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

- The punctualist model of evolution has sometimes erroneously been confused with the models of saltationist evolution, i.e. models that assume the existence of typostrophic saltation – sudden instantaneous phenotype changes of major extent. According to saltationists, all important evolutionary changes occur in jumps, basically from one generation to the next. The mechanism of the relevant changes leading to the particular evolutionary jump mostly includes macromutation, a genetic change with major phenotype impact. For example, some mutations in the genes controlling the progress of the early stages of ontogenesis could be considered to be macromutations. This type of mutation, leading to the instantaneous formation of hopeful monsters, could be feasible in the emergence of biological diversity and especially disparities and could thus occur in the evolution of some large taxa that substantially differ in the basic organization of their body structure and thus in the formation of the individual strains. However, it could not be very important for the evolution of adaptive traits, as it is highly improbable that a random change of major extent could increase the functionality of a complicated organism. The vast majority of evolutionary changes occurred through the gradual accumulation of mutations with minor impact.
            However, the punctualist model of evolution, similar to the gradualist model, does not require the participation of sudden phenotype changes, saltations. The time during which evolution occurs according to punctualists is of the order of tens of thousands of years; this is a very short time on the scale employed by paleontologists; however, from the viewpoint of the usual rate of microevolution, this is quite adequate for the gradual accumulation of normal mutations to collect a sufficient number of anagenetic changes that would be quite sufficient for the formation of a new species. Thus, it is erroneous to confuse the punctualist model with the saltationist model.

see History of evolutionism – classical Darwinist period

The zygote, i.e. the cell formed by fusion of two parent gametes, bears two sets of chromosomes from the two parents. Random separation of chromosomes into the daughter cells occurs during nuclear division, mitosis and meiosis, so that each of these cells contains a unique genotype formed by mixing the chromosomes derived from the two parents. Simultaneously, the mechanism of nuclear division ensures that each of the cells obtains a complete set of chromosomes, i.e. one chromosome of each type of chromosome.

see Genetic draft

see Selection disruptive, stabilizing and directional

see Selectiondisruptive, stabilizing and directional

see Selection – the relationships between natural andsexual

The biological fitness of an individual is frequently determined, not only by his phenotype, but also by the phenotypes of the other members of the population. For example, in any form of soft selection, the chances of survival of an individual depend not on the absolute value of his traits, but on the degree to which and the direction in which his traits differ from the traits of an average member of the given population.

However, more complicated cases also frequently occur, where the fitness of an individual changes stepwise in dependence on the frequency of his allele in the remaining population, even under the conditions of hard selection.  An example is the situation in which a population of prey, exposed to the activities of a certain predator, finds itself. It is known that a predator will frequently select the commonest type of prey as a target in a particular environment (Amalraj & Das 1996; Allen 1988; Gotmark & Olsson 1997). If the prey occurs in two different colour forms, determined, e.g., by a pair of alleles, then the predator will always concentrate on the bearer of the more common allele. Thus, the frequency of this allele will decrease in the population as a consequence of “apostatic selection” (Allen, Raison, & Weale 1998)until the bearers of the alternative allele predominate in the population. Then, the predator will concentrate on the bearers of the alternative allele, so that the fitness of the individuals with the originally frequent allele (now rare) will suddenly increase.

Frequency-dependent selectionoccurs, e.g., in some types of sexual selection. In some species of organisms, the rare-male advantage phenomenon  is active. Here females mate preferentially with the bearers of rare traits, i.e. the bearers of rare alleles (Dernoncourt-Sterpin, Leichien, & Elens 1991; Depiereux et al. 1990). Because of the preference for these males, the frequency of the rare alleles increases and thus other alleles become rare, i.e. advantageous. On the other hand, in some species, females can prefer the bearers of the most frequent alleles; in this case, we once again speak of frequency-dependent selection; however the less frequent alleles then rapidly disappear from the population.

Frequency-dependent selection acting in favour of less frequent alleles is probably one of the most important mechanisms for long-term maintenance of polymorphism in the population (Antonovics & Ellstrand 1984; Elena & Lenski 1997; Benkman 1996). As this type of selection can occur not only within populations and within species, but is also a matter of interspecies competition (a predator can select the members of the commonest species), frequency-dependent selection can create the preconditions for the long-term co-existence of two various species at a single location.

Frequency-dependent selection occurs if the selection coefficient for an allele is not constant, but changes in dependence on the frequency of this allele in the population. If this type of allele is to maintain polymorphism in the population, it is necessary that the selection value of this allele increase with decreasing frequency of this allele in the population. Then, if this allele is rare in the population, the fitness of its bearers is high; if it is frequent, the fitness of its bearers is low. A typical example is the situation occurring in a species that is capable of using two different resources in the environment. Only one of the two alleles of a certain gene is advantageous for using each of the two resources. If there is a greater frequency of one of the alleles in the population, most individuals will preferentially use the given resource, this will be rapidly exhausted, the bearers of the allele will begin to starve and will reproduce more slowly and their frequency, i.e. the frequency of the relevant allele in the population, will decrease.

