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Macroevolution

- Evolutionary processes occurring above the level of a species are mostly designated as macroevolutionary processes. The action of macroevolutionary processes leads to the formation and development of higher taxa. Similarly as mutations are a source of new evolutionary features at a microevolutionary level, the individual speciations are a source of new features at a macroevolutionary level. The long-term fate of a new macroevolutionary feature, a new species, is determined by the ratio of the rate with which its and its daughter species undergo speciation and the rate at which they die out – are subject to extinction. The members of various taxa frequently differ substantially in their phenotypes. There are especially important differences in the adaptive traits that provide access to ecological niches that are not available for other taxa. For example, the existence of the photosynthetic apparatus of the plant type allows the organism to utilize carbon dioxide, water and solar radiation for synthesis of organic substances and thus to occupy ecological habitats in which there are no sources of organic substances. Study of the formation and development of new adaptive traits forms the main content of microevolutionary theory. The adaptivity (usefulness) of a trait is apparently the decisive criterion that affects the probability of whether a certain new evolutionary feature becomes fixed in the species or disappears. However, at a macroevolutionary level, aspects connected with the probability of speciation and extinctiontend to be more important. Adaptive traits are important for the course of macroevolution only if they negatively or positively affect the probability of one of these two processes. In a great many cases, a trait that is adaptive from the viewpoint of an individual is simultaneously advantageous from the viewpoint of survival of the species, as it reduces the probability of its extinction. In some cases, this need not be so and a particular trait may reduce the chances of survival of the species or higher taxon.

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more

Macromutations

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.

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more

Macroparasites

–see Infrapopulation of parasites

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Mafia effect

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).

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Major effect of the X-chromosome

see dominance hypothesis

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Malaria

see Sickle-cell anemia

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Males as cheap experimental material

Most of the males in the population can die without any detriment to the reproductive potential of the population. The relatively “cheap price” of male individuals allows males and females to divide some evolutionary roles between them. Females usually take on the function of a conservative agent, whose role lies in transferring tried-and-true traits acquired during evolution from one generation to the next, while males can act as cheap experimental material on which nature can “try out” evolutionary novelties.

            Experimental data related to various animal species indicate that the intraspecies variability of males is usually much greater than the intraspecies variability of females. Similar differences also exist in the death rates as a consequence of congenital deformities in embryos and adult individuals of the male and female sex. This phenomenon can be caused by epigenetic mechanisms valid during ontogenesis. However, in most cases, experimental results have unambiguously demonstrated that a greater number of mutations occur in males than in females. It has, for example, been found that, of 33 new mutations in the gene responsible for the formation of retinoblastoma, 31 were located on the chromosomes derived from fathers and only 2 on chromosomes derived from mothers (Kato et al. 1994). The actual mechanism causing elevated frequency of mutations in males is currently not known; however, this could be connected with the increased number of cell divisions occurring in the formation of male sex cells compared to the number of divisions occurring during the formation of female sex cells (Chang & Li 1995; Drost & Lee 1995; Lessells 1997). However, it can also be imagined that the male organism can, for example, turn off some processes of DNA reparation in the germinal line (Huttley et al. 2000).

 

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more

Manipulation hypothesis

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).

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Manipulation hypothesis of origin of sex

Intuition suggests that only structures and mechanisms that represent some kind of selection advantage for their carriers can emerge in evolution (an advantage for the individual, for the population or for the particular species). However, this impression is erroneous. There are a number of situations in which organisms exhibit properties that are clearly detrimental for their carriers, providing an advantage for someone else at his expense. This fact forms the basis for hypotheses about the emergence of sexual reproduction as a manifestation of a selfish gene or as a manifestation of a parasite (Hickey 1993; Bell 1993).

            The idea that one of the most obvious (and most pleasant) patterns of behaviour of contemporary organisms, sexual reproduction, could be a manifestation of the activity of a selfish gene or even a parasite is somewhat surprising. However, the unusualness of an idea is not an argument for or against the validity of a scientific hypothesis.s

During the evolution of any genome, genes could most probably be formed that would cause that their carriers exchanged genetic material with other organisms. While other genes were capable of spreading in the population only vertically in asexually reproducing organisms, i.e. from parents to offspring, through DNA replication, these mutated genes could also spread horizontally, i.e. from one individual to another (Hickey 1993; Bell 1993). One of the ways consists in transfer of a cytoplasmatic genetic agent, plasmid or virus with the relevant gene at the moment of physical contact of two cells. For example, during ciliate conjugation during exchange of nuclei between protozoa, the transfer of an infectious agent can occur very easily. A further type of horizontal spreading of a gene programming sexual reproduction is based on transfer of the gene from one chromosome to another within a single zygote by, for example gene conversion accompanying crossing-overs. The ability to force cells to reproduce sexually and thus create a precondition for horizontal spreading in the population is certainly advantageous for such a gene. It is thus probable that genes with this ability will be evolutionarily very successful and will be readily fixed by natural selection. It simultaneously makes no difference to the gene whether the actual process of sexual reproduction is or is not selectionally advantageous for the particular organism. Genes act selfishly; those that program their carriers so that they are themselves spread most effectively in the population are successful in evolution.

The F-plasmid of bacteria can serve as a prototype for such emergence of a sexual process. This plasmid contains genes encoding the formation of a sex pilus, through which bacteria containing an F-plasmid attach to another bacterial cell and the genes ensure transfer of a copy of the F-plasmid by this pilus to the cells of the recipient. Because the plasmid is capable of integrating into the bacterial DNA or is capable of integrating part of this DNA into itself, it can cause the transfer of bacterial genes during its transfer from cell to cell. Thus, it can be considered to be an adaptive structure that facilitates sexual reproduction for the bacterial cell. Similarly, however, the F-plasmid can be considered to be an infectious agent, a kind of bacteriophage, that has learned not to damage its host cell and that “doesn’t want anything else” than its own reproduction and spreading in the bacterial population. Integration into the bacterial DNA and transfer of bacterial genes thus can constitute only secondary improvement of the effectiveness of the process of plasmid reproduction. A plasmid that integrates into itself, for example, a gene for resistance to antibiotics (R-plasmid) or that is capable of being useful for the bacterial cell in some other way is, of course, at a substantial selection advantage compared to the original F-plasmid.

