See Evolutionary constraints.
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see Mutations at the level of the entire DNA section
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Paradox of genetic complexity
see Genome evolution
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The classical definition states that a parasite is an organism that, in some phase of its life cycle, utilizes the organisms of some other host as a source of food and as a permanent or temporary environment for its life, and thus harms it either directly or indirectly. Thus parasites are not defined taxonomically but ecologically and include organisms from viruses through tapeworms to the Amur bitterling (Rhodeus sericeus). Like most biological definitions, even this one is not capable of describing the facts in their full complexity. In a number of cases, especially for most phytoparasites, we are not able to exactly differentiate between a parasite and a predator. In addition, problems are encountered with nidicolous parasites, i.e. parasites that do not live in or on the bodies of their hosts, but in their dwellings. From the viewpoint of the negative impact on the host organism, there are a wide range of parasites, from species that are almost innocuous (in this case, we speak of commensals and not parasites) to species that almost always kill their hosts – parasitoids. Parasites differ from predators and micropredators (including, for example, mosquitoes) in that the hosts provide a permanent or temporary environment for their lives. This difference is of fundamental importance from the standpoint of evolution of parasitic species. While the relationships between a predator and its prey (as two individuals) are only antagonistic, the parasite – host relationship is, to a certain degree, asymmetric. The host has quite the opposite interests to those of the parasite In contrast, a parasite, in that it generally requires a live host as its environment for life, has at least a certain interest identical with that of its host – a host attacked by a parasite must live for at least some time and, in some cases, where possible, also reproduce, for example in the case of the possibility of transovarial transmission of the parasite from parents to progeny. This fact, together with the necessity of developing mechanisms capable of overcoming systems of specific physiological (immune) defense of the host requires maximal evolutionary adaptation of the parasite to the host. The host organism reacts evolutionarily in some way to this adaptation and develops the relevant counter measures, so that the evolution of a parasite tends to have the character of co-evolution of the parasite – host pair.
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Parasites and biodiversity
The pressure of parasites on a host population can be very intense. In fact, in some cases, it can be the basic element of the feedback regulation mechanism maintaining the size of the host population at a constant level. As the size of a parasite population bound to the population of a certain host is usually larger than the size of the population of a predator, the system is less susceptible to random fluctuations. Consequently, the equilibrium in the parasite-host system is usually more stable than in similar systems based on interactions of the predator-prey type. The greater host specificity of the parasite contributes to the stability of these systems. On the other hand, the frequently low food specificity of a predator allows the population of the predator not to be necessarily bound to the size of the population of a certain species of prey. As a consequence, a momentarily numerous population of a predator can completely exterminate the populations of some kinds of prey.
Similar to the predator-prey system, the parasite-host system also belongs, from the viewpoint of the host, amongst feed-back regulation systems of the turbidostat type (Flegr 1977) (see IV.4.1). This means that, in a system regulated by the action of the parasite, the host population is exposed to r selection, i.e. selection for a faster reproduction rate (and not for more effective use of nutrient sources). As a consequence, the species does not utilize the resources to the extreme of the capacity of the environment, so that a larger or smaller amount is left for other species occurring in the particular environment. Through this mechanism, the phenomenon of parasitism apparently contributes very effectively to maintenance of a high level of biodiversity in real ecosystems.
Maintenance of a high level of biodiversity through the presence of parasites is also augmented by the fact that specialized parasites add a further dimension to the multidimensional ecological environment in which organisms live. In section IV.4.1, we mentioned that two species utilizing a single resource can exist next to one another for a longtime in a single place if one of them is the subject of chemostatic and the other of turbidostatic regulation (see the caption for Fig. IV.4). Similarly, permanent coexistence is possible for two species whose populations are turbidostatically regulated through the action of two different species of parasites.
Overall, it can be stated that, in the absence of parasites, natural ecosystems would have far less biodiversity and would probably make less effective use of the available resources.
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Parasitic castration is a fairly common means of affecting the physiology of a host organism. In some cases, this occurs more or less incidentally; the parasite first consumes the tissues and organs that are not essential for the life of the host (Wilson & Denison 1980). However, in other cases, this is a targeted effect, brought about, for example, by the production of certain hormones. For example, in Biomphalaria glabrata snails infected with Schistosoma mansoni fluke worms, there is a substantial reduction in the level of biogenic monoamines (serotonin (5-HT), dopamine (DA) and L-dopa) in the plasma and in the central nervous system; the 5-HT level in snails is closely correlated with egg production (Manger et al. 1996). A different kind of fluke worm, Prosorhynchus squamatus, which parasitizes on marine mussels (Mytilus edulis), increases the level of the factor that reduces the intensity of division of future gametes (Coustau et al. 1991). Through temporary or permanent castration of its host, the parasite achieves a change in energy fluxes in the particular organism and specifically redirects that part of the energy, that the host would normally devote to its reproduction, towards growth and regeneration (Wilson & Denison 1980). In this way, it actually increases the viability of the host organism at the expense of reducing its fertility (Fig. XIX.13). While the host is concerned to optimize the ratio of energy invested into reproduction and into the other life functions, a parasite is usually primarily concerned with the length of survival of the infected individual, but not with its reproduction. It has been found, for example, that water snails of the Lymnaea truncatula species, infected and castrated by larvae of the fluke worm Fasciola hepatica, grow to as much as twice the weight of control snails (Wilson & Denison 1980). However, in some systems, castration of snails is only a side effect of parasitism and occurs through the effect of any kind of physiological stress.
The feminization of male mice apparently has a somewhat different purpose; this is caused by the larvae of Taenia crassiceps tapeworms through an approximately ten-fold reduction in the testosterone level and an approximately two-hundred-fold increase in the estradiol level in the serums of infected animals. It is known that mouse females are far less resistant against the infection than males and that, following hormonal feminization, the sensitivity of the two sexes (tendency to tolerate the growth and reproduction of tapeworms) is more or less equal. Some lymphokins (IL-6?), whose production is dependent primarily on the sex hormone level, are apparently of key importance here (Larralde et al. 1995).
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see Horisontally transmitted parasites and evolution of virulence
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Passive natural selection
Passive natural selection denote a form of selection that does not lead to an increase in the functionality of the structure, but does eliminate the consequences of evolutionary changes (mutations) that would otherwise lead to a worsening of the functionality.
