Frozen Evolution. Or, that’s not the way it is, Mr. Darwin. A Farewell to Selfish Gene.

Biologists study a great many evolutionary processes on the models of an adaptive landscape.The American biologist Sewall Wright introduced the model of the adaptive landscape into evolutionary biology at the beginning of the nineteen thirties. In actual fact, this consists of two quite different models, between which not even their author always sufficiently differentiated. This is an abstract model of either the environment and the individual organisms or the environment and populations. In the former case, the evolution of organisms in the environment can be conceived, e.g., as a three-dimensional topographical map, in which the x and y coordinates correspond to two qualities of a hypothetical organism (e.g. body weight and maximum speed of movement); in the second case, the frequency of the alleles are on the x and y axes at two different loci and the average biological fitness of the given population is on the z axis. Let us now return to the first model of an adaptive landscape. The shape of the surface of an adaptive landscape, the system of hills and valleys, is given independently of the properties of the organisms and determines the distribution of future niches in the particular environment. The projection of the points onto the surface of the adaptive landscape, i.e. coordinate z, determines the fitness of each individual organism (characterized in our model by properties X and Y). It is apparent that various combinations of X and Y are variously advantageous from the standpoint of natural selection. Mutations, i.e. a change in coordinate x or y, move the organism from one place to another, also shifting their projections onto the surface of the adaptive landscape. Only mutations that shift the projection of the organism uphill in the plane of the adaptive landscape, to places with larger coordinate z, can be fixed by natural selection. It is apparent that, under suitable circumstances, in time, organisms climb up to the peaks of the individual hills.

see Speciation by coevolutionary lift

Changes in time in the character of cladogenesis within a certain phylogenetic line are a striking and simultaneously difficult-to-explain macroevolutionary phenomenon. The paleontological record contains a number of phylogenetic lines that first continued in a state of evolutionary calm for a longer time after their formation, underwent speciation with only minimal frequency and their members also accumulated only a minimum of anagenetic changes. This was followed by turbulent evolutionary activity with splitting off and mutual phenotype diversification of a large number of species in a short period of time. On the phylogenetic tree, this phase appears as sudden radiation of a large number of phylogenetic lines from practically a single point. The period of radiation is again followed by a period of evolutionary calm, with a minimum of new branches, and evolution occurs only within the formerly split-off branches and tends to have the character of adjustment of the adaptation to the conditions of the environment rather than the creation of new diversity. In this period, specialized forms emerge in the line, frequently with large body dimensions that readily become extinct during the next mass extinction event. The last phase in the existence of a phylogenetic line from the viewpoint of its cladogenesis consists in evolutionary stagnation and decline – the species undergo speciation more slowly than extinction and thus the entire line gradually dies out. In some cases, rejuvenation can occur in any phase of the phylogenesis of the line, i.e. new radiation occurs in one of its branches and lines formed during this event then gradually replace most of the lines formed during the previous radiation (Fig. XXVI.2).

            The described process was sometimes interpreted in the past as maturing and ageing of the phylogenetic line. However, it is very probable that this is actually only a superficial analogy with the life cycle of a biological individual. In the life of a biological individual, i.e. in the section defined on the one hand by its birth and on the other hand by the physical destruction of its body, there actually do exist physiological processes determining the alternation of developmental phases, during which the viability of the individual and its ability to reproduce first increase and then decrease, with a proportional change in the probability of its death. However, this is not the case in the life of a phylogenetic line. Only individual species are formed and become extinct (and thus it is, at the very least, theoretically quite possible that the individual species can age, see XXVI.5), but the phylogenetic line encompassing all the species of organisms on the Earth lasts without interruption from the moment of emergence of life on this planet and only gradually branches over time. The individual lines (phylogenetic sublines) do, of course, disappear through extinction; however, the newly formed branches have, at the moment of their formation, the same age as all the branches existing on the Earth at the given moment. The individual taxa, monophyletic sections of the phylogenetic line defined on the phylogenetic tree by a taxonomist on the basis of an important trait, i.e. on the basis of the attained level of anagenesis, can, of course, emerge and disappear. The evolutionary emergence of a new taxon corresponds not to the formation of a new individual, but only to the formation of the relevant new anagenetic traits in a species within a long-existing phylogenetic line. Simultaneously, various taxa are delimited on the basis of very diverse traits. There is absolutely no reason to assume that the formation of basically an arbitrary trait would automatically initiate the process of ageing of the relevant phylogenetic subline. However, the anagenetic traits themselves, or rather the complex of anagenetic traits that characterize a new taxon, can age, e.g., can freeze, see below.

            It is highly probable that the “life cycle” of a taxon is not a result of its ageing and real changes in the traits of the relevant species. It is more probably a manifestation of mathematical laws following from the existence of fluctuations in speciation rates within a single phylogenetic line and also a consequence of the manner in which we obtain input data. A taxon that did not undergo at least one period of radiation has a very low chance of surviving in nature long enough for us to be able to observe it in the paleontological record and thus of being included in our considerations. There is low probability that a taxon will be subject to constant radiation; radiation is apparently always caused by some specific, relatively rare anagenetic change (see XXVI.2.1). The probability of radiation of a certain line is simultaneously apparently negatively affected by the overall biodiversity in the environment (see, e.g., the king of the hill effect, XXII.5.5, and the discussion of the model of the ecological network, XXII.7). As a consequence, a global balance is apparently maintained between the rate of speciation and the rate of extinction. However, this means that a taxon that does not undergo radiation in time becomes extinct. Obviously, once a taxon has become extinct, it can no longer undergo radiation and can thus not return to the paleontological record.

An alternative explanation is provided by the theory of frozen plasticity, according to which all evolutionary lines gradually age (and thus increasingly old lines emerge) {15429}. Old lines have reduced probability of evolutionary thawing and formation of new fundamental anagenetic features – and thus important evolutionary radiation, as more and more traits that were originally capable of thawing following peripatric speciation become permanently frozen. This phenomenon could explain why, for example, the great majority of disparities, the great majority of animal strains evolved in the Cambrian and, since that time, the number of basic body plans has tended to decrease on the Earth {12783}.

clinal variability

see Mutations at the level of the entire chromosome set

see Selection Intraspecific and  interspecific

Parasites can be divided into ectoparasites and endoparasites. Ectoparasites live on the surface of the bodies of the host or only in their “dwellings” (nidocolous parasites). In contrast, endoparasites live directly in the organs or tissues of the host species. A conspicuous anagenetic tendency is sometimes observed for endoparasites, i.e. a trend towards simplification of the body structure and individual physiological functions. This trend sometimes even goes so far that an originally multicellular organism becomes a more or less unicellular organism. A typical example is Myxozoa, a group of organisms parasitizing mostly on fish, in which the methods of molecular taxonomy have recently shown that these are not protozoa, but extremely reduced metazoa (Smothers et al. 1994; Siddall et al. 1995). A great many kinds of parasitic crustaceans have comparably greatly reduced body structure. Viruses are located at the other end of the scale of organismal complexity and they could well provide us with similar surprises in the future. It cannot be excluded that it will be found in time that some viruses are actually extremely reduced bacteria. (Well, probably not, but it would be nice, wouldn’t it?)

The reason for the simplification of the body structure of endoparasites is primarily the fact that a great many physiological functions related, for example, to maintenance of homeostasis, are left to the host organism by the parasite. The internal environment of the organism is relatively stable and rich in some easily processed nutrients. Consequently, a great many functions that are vital for freely living organisms are superfluous for a parasite and it can gradually get rid of them during evolution.

            It is even evolutionarily advantageous for a parasite if it manages to simplify its body structure as much as possible. The more differentiated tissues and organs its body contains, the greater the number of kinds of proteins that it must synthesize and the more easily can the immune system of the host recognize its presence and foreign nature.

            The specific cause of the reduction of the nervous system lies in the extreme predictability and stability of the environment in which the parasite infrapopulation lives. As a result of this predictability, the body of a host is sometimes designated as a third type of environment (in addition to aquatic and terrestrial environments) (Sukhdeo 2000). While every individual of nonparasitic species lives under quite unique conditions, parasites in the bodies of organisms are always in exactly the same, although highly heterogeneous environment. The distribution of the individual organs in the body of the host is almost identical in all individuals of a particular species. Consequently, while the nervous system and learning mechanisms are necessarily of great importance in controlling behavior in nonparasitic organisms, in parasitic organisms, these functions can be taken over by inborn fixed patterns of behavior, initiated without regard to stimuli from the environment (see XVI.2).

            In the past, the existence of predominating trends towards reducing complexity in parasitic organisms was considered to be a quite obvious fact (Poulin 1995b). As was later properly emphasized by a great many authors, the reason for general acceptance of this fact was an elementary methodical mistake. Instead of comparing the complexity of parasites in a certain phylogenetic branch with the complexity of nonparasitic organisms of the sister phylogenetic branch, the complexity of parasites was frequently compared with that of their hosts. It is obvious that, when a cow is compared to its tapeworm, the cow must appear more complex. However, when the complexity of parasitic and nonparasitic flatworms were compared, the result was far less obvious.

At the present time, the opinion pendulum has swung to the other extreme. To the contrary, especially amongst parasitologists and cladists, there is tendency towards throwing into doubt the trend associated with simplification of parasites (Brooks & McLennan 1993). Parastiologists have a quite understandable tendency to “favor” the objects of their study, so that they quite willingly accept the opinion that Sacculina barnacles, a crustacean that is most reminiscent of the mycellium of honey funguses, are, in fact, just as complicated as river crayfish; while it is true that they are lacking some organs, they quite certainly have a large number of evolutionarily new features, such as various types of receptors, at a microscopic or ultra-microscopic level. Support for this opinion of parasitologists by cladists then follows from their programmed lack of interest in similarity, and thus in the appearance of studied organisms. Cladists attempt to reconstruct the cladogenesis of organisms entirely on the basis of their mutual relatedness, where they estimate this relatedness wholly on the basis of sharing of new evolutionary features, synapomorphies (see XXIII.6). A new evolutionary feature could consist in both the acquisition and the loss of a certain body structure. Simultaneously, the complexity of the particular structures is of no importance in the formation of evolutionary hypotheses on the relatedness of organisms. If the particular evolutionary change occurred in one stage, then the loss of a complex structure, such as an eye, is equally important as the one-stage loss or acquisition of any other trait. Thus, if cladists attempt to compare the character of the evolution of nonparasitic and parasitic organisms, they first count the number of new evolutionary features that arose independently in a certain time interval. In this comparison, there understandably need not be any difference between parasites and nonparasitic species. When a cladist goes into greater detail and compares the number of new evolutionary features in both organisms, characterized by the loss of an organ and acquisition of a new organ, they do not in any way differentiate between the complexity of the lost and newly acquired organs. Simply on the basis of mechanical comparison of the matrices of evolutionary changes, they then come to the conclusion that tapeworms are an extraordinarily rapidly and progressively developing group. While they have lost a few organs, such as eyes and a digestive system, they have, on the other hand, acquired a large number of organs (mostly various types of chemoreceptors). Thus, only 6% of evolutionary changes here corresponded to the loss of organs (Brooks & McLennan 1993).

            Because of the difficulty of understanding the concept of complexity (see I.3), it will still long not be possible to exactly decide to what degree and whether trends towards a decrease in complexity predominate overall in parasites. It is, however, obvious that parasites provide us with a great many examples of secondary reduction of organs that have lost their original function in their new environment. In any case, the character of anagenesis of parasitic animals, i.e. at the very least the occasional trend towards simplified body structure, and thus towards reduction of the overall complexity of the organism, indicates that biological evolution need not always be connected with an increase in the complexity of biological systems. As was already pointed out in Sect. I.2, an increase in the complexity accompanies biological evolution; however, in a number of cases this parameter is quite independent of biological evolution. The only trait that differentiates biological evolution from other types of evolution is thus the formation of adaptive traits.

see Mutations at the level of the entire chromosome set

Presumed negative impact of evolution theory on people’s ethical attitudes

Warning coloration

Some authors are of the opinion that, under certain circumstances, the female can, to the contrary, create conditions for the most effective intergametic competition. It is known that the females of a great many animal species repeatedly copulate with a large number of different males. The arena hypothesis assumes that the purpose of this behavior consists in accumulation of sperm samples from a large number of males, thus creating conditions for effective competition between sperm derived from various individuals (Birkhead, Moller, & Sutherland 1993; Telford & Jennions 1998; Zeh & Zeh 1996). However, this hypothesis assumes that there is a positive correlation between the biological quality of sperm and the biological quality of the multicellular organism.

            The assumption that the biological quality of an individual is highly correlated with the competition potential of his sperm is rather bold; however, there is no reason why this should be rejected a priori. While organisms have created some mechanisms that prevent the emergence of competition between the sperm derived from a single individual (see, e.g., the above-mentioned inactivity of their genes), on the other hand the properties of the sperm are quite certainly determined by the quality of the genome of the male. Consequently, it can be expected that the quality of the sperm produced and thus its chance of success in the arena could depend on the biological quality of the males. Even if this were not true, it is still possible that sperm derived from various males compete in the arena independent of their quality but in dependence on their number. The situation is much more favorable in this case, as it can be expected almost with certainty that there exists a correlation between the quality of the male and the number of sperm that he can afford to produce.

            It has so far been verified only in a very few cases that promiscuity amongst females increases the fitness of the progeny. For example, it has been observed in the common yellow-toothed cavy (Galea musteloides) that females that were allowed to copulate with four males raised a larger number of healthy progeny that females that could copulate with only a single male; simultaneously, the size of the litter did not differ (Keil & Sachser 1998) (Fig. XIV.5)._s

Coevolution of a predator and its prey, parasite and its host or two species competing for utilization of a certain resource or having a common predator, and even the coevolution of two mutualistic species very frequently has the character of a sort of “arms race”. A certain new evolutionary feature emerges in one of the species, increasing the fitness of its bearers at the expense of members of another species, and thus it gradually spreads in the population of this species (Fig. XVIII.1). Such a new evolutionary feature could, for example, consist in stronger jaw muscles, enabling a predator fish to crack the shell of a certain kind of snail and include it in its diet. This would create a selection pressure on the snail to create a stronger shell, or to synthesize a poisonous or terrible-tasting substance to defend itself against attacks by the fish. The emergence of such an adaptation in the snails would produce a selection pressure on the predatory fish which, sooner or later, would lead to the creation of a suitable counter-strategy, enabling it to somehow overcome the effect of the new evolutionary trait in the snail – for example, through the formation of even stronger jaw muscles or of sharper horny jaws, or the emergence of some suitable pattern of behavior that would enable it to break even stronger shells. A new round in the arms race can be started by either the “attacker” or the “defender” and the participants in this race need not be only a pair of species, but can even consist in large groups of mutually interacting species.

            A great many paleontologists assume that some rapid changes in fauna that occurred in certain short periods in the history of the Earth, with the simultaneous participation of an enormous number of species, emerged as a product of just such arms races. A certain new evolutionary feature emerged in one species, creating a selection pressure on a great many species in the environment; they had to somehow react adaptively to this pressure, other species had to react to their reactions, so that the wave of anagenetic changes could finally affect a great portion of the species in the particular ecosystem in a very short period of time (Morris 1995).

            Arms races can also occur at an intraspecific level and this can happen on a relatively short time scale in microevolutionary processes. The members of the male or female sex can increase their fitness at the expense of the members of the other sex. Under normal conditions, the speed of evolution of males and females is comparable, so that it cannot be observed that the members of one sex would gain an apparent advantage over the members of the other sex. However, by suitably arranging an experiment, we can ensure, for example, that the females will not be able to respond to the evolutionary drives of the males. The experiment is performed in that the males are allowed to interact ecologically, ethologically and sexually with the females of a certain strain for a number of successive generations, where only the males of the obtained progeny are allowed to survive. The females are replaced in the experimental population in each generation from the stock population (and are thus completely “naive” from the standpoint of interaction with the particular selected line of males). The results of such an experiment performed on drosophila indicate that the males gained a considerable advantage over the females after 41 generations (Rice 1996). They achieved copulation with the females of the particular strain much faster; following copulation, the time before the females began to copulate with some other male was prolonged and, in case of multiple copulation with their own and foreign males, only a small percentage of the eggs were fertilized by the foreign males. The females lost out in the evolutionary battle, not only in the limited ability to chose, from their point of view, the best father for their progeny, but also in shortening of their lifetimes following copulation with the test males (but not with control males) (Fig. XVIII.2).

            According to some authors, the coevolutionary battle between the sexes in sexually reproducing species is the main reason for the genetic divergence of allopatric populations and is thus indirectly an important motor for allopatric speciation (Martin & Hosken 2003).

see  Speciation by coevolutionary lift

see Extinctions types and also Extinction, viral theory of background extinction

see Selection for heterozygotes

However, parasites exploit their environment, which is generally very rich in sources of nutrients, only temporarily, sometimes even transitorily, in terms of their lifetimes. The parasite generally dies with the death of the attacked individual and, in the vast majority of cases, its death is accompanied by the extinction of the relevant infrapopulation of parasites (a population of parasites living in/on one host). While, for organisms living independently, the critical parameters determining fitness are generally the rate of reproduction or the economy of use of food sources, for most parasites, the ability to be transmitted from an infected host to an uninfected host is of key importance. A parasite has only a very limited ability to affect its fitness through reproducing within a single host. From the standpoint of fitness, the number of progeny is of key importance, but only if they manage to get into other individuals in the host population. Consequently, most adaptive traits that are encountered amongst parasites are in some way related to the transmission of the parasite in the host population.

            The effectiveness of transmission is characterized by the basic reproductive rate R₀, i.e. the number of individuals of the host species that are infected, on an average, by one already infected host in the population that has not yet been affected by the parasite, i.e. in a population of uninfected and not-immune individuals (see also XVII.5). In real populations there are, of course, individuals that have already been infected and immune individuals, so that the actual number of individuals infected from a single source, i.e. the actual reproductive rate, R, is usually much smaller. Its value can be calculated from the equation

where q is the fraction of susceptible individuals, i.e. not yet infected and not-immune individuals in the host population. For endemically occurring parasites, the actual reproductive rate is equal to unity in the long term, so that the number of infected individuals in the population remains constant over the long term. The actual reproductive rate is a very important parameter from the epidemiological standpoint. From the standpoint of study of microevolution in the parasite population, however, rate R₀ is of key importance. 

Optimization of the reproduction of the parasite, usually, although not necessarily, accompanied by optimization of pathogenicity and virulence, is a typical evolutionary adaptation permitting influencing of the effectiveness of transmission and thus maximizing of R₀.  The ability to form resistant latent stages is also common; these can survive in the infectious state in nature until they manage to enter a suitable host. This aspect also encompasses the frequently very complicated life cycles of parasites, which often include a number of intermediate host organisms, through which the parasite gets from one host to another. Other adaptive traits are related to the ability of parasites to adaptively change the traits and behavior of the host organism to assist in its reproduction and dissemination.

see History of evolutionism – classical Darwinist period

see clinal variabilit

The probability of superinfection and thus the optimal rate of multiplication of the infrapopulation and optimum parasite virulence do not depend only on the size of the parasite population at the given site, but also on the biodemographic parameters (life history) of the host population. If the host population is short-lived (for example small rodents) or if, for example, the host population at the given time exhibits a higher death rate for reasons not associated with the actual parasitosis, it is advantageous for the parasite to multiply more rapidly in the hosts and thus to damage them more than if the hosts were long-lived (Ebert & Herre 1996; Restif, Hochberg, & Koella 2002). This again contributes to an increase in the virulence of all parasites at times of famine, epidemics or military battles.

Similarly, greater mobility of individuals in the host population leads to an increase in parasite virulence. If the members of the given population exhibit low mobility and motility, infection is transferred especially between close neighbors. From the viewpoint of the rate of spreading, this is advantageous for those parasites that do not damage their hosts much (Haraguchi & Sasaki 2000). In contrast, if individuals of the host population move over large distances in their area of occurrence, low virulence does not constitute any advantage for the parasites.

More virulent parasite populations survive in more numerous host populations compared to small populations that are present, for example, at the edges of the areas of occurrence of a particular species,. Similarly, more virulent strains of parasites are usually at an advantage in growing host populations; while parasites with lower virulence are at an advantage in populations with constant or even decreasing size. This is a result of the fact that, in a growing population, there is a high probability that the infectious stage of the parasite will encounter an uninfected and unimmunized host, while this probability is lower in a stagnant or decreasing population and thus it is preferable for the parasites in a shrinking population to harm their hosts less (Knolle 1989; Combes 2001; Ebert 2000). In tropical areas, mosquitoes, acting as vectors for malaria (i.e. hosts whose role in the life cycle of the parasite is to provide mobility for immobile parasites), are active throughout the year and thus infection is transmitted throughout the year. This is perhaps why Plasmodium species causing malaria (Plasmodium falciparum) are more virulent in these areas than in subtropical or temperate regions. In areas where the frequency of transmission of a disease is decreased in some seasons of the year, for example because of the absence of insect vectors, species that are capable of forming latent stages in the host or species that have a long incubation time (Plasmodium ovale, P. vivax) are at an advantage. A similar phenomenon can be observed for Leishmania (Combes 2001).

Biodiversity denotes the mutual diversity of living systems. It has two components, the diversity (biodiversity), i.e. number of species, and disparity, i.e. the diversity (dissimilarity) of various forms of life.

Biological evolution is long-term, spontaneously occurring process, during which living systems are formed or were formed singly from nonliving systems, and these living systems then develop and mutually diversify.

see Extinction predispositio

A temporary, frequently very drastic reduction in the size of the population, followed by a return in the number of individuals in the population or species to the original size, is apparently important in evolution. This process and the evolutionary and genetic processes that accompany it are called the bottle-neck effect. The bottle-neck effect occurs, for example, when the size of the population is radically reduced by a certain biotic or abiotic factor whose action is only temporary. The same effect occurs when a new location is colonized by a small group of individuals of a certain species, in the extreme case one fertilized or even parthenogenetic female. Such an event can lead to accelerated evolution through accelerated anagenesis, as the gene pool of the founding population can differ drastically from the gene pool of the initial population (see XXVI.5).The direction of evolution is determined not only by the selection pressures, to which the population is exposed, but also by the structure of the gene pool of the given population. As the gene pools of the original and founding populations differ, the course of their evolution can also differ. This founder effect (Mayr 1963)has a number of genetic consequences and can even lead to the formation of a new species. In addition, as was discussed in Section VII.3, selection pressure does not act as strongly in small populations as in large populations, so that mutants that would be rapidly eliminated by natural selection can survive here.The bottle-neck effectthus allows evolution to overcome shallow valleys in the adaptive landscape (Wright 1931; Wright 1982).

At first glance it might seem that the bottle-neck effect would lead to the same decrease in polymorphism as a reduction in the size of the population. However, theoretical models of this phenomenon indicate that this need not be true, that the bottle-neck effect frequently does not lead to a substantial reduction in polymorphism. This is a result of the fact that the reduction in the size of the population is followed by its re-expansion, during which no alleles basically become fixed. The population expands into free ecological space and is thus not exposed to almost any intraspecies competition, so that the bearers of all the alleles transfer their genes to their progeny. If an allele “survives” the process of reduction of the population, in the following period of exponential increase it will apparently not be eliminated, even in the period when the number of individuals in the expanding population is still very small compared with the size of the original population. It is, however, apparent that a temporary reduction in the size of the population always leads to the loss of most rare alleles, i.e. alleles that were present in such low frequency in the original population that they disappeared from the gene pool at the instant when the size of the population was reduced. In this case, however, these are mostly neutral or almost neutral mutations that are maintained in the population by mutation pressure, i.e. as a consequence of constant formation of the same alleles through mutations. Thus passage through the bottle neck affects primarily type 1 polymorphism that is not of such fundamental importance in evolutionary and ecological processes as type 2 polymorphism (see VIII.3).

Study of the genetic polymorphism of a certain population yields information on whether it passed through a bottle-neck in the past (Emerson, Paradis, & Thebaud 2001). If a certain DNA segment is sequenced for a greater number of representatives of the relevant population and the mutual similarity of all pairs of sequences is compared, three fundamentally different results can be obtained. If the population was stable for a prolonged time and was relatively large, it contains a large amount of polymorphism, where some pairs of alleles differ in many positions, while other pairs differ just in few positions. A histogram of the number of mutations in which a pair of sequences differs is very irregular – it does not have one clear maximum. If the population was limited in size for a long period of time, the overall polymorphism, both in the numbers of alleles and in the numbers of differences between the alleles, is substantially smaller but the histogram of positions in which the individual alleles differ from one another is also irregular. If the population passed through a bottle neck and later substantially increased in size, the amount of polymorphism is also large, while the histogram of the number of different positions has a regular bell shape (Vonhaeseler, Sajantila, & Paabo 1996)(Fig. V.6).

It is known for a great many species of animals living in groups that, at the moment of a sudden change in the social structure of the group and immediately after this, especially in situations where there is a change in the alpha male in the group, massive infant mortality occurs. In some cases, the progeny are killed by the new head of the harem, but in other cases it seems that their mothers kill or abandon the offspring. The Bruce effect is the best-known example of such a phenomenon; this is encountered in mice and other species of rodents (Bruce 1959). If we remove the original male from a pregnant mouse and replace it by a foreign male, the female usually very rapidly aborts.

            These and related phenomena apparently accompany intersexual competition. From the viewpoint of the male, it is extremely important to be the biological father of the greatest possible number of offspring in the population. Any behavior that contributes to this goal is selectionally advantageous and will apparently become fixed during evolution. The male can best shorten the time until the individual females become pregnant with him by removing all foreign offspring as soon as possible. From the viewpoint of the female, such an approach is, of course, extremely disadvantageous, because she has already invested a great deal in the offspring. However, she mostly has no effective defense against this male strategy. To begin with, the females of a great many species are weaker than the males and, in addition, an offspring can be killed very quickly, while defense of an offspring against killing requires constant alertness and care. This asymmetry means that the females generally lose the battle for the young in advance, so that it is fundamentally more evolutionarily advantageous for her to cooperate with the male and to rapidly get rid of her own young or embryos.

            It should be stated that there are a number of other explanations for confirmation of the Bruce effect, including unilateral, pheromone-mediated manipulation on the part of the male or hidden (post-copulation) female choice – preferential conception with the winning – and thus genetically better partner (Storey 1994).

see Genome evolution

Cause – see Goal-orientation.

see History of evolutionism – classical Darwinist period

see Selection of chemostat type and turbidostat type

Simple chromosome mutations very frequently spread in the population without their presence substantially affecting the fitness of their carriers. In fact, even heterozygote individuals, which frequently bear very drastic chromosomal mutations, frequently exhibit more or less the same fertility as homozygote individuals. In this case, a relatively large part of the population, usually in the territory where this mutation emerged, can exhibit the mutated karyotype. The territory in which this karyotype variant occurs can grow in time at the expense of the territory occupied by the original variant. In this case, karyotype variants are generally termed chromosome races. The members of new chromosome races freely cross with members of the original race and regular recombination occurs between their chromosomes. Although they differ in the chromosome number or morphology, they need not differ in the frequencies of the individual alleles on these chromosomes and therefore in their phenotype. However, if two different chromosome mutations spread simultaneously in the population, heterozygotes with reduced or even zero fertility can be formed at their site of contact. The chapter on meiotic drive (VI.3.5.1) described a case where two metacentric chromosomes with a single common arm formed by Robertson translocation, with participation by the same acrocentric chromosome in both cases, but in each case in combination with a different acrocentric chromosome, met at a certain place in the range of occurrence. In this case, complicated multivalents are formed in meiosis, which can substantially disturb the course of reduction division. The infertility of these heterozygotes can result in the formation of a very effective reproductive barrier between these two chromosome races and the races can gradually differentiate into completely separated species. 

In this test, two mutants with mutations manifested in the same way in the phenotype of their carriers are first prepared or isolated from nature. If we are interested in whether both mutations are found in the same cistron, then a sufficiently long continuous DNA section bearing the mutation is transferred artificially, e.g. through transfection, or naturally, i.e. through crossing, from one mutant to cells containing the DNA of the individual with the other mutation. The obtained individual carries the given section in two copies, each of which bears one mutation. If the functioning of the particular gene is renewed in it, i.e. the original form of the trait corresponding to the unmutated form of the given gene is formed, it will be very probable that the relevant mutation will be located on two different cistrons. In the opposite case, this will correspond to a mutation on a single cistron. This test can be employed in this simple manner only if the wild form of the trait is dominant, i.e. when the presence of only a single copy of the given gene in the genome is required for its occurrence. Simultaneously, it is necessary to exclude (technically in advance or at least subsequently when evaluating the data) the possibility that the functioning of the given gene was renewed as a consequence of genetic recombination occurring directly in the studied DNA section. See also Gene

The process of cladogenesis mostly takes place by gradual branching apart of the individual lines of organisms. If a speciation event occurs, two daughter species are formed in a certain moment from a single parent species. One of these species can be basically identical in its phenotype with the parent species for a long time. Nonetheless, in the first phase of reconstruction of cladogenesis, it is preferable to consider both daughter species to be new species. The evolutionary fates of the parent and daughter species differ substantially. All the genetic changes relating to the parent species can be passed on to both the daughter species and subsequently to both phylogenetic lines that can be formed from them by repeated speciation. In contrast, the genetic changes that occur after splitting off of the daughter species can affect only the progeny of one of the two daughter species and cannot be transferred to the sister phylogenetic line.

Speciation can occur in rapid succession in a certain phylogenetic line. In fact, in some cases, a certain species can decompose into a whole series of daughter species at a single moment. For example, such a situation can occur on a decrease in the water level in a lake and subsequent division of the original continuous population of a certain aquatic species into a number of isolated populations (Fig. XXIII.1). In this case, it is also useful, although not always technically feasible, to express the entire process of cladogenesis as a sequence of binary branchings of the particular phylogenetic line. In actual fact, the physical division of the population occurred at a single moment on a decrease in the water level in the lake; however, branching of the population probably occurred gradually, as the individual parts of the population occupied the individual parts of the original lake. Simultaneously, it is highly improbable that two populations that will, in the future, occupy two different parts of the lake and that led to the formation of the two new species would split off from the parent population at the same instant. Consequently, in reconstruction of cladogenesis we primarily attempt to express this process as a sequence of binary branchings of the particular phylogenetic line and, only if the available data do not make this possible, can we create a scheme of cladogenesis including multifurcation.

In rare cases, two originally independent lines can merge to form a single line, which can then branch apart. Fundamentally, there are two basic mechanisms of syngenesis, i.e. the formation of a new phylogenetic line by the merging of two older lines: symbiogenesis and interspecies hybridization (Fig. XXIII.2). Symbiogenesis refers to the formation of a new species of organism by the integration of two unrelated organisms that live for some time in some form of symbiosis, most probably parasitism or mutualism, into a single organism. If both symbionts begin to reproduce together in a coordinated manner, i.e. so that each daughter organism of symbiotic origin begins to inherit from its parents only the genetic material of both symbionts, the evolutionary fates of the two original species become so interconnected that they sooner or later merge into a single species. Evolutionary dissolution of one species in another species, for example a microscopic parasite or mutualist in its macroscopic host, is sometimes term the Cheshire cat effect (unfortunutly, this term is also used for at least two unrelated phenomena). The relevant literary sources state that, under suitable conditions, a Cheshire cat can gradually disappear and, in the last stage, only its smile remains and, after a certain time, this also disappears. If both symbionts that form a common symbiotic organism produce independent progeny and a new symbiotic organism is formed each time (or at least frequently) through new integration of both symbionts that grew from embryos produced by two unrelated and independent individuals, both species will most probably preserve their species identity (Fig. XXIII.3). This is the frequent case of the symbiosis of fungi and vascular plants. The best known opposite case is the formation eukaryotes, occurring through gradual integration of the members of several unrelated lines of prokaryotic organisms. Completely unrelated phylogenetic lines of organisms can merge through symbiogenesis.

Two lines can also merge through interspecies hybridization, i.e. accidental crossing of the members of two different species. However, in contrast to symbiogenesis, this mechanism can occur only in closely related species with sexual reproduction. The effect of symbiogenesis and hybridization on the topology of the phylogenetic tree is the same; in both cases, the cladogenesis scheme can have a recticular structure instead of a tree structure at some places.

A. Graham Cairns‑Smith formulated Clay hypothesis of the origin of life (Cairns-Smith 1982). He based this on the concept that the original structure that provided for transfer of information could have been a clay-type inorganic substance rather than an organic compound.

            The microstructure of clay is formed by an irregular crystal, in which the individual series of silicate molecules lie above one another in regularly ordered layers. However, the overall structure of clay is in no way monotonous, as the layers copy the surface on which they lie and also contain a number of defects that are then copied in further layers of the molecule. The fact that the defects are thus copied ensures a certain mechanism of heredity. Clays containing various types of defects can be variously successful. Some grow and enclose further layers faster than other ones, some dry out faster and, after disintegration into smaller particles, can be readily dispersed by the wind and can thus “infect” other locations on which clays settle. A certain type of natural selection can thus occur between various types of clays.

            Similar to nucleic acid in the genetic model of life, clays can also “learn” to cooperate with some other substances, for example with proteins, whose synthesis they can catalyze on their surface (Coyne 1985b; Ferris, Huang, & Hagan 1988; Ferris et al. 1996).

            The Cairns-Smith hypothesis is certainly very interesting and inspiring; however, it is hard to imagine a way in which a transition could occur from a system of storing genetic information in a set of defects in pseudocrystalline clays to a system of storage of information in sequences of nucleotides in nucleic acids. The hypothesis also in no way resolves the problem of the evolution of the genetic code and proteosynthetic apparatus.

The subpopulation of parasites in one host very frequently corresponds to a clone of genetically identical individuals. There is minimal variability within the clone and thus the effectiveness of individual selection that would favor selfish individuals is also minimal. If an individual in the subpopulation mutates towards a greater rate of reproduction, its progeny are at an advantage only in the first host; following transmission to another host, they yield a clone of identical individuals, so that any selectional advantage of the particular mutation disappears. To the contrary, the disadvantage connected with the deviation from optimum virulence is manifested and the entire daughter subpopulation finally produces less infectious stages than the subpopulation of unmutated individuals.

The advantage of the limited effectiveness of individual selection within an infrapopulation is apparently a cause of the fact that asexual reproduction is very frequently encountered in parasitic organisms, for example parthenogenesis and polyembryony (division of the embryo into several or even many embryos) which occurs in taxonomic groups in which wild species reproduce mainly sexually. Parasites sexually produce practically only the invasive stages, which leave the host for the outside environment. Whenever the progeny could compete with one another or with the parent individuals, they are produced by asexual reproduction, where new genotypes are formed only by the slow route of new mutations, and not by the rapid process of genetic recombination.

It is mostly stated that the reason for the emergence of secondary forms of asexual reproduction lies in the necessity of ensuring reproduction even when only a single parasite is capable of entering the host. However, this is inadequate to explain the repeated formation of asexual reproduction. The same goal could be achieved in a far simpler way by the emergence of hermaphroditism, the production of a microgamete and a macrogamete in a single individual. Although sexual reproduction is the commonest means of reproduction in nonparasitic eukaryotic organisms and thus it can be assumed that it is evolutionarily very advantageous, a great many parasitic species apparently are not capable of sexual reproduction or are capable of reproducing in their life cycle only in one of their hosts, i.e. in the definitive host. It is very probable that the selection pressure that, through interspecies selection, has led in parasitic species to the formation of this otherwise unexplainable “sexual abstinence” consisted in the necessity of limiting individual selection in favor of group selection.