For example, this phenomenon has been described for predaceous cichlids (Perissodus microlepis) (Hori 1993). Fish of this species feed on the scales off the bodies of other fish. They are adapted to this means of obtaining nutrition, amongst other things, in that their jaws are asymmetrical. Without regard to the external conditions in the individual water reservoirs, they all contain the same numbers of cichlids with left-handed and right-handed asymmetry. Research has shown that right-handed asymmetric cichlids can effectively bite off the scales on the left-hand side of fish and vice-versa. If right-handed asymmetric individuals multiply excessively in the reservoir, other fish will be wary of danger coming from the left, so left-handed asymmetric cichlids will be more successful and will, as a result, multiply more rapidly.

The right-handed and left-handed curvature of the bills of crossbills (Loxiacurvirostra) is a somewhat less exotic example. Once again, the ratio of the two forms in a flock is frequently just 1:1 and here it is also assumed that frequency-dependent selection is responsible for maintaining this ratio.In this case, the curvature of the bill is related to the effectiveness of removing seeds from tree cones; one curvature can utilize only half the seeds from poorly accessible cones, while the beak with the opposite curvature can reach the other seeds (Benkman 1996). The crossbills with the less common form of beak will thus be able to obtain more food than crossbills with the more common form and will thus multiply faster.As a consequence, the ratio of the two forms reaches an equilibrium value of 1:1 in every population.

Another, in principle, similar case occurs when the size of the population of a certain organism is limited by the activities of a predator that is capable of differentiating between the individuals of the two phenotypes.It has been repeatedly demonstrated in experiments with various model organisms that some kinds of predators regularly select the more common type as their prey (Brockmann 2001). If there are two very different forms in the population of prey, e.g. two coloured forms of grove snails (Cepaea nemoralis), these kinds of predators (in this case, thrushes (Turdus), concentrate on the type that is momentarily more common (Brockmann 2001). The less frequent type is attacked less and its frequency in the population can increase. As soon as it predominates in the population, it attracts the attention of thrushes and the size of its population again decreases.

Similar phenomena of preference for individuals with a less common phenotype is frequently important in sexual selection, where the females of some species of birds, mammals and even insects mate preferentially with males of the less common phenotype (Singh & Sisodia 2000). However, this rare-male phenomenon occurs only in some species; in others, to the contrary, males with the more common phenotype are preferred (see XV.4.3).

We speak of hard selection if the selection removes from the population all the individuals whose critical biological parameter, i.e. property that is a measure of the success of the individual under the given conditions, does not attain certain limiting values. For example, all individuals whose body weight is less than 30 kg could be eliminated. In contrast, soft selection ignores the absolute values of a critical trait and eliminates from the population individuals that do not achieve a certain relative value of the given trait, e.g. it eliminates 25% of the smallest individuals in the population. Elimination of the slowest individuals in a herd of ungulates by predators could be an example of soft selection.

From the standpoint of microevolution, soft selection is apparently a more effective evolutionary factor than hard selection (Fig. IV.1). While a species can extricate itself from the effects of hard selection (for example, by increasing its bodily dimensions above a certain critical value), it cannot escape from soft selection; a constant percentage of individuals will be eliminated in every generation without regard to an increase in the mean value of the critical parameter. However, hard selection can be effective over prolonged period of time in a changing environment or in an environment whose properties oscillate in the medium-term. Similarly, from the standpoint of macroevolution, hard selection which, under certain circumstances, can lead to the extinction of a particular species, can apparently be of substantial importance.

The term natural selection is sometimes erroneously extended to include two completely different phenomena, intraspecies andinterspecies selection, also denoted(especially by ecologists) as interspecies competition. Another evolutionary mechanism – species selection – is based not on mutual ecological competition between the members of various species, but rather on the competition between entire evolutionary lines, and follows from the existence of differences in the rates of speciation and extinction of various taxons (Stanley 1975). This mechanism was first described relatively recently and will be discussed in part IV.8.4 and also in the part concerned with macroevolution (XXVI.3). All the phenomena described to date were related to intraspecies selection and Darwinism as a whole can, with certain simplifications, be understood as the theory of emergence and gradual development of modern organisms through the mechanism of intraspecies selection.

Intraspecies selection andinterspecies competition are two phenomena that are incomparable in their biological importance. While intraspecies selection is capable of gradually forming and improving various useful biological structures, organs, macromolecules and patterns of behaviour, interspecies competition functions only as a one-step process capable, in the final analysis, of  deciding which of the mutually competing species is better at the given time and place. Species with worse parameters mostly do not have a chance to evolutionarily adapt to the competition and are usually immediately eliminated on an evolutionary time scale.  If two competing species have only partly overlapping niches and only partly overlapping areas of occurrence, the weaker species need not be completely eliminated; however, there can be a drastic change in its niche and, because of interspecies competition, it can successfully survive only in certain, strictly limited types of biotopes or only in those parts of its original area of occurrence in which the other species is not present. Thus, it can gain time for the relevant evolutionary changes and could, in time, eventually expand back into its original biotope or to other parts of its original area of occurrence. However, in this case, the relevant evolutionary changes accumulate through the classical mechanism of intraspecies selection.

While intraspecies selection is apparently the most important factor in biological evolution, interspecies competition, similar, e.g., to genetic drift and sexual selection, is only an important factor in evolution, affecting some of its properties and determining some properties of the organisms. Its main importance apparently lies in “niche reduction”. The fact that each kind of organism is limited to only a relatively narrow niche forces it to specialize, to select only a specialized life strategy and to improve this strategy as much as possible through intraspecies selection If there were no interspecies competition, e.g. if only one kind of organism were to live on the Earth, this would probably be an unspecialized species, capable of living under various conditions and utilizing various resources. Its individual organs and life functions would probably not be as well adapted to the environment as those of contemporary, mostly highly specialized species. If the survival of a member of a certain species is dependent on how fast it can run, the evolution of the motor system will occur much more rapidly for this species (and will advance much further) than if its survival were determined by a number of various factors or even by chance.