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Pathogenic manifestations of infection
The ability of a parasite to survive and reproduce in the host organism and the ability of the parasite population to survive consistently in the population of the host species are a consequence of gradual evolutionary adaptation of the parasite to the particular host species (Kaltz & Shykoff 1998). If the host species comes into contact with a new range of potential parasites, for example if it invades a new territory, it is generally resistant to parasitization by unspecialized parasites. Escaping from the reach of the original parasites is usually considered to be the most important cause of the ecological success of a great many invasive species (Mitchell & Power 2003; Torchin et al. 2003) (Fig. XIX.5). Only after a longer period of time are some parasites that occur in the given territory able to adapt to a new host sufficiently to survive consistently in the population of new hosts and are thus able to bring the spreading of the invasive species under control.
However, in some cases, the pathogenic manifestations of infection by an unadapted parasite are very drastic, so that in a great many cases it ends with the death of the host organism. These cases are apparently far rarer than cases where an unadapted parasite is not capable of reproducing at all and of substantially damaging the new host. However, from the viewpoint of humans, these cases are more obvious and thus they get far more publicity. If the population of hosts survives the meeting with the new parasite, changes gradually occur in the progress of the infection and, understandably, also in the dynamics of its spreading in the host population. Specifically, the pathogenic manifestations of parasitosis are reduced, so that the originally fatal infection is gradually reduced to a milder sickness and, in extreme cases, can even end up practically free of symptoms (asymptomatic) (Combes 1997). The well-documented history of the intentional introduction of the virus of rabbit myxomatosis into Australia (Fig. XIX.6) is a textbook case of reduction of the pathogenicity of infection that has been well documented.
The phenomenon of gradual reduction in the pathogenicity of parasites, described commonly but rather inaccurately as the phenomenon of reduced virulence (see XIX.4.1), is, on the one hand, influenced by evolution of the host organism and selection of individuals that are more resistant to reproduction of the pathogen and to the pathological manifestations of its action in the organism and, on the other hand, selection within the parasitic species is important here, as parasites that do not excessively damage their hosts can produce more infectious stages and infect more hosts during their existence in a single host organism.
However, it should be pointed out that, in a great many cases, the pathogenic processes that accompany parasitosis are directly connected with the reproduction of the parasite – the more invasive stages it forms during the overall time of infection, the more intense are the pathogenic processes and their consequences (Fig. XIX.7). In this case, to the contrary, the pathogenicity gradually increases with gradually increasing adaptation of the parasite. Even cases where the pathogenic processes are part of manipulative behavior of the parasite and participate substantially in the effectiveness of spreading of the parasite in the host population are not exceptional (see below). Also in these cases, the virulence of the parasite is not reduced; to the contrary, the parasite is able to do more damage to the members of species or populations to which it is adapted in the long term (Ebert 1994; Ebert & Herre 1996).
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From the viewpoint of game theory, even the Generous Tit for Tat strategy is not an evolutionarily stable strategy in the stochastic world, because its temporary success enables the always cooperate strategy to spread and this allows the successful return of the always betray strategy. So the game does not have a stable solution, and the representation of individual strategies in the population circulates constantly. It seems so far that the only evolutionarily stable strategies are those that do not direct their behavior according to the opponent’s behavior in the last round, but according to how they behaved in the last round and what profit they got from it. A fairly successful, even though not evolutionarily stable strategy of this kind is a strategy named Pavlov (Nowak & Sigmund 1993). It is directed by a simple rule: repeat your behavior from the last round, if it was successful (i.e. you betrayed and the opponent cooperated or you both cooperated), change your behavior if you lost in the last round (i.e. you cooperated and your opponent betrayed or you both betrayed). The Pavlov strategy, similar to the Generous Tit for Tat, does not allow the always cooperate strategy to spread in the somewhat unpredictable world, but it enables the always betray strategy to spread. Existing results show that even the simplest so-far described evolutionarily stable theories have to be capable of learning, i.e. they must have memory and the ability to remember the results of a number of previous rounds when choosing a strategy for a new round (Wakano & Yamamura 2001). Experiments performed using experimental games with human volunteers have shown that, actually, in a normal population, people mainly follow strategies similar to the Generous Tit for Tat as well as the Pavlov strategy (Fig. XVI.6). At the same time, it has been shown that the actually used strategies were somewhat complicated and also more successful than the Generous Tit for Tat or Pavlov and that the players used information from a number of previous rounds in the strategies (Wedekind & Milinski 1996).
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- The hypothetical model of adaptation of the peptide vocabulary of a parasite to the peptide vocabulary of the host is an example of molecular mimicry. This model could also explain the process of speciation of a host species through development of the host vocabulary and its divergence in various subpopulations. If, for example, a certain subpopulation of hosts achieved a change in its peptide vocabulary, for example, if it removed a certain peptide from its vocabulary through substitution mutations, it would, to a certain degree, escape from the reach of a parasite whose vocabulary is adapted to the original host population. The members of this population would begin to identify the relevant peptide in the parasite proteins as a foreign element. It is apparent that vocabulary differentiation can fulfill a protective function only if crossing does not occur between individuals of the two host subpopulations. The advantageousness of genetic isolation can thus lead to the creation of selection pressure on the formation of reproduction barriers.Thus, pressure from parasites could indirectly lead to the formation of isolated species.
The increased susceptibility of crossed individuals occurring in the hybrid zones of some species could be related to differentiation of the peptide vocabularies of two related species. Such a greater susceptibility has been observed, for example, in mice caught in the hybrid zone of the species Mus musculus and Mus domesticus (Moulia et al. 1991; Sage et al. 1986; Moulia et al. 1995) (Fig. XIX.4). The hybrid mice necessarily have a more extensive peptide vocabulary, so they are unable to identify a great many more peptides as foreign than either of the parent species.