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more

Mass extinction

see Extinctions types

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more

Mass extinction, after the end of mass extinction events

In the typical case, a mass extinction event is accompanied by a substantial reduction in biodiversity, very frequently not only on a local, but also on a global scale. The individual ecosystems degrade substantially and only a few species remain, which were originally rare before the mass extinction event but subsequently relatively abundant. For example, the beginning of the Mesozoic was characterized by an enormous expansion of stromatolites, while the beginning of the Tertiary witnessed an enormous increase in Foraminifera of the Guembelitria group (Erwin 1998). Many of these species tend to be characterized by small body dimensions – this phenomenon has been described as the Lilliputian phenomenon. These pioneer species are apparently capable of utilizing the degraded environment effectively but are not capable of surviving in competition with other species under normal conditions. Thus, they are a sort of macro-evolutionary analogy of ecological r-strategists. However, in contrast to r-strategists, they apparently did not adapt evolutionarily to the conditions prevailing after mass extinction, but their adaptation, to be more exact exaptation, occurred accidentally or as preadaptation through the action of different selection pressures.
            Over a longer period of time, some of the original species that avoided extinction in locally limited refuges reappear in ecosystems. Of course, some species completely die out and completely disappear from the paleontological record. Some species reappear in the biotope only after a very long time, during which the paleontological record did not contain any traces of them. These species are termed Lazarian species. In contrast to Lazarus of the Bible, we do not know who and why they were called back to life; however, the results of radioactive dating indicate that the personal intervention of Jesus Christ can most certainly be excluded. Cases of “living fossils”, i.e. evolutionarily ancient species or lines that are known in recent fauna and flora and that simultaneously did not occur for long periods of time in the paleontological record, nonetheless indicate that, in some cases species (to be more exact evolutionary lines of subsequent species) can survive tens or even hundreds of million years in geographically or ecologically narrowly defined refuges without leaving any traces in the fossil record.  
            A less fortunate category of species consists in those that also survived a mass extinction, but then died without any successors after its end, usually at the time when the original biodiversity was renewed (Jablonski 2001). These need not be only individual species, but can even correspond to whole higher taxa which, in addition, could have undergone speciation at the normal rate before the beginning of the mass extinction. This is a quite common and striking phenomenon and has been termed “dead clade walking” by paleontologists, an analogy of the 1995 film Dead Man Walking (Jablonski 2002). Once again, it is not apparent why species or higher taxa that prospered in the period prior to a mass extinction and were capable of even surviving through the mass extinction finally succumbed without successors in the subsequent period. It is quite possible that this mass extinction was survived only by those species that were relatively resistant compared to the other species in the taxon but, for some reason, had a reduced rate of speciation.

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more

Mass extinctions impacts on the course of macroevolutionary processes

 

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)

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more

Mass extinctions ecological and taxonomic specificity of

The individual periods of mass extinction also differ in their degree of specificity, i.e. range of species that are primarily affected. Taxonomic specificity is generally rather low. The members of various developmental lines that live in a similar environment and have similar ecological requirements tend to be affected to the same degree (Raup 1994) (Fig. XXII.7). Nonetheless, it seems that, at least in some cases, a certain taxonomic specificity is manifested For example, mass extinction at the boundary between the Mesozoic and Tertiary affected mainly dinosaurs on the continents, while mammals crossed this boundary with substantially smaller losses. A study performed on 117 North American genera of mammals, reptiles, amphibians and fish demonstrated that 43% of genera became extinct at the end of the Cretaceous. Simultaneously, however, all 22 genera of dinosaurs became extinct, while only 8 of 24 genera of mammals died out. Similarly, only 4 of 12 genera of amphibians became extinct (Raup 1994).
Ecological specificity is usually somewhat greater. Certain communities of organisms were especially affected during some periods of mass extinction, for example communities of marine or, on the other hand, terrestrial ecosystems (Benton 1995). In some cases, on the basis of affecting of the individual types of organisms, it was possible to estimate what was the immediate cause of extinction of organisms in a particular period.

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more

Mass extinctions periodicity

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).

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Mass extionction causes

The irregular occurrence of natural catastrophes of various intensities and various geographic extents is a highly probable cause of a substantial number of the episodes of mass extinction. A natural catastrophe is considered to correspond to a change in the environment to which the local organisms are not evolutionarily adapted and that occurs so suddenly or is so radical that the organisms are not capable of evolutionarily adapting to the new conditions. The catastrophe can be of biotic or abiotic origin. In the former case, the cause of the catastrophe could lie in the arrival of a foreign invasive species that uses up or destroys the resources of the local species, or the disappearance of a key species whose presence is essential for the maintenance and proper functioning of the local ecosystems. In the latter case, the cause in the catastrophe could lie in a permanent increase in the water level and flooding of terrestrial ecosystems or a decrease in the water level, destroying the species-rich ecosystems of the continental shelf (Hallam 1989; Raup 1986), a decrease in the oxygen content in a global ocean (Isozaki 1997; Rampino 1996), the eruption of a volcano or the impact of a large cosmic body accompanied by mechanical and thermal destruction of ecosystems, frequently over an extensive area (Renne et al. 1995; Alvarez et al. 1984).
A number of other theoretically possible causes for mass extinction have also been proposed, for example a sudden increase in radioactivity or electromagnetic radiation, caused either by the explosion of a supernova close to the solar system (Ellis & Schramm 1995), or the temporary disappearance of the Earth’s magnetic field that, under normal conditions, blocks the action of cosmic radiation in the surface of the Earth (Loper, McCartney, & Buzyna 1988; Raup 1985). Mass extinctions were apparently connected with the complete or almost complete freezing of the surface of the global oceans to a depth of possibly one kilometer, which most probably occurred at least twice in the Late Precambrian (850 – 590 million years ago) and apparently several times in the Early and Middle Precambrian (the Snowball Earth hypothesis) (Hoffman et al. 1998). The reason for the freezing of the Earth was apparently primarily a slight decrease in the intensity of solar radiation and the secondary existence of positive feedback consisting in greater reflectance of radiation from the frozen surface. No fossils remain from the period of the frozen Earth that would help us to evaluate the effect of this phenomenon on biodiversity; however, the results of physical measurements confirm that almost all photosynthesis disappeared at that time and only bacteria and some anaerobic protozoa could live in the anoxic environment under the ice. However, the results of molecular phylogenetics indicate that the Metazoic divergence is apparently older and it is thus very probable that a suitable refuge must have existed somewhere even in the periods of the frozen Earth, allowing some of the species to survive and to expand to the rest of the territory after melting of the oceans (Runnegar 2000; Hyde et al. 2000)
            In general, it is necessary to recall that the individual causes of mass extinction are not mutually exclusive but, to the contrary, direct causal connections could exist between them. The impact of a cosmic body can initiate flood volcanism, volcanism can (in fact must) cause changes in the atmosphere and subsequently in the climate, changes in the climate can cause both a variation in the sea level and glaciation, where glaciation can subsequently lead to a decrease in the oxygen content in the ocean. Thus, the immediate cause of extinction can be an entirely different phenomenon than that which originally caused the catastrophe.