During evolution, organisms adapt, not only to the conditions of the abiotic environment, but also to the effects of the biotic environment, i.e. they create traits and patterns of behavior through which they react effectively to the presence and actions of the other species of organisms in their environment. Evolutionary adaptation to the biotic environment differs from adaptation to the abiotic environment in two primary aspects. To begin with, the biotic component of the environment changes much faster than the abiotic component. While it is true that some local changes in the climate take place quite rapidly, in most cases rapid changes are temporary or even cyclic in character and, after a certain period of time, the climate returns to the original state. The abiotic environment is usually quite stable on a scale of 106 to 107 years, which is the usual duration of the existence of a species. The individual species can react to temporary changes through temporary changes in their areas of occurrence, for example, through withdrawing to refuges, more easily and especially more rapidly than through evolutionary changes in their phenotype traits.

            The other way in which adaptations to biotic and to abiotic environments differ fundamentally is in that the biotic environment is not passive, but also reacts effectively to ongoing evolutionary changes. For example, if a predator evolves a certain anatomic trait or a certain pattern of behavior that enables it to acquire a certain prey more effectively, then the newly emerging evolutionary pressure will sooner or later lead to the evolution in the prey of a trait that enables it to defend itself more effectively against the new hunting strategy of the predator. Rather than independent evolution of the individual species, mutually interconnected and mutually dependent evolution occurs in pairs of species or larger groups of species – coevolution.

            While the abiotic factors in the environment are more or less stable on the time scale of biological evolution, or only fluctuate cyclically or randomly in time, changes in the biotic factors in the environment tend to have a cumulative character and are frequently irreversible. The irreversibility of changes in biotic factors is a result primarily of the irreversibility of macro-evolutionary processes, anagenetic and cladogenetic processes in biological evolution. Stochastic processes constitute an important factor in these processes, whether genetic mutations or mass extinction caused by catastrophic events in the environment. Although the environment otherwise changes periodically, for example when there is a periodic alternation of warm and cold periods, species react to these cyclic changes through irreversible evolutionary changes. For example, Dollo’s law expresses the irreversibility of evolutionary processes. According to this law, an organ that disappears during the evolution of a certain species never reappears in the future in its original form, even if the relevant selection pressures that led to its formation in the original species are renewed. It is not necessary to emphasize that, similar to all biological laws, Dollo’s law also has a number of exceptions.

            The biological species that occur at a particular moment constitute a key factor in the evolution of the biosphere. The fact that these species undergo cumulative and irreversible evolution means that changes in the biosphere as a whole also have a cumulative and irreversible character.

The essentialist concept of species is based on the idea that that members of the same species objectively share a certain inner quality, essence, that sets them apart from members of other species. According to essentialists, the number of species or organisms and boundaries between these species is unambiguously determined beforehand, similarly as, for example, the number and shape of Platonic bodies are determined beforehand. Essentialists explain the existence of species internal variability as being a consequence of a different degree or quality of expression of this essence, where this unequal degree of expression has its origin in unforeseeable random effects of the surroundings on a particular organism. Philosophically, the essentialist concept is based in Plato’s world of ideas (where Plato’s own approach to classification of objects was based on other principles and it is improbable that he would consider himself an essentialist in the modern definition of this term). Similarly as transitions between triangle and rhomboids cannot exist in an ideal world, according to essentialists there cannot exist transitions between individual species. However, transitions between species can, of course, exist in our real (and imperfect) world. Here, however, it is frequently useful to differentiate between the essentialist and nonessentialist explanation of the difference between species (or between anything at all). For example, there are certainly several ways in which clocks can be formed. Simultaneously, it is hard to image a transitory type between pendulum clocks and crystal clocks – the differences are essential. In contrast, there can be quite continuous transitions between detergent powders and the fact that only a certain number of kinds of detergent powders are available in stores is not a consequence of the fact that transition kinds couldn’t be mixed or that transition forms would wash less efficiently. This is given by “external factors”, the business strategy of the manufacturer or seller or the laws of competition amongst individual market entities. 

            It is not probable that the essential concept of a species, at least in its original sense, would be very useful for description and explanation of the phenomenon of the existence of species in live nature. Species are not crystals or geometric objects, but products of a unique series of historical events, whether this series of historical events is considered to consist of biological evolution or biblical creation. This means that this development into the present-day form was affected not only by deterministic processes that necessarily followed from the properties of the particular system, but also, to a substantial degree, by chance. To assume under these conditions that the individual species should differ in a certain special category of properties, i.e. essential properties, is perhaps not completely naive, but is certainly very impractical. It is, of course, possible and, in fact, quite probable that any two species will differ from one another in a specific property, whether this is a particular biochemical or physiological property of their members or a certain aspect of their position in the ecosystem. However, this property is “essential” only in that it differentiates the two particular species. It is more than questionable whether the concept of a species based on “essential” properties defined in this way could be included in the category of an essential concept of species.

The nominalistic concept of species assumes that a natural property of all biological objects lies in their variability. Nominalists consider that only individuals and not taxons realistically exist. According to nominalists, the sharp boundary between species is basically artificial and, similar to higher taxons, is only a matter of convention.

            If the discussion between nominalism and realism is limited to the aspect of the existence of an objective boundary between species at a single level in time, specifically at the present time, most of the available empirical data will tend to throw doubt on the nominalist concept. While the delimitation of the boundaries between individual colors in a spectrum is a matter of convention and various cultures have resolved this task with different results, when delimiting the boundaries between species living in a certain territory, mostly not only scientists working independently using different methodical approaches, but most scientists and nonscientists, i.e. representatives of pre-industrial ethnic groups living in the particular area, will tend to agree in terms of rough characteristics (Gould 1979). This is, of course, only an argument against cultural relativism and it can, in addition, be objected that both the scientist and the “savage” are members of the same species and have, for example the same sensory organs and the same architecture of their brain structure. It will probably not be possible to perform a real experiment any time in the near future; nonetheless, it seems highly probable that a sufficiently motivated Martians equipped with the corresponding Martian instrument (e.g. a DNA sequencer) would differentiate terrestrial organisms into a similar system. Nothing personal, but the occasional excursion of molecular biologists into the field of systematic biology does not differ much from the above described hypothetical experiment.

It necessarily follows from the existence of individual variability of organisms that some individuals in the population will be more or less similar and thus that the boundaries between the individual species will be “fuzzy”; consequently, in some cases, it will be difficult to differentiate the individual species from one another. In contrast, the fact that, nonetheless, there are mostly objectively more or less definable boundaries between the individual species, does not necessarily follow from anything and thus is a special natural phenomenon that is contradictory to the starting premises of nominalism and that requires a separate explanation.

The discovery of evolution led to extension of the discussion between nominalists and proponents of other concepts about the boundaries between the species over time. The nominalist concept assumes that daughter species are formed in evolution more or less through continuous development from parent species, where the specific moment from which an individual in a particular related line can be considered to be a member of a new species is only a matter of convention. In contrast, a different concept of species assumes that, at a certain historical moment, a new species is formed in a particular related line, and is qualitatively different from the parent species. The decision as to which concept to favor is fundamentally complicated by the fact that a species is a set of a great many individuals and a great many related lines and no just a single entity. Individuals can differ substantially within a single species. Even if we were to come to the conclusion that a fundamental change occurs at a particular moment in a particular related line, which allows us to consider the particular individual to be a member of a different species, the frequency of the individuals with the particular property in the population is a continuous quantity that can gradually change over time or even fluctuate irregularly (Fig. XX.2). This means that the nominalist concept of species developing and splitting apart in time is quite legitimate and has a great many proponents at the present time.

Essentialism can, in a certain sense, be considered to be a certain, rather extreme form of structuralism. The structuralist concept of species is based on the idea that the phenotype of organisms is determined primarily by almost deterministic processes following from the properties of their structural elements and also the character of the mechanisms governing ontogenesis. In contrast, the action of external factors is assigned a secondary role, either in the basically deterministic processes of selection or in random historical processes of the type of drift and speciation. According to structuralists, there is only a limited number of ways in which a functional organism can be formed from biomolecules through existing ontogenetic processes. According to them, each species is a specific manifestation of one of these means. Thus ontogenic constraints play a decisive role in determining the phenotype of an organism and, consequently, the evolution of a new species. The Vavilov model of homologous series (Vavilov 1967), one of the oldest complete structuralist concepts of the character of species, was proposed in the 1920’s. The Russian geneticist N.I. Vavilov noticed that a certain combination of phenotype traits occurs in various genera of plants, permitting the individual species to be distinguished. On the basis of study of the morphology of the members of a certain genus, he was thus capable of predicting the existence of so-far unknown species in a different genus and a great many of these predicted species were, in fact, discovered (Fig. XX.3).

            It is probable that developmental limitations can be of substantial importance in the evolution of viruses. For example, in these cases, the morphology of the virus capsid is actually determined to a major degree by the laws of crystallography rather than by the character of selection pressures acting on viruses. In more complex organisms, developmental limitations can very substantially predetermine the evolution (and thus also the phenotype diversity) of the individual traits (for example the possible shapes of mollusc shells (Raup 1962; Raup 1966)). The structuralist model could also explain the diversity of the patterns on the wings of butterflies and on the body cover in general. Another area where the structuralist explanation could be important consists in the nonadaptive variability in the individual traits between species within a single genus. As an enormous number of traits contribute to the phenotype of more complicated organisms, the total number of possible combinations of these traits is infinitely large. Thus, it is not very probable that structuralist laws would determine which species would be formed in evolution and which not. This factor tends to rather have a limiting and defining role; of the enormous number of phenotypes that would correspond well to the requirements of the environment, it eliminates a certain percentage of those that, in actual fact, cannot be formed for internal reasons. However, I am of the opinion that this will tend to be a small percentage, but cannot, of course, be certain of this. Which of the species amongst the almost infinite number of other possibilities are actually formed tends to be determined rather by chance, selection and evolutionary drives. 

Reconstruction of phylogenesis by the maximum parsimony method very frequently yields several trees that do not differ at all or differ very little in the anticipated number of evolutionary changes. If there is no statistically significant difference amongst them, it is not possible to decide which of them best corresponds to the progress of cladogenesis of the relevant group. Similarly, in cases where the cladogenesis of a single group is reconstructed several times in succession on the basis of a different set of traits, mostly trees are obtained that differ in more or less important details. In these cases, it is correct to create one consensus tree on the basis of several trees, which summarizes the information contained in all the obtained trees.

            The degree of consensuality can be selected according to the purpose that the study is to serve. If we require one-hundred percent consensuality, we must denote only those binary branches on the final tree that occurred on all the individual trees. If the order of branching off of species differed in some places on the individual trees, the corresponding place on the consensus tree is designated by multifurcation, i.e. a node from which more than two branches originate. The presence of multifurcation on a consensus tree does not mean that we think that the particular species underwent adaptive radiation in the past from one place at a single moment, but only that we are not capable of deciding on the order of branching apart of the particular species on the basis of our data. When creating consensus trees, we need not always require one hundred percent consensuality; for example, for some purposes 90%, 75% or even only a majority consensus is sufficient (Fig. XXIII.10). A supertree is a special type of consensus tree. A supertree summarizes information from trees created for partially overlapping sets of species.

            A condensed tree differs in principle from consensus trees. A condensed tree is not created on the basis of a greater number of individual trees. Multifurcations on a condensed tree once again designate sites where we are not certain of the order of branching; however, this time this is not because of conflicting results but rather, for example, because of the absence of the relevant data (for example, lack of suitable synapomorphies).

see Condensed tree

– see Evolutionary constraints.

The fact that some groups of parasites are closely adapted to a particular host species or small group of host species means that transmission from one host species to another is relatively rare in these parasites even on an evolutionary scale or occurs only within a group of related species. However, this means that, as the host species is subject to speciation, i.e. individual daughter species split off during evolution, the parasite must also undergo speciation. Cospeciation occurs in the parasite and the host. Enforced speciation of the parasite may be caused by genetic drift following separation of a subpopulation bound to both daughter species and thus after separation of their gene pools. In many cases, however, this is apparently also strengthened by natural selection, adaptation to two, now mutually different, host species. Of course, sometimes host speciation need not necessarily be followed by speciation of the parasite; a single species of parasite can attack a relatively broad group of mutually related species. However, such a situation generally occurs when the host species live in the same territory (sympatrically) or when the parasite is spread by intermediate host species, which have sufficient mobility and habitats encompassing the habitats of all the related host species._s

The fact that the sequence of parasite speciation must frequently copy or at least respect the sequence of speciation of the host taxon means that the cladograms (phylogenetic trees) of the host and parasite will be similar to a certain degree (Thomas et al. 1996) (Fig. XIX.19). Thus, if we know the phylogenetic tree of the host taxon, it is often possible to approximately estimate the phylogenetic trees of its parasites (and vice versa).  This Fahrenholz rule was first apparently published in 1896 by Kellogg (Brooks & McLennan 1993). It is, of course, possible that, in some cases, the parasite can transfer to some other host organism, especially if the parasite is not particularly specialized, i.e. has a broader host spectrum. A parasite can also “miss the boat”, i.e. may be absent at the critical moment in the host subpopulation that, in time, results in the formation of an independent species, or could become extinct over time in a host species. In this case, the phylogenetic trees of the parasite and host need not be identical or can contain individual anomalies that are externally manifested, for example by crossing of the relevant branches of the cladograms. Empirical data indicate that better similarity is exhibited between the cladograms of hosts and their parasites when the relationship of the two organisms tends to be mutualistic and that the similarity is less in cases of actual parasitism. For example, the cladograms of Wolbachia bacteria in insects are far less similar to the cladograms of their hosts than those of Wolbachia bacteria and Filaria (Moran & Baumann 1994; Casiraghi et al. 2001). This is apparently a result of the fact that a coevolutionary “arms race” occurs between the parasite and the host, in which the host occasionally manages to successfully shake off its parasite. However, this success is usually only temporary; the empty niche can be secondarily occupied by a different species of parasite that is often not related to the original species.

see Two-fold genetic cost of sex

The phenotypes of existing species are more or less adapted to the conditions of the environment in which they live. If they are to start to use a new niche and enable the formation of a new species by branching speciation, they must first adapt to this new niche. This evolutionary change can only rarely occur in a single step, i.e. can occur as a result of a single mutation. Mostly a number of gradual evolutionary changes are necessary for exploitation of a new niche; these change the phenotype corresponding to the requirements of the original niche to a phenotype corresponding to the requirements of the new niche. There are a number of intermediate stages between the terminal states of the particular evolutionary pathway, where the particular intermediate links, transition forms, will probably exhibit suboptimal phenotypes from the viewpoint of both the old and new niches. Thus, their carriers will be at a disadvantage compared to the carriers of the original phenotype, which will substantially retard the progress of speciation. The entire phenomenon can be elegantly described by the model of the adaptive landscape (see I.13). There are a number of peaks in the adaptive landscape to which the individual species can gradually climb through the action of natural selection. Each of the peaks corresponds to a potential niche. Some of the peaks are occupied (exploited niches), while others are empty. In order for the members of a certain species to move from one peak to another, i.e. in order for them to form a new species, they must be able to first “climb down” from their adaptive peak and overcome the valley in the adaptive landscape, i.e. they must survive with a suboptimal phenotype from the viewpoint of fitness for a great many generations (Fig. XXI.4).

            In some types of speciation, suboptimality of the transition phenotypes is not a great drawback. For example, if part of the population finds itself in an isolated territory with very different conditions than those to which the phenotype of the original species was optimally adapted, the phenoptype of the population can begin to adapt to the new conditions even if the changes lead to temporary or permanent loss of fitness under the original conditions. Because the members of the population will not find themselves in the original conditions for a long time, their potentially worse competitiveness will not be a detriment. However, in some types of speciations, the newly formed species is in constant contact with the original species and, in this case, the reduced competitiveness of its members can be detrimental. Prevention of speciation that is based on worse adaptability of the individuals with transition phenotypes can be an important factor in those types of speciation where the new species evolves in close contact with the parent species. There are two basic factors that can facilitate the formation of a new species, to be more precise phenotype differentiation, under these conditions. The first factor is the multidimensionality of the actual adaptive landscape. While the landscape to which we are accustomed is three-dimensional, the adaptive landscape is actually multidimensional and each of these dimensions corresponds to one phenotype trait of a living organism. There are valleys between the individual peaks in a three-dimensional landscape that correspond to an area with suboptimal phenotypes in the three-dimensional model of the adaptive landscape. In contrast, in a multidimensional adaptive landscape, there are sorts of ridges or upland plains between the individual, often very distant peaks, along which the population can move, through the action of suitable selection pressure, from one peak to another without first climbing down to the valley.

            Another factor that allows species to pass from one adaptive peak to another is genetic drift and the related possibility of neutral evolution. In small populations, to be more exact in populations with small effective size, selection has rather low efficacy. This means that, in small populations, individuals with suboptimal phenotypes, located in deep valleys of the adaptive landscape, can survive for long times and even predominate through the effect of genetic drift. Then, when the effective size of the population again increases, the progeny of these individuals can climb back to the surrounding peaks in the adaptive landscape, including formerly unoccupied peaks. Sewall Wright explained adaptive evolution and certain forms of speciations by his shifting balance hypothesis, which is based on the principle of alternation of the effect of genetic drift with that of natural selection (VII.3)._s  

Cryptic choice hypothesis assumes that the processes occurring in the female reproductive organs are a continuation of sexual selection (Birkhead 1995). Through manipulation with the ejaculate, the female is capable of subsequently determining which sperm of the males with whom she recently copulated will finally fertilize the egg cells. Some authors have even suggested that, in this “decision-making”, the females are capable of “taking into consideration” the genotype of the individual sperm and their own genotype so that, in the final analysis, they allow the egg to be fertilized, for example, only by those sperm that ensure heterozygosity of the progeny for genes important for resistance, for example genes for MHC-antigens (Wedekind 1994; Lopez-Leon, Cabrero, & Camacho 1996; Stockley 1999) (Fig. XIV.3). Similar phenomena have also been observed for plants. Here, selection apparently occurs through affecting the rate of growth of the individual pollen tubes (Matthys-Rochon, Gaude, & Dumas 1987; Charlesworth, Schemske, & Sork 1987; Wendel, Edwards, & Stuber 1987)._s

            Unambiguous interpretation of the results of experiments studying cryptic choice is somewhat complicated by the ability of females to affect the viability of progeny through uneven investment into the individual embryos. It has, for example, been observed that the females of zebra finch (Taeniopygia guttata) that were able to copulate with more attractive males produce eggs with higher testosterone concentrations (Vogel 1999). In the traditional arrangement of experiments, i.e. without the use of artificial insemination, it is thus frequently not possible to decide whether the uneven success of the individual males is a result of cryptic choice occurring at the level of competition between sperm or classical sexual selection occurring at the level of the adult individuals. Results to date using artificial insemination indicate that it is possible that the cryptic choice mechanism also allows females to select males exhibiting quite specific phenotype traits, including the degree of expression of classical secondary sexual traits or body size (Evans et al. 2003) (Fig. XIV.4).

Traits formed in biological evolution are transmitted genetically, most frequently in the form of information written in the primary DNA structure of the relevant species. Simultaneously, in a great many cases, the genetic relatedness of the population is not correlated with the similarity of the patterns of behavior transmitted in the particular group through imitation. For example, in individual populations of chimpanzees monitored for long periods of time in their natural environment, a great many patterns of behavior have been observed that were specific only for the population occurring in a certain territory. Systematic studies have demonstrated that, because of these differences, groups in populations of chimpanzees form a sort of cultural spheres that are strikingly similar to human nationalities. Simultaneously, the similarities of the individual cultures were related only very little to the genetic relatedness of their bearers (Whiten et al. 1999). A similar phenomenon was subsequently observed in orangutans (van Schaik et al. 2003). It is thus apparent that cultural patterns are transmitted to a substantial degree independently of gene flux.
Traits formed as a consequence of cultural evolution are transmitted nongenetically, by social learning, occurring in the simplest case by imitative learning (observational learning), i.e. imitation of the behavior of the individual members of the social group (Fawcett, Skinner, & Goldsmith 2002). If, for example, a rat observes that another rat prefers one kind of food of two possible kinds, then it also prefers this type of food for several days (Galef & Whiskin 2001). Only subsequently can individual experience with the two types of food predominate over the learned patterns of behavior and the animal begins to prefer the actually better type of food (Fig. XVII.2). In humans, imitative learning is the most important mechanism of cultural evolution and, according to some authors, it was its development that triggered and facilitated the rapid evolution of our species (Blackmore 2001). However, in most species, social learning does not have the character of imitating the behavior of another individual. Very frequently, the “imitated” individual only draws attention to the possibility of attaining a certain source through its behavior and the “imitating” individual then “finds” a way of getting to this source by itself (Reader & Laland 1999; Blackmore 2001). This mechanism, denoted as stimulus enhancement, is apparently also operative in probably the best known example of cultural evolution, adaptation of English tits to new ways of obtaining food (Hinde & Fischer 1952; Lefebvre 1995). Some time around 1921, blue tits in the Swaythling area learned to peck through the wax closings on milk bottles and peck up the cream from them. The habit gradually spread to other areas of England. Simultaneously, the individual birds used different techniques to open the lids. This indicates that only information on the fact that cream can be obtained by opening a bottle was spread culturally, but not the technique of how to open the bottle (Sherry & Galef 1984; Blackmore 2001).
However, in some species, in addition to stimulus enhancement, imitative learning also plays a role (Fawcett, Skinner, & Goldsmith 2002)(Fig. XVII.3). Imitation of behavior is mostly highly selective. Young animals very frequently imitate their parents or the behavior of other adult members of the population. Another fairly common means of learning consists in imitation of the behavior of the highest-ranking individuals in the social hierarchy. It has been observed, for example for Japanese macaque apes, that if only a low-ranking individual was capable of removing sand from grain (by throwing the mixture into water and collecting the floating grains from the surface), no one tried to imitate it. Only when a dominant male learned this from him did this skill rapidly spread to the whole group (Kawamura 1963). This means of accepting cultural traits is understandably advantageous – from the viewpoint of fitness it makes sense to accept behavior from successful, i.e. from higher ranking individuals.

see Selection cyclic

Charles Robert Darwin (1809–1882) (Fig. XXVIII.6) is certainly the most famous biologist of all time. Even in the absence of his work on the theory of evolution, his other discoveries in various fields of biology would be sufficient to make him renowned. Amongst other things, he discovered the mechanism of formation of corral atolls and the mechanism of the formation of soil through the activities of earthworms, he wrote a number of books, for example books about emotions in animals and about movement in plants, and also compiled an extensive monograph about barnacles. Simultaneously, Darwin had no formal education in biology. According to the wishes of his father, he began to study medicine, but was so bored that he abandoned his studies after one year. In the end, he completed three-year bachelor’s study in theology. During his studies, he was constantly interested in nature, especially geology and biology. He maintained contacts with the best scientists in his surroundings, collected various natural materials and systematically extended his knowledge through his own studies. After completing his studies, he took part in a five-year oceanic expedition, intended for mapping and exploring the shores of South America. Although he was originally accepted on board the research ship Beagle mainly because captain Fritzroy wanted company, he originally unofficially and later officially held the position of natural scientist of the expedition. During the expedition, he collected a great deal of knowledge in the fields of geology and biology, which later substantially affected his scientific ideas, and also gathered a extensive material in his collections, which he regularly sent to England. When he returned to London after the end of the expedition, at the age of 27, he already had the reputation of an important natural scientist. After his return, he married within 2 years and moved to the countryside after three years. He travelled to London only sporadically and travelled around England only to attend scientific meetings. However, he maintained very intense and extensive correspondence with domestic and foreign scientists and carefully followed all the contemporary professional literature. Darwin’s entries in his working daybooks indicate that he began to formulate his theory of evolution around 1837. In 1844, he drew up a 230-page description of his theory of evolution and asked his wife to publish it if he were to die prematurely. Until 1858, he systematically prepared for publication of his theory of evolution and gradually gathered evidence and arguments in its favor and established a sufficiently strong scientific and social position to allow him to publish and defend his ideas. However, he never completed his fundamental and very extensive evolutionary work because, in 1858, a different British biologist, Alfred Russel Wallace (1823–1913) (Fig. XXVIII.7), sent him the manuscript of his work, in which he described his own version of the theory of evolution, asking him to evaluate and potentially publish it. Except for minor details, Wallace’s theory was practically identical with Darwin’s. Darwin’s friends finally arranged for Wallace’s manuscript to be read together with excerpts from Darwin’s manuscript of 1844 at the same meeting of the Linnean Society and both papers were subsequently published in the same edition of the Proceedings. In addition, Darwin interrupted his efforts on his extensive work and, instead, rapidly prepared an abbreviated version of “On the Origin of Species through Natural Selection” for publication.

Darwin’s theory of evolution, published in 1859, actually consists of at least five mutually complementary theories (Mayr 1982). Most of them had already appeared at the very least in intimations in the works of his predecessors; however, Darwin was the first to present them to the public in comprehensive form and to demonstrate their veracity by empirical facts.

The first of Darwin’s theories is the theory of the existence of the evolution of species. According to it, species are not invariant, but vary and can evolve over time. Lamarck propounded the same theory before him, but Darwin was the first to collect sufficient data (and social capital) to convince a large part of the professional public.

The second theory is the theory of the common origin of all species. Darwin postulated that species were formed and are still formed in evolution by divergence from a common ancestor. This theory meant a radical rejection of all the ideas about the independent, either natural or supernatural, creation of the individual species.

The third theory is the theory of the divergence of species in their phenotype traits. Darwin even proposed a mechanism that could lead to the divergence and mutual differentiation of individual species. This mechanism was founded on centrifugal selection and we now know that it is actually not very important in evolution in the suggested form. However, the fact that the organisms that are formed by divergence from a common ancestor can gradually differ more and more through the continuous accumulation of changes over time is more important than the actual mechanism of phenotype divergence. The general acceptance of this fact led to fundamental changes in the concept of systematic biology and in the approach to the creation of a taxonomic system.

            The fourth theory is the theory of gradualism. According to it, species gradually evolve and change from one to another through the slow accumulation of minor changes. In his work, Darwin explicitly rejected the opposite possibility, i.e. saltationism, i.e. sudden changes in jumps from one species to a different species.

            The fifth theory was the theory of natural selection as the main mechanism driving all evolutionary changes, whether the formation of adaptive traits, the formation of complexity or the formation of biological diversity. At the time of its publication, this part of the theory of evolution met the greatest resistance amongst the professional public. Especially paleontologists, but also a great many biologists, including Darwin’s greatest supporters, had serious doubts about the importance of natural selection. In fact, their arguments convinced Darwin to gradually admit the possibility of other mechanisms, including the heritability of acquired traits, in his later editions of the “On the Origin of Species”.

            Before he died, Darwin published a number of other extensive works, in which he elaborated his theory of evolution. Of his most important evolutionary discoveries, mention should be made of the discovery of sexual selection as a mechanism acting independently of natural selection. According to Darwin, sexual selection, i.e. selection that occurs in the choice of sexual partners, enables explanation of a number of biological phenomena, including a great many aspects of human evolution. On the other hand, another of Darwin’s theories of evolution, i.e. the theory of inheritability, was erroneous right from the beginning and is currently only of historical importance.

see Dawkinsian evolution

The emergence of amphimixis also brought about the creation of extraordinarily favorable conditions for the spreading of a number of types of ultraselfish genes, i.e. genes that spread in the population even when they simultaneously reduce the fitness of their carriers. While, in asexually reproducing organisms, the fate of the individual gene is permanently connected with the genome in which it occurs, and the gene must thus be more or less loyal to the other genes, in organisms with amphimixis, a gene or, to be more exact, the allele of a certain gene appears in a different genome in every generation. As a consequence, classical Darwinian evolution, in which those alleles that increase the fitness of their carriers are fixed, changes into Dawkinsian evolution (see IV.9.1). During Dawkinsian evolution, preferentially those alleles that are capable of ensuring propagation of their copies at the expense of copies of other alleles in the same locus and sometimes at the expense of the fitness of their carrier are preferentially fixed – see the bluebeard model in Section IV.9.1 (Dawkins 1976; Dawkins 1982). The main driving force for evolution ceased to be competition between individuals within a population and became competition between alleles within the individual loci (Tab. XII.1). The ability of alleles to program the traits or behavior of their hosts so as to gain advantages in intra-species competition became only one of many strategies through which the allele can ensure its preferential spreading within the population.

see Mass extinction, after the end of mass extinction events

see Point mutations and also Mutations at the level of the entire DNA section

The progress of cladogenesis can be depicted in a graphical form, called a tree graph, a dendrogram, by mathematicians, and simply a tree by biologists. It would be logical to call a tree depicting cladogenesis a cladogram. However, at the present time, a large number of authors use the term cladogram to denote the tree formed using cladistic methods, not depicting the progress of cladogenesis but rather the distribution of apomorphies (i.e. new evolutionary features – see below) within studied taxonomical units, most frequently species. Consequently, the tree describing cladogenesis will be denoted in the following text by the rather awkward term scheme of cladogenesis. The tree consists of a system of gradually branching out lines, termed branches, where the order and sites of branching, i.e. distribution of nodes, reflects the time order of the mutual splitting off of the phylogenetic lines (Fig. XXIII.4). Each branch (line joining two nodes) depicts a single species and its final node corresponds to the particular species at the instant of speciation. The branches originate from a particular single node denoting the individual phylogenetic lines of organisms. The phylogenetic line can contain several species or just a single species. For the purposes of phylogenetic studies, the species of a single phylogenetic line form an operational taxonomic unit (OTU). For example, however, in phenetics (see XXV.2.1), OTU need not be formed of species of the same phylogenetic line, but of species that have a certain type of phenotype similarity. In contrast to regular taxa, it is not necessary to name the individual OTU or to find a formal taxonomic level (rank) for them. The root of the tree, i.e. the lowest branch, from which all the other branches split off in a certain order, denotes the common ancestor of all the studied species, and the terminal branches correspond to the individual species that were included in the analysis. The arrangement of the inner branches in the direction from the root to the terminal branches of the tree denotes the order of splitting off of the ancestors of the individual species included in the analysis. As the species last for only a limited period of time and sooner or later die out, most of the inner branches of the tree denote already extinct ancestors of modern species. If the analysis includes only living species of organisms, the ancestors are hypothetical, whose existence has been derived on the basis of the traits of modern, i.e. neontological species. In contrast, if the scheme also includes species living on the Earth in the past and thus known only from the paleontological record, these species can also be placed on one of the inner branches of the graph depicting the cladogenesis scheme. However, even in this case, all the species are again placed on terminal branches on trees if they are created by cladistic methods. The length of the branches on the graph and the angles enclosed by the individual branches do not have any biological meaning. If the length of the branches were to correspond to the duration of the individual species or number of evolutionary changes that occurred in the individual branches, this would no loner be a cladogenesis scheme, but rather a phylogenetic tree, i.e. a phylogram.

It is quite clear that the process of evolutionary biology is a stochastic process. Living organisms and their environment, i.e. the system in which the process occurs, contain an enormous number of elements whose behaviour is determined to a greater or lesser degree by chance.

If an advantageous new mutation appears in the DNA of an individual, that brings its bearer increased resistance to a certain disease, we could theoretically expect that the descendants of this mutant will gradually become predominant in the population, i.e. that the particular mutation will become fixed. In actual fact, this need not occur. The resistant mutant could be killed while still young by a falling tree, could be eaten by a predator, or the particular population need not necessarily encounter the relevant disease for a long time. Thus, the potentially advantageous mutation will most probably be eliminated by genetic drift.

Mutations themselves occur more or less by chance, so that the character and order in time of their occurrence cannot be in any way predicted. On the other hand, it must be admitted that some micro-evolutionary processes are highly deterministic, such as natural selection, molecular drive, meiotic drive. This means that, in short experiments, we are frequently capable of predicting the course of the relevant micro-evolutionary changes on the basis of the properties of the individual organisms. When several islands in the Greater Antilles were experimentally colonized by populations of small lizards of the Anolis genus, it could be observed that genetic fixation of very similar morphological changes occurred in all the populations after several years. In contrast, as a consequence of participation in the random process of mutagenesis, the results of repeated laboratory experiments, in which the microevolution of bacterial populations is modelled under strictly controlled conditions of continuous cultivation, are frequently quite different.

Biological evolution as a whole, i.e. encompassing both microevolutionary and macroevolutionary processes, is a very long-term process. Simultaneously, organisms are systems with a memory, whose future development depends on the development that they underwent in the past. The effects of random processes also logically accumulate andare amplified. If it were possible to perform a long-term evolutionary experiment consisting, for example, in colonizing completely identical islands with completely identical species of organisms and subsequent long-term observation of the evolution of these species on the individual islands, it is quite certain that the flora and fauna of the individual islands would gradually become different through the effect of random processes.

Evolutionary processes are governed by their own laws. As we gradually come to understand these laws, we are increasingly capable of predicting the course of evolutionary processes. As the element of chance plays a role in evolutionary processes in many respects, it is quite impossible that we would be able, sometime in the future, to specifically (and thus not statistically) predict the course of biological evolution of some species of organism. The influence of chance similarly excludes the possibility that evolution could occur in exactly the same way at two places in the universe, i.e. that the same kinds of organisms could develop on two different planets.

It is advantageous for organisms if they are able to modify their ontogenesis in dependence on the local conditions in which they find themselves. This ability is especially advantageous for immobile organisms that are bound all their lives to the place where they were born and grew up.  It is thus encountered primarily in plants (Pigliucci 1998) and to a lesser degree in other organisms (Gotthard & Nylin 1995; Brönmark & Miner 1992). In a great many species of plants, the phenotype of individuals growing at relatively dry sites differs from the phenotype of individuals at damp sites; however, frequently even the phenotype of separate parts of a single individual differs in dependence on the local conditions (Fig. XII.12). The phenotype of water plants differs according to the speed of water flow at the particular sites. In a great many species of plants, preference is given to the phase formed by the vegetative or by the reproductive organs, in dependence on the amount of resources available to the particular individual. Development of the organism is thus programmed so that it occurs in dependence on the external conditions and so that it results in an individual with the phenotype that is best adapted to these local conditions. The ability to purposefully modify ontogenesis in dependence on the external conditions is called developmental plasticity. From the viewpoint of the individual, it is advantageous if its phenotype corresponds best to the local conditions of the environment in which it finds itself. However, from the standpoint of the existence of the species, adaptive developmental plasticity reduces the ability of the species to submit to the action of selection pressure in the environment, and thus to evolutionarily adapt to changing conditions. If the environment undergoes cyclic changes, i.e. oscillates between several different states at regular or irregular intervals, this evolutionary stability of the species can be advantageous, as it reduces the substitution burden to which the species would otherwise be exposed. In contrast, if the changes are acyclic and irreversible or cyclic, but with a periodicity that is comparable with the usual length of existence of the species, developmental plasticity and the related reduced evolutionary plasticity will decrease the chance of long-term survival of the particular species. While species without developmental plasticity have a chance to gradually adapt to the particular changes in the environment as a consequence of the action of selection, a developmentally plastic species only avoids the relevant selection pressure temporarily and frequently imperfectly within the limits of its developmental plasticity. Whether and how much developmental plasticity actually reduces the evolutionary potential of a species is still a subject of discussion. The fact that, on a drastic change in the conditions in the external environment, it partly protects the species against the action of selection, simultaneously provides the species with time to accumulate mutations that gradually lead to the formation of adaptive adjustment to the new conditions (see XVI.3.1). See also developmental canalization.

see History of evolutionism - pre-Darwinist period

see Environmentally directed mutations

See Biodiversity.