Natural selectioncould theoretically occur even at higher levels than the population or species. Consequently, it is possible that entire flora and fauna communities could compete together or, on a cosmic scale, entire biospheres of various planets. Ecological data indicate that competition between communities does actually occur and sequences of succession stages have been described, which regularly alternate in a certain biotope. However, from the standpoint of evolutionary biology, competition at a higher level than intraspecies is a rare phenomenon. The main factor responsible for minimal effectiveness of selection at a community level consists in low heritability of the properties of communities. If selection actually occurs at the level of ecological communities, then everything that was said of group selection is also true here (to an elevated degree).

Natural selection is defined as the process of uneven transfer of alleles derived from particular individuals to the gene pool of the following generations through their progeny.This process can occur in a number of quite different ways, and thus it is possible to differentiate several basic types of natural selection and also their combinations.The individual types of selection can be studied from the standpoint of their impact on the course of evolution, i.e. on the speed and direction of changes that they cause in the gene pool of the population, and from the standpoint of the level at which the selection acts (alleles, individuals, populations, etc.).

One of basic preconditions for the functioning of natural selection is the existence of heritability of the properties of organisms (I.9). Over time, organisms can develop complicated adaptive structures and patterns of behaviour only if randomly formed mutations and phenotype manifestations of these mutations and their consequences for the biological fitness of the individual are transferred from the parent organisms to their progeny. This precondition is fulfilled for organisms reproducing asexually – an individual with a certain mutation produces progeny whose genome contains copies of the same mutation and, if further mutation does not occur in the progeny that would somehow change the manifestations of the original mutation, the phenotype manifestations of this mutation and their impact on the biological fitness of the individuals will be the same as for the parent organism. However, a very different situation occurs in organisms with sexual reproduction. In these organisms, the progeny do not receive a copy of the genome of their parents, but rather their zygote is formed with a unique genome through combination of the genes derived half from the mother and half from the father. Although the newly formed mutations are also transferred (with a probability of 50%) from the parents to the progeny, their impact on the phenotype and thus on the biological fitness of the individual is usually fundamentally different than for the parent organism. Compared to asexually reproducing organisms, sexually reproducing organisms have substantially limited heredity of phenotype properties as, because of epistatic interactions between the individual genes, the same allele in the context of various genomes can cause the formation of completely different phenotype traits. Similarly, they have substantially limited heritability of biological fitness as, in the context of certain phenotype traits, a single trait can increase the biological fitness of its bearers, while it can reduce it in the context of other traits. This means that a great many mutations cannot become fixed in the population because, while they can contribute to increasing the biological fitness in the genomes of some individuals, and are thus preferred by natural selection here, in the genomes of the progeny of these individuals they can, on the other hand, reduce their fitness and their frequency is then reduced by natural selection. The degree to which the heritability of properties in sexually reproducing organisms only reduces the effectiveness of the functioning of Darwinist evolution and the degree to which it prevents its functioning is a question that has not yet been resolved.

Attempts to come to terms with the problem of the apparent existence of biological evolution under the conditions of low heritability of traits and biological fitness in sexually reproducing organisms are exemplified in the theory of the selfish gene (Dawkins 1976)and thetheory of frozen plasticity (Flegr 1998).

Although the death rate and the rate of reproduction of organisms in time vary very irregularly and very strongly, from the long-term perspective, the sizes of the populations of the individual species remain constant. This long-term stability can be ensured only by the existence of some kind of negative feedback regulating the size of the population and compensating random effects of the varying intensities of reproduction and death. In principle, there can be only two types of this feedback and technical laboratory models exist for both types (Flegr 1997)(Fig. IV.3). The first of these, “top-down regulation”, can be modeled in the laboratory in continuous cultivation systems of the turbidostattype. In this system a sensor (mostly optical) monitors the size of the population and, when it increases, the instrument increases the flow of nutrient medium through the cultivation vessel and thus increases the rate of flushing organisms out of the vessel. Thus, an increase in the population increases the rate at which individuals are flushed out of the vessel, subsequently leading to reduction in the size of the population to the original value. In nature, negative feedback of the turbidostat type is functional for systems in which an increase in the population leads to an increase in the death rate of its members. This occurs, e.g., in populations in which the size of the population of prey is regulated by the activity of predators. An increase in the number of prey leads to an increase in the number of predators, leading to increased predation and thus to a decrease in the size of the population of prey (and subsequently to a decrease in the size of the population of predators). Similar negative feedback exists in systems in which the size of the population is regulated by the action of an infectious agent (a contagious disease, a parasite). In this case, the effectiveness of spreading of an infectious agent is frequently directly proportional to the number of contacts between members of the population and the frequency of these contacts is directly proportional to the density of the population of hosts or, to be more precise, to the square of the population density.