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The multidimensional statistical method of cluster analysis permits the creation of clusters of objects on the basis of the similarity of the individual objects, where the distance between these clusters and the manner in which they are gradually immersed in one another express the degree and character of mutual similarity amongst the classified objects. If these objects are individual species of organisms and the degree of mutual similarity consists, for example, in the number of shared traits, then the created system of clusters can be used as a taxonomic system for this group. More serious attempts to create systems of some organisms using the methods of cluster analysis were made only in the middle of the last century (Michner & Sokal 1957). The usefulness of the relevant methods in biology was dependent on the existence of computers, as it required the processing of a large amount of data. This procedure came to be called numerical taxonomy or numerical phenetics. Numerical taxonomists assumed that, if the initial data set contains information on the maximum number of traits for all the studied species, the outputs of the relevant programs would be a hierarchically ordered system of clusters, objectively expressing the existing relationships amongst the studied organisms. Such a system could form a good basis for taxonomic classification of organisms. Experience in the use of the methods of numerical taxonomy has shown that, for a sufficiently large number of traits and using the same methods of cluster analysis, the results obtained are truly objective, i.e. individual taxonomists processing the same group of organisms come to more or less the same results. However, the choice of suitable methods of cluster analysis remains a problem. There are a great many ways of calculating the phenetic distances (or similarities) amongst the classified species on the basis of the individual traits and also a great many methods that can be used to form clusters on the basis of the phenetic distances, where each method usually provides qualitatively different results. Simultaneously, it cannot be stated that one method is the right one and the others are wrong. The choice of methods is a matter for the subjective decision of each taxonomist and thus the consequent taxonomic system is subjective.
When any phenetic taxonomic system is used, it must be constantly borne in mind that the system expresses only the similarity but not the relatedness of the organisms. In a great many systems this does not matter much, for example, if it is necessary to classify species that diverged apart at a single moment a long time ago. At other times, the use of a phenetic approach seems more like the only solution in a bad situation. If no traits are available, on the basis of which we could reconstruct the cladogenesis of the particular group, we will have no choice but to use phenetic classification. Finally, it should be pointed out that, where the input data consisted in selectively neutral traits, which changed during evolution at roughly a constant rate in all the species in the studied line, the obtained phenogram should be identical with the cladogenesis scheme and should allow us to reconstruct the relationships amongst the species of the particular phylogenetic line (see XXIV.6).
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- However, anagenetic changes can complicate the reconstruction of cladogenesis. If anagenesis occurs similarly in two distant phylogenetic lines under the influence of the same selection pressures, even unrelated species of organisms may have similar appearances. Then we could have a tendency to place these organisms close together on the tree. This approach is obviously erroneous; the cladogenesis scheme must express only the degree of mutual relatedness of organisms, while the degree of their phenotype similarity should not have any effect here. If the mutual phenotype similarity of individual groups of organisms is expressed graphically, a phenogram is obtained. The topology of a phenogram allows us to estimate which of the compared species exhibit similar properties and thus were, during their evolution, probably because of a similar life style, exposed to similar selection pressures. In cases where, for some reason, we cannot reconstruct the progress of cladogenesis, for example when all the studied species evolved during a historically short period of adaptive radiation (see XXVI.2.1.1) and did not further undergo speciation, or when all the species were formed gradually but from the same parent species, the phenogram can act as a basis for taxonomic classification of the given group of organisms. If a phenogram is formed on the basis of selectively neutral traits which change in all the phylogenetic branches at approximately a constant rate, i.e. for example on the basis of mutations accumulating in pseudogenes, i.e. in genes that have lost any biological function due to some critical mutation, and, if there is a sufficient amount of data, the topology of the phenogram should be identical with the topology of the graph describing cladogenesis. In this case, the phenogram can also be used for reconstruction of the course of cladogenesis.
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Phenotype of an individual can be understood to consist in the set of all the properties that the particular individual exhibits. Some of these properties are genetically determined, i.e. their occurrence is determined by the presence of specific genetic information in the genome of the particular individual. Other properties, such as behaviour in an environment with a temperature of 3000 oC, are not genetically determined but follow from the properties of the substances from which the bodies of organisms are composed. A great many properties are simultaneously determined genetically and by the environment. In this case, the occurrence of certain properties is dependent, e.g., on the character of the external environment in which the particular individual occurs, or on the internal environment of the particular organism, which parameter is, once again, frequently determined by the overall genotype of the given individual.
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During phylogenesis, not only individual species, but entire higher taxa very rapidly emerge and develop to their typical form. G.G. Simpson pointed out this fact in the middle of the last century and proposed the name quantum evolution for this phenomenon, in contrast to phyletic evolution (Simpson 1944). In modern terminology, we would most probably speak of quantum or phyletic anagenesis. While the punctualist model of evolution refers to the fact that a species changes only immediately after the time of its formation, the quantum evolution model refers to the fact that fundamental anagenetic changes typical for the members of a particular taxon also occur very rapidly, almost in a jump on a paleontological scale, in sequences of (punctualistically or gradualistically evolving) species forming a certain phylogenetic line. Simpson explained this by suggesting that the formation of a new taxon is dependent primarily on key anagenetic changes that enable the hosts to occupy a new adaptive zone. However, passage to a new zone frequently has the character of “all or nothing”, so that organisms with transition forms of the particular traits are exposed to very strong selection pressures that cause a very rapid passage to a new adaptive zone. Consequently, species with transition traits practically do not occur in nature or have such short lives that they are not even observed in the paleontological record.
At the present time, it is not clear whether the quantitative character of anagenesis requires separate explanation or whether it can also be a consequence of the punctualist character of anagenesis of the species.
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During phylogenesis, new phylogenetic lines of organisms are formed from the original single line (denoted as the phylogenetic line, evolutionary line, monophylum or clade), i.e. from a branched or unbranched series of species that have a mutual relationship of ancestors and descendants, by splitting off in the process of branching speciation. These lines can then survive for long times in nature or disappear after a shorter or longer period of time. A phylogenetic line becomes extinct when all its members die out. Individual species are constantly formed and disappear within the individual phylogenetic lines, where the phenotype properties of the new species can differ from the phenotype properties of the older species. Just as the species composition of the individual phylogenetic lines changes during evolution, the phenotype composition of their living members also changes. The process of mutual splitting and, to the contrary, in isolated cases, merging of phylogenetic lines is termed cladogenesis, while the process of accumulation of phenotype changes within the line is termed anagenesis. The entire historical process of gradual splitting off of the individual phylogenetic lines and accumulation of their anagenetic changes is termed phylogenesis. It should be pointed out that the term anagenesis was used for some time in the past in different senses, for example in the narrower meaning of accumulation of progressive evolutionary changes, i.e. changes improving a certain structure and its functions (Rensch 1959).