See Biodiversity.

see History of evolutionism - neo-Darwinist period

see Coevolution

Dominant and recessive relationships are the best known forms of gene interaction between alleles within a single locus. (See also Gene interactions). Diploid organisms have two alleles from each gene. If both alleles at a given locus are the same, then (from the standpoint of the particular gene) this is termed a homozygote individual, a homozygote. If the two alleles differ, then this is a heterozygote individual, a heterozygote. The manifestation of each allele can depend on the second allele in the given locus for the particular individual. It very often happens that a particular allele is recessive, i.e. it is manifested in the phenotype only when present in two copies in the given individual, i.e. in a recessive homozygote. A dominant allele is the opposite of a recessive allele. Its presence is manifested in the same way both in a carrier of two copies of the given allele, i.e. in a dominant homozygote, and in a heterozygote, i.e. in an individual in which it is present in only one copy. The degree to which semi-dominant alleles, i.e. alleles with partial dominance, are manifested in the phenotype of an individual depends on whether they occur in the genotype of the given individual in one or both copies. In co-dominance, the two alleles present are manifested to the same degree to which they would be manifested in the relevant homozygotes. While, in partial dominance, the degree of manifestation of the two alleles in a heterozygote is less than for one or the other homozygote, in super-dominance, the expression of the given trait is greater in a heterozygote than in either of the two homozygotes. Interactions between alleles of a single locus can be divided schematically only if these alleles are manifested in the degree of the phenotype expression of a simple quantitative trait. For traits of qualitative character, it is mostly possible to differentiate only between dominant and recessive alleles; mutual differentiation of alleles with partial dominance, super-dominance and co-dominance is usually rather difficult or even impossible.

The picture is further complicated by the fact that that there are usually more than two alleles of a single gene and also by the fact that dominance is a relative matter, i.e. the matter of the relationship between two specific alleles of a given gene, rather than an absolute property of a particular allele. Allele a₁ can act as dominant in relation to allele a₂, allele a₂ as dominant in relation to allele a₃ and simultaneously allele a₃ as dominant in relation to allele a₁. So that the subject of dominance and recessivity is even more complicated, it is necessary to point out the fact that a particular relationship between two particular alleles can also depend on the context, i.e. the effects of genes present at other loci can also be important. In the presence of a particular allele at locus B, allele a₁of locus A can be dominant in relation to allele a₂; in the context of a different allele at locus B, allele a₁can, on the other hand, act as recessive towards allele a₂

A certain amount of direct and indirect evidence demonstrates that the dominance of alleles is actually a more complex phenomenon that is, itself, the subject of biological evolution (Bourguet 2001). For example, it was repeatedly found that, in the natural population, the most common alleles are usually dominant and, on the other hand, minority alleles are frequently recessive. If, on the other hand, we isolate individuals in the laboratory that bear two newly formed mutated alleles, or if we obtain individuals bearing minority alleles in mutually isolated natural populations, then the relationship of partial dominance is mostly found between their alleles. For different explanation of the phenomenon see also Haldane’s sieve.

see Evolutionarily stable strategy

see Anagenesis in parasites

In describing the dynamics of fixation of mutations, it is necessary to consider not only the probability with which a mutation will become fixed in a population of a certain size, but also the time required on an average for fixation of a mutation. The probability that a newly formed mutation will be fixed is equal to 1/2N. Similarly, the average time required for fixation of one mutation is proportional to the size of the population. However, this is a case of direct proportionality. M. Kimura derived that the average time for fixation of a mutation by genetic drift is equal to 4N_e generations, where N_eis the effective size of the population (the effective size of the population is a term that will be explained in Section V.3.2.1) For a population with an effective size of 30,  fixation of a neutral mutation will thus require an average of 120 generation periods.

The graph describing the shape of the time distribution required for fixation of a mutation by genetic drift is highly asymmetric. The asymmetry of the graph reflects the fact that it is highly improbable that a mutation will become fixed sooner than in 0.8N_e generation periods and a great many mutations require substantially more time than the average 4N_egeneration periods.

History of evolutionism – post-neo-Darwinist period

The closest form of cooperation and the closest interconnection  exists between intracellular endosymbionts, called endocytobionts, and their host organisms or, to be more exact, their cells. When the intracellular endosymbiont begins to be transferred from one host to another solely through the sex cells of the host, its fitness becomes completely dependent on the fitness of that host. This basically ends any further “arms race” between the host species and the endosymbiont, as the selection pressure on the creation of traits permitting an increase in its own fitness at the expense of the other organism completely disappears. From that moment on, it is advantageous for both species to only cooperate and the coevolution of the two species ends with the two species dividing up the individual biological functions so that the chimeric cell formed can work as effectively as possible (see XIX.5.5.1). This division of functions sometimes goes so far that both species eliminate, from their genomes, the genes whose function would  be doubled or even replace their own genes in the genome by the genes of their partner – symbiont. Important organelles of eucaryotic cells, including mitochondria and plastids, evolved through this mechanism, (Margulis 1981). However, extensive results indicate that the endosymbiotic formation of mitochondria and plastids was probably not the first symbiogenetic event in the history of eucaryotic cells. Comparison of phylogenetic trees formed on the basis of various proteins has shown that the actual nucleus of the eucaryotic cell was most probably formed as a chimera through the combination of genomes, probably from two symbionts, one of which was a related gram-negative eubacterium and the other an archaebacterium (Golding & Gupta 1995; Gupta 1998). Study of the metabolic pathways of contemporary organisms and their organelles leads to similar conclusions (Martin & Müler 1998)(Fig. XVIII.3). It could be speculated that it was an increase in the size of pre-eucaryotic cells (by a volume 3-4 orders of magnitude greater than the procaryotic cells) that became a pre-adaptation for the emergence, first of the ability to phagocytose larger particles of food and, in direct connection with this ability, also pre-adaptation for the emergence of endosymbiosis. A series of subsequent endosymbiotic events could finally have led to the formation of modern eucaryotic cells and subsequently of multicellular organisms (Flegr 1990). Such an increase in the size of a eukaryotic cell could be made possible, for example, by the formation of a mechanism that permits overcoming the limitation of the rate of biochemical reactions by the slow rate of diffusion of the individual reactants in the cytoplasm (Flegr 1990).

Endosymbionts and their hosts have gone very far in mutual integration. Endosymbionts live directly inside the bodies of their hosts. In the vast majority of cases, the symbiosis of the two organisms is so close that one species cannot survive without the other one and does not even occur in isolated form in nature – with the exception of the invasive stage of an endosymbiont and new-born young of the host, which have not had time to become “infected” by their parents or the environment. Ruminant ciliates and bacteria are known examples of endosymbionts, as are endiosymbiotic protozoa in the digestive tracts of termites.  In the absence of these organisms, the host organism would not be capable of utilizing its main source of food, plant polysaccharides, especially cellulose. However, symbionts in the digestive tract are also important for other species, such as humans. Experiments with rodents freed of microbial symbionts and kept permanently under these conditions have shown that these animals require, for their lives, approximately one third more food than animals kept under normal conditions (Hooper & Gordon 2001). The symbiosis of fungi and algae (or blue-green algae) in the form of lichens is an obvious textbook example. It is less widely known that, according to some (very bold) ideas, terrestrial plants are also actually a sort of inverse lichens, i.e. the products of ancient symbiosis between algae of the Charophyceae genus and a fungus. Here, the algae would provide the mechanical support, protection against UV radiation and a number of other functions and the fungus would provide the cytoskeletal apparatus required to prolong the growth of cells, employed, for example, in the growth of pollen tubes and hair roots (Atsatt 1993; Jorgensen 1993)
            Thus, very few species of animals can survive in the absence of endosymbiotic organisms. If nothing else, the symbionts at least provide them with some essential substances, for example some vitamins, that they are not capable of synthesizing themselves. However, in a great many cases, cooperation amongst the relevant species of organisms need not be especially close; the individual species of endosymbionts and the individual species of hosts can be mutually substituted.

Genetic information is defined as information entered in the primary structure of a nucleic acid, i.e. in the order of the nucleotides in the DNA molecule or (in some viruses) in the RNA. However, organisms also contain a large amount of further information in the structures of their cells and multi-cellular bodies, which also co-determine the course of all the molecular, biochemical and physiological processes, including ontogenesis, and thus co-determine both the characteristics and the behaviour of the organisms. This is called epigenetic information.

The entire molecular apparatus of the cell determines which DNA sections will be transcribed to the RNA at a given moment and which RNA molecules will be further translated to proteins.  If an important regulation molecule were missing in the zygote, the course and result of the ontogenesis of the given organism could be seriously disturbed and altered, even if the genetic information in the zygote gene pool is not disturbed. According to some authors, the importance of the molecular apparatus interpreting the genetic information for the progress of ontogenesis is similarly important as the genetic information located in the genome.

It cannot be denied that, for setting into motion and directing the individual development of an individual, the presence and functioning of both components is absolutely essential. Interventions into any of them can lead to similarly important influencing of the progress and results of ontogenesis. Nonetheless, from an evolutionary standpoint, genetic information encoded in the primary structure of the nucleic acid plays a quite primary and incomparably important role. A random change in the molecular apparatus of a cell can, of course, affect the result of the relevant ontogenetic processes, i.e. the characteristics of the particular individual. However, it is very probable that the changes caused in the characteristics of the organism would lead to repetition of the same changes in the molecular apparatus of the cells in the offspring and that the given change would be transferred to further generations. In certain, quite exceptional cases, the particular change can cause the occurrence of the same changes and thus be passed on from one generation to the next. An example could consist in prions, protein molecules that can adopt two different conformations, where the presence of the less common of them can induce the transition of other molecules to this conformation. However, only a negligible percentage of molecules or other cellular structures have this characteristic and thus it cannot be expected that heredity based on this principle could occur to a greater degree in evolution. In contrast, if mutation occurs in the DNA, the relevant change is automatically transferred, because of universal copying of the primary DNA structure during the replication, to subsequent generations, and causes the same changes in ontogenesis in progeny organisms as it caused in the parent organisms. While primary those genetic changes that are in some way advantageous for their carriers have a chance to be fixed evolutionarily, only epigenetic changes that are not only advantageous, but also cause their own occurrence and can thus be transferred from one generation to the next, have a chance of evolutionary fixation. Put simply, all DNA changes have high heritability, but epigenetic changes in the molecular apparatus interpreting genetic information have much lower heritability, generally approaching zero, in the vast majority of cases. As the heritability of changes is an essential condition for the functioning of biological evolution, especially the formation of adaptive characteristics of organisms, it is almost certain that genetic and not epigenetic information acts as the main medium for the evolutionary memory of contemporary organisms.

The development of a multicellular individual (ontogenesis) constitutes a set of extremely complicated and simultaneously precisely spatially and temporally coordinated steps.

Epistatic interactionsare interactions amongst genes occurring at different loci on the genome. The effect of a certain gene or some alleles of a certain gene is frequently quantitatively and qualitatively dependent on the presence of quite specific alleles in a completely different locus. Genes and thus also polymorphism in these genes can be functionally interconnected and the fitness of the bearers of certain alleles can be dependent, not on their frequency in the population, but rather on the frequency of certain alleles in completely different loci in the genome.

For example, if allele a₁ of gene A is selectionally more advantageous (than allele a₂) in combination with allele b₁ of gene B and selectionally less advantageous (than allele a₂) in combination with allele b₂ and if polymorphism is maintained in gene B by any of the above-mentioned mechanisms (for example, selection for heterozygotes), then polymorphism will exist permanently in gene A (Fig. VIII.10).If, for example, a certain form of the enzyme were to function better in black two-spotted lady beetles and a different form in red lady beetles (for example, because, as a consequence of differences in the degree of reflection and absorption of solar radiation, the body temperature of dark-colored lady beetles in the sun were higher than that of red lady beetles), then both alleles of the relevant gene would remain in the gene pool of the species A. bipunctata for prolonged periods of time.

As most genes are apparently functionally interconnected in various ways, it can be assumed that epitstatic interactions will be very important in maintaining the polymorphism of a great many traits and, because of the existence of gene linkage, also the maintenance of polymorphism in selectively neutral traits (mutations) (Kel­ly & Wade 2000). See also Frozen plasticity theory.

Evolution means the accumulation of changes in any system with a memory. A special for of evolution is the biological evolution, which is characteristic by involvement of natural selection.

Behavior can be defined in various, generally unsatisfactory ways. In this chapter, behavior will be considered to constitute the responses of different organisms to stimuli coming from their external and internal environment, where these responses most often consist in the changes of their position or in the position and state of their organs. The integration of signals and storage of the information that directs an individual’s behavior is not performed at the genome level, but at the level of specialized organs or organ systems and, in animals, especially at the level of the neural system. Behavior is basically an integral compound of the organism’s phenotype. In some cases, it is quite difficult to distinguish the point where the individual’s traits (morphological, physiological or molecular) end and its behavior begins. Even the body color, i.e. the part of its phenotype that, at first sight, definitely belongs to the category of morphological attributes, can be (and in animals often is) a result of the behavior of the organism – for example, the seasonal changes in skin color in beach volleyball players or similar, only slightly more spectacular changes in chameleons, cephalopods and some fish. Comparing the morphological attributes to computer hardware and behavior to software may seem to be a useful analogy. The genotype of an individual during the ontogenetic process determines the attributes of the organism. The way the organism will handle these attributes, how is it going to use the organs that nature has given it during the ontogenetic process, i.e. how is it going to behave, depends on its software. The same morphological structure (hardware) may be used for completely different purposes – the same beak can be used with the same success for shelling seeds or breaking snails out of their shells; prehensile primate limbs are even more universal. While the hardware, i.e. the body structure, remains practically unchanged during the adult’s lifetime (at least if we ignore the manifestations of wear and tear), the software can develop continuously; the individual is able to change its behavior, for example, as a result of accumulated experience. It is obvious that components of behavior exist that, in principle, resemble software, e.g., learned patterns of behavior whereas others are more reminiscent of hardware, e. g. inherited fixed behavioral patterns.

The biological importance of the existence of functional anisogamy lies in the fact that it ensures that zygotes are not formed by combination of mutually related cells, in the extreme case gametes produced by a single individual (autogamy) but, where possible, by cells derived from different individuals (alogamy). However, the advantages of alogamy are not entirely apparent at first glance, especially the advantages for the individual. It can be advantageous for a population or the species as a whole if unrelated individuals can mate together. It holds more or less for most of the models that explain the existence of sexual reproduction as a mechanism increasing the evolutionary potential of the species that the favorable effect of sexual reproduction increases with increasing genetic difference of the mating individuals. However, for the individual, the inability to mate with the members of the same mating type is a limiting factor and thus generally disadvantageous. Thus, it is necessary to explain why individuals do not emerge in the population that would be capable of mating with all the members of their species, without respect to their mating type.

Although a single male can frequently ensure the production of sufficient microgametes to cover the needs of the entire population, the ratio of the number of progeny of the male and female sex, i.e. the secondary sex ratio of the population, is close to one with surprising frequency. The mortality of males and females frequently differs during maturing and finally also in adulthood. Consequently, in adulthood, the tertiary sex ratio can be very different, usually biased in favor of females. In contrast, the primary sex ratio, i.e. the ratio of male and female zygotes immediately following fertilization of the eggs, is, to the contrary, usually biased in favor of the sex whose embryos die more frequently prior to birth. For example, in human beings, there are 160 male zygotes for every 100 female zygotes, while only 106 boys are born for every 100 girl babies (Dorak et al. 2002). It is obvious at first glance that a secondary sex ratio equal to one is not optimal from the standpoint of the population for a great many species. If more females were to be born at the expense of males and every male were to fertilize a greater number of females, the population as a whole could grow faster than when the numbers of males and females are approximately equal.

            This paradox has long drawn the attention of a number of biologists. Consequently, a number of hypotheses have emerged in to explain its existence. Hypotheses considering the same numbers of males and females to be a consequence of a genetic mechanism of determining the sex of the embryos are currently falling into disfavor. A genetic mechanism of determining sex should primarily affect the ratio of the two types of heterogametes and thus the ratio of male and female zygotes immediately after fertilization. This ratio, the primary sex ratio, however, frequently deviates substantially from a value of 1 and, as already mentioned above, approaches a value of 1.6 in favor of male zygotes in humans (Dorak et al. 2002). Similarly, comparative and experimental studies have demonstrated beyond the shadow of a doubt that a genetic mechanism of determining the sex of a zygote is extremely plastic at both the interspecies and intraspecies level. It is known that completely different mechanisms that, together, could theoretically ensure a quite arbitrary ratio of males and females in the progeny, exist in the individual taxa. Simultaneously, it is apparent that a population exposed to a selection pressure for a change in the sex ratio usually reacts quite easily to the given pressure and changes the sex ratio in the appropriate manner (Orzack & Gladstone 1994). It is thus apparent that a secondary sex ratio of 1 is not a consequence of the mechanism employed to determine the sex of the embryo but rather a result of quite specific selection pressures and that it is adaptive.

            A value of the secondary sex ratio equal to one can also be explained by the action of individual selection. The effect of this factor on the secondary sex ratio is expressed in the Shaw-Mohler principle (Shaw & Mohler 1953). Translated from the language of mathematics to normal language, this principle says that, at the instant when, because of the momentary ratio of males and females in the population, it is preferable to produce members of one sex rather than members of the other sex, those individuals, who produce more progeny of momentarily more valuable sex, will be at an advantage.

            Under normal circumstances, a population is in equilibrium in the numbers of males and females. The selection value of males (most readily expressed as the number of progeny that they leave behind) is the same as the selection value of females. Simultaneously, it is not important that all the females in the population have approximately the same number of progeny, while there are frequently enormous differences amongst males in the number of progeny. The variance value has no effect on the selection value of a member of a certain sex, only the value of the average number of progeny per member of that sex is important. If males predominate because of a random fluctuation in the population, then those individuals that, on the basis of their genetic predisposition, produce more progeny of the female sex are at an advantage. Thus, the population gradually returns to equilibrium. The temporary increase in the sex ratio amongst humans in the post-war years has been cited as an example of this phenomenon in the past. However, newer studies have shown that, for example, the men that returned to England from the battlefields of the I^st World War were more than 3 cm taller than those that died. As taller men exhibit a higher sex ratio in their progeny, the increased sex ratio in the post-war years can be fully explained by the higher death rate of shorter men in the military conflicts {13730}.

            It follows from game theory that the optimal strategy for an individual is to invest the same amount of energy into production of sons as into production of daughters. Under conditions where the production of sons is just as costly as the production of daughters, the ratio of young of both sexes in the population settles at a value of one.

            This explanation of maintenance of equal numbers of the two sexes was apparently first proposed by R.A. Fisher in 1933 (Fisher 1958). However, it must be admitted that later mathematical analyses of the relevant model demonstrated that establishment of equilibrium through such individual selection is too slow and that some other mechanisms are apparently also active in a great many species (James 1995).

In a great many cases, the fitness of the bearers of a trait depends only very indirectly on its frequency. An increase in the frequency of a particular trait increases the fitness (and subsequently also the frequency) of the bearers of another trait, an increase in the frequency of the bearers of a different trait increases the fitness of the bearers of this other trait and this subsequently reduces the fitness of the bearers of the first trait. In these complicated interconnected systems, the fate of new mutations is decided not so much by the Darwinist fitness of its bearers as by whether the presence of the given trait is an evolutionarily stable strategy (ESS) in the sense of game theory. Evolutionarily stable strategy is considered to constitute strategy that, as soon as it predominates in the population, will be more successful in every situation than any other minority strategy (Maynard Smith & Price 1973). Thus, if an allele that codes behaviour of an organism (strategy) that is evolutionarily stable predominates in the population, then no other allele that occurs in the population through migration or mutation can force it out of the population – see the definition of ESS above.

A classical, albeit simplified example encompassing only two strategies in the basic variant, competition of only two strategies, on the basis of which evolutionarily stable strategy is studied, is the model of the dove and the hawk (Fig. IV.5).  Dove and hawk are names for two alternative strategies that can be adopted by two members of a single species when they clash, e.g., over a piece of food or some other scarce resource. The strategy of the dove consists in that the two individuals divide up the food. In contrast, the strategy of the hawk is dependent on the fact that the two individuals fight for the food, the winner gains the whole piece and the loser remains only with its injuries. If a dove encounters a hawk, it retreats without a fight (and thus without injuries) and the hawk gains all the food for itself. Changes in the frequencies of the two strategies are dependent on how successful its bearers are in competition with the other members of the population, i.e. how much food (and how many injuries) they gain from mutual encounters. If a hawk comes into a population of doves, it is initially very well off as it wins all the encounters without a fight and obtains all the food. The frequency of hawks thus increases in the population. Similarly, if a dove enters a population of hawks, it has an advantage in competition with the other members of the population. It always gives up in advance in any fight for food (however, it will certainly occasionally find some food when a hawk is not close-by); however, in conflicts with other hawks, an average hawk will end up with injuries in half the cases. It is apparent that, in the end, a stable ratio of doves and hawks will be established in the population, at which the average fitness of doves and hawks will be identical. The specific value of this ratio is determined by the by the values of the pay-off matrix. The following scheme gives an example of such a matrix. If two doves meet over a piece of food, each obtains an average gain of o/2 (where o is the average value of one piece of food expressed as input of biological fitness for the individual that consumes it). If two hawks meet, each of them gains, on an average, (o – c)/2 (where c is the average loss connected with injuries suffered in conflict of two hawks over prey, again expressed as the reduction in biological fitness of the injured individual). If a hawk encounters a dove, the hawk obtains gain o and the dove does not obtain any gain (but also suffers no loss). The average gain of a hawk in all conflicts (with doves and hawks) depends on the presence of the two strategies in the population and is equal to

(1)

where p is the frequency of hawks in the population. The similar average gain of a dove is

(2)

The population moves towards an equilibrium state, at which the average gain of the representatives of the two strategies is equal and where it holds that Z_h = Z_d. Substitution into equations (1) and (2) yields

(3)

Following simple modification, this equation yields the frequency of hawks in the equilibrium population

(4)

Neither the strategy of the dove nor the strategy of the hawk is evolutionarily stable. On the other hand, the strategy “behave like a hawk with frequency o/c and like a dove with frequency of (1 – o/c)” is evolutionarily stable; if an allele that determines this behaviour predominates in the population, no other allele will be capable of successfully penetrating into the population. The basic model of the dove and hawk can be variously further developed (see also XVI.9). For example, interesting situations occur if we admit the existence of other strategies, such as the strategy “act like a hawk at the beginning of an encounter but, as soon as you encounter resistance, run away” or the strategy “act like a dove initially but, as soon as you are attacked, begin to fight like a hawk”. In some models, we find that a particular strategy acts as evolutionarily stable only until two different alternative strategies are present in the population; in other cases, the frequency of a certain strategy begins to increase but is completely forced out by some other strategy after a certain period of time (a strategy that had no chance of spreading under the initial conditions).

Most people erroneously understand strategy to refer to the particular behaviour of an animal or human being. However, the theory of evolutionarily stable strategies is certainly not related only to the evolution of individual patterns of behaviour. From the standpoint of the theory and the mathematical apparatus employed, it makes no difference whether we study the competition of the alleles that code a certain pattern of behaviour of their bearers, or alleles that code, e.g., the synthesis of a certain pigment or enzyme. Competition for an evolutionarily stable strategy is applied almost universally for sexually reproducing organisms. In these organisms, the fitness of the bearers of certain alleles is rarely determined by an unvarying selection coefficient, but is rather usually dependent on the frequency with which it encounters other alleles of the same or some other gene in the future embryos, i.e. on which alleles will probably be borne by both parents of the future progeny.

The fact that the advantageous or disadvantageousness of a certain strategy (in general a certain trait) depends on the frequency of alternative strategies (traits) in the population indicates that it is necessary to quite fundamentally reassess the original Neodarwinist concepts of the mechanisms of biological evolution.While the simple Neodarwinist model quite naturally assumes that the criterion of evolutionary success of a particular trait (characteristic or pattern of behaviour) consists in the average biological fitness of its bearers, contemporary theory indicates that, in the long-term perspective, the evolutionary stability of the given strategy is a more important criterion (given by patterns of behaviour or the presence of a particular trait).At the very least since 1973, when John Maynard Smith and George Price published the concept of evolutionarily stable strategy, this rendered completely irrelevant the popular dispute between the proponents and opponents of Darwinism as to whether the principle of natural selection and the principle of biological fitness are or are not circular definitions and whether Darwin’s explanation of the formation of adaptive traits is or is not a tautology from the standpoint of formal logic (see I.10.1)The development of the theory of evolutionarily stable strategy demonstrated that this explanation is primarily a scientific error – mutants whose mutated trait gives them greater fitness at the present time or in the future do not predominate in evolution, but rather mutants whose mutated traits represent evolutionarily stable strategy in the sense of game theory.We could, of course, begin to consider evolutionary stability to be a criterion of fitness.However, this would constitute a very fundamental redefinition of the Neodarwinist concept of fitness (as a technical term encompassing a set of quite specific and, under various circumstances, different characteristics affecting the chance of an organism to leave progeny, see I.10.1) and the term fitness would then really lose meaning to a substantial degree.

If we return to the original model of the dove and the hawk, we can see that, from the viewpoint of classical Neodarwinist theory, the dove strategy should win out in a structured metapopulation, as local subpopulations consisting of only doves would contain individuals with the greatest average biological fitness and migrants originating from this population would contribute to the greatest degree to the subpopulation of migrants, so that they would “infect”, with their genes, the greatest number of surrounding populations and would establish the greatest percentage of new populations.“Infection” of already existing populations would, however, be unsuccessful in a great many cases or would be only temporarily successful, as the dove strategy is not ESS.The theory of evolutionarily stable strategies shows that, in the long-term perspective, the substantially less advantageous mixed strategy from the standpoint of average biological fitness “behave as a hawk with probability p and like a dove with probability 1-p” is more successful.While this strategy is suboptimal from the standpoint of the average reward that the two individuals carry away from the encounter (compared to the average reward in a population consisting of only doves), it is, however, evolutionarily stable and, because the relevant population cannot be infected with any other strategy, it will, in time, predominate in all the local populations, and thus also in the subpopulation of migrants – potential founders of new subpopulations.

The concept of evolutionarily stable strategy thus apparently represents one of the deepest and most important blows to the very foundations of Darwin’s theory of evolution since the emergence of Neodarwinism.It is interesting and apparently quite significant that this aspect of the theory of evolutionarily stable strategies is currently not assigned its true worth and is even not much taken into account amongst evolutionary biologists.

Some authors assume that the relationship between a morphological trait that is useful from the viewpoint of specific behavior of an organism and the behavior itself is exactly the opposite of how it is described by the Baldwin effect. They assume that the relevant (incidental) phenotype change is primary and useful exploitation of the change by creating an appropriate behavioral pattern is secondary. Returning to the example in Chap. XVI.3.2, we find that birds with large strong beak first arise and that they then look for ways to use it and then, finally, by the trial-and-error method, they find that it can be used for shelling snails. According to these conceptions, in evolution,  the phenotype of organisms does not adapt itself to activities and the environment through adaptations, but rather by adoptions – by actively creating those behavioral patterns that best utilize the changes in the phenotype made by mutations and by seeking an environment where these phenotype changes can be best used (Piaget 1979; Ho & Saunders 1982).
            It may seem that both variants of the origin of usefulness are possible and even highly probable for adaptive traits that are conditioned by only one mutation. Actually, egression of the usefulness of adaptations by the Baldwin effect is much more probable. If a new mutation arises, e.g. one that leads to egression of a large strong beak, and the mutant would be lucky enough to find a way of using it sensibly, for example for cracking snails’ shells, it (the now useful mutation) can be passed on only to the organism’s offspring . However, it would be a prolonged and rather improbable process for the mutant’s offspring to prevail in population. Most – even very useful – mutations vanish from the population during a few generations because of genetic drift. If more mutations are required for the optimal value of the trait (the optimal beak size in our case), all of them have to appear in the offspring of the particular mutant. On the contrary, when the evolutionary novelty is made by the Baldwin effect, i.e. a particular behavior pattern is created first (birds start to crack the snails, even imperfectly because of a weak beak), this behavior pattern can spread horizontally into the whole population by imitation and the useful mutations (e.g. for a strong beak) can consequently arise in any individual. The speed and probability of development of evolutionary novelties by the Baldwin effect, i.e. by adapting the organisms to their environment and behavior through mutations, is much greater than if the organisms would have to look for an environment and behavior that would suit their mutations.

Evolutionary constraints are generally understood as properties of the structural elements of an organism that constrain the pathways that the evolution of the given species may or may not follow. Some biologists, called particularly by their opponents selectionists (functionalists, panselectionalists) are of the opinion that the only constraints that stand in the way of evolution follow from external constraints, i.e. from the laws of mathematics, physics and chemistry. If the existence of a certain structure is not excluded by the laws of the surrounding nonliving nature, then this structure (e.g. flying ears) must be formed in evolution through the effects of the relevant selection pressure. In other words, what is suitable and functional from an evolutionary standpoint and is not prohibited by natural laws will be formed sooner or later.

Other biologists, frequently designated as structuralists, on the other hand, think that certain mutations and thus certain structures can never be formed as, objectively, there exist certain internal constraints, barriers that evolution cannot overcome. In the extreme case, they state that the direction of macroevolutionary development is determined by just these evolutionary constraints, which decide which genetic changes will occur in the particular species. In macroevolution, they attribute a secondary and passive role to selection; according to them, it cannot form new evolutionary forms, but can only constrain the fixation of new forms that are unsuitable from the standpoint of survival of the organism or can hinder this.

According to structuralists, an important category of evolutionary constraints consists in the (evolutionarily) historical internal constraints, specifically ontogenetic constraints.These constraints determine which structures can or cannot be formed in the context of the existing ontogenesis. For example, if a certain pattern on butterfly wings is formed by the diffusion of a morphogen from a single place and if, after a certain time, individual dyes begin to be formed at places with certain concentrations, it is clear that only concentric patterns can be formed on the wings and not patterns of a different type (Beldade & Brakefield 2002). It is apparent that, if a certain structure cannot be formed in ontogenesis, it can also not become fixed during the course of evolution.

The existence of evolutionary constraints could be the cause of the preservation of sexual reproduction. Although it could provide a sort of evolutionary advantage for the organism, the transition from sexual reproduction to asexual reproduction in such a complicated organism as a mammal or bird would require such fundamental and extensive changes in the physiology and anatomy that the probability of their occurrence is negligibly small. A less drastic variant of this hypothesis points out the fact that, while the transition to parthenogenesis is, in principle, possible, this would be such a drastic intervention in the physiology of the organism that the parthenogenetic individuals would necessarily have substantially reduced viability and fertility compared to the other members of the population for a great many generations (Uyenoyama 1984).

            The existence of a great many parthenogenetically reproducing species in such complicated organisms as reptiles, amphibians or fish, however, indicates that evolutionary constraints will probably not be the main reason for preservation of sexuality in the vast majority of species.

There is a very obvious inverse dependence between the length of a time period in which the rate of evolution of a quantitative trait is measured and the measured rate of the corresponding evolutionary changes. If we measure the rate of evolution that occurs during a laboratory experiment, values are obtained that are an order of magnitude larger than when the rate of evolution is measured in long-term observations in the field, and the rates of evolution measured in these observations are again many orders of magnitude greater than the values measured on the basis of studies of paleontological material that include a long period of phylogenesis. There are several explanations for this dependence.
Probably the simplest explanation assumes that frequent changes in the direction of evolution are responsible for the given phenomenon. In a short experiment or in medium-long observations in the field, we catch the species or population in a phase when the action of a particular selection pressure leads means that changes in the particular trait consistently occur in a single direction. However, if our observations cover a longer time interval, which is generally true in the study of paleontological material, the species or phylogenetic lines are gradually exposed to various selection pressures that are frequently contradictory from the viewpoint of the monitored trait. Thus, this trait alternately increases and decreases, so that the resultant rate of change in its size over the entire monitored period is necessarily smaller.
Other explanations are based on the fact that, as a consequence of the existence of various evolutionary limitations, any structure can change at a high rate for only a short period of time, while it can change at a low rate over a longer time. For example, if humans were to increase in size by a single millimetre from one generation to the next, i.e. about every 20 years, they would be over 50 metres tall after a million years. It is quite obvious that even a growth rate of 1 millimetre per generation is too large for humans to change size at this rate for a period of a million years. Simultaneously, such a rate is too small for us to be able to register and measure in a laboratory experiment. It is quite logical that laboratory experiments or observations in the field will provide information on evolutionary changes that are fast enough to be registered, while the paleontological record contains information in changes that are sufficiently slow that they can occur over a sufficiently long time.
Another explanation of this phenomenon is based on the idea that the microevolutionary changes studied in experiments or in the field are of a different nature than actual evolutionary changes, which are encountered only in the paleontological record. While microevolutionary changes are based on selection of alleles that were already present in the population beforehand or in the species in the form of intrapopulation or intraspecies variability, macroevolution must wait for the formation of new genetic variants, for new mutations. This idea is also supported by the results of medium-long genetic experiments demonstrating that the rate of change of the relevant selected trait generally decreases gradually during the selection experiment until, after a certain time, the population ceases to respond evolutionarily to the given selection pressure (Fig. XXVI.7). These results are sometimes interpreted in that, during the first phase of the selection experiment, the genetic variability in the population is exhausted and further evolution of the trait is limited by waiting for a new mutation. This simple explanation is, however, most probably erroneous and the retardation or even stopping of evolution is more probably caused by genetic homeostasis (see IV.9.2).
It is apparent that none of the above mechanisms can, in itself, explain the negative correlation between the rate of evolution of a quantitative trait and the length of the time interval during which the particular evolutionary process is monitored, observed on all time scales. However, all of these mechanisms can operate simultaneously and can jointly explain the existence of this correlation very well.

see History of evolutionism - neo-Darwinist period

Evolutionary systematists took a formalized Linnaean system of taxa at various levels, including their nomenclature, from their structuralistically oriented predecessors. They differentiated the originally hierarchical system of organisms into the lowest super-species level of the genus and then gradually into the family, order, class and phylum. As this number of hierarchical levels (ranks) was insufficient for some evolutionary lines, further levels were gradually introduced; for example supplementary categories were created by adding the prefixes sub-, super- and infra- and thus, for example, subgenuses, subfamilies, infrafamilies, superfamilies, and additional categories, for example tribes and cohorts. Basically, it is a matter of convention which taxonomic levels are differentiated for the individual taxon. For example, it is certainly not possible to compare taxa at the same level that belong to different groups of organisms, such as the families of crustaceans and families of birds, on the basis of their evolutionary age or degree of mutual phenotype similarity of their members. In the past, attempts were made to determine the level of a taxon on the basis of its evolutionary age, but this approach has not become established.
            Cladists were forced by objective circumstances to abandon the system of formal taxonomic ranks. As they attempted to create a system of strictly monophyletic taxa (see below), the number of taxonomic levels increased disproportionately, so that it was no longer possible to introduce separate names for them. Consequently, cladists mostly restrict themselves to expressing the rank of a taxon by a number or graphically, by placing (offsetting) the relevant name of the taxon (in cladistic terminology, clad) on the page. They do not attempt to classify the created clads into predetermined categories according to their taxonomic rank. Consequently, evolutionary taxonomists sometimes (pejoratively) call their work, not classification but rather cladification. The cladistic system is less illustrative and less didactic, but contains all the information obtained on the cladogenesis of the studied evolutionary line.