The second type of negative feedback, “bottom-up-regulation” is modelled in continuous cultivation systems of the chemostat type. In these systems, nutrient medium flows into the cultivation vessel at a constant rate. If the population increases, nutrients are consumed more rapidly from the medium, their concentration decreases, the organisms begin to suffer from a lack of nutrition and the rate of reproduction is reduced. Thus, the natural death rate predominates over the rate of reproduction and the size of the population begins to decrease, the consumption of nutrients also decreases and the rate of reproduction of the population increases again. In nature, this type of negative feedback occurs everywhere where the size of the population is limited (and regulated) by the amount of some resource. For example, the population of predators in the previous case is limited by the size of the population of prey; however, a population can be similarly limited by any scarce resource, such as the number of available hiding places. In case of regulation of the population by lack of hiding places, the “superfluous individuals” are finally eliminated by predators, but the primary reason for their superfluousness is that lack of a resource (hiding places) and thus the growth of the population are regulated by negative feedback of the chemostat type.

The type of negative feedback determines which of the parameters of the organism will decide on the success of the individual and thus which will be the subject of natural selection. It follows from theoretical analysis (Flegr 1997) that the maximum rate of reproduction is the critical parameter in systems of the turbidostat type, e.g., the number of glucose molecules that the organism is capable of converting to biomass per time unit in the presence of an excess of all resources. In contrast, in systems of the chemostat type, the critical parameter is the effectiveness of utilization of a limiting resource, thus, e.g., the number of ATP molecules that a given individual is capable of forming from one glucose molecule (Fig. IV.4). Recalling the properties of r-strategists and K-strategists in the previous part, it can be seen that the properties of r-strategists, i.e. greater rate of reproduction, shorter life cycle, greater number of not very fit progeny, poor ability to compete with other species in stabilized biotopes, can be interpreted as the result of selection for the maximum rate of reproduction under turbidostatic conditions, while the opposite properties of K-strategists can be interpreted as being a result of selection for maximum effectiveness utilizing a limiting resource. This means that the long-known existence of two distinct ecological strategies could be related to the existence of two, and only two, types of negative feedback capable of maintaining a constant size of the population.

 see selection negative

The model of r- and K-selection, also presented as the model of r- and K-strategy, was a popular concept of field ecology in their time (Pianka 1970). In nature, organisms with two fundamentally different life strategies can be encountered. One group of organisms prefers rapid reproduction. Its members are called r-strategists and the natural selection that they undergo is called r-selection. The second group tends to prefer the ability to compete with other organisms. The members of this group are called K-strategists and the relevant selection is called K-selection.

The ecology of r-strategists differs from that of K-strategists in a number of respects. Compared to K-strategists, they have shorter life cycles, greater maximum rate of reproduction, reproduce sooner, are usually smaller in size, frequently reproduce only once in their lifetime, and usually have a large number of progeny that, however, are not very viable and most of which do not even reach adulthood. The size of the populations of r-strategists tends to fluctuate in time and is mostly much smaller than would be permitted by the capacity of their environment, and thus within-species competition is very low. Death is usually caused by factors that do not differentiate amongst individuals according to genotype (random elimination, see below).r-Strategists occur particularly in a variable and unpredictable environment that is typical for the habitat in the early stages of succession. K-Strategists behave in the opposite way in all these respects.

The names of the two ecological strategies were chosen on the basis of the traditional designation of the constants in the logistic equation(Fig. IV.2), i.e. the equation describing the growth of a population in an environment capable of sustaining only a limited number of individuals:

where N denotes the number of individuals in the population, r is the rate of growth and K is the capacity of the environment, corresponding to the maximum number of individuals that the given environment is capable of sustaining. The logistic equation is fundamentally only a modification of the polynomial

where a = r, b = – r/K,i.e. an equation that successfully describes the shape of the growth curve (rapid, almost exponential growth at the beginning and slowing down or even stopping after a high population density is achieved); however, in fact, it has very little in common with the actual mechanisms of regulation in populations limited by the availability of nutrition.

The naming of the two types of natural selection according to the designation of the constants in the logistic equation is a very illustrative approach, but is rather unfortunate. To begin with, the logistic equation describes only a single, rather specific model of population growth, the specific case where the rate of reproduction is directly proportional to the size of the population and the death rate is directly proportional to the square of the size of the population – i.e., for example, population growth limited by a parasite transferred by direct contact. In addition, some authors noticed in the past that the existence of two types of natural selection does not follow from the logistic equation (Ginzburg 1992). We would expect that constant K would not play a role in a population of r-strategists and that the fitness of the organisms would be decided only by constant r, while the situation should be just the opposite in a population of K-strategists. However, in a population whose growth is described by the logistic equation, the fitness of an organism is affected to the same degree by constants r andK, so that there is only one strategy here, increasing r and/or K. Thus, although the concept of r- andK-strategies is one of the best known concepts in general ecology, the theoretical background of the relevant ecological phenomenon has so far been studied quite inadequately.

see Selection – the relationships between natural andsexual

see Selection hard and soft

see Selectiondisruptive, stabilizing and directional

Darwin introduced the expression natural selection as an analogy or rather as an antithesis of the term artificial selection,i.e. selection performed by humans. Later, it was found that natural selection consists of at least two components, of selection performed by the environment, i.e. environmental selection, and of selection that occurs through the competition of members of the same sex for partners for reproduction, i.e. sexual selection (Darwin 1909). However, Darwin did not explicitly introduce the term environmental selection as supplementary to the term sexual selection and used the expression natural selection in both a broader and a narrower sense.

