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

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

see Reproductive isolation postzygotic

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

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

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

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

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

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

.

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

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

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

.

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

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

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

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

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

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

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

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

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

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

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

see Sisyphean genotypes model of advantage of sexuality

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

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

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

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

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

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

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

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

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

Theory of neutral evolution

see History of evolutionism – classical Darwinist period

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

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

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

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