In sexual reproduction, the accumulation of a large number of lethal or more or less semi-lethal recessive alleles can represent an evolutionary trap; these alleles occur with low frequency in the gene pool of every diploid organism but cannot accumulate in haploid organisms. These mutations are active only in the homozygote or hemizygote state and thus are not very influential in an outbred population. However, as soon as a diploid organism begins to reproduce asexually, its offspring become homozygote in the given recessive lethal and semi-lethal genes, which results, at the very least, in reduction of their fitness. Consequently, only a small percentage of mutants can go back from sexual reproduction to asexual reproduction. Transition from asexual reproduction to sexual reproduction (permitting the persistence and accumulation of recessive lethal mutations), similar to transition from haploidy to diploidy, can be a one-way route for more complex organisms, a sort of evolutionary trap, in which most species of organisms finally end up (Bernstein et al. 1985; Crow 1994).

The action of environmental selection can lead to the formation of structures or patterns of behavior with a positive adaptive value, i.e. those that either directly or indirectly improve the chances of survival of organisms in their natural environment. In contrast, the action of sexual selection can lead to structures or patterns of behavior that are detrimental for their bearers, i.e. reduce their viability {10856}.
            The extremely long feathers in the cocks of argus pheasants (Argusianus
argus), which apparently greatly hinder their bearers in flying and moving over the ground, are frequently mentioned as an example. The about 40 kg antlers of the Pleistocene elk Megaloceros giganteus constitute another frequently mentioned example. With a span of 3.5 meters, this weapon for combat between males represented a considerable burden for their bearers, either as a mechanical obstacle to motion in the natural terrain or as a weight that the males had to constantly drag around, and also as the amount of organic matter that they had to grow each year. This example is now frequently thrown into doubt - Megaloceros lived in a landscape without forests and the size of its antlers related to its overall body weight was not greater than that of the other members of the deer species, etc. (Gould 1974). However, a definitive answer to such questions could only be provided by an experiment comparing the rate of growth of a population of elks with antlers and without antlers occurring under otherwise identical conditions. 
            However, the viability of individuals need not be reduced only by hypertrophic body structure. Males could also live to a lower age because of brighter coloring, which increases the risk of attack by a predator. Probably for this reason, secondary sex traits are expressed in some species only at the time of reproduction.
            It has been observed amongst extinct mammals that the length of existence of a species is negatively correlated with the body size of the individual species. Simultaneously, some authors are of the opinion that the main evolutionary motor for an increase in body dimensions in mammals lies just in sexual selection (Mclain 1993). It has been observed for birds artificially introduced on individual islands that the probability of successful introduction is substantially lower for species with sexual dimorphism than for species without marked sexual dimorphism (Mclain, Moulton, & Redfearn 1995). Newer studies performed on North American birds have shown that species with greater sexual dimorphism, to be more exact dichromatism (differences in coloration of males and females) more readily become locally extinct (Doherty et al. 2003).
            The disadvantageousness of some traits acquired through sexual selection has also been observed in intraspecific comparative studies. For example, it has been found that the sexually most attractive guppy males have the lowest viability (Brooks 2000; Godin & McDonough 2003) (Fig. XV.2). However, the results of meta-analyses have shown that the degree of expression of secondary sexual traits is generally positively correlated with the viability of males (Jennions, Moller, & Petrie 2001). This result can have a number of causes. To begin with, the degree of expression of sexual traits can be determined directly by the fitness of the males, so that only extremely fit males can allow themselves to form more obvious secondary sexual traits. In addition, in other species, the formation of secondary sexual traits need not be influenced by the fitness of the individual, but this fitness can fundamentally affect the probability of whether males with extremely accentuated secondary sexual traits survive in nature and whether they can be included in comparative studies.s 

It follows from theoretical models and empirical data that more intense sexual selection acts on the members of the sex for which the dependence of the number of fertilized offspring on the number of sexual contacts has the greatest slope, i.e. on the sex exhibiting the steepest Bateman gradient (Andersson & Iwasa 1996) (see Fig. XV.1). The reasons for the steepness of the Bateman gradient can differ for the two sexes. The commonest factor consists in the uneven costs of the production of microgametes and macrogametes (see above). However, there are a number of species of animals for which the two sexes exchange roles and the male invests a greater amount of energy into the production of progeny. In these cases, the male and female frequently also exchange roles in sexual selection; the males are more choosy and more obvious secondary sexual traits appear in the females. The reasons for exchange of parental roles are known in only a few cases.
            Exchange of parental roles occurs relatively frequently in fish. In some species, the male carries the eggs and fry in a special cavity in his body (sea horses); in other cases the male builds a sort of nest in which he cares for the eggs and fry. At the present time, the opinion predominates that exchange of roles occurs in connection with territoriality in males. If a male must fight for and defend a territory, then he invests more in reproduction than the female. In addition, spawning occurs in this territory so the eggs and fry remain in the care of the male.
            Some authors think that exchange of roles in fish could be related to a greater rate of diffusion of milt compared to the diffusion of eggs (Dawkins 1976). This difference means that the male must wait to release the milt into the water until the female releases her eggs. He thus finds himself at a certain disadvantage; at the moment when he fertilizes the eggs, the female can have already left. Consequently, the male must make the choice of whether to care for the embryos and ensure they survive, or to also leave and waste all the expended energy. While it may be advantageous to leave first (the partner must care for the progeny), it is clearly disadvantageous to leave second (there will be no offspring). It is quite possible that the short time that the male must remain at the spawning site after the female could play a decisive role, i.e. can decide who will finally care for the fry. It is good to recall that, in sessile aquatic organisms, the greater rate of diffusion of microgametes means that it is necessary to release microgametes first, where the release of macrogametes is frequently triggered by the presence of microgametes. However, in immobile organisms, the investments into the two types of gametes are the same, the male and female investment into care for progeny is zero and consequently ecological and ethological differentiation of males and females need not occur (Williams 1975).
            Exchanged roles have been observed in insects, for example in some species of water bugs of the Belostomatinae family (Smith 1979). The female lays her eggs on the back of the male and he then carries them, defends them and ensures that they get enough oxygen for about three weeks. The total number of eggs corresponds to twice the weight of the male and care for them is a substantial burden for him. Females can copulate with a number of males, but a male decides whether he will accept eggs from a female or not. As the area of the backs of males is a factor limiting reproduction, fierce competition occurs amongst females for males willing to accept batches of eggs.

As was already mentioned in the part dealing with mass extinction, the members of certain groups of organisms were affected more by extinction in the individual periods of the history of the Earth. The sensitivity of the individual groups differed in the various cases, apparently in dependence on the immediate cause of the particular mass extinction. However, irregardless of the cause of the particular mass extinction, certain long-term trends and long-term patterns can be seen in the sensitivities of the members of the individual groups of organisms to extinction. In general, it can be stated that the probable length of existence of a species differs substantially in dependence on its taxonomic affiliation and its life style. Marine species of mussels and snails exist for an average of 10 – 20 million years. In contrast, the average lengths of the lives of mammal species are far shorter, generally substantially less than 5 million years. Amongst marine invertebrates, plankton species have shorter lifetimes than benthic species. If we ignore the theoretical possibility that a great many extinctions actually correspond to pseudo-extinctions and that the rates of extinctions actually correspond to the differences in the rates of anagenesis or even the convention of taxonomists dealing with the particular group of organisms, the main reason for these differences lies in the unequal probability of extinction of species within the individual groups of organisms. As the most intense competition can be expected for mutually closely related species, it is probable that the frequency of extinction can also be increased by increased frequency of speciation. According to some authors, the very fact that a certain species splits off a daughter species substantially increases the probability of its extinction (Pearson 1998) {5302}. In relation to the duration of existence of higher taxa, on the other hand, the species abundance of the taxon will reduce the probability of its extinction and taxa including a greater number of species will, on an average, exist for a longer time.
            The individual species differ in the width of their ecological valence. Eurytopic species are capable of utilizing a wider range of resources and successfully surviving in various types of habitats; in contrast, stenotopic species specialize on a narrow range of resources and are capable of surviving only in a narrow range of conditions. Comparative studies have shown that stenotopic species have a far greater tendency to become extinct than eurytopic species (Purvis, Jones, & Mace 2000). This is undoubtedly a result of the fact that eurytopic species are capable, when necessary, of reorienting themselves to a different type of resource, are capable of tolerating quite drastic climatic changes and generally occur over a broader area than stenotopic species. As will be mentioned below (XXII.6.3), the size of the geographic range tends to be the decisive factor from the viewpoint of survival of the species.
 
            At least in some cases, physical proportions affect the probability of survival of a species; specifically they are negatively correlated with the length of existence of a species (Raup 1994). However it is probable that the lower rate of reproduction of large species is important here. This dependence was quite apparent in the Late Pleistocene, although the causes were rather atypical. At that time, primarily large mammals and birds became extinct, specifically species weighing more than 44 kg (Gittleman & Gompper 2001). These species became extinct almost all around the planet over a very short period of time. Simultaneously, this extinction occurred at different times in the individual parts of the world. For example, in North America, this extinction event lasted approximately 200 years, in a period about 10,800 to 11,000 years ago, during which 72% of large animal species and only 10% of small animal species became extinct. This selective extinction was greatest in South and North America, Australia and Madagascar, while Africa and Asia were affected far less. The most probable cause of this extinction, which is also termed Blitzkrieg extinction, was hunting of large animals by humans. The time of disappearance of animals at the individual places correlated very well with the arrival of humans in this territory. The extinction was not so marked in places where settlement occurred gradually or where humans had lived from the very beginning, as the animals apparently had time to adapt to this dangerous predator; in contrast, the extinction was greater in territories that were settled rapidly.
            Greater sensitivity of large animals to extinction was also manifested at other times. It is highly probable that it could be connected with the relatively smaller sizes of the populations of larger organisms. The resistance to extinction is positively correlated with the size of the population and is thus negatively correlated with the size of the members of a particular species.

Most of the species that ever existed on the Earth became extinct at some time in the past. It has been estimated that the number of species existing at the present time corresponds to the order of one per mille to one percent of the number of extinct species (Raup 1994). It is rather difficult to perform a more exact quantitative estimate as the probability that a certain species will be found in the paleontological record is directly proportional to the duration of its existence. It is thus apparent that the major part of preserved fossils will correspond to species that survived for a sufficiently long time on the Earth and, to the contrary, we will learn nothing from the paleontological record about the existence of short-lived species. Similarly, it is obvious that a great many of the traits, on the basis of which modern species are distinguished within a certain taxon, are apparent only on the soft parts of their bodies and were thus not preserved in fossils. Nonetheless, the paleontological data clearly demonstrate that species are formed at a certain moment, survive for a longer or shorter time and finally disappear, become extinct. The situation is similar for higher taxa – however, they understandably exist far longer than individual species and become extinct only when their last members become extinct.
            At a general level, the most common cause of extinction of a species is “bad luck”, the fact that it was present at the wrong time in the wrong place. Losing the coevolutionary battle with another species apparently occurs far less often. It seems that, at the very least for tetrapod vertebrates, new species mostly expanded into a previously vacated ecological space (Benton 1996). Apparently the vast majority of extinctions occurred in that, at a certain moment, the species was suddenly exposed to conditions that it had not encountered in the past and to which it was thus not adapted. Of course, amongst other things, this means that it is not species and developmental lines that were best able to adapt to the current conditions in their environments that survive for long times, but rather species and evolutionary lines that were fortunately able to survive in situations that they had never encountered before. Thus, paleontologists often point out the contrast between microevolution, based on survival of the fittest, and macroevolution, based rather on survival of the luckiest. Obviously, the degree to which this sharp division corresponds to facts could be a matter for long discussions. In any case, compared to microevolutionary processes, luck certainly plays a much greater role in macroevolution (Raup 1994).
            A species become extinct when all its members die. Higher taxa become extinct when all the species that they encompass become extinct. The basic model of extinction assumes that the individual species become extinct independently of one another. If, for example, ten taxa at the highest level are considered, of which each can be divided into ten taxa at the central level and each of these taxa contains ten species then, for example, if, during a certain period in which speciation does not occur, 90% of species die at random, simultaneously 35% of taxa at the central level become extinct and probably only 0.003% of taxa at the highest level (i.e. in this case, probably none). More realistic models, which consider unequal numbers of species and taxa in various taxa at the same level, yield somewhat different numbers, but the results are basically similar.
For example, the number of species that became extinct during the greatest known mass extinction 248 million years ago at the end of the Permian has been estimated by the method of reverse rarefication on the basis of the number of extinct genera and families on the actual distribution of species in the individual taxa as 96% (the newest estimates yield somewhat lower values). The model describing the extinction of higher taxa on the basis of the independent random extinction of their individual species is called the foot soldier in the field model. Even if 90% of foot soldiers were shot and killed, most probably “only” 35% of ten-membered squadrons would be killed, only about 4% of platoons consisting of 3 squadrons and only about 0.008% of troops consisting of 3 platoons, etc. It is apparent that such a model would not apply to a real battle. Either the individual troops and their platoons wouldn’t all attack at once and be mixed up, but in a certain order, or, for example, some of the members of each formation would be left behind somewhere and would most probably survive. In the former case, more of them would be wiped out while, in the second case, fewer higher formations (higher taxa) would disappear than would correspond to the number of dead foot soldiers.
            Study of paleontological material demonstrates that, even for the extinction of higher taxa, the foot soldier in the field model does not adequately describe the real situation. For example, it is improbable that all the taxa of the numerous and extremely diversified trilobite taxon could have died in the Paleozoic or that both orders of dinosaurs (Saurischia and Ornithischia) would have become extinct at the end of the Mesozoic. It is apparent that, at least in some periods of the history of life, membership in a taxon affected which species would become extinct and which would survive. However, the foot soldier in the field model is an extremely useful instrument from the methodological point of view as it represents the zero hypothesis against which other more complicated and more realistic models can be tested.

Species became extinct throughout all the periods in the history of the Earth. However, relatively few species become extinct in some periods while, at other times, the rate of extinction, i.e. the number of species that became extinct over a certain time interval, temporarily increased drastically (Fig. XXII.2.). On the basis of Sepkoski’s database of 17,621 genera of marine fauna, it has been estimated that the average risk of extinction of a species is 0.25 per million years. However, this value was calculated as an average of the negligible risk of extinction over long periods of time and the very high risk during other periods (Raup 1991). In some periods, the majority of existing species became extinct almost at a single instant, so that even entire higher taxa died out. Extinction is usually classified as mass extinction and “normal” extinction, which is usually termed background extinction. Sometimes, only the “big five” extinctions are classified in the category of mass extinctions, i.e. extinctions at the end of the Ordovician, in the later Devonian, at the end of the Permian, Triassic and Cretaceous (Fig. XXII.3). Simultaneously, some authors do not consider the extinctions before the end of the Devonian and at the end of the Triassic to be real mass extinctions as, in contrast to other periods, the mass extinction was not accompanied by a substantial reduction in the overall biodiversity (Kerr 2001). However, fundamentally, it is highly questionable whether there is actually a difference in principle between mass and background extinction. There were certainly more than five periods with elevated intensity of extinction. In all probability, these periods differed both in the intensity, i.e. number of species affected, and in selectivity. However, there were smooth transitions in both the intensity and selectivity of the extinctions and there were also only rather loose correlations between the selectivities and intensities. For a number of reasons, it is practical to classify extinction as mass and background and thus this will be retained here. However, it is necessarily to constantly bear in mind that the individual periods of extinction always had a specific cause and specific course and that any generalization on the differences between mass and background extinction can hold only under certain conditions.

Extra-pair copulation - For a female, an ideal sexual partner should simultaneously be maximally fit, sufficiently sexy and simultaneously willing to invest the greatest possible amount of time and energy into care for his offspring. It follows from the existence of conditional strategies that it is very improbable that such a partner will be found. Thus, the female must decide on some sort of compromise, reducing her demands in one or the other area or must find a suitable counter-strategy.  The most effective strategy according to which the female can resolve problems connected with selection of a sexual partner consists in separation of the roles of care-giver and biological father. She can achieve this shrewd solution in a simple way, which is called extra-pair copulation (EPC) in animals, while we use a commoner term amongst humans – partner infidelity. For females, the optimum state exists when the partner in biparental care for offspring (or even exclusive care for offspring) is the winner in the game for “who is the dumbest”, a male willing to invest the greatest amount into care for his offspring, while the biological father of the greatest number of progeny will be the male with the best combination of viability, fertility and sex-appeal. Direct observations in nature, in combination with modern molecular-biological methods of determining paternity, have shown that, in a large number of species of mammals and birds, females achieve this result with surprisingly high frequency (Sundberg & Dixon 1996), {12659} (Fig. XIV.9).

            It is obvious that a situation that is optimum from the standpoint of the female is disadvantageous from the viewpoint of the male caring for foreign progeny, and thus that the emergence of an appropriate male counter-strategy can be expected. The males mostly try intensely to prevent partner infidelity. They guard the female in the critical period and chase other males out of the territory. In a great many species, the male delays the first copulation to a time when it is obvious that the female has not been previously fertilized by a different male. In other cases, he mechanically prevents entrance into the sexual organs of the female following copulation. For example, some spiders create such a “chastity belt” in that, following copulation, they break off and leave part of their own sex organs in the sex organs of the female. In a great many species of mammals, including those species of primates in which their life style and reproduction strategy make competition of sperm very probable, the sperm coagulate in the female reproductive organs and form a copulation plug (Polak et al. 2001; Baumgardner et al. 1982; Dixson & Anderson 2002).

            A very common counter-strategy, through which the male at least minimizes losses following from partner infidelity, consists in reducing care for those offspring for which there is a greater risk that that they come from foreign fathers. In starlings and warblers, it has been found that the amount of paternal care is directly proportional to the time during which the male had the female “under control” in the critical period (Wright & Cotton 1994; Dixon et al. 1994) (Fig. XIV.10).

            In humans, it has been found that children, according to newer studies only sons, are similar to their fathers, especially in the first years of life, when it could be useful to ensure a suspicious father that the offspring is really his (Christenfeld & Hill 1995) {12874}. It has also been found that fathers, in contrast to mothers, were willing to invest in their children in proportion to how similar these children (on computer-modified photographs) are to them {11457}. Critics of these studies objected that, in prehistoric time, fathers did not have any mirrors, so that they had limited information about their own appearance (Bains 1996). However, it can be assumed with probability bordering on certainty that malicious uncles, aunts and friends were very willing to provide them with the relevant information even in prehistoric times.

            The male can also attempt to increase the probability of his biological paternity by copulating with the female repeatedly and, in some species, with high frequency. Simultaneously, the amount of sperm in the ejaculate is frequently far greater than the theoretical biological requirement. If the female is guilty of only isolated partner infidelity, there is high probability that the less numerous sperm of the foreign male will lose out in competition with the more numerous sperm of the social partner. It is known that, in many taxa, the size of the testicles and thus the number of sperm produced is positively correlated with the probability of repeated copulation of a single female with particular males (Hosken 1997) (Fig.. XIV.11 and Fig. XIV.12). Studies performed on humans (Baker & Bellis 1993a) have also shown that the amount of ejaculate in sexual intercourse is increased with the length of time during which the partners were not together in the previous period (and thus with the probability of partner infidelity and possible sperm competition).

            Thus partner infidelity is extremely advantageous for females for two reasons. On the one hand, it can lead to the optimum result (a male willing to invest the maximum amount of energy in care for progeny will take care of the offspring of a genetically ideal male) and, on the other hand, forces the male to invest substantial efforts in ensuring his biological paternity in the initial stages of reproduction (production of a large number of sperm, guarding the female, etc.), so that this reduces the advantageousness of the male strategy “if not this one, then another one”.

Another explanation of the Haldane rule is based on the existence of intense sexual selection amongst males and thus the anticipated greater rate of evolution of genes participating in reproduction amongst males than the corresponding genes in females (Wu & Davis 1993) (Fig. XXI.10). It is obvious that the faster male hypothesis can explain the existence of the Haldane rule only for species containing heterogametic males. The hypothesis could also explain only the differences in the level of fertility, but not in viability. While the sets of genes affecting the fertility of males and females mostly do not overlap, viability is affected by the same genes in males and females (Hollocher & Wu 1996; Turelli & Orr 2000). In species with heterogametic females, this effect has the opposite influence than the dominance effect; if it were to predominate, homogametic males would be affected more by the results of hybridization. Comparative studies confirm this theoretical conclusion. While, in Diptera insects, 81% of hybrid males have primarily affected fertility and only 19% viability, amongst butterflies and birds (where the females are heterogametic and thus the faster male effect acts in the case of genes for sterility against the effect of interactions of the sex chromosome with autosomes), 60% of cases of reduced fitness of hybrid males have lowered viability and only 31% have lowered fertility (Laurie 1997; Presgraves & Orr 1998). Further evidence for the faster male effect was provided by the results of studies performed on mosquitoes of the Aedes and Anopheles genera (Presgraves & Orr 1998). In the Aedes genus, the Y-chromosomes are characterized by an extensive pseudoautosomic area, i.e. an area that contains the same genes as the corresponding section of the X-chromosome. In contrast, members of the Anopheles genus have similar Y-chromosomes as humans and thus only a small fraction is formed by a pseudoautosomic area and contains normally expressed genes, while most of the Y-chromosome cannot recombine with the X-chromosome and contain only a minimum amount of expressed genes. In the Aedes genus, the X-chromosome should behave like an autosome in many respects, as a large part is located in two copies in the cells of both sexes. According to the dominance hypothesis, the Haldane rule should not be valid, either in reducing the viability or in reducing the fertility of hybrid males. In contrast, according to the faster male hypothesis, which, it will be recalled, explains only differences in fertility but not in viability, the Haldane rule should be manifested in a relative reduction in the fertility of hybrid males in the same way in the Aedes and Anopheles genera, because it should not depend on the size of the pseudosome areas. Experiments have shown that the reduced fertility of hybrid males is manifested in members of both genera, indicating that the effects described by the dominance hypothesis, i.e. effects connected with the presence of classical X-chromosomes, cannot be the only explanation of the reduced fertility of members of the heterogametic sex. The fact that, in accordance with the predictions following from the faster male hypothesis, the Haldane rule for inviability is not really valid for the Aedes genus, suggests that this hypothesis is another mechanism responsible for the Haldane rule.
As mentioned above, in species with heterogametic females, the faster male effect acts in the opposite direction to the dominance effect. The fact that members of the heterogametic sex are affected by reduced fertility in these species clearly indicates that the faster male effect is weaker than the dominance effect.

The evolutionary mechanism of the emergence of secondary sexual traits – sexual selection – is relatively simple. This is true both for traits occurring on the basis of direct competition between the members of one sex (most frequently between males) and also for traits occurring on the basis of selection performed by the members of the opposite sex (most frequently females). However, an important question remains: what is the mechanism in females that fixes the tendency to prefer a certain type of male? This is especially true for those species where the striking sexual trait entails a reduction in the viability of the males and the actual process of selection of a male constitutes, at the very least, a loss of time for the females.
            At the present time, there are a number of theories that explain the emergence of female preferences. The oldest theory is based on Fisher’s model of co-evolution of male traits and female preferences; however, models of sensory drive, intraspecies recognition and models included in the group of hypotheses of good genes are also popular. It is very probable that all the considered mechanisms are valid to different degrees in various species.

Fitness in the sense of biological fitness is a key term in evolutionary biology. The fitness of individuals under specific conditions and in specific situations can be measured with greater or lesser ease; however, it is not a simple matter to define it in general terms. The fitness of two organisms can be evaluated only in retrospect, in relative values, on the basis of the number of progeny that each of them leaves in the population after a sufficiently large number of generations. If one of them leaves twice as many descendants, it is assumed that it probably has twice the fitness. However, it is not possible, for example, to measure the physical parameters of an individual and to determine his fitness on the basis of the data obtained. Fitness depends not only on the qualities of the particular individual, but also on the fitness of the other individuals in the population. In addition, it is closely related to the external conditions. Individuals with a certain phenotype can have greater fitness under certain conditions in certain habitats, while different individuals can have greater fitness in the same population under different circumstances.

The fact that the fitness of an individual can be estimated on the basis of the number of his progeny could lead to the erroneous impression that fitness is equivalent to fertility or the rate of reproduction. However, this is an entirely erroneous impression. Under certain conditions, organisms that reproduce more slowly have a longer generation period or a smaller number of progeny can have greater fitness. For example, if the blood of a host simultaneously contains two populations of the parasitic protozoa Trypanosoma, which differ in a surface antigen and the rate of growth, then the more rapidly reproducing protozoan variant will cause a stronger and more frequent immunity reaction of the host and will generally be more rapidly liquidated. The more slowly reproducing variant survives longer in the blood and thus has a greater chance of being transferred to a new host by blood-sucking insects. A different but, in its consequences, identical situation occurs if the immune system is not capable of eliminating the parasite and the host is killed by the parasite. The more rapidly reproducing parasite will kill its host faster, so that it has a lesser chance of being transferred to a new host. Thus, it has lower fitness.

Classical population genetics employs the term fitness (adaptive/selection value, w) in a more exact and simultaneously narrower sense. Here, fitness characterizes the degree to which a certain genotype contributes to the gene pool of the next generation through its progeny, compared to the genotype of the fittest individuals against whom no selection is acting. The genotype of individuals against which no selection pressure is active (population genetics studies ideal models, such a genotype doesn’t exist in real populations) has a selection value of w = 1, while other i genotypes have selection values w = 1 – s_i, where s_i is the selection pressure against individuals with the i-th genotype. Thus, in population genetics, fitness, as a relative quantity, can assume values from 0 to 1; in evolutionary biology it is legitimate to consider things in terms of absolute fitness, i.e. in the entire range of positive numbers.

In the fluctuation tests (Fig. III.7), we also determine whether the mutation providing resistance against a certain toxic agent occurred before addition of the selection agent or after its addition. The experiment can be performed by growing a larger innoculum of genetically identical bacteria from one cell, adding this innoculum in the same amount to a series of test tubes with fresh nutrient medium and leaving the bacteria to further multiply here, e.g., for 24 hours. Then a sample of bacteria from each test tube is seeded on one Petri dish containing an antibiotic to which all the bacteria were sensitive at the beginning of the experiment. After a certain time, e.g., after two days, we count the colonies of resistant bacteria on the individual dishes (unmutated bacteria, i.e. those sensitive to the antibiotic, do not grow on the dishes). If the mutations occurred only as a reaction to the presence of the antibiotic, then there should be approximately the same number of colonies on all the dishes or, to be more exact, the number of colonies should have Poisson distribution (Fig. III.8). If the mutations occurred spontaneously, i.e. before the bacteria came into contact with the antibiotic, the numbers of colonies on the individual dishes should differ substantially, i.e. should substantially fluctuate. This is a result of the fact that a mutation can occur in the test tube prior to seeding on the dish at any moment; the mutant could multiply exponentially in the particular test tube up to the moment of seeding on the dish. If approximately the same number of mutations occurred in each test tube, the resultant numbers of colonies in the dishes would differ according to when the mutations occurred. If the particular mutation occurred just before seeding on the dish, then a single colony is obtained; however, if the same mutation occurred 3 hours prior to seeding then, for a generation time of the bacteria of, e.g., 30 minutes, the particular mutation can appear as the presence of up to 64 colonies on the dish. As the number of colonies on the dishes actually differed substantially in the laboratory experiments, fluctuation tests were considered until recently to be the strongest proof that mutations always occur randomly, spontaneously, and are not environmentally directed, i.e. induced  by the presence of an antibiotic.

Competition between individuals of the same sex can assume very diverse forms. This can take the form of a physical battle between members of the same sex, which might even lead to the death of one of the combatants (elk, elephants, some species of crickets). Mostly, however, the opponent is not killed, as the species has created ethological inhibitions that do not allow the competitors to use their frequently fatal weapons (caribou, some snakes, spiders, canine carnivores). The battle thus becomes a sort of ritualized combat, which lasts only until the stronger combatant is decided, It should be pointed out that, under unnatural conditions, for example when individuals are kept in captivity, these ethological mechanisms cannot come into action and the competitor is finally killed. Ritualization of the battle is certainly advantageous from the point of view of the species, because young or temporarily weak individuals are not killed. Ritualization is also advantageous from the viewpoint of the individual: if combatants do not fight to the death, the winner saves a lot of energy and avoids potential injuries (Lumsden 1983).s
            However, competition between individuals of the same sex can also take the form of more or less passive submission to the selection made by individuals of the opposite sex. This situation is very frequently encountered amongst vertebrates (Westcott 1994). In 232 works concerned with sexual competition, selection performed by females was observed for 186 animal species in 167 works, selection by males in 30 works, battles between males in 58 works and, in 14 cases, a sort of competition was observed amongst males as to who could last the longest (stamina competition) (Andersson & Iwasa 1996). In contrast to competition in the form of a battle or stamina competition, in which the chance of success depends on size, dexterity or strength, and thus on the viability of the individual, in cases where the choice is made by a member of the opposite sex, the criteria for selection can be quite arbitrary. Thus, sexual selection can lead to evolution of various structures and patterns of behavior, from bright colors and remarkable body organs to the complicated songs of birds and intricate courtship dances of some species of insects.
            Both types of selection can occur simultaneously in a single species and can even be directed against one another. Males can compete together for access to females while, at the same time, females can attempt, with greater or lesser success, to choose the optimal male on the basis of completely different criteria.

- The age of fossils can be determined on the basis of leading fossils present in the particular layer. Redeposition, i.e. release of fossils from the original rocks during weathering and secondary transport to layers of a different geological age, can, of course, lead to certain complications. However, the main problem associated with dating of evolutionary events is related to the problem of how to determine when the particular species evolved and became extinct on the basis of the discovered fossil. Basically, the discovery of a fossil of a certain age only allows us to state that the particular species was already and simultaneously still present in nature at the particular time. However, it is not possible to determine when the species appeared in nature or when it disappeared. If a certain species disappeared during a well-dated event, for example during a mass extinction event, its fossil documents will most probably disappear from the paleontological record at an earlier date (Signor & Lipps 1982). For abundant species, it is possible that the youngest fossils will be present close to the layer whose age corresponds to the time of extinction of the particular species. However, if a relatively rare species was involved, only a very few fossils will be available. In this case, it is probable that even the youngest fossils will come from layers that are substantially older than the time when the species still actually existed. This phenomenon is denoted as the Signor-Lipps effect and is valid both for dating the extinction of a species and also for dating its evolution; here, this is sometimes (humorously) called the Lipps-Signor effect. These effects do not constitute such a great problem for marine invertebrates, because their fossils were mostly preserved in large numbers. However, it constitutes a major problem in dating the evolution of terrestrial vertebrates, only a few of whose fossils are found.
            The apparent time shift in the fossil record as a consequence of the Signor-Lipps effect introduces substantial uncertaintyinto determination of the causes of extinction of entire taxa. For example, for dinosaurs, there is considerable uncertainty as to whether their extinction was caused by a catastrophe at the boundary between the Cretaceous and the Tertiary, at the KT-boundary, or whether the diversity of this long-successful taxon began to decrease long before this event. In this case, terrestrial vertebrates were involved to a major degree; while their fossils are striking, not many of them have been preserved. Approximately half of approximately 350 species of dinosaurs have been described on the basis of a single preserved specimen (Raup 1994). Under these conditions, it is very difficult to determine the moment of emergence and disappearance of the individual species. Even if an entire taxon were to become extinct at a single moment, most of the rarer species would disappear from the paleontological record long before the Cretaceous-Tertiary boundary.
            The pull of the present and the consequent “telescopic character” of the fossil record constitute a further confusing factor affecting the information that can be obtained from the fossil record and the accuracy of dating evolutionary events. Fossils in the younger layers are better preserved and have mostly been preserved in greater numbers than older fossils. Consequently, when, for example, we study the development of biodiversity over time and find that the biodiversity gradually increased, this could possibly actually only correspond to the pull of the present. The same is true of comparison of the rate of extinction on the basis of the number of species or number of higher taxa that became extinct at the given time; this would necessarily yield a greater number of recent extinctions and a lower number of ancient extinctions.
            Further substantial distortion can occur if recent species, i.e. contemporary species, are also included in the study. Recent species are far more accessible to study than extinct species and far more traits can be distinguished in them. As a consequence, we are capable of distinguishing a far greater number of species within most taxa than we would be able to distinguish if we were to study the same set on the basis of paleontological material alone. This problem is mostly resolved by not including contemporary species in paleontological comparative studies.

see Point mutations in the protein-encoding DNA.

Frozen accident hypothesis assumes that the formation of the genetic code is an example of a frozen accident (Crick 1968) According to this hypothesis, the genetic code was formed through a random, highly improbable combination of its components formed by an abiotic route. Because of its great evolutionary potential, this system was successful in competition with all the other systems and has survived as the sole universal system to the present day. However, the complicated nature of the proteosynthetic apparatus and the age of our universe mean that there is very low probability of the correctness such a hypothesis.

The theory of frozen plasticity assumes that species of sexually reproducing organisms exhibit evolutionary plasticity only immediately after emergence, before genetic polymorphism builds up in their genetic pool.

The main drawback of the selfish gene theory is that it does not take into account the existence of epistatic interactions between individual genes and the consequent dependence of the phenotype manifestations of the individual alleles on their own frequency and on the frequency of alleles in other loci. The model of inter-allele selection tacitly (and erroneously) assumes that the effects of the individual genes on the phenotype of the organism and, indirectly, on the biological fitness, are simply additive. In actual fact, this is frequently not true (Chippindale & Rice 2001).  Two alleles, each of which can be advantageous on its own for its bearer, can frequently substantially reduce the biological fitness of their bearer if they are in the same genome. On the other hand, two independently harmful alleles can, together, increase the fitness of their bearer. This means that the fact that the actual allele (in contrast to the overall genotype) is inherited from one generation to the next in unaltered form still does not ensure that its phenotype manifestations and their effect on the biological fitness of the individual will also be inherited (Fig. IV.13) and that they can spread through the Darwinistic mechanism of natural selection.

For example, in most individuals in the human population, the effect of loss mutations on the gene encoding the α-chain of haemoglobulin is highly negative, as inadequate production of this chain causes α-thalassemia. However, in bearers of a similar mutation in the gene for the β-chain of haemoglobulin, the same mutation is manifested in an increase in their biological fitness, as it prevents the occurrence of relative excessive production of the α-chain and thus also the occurrence of pernicious β-thalassemia (Wainscoat et al. 1983; Kanavakis et al. 1982). Thus we cannot assign any specific selection coefficient value to the individual alleles. In addition, even if we could do this, the evolutionary fate of the alleles will not be determined by the value of such a coefficient, but rather by whether the allele determines an evolutionarily stable strategy (see IV.5.1.1). Thus the solution to the problem of inadequate heritability of biological fitness suggested by Dawkins in his selfish gene theory (the model of interallelic selection) is inadequate.