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Maupertuis

see History of evolutionism - pre-Darwinist period

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Maximum parsimony principle in phylogenetics

If the relevant paleontological data are not available or do not permit us to draw unambiguous conclusions and if approaches based on comparison of the ontogeneses of the given forms of the trait similarly fail, we can attempt to differentiate homology and homoplasy on the basis of the maximum parsimony principle. The maximum parsimony principle as employed in phylogenetics states that that the most probable course of cladogenesis is the one that can explain the distribution of the individual forms of traits within the phylogenetic tree through the smallest number of anagenetic changes, i.e. smallest number of transitions from one form of the trait to another. Thus, in looking for the maximally parsimonious tree (Fig. XXIII.5), first all the conceivable trees are created for the studied species, on which the studied species form only the terminal branches, where the form of the trait carried is drawn in next to each species. For all the hypothetical ancestors, i.e. for the inner branches of the tree, the most probable forms of the individual traits are also estimated. The most probable combination of forms of traits for the hypothetical ancestor is then chosen so that the total number of evolutionary changes cable of explaining the distribution of traits in the real studied specie sis as small as possible. If, for example, sister species 1 and 2 carry the trait in form A, then it will be assumed that this form of the trait was also carried by their common ancestor. For each created tree, the number of evolutionary changes in all the traits required to explain the distribution of the individual forms of the traits in the studied species and the tree with the smallest number of necessary changes, i.e. the maximally parsimonious tree, will be considered to be the most probable scheme of cladogenesis for the given phylogenetic line. For a small number of species and small number of traits, the maximally parsimonious tree can be sought for “manually”; however, in the vast majority of cases, a sufficiently powerful computer must be used to solve this task.
            The topology of the resultant tree corresponds to the distribution of most of the traits, i.e. minimizes the overall number of changes in all the traits together, but is usually in contradiction with the distribution of some traits. Traits whose distribution corresponds to the topology are probably homologies. On the other hand, traits whose distribution is contrary to this topology, i.e. traits whose distribution would best suit some other topology, are most probably homoplasies.
            In reconstruction of cladogenesis on the basis of the maximum parsimony principle, we simultaneously form hypotheses about phylogenesis on the basis of hypotheses as to what is a homoplasy and what is a homology and formulate hypotheses on division of traits into homologies and homoplasies on the basis of our hypothesis about the phylogeny of a particular taxon. Thus, there is a danger that, while the created hypotheses will be compatible, both the differentiation of homologies and the reconstruction of phylogenesis will be erroneous. If the obtained phylogram assumes substantially fewer evolutionary changes than the phylograms of other topologies, it is highly probable that it is correct. If the differences between phylograms are not very great in this aspect, it is not possible to rely on the obtained results and it is necessary to obtain new data or use a different method for their processing.
 

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Maynard Smith

History of evolutionism – post-neo-Darwinist period

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Mayr

see History of evolutionism - neo-Darwinist period

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Meme

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.

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Meme competition

The individual variants of genes (alleles) compete together in biological evolution as to which
will be successfully transmitted to further generations. In cultural evolution, the individual meme variants compete similarly. However, in this case, the competition is not limited only to transmission to the next generation, but also includes effective spreading within a single generation. The meme that is copied (imitated) most often by the members of the population or the members of other species will be most successful. There are various reasons why some memes are imitated more frequently than other memes. Frequently, those memes that are advantageous for their host, bring it some benefit, are copied. However, this is far from being the only reason. Some memes spread because they are easier to copy than other memes, and others because their carriers frequently have a dominant position in the group and the behavior of dominant individuals is usually preferentially copied (Benskin et al. 2002)(Fig. XVII.6). Some memes preferentially spread because they enforce their spreading by some specific mechanisms. For example, the meme for destruction of heathens, either through physical liquidation or conversion to the faith will probably spread faster than the meme for religious tolerance. Analogously, the meme prohibiting the believers of some religions to use contraception will also be successful (Kirk et al. 2001). In the latter case, the effectiveness of the spreading of the particular religion is ensured by cooperation between memes and genes. The carriers of the relevant meme have more children than the carrier of other memes and these children will, with great probability, also inherit the relevant meme from their parents.s

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Meme pool

see meme

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Memes origin of new

The Darwinian model of biological evolution is characterized by the fact that new useful phenotype traits, to be more precise new alleles, which determine their formation, are formed only by random mutations during evolution. In contrast, an important feature of cultural evolution is that a new meme variant can also be formed as a consequence of targeted, i.e. the purposefully directed activities of an individual.
Ethological experiments on a number of animals have unambiguously demonstrated that individuals faced with a problem, for example the necessity of reaching food that is too high to reach, begin to purposefully look for a suitable way of resolving the particular problem. Simultaneously, they need not progress only by the method of trial and error, but can combine previous experience in dealing with a similar situation. Although the method of trial and error is, for many species, a basic method of creating a great many useful patterns of behavior, the members of some species can employ insight in such a situation. For example, if an experimental chimpanzee could not reach a banana that was suspended high up and was also not even able to knock it down with a stick or by throwing various objects at it, it thought the problem over and, after some time, moved a box under the banana, climbed up on it and picked the banana (Lorenz et al. 1974). Once a successful solution has been found to the particular problem, this is very frequently preferentially adopted by the other animals in the population. Thus, cultural evolution can take place, not only by the mechanism of Darwinian evolution, but also by the mechanism of Lamarkian evolution, i.e. preferential emergence of useful (adaptive) memes and preferential inheritance of just these useful memes.

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Memes spreading of

- 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.

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Memes spreading of thouse reducing fitness

Some memes can spread very effectively even though they are disadvantageous for their bearers. The meme for smoking spreads in spite of the fact that smoking demonstrably shortens life expectancy and worsens the health of its bearer and persons living in his vicinity, i.e. most frequently his biological relatives, and thus reduces his inclusive fitness (Kunzle et al. 2003; Munafo et al. 2002). The success of the meme for smoking is not only a result of its physiological addiction and the fact that it is imitated by adolescents as a symbol or maturity (and the maintenance of the smoking habit in adulthood is then ensured by the already-mentioned addiction). Smoking, similar to the consumption of chocolate or hard drugs, is pleasant for the individual, at least initially or at the time of consumption. The memes that an individual will attempt to adopt are decided, not by the degree to which they increase or decrease his fitness but by the degree to which they increase his feeling of pleasure or reduce feelings of stress (see XV.2). Even such obviously disadvantageous behavior as suicide, or behavior disadvantageous for its bearer but advantageous for his surroundings, such as some patterns of altruistic behavior, tends to be imitated. Because cultural evolution occurs incomparably faster than biological evolution, there is very little hope that selection against genes that are biologically disadvantageous, i.e. genes determining that biologically disadvantageous behavior will be perceived as unpleasant, could make a species immune to spreading of the particular disadvantageous memes. For example, it cannot be expected that the bad habit of smoking or over-eating sweets would, in time, be reduced by natural selection in that the individuals that find these bad habits pleasant would gradually disappear from the population because they would produce fewer offspring on an average.
            In general, the same rules apply to the spreading of memes as to the spreading of infectious diseases and the relevant processes can also be described by the same formal models (Anderson 1993). The most important parameter that determines the efficiency with which a meme will spread is its basic reproduction constant R0, a dimensionless constant equal to the average number of individuals “infected” by the relevant meme by one bearer of the particular meme in the “naive” population, i.e. a population whose members had not previously encountered the meme. If this constant is larger than 1, the given gene can spread in the population and be retained in it for a long time, even if it is harmful to its bearers, i.e. if it reduces their fitness. The actual reproduction constant, R, in a population in which a certain fraction of individuals, q, was “infected” by the meme in the past, is understandably lower and decreases linearly with increasing fraction of infected individuals. If R decreases to a value of 1, the fraction of infected individuals remains constant in the population and the particular meme is retained endemically in the population. Each meme is differently “infectious” and each has a different threshold intensity, NT, i.e. number of susceptible individuals, at which it can begin to spread in the population. A simple equation exists between the threshold density and R0 
 
      (1)
 
where N is the size of the population. If “meme infection” has occurred in the population, the value of R0 can be calculated from the fraction of individuals that remained unaffected by the meme (s), as it holds that
 
     (2)
 
On the basis of R0 we can then easily calculate the size of the fraction of persons in the population that it would be required to make immune to the particular meme through an effective campaign so that this meme would not be able to spread by horizontal transmission.
 