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One of the most obvious properties of life on Earth is that its organisms form a hierarchically ordered system of mutually immersed groups. The lowest level represents species, groups of mutually similar individuals. A separate chapter, Chapter XX, was concerned with the aspect of species and the existence of species. Species can be ordered into higher groups on the basis of similarity of their members and these groups of species can again be classified in groups at higher and higher levels. We are currently aware that the reason for hierarchies in taxa lies in the mechanism through which the individual species emerged during evolution. Species gradually branched off from a common ancestor and the individually established phylogenetic lines subsequently further branched or some of them disappeared as a consequence of extinction of all their species. The lines that branched off only recently contain a number of mutual relative, and thus more similar species than the lines that branched off at an earlier time. The subject of study of phylogenetics consists in phylogenesis, i.e. the formation and evolution of the individual phylogenetic lines. Phylogenetics attempts particularly to reconstruct the course of cladogenesis, i.e. the order and manner of branching of all the phylogenetic lines during evolution. Simultaneously, it must necessarily be based on the study of anagenesis, i.e. on the study of the evolution of the individual properties of organisms within relevant phylogenetic lines. Thus, phylogenetics studies both the mutually interconnected aspects of phylogenesis - the specific history of the evolution of life on the Earth.
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A great many contemporary embryologists are of the opinion that, in embryo development, a certain stage exists for the individual animal phyla in which all the representatives of a certain phylum are most similar. This is called the phylotypic stage. The phylotypic stage in vertebrates is the pharyngula stage, while in arthropods this is the segmented germ-band stage (Fig. XII.10). According to the original concepts, the phylotypic stage corresponds to the developmental stage in which the basic body structure is formed, a bauplan, which is characteristic for the given animal phylum.
The concept of the existence of a uniform phylotypic stage is probably somewhat simplified. Numerous heterochronies occur in the development of the individual species of organisms; i.e. the individual organ systems develop at different rates in various species (Palumbi 1997). It thus follows that the members of two taxa of a single phylogenetic line can be most similar at a certain stage in development, while the members of two other taxa are most similar in a different stage (Richardson et al. 1997; Richardson 1995).
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- A trait is understood to refer to any structure, function or behavior that occurs in various species in at least two different forms. From an evolutionary standpoint, the individual forms of a certain traits are not equivalent; one of them, the plesiomorphic form, for short plesiomorphy, is evolutionarily older in the particular phylogenetic line and the other forms were formed secondarily all at once or in a certain order as a consequence of anagenetic changes in the original form of the trait. These evolutionarily derived forms are termed apomorphic forms, abbreviated apomorphies.
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Point mutationsmost frequently consist in the replacement of one nucleotide by another; these are replacement mutations, substitutions.If a nucleotide with a certain type of base, e.g. pyrimidine (C, T), is replaced by a nucleotide with a different type of base – purine (A, G), then this corresponds to transversion; if it is replaced by a nucleotide with a base of the same type, then this is a transition.Point mutations also include deletion and insertion, in which the number of nucleotides is changed at a certain place in the DNA, usually by one; however dinucleotide insertions anddeletions are also quite frequent.The frequencies of the individual types of mutations differ considerably and depend not only on the type of organism (bacteria, eukaryote) and on the genome, in which the mutation occurs (nucleus, mitochondria, plastid), but also on the nucleotides occurring close to the given position.For example, it was found for chloroplast DNA that, if a certain nucleotide is adjoined from both sides A and T, then the probability of transversion is 2.2 times greater at this site than the probability of transition.However, if at least one of the neighbouring nucleotides is G or C, then transitions are 1.5 times more probable at the given site than transversions (Morton & Clegg 1995).However, these ratios differ somewhat for various genes, so that it is apparent that the probability of the individual types of exchanges is not affected only by the immediately neighbouring nucleotides.
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Point mutations in the protein-encoding DNA
If point mutations occur in the DNA protein-encoding section, it is possible and frequently useful to classify mutations according to their effect on the structure of that protein.Because of the degeneration of the genetic code, i.e. in relation to the fact that a single aminoacid is encoded by a number of various codons, i.e. nucleotide triplets, replacement of a nucleotide in the codon need not be manifested in the structure of the protein.These are termed synonymous (samesense) mutations.Mutations of this type, similar to most mutations in the area of introns or pseudogenes, i.e. in genes that have lost their functionality and are not rewritten in the cell and translated to proteins, are important in that they are invisible, neutral, from the standpoint of natural selection.However, in actual fact it was found that synonymous mutations are not neutral in the true sense of the word.It can be important for the organism whether a certain triplet-encoded aminoacid is translated by rare or common tRNA.In addition, synonymous mutations also affect the regulation of transcription of the given gene, the secondary structure of the synthesized RNA, its stability and the intensity of the translation.In drosophila, the average selection coefficient acting against mutation in the synonymous site has been estimated at s= 2,3/Ne, where Ne is the effective size of the population (Akashi 1995).In human beings, it has been estimated that approximately 3% of synonymous, 12% of nonsynonymous and 100% of nonsense mutations (see below) are detrimental.
Missense (nonsynonymous) mutations are mutations through which one aminoacid is replaced by a different one.If the aminoacid is replaced by an aminoacid with similar physical-chemical properties, then this is termed a conservative substitution.A conservative substitution need not substantially change the tertiary structure and biological function of the protein.The genetic code is arranged so that most aminoacid substitutions that can occur through mutation of a single nucleotide in the triplet are conservative.For example, 97% of transitions at the third position of the codon are synonymous and the remaining 3% lead to conservative substitutions.Of the less common transversions, 59% of those in the third position are synonymous (Wakeley 1996).It is not currently apparent whether this arrangement of the genetic code is a useful adaptation of organisms preventing drastic changes in the protein structure as a consequence of substitution mutations or whether this is only an indication of the way in which the evolution of the genetic code occurred (see X.3.3).The individual aminoacids differ very substantially in their degree of conservativeness.For example, during evolution in proteins, the aminoacid glycine is substituted by another aminoacid only very rarely, while, in contrast, asparagine is replaced far more frequently.Differences in the rates of evolution of the individual proteins can be explained to a considerable degree by various contents of conservative and nonconservative aminoacids.For example, the differences in the content of glycine alone can explain 39% of the total variability in the rate of development of 27 studied mammal proteins; if we take into account the content of 5 aminoacids with the greatest effect on the rate of evolution, then 73% of the variability can be explained (Graur 1985).