As a single mutation occurs in the context of other genes in each generation as a consequence of mixing of the genomes in sexual reproduction and its effect on the properties of the bearer thus changes, a major proportion of mutations cannot become fixed in the gene pool of the species. Thus, sexually reproducing species gradually begin to exhibit an increasing degree of genetic polymorphism. Increased polymorphism again increases the probability that the new mutation will find itself in the context of a different gene pool in each generation. This viscous circle of positive feedback, together with a common phenomenon of frequency dependent selection (see chapters IV.5, IV.5.1 and IV.5.1.1), finally leads to the formation of genetic homeostasis, a phenomenon that was recognized long ago in their experiments by classical geneticists (Lerner 1958). Initially, a species changes readily under the effect of any selection pressure; however, as the frequency of the individual alleles gradually shifts away from equilibrium, the selection coefficients of the individual alleles present also gradually changes until the selected population ceases to respond to the relevant selection pressure (Fig. IV.14). This phenomenon is sometimes interpreted in that, during the selection experiment, the genetic variability in the population is exhausted and further evolution of the trait begins to be limited by waiting for a new mutation. This explanation is, however, apparently erroneous. If, at the moment when the evolution of the given trait stops, we begin to exert pressure the opposite direction, for example, instead of individuals with large dimensions of the given trait, we begin to select individuals with small dimensions of the trait, the population begins to respond quite willingly to the new pressure and the relative trait will become smaller. However, this means that, at the time when the population does not react to the original selection pressure, it still contained the genetically-dependent variability. The most probable explanation for genetic homeostasis consists in pleiotropic negative effects on the genes responsible for the given trait. Some alleles that became fixed through selection pressure of the experimenter, or at least increased their frequency, simultaneously negatively affect the biological fitness of their bearer. This means that, from a certain instance, the bearers of a particular combination of alleles continue to be at an advantage through the artificial selection of the experimenter, but are increasingly at a disadvantage in relation to natural selection. At the moment when the artificial selection and natural selection become equal, the development of the given trait stops. After termination of the selection pressure of the experimenter, a sufficiently large population will return to the original state through the action of natural selection, and the original frequency of the individual alleles and also the original phenotype (appearance and behaviour) of the individuals in the population are renewed in the population. In a small population, the return to the original state need not be complete, as some less frequent alleles disappear from the population through drift (see chapter V).

The theory of frozen plasticity (Flegr 1998), (Flegr 2008) assumes that, as a consequence of the occurrence of genetic homeostasis, clearly punctuated evolution (see XXVI.5) is characteristic for sexually reproducing species. Throughout most of their existence, species more or less do not change or change only temporarily, in spite of frequently dramatic changes in their environment. Irreversible changes in the properties of a species, i.e. anagenesis, occur only immediately following speciation, when the size of the originally small population of the newly formed species has already grown (therefore the destiny of an individual is already directed by selection, not by chance, see Chapter V.4) but the population still bears only a small fraction of the polymorphism of the parent species. The drastic reduction in the genetic polymorphism in the new species means that new mutations are present in the company of the same genes even in sexual reproduction. Until sufficient genetic polymorphism accumulates in the gene pool of the population, the species is evolutionarily plastic and can respond adaptively to selection pressures of the environment similarly to asexual species. Following accumulation of polymorphism, the species evolutionarily “freezes” (becomes evolutionary frozen on macroevolutionary time-scale and evolutionary elastic on microevolutionary time-scale) and, for the rest of its existence, only passively waits until a change in its environment causes its extinction.

Frozen plasticity may also play an important role in some processes at an intraspecies level.. Cultivated plants include both autogamous (e.g. wheat) and also heterogamous (e.g. rye) species and varieties. It follows from the theory of frozen plasticity that the properties of heterogamous species and varieties should be more stable on a micro-evolutionary scale than the properties of autogamous species or even varieties that reproduce predominantly or only vegetatively (Flegr 2002). In the former case, the alleles are in the presence of other alleles in each generation, so that their selection coefficient changes unpredictably. Thus, it is difficult for selection pressure to act consistently leading to their elimination or fixation. In contrast, for autogamous or vegetatively reproducing species, the genetic environment of the individual alleles is the same in each generation and thus the selection value remains stable from one generation to the next. Thus, the genetic composition of the population can easily submit to the effect of selection through evolutionary changes.

The different response capacity of sexual and asexual (and autogamous) species and varieties for selection pressures is apparently also very important in plant improvement and normal farming practice. It is relatively difficult to select new varieties in sexually reproducing species (or amongst the above-mentioned heterogamous plants). In order for the organisms to respond to the relevant selection pressures, it is mostly necessary to work with relatively small populations and to employ a high degree of inbreeding, to reduce as far as possible the genetic variability of the population and thus to increase the heritability of the phenotype manifestations of the relevant selected alleles. In asexual (and autogamous) species and varieties, it is possible and, because of the relative lack of genetic variability, frequently also necessary to perform selection in large populations. On the other hand, the newly obtained varieties are more stable for sexual (and heterogamous) varieties than for varieties reproducing asexually or autogamous varieties. Their advantageous properties should not gradually disappear as a consequence of the action of natural selection, which constantly increases the biological fitness of the organisms, frequently at the expense of their usefulness (Flegr 2002).

As, until recently, these phenomena had practically no support in genetic or evolutionary theory, they are very rarely described in the biological literature. The publications of the Lysenkoists constitute an exception; these results follow very well from consideration of their absurd theories. In their work, these Soviet “researchers” described the low stability of the evolutionary properties of autogamous varieties of cereals compared to heterogamous varieties and also promoted agrotechnical procedures based on intraspecies crossing of autogamous plants, which led to prolonged maintenance of the useful properties of the given varieties (Lysenko 1950). It is probable that a major part of the results published by Lysenkoists were falsified or even fabricated and it is, understandably, necessary to approach their data with a maximum of caution (Medveděv 1969). Nonetheless, it is not possible to completely ignore the fact that a certain part of the information was passed down from the experienced empirical agronomists of previous generations.

see Mutations at the level of the entire chromosomes

Game of Life is model of evolution powered by  sorting from the standpoint of stability.  In this game, space is conceived in the form of a large chess board. Each square neighbours on other cells along its sides and in its corners and can be in one of two alternative states, for example black and white. Development of the system occurs in discrete cells according to the following rules: As soon as a white cell is next to three black cells, it becomes black in the next step; as soon as a black cell is next to less than two or more than three black cells, it becomes white in the next step. If a black cell is next to two or three black cells, its state does not change in the next step. On the basis of these simple rules, a system develops from the originally disordered state of randomly distributed black and white cells to a much more ordered state. At various places on the chessboard, relatively large black shapes are formed, which grow or move about (Fig. I.6). Some shapes generate and, on various sides, periodically emit other forms, where the meeting of two forms on the surface can lead to the disappearance of both or only one of them, or several new separate forms are created.

see Reproductive isolation postzygotic

Gene flow, which consists inthe transfer of genes between populations, most commonly via migrating individuals, is an important factor in evolution. Depending on its intensity and on the structure of the population, it can either speed up evolution, or, on the contrary, slow it down significantly. Gene flow becomes an important factor in mobile organisms as well as in organisms that never move during their lifetimes, i.e. also in sessile animals and in plants. This is because, for the purposes  of gene flow, the most important parameter is not based on an individual’s mobility within the population of its species, but rather the ability to migrate, i.e., the usual distance between the place where a particular individual is born and where its offspring are born. Consequently, a pine-tree population whose pollen is spread over large distances by wind has a much greater migration ability, and thus also much more intense gene flow, than a bat population, whose members fly thousands of kilometers in their lifetime, but ultimately breed in the same cave as that in which they were born. It should be mentioned that, in single-cell organisms, especially prokaryotic organisms, the gene flow between populations can take the form of transfer of the genes themselves, such as in a viral transfection. Analogical processes of horizontal gene transfer between individuals of the same species, as well as between different species, can also occur in multicellular organisms. In this case, however, the mobility of individuals tends to be much higher than the mobility of the genes or viruses, rendering these processes practically negligible in gene flow.

While, within a metapopulation, evolutionary novelties arise primarily frommutation processes, gene flow is a much more likely within a population and is therefore more important source of novelties, such as mutated alleles. The incidence of migrants is usually much higher than the frequency of mutations in a population, with each migrant contributing his entire genome, i.e. a large number of alleles that may differ significantly from the alleles present in that population.

While the impact of gene flow is clearly positive in that it helps to maintain genetic polymorphism and thus also the ability of the local population to optimally respond to changes in the environment, from the perspective of the population’s ability to adapt optimally to long-term stable conditions in a given environment, its impact is rather negative. Microevolutionary adaptation of the population to local conditions is achieved by fine-tuning the frequency of the alleles in the population’s gene pool. The frequency of the alleles introduced into local population’s gene pool by migrants equals that of the surrounding populations, which constantly tips the composition of the local population’s gene pool off its optimal value. 

It has been observed, for example, that a relatively isolated blue tit population living in the evergreen forests of Corsica nests later than the tit population on the continent, a beneficial behaviour in that particular environment because it ensures that the time of feeding the offspring coincides with the peak insect levels in the evergreen forests. On the other hand, a minority tit population living in the evergreen forests on the continent nests earlier, simultaneously with the tit populations living in the surrounding dominant deciduous forests, which makes the timing of feeding its offspring inconvenient in relation to insect rates in the relevant locations. It is assumed that gene flow from the surrounding populations prevents the populations on the continent from adapting optimally to the conditions of their local environment (Dias & Blondel 1996).

Gene flow and mutation processes as two sources of evolutionary novelties do not differ only in quantity. While an evolutionary novelty arising from mutation is harmful for its bearer in the absolute majority of cases, novelties acquired through migrants have already passed the natural selection test in another population and are therefore much more likely to be useful or at least selectively neutral. 

Genetic drift is one of the most important mechanisms contributing to changes in the composition of a population’s gene pool. If a population disintegrates into several partial populations isolated in terms of reproduction, the drift effect gradually changes the frequency of alleles in each of these populations. As genetic drift is a stochastic process, allele frequencies in the populations move in different directions. A mathematical model of the genetic drift suggests that genetic diversification should occur very rapidly in populations. However, studies of real populations of the most varied animal and plant species have shown that the frequencies of alleles that can, for some reason, be considered selectively neutral are, in fact, very similar in different populations (Lewontin 1974). It can be demonstrated that the uniformity of selectively neutral alleles within a metapopulation is most likely to be the result of gene flow. Calculations show that even a surprisingly small number of migrants can prevent subpopulations from diversifying genetically through genetic drift (Wright 1931). If we take two populations, each with size N, with an average frequency of the various gene alleles equal to p, subject only to the effects of genetic drift, not selection, and exchanging a certain share m of their genes via migrants in each generation, then the average difference d in the frequencies of the relevant alleles between the populations, or more precisely its absolute value, can be calculated as follows:   

.

For example, if we take populations of 10 000 individuals that exchange 10 individuals in one generation (m= 0.001) and that had an initial average allele frequency of 0.5 then, at equilibrium, the average difference in allele frequencies will equal 0.156. As m in the equation represents the ratio of the number of migrants to the population size, then Nm term is equal to the absolute number of migrants and the effects of gene flow consequently do not depend on the size of the population but only on the absolute number of migrants per generation. It follows that, in terms of neutralization of the impact of genetic drift, the same number of migrants will have a comparably strong effect on a population of 10 thousand and on a population of 10 million. Although this number will introduce a relatively smaller share of foreign genes into a large population, genetic drift in this population is also proportionally slower than in a small population. 

As early as in 1931, Sewal Wright deduced that the exchange of 1-2 migrants between partial subpopulations can prevent genetic differentiation and thus speciation of subpopulations within a metapopulation as a result of genetic drift and will ensure that the metapopulation develops synchronously as a single evolutionary unit (Fisher 1958). This conclusion has also been verified experimentally, for example, by studies of differentiation in red flour beetle populations (Schamber & Muir 2001).

Calculations show that, if the diversification of subpopulations is the result of natural selection and not genetic drift, the number of migrants required to maintain the genetic cohesion of the metapopulation is substantially higher (Gavrilets 2000; Rieseberg & Burke 2001). If a dominant allele is being eliminated in a given local subpopulation by natural selection with intensity s, i.e. at the rate of ps per generation (p corresponds to the frequency of the allele in the subpopulation, s – selection coefficient) and, at the same time, it enters that subpopulation via gene flow at a rate of  (P – p)m from surrounding subpopulations (P corresponds to the frequency of the allele in the surrounding subpopulations, m – the intensity of gene flow), any particular ratio of the selection and gene flow intensity can ultimately result in a balanced frequency of the given allele in the subpopulation

.

If selection is much stronger than gene flow, the allele can practically disappear from the local subpopulation and, analogously, if gene flow is much stronger than selection, the frequency of the allele in the local subpopulation can very closely resemble its frequency in the surrounding subpopulations.

The intensity of gene flows detected in real populations is so high that, even in the case of plants, a useful allele can spread quite rapidly to all the subpopulations within the whole range of the given species, allowing the species to behave as an evolutionary unit in terms of adaptive evolution. Subpopulations tend to differ in non-adaptive traits or in traits expressing low additive heritability that are difficult to select (Rieseberg & Burke 2001).

Different types of organisms are present only in a specific limited area. This area is called the range of the species. In some cases the range is delimited by natural barriers, continental edges, mountain ranges or rivers. Quite often, however, we are not able to discern any natural barriers of this kind – the natural conditions in the given territory change more or less gradually. In species with discontinuous range, conditions in the individual areas of that range are often very different but local populations are able to adapt to these differences through microevolution. It follows from what has been stated above that the geographic delimitation of range is probably the result not of some natural abiotic barriers in the environment but rather of a biological phenomenon. One of the possible reasons was already suggested in the middle of the twentieth century by Haldane (Haldane 1956). According to his hypothesis, spatial delimitation of ranges is the consequence of gene flow. As the natural, for example climatic, conditions gradually change within the range, local populations of the species adapt to these local conditions. The effect of natural selection, which optimizes the composition of the gene pool with respect to local conditions, is, however, simultaneously countered by gene flow, introducing alleles from other populations’ gene pools via migrants. These alleles tip the local population’s gene pool composition off its optimal balance. Considering that populations are more numerous towards the centre of the range and less numerous towards its edges, the impact of migrants on the composition of local populations’ gene pools grows with an increase in the distance from the centre. At a certain distance from the centre, local populations are so sparse that even relatively weak gene flow can prevent their microevolutionary adaptation to local conditions. This is the distance at which the natural limit of the species’ range will be found (Garciaramos & Kirkpatrick 1997).

This model also serves to explain Rapoport’s rule (Case & Taper 2000). According to this empirically derived, biogeographic rule, ranges of species living at low latitudes, i.e. mainly in the tropics, are usually smaller than the ranges of similar species living at higher latitudes. For species living near the equator, as a rule, environmental productivity decreases as we move away from the centre of its range, i.e. from the equator and, consequently, the density of the local populations also decreases. This means that the impact of gene flow on the composition of a local population’s gene pool increases rapidly with increasing distance from the equator, preventing microevolutionary adaptation of these populations to local conditions even at a relatively short distance from the centre of the range. To the contrary, species with ranges centered at high latitudes reach a more productive environment as they penetrate towards the equator and can therefore create more numerous populations in these areas. Consequently, the flow of genes from the centre of the range has a smaller impact on the composition of the local populations’ gene pools and does not hinder their microevolutionary adaptation to local conditions. As a result of their higher microevolutionary plasticity, species at higher latitudes can, on an average, have larger ranges. Naturally, there are other explanations for Rapoport’s rule, such as the selection for broader environmental tolerance in species living in the less stable and rougher conditions of the higher latitudes (Stevens 1989).

Individual genes and, in fact, also individual factors in the external environment work together in various ways, interfere or replace one another in their effects in creating the final forms of the traits. Current molecular biological studies, for example, indicate that a major part of genetic information is redundant. If both copies of a certain gene (i.e. cistron) are artificially inactivated, it very frequently happens that the phenotype manifestation of the given mutation is very small or even negligible.

Experiments performed with baker’s yeast, for example, have shown that loss mutations in only 1100 genes (i.e. cistrons) of the total number of 6200 tested have lethal character. Inactivation of a further 291 genes has lethal character only if some other gene is simultaneously inactivated.

Genes or, to be more exact, their specific alleles can thus interact, i.e. mostly mutually augment or cancel their effects. In the case of an interaction within a single locus, we then speak of allele dominance in this context. If similar interactions occur between two different loci, then these are termed epistatic interactions. Of course, the actual interaction occurs physically as a rule, but not necessarily always, at the level of the products of the relevant genes and not at the level of the DNA.

The existence of interactions greatly complicates both the search for the locus at which the gene determining a certain trait is located and also the delimitation of the particular gene. Basically, it even complicates the very concept of a gene and especially the molecular biological definition of a gene as a cistron. If the interaction amongst several genes, and not a particular gene, is responsible for the formation of a particular trait, then there is no point in searching for the locus at which the particular gene is located. However, interactions reduce the effectiveness of the action of natural selection in evolution. If several genes located at various places on the genome participate in the formation of a particular trait, then its heritability is substantially reduced (see also Section II.7). The trait in the original form in which it occurred in the parents will develop only in those progeny that have the same allele at all the participating loci as their parents. However, in a polymorphous population, recombination and segregation of chromosomes leads to mixing of the genes of the two parents so that the probability that any of the progeny would inherit exactly the same combination of alleles as one of the parents would be very low. If the particular combination of alleles and thus the particular trait is transferred from the parents to the progeny, it is very probable that the particular allele will fall apart in one of the subsequent generations. See also Frozen plasticity theory.

Organisms live in the real world, not in the world of idealized models. One of the basic differences between models and reality is the fact that the real world is always more or less unpredictable (stochastic) and errors happen there with a certain probability. An individual can, by mistake or accidentally, betray its opponent or, to the contrary, cooperate in error, or its behavior can be misinterpreted in the same way by the opponent. In the real world, Tit for Tat is not an optimal strategy and can be forced out of the population by other strategies. An example of a strategy that is more successful in the unpredictable real world is “Generous Tit for Tat”, sometimes also called “Firm but Fair” (Nowak & Sigmund 1992). This strategy forgives sporadic betrayal with a certain probability (30 %), i.e. it responds by cooperation in the next round of the game. If two bearers of the Tit for Tat strategy play against one another and one of them betrays by mistake, it launches a long series of mutual punishment and both opponents fail to profit. On the contrary, if this situation occurs for two bearers of the Generous Tit for Tat strategy or one Generous Tit for Tat bearer and one Tit for Tat bearer, the mutual punishment series will be terminated quickly as soon as the Generous Tit for Tat bearer responds to the betrayal by cooperation in the next round.

Genetic assimilation is responsible for genetic fixation of a phenotype trait originally produced non-genetically in the individual. For example, in the nineteen fifties, Conrad Hal Waddington observed that during artificial selection, a certain change of wing morphology in drosophila (absence of certain veins – i.e. cross-veinless phenotype), originally a response to heightened temperature during larvae ontogenesis of a small portion of the flies population, occurs in the offspring of altered individuals in further generations more and more often. After 23 generations of the selection, 96% of the flies respond to increased temperature by change of  the wing morphology. Most importantly, the morphological change started to occur also in flies that were not exposed to increased temperature. (Waddington 1961; Grodnitsky 2001) (Fig. XVI.4). This means, that during several generations of selection for the ability to response to increased temperature through wing modification, a phenotype change that was originally conditioned by the environment (phenocopy) has become genetically dependent.
At the present time, it is assumed that genetic assimilation occurs in that changed environmental conditions or a behavior pattern achieved by learning cause manifestation of already existing minor inter-individual genetically dependent differences in a particular trait in the individual members of the population (i.e. manifestation of latent genetic variability). Manifestation of these differences subsequently enables selection and thus genetic fixation of the new forms of the traits  (Hall 2001; Flegr 2002). In the above mentioned hypothetical snail-shelling case, both genetic assimilation and the Baldwin effect can play a role. When the organisms start to exhibit a certain behavioral pattern, the so-far hidden differences in the predispositions of the individual members of the population for performing a certain activity, in our case the predispositions for snail-shelling became “visible” for natural or artificial selection. This enables spreading and finally fixation  of already existing alleles that cause or at least facilitate development  of a particular trait, e.g. launching a particular behavioral pattern (snail-shelling in a bird) or  modification of wing morphology (in drosophila), even without the necessity to learn it individually or without any  external stimulus.
Along with this, the Baldwin effect is responsible for the fact that selection makes this behavioral pattern more effective in time by suitable modification of the organism’s phenotype – e.g. by selecting birds with larger or stronger beaks. 

If an advantageous mutation occurs in an individual whose genome carries a disadvantageous mutation, an advantageous mutation cannot be fixed in asexually reproducing organisms or it becomes fixed together with the disadvantageous mutation. In contrast, in sexually reproducing species, an advantageous mutation sooner or later during genetic recombination gets rid of its unpleasant neighbourhood and “moves” to a chromosome without a disadvantageous mutation (Fisher 1958). This model is currently considered to be extremely important, as it is capable of explaining the advantageousness of sexual reproduction in a wide range of ecological and genetic parameters in organisms with very diverse reproductive systems (Crow 1994). Experiments with cultures of the yeast S. cerevisiae have demonstrated that sexuality increases the average fitness of individuals especially under stable conditions, to which the yeast is adapted, but not under altered or changing conditions. This indicates that sexuality is apparently of fundamental importance for elimination of detrimental mutations from the genome, but not for fixation of new adaptive mutations required for adaptation to changing conditions (Zeyl & Bell 1997).

see Sisyphean genotypes model of advantage of sexuality

Genetic information is defined as information entered in the primary structure of a nucleic acid, i.e. in the order of the nucleotides in the DNA molecule or (in some viruses) in the RNA. See also Epigenetic information.

Eldredge and Gould originally suggested that the punctualist character of evolution is a result of a genetic revolution that occurs through the founder effect. This was based on the peripatric speciation model, created by Ernst Mayr (Mayr 1963). Mayr emphasized that a large population located in the central part of the geographic area of the particular species has only limited potential for the formation of anagenetic changes. As a result of migration, alleles constantly flow in from the other parts of the geographic area of the species and these alleles prevent the formation of optimal adaptations to local conditions. Thus, only those alleles that are capable of withstanding the competition from alleles coming in from the rest of the population survive in the long run, i.e. alleles that are capable of providing their carriers with reasonable fitness in combination with the widest possible spectrum of the alleles of other genes and not, for example, alleles that provided their carriers with ideal adaptation to local conditions and possible changes in these conditions. In addition, normalizing natural selection is much more effective in large populations compared with small populations. If it was necessary to overcome a valley in the adaptive landscape for a change in the phenotype to become possible, i.e. if the transition form between the old and new forms exhibited lower fitness, the emergence of new forms in the population would be impossible. The genetical composition of the gene pool of large populations located in central parts of the area of occurrence thus remains unchanged over long periods of time and reacts very slowly to any changes in the environment. In contrast, much more favorable conditions for anagenetic evolution occur during peripatric speciation in small populations, which are constantly formed and disappear at the edges of the area of occurrence of the given species. The populations are smaller so that their members can more easily overcome valleys in the adaptive landscape through genetic drift. The populations are also geographically and thus also genetically isolated from the other populations of the given species so that foreign alleles do not enter their gene pool and the composition of the gene pool can better adapt to the momentary local natural conditions. It is an important property of small populations that the composition of their gene pool can differ very substantially from that of the parent population thanks to the founder effect. The particular population was most probably established by only a very few, frequently mutually related individuals, so that their genetic composition could differ at random from that of the parent population. As a result of genetic drift acting in small populations, other alleles can disappear from the gene pool. A genetic revolution can occur in the population as a result of the altered composition of the gene pool. The selection values of the individual alleles are mostly affected by their own frequency and the frequencies of the other alleles in the same locus or in other loci. If the frequency of an allele increases through the effect of selection pressure or randomly (by genetic drift), its selection value changes and the relevant selection pressure ensures that, in time, its frequency will return back to the equilibrium value. This genetic homeostasis (see IV.9.2) is capable of maintaining approximately constant frequency of the individual alleles in the gene pool of the population even when the natural conditions and thus also the external selection pressures acting on the population change. The most important component of the external environment of an allele consists in the frequencies of the other alleles, because these frequencies determine which alleles a certain allele will most often encounter in future zygotes and thus what its selection value will be. Where, as a consequence of the founder effect and as a result of subsequent genetic drift, a great many alleles disappear from the gene pool of the population and the frequencies of other alleles change drastically, a number of the remaining alleles escape from mutual bonds and thus also the phenotype of organisms in the population can begin to change through natural selection. Thus, in contrast to large, genetically interconnected populations, small populations can evolve and can lead to the formation of a new species with a different phenotype. The appearance of a new species in the paleontological record at a certain location thus reflects, not the formation of a new species at the particular location, but rather the invasion of a species that was formed by peripatric speciation at some other location. The population in which the new species evolved was small and the anagenesis of its members was relatively rapid because of genetic revolution, so that it is not very probable that its members would be preserved in the paleontological record.
            In later works, Gould abandoned the model assuming the participation of genetic revolution (Gould 2002). He stated that his main reason for abandoning this model was the fact that, at the present time, geneticists tend to think that selection occurs more effectively in large populations than in small populations. The fact that the existence of genetic revolution was not confirmed experimentally also probably played a certain role. Gould also concluded that the participation of this mechanism is not necessary for explaining the punctuated character of evolution and that the mechanism of peripatric speciation alone explains it sufficiently. In his opinion, it is not necessary for acceleration of anagenetic processes in small populations, as a period of the order of 10,000 years is adequate for the accumulation of a sufficient number of evolutionary changes even at the normal rate of evolution. The fact that the population is located close to the edge of the geographic area of the species, where different natural conditions are most probably present, that it is genetically isolated from the rest of the species, so that it can adapt to these conditions and that, because of its smaller size, it can overcome any valleys in the adaptive landscape through genetic drift apparently provide sufficient explanation for the faster anagenesis of these populations. As soon as a reproduction barrier is formed between species, the members of the new species can invade the geographic area of the old species without the newer species becoming “dissolved” in the more numerous population of the old species.
            Personally, I am of the opinion that Gould abandoned the genetic revolution model prematurely. The present-day skeptical opinion of this mechanism on the part of a large fraction of geneticists is probably a result of the methodical difficulties associated with its experimental verification rather than the existence of data that would be contrary to it. The fact that selection is more effective in large populations than in small populations is undoubtedly true; however it is in not way contrary to the statement that selection is more effective in genetically homogeneous populations than in genetically polymorphic populations. The polymorphism of the population is the critical parameter here. A small population can very rapidly grow into a large population, while the original degree of polymorphism is renewed in the population much more slowly. Thus, for a very long time after splitting off, the population can remain in a completely ideal state from the viewpoint of selection, i.e. in the state of a very numerous, genetically uniform and thus evolutionarily plastic population. Only after a longer time is polymorphism accumulated in the population, as a consequence of which the heritability of the individual phenotype traits and the heritability of the overall fitness are reduced (see IV.9.2). As a consequence, the particular species becomes evolutionarily frozen and, for the rest of its existence, more or less passively awaits a change in the external conditions that will lead to its extinction or to new peripatric speciation which will renew its evolutionary plasticity (Flegr 1998), {14400, 15429}. I am of the opinion that, in the field of genetics, the research related to the mechanisms of genetic homeostasis and conversion of nonadditive heritability to additive heritability in small or genetically homogeneous populations will lead to great support for this model of evolution. In the field of paleontology, the model of punctualist evolution encompassing the genetic revolution mechanism could substantially support or confirm current indications that suggest that the punctualist model better describes the evolution of sexually reproducing species, while the gradualist model better describes the evolution of species whose members reproduce asexually.

Individual, frequently even closely related species of organisms can differ very substantially in the sizes of their genomes. The genetic complexity (C-value), i.e. put simply, the total amount of DNA recalculated to the haploid genome, differs more than 80,000-fold for eukaryotes, 5800-fold for protozoa, 250-fold for arthropods, 350-fold for fish, 5000-fold for algae and 1000-fold for angiosperm plants (Cavalier-Smith 1985; Petrov 2001). Such large differences cannot be caused by differences in the number of genes in the genomes of the particular species and are certainly not correlated much with the complexity of the individual organisms (Fig. VI.3). Consequently, this phenomenon is called the paradox of genetic complexity – the C-value paradox.

A frequent explanation of the C-value paradox could consist in the tendency of certain species or groups of species towards (repeated) polyploidization of the genome or part thereof. Another quite probable explanation is that mutations of the insertion type predominate in the genomes of some species of organisms, while mutations of the deletion type predominate in the genomes of other organisms. This hypothesis has been tested by comparing the frequencies of the individual types of evolutionarily fixed mutations in the genomes of drosophila and in crickets of the Laupala genus (Petrov et al. 2000). The genome of crickets is approximately 50 times larger than that of drosophila. In agreement with the expectations following from the tested hypothesis, it was found that the mutations in drosophila contain a greater number of deletions and fewer insertions than those of crickets. Very marked differences have also been observed in the range of the relevant mutations; the average length of deletions in drosophila equals 24.9 nucleotides, while that in crickets equals 6.0 nucleotides. On the other hand, the length of insertions was larger for crickets. The results of this study did, of course, not demonstrate that the cause of the different sizes of the genomes lies in mutation bias. The initial data do not permit determination of whether the discovered differences in the sequences of the individual species of crickets and individual species of drosophila are caused by differences in the probability of the individual types of mutations or differences in the probability of evolution fixation of the individual types of mutations. In any case, the action of mutation bias remains a highly probable explanation of the existence of the complexity paradox. Alternative explanations of this phenomena are, however, provided by other, basically different hypotheses, some of which assume that noncoding DNA in the nucleus can have functional importance for the cell – e.g. it permits maintenance of a constant ratio between the size of the nucleus and the volume of cytoplasma (Beaton & Cavalier-Smith 1999).

Individual, frequently even closely related species of organisms can differ very substantially in the sizes of their genomes. The genetic complexity (C-value), i.e. put simply, the total amount of DNA recalculated to the haploid genome, differs more than 80,000-fold for eukaryotes, 5800-fold for protozoa, 250-fold for arthropods, 350-fold for fish, 5000-fold for algae and 1000-fold for angiosperm plants (Cavalier-Smith 1985; Petrov 2001). Such large differences cannot be caused by differences in the number of genes in the genomes of the particular species and are certainly not correlated much with the complexity of the individual organisms (Fig. VI.3). Consequently, this phenomenon is called the paradox of genetic complexity – the C-value paradox.

A frequent explanation of the C-value paradox could consist in the tendency of certain species or groups of species towards (repeated) polyploidization of the genome or part thereof. Another quite probable explanation is that mutations of the insertion type predominate in the genomes of some species of organisms, while mutations of the deletion type predominate in the genomes of other organisms. This hypothesis has been tested by comparing the frequencies of the individual types of evolutionarily fixed mutations in the genomes of drosophila and in crickets of the Laupala genus (Petrov et al. 2000). The genome of crickets is approximately 50 times larger than that of drosophila. In agreement with the expectations following from the tested hypothesis, it was found that the mutations in drosophila contain a greater number of deletions and fewer insertions than those of crickets. Very marked differences have also been observed in the range of the relevant mutations; the average length of deletions in drosophila equals 24.9 nucleotides, while that in crickets equals 6.0 nucleotides. On the other hand, the length of insertions was larger for crickets. The results of this study did, of course, not demonstrate that the cause of the different sizes of the genomes lies in mutation bias. The initial data do not permit determination of whether the discovered differences in the sequences of the individual species of crickets and individual species of drosophila are caused by differences in the probability of the individual types of mutations or differences in the probability of evolution fixation of the individual types of mutations. In any case, the action of mutation bias remains a highly probable explanation of the existence of the complexity paradox. Alternative explanations of this phenomena are, however, provided by other, basically different hypotheses, some of which assume that noncoding DNA in the nucleus can have functional importance for the cell – e.g. it permits maintenance of a constant ratio between the size of the nucleus and the volume of cytoplasma (Beaton & Cavalier-Smith 1999).

can constitute another evolutionary trap in organisms in which the embryos develop inside the maternal organism (II.8.3) (Fundele & Surani 1994). This phenomenon is known, for example in mammals and plants. This is manifested in that some genes derived from the gametes of the father and gametes of the mother fulfill different functions in the development of the embryo. The copies of a certain gene derived from the sperm can be active in the embryo and, for example, control the production of the growth factor, while a copy of the same gene derived from the egg need not even be transcribed. This strange behaviour of the genes may (but, of course, need not, see e.g. (Skuse & et al. 1997)), be highly useful from the viewpoint of the father or mother; both individuals modify and thus program the genes of their gametes so that, after formation of the embryo, they “defend the interests” of their original carrier, frequently at the expense of the interests of the other parent (Moore & Haig 1991).

             In the above case, the male tries to program his genes so that the newly forming embryo is as large as possible, even at the expense of other developing embryos or even at the expense of the overall state of health of the mother. The other embryos could have different fathers, a very frequent phenomenon in mammals, birds and a great many plants. Even a certain damage to the mother during gravidity or parturition is not detrimental from the viewpoint of the father in a great many animals, as he can have future progeny with other females. The female must program her genes so that they compensate the relevant activity of the paternal genes in the embryo. In the above case, she apparently does this in that she programs her genes to synthesize receptor proteins capable of capturing and thus deactivating the growth factor synthesized under the control of the paternal genes. If a similar battle occurs between the paternal and maternal genes in embryogenesis, then it is practically impossible for the species to change from sexual to asexual reproduction and for a viable embryo to be formed, for example, by the combination of two female gametes – production of the growth factor would be missing. The phenomenon of genome imprinting and some of its other consequences were also described in Section II.8.3.

The combination of the specific alleles in all the loci present in the genome of the particular individual is called the genotype. If we are interested in alleles present at a specific locus or in several particular loci in the given individual, in this connection we can also use the term genotype for the particular combination of alleles.

Theory of neutral evolution

see History of evolutionism – classical Darwinist period

 In a number of multicellular organisms, microgametes and macrogametes are produced in the specialized organs of a single individual. This state is termed hermaphroditism. This is a derivative state in most modern multicellular organisms, which emerged secondarily during evolution, for instance as a consequence of the specific ecological requirements of the individual species. For example, adaptation to a parasitic life style is a frequent reason for the emergence of hermaphroditism. Macroparasites, of which human tape worms are a typical prototype, frequently enter the bodies of their hosts or can survive there only as a very few specimens. Thus, as gonochorists, they would be faced by the danger that they would not be able to find an individual of the opposite sex in their vicinity as adults. It is thus advantageous for them if any given individual can function as both a male and a female. Similarly, hermaphroditism is advantageous from an ecological viewpoint in sessile, immobile organisms (e.g. plants).

            Some hermaphrodites can use either a uniparental or a biparental mode of reproduction. From the viewpoint of exploitation of the advantages of sexual reproduction, biparental reproduction is preferable, where the microgametes and macrogametes forming the zygote are derived from different individuals. However, sometimes a situation occurs where the hermapahrodite is dependent on uniparental reproduction, i.e. fertilization of the macrogametes by its own microgametes. So far, it seems that a great many hermapahrodites are capable of self-fertilization in such a situation; however, it is mostly not clear how long the individual hermaphroditic species are capable of surviving without biparental reproduction.