This inadequacy in the professional terminology leads, for example, to frequent misunderstanding in relation to the position of sexual selection. One faction of biologists considers this to be part of natural selection, while another faction considers it, as Darwin did, to be the biological process itself, operating independently of environmental selection and acting in the same population, frequently in the opposite direction to environmental selection.  It is apparent that the proponents of the former concept understand natural selection in the broader sense of selection that is natural, not artificial, while the proponents of the latter concept understand it in a narrower sense, i.e. in the sense of selection performed by the environment (Flegr 1996b).

The category of natural selection can also include parental selection, i.e. selection performed by parents amongst their progeny. For example, it is assumed for altricial birds that the brightly coloured lining of their beaks and mouths emerged because parents preferentially fed young with the most obvious, i.e. most brightly coloured beak linings (Lyon, Eadie, & Hamilton 1994). With certain reservations the category of natural selection can also be considered to include subconscious selection performed by humans. It is quite possible, for example, that the phenotype of house cats (appearance, behaviour) was created through just this mechanism, through a form of unconscious domestication. People preferentially kept in their houses individuals that exhibited traits reminiscent of human young and that were also clean and affectionate.

see Genetic draft.

- The term selfish DNA, i.e. designation for DNA segments that proliferate in the gene pool through molecular drive, must not be confused with the similar, but totally unrelated, term selfish gene or the somewhat related term ultraselfish gene.The selfish gene is the central concept of Dawkin’s model of biological evolution (Dawkins 1976)This model, based on the theoretical work of W.D. Hamilton (Hamilton 1964a; Hamilton 1964b; Hamilton 1967), assumes that the objects of selection in evolution are not individuals, and certainly not populations or species, but only the alleles of the individual genes. From the viewpoint of this hypothesis, all genes are selfish or, to be more exact, all the alleles of all genes are selfish. Selfishness here means that every allele is “out for itself”. Only an allele that affects the properties of an organism so that it increases the probability that it will be replicated and transferred down to future generations more frequently that other alleles of the same gene can be successful in evolution. In most cases, a successful allele somehow increases the biological fitness of the individual in whose gene it is contained. Consequently, the selfishness of genes is not fully apparent at first glance. It might seem that alleles that bring an advantage to individuals are most successful in evolution.

An ultraselfish gene is a gene or, to be more exact, an allele that, in order to increase the probability of its proliferation in the gene pool of the species, reduces the biological fitness of its bearers (see, for example, the bluebeard model in Section IV.9.1).

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.

An individual receives signals from the environment through its sensory organs. This also applies to signals allowing the organism to obtain information on the presence or quality of a potential sexual partner. Any sensory organ has different sensitivity for various types of stimulation. For example, vision better differentiates certain colors or certain shapes and recognizes other colors and shapes less well. This kind of selective sensitivity of the sensory organs and related brain centers can be manifested in evolution as sensory drive (sensory bias, sensory exploitation) (Enquist & Arak 1993; Enquist & Arak 1994). Sensory drive can decide which traits will finally be fixed by sexual selection. If, for example, the vision of a pheasant is better capable of differentiating the horizontal than the vertical dimensions of an object, females will consider a male with long tail feathers to be a larger male than one that is actually larger, but has shorter tail feathers.
            In a number of species, individuals with symmetric patterns are preferred (Ridley 1992; Swaddle & Cuthill 1994) (Fig. XV.5). It has been found that even artificial neuron networks capable of learning are able to more readily identify symmetrical shapes than asymmetrical ones (Enquist & Arak 1994; Johnstone 1994). Females preferring males with symmetrical patterns are probably capable of identifying the presence of a male of their species at a much greater distance or under conditions of much worse visibility than females preferring asymmetric patterns.
            Even a very weak sensory drive can start a cycle of positive feedbacks that can lead, for example with contributions from the Fisher mechanism, to fixation of genes for preference for a certain trait and simultaneously fixation of the genes for the trait.

In species in which uniparental care for progeny is possible, r-strategy, mostly of males, the greatest possible promiscuity, copulation with the greatest possible number of females, is evolutionarily advantageous. In contrast, careful choice of the biological fathers of their offspring, i.e. copulation with the best male in the population, is more advantageous for K-strategists, mostly for females. However, this theoretical conclusion has been repeatedly thrown into doubt by the results of the observations of the behavior of organisms in captivity and in nature. It has been found in a number of species that, not only males, but also females copulate with a great many partners.

            The simplest explanation of this, at first glance illogical, behavior of females is that organisms do not subject their reproductive behavior to attempts to achieve the greatest possible fitness, but to attempts to gain a reward in the form of satisfying feelings of physiological pleasure. However, this explanation is apparently not sufficient. An individual can subject and probably does subject his behavior to this aspect, to what his/her nervous system feels to be pleasant; however, evolution makes the final decision. With a certain degree of exaggeration, we can say that we do not eat an apple because it is sweet but that we experience an apple as being sweet because it is evolutionarily advantageous to eat it. Like almost everything in biology, this principle is not one hundred percent valid. A smoker doesn’t enjoy a cigarette because it is evolutionarily advantageous to smoke, not to mention other types of addictive drugs.

            The above-mentioned arena hypothesis is a frequently mentioned hypothesis explaining the function of female promiscuity. This hypothesis assumes that a female copulates with a greater number of males to obtain sperm from various individuals in the population to create conditions for intergamete competition. Through copulation with a greater number of males, the female can insure herself against infertile males or against males with reduced fertility.