   (3)
 
If, for example, a certain meme affects an average of 70% of individuals during its natural horizontal spreading in the population, then it would be necessary to “immunize” 41% of the so-far unaffected population in advance to prevent a future meme epidemic. Because the fraction of immunized persons gradually decreases in a natural way after the end of the epidemic, either through the deaths of immune individuals or forgetting, some meme epidemics can have a regular cyclic character, where the periodicity of the cycle will depend on the size of the population.
            Some other interesting laws, which have already been described for classical epidemiology, also govern the spreading of memes (Ewald 1994), see also the chapter XIX.5. Memes (similar to parasites) transmitted exclusively or predominantly vertically, i.e. from parents to children, generally do not harm their bearers, as their successful spreading is closely connected with the fitness of their bearers. In contrast, memes that can spread horizontally can be far more harmful for their bearers. This is especially true of memes that are not transmitted horizontally by direct personal contact between neighbors, but tend to be transmitted over long distances, in the modern world, for example, through the press and television, and are simultaneously not bound to a particular culture, so that they can spread transculturally. Especially harmful memes can spread in populations whose members have a reduced life expectancy for some reason, for example as a result of a war, poor nutrition or diseases. The positive feedback effect can also be important here, where the spreading of the harmful meme reduces the life expectancy of the members of the population, enabling effective spreading of even more harmful memes. The gradual reduction in the occurrence of all possible forms of individual or mass aggression during the second half of the 20th century can be most readily explained as a side effect of the prolonged life expectancy of human beings. The longer this life expectancy, either as a consequence of improved hygiene or advances in medicine, the greater are the penalties for memes that might be successful in the short run, but harm their bearers in the longer term.
The harmfulness of memes is further increased by the possibility of “superinfection”, i.e. increased probability of simultaneous infection of a single person by several memes. If this possibility is negligibly small, an advantage is usually given to those memes that allow their hosts to live as long as possible, so that they are capable of “infecting” a large number of other individuals in the population. However if, during infection by one meme, there is a danger of infection by another meme, even memes that harm their bearers very rapidly can be successful, for example the meme for use of hard drugs. Mutability of memes acts similarly to superinfection. From this point of view, for example, religious systems based on canonized texts will probably be less harmful to their adherents than the religious systems of various sects. Population growth is a factor that can promote the spreading of dangerous memes; memes that are beneficial for their bearers tend to spread in populations with stable sizes or those that are diminishing in size.s

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Memes spreding by enhancing fitness and reducing quality of life

- 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.

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Memes vertically transmitted

A number of memes are transmitted in the population entirely or primarily from parents to offspring, i.e. via the same direction pathway as genes. As a consequence, together with the successful meme, i.e. with a meme that increases the inclusive fitness of its bearer, the genes that the bearers of the particular gene have in their genome can also spread in the population. However, this can happen only if the bearers of the relevant meme do not reproduce with individuals that do not carry the particular meme. This is generally a rather difficult condition to fulfill, so that ideally this situation can probably occur only for the spreading of the already mentioned meme for killing heathens. However, for a certain structure of the population and means of transmitting memes and genes, the progress of biological evolution can also be affected by cultural evolution when the bearers of the various memes reproduce together. In studies of the genetic polymorphism in four types of cetaceans, it was, for example, found that the mitochondrial DNA of each of the species is practically identical in the entire area (Whitehead 1998; Whitehead 1999).  Similar to most other species of animals, here also the mitochondrial DNA is inherited only from the mother and is practically not subject to genetic recombination. From the viewpoint of population structure, these were matrilinear species in all cases, i.e. species in which the offspring remain in the original herd, while adult males visit other herds for short periods for the purpose of mating. As a result of this type of population structure, memes will also be inherited in the same way as mitochondrial DNA, i.e. down the maternal line. It is known that very intense cultural evolution occurs in cetaceans and the individual herds differ substantially, for example, in the means of obtaining food; the members of a single species catch completely different food in various areas and use very different hunting techniques (Rendell & Whitehead 2001). In some cases, vary rapid spreading of a new pattern of behavior has been observed, for example new hunting techniques within the entire area of occurrence of a particular species (Fig. XVII.7). The authors of the relevant molecular biological studies assume that the  particular mitochondrial DNA variant spreads together with the spreading of the biologically successful meme, i.e. the meme increasing the fitness of its bearer, and that it finally replaced all the other variants in the gene pool of the species.

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Memetic drives

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).

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Mendel

see History of evolutionism - neo-Darwinist period

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Mendel’s genetic laws

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 19th 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.

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Meoitic drive

Meiosis is a process that should theoretically ensure that homologous chromosomes from the original diploid chromosome set of maternal cells enter the haploid chromosome set of sex cells entirely at random regardless of the alleles that the individual chromosomes contain. However, in actual fact, this is frequently not true and the structure and gene content of the individual chromosomes frequently affect which of the pair of homologous chromosomes finally ends up in the sex cells and which does not. The process of differential transfer of genes to the sex cells through differential transfer of the individual chromosomes is called meoitic drive (Zimmering, Sandler, & Nicoletti 1970; Prout, Bundgaard, & Bryant 1973; Thomson & Feldman 1974).In most cases, meoitic drive occurs during meiosis; however, in some cases, the relevant processes already occur during mitosis, which precedes meiosis or, to the contrary, follows it. To the present day, a number of processes that lead to the origin of meiotic drive have been described.