            The differentiation of organisms into individuals producing microgametes and individuals producing macrogametes, gonochorism, is advantageous for two reasons. To begin with, it prevents uniparental reproduction, i.e. it ensures that the microgametes and macrogametes forming the zygote are derived from two different individuals. In addition, it allows organisms to be differentiated morphologically, physiologically, ecologically and ethologically into males, producing microgametes and females producing macrogametes. The production of microgametes and macrogametes places somewhat different demands on the properties of the organism. The properties of hermaphrodites must necessarily be only a certain evolutionary compromise in this respect. In contrast, the evolution of the properties of gonochoristic organisms can proceed in both males and females separately and can optimize the relevant properties for each sex separately.

The hypothesis of greater robustness of oogenesis assumes that the formation of sperm is generally more sensitive to disturbances than the formation of oocytes (Hunt & Hassold 2002). It follows from experiments that, compared to the differentiation of sperm, the differentiation of oocytes more frequently progresses successfully to the end, even when the individual bears genetic defects or when this occurs under abnormal external conditions. A female with a certain genetic disorder is still fertile, while a male is not. It is possible that this is a manifestation of the general phenomenon of the greater intra-population cost of females (see XIV.7.1). Thus males can act in evolution, not only as cheap experimental material for testing new evolutionary features, but also as a “waste basket”, i.e. a means of cheap elimination of unsuitable alleles.

see hybridogenesis

History of evolutionism - neo-Darwinist period

Most models of evolution in the area of population genetics consider only hard natural selection. Consequently, geneticists occasionally encounter apparently unsolvable paradoxes. An example is Haldane’s dilemma (Haldane 1957), describing the substitution cost accompanying the replacement of one allele in the population by some other, more advantageous allele. The substitution cost (L) is defined by the equation

where W_opdenotes the fitness of an individual with optimal genotype and W is the average fitness of individuals in the population i.e. a parameter expressing how many times the average fitness of individuals in the population is lower than would be the average fitness in a population formed exclusively of individuals with optimum genotype. In models describing hard selection, the magnitude of the substitution cost for the population is directly proportional to the number of genetic deaths, i.e. the number of organisms eliminated by natural selection in substituting a suboptimal allele by an optimal allele. If new alleles constantly appear in the population, increasing the fitness of their bearers, the relative fitness of all the bearers of the other alleles is reduced (W_op, i.e. the fitness of individuals with optimal phenotype is always set at 1), increasing the substitution cost for the population. Haldane pointed out that, with simultaneous selection in favour of a greater number of suitable alleles from various genes, the substitution cost for a particular population can attain unrealistically high values and the number of genetic deaths can easily exceed the reproduction potential of the population.

However, when we take into consideration that the individual alleles can be eliminated by soft selection, the situation looks rather different. The cost is constant in each generation, i.e. actually equal to zero. Natural selection always eliminates a constant percentage of individuals from the population without regard to the specific values of the average fitness of individuals in the population (Nunney 2003). On the other hand, it is apparent that selection can occur simultaneously in favour of only a limited number of traits; if selection occurs to the benefit of a great many traits, the viability of the population is not endangered (as it would be if hard selection were active), but the effectiveness of the selection of the individual traits would be proportionally reduced, and the Hill-Robertson effectwould be manifested. This effect is especially marked when there is a close genetic connection between the loci in which selection occurs, i.e., e.g., in asexually reproducing organisms or for loci in areas in which genetic recombination does not occur for some reason (Charlesworth & Charlesworth 2000). The reduced effectiveness of simultaneous selection for a greater number of traits can play a significant negative role in the evolutionary response of the population or species to a rapidly changing environment (Nunney 2003).

It was repeatedly found that, in the natural population, the most common alleles are usually dominant and, on the other hand, minority alleles are frequently recessive. If, on the other hand, we isolate individuals in the laboratory that bear two newly formed mutated alleles, or if we obtain individuals bearing minority alleles in mutually isolated natural populations, then the relationship of partial dominance is mostly found between their alleles. The explanation suggested by Haldane says that suitable dominant alleles will be more readily spread in the population and will thus become majority alleles more readily than similarly advantageous recessive alleles. While the usefulness of dominant alleles is also manifested in a heterozygote, the usefulness of similar recessive alleles is manifested only in recessive homozygotes, in the outbred population, i.e. in a population in which random crossing occurs between its members, i.e. only when its frequency is substantially increased.

History of evolutionism – post-neo-Darwinist period

History of evolutionism – post-neo-Darwinist period

The handicap hypothesis, which was formulated in 1975 by A. Zahavi (Zahavi 1975), assumes that, under certain conditions, it may be advantageous for the female to choose, as the father of her offspring, a handicapped male, for example, a male with long tail feathers. The long feathers represent a substantial handicap for their bearer in the fight for survival. Thus, if a male with abnormally long tail feathers, i.e. with an abnormally large handicap, has survived to reproductive age, it is almost certain that this must be an abnormally fit individual.
            Simultaneously, this handicap need not be only a secondary sexual trait. It could, for example, be a physical defect incurred through an injury or even the old age of the individual (Kokko & Lindstrom 1996; Sundberg & Dixon 1996). It has been observed, for example, for sparrows and finches, that, in extra-pair parentage (EPP), females prefer old males (Wetton et al. 1995; Sundberg & Dixon 1996). Simultaneously, the frequency of extra-pair copulation (EPC) with old and young individuals is the same. In perching birds (Passeriformes), the female determines whether copulation will leads to transfer of sperm or not. The fact that, for the same frequency of EPC, a greater number of offspring are fathered by older males suggests that the purpose of this “gerontophilia” lies in an attempt of the female to obtain the best genes for her offspring. 
            The handicap hypothesis on the origin of secondary sexual traits has been subject to fundamental criticism in the past. Mathematical analysis of the effect of a handicap of the father on the fitness of offspring has shown that the advantage represented by the greater fitness of the father is exactly compensated in the offspring by the existence of the handicap that the progeny also inherit. However, at the present time, it seems that the model could work in a number of situations (Pomiankowski 1987; Siller 1998; Hastings 1994).  At the same time, it is important that the coefficient of heritability of the handicap, a factor reflecting the probability that the offspring will inherit the particular trait, for example long feathers, is less than the average coefficient of heritability of the other traits determining the fitness of the individual. If, in addition to genetic factors, the effect of the environment also has a substantial effect on feather length, the coefficient of heritability of this trait can be very low. Under these conditions, it is really advantageous for the female to prefer reproduction with a handicapped male.s

The frequency of the individual genotypes in the equilibrium state can be readily calculated from the frequency of the alleles in a certain locus. This equilibrium state is called the Hardy-Weinberg equilibrium. In a large panmictic population, i.e. in a population whose members reproduce together quite at random, this equilibrium is established during a single generation. It follows from the laws of combinatorics that, at equilibrium, genotypes a₁a₁, a₁a₂ and a₂a₂ will be present in a ratio of ¦²: 2¦_a¦_a:¦², where ¦_aand ¦_adenote the frequency of alleles a₁ and a₂ in the previous generation (Fig. II.14).  Here, the ratio in which the individual genotypes were present in the previous generation is not in any way important. During a single generation, the same representation of the individual genotypes is established, regardless of whether the original population contained, for example, only homozygotes a₁a₁ and a₂a₂, or only heterozygotes a₁a₂.

If we study several genes, amongst which there is no genetic linkage, for example, if each of them is located on a different chromosome, equilibrium is again established within a single generation; the numbers of the individual genotypes can be calculated for this state according to the simple rules of combinatorics.

Ability to passed the individual characters between generations that is responsible for the resemblances between parents and offspring.Natural selection is effective, and the biological evolution can operate, only if individual differences between organisms are hereditary.Various degrees of heritability of properties can exist; in some systems, a characteristic property of a certain individual can be passed on to its progeny in unaltered form and degree, at other times to a lesser degree or may appear in progeny only with increased probability.

Amongst modern organisms, heredity is based on copying genetic information, instructions for creation of the body of organisms. Theoretically, completely different mechanisms could also exist, based, for example, on direct copying of the actual structure of the organism itself.

see Gonochorism

The heterozygosity index (H), which is basically the frequency of heterozygotes in the population, is another commonly employed measure of the degree of polymorphism in the population. For the individual genes, this index is usually calculated from the frequencies of the individual alleles:

where x_i  is the frequency of the i-th allele in the population. Thus, a population containing a large number of alleles with the same frequency has the largest H value. The average heterozygosity index for the given population can be calculated on the basis of the heterozygosity indices as the arithmetic mean for the individual genes. If the heterozygosity index is calculated on the basis of sequence data, it is also sometimes called the gene diversity index. The nucleotide (aminoacid) diversity index (B) can also be calculated on the basis of sequence data; this corresponds to the average number of nucleotide (aminoacid) differences between all the pairs of alleles in the sample divided by the length of the sequences of the relevant alleles. The average number of pair differences Π can be calculated for the whole population or, to be more precise, for the population sample, as

where n is the number of observed sequences (so that  is the number of various pairs of sequences) and Π_ij is the number of differences between the i-th and j-th sequence.

The emergence of genetics, a field of science whose theoretical foundations were established in the 19^th century by Johann Gregor Mendel (1822–1884) (Fig. XXVIII.9), greatly assisted in the development of the theory of evolution. Genetic knowledge especially assisted in eliminating the greatest conceptual inadequacies of Darwin’s model of the evolution of adaptive structures by natural selection. As long as biologists assumed that the predispositions derived from both parents are mixed together and “averaged” in sexual reproduction, Darwin’s model was incapable of functioning. The hereditability of traits, including evolutionary innovations was necessarily vanishing; a substantial trait in a parent appeared to a lesser degree in its progeny, even less in its grand-descendants and basically disappeared, i.e. was lost in the standard population, over a few subsequent generations. In order for Darwin’s model to be functional, it would require an unrealistically high rate of formation of new inheritable variability. The rediscovery of Mendel’s laws around 1900 demonstrated that the predispositions for the individual traits actually do not affect one another during sexual reproduction and, to the contrary, are transferred from one generation to the next in unaltered form. However, over time, the frequency of the individual predispositions (alleles) can change in the gene pool of the population, enabling Darwinistic evolution. As the proponents of the other concepts gradually died, the study of evolution slowly became identical with study of the changes in the numbers of the individual alleles in the gene pool of the population and all evolutionary phenomena taking place above the level of the species began to be considered to be simply evolutionary consequences and accompanying phenomena of processes occurring at the intraspecific level.

            The geneticist Theodosius Dobzhansky (1900–1975), paleontologist George Gaylord Simpson (1902–1984), zoologist Ernst Mayr (1904-2005) and botanist George Ledyard Stebbins (1906–2000) are generally considered to be the main representatives of Neo-Darwinism responsible for evolutionary synthesis. Bernhard Rensch (1900–1990), Julian Sorell Huxley (1887–1975), Ronald Aylmer Fisher (1890–1962), Sewall Wright (1889–1988), John Burdon Sanderson Haldane (1892–1964) and a great many others also contributed substantially to the formulation of Neo-Darwinism. The Neo-Darwinist period is characterized by emphasizing and stressing the importance of selection in evolution. Other mechanisms, with the possible exception of genetic drift, are considered to be marginal. The main scientific efforts were concentrated on the study of evolutionary processes occurring at the intraspecific level or speciation processes. Study of macroevolutionary processes lies, to a substantial degree, outside of the main sphere of interest of a major portion of evolutionary biologists.

Just as, in his work, Darwin admitted the importance of a number of independent evolutionary mechanisms acting on organisms together with natural selection, a similar plurality approach to the theory of evolution was prevalent in the entire professional community (Gould 2002). Amongst the non-biological public, Darwinism was almost universally identified with his theory of natural selection. This theory was attractive for a large part of society, because it agreed well with the general experience of the inhabitants of England and the rest of the developed world with the functioning of human society in the period of emerging capitalism. Competition amongst individual entities and the success and preservation of the strongest and best adapted to the prevailing conditions was generally recognized as a motor for social change and social, of course primarily material, progress. In contrast, professionals were frequently aware that Darwin’s theory of natural selection has a number of obstacles and that some of the conclusions following from this theory were even contradictory to the then-known empirical facts.  For these reasons and also because of the absence of centralized supranational science, a great many various concepts of the theory of evolution, based on a number of fundamentally different mechanisms, coexisted for a period of at least 60 years. Various autogenetic concepts, which assumed that living organisms are characterized by a certain internal tendency towards gradual directed development (Galton, Chambers, von Nägeli, Eimer, Osborn) and frequently even towards gradual perfection (Teilhard de Chardin) always held a very strong position. Other theories assumed that Lamarckian mechanisms of strengthening of highly utilized structures and inheritance of acquired traits are of great importance in the evolution of adaptive structures and in mutual divergence of individual species of organisms (partially also supported by Darwin himself). Some theories considered the direct effect of environmental factors on the properties of organisms (St. Hilaire). Others assumed a fundamental effect of sudden jump-like changes in the properties of organisms (Bateson, de Vries, Goldschmidt, Schindelwolf). Of course, theories assuming the fundamental effect of natural selection also maintained a strong position (Wallace, Weismann).

see Genetic draft

While phenograms are formed on the basis of all the traits that can be differentiated in the members of the studied species, a scheme of cladogenesis, which is intended to express not similarity but rather relatedness of species, must be expressed solely on the basis of certain subsets of these traits. For example, it is quite obvious that relationships between species cannot be derived on the basis of shared traits, formed in the individual species during evolution independently of one another, i.e. traits that were not present in the closest common ancestor of the compared species. Such a trait is termed homoplasy. Homology is the opposite of homoplasy; this is a common trait of two or more species that these species inherited from their closest common ancestor.
The definition of a homological trait is, in a certain sense, relative. On the one hand, the wings of birds and the wings of bats are homoplasies, as no exclusive common ancestor of birds and bats had wings. However, wings evolved only once in the line of birds and the line of bats. The presence of wings in birds and bats is thus homoplasy from the viewpoint of the two groups together and is a homological trait from the viewpoint of each group separately. The situation is further complicated by the fact that, in both birds and bats, wings were formed from the front limbs of vertebrates and the common ancestor of these two groups had front limbs. Thus, the presence of front limbs must also be considered to be a homological trait that birds and mammals inherited from their common ancestor.

see Homological trait in phylogenetics

- If a parasite is transmitted horizontally through direct contact between an infected and uninfected individual, parasitosis is generally less virulent. From the standpoint of spreading of the parasite, it would be inexpedient if it were to substantially harm the state of health of the infected host and thus limit its number of contacts with healthy individuals. To the contrary, the virulence of parasites tends to be greater for some other means of spreading parasitosis. For example, parasites spread by vectors tend to have high virulence. This is true both for parasites spread by animal vectors (Ewald 1983), such as mosquitoes (Fig. XIX.10), as well as parasites spread by abiotic vectors, for example flowing water. (Ewald 1991) (Fig. XIX.11). The infected animal can be harmed by the parasite or even immobilized, as the vector is responsible for transfer of the infection to another individual in the population. If water acts as the vector, high virulence of the parasite is also enhanced by a large size of the infection inoculum, which generally enters a single host during infection, with the related high genetic variability within the infrapopulation (see XIX.4.2.2). If the vector is an animal, its manifestations of parasitosis are generally much milder than those in the actual host. It is the role of the vector in the life cycle of the parasite to spread the infection in space and any damage to its state of health would be detrimental to this function. 
 
Parasites capable of independent active motion from one individual to another within the host population, for example, parasitic Hymenoptera or Diptera, also frequently exhibit high virulence. In this case, the parasite is very frequently converted to a parasitoid during evolution, i.e. a parasite that kills its host after a certain period of symbiosis with the infected individual.
Parasites spread alimentarily, specifically by predation, also exhibit high virulence (Ewald 1995). In these cases, the pathological manifestations of parasitosis can increase the chance that the infected individual will be caught by a predator, leading to transfer of the infection. Simultaneously, the predator is usually harmed substantially less than its prey. Otherwise, it would be a relatively easy matter for individuals to be selected in the population of predators that would learn to avoid infected individuals amongst prey when hunting. It could also be important that the definitive host often also acts as a vector and harming the vector would be detrimental to its function in the life cycle of the parasite – spreading infection in space. Simultaneously, the frequent combination of the function of a vector and definitive host need not be accidental and can have a certain importance. During spreading of parasites in space, offspring can frequently encounter conditions differing from those under which their parents lived; under these circumstances, even temporary variability, formed during multiplication through recombination and segregation, can be an advantage (see for example, XIII.3.2.2.2).
High virulence can be exhibited by sit-and-wait infections, i.e. infection transmitted through long-lived resistant stages, spores and cysts, which remain where the infected host died and then infect another host that comes some time in the future (Ewald 1995). Anthrax and smallpox are typical examples of sit-and-wait infections and their spores can remain in the environment for years or even decades. The high virulence of infection in these parasites is a result of the fact that the probability of infecting another host is proportional to the number of spores that remain at the site of death of the infected individual. Consequently, a parasite will attempt to convert as large a part of the body of its host into its own spores or cysts as fast as possible. This is, of course, mostly incompatible with the life of the host organism.

The evolution of a parasite and its host often has the character of an “arms race”, in which the host develops more or less specific mechanisms of defense against parasitization and the parasite, on the other hand, develops mechanisms allowing it to avoid or overcome these defense mechanisms. However, the fact that a parasite adapts perfectly to a certain species of host means that it closes the route to parasitization on other species. Thus, “arms races” frequently lead to very narrow specialization of the parasitic species and often result in narrow host specificity of the parasite. Narrowing of the host spectrum frequently ends with a state where the parasite is capable of completing its life cycle only in the members of a single host species and does not attack even closely related species at all (Fig. XIX.3). This is in sharp contrast with the situation for a number of groups of predators, where narrow specialization of the predator on a single species is certainly not the rule.
For example, molecular mimicry is characteristic for some parasitic microorganisms (including viruses) (Moloo, Kutuza, & Boreham 1980). The parasite adapts the structure of its macromolecules to the structure of the relevant macromolecules of the host organism. If, for example, a certain virus were capable, through gradual accumulation of substitution mutations, of eliminating, from its proteins, all the peptides that are recognized as being foreign by the immune system of the host species, and thus adapt its “peptide vocabulary”, i.e. the set of peptides occurring in its proteins, to the vocabulary of its host, it would quite certainly escape from the reach of the immune system of the host, and could thus spread uncontrollably in the relevant host population. (The fact that it is not an easy matter for the parasite to achieve this final state and the role of MHC-antigens and sexuality in the defense of the host were described in Section VIII.4.3.1.) However, if the peptide vocabularies of two host organisms are very different, and this is highly probable as a result of the relevant selection pressure from parasites (see below), then a parasite cannot simultaneously adapt its vocabulary to two different vocabularies of two host species, except at a cost of drastic limitation of its own peptide vocabulary, which is incompatible with functionality of the proteins. Any form of utilization of the principle of molecular mimicry thus again creates selection pressure for gradual narrowing of the host spectrum of the parasite.

The biogeography, i.e. study of the distribution of the individual species provides an enormous amount of evidence for the evolution of species of fauna and flora through gradual branching off from a common ancestor. If the individual species of organisms were to be formed independently at the same time or one after another, the distribution of their occurrence over the surface of the Earth should also be independent or this distribution should reflect only the differences in natural conditions in various parts of the Earth. However, reality is quite different. Species belonging in a particular taxon very frequently occur in the individual areas of the Earth, although species belonging in other taxa could also be very successful there. The reason why, for example, there are no local species of big cats in Australia is certainly not that there were not suitable conditions there for them, but that they did not have any species from which they could evolve, there was no species of cat that they could gradually evolve from. On the other hand, it is clear why there are a great many local species of bats there – their ancestors could quite easily get there by air. This phenomenon is particularly obvious on islands. As soon as an island is far from the mainland, there is a lack of the members of taxa for which the ocean represents an obstacle to spreading. In contrast, these species are present on islands located at suitable distances from the mainland and they very frequently form separate species that are different from the species occurring on other islands or on the mainland.
            Another obvious phenomenon that is encountered on islands and groups of islands consists in radiation of taxa, whose members have only a very narrow niche on the mainland. Darwin’s finches are mostly given as a typical example; in actual fact, these are a group of closely related buntings occurring on the individual islands of the Galapagos Islands. The individual species became morphologically differentiated in the local environment and divided up various ecological niches that are occupied on the mainland by birds of various taxa. Numerous species of Drepanididae on the Hawaiian Islands represent a similar case (Fig. XXVII.3). The theory of evolution predicts the formation of species with this character of distribution of occurrence the individual species. Local species of woodpeckers cannot exist in the Galapagos simply because no common ancestor got there. If the relevant niche were to be filled, a species of bird that got to the island in the past, in this case a bunting, would have to (at least imperfectly) adapt to it. In contrast, other theories of the origin of species would encounter substantial difficulties in explaining similar data. If the species were to have been formed independently, for example by autogenesis, or if they were to have been formed in a single instant, either in one place or in a great many places by a rational being, either there would be woodpeckers on the Galapagos, or they would not be there; however, they would apparently not be replaced by a local species of bunting and quite certainly closely related species of this species of bunting would not replace several other unrelated groups of birds in their very different ecological niches in the Galapagos.

It was very soon found from study of the anatomy of various species of organisms, and especially in studying the ontogenesis of their individual organs, that the structural plans of the bodies of even very dissimilar organisms within the individual taxa are extremely similar in their individual details. For example, amongst vertebrates, the human hand, the digging limb of a mole and the wing of a bird contain the same groups of bones (Fig. XXVII.4). We say that the individual bones in various species can be homologized, i.e. that they are homologous structures, homologues. In addition, these bones were formed in the course of ontogenesis by basically the same mechanisms from the same basic forms. Simultaneously, if we compare the limbs of other groups of organisms, for example the limb of a mole and the limb of a mole cricket, it is immediately obvious that functionally identical types of limbs can be formed by completely different means, from completely different parts and through completely different ontogenetic mechanisms.
The occurrence of homologous structures within individual monophyletic taxa is now considered to be a consequence of the fact that the individual species were formed by divergence from a common ancestor. As biogeography has demonstrated that daughter species can be formed only from some parent species, comparative anatomy has also confirmed that a new anatomical structure can be formed only by modification of a different structure that already existed in the parent species.
The existence of rudiments and atavisms also confirm that the occurrence of homologous structures actually does not have a functional cause. Rudiments are residual organs that occur in all the individuals of a certain species, where they do not fulfill any function in this species. Thus, they are mostly much smaller and structurally simpler than where they fulfill some sort of function (Fig. XXVII.5). Some rudiments in the given species of organism are formed only during embryonic development and cannot be found in adult individuals. The appendix, a worm-like protuberance of the intestine, is considered to be a rudiment in humans. In a great many taxa, the appendix plays a very important role in digestion and is quite large (Fig. XXVII.6). It has been substantially reduced in humans and its removal apparently does not negatively affect the fitness of the individual.
Atavisms represent a similar case to rudiments. Atavisms are structures that, in contrast to rudiments, occur in only some individuals of a particular species, have no functional importance for their bearers and simultaneously occur in all the members of some other species, where they do have functional importance. For example, in humans, individuals occur very rarely that have an atavism in the form of a tail (Fig. XXVII.7). The occurrence of atavisms is once again very good evidence for the evolutionary mechanisms of the origin of species. The organisms can manage quite well without these structures, so that their presence has no functional basis. They are not formed in most individuals, so that their presence necessarily cannot follow from the properties of the components from which the body of the organism is formed or from the character of the processes of ontogenesis (see the structuralist explanation of evolutionary trends, XXVI.7.4). The only reasonable explanation that remains is the evolutionary explanation – the occurrence of rudiments and atavisms follows from the fact that these organs existed in functional form in an ancestor of the given species, so that the ability to form them is also borne by the members of successor species.

- Paleontology, the study of fossils, provides us with a great deal of evidence for the simple fact of evolution. However, the existence of fossils is not, in itself, evidence for evolution. Nonetheless, because of the possibility of dating fossils using a number of physical methods, at the very least it reliably overturns the ideas of some opponents of evolution about the recent emergence of animals, plants and humans on the Earth approximately 6000 years ago. While there are not now a great many proponents of the “Young Earth” theory, relying on a literal interpretation of the Bible, they are disproportionately vociferous. However, the results of stratigraphic analysis document the evolution of organisms from a common ancestor, showing that the individual organisms do not appear in the paleontological record at random, but rather in the order that corresponds to their mutual similarity and thus assumed relatedness. On the basis of the similarity of the members of the main taxa of vertebrates – fish, amphibians, reptiles and mammals – it can be concluded that they were most probably formed one from another in this order. Theoretically, it would also be possible that they would be formed from one another in the opposite order, i.e. that first mammals would be formed, from them reptiles, then amphibians and finally fish. However, this possibility can be refuted by comparison of fish and mammals with invertebrate fauna, which certainly have far more common traits with fish than with mammals. Perusal of the paleontological record reveals that, of these groups, fish actually did appear first on the Earth, followed by amphibians, reptiles and finally mammals. The same analysis can be performed in any monophyletic taxon, i.e. within a group of organisms for which it can be assumed, on the basis of independent data, that they evolved from a common ancestor. In every case, we obtain results that are in full agreement with the predictions made on the basis of the theory of evolution. This indicates that the individual groups of organisms emerged gradually over time through divergence from a common ancestor 

see History of evolutionism - neo-Darwinist period

see Speciation hybridization

Amongst sexual organisms, species frequently evolve allopatrically or peripatrically (in geographically separate regions) from a common ancestor, so that their original areas of occurrence are not in contact or are in contact only at a place where, because of the presence of a certain barrier in the environment (mountain range, river), there is only very limited gene flow between the two species. The places, where the areas of occurrence of emerging species are in contact and where a certain degree of gene flow occurs between the species, are called primary hybrid zones. Primary hybrid zones are apparently rather rare (Jiggins & Mallet 2000). If this were not true and if substantial gene flow were to occur between emerging species, in most cases a new species could not even be formed or, after formation, would again merge with the original species. However, the areas of occurrence of the individual species are frequently not static and grow larger or smaller or are shifted in response to changes in the natural conditions. Thus, it can occur that, in time, two species, that were not originally in contact or were in only very limited contact, come into close contact or their areas of occurrence can even merge. Under these circumstances, there are three possible consequences. If internal (e.g. ethological or ecological) barriers have formed in the species to prevent crossing, the two species can live sympatrically, i.e. in the same territory, one next to the other, or the ecologically better adapted species can suppress the less well adapted species over a certain area. If no reproduction barriers have been formed in the species, the two species can fuse to form a single species, even if they were not originally sibling species – i.e. species that were formed by a single speciation from a common ancestor. If the species have already formed certain reproduction barriers, the contact of the areas of occurrence of two related sexual species usually leads to the formation of a secondary hybrid zone along the line of secondary contact of the two areas. Crossing of the members of two different species occurs at sites in the hybrid zone and thus their hybrids are encountered here. This zone is usually very narrow but may extend for hundreds of kilometers across a continent. The alleles of the individual genes characteristic for one or the other species penetrate through the hybrid zone into the area of occurrence of the other species to different depths (Fig. XX.7), so that detailed genetic studies generally demonstrate that the edges of the hybrid zone are fuzzy (the zone has a different width for each gene) and asymmetric from the viewpoint of the two species – the alleles of a certain gene of the first species penetrate deep into the area of the second species, while the relevant alleles of the second species do not penetrate at all or penetrate to only small distances into the area of the first species (Gündüz et al. 2001). The depth to which a particular allele penetrates depends on the degree to which this allele is compatible with the alleles occurring in the neighboring species, i.e. the degree to which it reduces the fitness of its carrier when combined with the alleles of the genes of the foreign species. However, other phenomena also contribute to the formation of asymmetry, for example differences in the migration activities of the two species and asymmetry in the reproduction barriers – the males of the first species might be able to successfully reproduce with the females of the second species, but the males of the second species are not capable of successful reproduction with the females of the first species (Tiffin, Olson, & Moyle 2001). Some zones are static and remain in the same place for a long time, while others are mobile and move at a certain rate in both directions. In this case, the area of occurrence of one species will gradually expand at the expense of the area of occurrence of the other species.
At a genetic level, a hybrid zone is typically characterized by unusually high occurrence of some otherwise very rare alleles (Schilthuizen, Hoekstra, & Gittenberger 1999; Schilthuizen, Hoekstra, & Gittenberger 2001). Their elevated occurrence is apparently a consequence of epistatic interactions between the alleles derived from one or the other species. Such a combination of alleles cannot occur outside of the hybrid zone, so that the alleles that function very well for these combinations, i.e. increase the fitness of the carriers of alleles derived from different species, are rare there.

The hypercycle model, which was developed mainly by Nobel prize winner for chemistry, Manfred Eigen, is a theoretical model of a self-replicating system, whose elements are arranged in a cycle, in which every element (enzyme, protoenzyme?) somehow assists in the formation of one or more further elements (Eigen & Winkler-Oswatitsch 1992). Simultaneously, the elements of a cycle are mutually connected only functionally, i.e. through their functions in the cycle, and need not be spatially related, e.g. concentrated in structures of the coacervate type. Mathematical models have demonstrated that mutual competition may occur in a medium containing the components of several different hypercycles. Thus, biological evolution can occur under certain conditions.

            The hypothesis is very interesting from the point of view of the theory of systems. Its chief importance for protobiology lies in the fact that it permitted study of the aspect of whether the formation of spatially delimited structures is a necessary condition for the functioning of natural selection and thus a necessary condition for the emergence of biological evolution. However, the hypothesis does not deal with how systems of the hypercycle type could be specifically formed in an abiotic medium, i.e. from which chemical components they could be formed. Moreover, the most frequently considered hypercycle model, consisting in a system of functionally interconnected molecules with enzymatic activity capable of self-reproduction as a whole (Fig. X.5), seems somewhat unrealistic from the viewpoint of modern protobiology. The study of mathematical models of competition between spatially undelimited hypercycles finally indicated that the stability of such a system is seriously endangered by the possibility of formation of parasitic hypercycles, i.e. hypercycles that take some components from other hypercycles, but do not return anything to the system in their place. These parasitic hypercycles can reproduce substantially faster than complete hypercycles and can thus relatively easily disrupt the entire system (Cronhjort 1995). This indicates that compartmentation of the individual proto-organisms is apparently an essential precondition for the emergence of biological evolution.

see Cultural traits transmission of

Formation of conditioned reflexes and other types of learning provide animals with good behavioral plasticity. They enable each individual of the given species to adapt to the particular local conditions, which can differ from the long-term conditions under which the majority of this kind lives. The individual can even adjust its behavior to stimuli it never experienced before. If an adaptation to a unique lifetime situation is to be created (e.g. the need to recognize its parents), learning may occur in the form of imprinting. If the individual encounters the appropriate stimulus at a given moment, e.g. when a freshly hatched young goose meets a colored ball or Professor Konrad Lorenz, it will imprint the particular object into its memory as its mother and for the rest of its life this stimulus will remain a trigger for particular behavioral patterns. Behavioral patterns created by imprinting are long-term or permanent and do not need strengthening to last. On the other hand, once they are created they are usually irreversible; they can not be changed when the external conditions change. In contrast, standard learned patterns can disappear more or less rapidly. To last, they need to be strengthened continuously by a repeatedly occurring combination of the stimuli that produced the patterns. In a changeable environment, this is advantageous because reflexes that are no longer useful for the organism can give way to new ones. Conversely, imprinting is useful for stimuli that will probably not change during the individual’s life, e.g. recognizing its mother or members of its own species.

Inborn reflexive behavioris a type of behavior that is one step more complex. The unconditioned reflex is a prototype of this kind of behavior, but it is necessary to bear in mind that a simple reflex can be followed by a long sequence of other elements of behavior, of  which some are fixed and some learned (see below). The organism’s reaction to a specific external starting stimulus consists in the activation of another specific pattern of behavior (e.g. the familiar patellar reflex). The specificity of the external starting stimulus ensures that the given patterns of behavior will be initiated in situations that are advantageous for the organism. This type of control lacks plasticity; it develops entirely in the process of natural selection which does not enable the organism to react to the momentary situation. From a statistical point of view and in the long-time perspective, the existence of a fixed pattern of behavior can be advantageous, but in some situations, especially under changing conditions, such a behavioral pattern can be fatal. Moths would certainly tell us something very ugly, if they could, about their current experience:  For millions of years, they have oriented themselves according to light sources when flying in the dark; i.e. according to the position of moon and stars, objects infinitely far away from the practical point of view. If they were to do this in the present-day populated landscape, they would most likely end their lives by spiraling into hot light bulbs.

Inclusive fitness is one of two components of fitness, direct fitness and inclusive fitness.. Direct fitness takes into consideration reproductive success only of the particular individual, while inclusive fitness considers the reproductive success of both the particular individual and of his relatives.

For example, if the population contains an individual who helps his siblings, these individuals have, on an average, greater fitness than the other members of the particular population, even if they leave behind the same number of descendants. Their nephews and nieces have, in any case, at least ¼ of their genes in common because of their relatedness (the fraction of common genes can often be greater as a consequence of relatedness, as the relatives of particular individuals could have reproduced together in previous generations). From the standpoint of evolution it thus makes no difference if an individual assists in reproducing himself or two of his direct relatives or siblings (with whom he has at least ½ of their genes in common because of their relatedness) or 4 descendants of his descendant or sibling. Altruistic behaviour of individuals is thus worthwhile if

rb>c,

where r is the relationship of mutually assisting individuals, basically indicating how much larger will be the probability that an allele of the gene for altruistic behaviour will be shared by two specific individuals than that it will be shared by two randomly selected individuals in the population, b – the advantage that altruistic behaviour provides to the assisted individual and c – the cost that the assisting individual must pay for assisting. The price and the advantage are measured in terms of the relevant biological currency, i.e. in the biological fitness. Thus, under certain conditions, an organism can increase its fitness either by producing a greater number of descendants or by assisting its relatives.

An interesting property of sexual selection lies in its marked inertia. At first glance, it might seem that, under conditions where feather length attains dimensions that are disadvantageous for their bearers, sexual selection should “shift to another track”. Females should appear in the population that would begin to select a sexual partner according to other criteria. However, imagine the situation encountered by a female that would begin to prefer males with shorter feathers. Her sons would inherit shorter feathers from their father and will thus have a greater chance of living to reproductive age than their competitors. It might seem that the offspring of the mutated female would have greater fitness. However, this is not true in actual fact. Most of the females in the population will continue to prefer cocks with longer feathers, so that the sons of the mutated female will have reduced sexual attractivness and therefore reduced fitness.
            It can be demonstrated that the predominant taste of the females in the flock has a major effect on the reproductive success of males with various phenotypes, especially in polygynic species. In some species of fauna there is even a special ethological mechanism that further strengthens the inertia of sexual selection. It has frequently been observed in birds, mammals and fish (Dugatkin 1996; Agrawal 2001b) that females employ a male’s success with the other females in the flock as one of the most important criteria for selection of a sexual partner (Fig. XV.3). A female who saw that a certain male copulated with a great many other females also frequently prefers this male. This mechanism ensures that the females “need not” rely on their individual taste, but can base their selection of a sexual partner on the predominant taste of females in the particular population. This mechanism is especially advantageous when a female becomes part of a new flock. In order for her sons to exhibit sufficient sex-appeal in the new environment, it is advantageous if the female is able to subject her selection of a sexual partner to the momentary taste of most of the females in the flock.
            This model can, of course, not be generalized; in some situations, to the contrary, the effect of the rare male is important. It has been observed in a great many species that above-average success in intrasexual competition is exhibited by males with rare, frequently striking phenotypes (Singh & Sisodia 2000). As was probably first noticed by Daniel Frynta of the Prague Faculty of Science (who, after his custom, did not publish it), the two contradictory effects are, in actual fact, not mutually exclusive and can be active simultaneously in a single population. While most of the females in a particular population systematically prefer males with the most common phenotype, these males tend to compete with one another. When a male with unusual phenotype appears in the population, he has a chance that he will have great reproductive success amongst some females whose individual taste he satisfies. Although most females will prefer the male with the common phenotype, males with unusual phenotype could exhibit the greatest “sexual fitness”.