            There are a number of other hypotheses that attempt to explain the phenomenon of female promiscuity. In some species, it can be assumed that the sperm or other components of the ejaculate constitute not only a source of genetic material for the female, but also a source of energy for nourishment of the developing embryos or even for herself (Wedell 1994). In other species, it is assumed that the females ensure greater genetic diversity of their offspring in this way, reducing their mutual competition for resources (see the elbow room hypothesis, XIII.3.2.2.1) and also increasing the chance that an individual ideally adapted to the conditions of any particular micro-habitat will be present amongst the offspring (see the lottery model, XIII.3.2.2.2).

            Other models assume that, in species living in groups, it is advantageous for females if they prevent the males from finding out with certainty who is the biological father of the offspring. If the female copulated at least once with any male in the group, then no male can exclude that he is actually the biological father of any offspring and will thus not behave in an unfriendly manner towards the offspring. The phenomenon of concealed ovulation, which is encountered in many species of animals, and the ability of the female to manipulate the ejaculate inside her reproductive organs simultaneously allows the female to affect which of the copulating males finally becomes the biological father of the offspring (Pizzari & Birkhead 2000; Pizzari, Froman, & Birkhead 2002). In human beings, similar to other animals, these processes frequently occur to a major degree outside of the consciousness of the woman. However, experimental studies have shown that, in the fertile phase of the menstrual cycle, women prefer different types of short-term sexual partners (more dominant and masculine types) than in phases where conception is less probable (Penton-Voak & Perrett 2000; Penton-Voak et al. 1999). The results of studies performed on the students of the Prague Faculty of Science of Charles University also demonstrated that the smell of dominant males was preferred in the fertile phase only by women who had a long-term partner at the time of the experiment and who were thus probably unconsciously more interested in “good genes” than in a “good care-giver” for their offspring {12514}.

The greater probability of conception in cases of rape than during normal sexual intercourse could also be connected with concealed female choice at subconscious level (Starks & Blackie 2000). A study in the U.S.A. showed that, in a single year, 32,000 pregnancies resulted from rape, of which 38% of the women finally gave birth to their babies. The data indicated that the probability of conception following rape was 5%, compared to approx. 1.2% in normal sexual intercourse. Only 11.8% of the pregnancies ended in spontaneous abortion, compared to 13.8% of normal pregnancies. Because of the size of the data set, all the observed differences were statistically highly significant. 

            Female (and male) promiscuity is, however, sometimes explained in an entirely different way. This need not in any way be behavior advantageous for its bearer, the promiscuous female, but may consist in behavior controlled by a parasite and advantageous only for this parasite.

            Control of the behavior of a host by a parasite is apparently a very common phenomenon (see XIX.6.5). There are a great many parasites whose transmission from one host to another occurs at the moment of copulation or during behavior directly or indirectly connected with reproduction of the host species. Promiscuity could provide certain advantages for the host species; however, for the sexually transmitted parasite, it is the most important parameter influencing the effectiveness of its spreading in the population, thus a question of life and death. If a mutation occurs in a parasite that allows it to affect the nervous system of the host organism in a way so that it will behave in a more promiscuous manner, this will greatly increase the chance for the parasite that it will spread in the population horizontally from one individual to another. It is understandable that such a mutant very rapidly predominates in a population of parasites. A parasite can achieve the required result in various ways, either by direct intervention in the nervous system of the host or through its endocrine system, through production of suitable hormones or their analogues, or very indirectly, for example in that it causes itchiness of the sexual organs of its host (Dawkins 1976).

            The parasite need not be transmitted during the actual copulation. It is, at the very least, suspicious how frequently the mouths come into contact as part of the precopulation behavior of various species (mutual feeding, licking, kissing). In general, it can be stated that we kiss one another because it is pleasant. This undoubted fact is, however, uninteresting from an evolutionary standpoint. What requires an explanation is who and why programmed our nervous system so that kissing is pleasant. One of the surprising answers could be – a parasite.

Several key moments are important in the game for the laziest parent, which takes place between males and females in a great many species. The female attempts to delay the actual act of copulation for as long as possible, so that the male has already invested as much as possible at the beginning of reproduction. Simultaneously, she cannot postpone copulation disproportionately long, because the male could lose patience and could try to obtain a more compliant (and more permissive) female. Simultaneously, intrasexual competition takes place amongst the males in the population – the evolutionary game of “who’s dumbest”, i.e. a competition for the most patient suitor, “if not this one, then another one”, i.e. a competition for the most successful searcher for a permissive female, “for the dude”, i.e. a competition in willingness to risk invested precopulation efforts and, after achieving copulation, go on to the next house, and a great many more, at least as interesting games.

            A number of evolutionary games also take place within the population of females; I will leave their designation to the fantasy of the reader. Simultaneously, choice of suitable strategy is frequently even more complicated for females in that the choice of a suitable sexual partner must be subject to other criteria to a far greater degree than only the probability of immediate gain from the game as to who is the laziest. While the optimal (although not always evolutionarily stable) strategy of males lies in maximum quantity, i.e. in lack of selectivity in reproduction, females must rather favor the qualitative aspect. They can influence their probable reproductive success primarily through selection of the best sexual partner, i.e. the male with the greatest fitness. Thus, for a female it is not a simple matter to determine the criteria according to which she should chose a suitable male. The fitness of a male need not be in any way correlated with his willingness to contribute to care for his progeny. In most cases, we can probably expect negative correlation, following from the existence of evolutionarily advantageous conditional strategy. If you are beautiful  and strong, then play the game of “if not this one then another one”; if you are low on sex appeal, than you still have a chance in the game of “who’s dumbest” {11547}. Observations of swallows has shown that females prefer to copulate with individuals with long tail feathers, while these individuals provide the least paternal care for their offspring (Reynolds 1996).