Meiotic drive occurs very frequently in egg formation. During this process, only one haploid set of chromosomes ends up in the nucleus of the female gamete, while the remaining three sets are eliminated into the polar bodies. In heterozygote females, it very frequently occurs that the probability with which a certain allele will end up in the nucleus of the oocyte or in the polar body, i.e. the probability with which the allele will be transferred to the next generation, differ considerably (Fig. VI.10). (Crow 1979). In some cases a certain allele of a specific gene is proliferated in this way in the population while, in a different case, this can be a certain chromosome mutation (Ruvinsky 1995). If, for example, a laboratory mouse is crossed with a wild house mouse, whose karyotype contains a metacentric chromosome formed through Robertson translocation, i.e. fusion of two acrocentric chromosomes, it has been observed in five cases out of ten that the metacentric chromosome occurs in less than 50% of the progeny of heterozygote females. In some cases, the ratio of the two types of oocyte was as much as 3:1. The authors assumed that the metacentric chromosome would most probably end up in the primary polar body. In another study, monitoring the behaviour of a metacentric chromosome in a population of wild mice, it was observed, on the other hand, that the metacentric chromosome had the greatest probability of ending up in the nucleus of the oocyte (King 1993).

Similar phenomena were also observed for other organisms. For example, it has been observed in sorrel (Rumex acetosa) that only four of nine randomly selected chromosome mutations of the reciprocal translocation type or mutations externally manifested as a shift in centromers exhibited normal Mendelian heredity. In the remaining five, meoitic drive appeared to some degree, in the female or the male plants.

DNA sequencing in the area of the centromere (the site of attachment of microtubules of meiotic spindle and therefore probably an important battlefield for meiotic distorters) in closely related species indicated that these areas are subject to very rapid evolution. It is highly probable that this is the result of a battle between genetic elements proliferating through meoitic drive. According to some authors, a significant part of the DNA in the area around the centromere is formed of these active or inactive elements – meiotic distorters. The predominance of nonsynonymous mutations in the histones that are bonded to the DNA in the area of the centromere, is interpreted in a similar way (a battle between meiotic distorters).Meiotic drive occurs very frequently in egg formation. During this process, only one haploid set of chromosomes ends up in the nucleus of the female gamete, while the remaining three sets are eliminated into the polar bodies. In heterozygote females, it very frequently occurs that the probability with which a certain allele will end up in the nucleus of the oocyte or in the polar body, i.e. the probability with which the allele will be transferred to the next generation, differ considerably (Fig. VI.10). (Crow 1979). In some cases a certain allele of a specific gene is proliferated in this way in the population while, in a different case, this can be a certain chromosome mutation (Ruvinsky 1995). If, for example, a laboratory mouse is crossed with a wild house mouse, whose karyotype contains a metacentric chromosome formed through Robertson translocation, i.e. fusion of two acrocentric chromosomes, it has been observed in five cases out of ten that the metacentric chromosome occurs in less than 50% of the progeny of heterozygote females. In some cases, the ratio of the two types of oocyte was as much as 3:1. The authors assumed that the metacentric chromosome would most probably end up in the primary polar body. In another study, monitoring the behaviour of a metacentric chromosome in a population of wild mice, it was observed, on the other hand, that the metacentric chromosome had the greatest probability of ending up in the nucleus of the oocyte (King 1993).

Similar phenomena were also observed for other organisms. For example, it has been observed in sorrel (Rumex acetosa) that only four of nine randomly selected chromosome mutations of the reciprocal translocation type or mutations externally manifested as a shift in centromers exhibited normal Mendelian heredity. In the remaining five, meoitic drive appeared to some degree, in the female or the male plants.

DNA sequencing in the area of the centromere (the site of attachment of microtubules of meiotic spindle and therefore probably an important battlefield for meiotic distorters) in closely related species indicated that these areas are subject to very rapid evolution. It is highly probable that this is the result of a battle between genetic elements proliferating through meoitic drive. According to some authors, a significant part of the DNA in the area around the centromere is formed of these active or inactive elements – meiotic distorters. The predominance of nonsynonymous mutations in the histones that are bonded to the DNA in the area of the centromere, is interpreted in a similar way (a battle between meiotic distorters).

Another way in which an allele can spread through meoitic drive consists in programming the chromosome that carries the alternative allele to destroy or damage the gamete in which it will end up after the completion of meoisis. This mechanism occurs, e.g. in known systems in the fruit fly Drosophila melanogaster (segregation distortion, SD-systém) and in the house mouse Mus musculus (t-haplotype) (Carvalho & Vaz 1999; Ardlie 1998; Vanboven et al. 1996) (Fig. IV.11). In both cases, meiotic drive occurs during sperm formation and, in both cases, this leads to a smaller number of viable sperm in the ejaculate of a heterozygote male and, in both cases, most of the viable sperm contain the allele that causes this effect. Simultaneously, the destruction of the sex cells containing the normal allele is an active process from the standpoint of the normal allele. If the relevant chromosome does not contain the normal allele in the relevant locus because of deletion, the sperm is not destroyed. This means that the allele responsible for meiotic drive somehow manages to reprogram the normal allele so that, after completion of cell division, it actively damages the spermatid or sperm, in which the nucleus is located. However, it is a certain simplification to speak of an allele in this case; in actual fact, the relevant “allele” consists of a combination of several genes in closely adjacent loci.

The mechanism of meiosis should ensure, amongst other things, that the members of a heterogamete sex will produce the same number of gametes with two different sets of sex chromosomes and thus the ratio of males and females in their progeny will equal 1:1. However, for a number of species, populations are known in which the ratio of males and females differs substantially from the theoretical ratio of 1:1. In some cases, meiotic drive is responsible for this deviation (Carvalho & Vaz 1999). Alleles proliferating in the gene pool through the action of this mechanism are denoted as SRD (sex ratio distorters). For example, in the mosquito Aedes aegypti, gene D (distorter), whose active allele causes decomposition of the X-chromosomes in future sperm, is located on the Y-chromosome close to gene M, i.e. the gene that determines male sex. Males with active allele D thus produce far fewer viable sperm, and most of them contain a Y-chromosome and thus lead to the formation of males. The SRD system on the X-chromosome of several species of drosophila acts similarly, but in the opposite direction.

The distortion of the sex ratio in favour of males (Aedes) or in favour of females (Drosophila) can, of course, seriously affect the existence of the population. According to some authors, in many species this process can substantially affect the behaviour of the entire meta-population, specifically the rate of formation and disappearance of local subpopulations (Carvalho & Vaz 1999).

Large evolutionary plasticity and the great variety of genetic sex-determining mechanisms is currently explained by the existence of the selection pressure of the SRD-allele, specifically the necessity from time to time of formation of substitute mechanisms capable of compensating the distorted sex ratio that occurs with proliferation of certain SRD alleles (Werren & Beukeboom 1998).

 

It has been estimated that more than 90% of speciation events are accompanied by the formation of a modified karyotype in a daughter species (White 1978). It is probable that, in the case of allopatric speciation, meiotic drive is responsible for this phenomenon or, to be more exact, the fact that the karyotype of the species changes much faster through the effect of meiotic drive than new species are formed. Speciation events only conserve differences in the gene pool of the two populations existing at the given instant and simultaneously create a barrier capable of preventing spreading of chromosome mutations from one population to another. Thus, the karyotypes of two daughter species can diverge. As this divergence occurs through the effect of relatively fast meiotic drive, divergence of karyotypes occurs faster than divergence of phenotypes, which change through the action of the slower processes of genetic drift and selection.