Frequently, only a small number of infectious stages of the parasite, and sometimes only one individual, enter the host organism. This individual can reproduce here and must form the infectious stage. A subpopulation of the parasite bound to a single host organism, called an infrapopulation, survives there for a certain time; this period of time is limited at one end by the moment of infection and, at the other end, by the moment when the host manages, for example through immune mechanisms, to destroy the parasite or when the host organism dies a natural death or as a result of pathogenic manifestations of parasitosis. From the standpoint of the growth rate of the overall parasite population, and thus from the standpoint of the evolution of the relevant parasite species, two parameters are most important – the number of infected individuals and the number of propagules, i.e. infectious stages that the individual parasite infrapopulation produces. In general, we can state that, under certain conditions, the rate of production of infectious stages by the particular subpopulation per time unit is more important while, under different conditions, the number of infectious stages produced over the entire time of existence of the parasite subpopulation, i.e. for the duration of infection of a single host, is more important. This is thus a system that, in a certain sense, is analogous to the model of turbidostatic and chemostatic selection. Parasite subpopulations bound to individual hosts can be exposed either to selection for greater rate of reproduction, for example, when there is a danger of frequent superinfection (i.e. the infection of an already infected individual), or selection for better (more economical) use of resources, in this case infected hosts. In the latter case, the critical parameter is not the actual growth rate of the infrapopulation, but the effectiveness of use of the infected host individual. Because the growth rate is not of fundamental importance, it can be quite low in some parasites and, in some cases, even zero. The parasite does not reproduce in the infected individual, only survives in a constant number of individuals and produces infectious stages.
A low or zero growth rate of the parasite infrapopulation is, in addition, also advantageous from the standpoint of protection against identification by the immune system of the host. Some components of this system react, not to the presence or absence of a foreign antigen, but rather to its potential dangerousness and thus, for example, to damage to the tissues of the host organism or to the very dynamics of increase in the amount of antigen in the organism. If a parasite reproduces exponentially in an organism, it becomes an easy target for the sensory components of the immune system and thus a probable object of attack by its effector components. If, on the other hand, the concentration of antigens does not change in the organism, or if it increases only slowly, the immune system does not act against the particular instigation. This “sneaking through” of an antigenic agent plays a negative role, not only in defense against a slowly reproducing parasite, but also in antitumour immunity, specifically in immunity failure against slowly growing tumours.
            Reproduction or, to the contrary, absence of reproduction of a parasite infrapopulation in an organism currently forms a basis for separation of parasitic organisms into macroparasites and microparasites. While this division is correlated to a certain degree with parasite size or, to be more exact, with the ratio of the size of the bodies of the parasite and the host, the decisive criterion is, however, whether the size of the infrapopulation and thus most pathological manifestations of the infection are proportional to the number of parasite individuals infecting the particular host. Such a direct dependence exists for macroparasites, including, for example, tapeworms, nematodes and ticks; however, such a dependence is more or less lacking for microparasites, including, for example, Plasmodium, Toxoplasma, bacteria and viruses. Thus, from an ecological standpoint, some microscopic parasites belong amongst macroparasites, e.g. the cilita protozoan Ichthyophthirius, and, on the other hand, some macroscopic parasites would tend to be classified amongst microparasites, e.g. the larvae of flukes in snails, barnacles of the genus Sacculina (Kuris & Lafferty 2000).

see Point mutations and also Mutations at the level of the entire DNA section

See replicator

 In unicellular organisms, cells are only rarely differentiated morphologically into microgametes and macrogametes. This is apparently a result of the fact that the unicellular organism and the unicellular gamete are exposed to very similar selection pressures in their environment, which does not permit them to differ much from the common structural plan in their morphologies. However, the situation is somewhat different for permanently attached (sessile) unicellular organisms. A different selection pressure acts on the gametes than on the sessile individual, as they must, at the very least, be capable of looking for one another. In this case, it can be expected that differentiation into microgametes and macrogametes will occur.

            Differentiation into microgametes and macrogametes is more or less a general rule in unicellular organisms forming colonies and in true multicellular organisms. The phase of a multicellular, frequently macroscopic organism regularly alternates in the life cycle of the species with a mostly unicellular gamete phase. It is evident that the selection pressures acting on a macroscopic organism and a microscopic gamete are different. Simultaneously, especially microgametes are frequently produced in an enormous excess compared to macrogametes, so that the intensity of their mutual competition to find and fertilize macrogametes can be extremely high.

            The aspect of intergamete selection warrants closer attention. At first glance, it may seem that its effectiveness must be incomparably greater than the effectiveness of selection at the level of an adult multicellular individual. One sperm from amongst millions participates in fertilization of an egg. However, it should be borne in mind that each gene occurs in the set of sperm derived from a single individual in only two variants, where 50 % of the sperm carry one variant and 50 % the other one. Thus, if the concepts of the theory of interallele competition are considered (see IV.9.1), it is apparent that, from the viewpoint of the individual alleles, this does not involve selection of one in a million but one of two. It is, of course, necessary to point out that new mutations formed during gametogenesis will be selected with an effectiveness of one in a million if they occur in the sperm population with this frequency.

            Gametes and their multicellular organism have a common gene pool for their evolution. However, because they are exposed to different selection pressures, situations must necessarily occur in which a certain gene is exposed to two opposing pressures. From the standpoint of the chance of a multicellular organism surviving to reproductive age, it could, for example, be advantageous if the Michaelis constant for a certain substrate is a reduced for a certain enzyme while, from the viewpoint of the chance of microgametes rapidly finding macrogametes, it could be, to the contrary, advantageous if this constant is increased. As the intensity of the selection pressure on the gamete can be greater than the intensity of the selection pressure on its multicellular organism, it could easily happen that the interests of the gamete would predominate over the interests of the organism and evolution would proceed towards an increase in the Michaelis constant and thus in an undesirable direction from the viewpoint of the multicellular organism.

            While the gamete can hardly affect the selection pressures to which the multicellular organism is exposed, the multicellular organism can very easily and very substantially alter the environment in which the gametes will live and thus the selection pressures to which they will be exposed. Some facts indicate that this targeted influencing of the gametes actually occurs.

            The most effective mechanism capable of limiting inter-gamete competition and thus also the subsequent autonomous evolution of gametes consists in inactivation of genes in the mature gametes. For example, it is known that most of the genes in the sperm of vertebrates are completely inactive and that neither transcription nor subsequent translation occurs on them (Ward 1994). Highly condensed nuclear material, i.e. an indirect indication of gene inactivity, is found in the microgametes of most animals, plants and protozoa. Thus, most of the properties of sperm are not determined by the set of genes borne by the particular sperm, but by the set of genes of the multicellular organism controlling the processes of spermatogenesis and spermiogenesis in the sex organs. However, recent results have indicated that, in spite of the condensation of chromatin, expression of a great many genes occurs in microgametes. In plants, possibly up to 20 thousand genes are expressed in pollen grains and it has even been observed in vertebrates that some of the expressed genes affect such an important trait from the viewpoint of intergamete selection as flagella mobility (Olsson & Madsen 2001).

            It is also known for a great many animals that the female does not leave the sperm to their fate in her reproductive organs following copulation (Pizzari & Birkhead 2000; Tschudirein & Benz 1990). Cases have been described in many species of animals, including human beings where the sperm in the reproductive organs are passively drawn in or rapidly moved by peristaltic motion to the sites where fertilization is to occur (Baker & Bellis 1993b). It cannot be excluded that the female thus prevents intergamete competition, here a race amongst the sperm for the fastest pathway to the egg.

Reduced virulence amongst long-term adapted parasites is sometimes explained as a result of the action of interpopulation, interspecific or species selection. Some authors assume that populations or species of parasites that rapidly liquidate their host population are at a disadvantage compared to populations or species that spread more slowly and thus leave their host population time to regenerate. Consequently, parasites with greater infectiousness are at a disadvantage in interpopulation or interspecies competition.  
This mechanism could actually participate to a certain degree in reducing virulence; on the other hand, as has been mentioned repeatedly, the effectiveness of interpopulation and interspecific selection is generally rather low. If the altruistic behaviour of parasites (for example a reduced rate of multiplication) is maintained only by interpopulation selection, then selfish individuals with greater virulence than that exhibited by the other members of the population can very readily emerge and predominate in the population.
Species selection has a somewhat greater chance of affecting the situation. This could be true in the given case because species of parasites with high virulence endanger the existence of their host population and thus simultaneously increase the probability of their own extinction. In nature, there is a greater chance of encountering parasites exhibiting lower virulence towards their natural hosts, as species with high virulence have probably long been extinct.

 Affecting the sex of offspring is one of the areas in which a conflict of interests can occur between the interests of males and females. The most extreme cases occur once again amongst hymenopterous insects, where the males do not have the least interest in their sons with whom they do not share any part of their genome (daughters obtain half their genes from their father and half from their mother, sons have all their genes from their mother). In the mentioned parasitic wasps of the Nasonia genus, the male cannot affect the decision of the female in any way; in another hymenopterous insect Tripoxylon politum, it seems that it at least tries to (Dawkins 1976). In this case, the female lays the eggs immediately following copulation. The male holds the female by the head for about 30 seconds after copulation and apparently attempts to prevent her from laying any eggs. It cannot be excluded that, through this forced prolonging of the interval between copulation and laying of the eggs, it could perhaps increase the chance that the eggs will be fertilized prior to laying.

            The conflict of interests between the male and female is not as strong in diploid organisms, but still occurs to some degree. This could follow, for example, from the fact that the female must invest substantially more in the production of offspring than the male. Consequently, for example, situations can occur where it would be more advantageous for the father to kill embryos or zygotes of a certain sex, while this would not be worthwhile for the female.

see Cladogenesis

see Selection intraspecific and  interspecific

Intra-individual competition and the consequent intra-individual cell line selection are mostly, but not necessarily always (see XII.6.1.2.1) undesirable from the standpoint of maintenance of the integrity of a multicellular organism. If the cells could compete together, those that were capable of the fastest reproduction and the most effective spreading in the body of the organism would, in time, predominate in the individual. Then these cells would multiply at the expense of those that invest their energy into performing their physiological functions in the body of the multicellular organism rather than into their own reproduction. Those cells that would be capable of preferentially occupying the position and function of precursors of germinal cells would then predominate at the population level. The most important consequence of the existence of a single-cell phase in the life cycle of organisms is that all the cells in the body of a multicellular organism are mutually genealogically related and thus genetically more similar than the cells occurring in the bodies of two multicellular individuals. Genetic similarity and, if we ignore newly formed somatic mutations, even genetic identity of cells in an organism fundamentally limit the occurrence of mutual competition of cells and cell lines within the multicellular organism – intra-individual competition of cell lines.

see Impacts theory of mass extinctions

This popular objection is again untrue. To begin with, it is necessary to clarify what we mean by the formation of a new species. A great many breeds of dogs have been bred over a time period of the order of hundreds of years. In their phenotype, they differ to such a degree that, if a paleontologist were to discover their skeletons, he would not hesitate a moment to assign them to different species or even genera. Nonetheless, we do not consider them to be separate species because they can interbreed. The formation of a new species amongst sexually reproducing organisms is considered to occur when a reproduction barrier is formed that prevents interbreeding between the members of the old and new species. We have repeatedly been witness to the formation of such a barrier in nature and in the laboratory. For example, it is sufficient for two lines of drosophila to be infected by different strains of bacteria of the Wolbchia genus so that they are no longer capable of interbreeding because of the “cytoplasmatic incompatibility” of their members (see XXI.5.4). Similarly, for example, if cholchicine is used to derive a tetraploid plant from a diploid plant and the former is propagated vegetatively, both the tetraploid and diploid plants will be capable to interbreed; however, frequently it will not be possible for the diploid plants to interbreed with the tetraploid plants. Simultaneously, tetraploid plants frequently have very different phenotype than diploid plants and also differ in their ecological requirements – thus they comply with both criteria for a separate species – i.e. they have a new phenotype and are reproductively isolated. If we really wanted to create a new species of dog, it would actually be possible. It would be sufficient to imitate extinction speciation (XXI.2) and kill off all breeds of dogs except St. Bernard’s and Chihuahuas...

At the present time, there are apparently no scientists concerned with the origin and development of life who would doubt the very existence of biological evolution and its importance for the origin and development of organisms. The individual mechanisms active in biological evolution and also their relative importance for the origin and development of organisms are understandably a subject of professional discussion and scientific research. In this area, the theory of evolution has, of course, undergone very significant development since Darwin’s time (see XXVIII) and it can certainly be anticipated that this development will continue.

Statistical reasons for the impossibility of the formation of an organism would be valid only for a single-step emergence. However, the theory of natural selection assumes the gradual, multi-step formation of living systems. The differences can best be illustrated using the well-known thought experiment (Fig. XXVII.1). If we sit a troop of apes down to typewriters and teach them to press the keys, there is only a negligible probability that any of them would write a sensible sentence within a reasonable period of time by only randomly pressing the keys, for example a sentence such as “Taken statistically, it is impossible that something as complicated as an organism could be formed by a random process of evolution.”. If, however, we have each ape press only one key, then send him back to the trees, we can find which of them wrote the letter “T”, copy this onto papers which we put in all the typewriters and request the apes to hit another key, etc. this sentence will be written with surprising speed. Darwin’s the theory of evolution assumes that random processes play an important role in the development of life, but not a decisive role. In the process of mutagenesis, random processes only generate the individual changes, from which the process of natural selection then non-randomly chooses those variants that improve the functioning of the whole system.

This is once again an argument that has arisen in various forms since the time of Darwin. Originally, anti-evolutionists liked to put forth these arguments in connection with the structure and function of the eyes of vertebrates. The eye has a great many components, where any of them would see to be essential for the creation of an image. However, the eye is a very unsuitable example for this type of argument. It is quite true that all the present-day components are necessary for perfect vision. However, it is simultaneously obvious that even the simple ability to differentiate light and dark is very useful for the survival of an organism; it is somewhat better to recognize the direction from which the light is coming and even better to roughly differentiate the shape of objects in the field of vision, etc. Thus, a perfect eye can be very easily formed by the gradual evolution of its components, where every evolutionary step put its bearer at an advantage compared with its less perfect predecessor.
            The opponents of the theory of evolution tend at the present time to concentrate on the purported irreducible complexity of molecular structures, such as the molecular apparatus employed for rotating a bacterial flagellum (Behe 2001a; Behe 2001b). These structures are usually less complicated than macroscopic structures, still their functionality , such as the ability to rotate a flagellum, is dependent on the existence and functioning of all the components. Anti-evolutionists argue that these components could not have evolved gradually in the process of evolution, as one of them makes no sense in the organism without the other.
A fundamental error in this argument is that it ignores the existence of exaptations, i.e. structures that developed in evolution in a different functional context than that in which they function in modern organisms (see I.7.1). The individual components of the flagellum apparatus most probably developed independently of one another, under the effect of various selection pressures and originally performed a completely different functions. At some point, the finished components were ordered in a functional apparatus, that began to be capable of performing, originally probably rather imperfectly, a new function, here rotating a flagellum and thus allowing the bacteria to move. The molecular apparatus of a bacterial flagellum has a great many components in common with the molecular apparatus employed by a great many bacteria for injecting toxin into the cells of an attacked organism, and also with the F1-ATPase molecular apparatus, i.e. the molecular complex synthesizing ATP at the expense of the transmembrane proton gradient (Block 1997; Noji et al. 1997).

Probably a very extensively used means of defense of a host organism, especially among plants, against parasites consists in the formation of substances that are released into the environment on attack by a parasite and that attract the natural enemies of the parasite, predators and hyperparasites. This type of kairomone, i.e. a substance used for exchange of signals between the members of different species, usually but not always useful mainly for the receiver, is released only under highly specific conditions. If the leaves of a plant are damaged by the caterpillars of the butterflies of a certain species, kairomones are released; to the contrary, if they are damaged to a similar extent by the caterpillars of a different species or mechanically, for example by the experimenter, the kairomone is not released (de Moraes et al. 1998) (Fig. XVIII.4). In fact, in some cases, the plant is capable of controlling the composition of the released kairomones in dependence on the species of natural enemies that are active at the particular time of day (de Moraes, Mescher, & Tumlinson 2001). Thus, a different mixture of kairomones is released in the daytime than at night.
            There are a number of indirect proofs that a great many animals also employ a similar strategy for defense. It is, at the very least, remarkable how many parasitoids are actually hyperparasites, i.e. species specializing in parasitizing other parasites or parasitoids. The reason for preferential attack on parasites could be the fact that the hyperparasite has a natural ally in seeking out its host – the host attacked by the parasite. From the viewpoint of this host, it is advantageous for several reasons if it attracts the attention of a hyperparasite by chemical or other signals. In some cases, a hyperparasite can completely exterminate a parasite and thus directly improve the fitness of the host; in other cases, the individual attacked by the parasite dies anyway; however, because the hyperparasite also exterminates the parasite, this can lead to an increase in the inclusive fitness of the host because a dead parasite cannot attack biologically related hosts in the vicinity.
            The third means is that a host can utilize the mafia effect, i.e. a strategy that is otherwise used by a number of parasitic species. This strategy consists in that the parasite does not damage its host much until the host begins to effectively to defend itself. As soon as the host initiates a defense mechanism, the parasite somehow “penalizes” it (Gadagkar & Kolatkar 1996). This phenomenon is most marked in cases where the interaction of a host with a parasite takes place at an ethological level. The cuckoos of some species remain in the vicinity of nests in which they lay their eggs and watch how the host bird acts toward their eggs. If the host throws the foreign egg out of the nest, then the cuckoo breaks all the eggs in the nest during the next inspection. It is thus better for the host to leave the egg alone because, for this species of cuckoo, the young bird does not destroy the whole brood and thus parents that tolerate the cuckoo have a chance of bringing up at least some of their progeny. Consequently, selection prefers birds that are not able to recognize a foreign egg in their nest or at least tolerate it (Zahavi 1979; Soler et al. 1995). A quite analogous strategy is apparently employed by a number of pathogenic organisms, including bacteria (Soler, Moller, & Soler 1998). A great many bacteria begin to release toxins only when they are attacked by the immune system of the host organism or when the host organism prevents them from having access to some essential resource, very frequently iron.
            The attacked host can also use the mafia effect in the above-described host – parasite – hyperparasite interaction. If the parasite does not damage it much, it is better to tolerate it. In plants, the presence of a benign parasite (microherbivore) can even protect the plant against other, more dangerous species (Saikkonen et al. 1998). If the parasite were to greatly damage it, it would attract hyperparsites and predators that destroy the parasite. In this case, once again, the species or lines of parasites that greatly damage their host are eliminated. Mathematical models indicate that a mechanism based on the mafia effect can be relatively easily fixed in a population and that, for example, when destruction of the egg batch does not require any great effort on the part of a cuckoo, this will even be an evolutionarily stable strategy (Soler, Moller, & Soler 1998).

see Theory of neutral evolution

see hybridogenesis

see History of evolutionism - pre-Darwinist period

To the present day, 1-2 million species of living organisms and hundreds of thousands of extinct organisms have been described. However, most living species and even more extinct species have not yet been identified and probably never will be. Generally accepted estimates place the number of species now living on the Earth at several tens of millions. While the latest results suggest that, at the very least for insects, these estimates will probably be excessive (Novotný et al. 2002), it seems, on the other hand, that the biodiversity of parasitic organisms could be substantially underestimated.
All these species apparently evolved in the past from a common ancestor. It is not clear how many times life evolved on the Earth or how many times it was transported from the surrounding universe. In the light of the speed with which it appeared as soon as conditions became favourable for its existence, i.e. after the end of the period of massive bombarding of the surface of the Earth by cosmic projectiles and after a solid cooling crust was formed, it is quite possible that life evolves relatively easily and thus that this occurred repeatedly on the Earth. No surprising events can be completely excluded; nonetheless, it is highly probable that the representatives of only a single line have been preserved to the present day, either by accident or as a result of mutual competition. Available information, especially related to the uniformity of the basic molecular apparatus of organisms and the similarity of basic biochemical processes, such as replication of nucleic acid or proteosynthesis, unambiguously indicate that all the known species of organisms have a common ancestor. This common ancestor most probably lived on the Earth 3.8 billion years ago (Holland 1997). However, we have no proof that the traces indicating the existence of life found in rocks of this age were actually left by the ancestors of modern organisms, and not by the members of some other, extinct line. However, it is almost certain that life did not cease to exist on Earth from the most ancient times to the present day and that organisms have been present on the Earth for at least 3.5 billion years in such large numbers that they fundamentally affected the development of the atmosphere, hydrosphere and geosphere of the planet. What this life looked like and when, not the first, but the last common ancestor of all contemporary forms of life, i.e. the organism from which modern bacteria, archea (archeobacteria ) and eukaryotes, branched off at a certain moment and in a certain order, remains an interesting and still unresolved question. This hypothetical organism is designated by the abbreviation LUCA (Last Universal Common Ancestor) in the English literature. On the basis of current knowledge in comparative molecular biology, it rather seems that this was a quite advanced organism with a modern-type, fully developed proteosynthetic apparatus. According to some hypotheses, it could have lived on the Earth at a relatively late date, possibly 2 billion years ago (Schopf 2000).

– see Mass extinction, after the end of mass extinction events

– seeCultural traits transmission of

From a general evolutionary standpoint, another phenomenon is very interesting and apparently determines to a substantial degree the result of the evolutionary battle between a parasite and its host. The two participants in the co-evolutionary process, here the parasite and its host, are not concerned to the same degree with the result of mutual interactions. While losing the battle with the host organism generally leads to death for the parasite (as an individual), for the host it generally leads only to a greater or smaller reduction in its fitness (Dawkins & Krebs 1979; Dawkins 1982). The fact that the host organism is sometimes killed by the parasite or is not able to reproduce and its fitness thus decreases to zero does not much affect the situation. This is not a typical situation as it is generally in the interest of the parasite not to kill its host and thus the relevant selection pressures to which the parasite is exposed mostly lead to a gradual reduction in its pathogenicity to a certain optimal level (see XIX.5).
The “life-dinner” principle is valid not only in the relationship between a parasite and its host, but also in a great many other inter-species and intra-species interactions. This principle was originally identified (and named) in systems of the predator and prey type. Put simply, rabbits run faster than foxes for the simple reason that they are running for their lives, while the fox is only concerned about its supper.

Equilibrium numbers of the individual genotypes corresponding to the numbers of the individual alleles will become balanced even if a genetic linkage exists between the studied loci; however, equilibrium will not be established immediately in this case, but rather gradually, where the rate of establishment of equilibrium is inversely proportionate to the strength of the genetic linkage. The population can be inthe linkage disequilibrium, i.e. the numbers of the individual genotypes need not correspond to their theoretical frequencies calculated on the basis of the relative numbers of the individual alleles, for several reasons. The degree of disequilibrium is most frequently expressed as the coefficient of linkage disequilibrium D which, for genes located in two different alleles, is calculated from the equation D= ¦_n¦_n- ¦_r¦_r, where ¦_nand ¦_nare the frequencies of the individual genotypes containing the unrecombined halotypes and ¦_rand ¦_rare the frequencies of individuals with genotypes containing recombined halotypes. Disequilibrium can, first of all, be caused by the fact that some genotypes are not viable and are continuously eliminated from the population by natural selection. In this case, zygotes with the individual genotypes are formed with the expected theoretical frequency, but some genotypes are frequently eliminated already during embryogenesis, prior to the birth of the individual. The second reason for the existence of linkage disequilibrium could be the existence of genetic linkage between the loci of interest. Each population has a unique history; at some point in the past, it was formed by splitting off from some other population or other populations. If a population was formed from more than one original population, the frequencies of the individual genotypes in the founding population will not apparently correspond to equilibrium values calculated on the basis of the frequencies of the individual alleles. Because of the existence of genetic linkage, the equilibrium frequencies of the individual genotypes will be established only gradually over a large number of generations

The rates of evolution can be compared on the basis of the number of quantitative changes that occur in a certain phylogenetic line within a given time interval. As various types of organisms differ in the number of traits that can be identified, it makes sense to use this means of estimating rates of evolution only to compare rates for similar organisms. This method is most useful for monitoring the changes in the rates of evolution within a single phylogenetic line. When, for example, this method was employed to follow the rate of evolution in lungfish, i.e. a group of vertebrates whose members appeared in the paleontological record approximately 340 million years ago, it was found that this rate achieved a maximum of 2.5 changes per million years at a time 290 million years ago, but decreased to about one tenth of this value 250 million years ago (Westoll 1949). Over the past 200 million years, the morphology of lungfish has practically not changed, so that their modern representatives are mostly given as examples of “living fossils”. Understandably, the rate of evolution in an evolutionary line depends not only on the rate of changes occurring in a single species, but also on the number of species in the given line. As, at the present time, there are only six known species of lungfish, it is not very surprising that the rate of evolution measured in terms of the number of evolutionary changes is very low at the present time.

The lottery model (sometimes also called the best man model) is based on the fact that the area of occurrence of any species is mostly heterogeneous to a greater or lesser degree (Williams 1975). Simultaneously, a more or less random sample of the offspring of various parents ends up in each microhabitat in each generation. The individuals compete together in the microhabitat and only the best of them or, to be more exact, those whose phenotype best corresponds to the properties of the particular microhabitat are successful in the competition and leave offspring. The progeny of asexually reproducing species would probably be very well adapted to some type of microhabitat. Those that end up in some other microhabitat would, however, most probably lose out in competition with the offspring of sexually reproducing parents. Because of their polymorphism, part of the progeny of sexually reproducing organisms would always have properties that would be especially suitable for any type of microhabitat.

Soviet Lysenkoism was an unfortunate chapter in the biology of the 20^th century. In connection with this subject, mention should be made of the aspect of jump transitions between two or more species. Lysenkians assumed that an organism is capable of reacting to some external stimuli in that it switches the ontogenetic system in such a way that, in a single jump, the progeny acquire the character of the members of a different biological species. Descriptions of observations in which poorly fertilized wheat suddenly began to form rye caryopses in its spikes or poorly fertilized rye began to form couch grass caryopses now sound like a students’ rag or April-fools joke.

Lysenkists completely discredited their learning, not only in that they physically liquidated their opponents in the interests of rapid dissemination of their ideas, or rather in the interests of fulfilling their ambitions of power, but also in that they extensively falsified their experimental data. Consequently, the results that were accumulated at the time of Lysenkoism are mostly worthless. The very idea of the transition of one species into another through switching of alternative ontogenetic programs cannot, however, be automatically rejected. However, contemporary knowledge related to the course and mechanisms of biological evolution exclude the possibility that such a phenomenon could have any importance in the evolution of organisms.

It is true that all organisms with sexual dimorphism and organisms whose life cycle includes a larval phase are capable of maintaining genes for two or more different, mutually exclusive ontogenetic programs in their genome. However, in these cases, natural selection constantly controls the functioning of the individual ontogenetic programs and greatly “penalizes” individuals that have a program damaged by mutations. However, if the population were to employ only a single program for a long time, it is probable that the genes for an alternative program would be gradually inactivated as a consequence of the accumulation of mutations. See also Frozen plasticity theory.

The existence and potential evolutionary importance of macromutations is an interesting and still-discussed aspect of evolutionary biology. Darwin’s theory of the development of living systems is based on gradual accumulation of micromutations, i.e. mutations that lead to slight changes in the phenotype of organisms. Only long-term accumulation of these minor changes, as a consequence of the consistent action of natural selection, can lead to major evolutionary changes in the structure of organisms. Darwinists assume that even very complicated structures like the eye or wing develop by this gradual accumulation of minor changes. On the other hand, some biologists, for example Richard B. Goldschmidtin the 1940’s and 1950’s (Goldschmidt 1998), were or are of the opinion that complicated structures and major changes in the body plan appear suddenly in evolution, in a sudden jump, as a consequence of “macromutations” (saltations, saltationism), which occur suddenly in some individuals in the population {9650}.

It is certain that mutations that can substantially affect the phenotype of an organism actually occur in the population with low frequency. These are mostly mutations in regulation genes and in genes that control the early stages of ontogenesis (Akam 1998). However, mostly these mutations lead to simplification of the body structure, to the loss of certain organs or, on the other hand, to a greater number of them or to replacement of one organ by another (antennae – legs in insects, etc.). In this sense, macromutations certainly exist. However, their evolutionary importance is rather questionable. We can imagine the formation of a basically new organ as the consequence of the accumulation of minor advantageous changes; on the other hand, the formation of a useful complex organ in a single large jump is a highly improbable event. However, even if such a change were to occur, the hopeful monster would probably encounter substantial difficulties in searching for an ecological niche and sexually reproducing organisms could find it difficult to find a sexual partner.

Some authors are of the opinion that, in addition to macromutations in the above-described sense, there are also other categories of macromutations. However, these would not be classical mutations with a large phenotype effect, but rather simultaneous changes at many sites in the genome, that would occur simultaneously, through a currently unknown, unspecified mechanism. A change in the structure of some tRNA could probably appear as such a change and this would cause that a certain aminoacid would be replaced by a different aminoacid in all the genes. As is already apparent from the above examples, the probability that such a drastic intervention in the genetic information could lead to the formation of a viable individual is quite small. The probability that a complicated adaptive structure could be formed in this way is probably zero.

A host can sometimes utilize the mafia effect, i.e. a strategy that is otherwise used by a number of parasitic species. This strategy consists in that the parasite does not damage its host much until the host begins to effectively to defend itself. As soon as the host initiates a defense mechanism, the parasite somehow “penalizes” it (Gadagkar & Kolatkar 1996). This phenomenon is most marked in cases where the interaction of a host with a parasite takes place at an ethological level. The cuckoos of some species remain in the vicinity of nests in which they lay their eggs and watch how the host bird acts toward their eggs. If the host throws the foreign egg out of the nest, then the cuckoo breaks all the eggs in the nest during the next inspection. It is thus better for the host to leave the egg alone because, for this species of cuckoo, the young bird does not destroy the whole brood and thus parents that tolerate the cuckoo have a chance of bringing up at least some of their progeny. Consequently, selection prefers birds that are not able to recognize a foreign egg in their nest or at least tolerate it (Zahavi 1979; Soler et al. 1995). A quite analogous strategy is apparently employed by a number of pathogenic organisms, including bacteria (Soler, Moller, & Soler 1998). A great many bacteria begin to release toxins only when they are attacked by the immune system of the host organism or when the host organism prevents them from having access to some essential resource, very frequently iron.
            The attacked host can also use the mafia effect in the above-described host – parasite – hyperparasite interaction. If the parasite does not damage it much, it is better to tolerate it. In plants, the presence of a benign parasite (microherbivore) can even protect the plant against other, more dangerous species (Saikkonen et al. 1998). If the parasite were to greatly damage it, it would attract hyperparsites and predators that destroy the parasite. In this case, once again, the species or lines of parasites that greatly damage their host are eliminated. Mathematical models indicate that a mechanism based on the mafia effect can be relatively easily fixed in a population and that, for example, when destruction of the egg batch does not require any great effort on the part of a cuckoo, this will even be an evolutionarily stable strategy (Soler, Moller, & Soler 1998).

see Sickle-cell anemia

The fact that a parasite is frequently in close contact with its host provides it with an opportunity for targeted interventions in the functioning of the host organism. Manipulation hypothesis suggests that parasites are capable of modifying for their needs various traits of the host, from the morphology through regulation of metabolism and allocation of energy for the individual life functions to specific interventions in the nervous system, leading to changes in the behavior of the host. Thus, parasites are typical organisms utilizing the extended phenotype principle (Dawkins 1982) (see XVIII.6). A number of their genes have become fixed in evolution, not because they would favorably affect the traits of the parasite organism, but because, through their products, they affect the traits of the host organism. Thus, the body of the host becomes part of the extended phenotype of the parasite and a great many of its traits assist not in spreading its own genes but rather in spreading the genes of the parasite. The genes of the parasite and genes of the host frequently have quite opposing interests in relation to the traits and functioning of the host organism. As was mentioned in Section XIX.2, the genes of a parasite in the co-evolutionary battle with the genes of the host are in a more advantageous position, so that their interests frequently predominate in the attacked organism.
            An important mechanism enabling an increase in the chance of transmission of a parasite between hosts consists in inducing behavioral changes in the infected host that can positively affect the probability of transmission of a parasite from one host to another (Barnard & Behnke 1990; Moore 1984). The parasite can cause these changes in various ways. The most specific mechanisms include direct intervention in the central nervous system of the host, through which the parasite is even capable of initiating very complicated patterns of behavior. The simplest mechanisms, on the other hand, encompass unspecific pathogenic effects on the host organism that, while they reduce the vitality of the host and thus increasethe chance that the parasite will kill its host and die itself, also can be very functional for the parasite in some special cases, from the standpoint of its transmission in the host population. The types of behavioral changes that the parasite induces depend primarily on the mechanism of its transmission. It is understandable that the behavioral changes that assist in transmission from an intermediate host to the definitive host through predation are completely different from changes that increase the effectiveness of transmission of sexually transmitted parasites.
            The effect of a parasite on human behavior has been observed in a great many systems. For example, explanations have been given for the negative effect of various parasitic infections (Ascaris, Schistosoma, Toxoplasma) on intelligence and learning ability (Nokes & Bundy 1994; Piekarski 1981; Saxon et al. 1973). (Cook & Derrick 1961; Ladee, Scholten, & Meyes 1966; Robertson 1965; Flegr & Hrdy 1994; Flegr et al. 1996){13300}.
However, in most of these cases, it is difficult to decide when this is a more or less unspecific symptom of the current or recent disease and when it is a manifestation of targeted influencing ofthe host’s behavior by the parasite. It is obvious that the behavior of a sick person will differ from that of a healthy person and that prolonged sickness can even be manifested in personality changes and thus, secondarily, on the way he will act in certain situations. In addition, most results are based on monitoring the correlation between the frequency of the occurrence of a particular parasite and a certain type of behavior in the monitored persons. In these situations, it is difficult to decide whether the presence of the parasite induced the observed changes in these persons, or whether a certain type of behavior in the observed persons increased the probability of infection by this parasite. Of course, a third possibility also exists, i.e. that both the changes in behavior and the infection by the particular parasite are both caused by a third, unknown factor. If the research is based on study of a large group of persons, then it would be possible to demonstrate statistically significant correlation arising as a consequence of the indirect effect of a very weak factor.
So far, the best-documented example of the existence of manipulative activity of a parasite in humans is the effect of latent asymptomatic infection by the protozoa Toxoplasma gondii on the psychological profile of humans, which was first described by Czech parasitologists (Flegr & Hrdy 1994; Flegr et al. 1996) {13300}.In nature, Toxoplasma is transmitted from its intermediate host, mostly mice rodents, to cats, its definitive host, through predation. An infected cat excretes resistant oocysts in its faeces, which can infect a wide spectrum of intermediate host species, including mice and humans. Infected persons generally have a mild form of the disease and, without realizing it, become carriers of the latent stage of the parasite to the end of their lives. It has been estimated that 30-50% of people in the Czech Republic have suffered from toxoplasmosis, while a figure of 83% has been given for Paris, France. Comparison of the psychological profile of persons infected and not infected by the parasite has revealed statistically significant differences in a number of monitored factors, including a tendency to look for new stimuli (Fig. XIX.15). It is interesting that different factors were affected in men and women and, when the changes were related to the same psychological factor, the shift mostly occurred in the opposite direction in men and women. When changes in these factors were examined for former patients who had suffered from acute toxoplasmosis in the past, i.e. persons for which records exist of when they were infected, it was found that there is a positive correlation between the time that had expired from the infection and the level of change in the psychological factors (Fig. XIX.16). This indicates that, at least in this case, the psychological changes were caused by the infection and not the infection by a change in psychological factors. In addition, latent toxoplasmosis is asymptomatic in practically all humans, so it cannot be expected that the psychological changes would occur as a result of unspecific deterioration of the state of health of the infected persons. However, the results of four studies of correlation between latent toxoplasmosis and the risk of traffic accidents indicate that the generally accepted assumption of harmlessness of latent “symptom-free” toxoplasmosis might not be valid and that this “harmless” parasitosis could, in fact, be responsible for more human fatalities than malaria (Fig. XIX.17).

see Extinctions types

The main impact of mass extinctions lies in the occasional elimination of successful taxa and creation of space for other taxa (Jablonski 2000; Raup 1994). It has been estimated that only 5 % of extinct species died out during mass extinctions, while the remaining 85 % of these species became extinct during background extinction (Raup 1994). In contrast, mass extinctions contributed to at least 35 % of extinctions of families (Newman & Palmer 2003). Without the existence of mass extinctions, a certain type of niche would apparently be occupied in nature for a long time or even permanently by the members of a certain taxon, but not because it would be better, for example because it would be more capable of utilizing the available resources. Their permanent dominance could be caused by the king of the hill effect. On a smaller time scale, the disappearance of a dominant species can release a certain resource for the other existing species. On an ecological scale, this effect is thus manifested in that the individual migrants of a single species can hardly occupy a territory in which a very abundant population of a species utilizing similar resources already lives (even though the latter species may use the resources less effectively). On an evolutionary time scale, the immediate effect of this ecological release can be supplemented by apparently the more important effect of extinction of a dominant taxon on the progress of species selection. The taxon with the greatest number of species, utilizing the widest spectrum of niches, has the greatest chance that it will occupy the newly formed niche through speciation, even if the species formed by speciation of the members of a different taxon were able to better utilize the particular niche. However, during mass extinction events, both successful and unsuccessful taxa are affected and the main criterion for the survival of a species becomes random preadaptation to the drastically altered conditions. As a consequence of this evening out of chances, a sort of alternation of dynasties can occur on a longer time scale, during which taxa that were completely dominant in various types of environment during a certain period, either in the number of species or in the abundance of their populations, can completely free the space for some other taxon in the period following a mass extinction event {11943}.

