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

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

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

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

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

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

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

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

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

see Point mutations in the protein-encoding DNA.

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

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

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

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

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

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

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

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

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