             The sexy-son hypothesis refers to the situation where it is more advantageous for females to choose a sexual partner that does not care much for his offspring, but which is most attractive for other females on the basis of different criteria. The disadvantage that choice of such a male represents for bringing up one’s own young is compensated here by the fact that the sons inherit attractiveness from their fathers and have a greater chance of reproducing in the next generation.

Relatively strong barriers to adaptive evolution exist in unstructured populations. This is because, in order to modify the phenotype of organisms – a prerequisite for a change in the environmental niche – the population must often pass through intermediate stages during which the organisms are already less adapted to utilize the old niche but not yet perfectly adapted to utilize the new niche. Another major obstacle to a population’s adaptive response to selection pressure lies in the genetic architecture of the phenotype traits, namely in the fact that alleles that, in their dominant status or in combination with particular alleles in other loci, help to create a particular trait very frequently in their heterozygotous state or, in combination with other alleles in other loci, participate in the creation of a completely different trait. The shifting balance theory formulated by Sewal Wright (Wright 1931; Wright 1982) in the 1930’s assumes that adaptive traits that cannot be fixed in a large unstructured population can be more easily fixed in a large structured population, i.e. in a population consisting of a large number of genetically and environmentally partly isolated small populations (Fig. VII.5). Dividing the population into a series of relatively isolated partial populations will, amongst other things, change non-additive genetic variability into additive genetic variability (Wade & Goodnight 1998)(see also II.7) which can, indeed, serve as the material for directional selection. Wright believed that evolution of an adaptive trait in a structured population has, in a certain sense, three stages. During the first stage, genetic drift in some small populations causes a shift in allele frequencies in favour of alleles that, in a particular combination, can determine a useful phenotype. During the second stage, the relevant alleles, and thus the relevant phenotype, are fixed in some of these populations through natural selection. In the third stage, group selection through migrants infecting other populations or establishing new populations causes the relevant alleles to spread newly throughout the metapopulation until they finally become generally fixed. Gene flow plays a crucial role in all three stages. In the first and second stage, high-intensity gene flow reduces the likelihood of useful trait fixation; in the third stage, on the contrary, it increases this probability. The validity of this model has repeatedly been confirmed by a number of theoretical (Barton & Rouhani 1993, 12322)and empirical studies (Katz & Young 1975; Wade & Goodnight 1991). However, some studies (Schamber & Muir 2001)did not confirm the conclusions of Wright’s shifting balance theory quite as clearly and the theory is therefore still a subject of discussion (Coyne, Barton, & Turelli 1997; Coyne, Barton, & Turelli 2000). Its opponents mostly argue that the theory is too complex and that the rise of adaptive traits through directional selection can be explained by even the simplest model of Darwinian selection in a large unstructured population. Its advocates, on the other hand, respond by arguing that the simplicity or complexity of a theory cannot be the final criterion of its accuracy (Peck, Ellner, & Gould 2000)and that Wright’s theory can explain even the fixation of alleles that, according to the simple neo-Darwinian model of selection, should not become fixed in large unstructured populations. 

see Fossils age of

Only a sort of sequential evolution can occur in asexually reproducing organisms, i.e. gradual fixation of advantageous mutations in a single genealogical line (Fig. XIII.6). If several advantageous mutations occur at once in the population, the carriers of various mutations will compete. Only the most successful of them will, in the end, survive and its progeny will have to again “wait” for another mutation to occur, even though it already existed in the population in the past. In contrast, in sexually reproducing species, the evolution of various traits can occur in parallel and the individual mutations are selected simultaneously in various individuals (Fisher 1958; Muller 1932). Recombinants are formed sooner or later during sexual reproduction and at least some of them carry the advantageous mutation from both parents. If the positive effect of the mutations is additive, then these recombinants and their progeny are positively selected with greater effectiveness than the original parent line (Muller 1964). Mathematical models have shown that acceleration of evolution through this effect can be significant, especially in populations of medium size {12233}. However, in normal-size populations, evolution tends to be limited by the number of newly formed mutations rather than by their mutual competition. Thus, the advantage of parallel selection is much smaller here (Crow & Kimura 1965; Crow 1994). Another reduction in the effectiveness of this process (even in large populations) follows from the Hill-Robertson effect (Hill & Robertson 1966), i.e. a reduction in the effectiveness of selection occurring in favour of several alleles at the same time (see IV.2.1).

The Sir Sebright effect can also apply at the individual level to organisms without a Weismann barrier. Lysenkoists described experiments in which two plants cultivated by cloning from a single rhizome were crossed together. They stated that the progeny obtained are more viable when the two plants were grown under different conditions, e.g. one in dry and one in damp soil, than if they are grown under the same conditions (Turbin 1952, p. 138). It is quite possible that the Lysenkoists thought up this result, similar to a great many others. However, it is also possible that the Sir Sebright effect was manifested in their experiments, i.e. that intra-organism cell-line selection selected genetically different cell lines of the parent plants under different conditions and that genetically different germinal cells gradually formed from them. The combination of genetically different germinal cells subsequently led to the formation of more viable progeny than would have been formed by combination of genetically more similar germinal cells derived from plant clones kept under the same conditions. In addition to classical somatic mutations, the source of variability for intra-organism selection could, of course, also have been epigenetic changes (see II.8).