            Mass extinctions can stop or even reverse evolutionary trends for a certain time (Fig. XXII.9). For example, amongst ammonites, the complexity of the sutures on their shells increased approximately 16-fold over 140 million years. Study of 469 species indicated that a daughter species had more complicated sutures on its shells approximately twice as often as its predecessor. However, during mass extinctions, the species with more complicated sutures disappeared preferentially, so that the anagenesis of this trait always moved back a bit (Saunders, Work, & Nikolaeva 1999)

When, in 1984, D. M. Raup and J. Sepkoski employed statistical and permutation tests to analyze the temporal distribution of periods of mass extinction over the past 250 million years, they found that especially intense mass extinction was repeated on the Earth with a periodicity of approximately 26 million years (Raup & Sepkoski 1984) (Fig.. XXII.5). The results that they obtained were highly statistically significant and later studies (Raup & Sepkoski 1988) tended to confirm the existence of a periodicity of 26 million years, or somewhat longer. However, some authors have thrown doubt on these figures, pointing out that the periodicity is an artifact caused by incorrect rounding off of the ages of some events (Jetsu & Pelt 2000; Jetsu 1997). Thus, at the present time, the existence of similar periodicity remains only a theoretically interesting possibility.
It is obvious that an event with such long periodicity cannot have its origin in processes occurring directly on the Earth, but rather in processes occurring in the cosmos. As the age of giant craters on the Earth indicates a periodicity of approximately 30 million years, it is generally assumed that mass extinctions could have been caused by periodic bombarding of the surface of the Earth by enormous cosmic bodies, the cores of comets or asteroids (Matsumoto & Kubotani 1996; Trefil & Raup 1987). The simplest model assumes that the Sun, similar to more than half the stars in the universe, could be part of a binary star, where the second part of the binary star, assigned in advance the name Nemesis (a substantially smaller red dwarf, orbiting at a distance of up to 3 light years) could approach the Sun, to be more exact to the Oort comet cloud, extending to a distance of almost one light year from the Sun, with a periodicity of 26 million years. According to some concepts, Nemesis could be a substantially less common brown dwarf, black hole or a planet on a very distant orbital path – however, in these cases, we would not have much of a chance of discovering it with contemporary technical means. It could affect the orbits of comets in the Oort comet cloud when it approaches the Sun and could send some of them towards the Sun and into the area in which the inner planets have their orbits. The impacts of their cores or the impacts of asteroids, which the comets forced out of their orbits, on the surface of the Earth could have caused the mass extinctions.
Astronomic research to date has not confirmed the existence of Nemesis. Consequently, at the present time, it is rather assumed that phenomena with a periodicity of the order of tens of million years could have their origin in the periodic passage of the solar system through the plane of the disk of the galaxy where a great deal of matter is present whose gravity could affect the orbits of comets in the Oort cloud (Sepkoski 1989; Rampino & Haggerty 1996). It is interesting that the periodicity of passage through the disk of the galaxy is currently estimated at 37 ± 4 million years (Stothers 1998), which is very similar to the periodicity of 37.5 million years, which was also observed simultaneously with the periodicity of 26 million years in the age of craters on the Earth (Yabushita 2002).

see History of evolutionism - pre-Darwinist period

History of evolutionism – post-neo-Darwinist period

The properties and patterns of behavior formed by biological evolution are recorded and transmitted as genes or groups of genes. Analogously, the name meme was introduced for information determining a trait transmitted culturally (Dawkins 1976; Blackmore 2001). For example, a meme can consist in knowledge of how to separate grain from sand thrown into water, a certain locally specific melody in finch song, the writing “Leroy was here”, or the formula E = mc2. While nucleic acid is a natural carrier of genes (the hard disk of a computer is an unnatural artificial carrier), the natural carriers of memes consist in the memories in the brains of animals. Genes and memes have a common important property in that they have variants (mutations) that can compete in their dissemination. In the former case, this corresponds to dissemination in the gene pool of the population while, in the latter case, within the meme pool, i.e. within the limited memory capacity of members of a particular species. However, there is one very substantial difference between genes and memes. Genes, i.e. the relevant sections of a nucleic acid, are transmitted directly by copying from one generation to the next and thus function as replicators. According to the information contained in them, the bodies of the organisms – interactors (vehicles) are newly formed in each generation (see also IV.9.1 and XII.4.1). Natural selection, but not molecular drive, occurs at the level of interactors, specifically uneven transmission of the individual replicators derived from various interactors to the following generations. Simultaneously, genetic information emerges (through mutations), is transmitted from one generation to the next and accumulates during biological evolution at the level of replicators. A change in a replicator is manifested in the properties of the interactor, while a change in the interactor cannot be manifested in the properties of the replicator and can thus not be transmitted to the following generation. For a meme, the replicator is very frequently, but not always identical with the interactor. Individuals directly copy” certain behavior, rather than a gene for the particular behavior. As a consequence, a random adaptive change in behavior can be a subject of imitation and can thus be transmitted to future generations. Acquired traits can thus be inherited here.

see meme

- If we ignore the modern ability of humans to sequence and synthesize genes and the possibility of natural, but, in multicellular organisms, relatively rare horizontal transmission of genes, genes can be transmitted under natural conditions only during reproduction. In contrast, memes can be transmitted in various forms and through various pathways. The most important difference in the spreading of genes and memes is apparently that a meme can be transmitted, not only vertically, from parents to offspring, but also horizontally, within a population between related and completely unrelated individuals. In fact, the spreading of a successful meme need not even respect the borderlines between biological species, as the members of one species can imitate the behavior of some other species. For example, 10 various species of birds gradually learned how to open milk bottles from tits. It has been confirmed in experiments that dogs are capable of obtaining useful information by observing the behavior of humans (Fig. XVII.5). Thus, spreading of memes is far more effective than spreading of genes. As a new allele of a certain gene can become fixed in the population only in that the carriers of other alleles will transmit their alleles to their progeny with lower effectiveness than the carriers of the new alleles so that, after a certain, frequently quite large number of generations, they become extinct, a new, useful variant of a meme can very easily spread at the expense of other variants of the relevant meme in the entire population during the lifetime of a single generation.

- The meme for divorce is an example of a meme that can be spread in an interesting way by biological evolution. It is known that the children of divorced parents have a greater probability of being divorced in adulthood than the children of complete families (Corak 2001). The meme for divorce can spread not only by simple imitation of the behavior of the parents, but its spread can be further strengthened by the fact that, in a series of consecutive marriages, the divorcing parents will finally have more children than persons living in a harmonic life-long marriage, especially in modern societies with developed social networks and 1-2 children in a family. Thus, this meme can increase the fitness of its bearer while not being transmitted genetically but only through children imitating the behavior of their parents. It is understandably possible that not only memes, but also genes capable of increasing the probability of an unsuccessful marriage ending in divorce could theoretically positively affect the fitness of their bearers through a quite similar mechanism. For example, a gene that would increase the probability of emergence of hysterical behavior in its bearer could be maintained in the population because its bearer would produce more offspring in a series of unsuccessful marriages and thus “enrich” the gene pool of future generations by more copies of his hysterical gene.

Just as biological evolution can be affected, not only by competition at the level of interactors, natural selection, and also competition for the most effective reproduction at the level of replicators, for example molecular or mutation drive, cultural evolution can also be very greatly affected by memetic drives, i.e. deterministic processes occurring at the level of replicators – e.g. at the level of a spoken language. The development of an orally transmitted story depends not only on how much the versions are liked by the individual story tellers and listeners and the probability with which they will pass on a particular variant, but also by the words that occur in the story and the errors occurring in the transmission of the story as a consequence of acoustic similarity of the words employed. Words that are difficult to pronounce or little known can, for example, be frequently replaced by other words, which can gradually change even the content of the story or song (Dawkins 1976).

The way genes are transferred from generation to generation is described by Mendel’s genetic laws. These laws were derived in the middle of the 19^th century by the Brno abbot Johann Gregor Mendel (1822-1884). He came to these conclusions without any knowledge of the mechanisms of transfer of genetic information, solely on the basis of the results of his hybridization experiments. These rules were later designated as genetic laws. The first law is generally termed the law of segregation and can be formulated roughly as follows using our contemporary terminology: two alleles of any gene present in a parent individual segregate into independent gametes in each generation without undergoing a change and thus without affecting one another. This law could seem trivial to us in the light of contemporary knowledge of the mechanism of storage and transfer of genetic information. In actual fact, however, its discovery meant a fundamental break-through in the thinking of biologists. On the basis of empirical observation of the heredity of phenotype traits, up to that time biologists automatically assumed that heredity is “soft”, that the predisposition for the formation of the individual traits, today we would say genes, that an individual acquires from both parents, mutually interact and mostly are basically “averaged” and are passed on to further generations in this altered form. The law of segregation basically states that, without regard to the mutual interaction of phenotype manifestations of the individual genes, the genes themselves do not affect each other in any way and are transferred from one generation to the next in unaltered form.

Amongst other things, this discovery eliminated one of the basic problems of Darwin’s theory of evolution. A serious argument of some of the opponents of the theory of evolution was that an evolutionarily advantageous new trait cannot be selected through natural selection simply because, amongst sexually reproducing organisms, it is gradually “dispersed” after several generations as a consequence of crossing of individuals with the new trait with the far greater number of individuals bearing the original variant of the particular trait. Henry Charles Fleeming Jenkin (1833-1885) graphically described this problem. Imagine that a white man is shipwrecked on a tropical island. Because of his excellent psychological and physical qualities (in all probability he was an English gentleman) he rapidly excels in competition with the local black men and becomes the head of their tribe He would certainly win out in competition for women and would leave the greatest number of progeny. All his descendants will, however, be half black and thus only half as good as the original shipwrecked man. If the population on the island is sufficiently numerous, only a few generations after the presence of the shipwrecked white man there will be only a minimal genetic trace, probably in the form of occasionally emerging blue eyes amongst the otherwise dark inhabitants of the island.

The whole problem can be described mathematically in a somewhat more politically correct manner. It can be derived that, if the predispositions from the father and the mother were actually averaged, exactly half of all the genetically determined variability present would disappear in each generation. After a few generations, only variability determined by the environment would remain and natural selection would not be able to make any choices. It is an interesting paradox that the greatest problem associated with Darwin’s theory of evolution was resolved by Mendel who expected to overthrow Darwin's theory through his experiments. It is quite possible that he was basically very lucky that his work remained unnoticed during his lifetime, safely buried in the local Brno bulletin, and that its importance for the theory of evolution was not understood, e.g. by Darwin, who is said to have owned a copy of the work. The abbot would apparently have received recognition and fame from evolutionary biologists, but the reaction of his superiors would probably have been less enthusiastic. I am not very well informed about the organization of church life, but I would guess that abbots are named and recalled more frequently by church dignitaries than by evolutionary biologists.

The law of independent assortment of predispositions is the second law of genetics. According to this law, the individual pairs of alleles of various genes segregate into the gametes independently of one another and the manner of distribution of one pair of alleles in no way affects the distribution of another pair.  The result is that the predispositions and the corresponding traits freely combine and the occurrence of the individual combinations of predispositions and traits is controlled only by the laws of combinatorics (Fig. II.12). If two genes are located on two different chromosomes, then, in accordance with the second law of genetics, the relevant alleles are freely combined. If one of the pairs of homologous chromosomes bears allele a₁ in locus A and the second has allele a₂ and one of the chromosomes of a different pair of homologous chromosomes has allele b₁ in locus B and the second of this pair has allele b₂, then 4 types of gametes bearing alleles a₁ and b₁, a₁ and b₂, a₂ and b₁, and a₂ and b₂ will be formed with the same probability. If two individuals with this genotype were to reproduce together, then 9 types of progeny would be created, with genotypes a₁a₁b₁b₁, a₁a₁b₁b₂, a₁a₁b₂b₂, a₁a₂b₁b₁, a₁a₂b₁b₂, a₁a₂b₂b₂, a₂a₂b₁b₁, a₂a₂b₁b₂ and a₂a₂b₂b₂ in a ratio of 1:2:1:2:4:2:1:2:1. It is apparent that this law is valid only for a pair of alleles from genes that are located on different chromosomes so that, during segregation of chromosomes, they segregate independently into different sex cells and also for genes that, while they are present on the same chromosome, are so far apart that crossing-over and thus genetic recombination will most probably occur in each meiosis in the section between them.

Alternation of the ploidy phases of the life cycle in multicellular organisms is called metagenesis. Very frequently the two ploidy phases differ in their means of reproduction, where the haploid gametophytes form gametes and the diploid sporophytes form spores. In some organisms, the gametophyte phase is more important, i.e. larger, morphologically more complicated and longer-lasting (mosses and lichens); in others, the sporophyte phase predominates (angiosperm plants), while the two phases do not much differ in other organisms (ferns,  Pteridophyta) (Jenkins 1993; Mable & Otto 1998). Alternation of phases with sexual and nonsexual reproduction also occurs in some animals (especially Turbellaria and Cnidaria). This process is also designated as metagenesis in this case, although the bodies of both the  sexual and nonsexual phases are composed of diploid cells under these circumstances.

see Infrapopulation of parasites

The microsphere hypothesis attempts to resolve the aspect of formation of molecules with enzymatic activity and thus the evolution of primitive metabolism. Heating a mixture of aminoacids in anhydrous medium leads to their condensation into an irregular polymer, a proteinoid, which has random sequence and only reflects the contents of the individual aminoacids in the original mixture. Following dissolution in water, these proteinoids form tiny, spherical, sometimes hollow species, microspheres (Muller-Herold & Nickel 1994) (Fig. X.3). Microspheres do not exhibit properties such as growth and reproduction and are not separated from the environment by a membrane. However, it has been demonstrated that they exhibit a number of kinds of catalytic activity (Fig. X.4). The formation of proteinoids is an approximation to a possible mechanism of the formation of the first enzymes and thus the first building blocks of future metabolism; however, it tells us very little about the mechanism of formation of systems capable of biological evolution.

see Gene flow

Mimetism (mimesis) is a very frequent and striking product of the coevolution of two or more species; this phenomenon consists in imitating the appearance (including imitation of the behavior) of the members of another, frequently completely unrelated species. The mimetized species are frequently especially dangerous or at least inedible (Alonsomejia & Brower 1994). To the contrary, the mimetizing species may be either some other dangerous or inedible species, where this phenomenon is termed Müllerian mimicry (according to F. Müller), or an innocuous and edible species, where this is termed Batesian mimicry (according to H. W. Bates).In the former case (Müllerian mimicry), the mutual imitation of the two various species is advantageous for both species, as predators are more readily capable of learning to avoid the relevant species. Thus, coevolution of the species progresses in the same direction, i.e. towards the greatest mutual similarity of the members of the two species (Brower 1996). The South American species of butterflies Heliconius erato and Heliconius melpomene are typical examples (Brower 1996). Because of their complicated evolutionary history, both species form allopatrically distributed strains, where strains of both species living in the same territory are generally very similar (Fig. XVIII.5). It has been verified experimentally that, after transfer of individuals imitating a certain pattern to an area in which a differently coloured strain of the imitated butterfly occurs, the butterflies with the wrong coloring rapidly succumb to predators (Fig. XVIII.6).
_{In the second case (Batesian mimicry), the mutual similarity is advantageous only for the innocuous (edible) species. This is frequently disadvantageous for the imitated species, as predators are less likely to consider these species inedible in the presence of mimetics. It is obvious that confusion of an innocuous species with a dangerous species is detrimental especially for predators; however, the attacked individual of the dangerous species is also frequently harmed in such an attack. When an inedible species is imitated by an edible species, this aspect is even more marked; it is of little advantage to the inedible species that the predator finally spits it out because of the unpleasant taste instead of swallowing it. From an evolutionary standpoint, it is important that Batesian mimicry can stably bring the imitating species an advantage, especially when its population is substantially smaller than that of the imitated species. In some species of butterfly, it thus occurs that the individual forms of a single species of butterfly, occurring together, have different phenotypes and imitate various species of inedible butterflies (Joron & Mallet 1998). In other species, e.g. Papilio dardanus, only the females imitate an inedible species and the males retain the original appearance of the relevant species (Komarek 1997). It is assumed that the failure of the males to adapt their phenotype is either a result of sexual selection (males with a different phenotype would not be recognized by the females of their own species) or because, compared to females, lesser selection pressure is exerted by predators on males compared to females (these would tend to attack the larger females) (Ohsaki 1995). However, it has also been suggested that, in these cases, mimetism constrained only to the females is related to heterogametic sex determination in male butterflies (Hastings 1994). According to these ideas, the genes that determine the preferences of the females in selecting a sexual partner are located on the female W-chromosome. If these genes ensure that the females will prefer males without the mimetic coloration, they will be spread by the mechanism described under the handicap hypothesis (and simultaneously sexual selection will occur in favor of the nonmimetic males). From the standpoint of functioning of the mechanism of handicaps, it is a key factor that the genes for preference for handicapped (nonmimetic) males located on the W-chromosome can never occur in the bodies of males (in contrast to genes on autosomes or on the Z-chromosome) and will always profit only from the advantages that the nonmimetic male phenotype provides without simultaneously participating in the disadvantages following from the given handicap (nonmimetic coloration). This hypothesis could, amongst other things, explain why butterflies and birds, i.e. taxons with heterogametic females, most frequently have brightly coloured males and more or less cryptically colored females.
In some cases, it is not possible to draw a sharp line between Müllerian and Batesian mimicry. For example, the brightly coloured butterflies of the Danaus plexippus species are poisonous when young, as they contain glycosides derived from plants of the Asclepias genus, eaten by their caterpillars. However, as they get older, the glycoside content in the bodies of the butterflies gradually decreases so that, at the end of the season, the older butterflies exhibit Batesian mimicry of the poisonous younger members of their own species (Alonsomejia & Brower 1994).}

see Is absence of missing links compatible with theory of evolution?

seeSelfish gene theory

see evolutionarily stable strategies

Molecular drive is a process through which mutations can proliferate within gene families (in process of homogenetization) and within the population (in process of fixation of mutations) through a number of mechanisms of nonreciprocal transfer of genetic information occurring on the chromosome or between different chromosomes (Dover 1986). Molecular drive differs from genetic drift in that changes in the frequencies of the individual alleles that occur through its action are not random in their direction. If a certain population of genetically identical organisms is divided into several smaller populations, then genetic drift will lead to fixation of different alleles in each population. In contrast, the effect of molecular drive should lead to fixation of the same alleles in all populations. Molecular drive differs from selection in that the alleles that are fixed through its action need not favourably affect the phenotype of the organism and can thus have a zero or even negative impact on the biological fitness of the individual. 

In molecular drive, one allele is replaced by another not because this is more advantageous for its bearer, but because, at the level of the DNA, it multiplies more effectively, either through a mechanism related to replication or through a mechanism related to gene conversion (see below).

Molecular drive differs from mutation bias and reparation drive mainly in that it is responsible for the proliferation of certain mutations in the genome or in the gene pool of the population, but not for their repeated formation.

Molecular driveentails a number of mechanisms connected primarily with replication, recombination and repairing of nucleic acids. These mechanisms favour the formation and proliferation of certain sequential motifs in the gene pool of the population regardless of the degree to which the existence of these motifs is manifested in the phenotype of the organism and the degree to which it affects its biological fitness. The best-known processes active in the functioning of molecular drive include gene conversion, transposition, and also processes directly dependent on replication, i.e.uneven crossing-over andslipped-strand mispairing (Tachida 1993).

The existence of molecular drive is most clearly manifested in the evolution of repetitive DNA segments in closely related species (Charlesworth, Sniegowski, & Stephan 1994; Petes & Fink 1982). These segments are frequently located in the genome in a great many copies, of the order of hundreds of thousands. The individual copies are very similar and frequently completely identical. Simultaneously, repetitive sequences in closely related species are very different. It is difficult to explain this phenomenon without postulating the existence of a specific mechanism capable, following the speciation event – after the splitting off of a new species, of causing parallel differentiation in the repetitive DNA segments in all the loci of the genome. As the speciation process can hardly cause or affect the differentiation of repetitive genes, it is more reasonable to assume that this process occurs continuously in the gene pool of each species. Speciation division of the originally uniform gene pool into two gene pools alone only makes this visible, i.e. permits the repetitive sequences in the two gene pools to develop in different directions.

At the present time, it is mostly assumed that a random process of differentiation of repetitive genes occurs continuously in the gene pool of organisms and thus that mutations are accumulated in the individual copies of the repetitive gene. However, the process of homogenization of the individual copies also occurs simultaneously, i.e. a process in which the variants of the repetitive genes that are most successful from the standpoint of replication, transposition or gene conversion proliferate in the genome at the expense of other variants. In sexually reproducing organisms, the process of homogenization exceeds the boundaries of a single genome and the most successful variant of the repetitive sequence gradually proliferates in the whole gene pool. This is certainly a long-term process; however, it is relatively rapid compared to other evolutionary processes (Fig. VI.9). New variants of repetitive sequences become fixed in a substantially shorter time than the interval separating two subsequent speciation events so that, when studying even closely related species, we find that different variants of the repetitive sequence became fixed in each of them.This fact can be utilized in molecular taxonomy – study of repetitive genes enables discrimination amongst representatives of even very closely related species (Grechko et al. 1998)(see also XXIV.3.9).

If a taxonomic system is to take into account the progress of cladogenesis, it would seem, at first glance, quite natural to require that each taxon include only those species that are mutually more related than any of them is related to any species classified under a different taxon. However, evolutionary systematists do not consider this to be a serious requirement and consciously ignore it in some cases. According to the usual definition, two species are more closely related than is either of them to a third species if they share a common ancestor which is simultaneously not an ancestor of the third species. The requirement of maximum mutual relatedness of species classified in a single taxon is sometimes erroneously interpreted as being equivalent to prohibition of creation of polyphyletic taxa, i.e. taxa including the members of two or more independent phylogenetic lines. A polyphyletic taxon would include at least two species whose immediate ancestors were not members of this taxon. The opposite of a polyphyletic taxon is a monophyletic taxon, i.e. a taxon including the members of a single phylogenetic line. A monophyletic taxon contains, or in the past contained, only a single species whose immediate ancestor was not a member of this taxon. (The topic of the taxa of organisms whose ancestor originated by symbiogenesis will be discussed in XXV.4.2.) The proponents of both the currently most influential directions of systematic biology, evolutionary systematists and cladists, agree on the prohibition of creation of polyphyletic taxa. However, they certainly don’t agree on where the boundary lies between polyphyly and monophyly.
            _{According to the cladist approach to monophyly, only a taxon, all of whose members have an exclusive common ancestor, i.e. an ancestor that is not simultaneously an ancestor of a species classified in a different taxon at the same taxonomic level, is considered to be monophyletic. Consequently, the thus-defined taxon contains the common ancestor of a certain line and all its descendants. In this strict interpretation, monophyly is sometimes called holophyly (Fig. XXV.1). In contrast, evolutionary systematists consider the taxon to be monophyletic when it contains its ancestor and all or only some of its descendants. Any species that was transferred from A to form separate taxon B need not simultaneously be an ancestor of any species that remained in taxon A. Taxa that comply with the evolutionarily systematic criterion of monophyly but not the stricter cladistic criterion, i.e. taxa of which some branches have been recognized to have the status of separate taxa at the same level, are called paraphyletic taxa. The class of reptiles is an example of a paraphyletic taxon. Within this class, the class of birds branched off, so that the common ancestor of all reptiles is also the common ancestor of all birds. However, none of the species of birds is simultaneously an ancestor of a species classified in the taxon of reptiles, so that reptiles still comply with the looser evolutionarily systematic requirement of monophyly.
            At the present time, the proponents of the cladistic approach tend to have the advantage; however, it is not clear which concept of monophyly and thus which concept of taxonomy will prevail in the end. Cladists primarily argue that paraphyletic taxa are our artificial constructs formed of species that, from the viewpoint of cladogenesis, do not exhibit any property that only they would have in common. On the basis of a system containing artificial, i.e. also paraphyletic taxa, for example, we cannot predict the distribution of properties that we did not yet know at the time of formation of the system. They further point out that, as soon as we admit the existence of paraphyletic taxa, the taxonomic system ceases to be hierarchical; to be more exact, situations will occur where a taxon at a certain level will be immersed in a taxon at the same level. For example, in the above-mentioned case, the class of birds will basically be immersed inside the class of reptiles. On the other hand, evolutionary systematists object that, from the viewpoint of cladogenesis, paraphyletic taxa (in contrast to polyphyletic taxa) have the common property that, with the exception of the species from which their common ancestor evolved, no other member of a different taxon is simultaneously a direct ancestor of any of its species. From the viewpoint of anagenesis, they have a common property not only in the absence of apomorphy, on the basis of which part of their line was classified in a separate taxon, but most probably also in the absence of other apomorphys evolving in the members of a split-off taxon. Simultaneously, these other apomorphies were not known at the time of separation of part of the evolutionary line into a separate taxon. According to evolutionary systematists, the objection about the unnaturalness and lack of usefulness of paraphyletic taxa is no longer valid – membership in a paraphyletic taxon permits us to predict the occurrence (or rather absence) of certain forms of traits. They respond to the second objection by stating that a system encompassing immersed taxa at the same level may be contrary to our aesthetic sense and sense of order but, in actual fact, only such a system properly reflects the real course of evolution. The individual lines now representing higher taxa actually branched off in the past within a taxon at a lower level. Most side branches of the evolutionary line, called stem group of the particular taxon, i.e. lines that branched off in the early stages of the particular evolutionary line, and their members carry only some apomorphys characteristics for modern representatives of this line, but a paleontological record of stem group species does not exist and has not been preserved. In contrast to lines of the crown group, i.e. lines that mutually branched off at later stages in the evolution of the particular taxon and who frequently still living members mostly exhibit characteristic apomorphies, they are thus not included in our analyses. Only this fact enables us to define a reasonable number of holophyletic taxa, of which a significant percentage would at least generally overlap with the traditional groups of organisms defined formerly on the basis of their mutual relatedness and phenotype similarities (Fig. XXV.2).}

Essentialist taxonomic systems were mostly monothetic, as they assumed that the presence or absence of a certain trait is decisive for inclusion of a species in a particular taxon. For example, monothetic systems classify angiosperm plants strictly on the basis of the number of individual flower components.
However, most modern systems are polythetic. Polythetic systems allow a taxon to be defined on the basis of a greater number of mutually interchangeable traits. In contrast to monothetic systems, polythetic systems are somewhat harder to use as classification schemes, i.e. as instruments for determination of organisms. On the other hand, only polythetic systems can be truly natural, i.e. can reflect the phylogenesis of the studied organisms.

The theory of the emergence and development of life through biological evolution is generally attacked from various angles and its opponents have various reasons for their criticism. However, basically, from the very beginning, three basic motives are continuously repeated: apparent or actual inconsistency with one’s own ideological model (concept) of the world, fear of the social consequences of general acceptance of the theory of evolution and specific substantive objections to the starting points or conclusions of the theory of evolution. All these motives can, of course, intermingle in the standpoints of individual persons. The opponents of the theory of evolution need not be aware of their actual motives and very frequently consciously and unconsciously copy the behavior of the social group to which they belong.

see Mimetism

is the number of mutations occurring in the given position per time unit for all the members of the population – compare with the substitution rate.

Mutations,the changes in the structure of genetic material respecting the rules of writing of genetic information, are the only source of variability and evolutionary innovation at the level of the species; in their absence, biological evolution would sooner or later stop.If more fundamental changes occur in the environment, organisms that would not be capable of undergoing mutation processes and thus of adapting to changes in the environment, would die out.However, at the level of individual populations, gene flow and genetic recombination are the main source of evolutionary innovation.In fact, even in species without regular sexual reproduction, for example bacteria, in which recombination must occur with the participation of relatively ineffective processes of transformation and transfection, the recombination is responsible for the formation  of new alleles 10x more frequently than mutations. Mutations can be differentiated according to a number of criteria.According to their physical nature, they can be classified as point mutations, mutations at the level of DNA sections (chromosomes) and at the level of the entire genome.Mutations can be encountered in the nuclear DNA and in the organelle DNA.“Mutations” that occurred during RNA transcription and that are thus not at all connected to the DNA exhibit the character of vanishing mutations, i.e. the mutations whose manifestation becomes weaker over time.In single-cell organisms with a short generation time and long mRNA lifetime, these mutations can peter out over many generations.On the other hand, mutation can occur in multicellular organisms only during ontogenesis or in the adult organism, so that the cells containing the given mutation can be present only in some tissues.If these somatic mutations do not reach the germinal organs and tissues, they are of no evolutionary importance.

According to their effect on the biological fitness, mutations can be differentiated as selectionally positive mutations (useful or also advantageous – increasing the biological fitness of their bearers), selectionally negative (detrimental or also disadvantageous – reducing the biological fitness of their bearers) and selectionally neutral (with no effect on the biological fitness of their bearers).In studying genetic drift, it was found that it is necessary to also differentiate the extremely numerous category of slightly negative mutations (see V.6).This category includes those mutations that, while they have a negative selection coefficient, this is simultaneously so low that their fate in the studied population tends to be determined by genetic drift (see Chap. V) or genetic draft (see IX.5.2) rather than by selection.

Mutations at the level of the entire DNA section can be classified into several types (Fig. III.2). In deletions, insertions andduplications, a certain DNA section is lost or, to the contrary, duplicated. The duplified section can either be immediately next to the original section (tandem duplication) or can be in an entirely different part of the genome. The sections that are, themselves, tandem duplicated can duplicate most readily. At the sites of tandem duplication, incorrect pairing and then  nonreciprocal recombination can occur between two homologous chromosomes, as a consequence of which deletion of a certain DNA section occurs on one chromosome, with insertion at another chromosome.

Translocation entails relocation of a certain DNA section to a different site in the genome. If this is reciprocal translocation, then two DNA sections exchange places on the chromosomes; in transposition, only one DNA section is relocated.

In inversion, a certain DNA section is cut out of the chromosome and inserted in the same place with the opposite orientation.  In mammals, the vast majority of chromosome restructuring  entails translocations; in contrast, inversions are involved in drosophila (Spradling & Rubin 1981). Drosophila are apparently pre-adapted to tolerate inversion in that recombination does not occur during meiosis in the nuclei of male gametes and thus deletion also does not occur in the inversion sections in heterozygote males.

Translocations and inversions can be of great importance in speciation as one of the mechanisms of formation of interspecies barriers. If two individuals differing in the presence of a greater number of chromosomal mutations breed together, they have greatly reduced fertility. In recombination including the restructured DNA sections, frequent deletions occur of entire chromosome sections, so that many of these recombinants are not viable (Fig. III.3). For example, if two individuals differ in the presence of paracentric inversion, i.e. inversion not including the centromere region, then recombination is prevented over entire long sections of the relevant chromosome or recombination leads to chromosomes without centromeres or with two centromeres, i.e. structures that reliably prevent nuclear division.

An increased frequency of inversion in some taxons could be the cause of an increased rate of speciation of these species and, as a consequence of the action of species selection (IV.8.4), also the cause of their evolutionary success (Trickett & Butlin 1994).

Natural selection is the process of uneven transfer of alleles derived from particular individuals to the gene pool of the following generations through their progeny.This process is fully responsible for the origin of evolutionary adaptations and partly responsible for increase of disparity during evolution. It can occur in a number of quite different ways, and thus it is possible to differentiate several basic types of natural selection and also their combinations.The individual types of selection can be studied from the standpoint of their impact on the course of evolution, i.e. on the speed and direction of changes that they cause in the gene pool of the population, and from the standpoint of the level at which the selection acts (alleles, individuals, populations, etc.). We can recognize for example environmental selection, sexual selection, parental selection, hard selection, soft selection, r-selection, K-selection, random selection, turbidostatic selection, chemostatic selection, frequency-dependent selection, apostatic selection, stabilizing selection, disruptive selection, directional selection, individual selection, group selection, kin selection, interspecies selection, intercommunity selection, interallele selection.