However, in the case of sympatric speciation, it is assumed that meiotic drive could sometimes participate directly in the creation of species barriers and that it could thus actively contribute to the origin of new species. If Robertsonian translocations gradually spread from various areas in the  area occupied by a given species, this entire area can disintegrate into a number of separate areas, where individuals of a different chromosomal race will live in each of them. The boundaries between these areas can be very sharp, especially if two races are next to one another, whose karyotypes contain two different Robertsonian translocations, in which the same acrocentric chromosome, as one of the pair of fused chromosomes, is present (see Fig. XXI.12). Because of the common branch, the two different metacentric chromosomes participate in creation of a chromosome tetrade during meiosis in  hybrids between the two races. Subsequently, disorders occur in the transfer of the chromosomes to the fields of the meiotic spindle and a substantial percentage of nonfunctional gametes is formed. In species in which more intense sperm competition occurs, because the female is often rapidly fertilized by several males in succession, the amount and quality of the sperm in the ejaculate or spermatheca decide the paternity of the individual embryos to a substantial degree. In this case, the heterozygote sons of a male that penetrated into the area of occurrence of a different chromosomal race have substantially reduced biological fitness. This can form a relatively effective barrier against spreading of metacentric chromosomes from the area of one chromosome race into the area of another. Because of the existence of crossing-over, such a barrier need not prevent the flux of the individual genes (or, to be more exact, alleles) between sympatric or parapatric (adjacent) populations of the two chromosome races.  However, reduced fertility of heterozygotes can create very strong selection pressure for the formation of specific recognition mechanisms, capable of preventing mutual crossing of the members of two different chromosome races. If the genes affecting this recognition occur in the area of chromosomes in which crossing-over does not occur for some reason, for example, in the inversion area, it is highly probable that meiotic drive will lead to the formation of two separate species.

Some authors (Ridley 2000)are of the opinion that meiotic drive is an extremely important evolution factor, where the effect of this factor on the average biological fitness of the members of the population is almost always negative. Meiotic drive could be manifested especially strongly in organisms in which crossing-over would not exist and in which alleles would thus not be mixed in pairs of homologous chromosomes. Competition of the individual chromosomes for the most effective spreading in the gene pool of the population through meiotic drive in these cases could generally predominate over competition between the individual alleles for the most effective transfer to further generations through the positive effect on the biological fitness of their bearers, i.e. over natural selection. Crossing-over, which breaks up alliances of alleles of individual chromosomes, is a very effective mechanism limiting the action of meiotic drive, and its development in evolution may even be a necessary condition for the existence of sexual reproduction based on meiosis and syngamy (Haig & Grafen 1991).

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Metagenesis

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.

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Metapopulations

Each species has a particular geographic range. Within that range, it exists in individual populations, some of which can be neighbours in terms of space while, on the other hand, others can be more or less isolated. Some populations are permanent, some gradually appear and disappear and some re-locate in space both in the long and in the short term, depending on how the natural conditions evolve in time. Members of these populations interact, including reproduction, mostly within their own population, less frequently with the members of the neighboring populations and least frequently with the members of the most distant populations. However, in many species, an even subtler structure can be discerned within each population, leading to the formation of subpopulations of individuals that are most likely to breed amongst themselves. These subpopulations are usually called demes. Thus, species tend to have a rather complex hierarchical structure, culminating in a metapopulation, i.e. the largest population unit whose members still share a common gene pool and can exchange genes with populations in their range via migrants, and a deme at the other end, whose adult members are most likely to breed amongst themselves. 

Metapopulations differ in both the intensity and the nature of migration occurring between their subpopulations. In some metapopulations, the likelihood of migrant exchange between two subpopulations does not depend on their relative distances, while in others migrants are exchanged primarily between neighboring subpopulations (Fig. VII.1). Migration sometimes occurs along a specific line, such as a coastline, or it can spread in two dimensions, together with the gene flow, covering an area. In the latter case, the rate at which, for example, a mutant allele spreads is substantially lower. Very frequently, one subpopulation produces a large number of migrants covering just a short distance, for example extending only to the neighboring subpopulations and, at the same time, a smaller number of migrants migrating over long distances. Theoretical analyses show that a quite small number of long-distance migrants is sufficient to bring the behaviour of a given system close to that of a system in which elements can interact over any distance. The large effect of a small number of long-distance migrants or a small number of individuals communicating with a large number of other individuals in the system is called the small-world network effect and the processes occurring in these systems are important, for example, in epidemiology (Lloyd & May 2001; Liljeros et al. 2001). Migration between subpopulations tends to be very asymmetrical; some populations produce many migrants, while others produce few but accept large numbers of foreign migrants. As migration often involves exclusively or at least primarily the members of just one sex or gamete (or gametophyte), such as pollen, the intensity of the gene flow on the autosomes, sex chromosomes and in the organelle DNA often varies. The nature of evolutionary processes is different in a metapopulation where the gene flow occurs between more or less permanent subpopulations and a metapopulation where subpopulations constantly disappear and the migrants themselves cause new ones to appear (see VII.8.2) (Shanahan 1998).

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Microparasites

see Infrapopulation of parasites

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Micropredators

see Parasites

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Microspheres

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.

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Migrants

In many species, the production of migrants is a costly investment that may not seem very efficient. Many migrants die without offspring, many reach locations that are less favourable in terms of chances for survival. Hamilton (Hamilton & May 1977; Comins, Hamilton, & May 1980) (Fig. VII.2) suggested reasons why many species nevertheless invest a large part of their reproduction potential into producing migrants.  By moving farther away from their parents, migrants reduce the chance of offspring competing with their own family. This situation is extremely beneficial from the point of view of individual inclusive fitness. Thus, an allele “programming” its bearer to produce primarily migrants will be preferred in interallelic competition over an allele reducing the number of migrants produced in favour of production of non-migrant offspring. Another advantage of investing in migrants lies in the fact that migrants have a non-zero chance of reaching an unoccupied location and also in the exponential rise of the newly established population producing more offspring in subsequent generations than the non-migrating individuals under the possibly better conditions in the territory of the parent sub-population, which, however, is already occupied by the species.   

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Migration

see Gene flow

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Mills of God model of origin of sexuality

One of the possible explanations of long-term survival of sexuality in the population is based on the same principle. The relevant model, which we will term the Mills of God model, was first described in detail by J. Maynard Smith (Maynard Smith 1993); however, he attributed authorship to M. Williams and G. Price. According to this model, the newly emerging parthenogenetic mutant originally has twice the fitness of its sexually reproducing competitor. However, wedging out the competitor took many dozens of generations in a large population. During this time, the traits of the members of the parthenogenetic clone did not change much, because the only source of its microevolutionary variability consists in rare mutations. In contrast, a population of sexually reproducing individuals permanently generates genetic variability and thus basically exhibits greater microevolutionary plasticity. Consequently, suitable adaptations are formed in time, allowing it to wedge out the parthenogenetic clone.