Another type of substitution mutation consists in nonsense mutations.In these mutations, one of the three termination codons is formed from the codon for the aminoacid, so that translation at this site leads to premature termination of synthesis of the protein chain.This is, of course, a drastic change in the protein structure, which mostly leads to the formation of a nonfunctional protein.
Drastic changes also occur through the effect of insertion ordeletion of a nucleotide.These changes, frameshift mutations, lead to a shift (disruption) of the reading frame so that a basically unaltered sequence of nucleotides is translated on the ribosome as a sequence of completely different triplets to a completely different sequence of aminoacids (Fig. III.1).In addition, the shift in the reading frame means that, sooner or later, a termination codon appears in the sequence of new codons, so that protein synthesis is prematurely terminated at the given site.
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Most natural populations are characterized by more or less obvious polymorphism. Individuals of the same sex and the same age in the population differ from one another in a number of quantitative and qualitative traits.
Part of this polymorphism is nonhereditary in nature and evolves as a response of the individual to the effects of the external environment that it or its immediate ancestors encountered during their lives or ontogenesis. However, a large portion of polymorphism is determined genetically and is thus hereditary to various degrees. Genetic polymorphism is a result of the existence of two or more variants (alleles) of the individual genes.
Genes were previously seen as hypothetical factors determining the value of the individual biological traits, the properties of living organisms. In order for the existence of such a gene to be distinguished, the relevant trait for which the particular gene was responsible had to assume at least two values.Monomorphic genes, i.e. the genes occurring in the population in a single variant, could thus not, in principle, be distinguished and described or studied.
Only with the ascendance of molecular biology and following revelation of the material nature of genes, i.e. DNA sections coding proteins or RNA molecules, did it begin to become possible to identify the individual genes without first knowing their phenotype manifestations. This permitted identification of monomorphic genes. Modern methods of molecular genetics, specifically the methods of reverse genetics, permit determination of the biological function of a gene even when only a single variant is known. It is possible to either transfer the relevant gene to the genome of a suitable recipient (through a cell of the germinal line) and thus prepare a transgenic organism or, on the other hand, to employ the gene targeting (knockout) method to inactivate the particular gene in the zygote. Study of the phenotype of these genetically modified organisms then assists in determining which traits a particular gene determines.
While molecular biology has made it possible to also study monomorphic genes, it has simultaneously demonstrated that, strictly speaking, monomorphic genes do not exist. Almost all genes studied in detail occur in populations in a great many variants that differ, at the very least, in the presence of individual point mutations. Most of these mutations are apparently neutral in relation to the phenotype and selection, and occur, e.g., on the third positions of the nucleotide triplets, where their occurrence does not lead to substitution of an aminoacid in the protein chain. Some mutations lead to these substitutions; however, only some substitutions simultaneously lead to changes in the biological functioning of the relevant proteins. A large part of the polymorphism at the DNA level is thus not polymorphism in the true sense of the word and is not manifested externally in any way. This type of “pseudopolymorphism” is important for study of evolutionary and population phenomena, but is of relatively little importance from the viewpoint of biological evolution. It arises from mutation processes and, on the other hand, is being continuously removed by genetic drift, genetic draft andmolecular drive.
If pseudopolymorphism is not taken into consideration, i.e. the presence of neutral mutations, that do not in any way appear in the phenotype of the organisms (i.e. if the location of zones on an electrophoretogram is not considered to constitute part of the phenotype), it is found that two groups of polymorphic genes exist. The first group consists in genes that occur in the population with great frequency in one standard form and in much lower frequency, usually less than 1%, in minority forms. For these alleles, it is generally assumed that they occur only temporarily here or that they are maintained as a result of the dynamic equilibrium of two processes – mutation pressure, i.e. constant formation of new alleles from the majority standard allele during mutagenesis, and selection, i.e. constant disappearance of the mutated alleles from the population.Polymorphism, caused by the temporary presence of rare alleles in the population, will be termed Type I polymorphism and will be discussed primarily in Chapter IX, devoted to the evolution of the DNA sequence and proteins.
However, for the second group of genes, it is difficult to say which allele is standard and which is mutated as they all, or at least a great many of them, occur in the population in high frequency (Fig. VIII.1). This type of polymorphism is maintained over long periods in the population through the action of specific mechanisms and is of incomparably greater importance from the viewpoint of evolutionary and ecological processes. Here, it will be termed Type II polymorphism and will constitute the subject of this chapter.See also Origin of Rh-blood group polymorphism and also Sickle-cell anemia.
The existence of polymorphism within a population is of substantial importance both from the perspective of ecological processes and also from the microevolutionary and macroevolutionary viewpoints. From an ecological perspective, it is important that a polymorphic population is capable of utilizing very varied resources and consequently of utilizing its environment more economically. A polymorphic species is also less vulnerable to random fluctuations in the environmental conditions, as at least part of the population can survive even during drastic changes.
Polymorphism also changes the microevolutionary potential of populations and species, i.e. the ability of populations and species to respond to short-term selection pressures in the environment,as it provides selection with genetic material from which it can choose suitable variants that better correspond to the altered conditions in the environment (Fig.VIII.11).Thus, populations need not wait for the formation of new mutations and can use the already-present variability. As the fate of isolated new mutations immediately after their formation is determined primarily by accident (see V.3.1), it is far more advantageous if potentially suitable variants occur in the population with sufficient frequency right at the beginning. In addition, in case of cyclic changes in the environment, it is ensured that the genetic composition of the population can readily return to the original state after the environmental conditions go back to their original values (Fig. VIII.12). According to some theories, it is this reversibility of microevolutionary changes that is mainly responsible for the greater evolutionary success of sexually reproducing species (Williams 1975, Flegr 2008). In asexual species, the composition of the gene pool of the population follows even temporary environmental changes. Thus, all the alleles that are essential for their bearers under normal conditions can be very easily lost from the population during short-term changes. This can understandably be very disadvantageous for an asexual species in the medium term.
From the perspective of long-term or even permanent changes in the environment, and thus, for example, from the perspective of macroevolutionary processes, the impact of polymorphism on the progress and rate of evolution can be quite the opposite (Flegr 1998). Due to the phenomenon of genetic homeostasis andepistatic interactions, the effectiveness of natural selection is greatly limited in polymorphic sexually reproducing populations (see IV.9.2). Thus, populations and species react to the action of selection pressure only through a shift in the frequencies of individual alleles that are already present in the gene pool, while the fixation of new alleles through selection is greatly limited. Thus, a genetically polymorphic species remains selectionally frozen and anagenetic changes can occur only following a drastic reduction in the polymorphism, for example, in connection with a long-term drastic reduction in population size(see V.2.2).
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Polymorphism of MHC antigens
An interesting example of the action of frequency-dependent selection is active in maintenance of polymorphism of the major histocompatibility complex antigens (MHC-antigens) (Klein & Ohuigin 1994). These proteins are of key importance in both cell and humoral immunity processes. They specifically bond, on their receptor region, some of the short peptides formed in the cells by enzymatic splicing of protein molecules and transport them to the cell surface. In this way, they determine the sections of the aminoacid chain according to which the immune system of the given individual will recognize the foreignness of a particular protein. If all the individuals in the population were identical in their MHC-antigen alleles, they would recognize the foreignness of the individual antigens, e.g. proteins derived from viruses and bacteria, according to the same criteria, i.e. according to the same sections of the aminoacid chain.In typical cases, evolution occurs much more rapidly amongst parasitic organisms than in their hosts. Thus, a parasite would be capable of rapidly changing the relevant site of its proteins, which would remove it from the action of the immune system of the host and it would be capable of attacking all the individuals in the host population. However, MHC-antigens are extremely polymorphic in real populations. Each MHC gene (MHC is a complex consisting of several genes) has a number of alleles (frequently dozens) that occur with quite similar frequencies in the population. For most species, with the exception of identical twins, it is thus not possible to find two individuals that would have the same combination of alleles of the major histocompatibility complex.
This extreme polymorphism was not formed to teach transplantation surgeons humility (without MHC polymorphism, some organs could be transplanted on an extensive scale) but as a defensive strategy of organisms against parasites. The individual alleles of MHC antigens specifically bind different peptides (Fig. VIII.9). Because every individual in the population has different MHC alleles, it recognizes the foreignness of the parasite proteins according to different sections of their aminoacid chain. Thus, the parasite cannot mutate the sequence of its proteins in a manner that would allow it to successfully attack all the individuals in the host population. The evenness of the frequency of the individual alleles of the MHC genes is apparently ensured by a frequency-dependent selection mechanism. If the frequency of certain alleles increases in the population, the individuals in the parasite population that mutated in that area of their proteins that was originally specifically bonded to the MHC-antigen coded by the particular frequent allele begin to have a selection advantage in the parasite population. Thus, individuals that, through mutations, have removed, from their proteins, sites capable of binding to the commonest MHC-antigen and that can thus not be recognized by the immune system of the host begin, in time, to predominate in the parasite population. Consequently, the parasite will multiply most successfully in individuals bearing the commonest MHC-allele.As a result, these individuals will be affected most and their frequency and the frequency of the relevant allele will decrease.
In many species, including man, the maintenance of polymorphism in MHC genes is also strengthened with different mechanisms, by assortative reproduction.For example the fertility of partners with different MHC alleles is in average higher than that the partners with higher representation of same MHC alleles in genotype.It is partly caused by higher frequency of abortion of embryos homozygous in one or more genes of MHC .
For a long time, immunologists discussed the question of whether the polymorphism of MHC-antigens is maintained in the population through the action of frequency-dependent selection or through the action of selection for heterozygotes. At the present time, it tends to be accepted that frequency-dependent selection plays the main role .The usual argument is that, if selection for heterozygotes were the main factor, it would be much more advantageous for the organism to increase the number of loci for MHC-antigens and thus the number of various kinds of MHC-antigens located on the surface of one cell, than to increase the number of alleles in a constant, not very large number of loci.However, the problem is somewhat more complicated (Takahata 1995). The number of various molecules of MHC-antigens on a single cell may, in actual fact, be limited from above by the necessity of eliminating all the T-cells that recognize an organism’s own peptide capable of binding one of its own MHC-molecules, during development of the lymphocytes in the thymus.Individuals with a large number of variants of MHC-molecules on the surface of their cells could thus have a substantially reduced range of T-cells and thus much worse immunity. Although it is more advantageous for the population as a whole to exhibit the greatest possible polymorphism of MHC molecules, there is a certain optimal number of MHC-alleles for individuals that, when exceeded, would lead to substantial reduction in the range of T-cells and thus to reduction in the ability to recognize the presence of foreign agents in the organism.It is apparently more advantageous for individuals to bear the less common variants of MHC-antigens than to bear the greatest number of these variants, i.e. to be heterozygote in the greatest possible number of loci.However, this once again indicates that polymorphism in MHC-antigens will tend to be a consequence of the action of frequency-dependent selection rather than selection for heterozygotes.
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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.
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Some metapopulations consist of local populations persisting in a given location in the long-term or relocating as a whole within the geographic range of the species. Individual populations exchange migrants but their gene pools exhibit long-term continuity in time. Other metapopulations, to the contrary, experience population turnover, i.e. a permanent emergence and disappearance of local populations (i.e. subpopulations). For example, species that sustain themselves on temporary sources of nutrients (such as rotting fruit, carrion) or whose range is linked to intermittent successive stages of some biotopes (forest openings, puddles) create local populations existing for only a more or less limited and transient period of time in a given location and then disappearing. In the meantime, new locations suitable for the creation and existence of local populations appear in other parts of the range of the given species and some of these locations are eventually actually colonized by representatives of the species. However, it is the migrants that colonize new locations. The way in which new populations are established, namely the genetic composition of the founding population, determines whether population turnover will further intensify or, to the contrary, will weaken the process of maintaining the genetic polymorphism of the local populations by gene flow (Fig. VII.3). If the founders of a new local population come from a small number of populations or just one single population, population turnover leads to a relative decrease in the genetic polymorphism within the local populations. On the other hand, if the founders come from a large number of local populations, genetic polymorphism of the local populations in a metapopulation with higher population turnover could even be augmented. However, the size and genetic uniformity of the founding population does not in any way affect the overall amount of genetic polymorphism in the metapopulation, but only changes its distribution. Although populations with large genetic polymorphism of the founders’ population exhibit greater founding population polymorphism, the genetic differences between the local populations are actually smaller (Harrison & Hastings 1996).