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Mimetism

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).

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Missense mutations

see Point mutations in the protein-encoding DNA

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Missing links

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

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Mitotic recombination

see Lamarckian microevolution in organisms without Weismann barrier

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Model bluebeard

seeSelfish gene theory

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Model of intralocus interallele selection

see Selfish gene theory

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Model of the dove and the hawk

see evolutionarily stable strategies

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Molecular clock

Part of neutral mutations is usually gradually fixed in the gene pool of a particular biological species through genetic drift. As the frequency of fixation of neutral mutations in time depends only on the mutation rate, of which it is assumed that it is roughly constant during phylogenesis for most organisms, it is possible for biologists to determine the time that has expired from the moment of divergence of two sister groups (taxa) from the common exclusive ancestor on the basis of the number of substitutions that occurred independently in the two lines from the moment of divergence. If we sequence a certain DNA section for two related species and determine the number of neutral mutations in which they differ, on the basis of a mathematical model that takes into account and eliminates the effect of possible repeated mutations in the same position, we can estimate how many fixation events occurred in the two species from the moment when they branched off from the common ancestor. If, in addition, we know the characteristic substitution rate for the given taxon and the given gene, i.e. the average number of mutations fixed for the given species per time interval, then we can calculate the time that has elapsed since the branching off of the relevant phylogenetic lines. Thus, fixation of neutral mutations can act as a molecular clock, permitting more or less exact dating of the individual events in phylogenesis or, to be more exact, the individual splitting events that occurred during the cladogenesis of the studied taxon.

            It is obvious that this substitution rate is frequently not known. However, in this case, we can calibrate the molecular clock on the basis of the number of evolutionary changes in which the two studied species differ from a third species for which we know the moment of divergence from the paleontological record (Fig. IX.6). If, for example, we know that the taxon including species A and B branched off from the taxon including species C at time T1 ago and, since that time, species A has collected KAC mutations in the studied gene and species B KBC mutations, where, since the time of splitting off of species A and B, i.e. over time T2, species A and B collected KAB mutations, we can calculate the time expired since divergence of species A and B according to the equation

 

T2 = (2KABT1) / (KAC + KBC)

 

If, on the other hand, we know the time that has expired since branching off of species A and B and we are interested in the time that has expired since the splitting off of these species from species C, we can use the equation

 

T1 =( KAC + KBC) T2 / 2KAB

 

Contemporary data and the current theory indicate that the rate of molecular evolution can increase substantially at the moment of speciation. Extensive studies performed on the representatives of a series of taxa have shown that the number of speciations can explain about 22% of the nucleotide substitutions in the DNA of two sister lines. In other words, the nucleotide divergence of two species does not depend only on the time that has elapsed since splitting of the two lines from the last common ancestor, but also on the number of speciations that the ancestors of the two species have undergone since that time (Pagel et al. 2006).  It is quite possible that acceleration of anagenesis in populations that underwent peripatric speciations (Flegr 2008) leads to fixation of many positive mutations by selection and a great many neutral and weakly detrimental mutations through the mechanism of genetic draft.

 

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Molecular drive

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).

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Molecular mimicry

see Host specificity

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Monophyly

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).

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Monophyly and Typological species

Most of the definitions of species require that the individual species be monophyletic, i.e. that they be formed in evolution through a unique speciation event. The definition of a typological species, at least in principle, does not entail this limiting requirement. A taxonomist usually considers that a separate species corresponds to a line of organisms that differ from other similar lines in an important phenotype trait. However, what an important phenotype trait consists in is often a matter of the subjective opinion of the scientist. Frequently, a quite inconspicuous trait is chosen, whose presence or absence has some sort of importance for humans. Amongst bacteria, this trait frequently consists in the ability to cause a certain disease or cause a certain symptom of a disease. As the genetic basis for such a trait in the individual lines of organisms need not be very complicated, its occurrence need not be correlated with the overall relatedness of these lines. For example, intestinal bacteria of the closely related species Escherichia coli, which exhibits pathogenic activity for humans, is frequently included under the bacterial genus Shigella. The genus was defined primarily on the basis of its pathogenicity; however, immobility and the inability to cause fermentation of glucose are used as diagnostic traits. In time, it was found that these traits need not always be correlated with the pathogenicity of these bacteria. Consequently, a great many pathogenic strains of Escherichia coli are now known. Molecular taxonomy studies later demonstrated that the genus Shigella is apparently polyphyletic and that its individual lines are variously scattered throughout the phylogenetic (more precisely genealogical) tree of the species E. coli (Pupo, Lan, & Reeves 2000) (Fig. XX.6).
While most modern definitions of species recognize only a monophyly as a species, i.e. a related line of the population derived from a single original parental population, it is almost certain that some biological species are formed polyphyletically, i.e. their members evolve several times independently within various populations. A typical example consists in botanical species formed by polyploidization of some existing diploid species (see XXI.5.2). Polyploid plants exhibit a different phenotype from their diploid ancestors and can also generally not cross with the original species because of differences in the number of chromosomes (however, some species of plants are capable of this across several ploidy levels (Petit, Bretagnolle, & Felber 1999)). However, they are usually capable of productively crossing with independently formed plants with the same ploidity level, i.e. with plants that have the same number of chromosomes. Tetraploids formed by duplication of the genome of a diploidal inter-species cross have relatively the greatest chance of full renewal of fertility. Their chromosomes will most probably not form an aberrant chromosomal arrangement containing tetrades during meiosis, but rather regular chromosomal arrangements containing twice the number of chromosomal pairs compared to the original diploidal species. It is apparent that some polyploids can be formed repeatedly within a species, and can successful reproduce together because of having the same number of chromosomes. As a consequence, they comply with the requirements of the definition of a biological species although, for example, they do not comply with the requirements of the definition of a phylogenetic species.

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Monothetic taxa

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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Morphological isolation

Reproductive isolation barriers internal

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Motives behind attacks on the theory of evolution

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.

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Muller's ratchet

see Stopping the Muller's ratchet hypothesis of advantage of sexuality 

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Müllerian mimicry

see Mimetism

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Mutation bias

Mutations are random changes in the sequence of nucleotides that occur mainly during replication or during repair of damaged nucleic acids, in most organisms in the double-helix DNA molecule. These mutations are random in direction and in the degree of their affect on the phenotype of the organism, however not in the sites of their occurrence or in their molecular nature, i.e. whether nucleotide substitution (insertion, deletion) or inversion of part of the DNA strand occurs. As we showed in Chapter III (Mutations), the type of mutation and the probability of its occurrence at a certain position in the nucleotide strand depend not only on the nucleotide that is present in the given position, but also on the nucleotides or sequence motifs that occur around this position. However, the types and frequency of mutations are also related to the mechanism of replication of the given DNA segment. Other mutations are formed in a continuously replicated strand (leading strand) and others in a discontinuously, through Okazaki fragments, replicated strand (lagging strand) (Lobry 1996). Mutation processes are also affected by whether the given segment is, or is not, transcribed and thus whether it is present in the cell temporarily in the single-strand or more or less permanently in the double-strand form, whether it is wound around the nucleosomes or whether it is located at a site between two neighbouring nucleosomes (Francino & Ochman 1997; Tillier & Collins 2000; Szczepanik et al. 2001; Holmquist 1994). 

The process of preferential formation of certain types of mutations in certain positions in the nucleotide strand is most frequently called mutation bias. In some works, this process is also called mutation pressure; nonetheless, this term should not be used in this sense, as it has long been used by geneticists and evolutionary biologists for another phenomenon that, however, occurs at the level of populations – the repeated formation of the same mutation in the population. As a large fraction of mutations occur during reparation processes, reparation drive is mostly recognized as an independent process.

It is highly probable that mutation bias and reparation drive and not, e.g., natural selection, genetic drift or genetic draft are responsible to a major degree for evolution of the overall structure of the genome, i.e. for its increase or decrease in size, changes in the content of GC pairs, formation of isochore structures and similar phenomena (Holmquist & Filipski 1994).

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Mutation rate

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.

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Mutationism

At the present time, mutation processes are considered to be a natural and essential part of Darwinistic evolution. However, at the beginning of the 20th century, this point of view was far from being a matter of fact and there was even a separate evolutionary theory, termed mutationism, which was considered by its proponents to be an alternative evolutionary theory that was incompatible with Darwinism. For example, when an orthodox mutationist explained the formation of wings in the ancestor of a certain clade of winged insect, he based his arguments on the concept that the members of the relevant clade of the wingless species produced winged mutants more rapidly than these mutants produced wingless individuals – revertants. Thus, winged individuals occurred in nature with increasing frequency until they completely predominated in the given clade.
Mutationists diminished the importance of natural selection and were willing to consider it to be, a most, a factor that removes unsuitable mutations. They overlooked the fact that, in the absence of this factor, they are not capable of explaining the most interesting phenomenon in biological evolution, i.e. the formation of adaptive traits, complicated yet useful structures and patterns of behaviour.

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Mutations

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.

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Mutations at the level of the entire chromosome set

Other categories of mutations, genome mutations, affect entire chromosomes or entire chromosome sets. In contrast to the previous types of mutations, these mutations are not formed as a consequence of irregularity in DNA replication or repairing, but as a consequence of irregularities and errors  in the progress of cellular division. As a consequence of these disorders, organisms can be formed in which a certain chromosome is multiplied or, on the other hand, is lacking (aneuploidy); in other cases, the entire chromosome series is multiplied (polyploidy). Depending on the number of specimens of a given chromosome occurring in the cell, this can correspond to nulisomics, disomics, trisomics, etc. On the basis of the number of chromosome sets, these are then haploid, triploid, tetraploid, etc. organisms. It was found in a study of human sperm that the frequency of diploid sperm varies around 0.2% and the frequency of haploid sperm with multiplication of one of the four monitored chromosomes varied from 0.1 to 0.17% (Miharu, Best, & Young 1994).

In most animals, the sex of the organism is determined by the gene dose and individuals with aberrant autosome ratios and sex chromosomes have transitory traits between males and females, i.e. are intersexes, and are mostly not capable of reproduction. Analogous disorders can occur for uneven gene doses at various chromosomes (cf. the Down syndrome in human beings, caused by trisomy of chromosome 21). Thus, these mutations are of only limited evolutionary importance for animals. However, the situation is very different, for example, for plants, in which the gene dose does not play a role in determining the sex and in which polyploidy thus generally does not have a detrimental effect on the viability or fertility of the mutant (Muller 1925).

A large proportion of these extensive genome restructurings cause partial or complete sterility in their bearers or at least form very effective interspecies barriers.However, polyploidization is simultaneously a mechanism that enables hybrid speciation.If two species cross, the zygotes cannot normally develop, because the gametes of the two species contain different sets of chromosomes.Thus, during cell division, they cannot form regular pairs of homologous chromosomes, so that the two chromosome sets divide unevenly into the daughter cells.As a consequence, most cells are not viable.However, if polyploidization occurs prior to hybridization, either autopolyploidization as a consequence of mitosis, which is not followed by cellular division, or alopolyploidization as a  consequence of fusion, e.g. of two diploid cells derived from two different  species in a single tetraploid cell or, more frequently, through a triploid intermediate stage (see XXI.5.3), the situation is substantially more favourable.If, for example, two tetraploid organisms cross together, their gametes already contain pairs of homologous chromosomes, so that a quite regular dividing spindles are formed during cell division and the chromosomes can be divided completely evenly amongst the daughter cells.Examples of hybrid speciation are encountered very frequently in some families of plants and also in animals with parthenogenetic reproduction, for example in some daphnia (Daphnia) (Dufresne & Hebert 1994).

 

 

Mutations at the level of the entire chromosomes – Translocationsof major extent can even be manifested in the structure of entire chromosomes.Simultaneously, classical cytogenetic methods can be employed to determine the occurrence of fusion or fission of chromosomes, i.e. processes entailing a change in the number of chromosomes in a chromosome set without a simultaneous change in the amount of DNA in the genome.A change in the number of chromosomes is not usually manifested in the phenotype of the organism, but often acts as a strong interspecies barrier.

Robertson transloctionis an interesting type of chromosome mutation in which one chromosome with a centromere in the vicinity of the centre (metacentric chromosome) is formed from two chromosomes with centromeres in the vicinity of the ends of the arms (metacentric chromosomes) (Fig. III.4).However, the altered karyotype contains one less chromosome, where the number of chromosomal arms does not change.There are a number of species, the best known of which are, e.g., the house mouse, in which the occurrence of local populations with one or more Robertson translocations is very common (Zima et al. 1990).It is very probable that meiotic drive is responsible for spreading of these chromosomal mutations (see VI.3.5) (Zimmering, Sandler, & Nicoletti 1970; Prout, Bundgaard, & Bryant 1973; Thomson & Feldman 1974), i.e. a phenomenon in which meiosis does not occur completely evenly and one of the pair of homologous chromosomes enters the sex cells preferentially.In case of polymorph populations, in which a certain chromosome with a Robertson translocation occurs and simultaneously two original unfused chromosomes are present in other individuals, it can readily happen that, in a heterozygote with two acrocentric and one metacentric chromosome, the metacentric chromosome will enter the sex cells with greater (in other species with lower) probability during meiosis (Gropp, Winking, & Redi 1982; Everett, Searle, & Wallace 1996).In this case, the particular type of chromosomes will spread in the population even under conditions when the heterozygotes will have reduced fertility compared to the original parent form because of the formation of part of the gametes with an incomplete (aneuploidal) chromosomal set – cf. the blue beard model (IV.9.1).

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Mutations at the level of the entire DNA section

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).

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Mutations directed

see environmentally directed mutations

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