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see Lamarckian microevolution in organisms without Weismann barrier
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Preadaptations are biological structures or patterns of behaviour that developed in a different selection context than that in which they later became advantageous. A great many biological structures or patterns of behaviour were formed as a consequence of completely different selection pressures than would follow from their contemporary biological functions and, in some cases, the reason for the formation of the original structure was not selection at all. In this case, evolutionary biologists speak about the formation of the relevant structures on the basis of already existing preadaptation and the relevant traits are mostly not termed adaptation but rather exaptation. For example, The wings of insects apparently developed from structures that originally served the processes of respiration or, according to another theory, for thermoregulation, and thus they emerged and were formed over a long time through the action of selective pressures following from this original function.
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– see Parasites
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see Extinctions types
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Presumed negative impact of evolution theory on people’s ethical attitudes
- Another motive that is employed by some opponents of the theory of evolution is the potential opinion that general acceptance of the conclusions following from the theory of evolution would unfavorably or even detrimentally affect the behavior of people in society. I am personally of the opinion that this motive is not currently very common; nonetheless, in contrast to the previous motive, it makes sense to discuss the matter with the proponents of these opinions.
The best known case of an attack motivated in this sense occurred in the 1920’s in Tennessee in the U.S.A. and was led by the lawyer and politician William Jennings Bryan. He first substantially helped his case by assisting in the passing of a law in that State that prohibited at all public schools “teaching of any theory that would deny divine creation as taught in the Bible and, instead of this, state that man evolved from lower animals”. In 1925 he also acted as a witness in the “ape process”, in which teacher John Scopes was sentenced to a fine for breaching this law. The process itself formed the basis for the well-known film Inherit the Wind. The film depicts Bryan as a reactionary and dullard who thoroughly made a fool of himself in the process and, in contrast, Scopes as a “martyr to truth and freedom of expression”, who was finally sentenced to a fine because of the existence of a stupid law. However, the actual facts were somewhat different. To begin with, Scopes, who taught mathematics, physics and chemistry and probably never taught the theory of evolution, volunteered for the process on the basis of an advertisement published in a newspaper by the opponents of this anti-evolutionary law. On the other hand, Bryan, three times candidate for the office of President of the U.S.A., Secretary of State in one government, important congressman and personal friend of a number of famous personages and state officials in the U.S.A. and around the world, was a widely recognized humanist and simultaneously a politician who promoted progressive movements and progressive laws throughout his life. The reason for his battle against the teaching of the theory of evolution in public schools most certainly lay in his conviction that teaching students evolutionary biology would most certainly turn them into atheists which would, in itself, have a negative impact on their morality and behavior in their future lives and would also encourage attitudes that, at the very least, would be in conflict with generally accepted ethics. In the former case, he based his opinions on statistical data that showed that, when entering secondary school, only 15% of boys believed in biblical creation and that, after graduation, this percentage increased to 40%. (A scientist would probably tend to ask to what degree this conviction increased in a control set of secondary school students who did not become acquainted with the theory of evolution during their studies.) In the second case, at that time, he didn’t have to search far for arguments stating that the theory of evolution promoted unethical attitudes and unethical behavior. Opinions that the theory of evolution teaches us that the strong have the right or even obligation to suppress the weak to avoid general degeneration of human beings, that altruism or compassion are unnatural and thus, in fact, detrimental, were very popular in some circles and this “social Darwinism” formed the ideological basis for the Prussian militarism and the ideological roots of the then-recent First World War. In the U.S.A., similar to a great many countries of Europe, state-supported eugenic programs were under way, intended to prevent entrance into the country of “biologically less valuable individuals” or to prevent such persons from reproducing. For example, tens of thousands or even hundreds of thousands of people with lower IQ values or developmental defects were subjected to compulsory sterilization in a great many countries, or were at least isolated from the rest of the population in special facilities. This mass practice basically ended when it was “perfected” and thus finally discredited in the eyes of the public by Hitler. However, it continued quietly behind the scenes in a number of countries even after the Second World War. Thus, it is not surprising that it was Bryan who did not want to accept this situation and attempted to eliminate what he though was its cause, teaching the theory of evolution at public schools.
The mistake made by Bryan and a great many others after him was apparently that they concentrated, not on combating social Darwinism, but on combating evolutionary teaching as a whole. In contrast to caricatures of evolutionary theory inspired by various social Darwinists, serious evolutionary theory certainly does not provide any basis for violation of ethical standards. At a professional level, it demonstrates, amongst other things, that, in a great many situations, cooperation or even altruism is evolutionarily more advantageous than selfishness or fighting competitors (see the chapter concerned with evolutionarily stable strategies, inter-allele selection, group selection and evolutionary behavior – IV.8.2, IV.9.1, XVI.4.1, XVI.5.3). It also very clearly demonstrates that any sort of eugenic program directed towards improvement of the human race must necessarily be hopelessly ineffective and predestined to failure in advance (see the sections concerned with selection against recessive or polygenic traits, the pleiotropic effects of genes or evolution in polymorphic populations – IV.9.2, XXVI.5.3). However, it then follows that, paradoxically, the greatest danger for society was not and is not represented by teaching the theory of evolution, but rather by its insufficient and unqualified teaching. However, something else is far more important. It cannot be in the least doubted that any theory of evolution, with any conclusions whatsoever, cannot justify unethical human behavior. Decisions on what is morally acceptable and what is not cannot be made on the basis of analogies with processes occurring in nature, but only on ethical grounds. Simultaneously, the actual ethical system can be based on various grounds; for some people, it can follow from Kant's categorical imperative, while for others religion forms the basis. However, the argument that a particular type of behavior is right because it is “natural” or because our animal ancestors behaved in this way exhibits a complete lack of logic. If evolutionary biology is capable of helping us in deciding questions of morality and ethics, then only in that it shows that our behavior must be subjected to the rules of ethics as understood by reasoning, and not our natural instincts. These instincts are frequently the result of individual natural selection and can thus be contradictory to the principles of ethics and sometimes even to the long-term biological interests of the individual, society or even the human species (XVI.6). If this seems somehow reminiscent of Christian teaching about original sin, then this need not be purely accidental....
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Prevalence of infection
– see superinfection and virulence
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History of evolutionism – post-neo-Darwinist period
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Principle of anchoring from above
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See Epigenetic information.
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– see Scientific nomenclature
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In a particular setting of the pay-off matrix, specifically in cases when betraying the cooperating opponent brings the greatest profit, mutual cooperation brings a lower profit, mutual betrayal an even lower profit and betrayal on the part of the betrayed brings the greatest loss and, at the same time, the total reward sum for one-sided betrayal for both participants is smaller than double the reward for mutual cooperation, the players get into situation called the prisoner’s dilemma. The prisoner’s dilemma game comes in several variants; one of them may be described as follows: Two prisoners got caught after they committed a serious crime together. There is no direct evidence against them, so if they will cooperate, meaning that they will deny the accusation, nobody will be able to prove they are guilty of committing a major crime. They will only be accused of committing a minor crime, e.g. having possession of a stolen object, and given a relatively mild sentence, like three years in prison. Each prisoner is now in his cell and gets the following offer. If he will own up first and accuse his accomplice of being the major culprit of the crime, he will get an even milder sentence, e.g. one year in prison. If he continues to deny his guilt, while the other prisoner, who got the same offer, pleads guilty first, he will get many years’ imprisonment. If both prisoners betray their accomplice, each gets five years in prison. Most works analyze the game where the reward for mutual cooperation is 3 points, for mutual betrayal 1 point and for one-sided betrayal the traitor gets 5 points and the betrayed 0 points. Mathematical analysis of this situation shows that, under the given conditions, it is most advantageous for any prisoner to betray his accomplice to avoid risk of being the second to come up with this solution. The course of a majority of actual processes shows that, to find the only right strategy, most prisoners do not need to know the mathematical apparatus of game theory.
Of course, a situation more or less analogous to the prisoner’s dilemma is also encountered in nature. An individual sometimes gets into a situation when it has to decide among betrayal that can bring either great profit or minor loss, cooperation that can bring average profit if the partner will also cooperate, and great loss if the partner betrays it. In a situation when the partners are not going to meet in the future or the organisms are not able to recognize or remember their ex-opponents, they are most likely to choose the strategy to always betray.
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- see Infrapopulation of parasites
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The emergence of living systems and thus the origin of life are the subject of an independent field of science that is only partly related to evolutionary biology, protobiology. This discipline is faced with two basic question areas. It should tell us how the basic building stones of living organisms were formed, i.e. simple chemical substances of the aminoacid and nucleotide type. These substances are currently formed under terrestrial conditions primarily through the activities of organisms; however, prior to the origin of life, they must necessarily have been formed by some other, abiotic route. Biological evolution must apparently have been preceded by rather complicated chemical evolution, during which the action of various abiotic factors led to the formation and accumulation in the environment of some simple and more complicated organic substances. In the laboratory, it has been possible to copy some of the conditions that could have prevailed on the Earth at the time prior to the origin of life and, under these conditions, scientists have been able to achieve the formation of almost all the important building blocks of present-day biological macromolecules (Fig. X.1).
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Some authors include pseudoextinctions amongst extinctions (Fig. XXII.1). This term is used to designate the disappearance of a certain species from the paleontological record as a consequence of its gradual transformation into another species. The average phenotype of the members of a certain species gradually changed over time so that, after a certain time, it differed from the original phenotype to such a degree that paleotaxonomists begin to consider it to be a separate new species. Species delimited in this way are sometimes termed chronospecies. Basically, during pseudoextinction, the original species did not actually die out in the true sense of the word, but was only transformed into new species. In most taxa, true pseudoextinction is a rather rare phenomenon (see the sections concerned with punctuated evolution). Nonetheless, its existence must be taken into account. A considerable number of pseudoextinctions reflect the tendency of paleontologists to call a single species occurring in subsequent paleontological zones by different names. Completely different laws govern pseudoextinction than those of real extinctions and it will not be further considered in this chapter. See alo Speciation branching
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Pull of the present
see Fossils age of
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see Extinctions types
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Punctuated equilibrium theory
Darwin repeatedly emphasized that evolution (i.e. anagenesis) is basically gradualist, and progresses alternately at greater and lesser rates through the accumulation of minor evolutionary changes. On the basis of these theoretical principles, evolutionary biologists long assumed that most evolutionary changes could occur at any time during the existence of the species, i.e. that anagenesis should not be bound to cladogenesis within the individual phylogenetic lines. Where it seems on the basis of the paleontological record that anagenetic changes occur in sudden jumps, that a new species with fully developed traits appeared instantaneously in the record and that there were no transition forms between it and its predecessor, then this is only a consequence of the imperfectness of the paleontological record, in which the transition forms were not preserved from the key period of the greatest anagenetic changes. It was only in 1972 that N. Eldredge and S. J. Gould pointed out that the absence of transition forms between the individual species is a practically universal phenomenon that cannot be explained by imperfectness of the paleontological record and lack of data (Eldredge & Gould 1972). They contrasted the gradualist concept of evolution with the nongradualist – punctualist concept (Fig. XXVI.8) and demonstrated that the available paleontological data tends to confirm that evolution occurs in the vast majority of cases in a punctualist manner, i.e. the species was formed very rapidly, acquired its characteristic phenotype and then practically did not change throughout the rest of its existence. Like every new theory, this theory of discontinuous progress of anagenesis, mostly termed the punctuated equilibrium theory, encountered considerable skepticism amongst evolutionary biologists and paleontologists. Data was repeatedly collected to test the theory. At the present time, it seems that, in cases where sufficient data is available, these data tend mostly to correspond to the punctualist model. New species appear in the paleontological record completely developed during a period of the order of 10,000 years and then do not change throughout their existence, which is usually 100 – 1000 times longer. They either force out the parent species or coexist for a long time with them until their extinction. The greatest amount of empirical evidence for the punctuated character of evolution is available for marine invertebrates as the best (most numerous and most complete) paleontological data is available for them; this is also confirmed by the available data relating to marine and terrestrial vertebrates (Benton & Pearson 2001). In contrast, the available data related to Foraminifera tend to support the gradualist character of their evolution.
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