The spreading of phenotype variability in sexually reproducing species allows generation amongst progeny of Sisyphean genotypes (genetic elite), i.e. individuals that are so well adapted to current conditions that they produce far more progeny during their lives than other individuals in the population. G.C. Williams introduced the term Sisyphean genotypes for them; the original name, genetic elite, was introduced by T. Dobzhansky. Williams’ name is probably more appropriate, as it primarily emphasizes the fact that the emerging genotype of these individuals appeared only because of segregation and recombination and thus has minimal heritability and must be formed anew in subsequent generations (Williams 1975). Both authors assumed that extraordinarily biologically fit individuals, whose direct or indirect descendants will subsequently constitute most of the individuals in the population, occur with very low frequency in very large populations of sexually reproducing species. _s

            It is very probable that this mechanism can work only for species with extremely high reproduction potential, i.e. where one individual produces so many embryos that its progeny could, in the ideal case, i.e. if all the embryos lived to maturity, maintain the existing population size even if the other members of the population did not reproduce at all. Williams introduced the term non-Markovian species for such species. While, in Markovian species, the number of individuals in the population depends on the number in the given population in the previous generation, this is not true in non-Markovian species, as the occurrence of only a single individual with optimum genotype (or with a good portion of luck) can supplement the size of the population from any random value to the maximum size, limited from above only by the relevant ecological regulation mechanisms (see IV.4.1). At the present time, only some species of wild fauna could fall in this category, possibly including fish, and also some endoparasites; however, in the past, the common ancestors of most of present-day Markovian species could have passed through this stage. Sexuality could be a trait that was advantageous in the past for non-Markovian species, as it allowed them to create Sisyphean genotypes; however this need not be advantageous from this viewpoint for modern species and could be preserved, for example, through the evolutionary trap mechanism (see XIII.3.3).

Slipped‑strand mispairing leads first to local short-term denaturing of the double-helix DNA molecule and subsequently to renaturation of the segment of the strand, not with the original complementary part of the opposing strand, but with some other area containing the complementary base. If this event is followed by reparation and further replication of the given DNA segment, this is followed by either multiplication or, on the other hand, deletion of a certain sequential motif (Levinson & Gutman 1987)(Fig. VI.7).

Slippagecan also occur during the replication itself by slippage of the template for the DNA-polymerase enzyme (Fig. VI.8). In the site where repetition occurs of a certain nucleotide or short oligonucleotide, the DNA-polymerase can “slip” backwards or forwards along the template at a certain moment and synthesize a new DNA strand twice in a row according to the same template section, or leave out a certain section of the template. The probability of this event is inversely proportional to the length of the oligonucleotide of which the given repetition consists and directly proportional to the number of oligonucleotides in the repetition. As a consequence, although slippage can be followed by insertion or deletion of the particular motif, there is clear asymmetry in the probability of the two events. Insertion of a new copy increases the probability of further slippage, while deletion reduces it. For example, it is known that the frequency of spontaneous insertion and deletion of A in pentanucleotide AAAAA is more than one order of magnitude greater than their frequency in tetranucleotide AAAA. This means that the familiar principle of positive feedback is important in multiplication of repetitive motifs and the entire process of multiplication of certain motifs has a marked accelerating, avalanche character.

Avalanche multiplication of motifs in the genome of the organism is responsible for a number of serious diseases. For example, multiplication of the (CAG)_n motif in the gene for androgen causes Kennedy’s disease, multiplication of the same motif on a different gene is responsible for Huntington’s disease, and multiplication of (CCG)_n is observed in all cases of the fragile X chromosome syndrome (Lubjuhn, Schwaiger, & Epplen 1994).

Multiplication and the general mutability of simple repetition segments form the basis for the microsatellite analysis technique (see XXIV.3.7).This technique, which is based on amplification and characterization of the individual loci containing simple repetitions, is broadly employed in various population studies. The mutability of these segments allows microsatellite analysis to monitor a large amount of genetic polymorphism even in mutually quite related individuals. This can be employed, for example, in determining paternity or in determining the internal structure of a population.

see Species recognition concept of species

see Mass extionction causes

see Cultural traits transmission of

- The hypothesis of somatic mutations (Gorshkov & Makarieva 1999) is based on the suggestion that one of the important functions of diploidy could consist in protection against somatic mutations. Somatic mutations occur during the ontogenesis of every multicellular organism. In large organisms, the number of cell divisions between the zygote and the adult organism is rather large. Consequently, during ontogenesis, a great many loss and thus frequently recessive lethal mutations accumulate in their cells. Their presence does not matter in diploidal organisms, as they do not enter the germinal line and are generally not manifested in the somatic cells, because there is only a small probability that similar mutations would occur in both copies of a single gene. However, sex chromosomes are present in the cells of members of the heterogametic sex in the haploid state which is quite fundamental for the viability of the organism in the case of the X-chromosome, which generally contains a large number of genes. While, in homogametic females, the X-chromosomes act as autosomes, so that loss somatic mutations of their genes are recessive and are not externally manifested, in members of the heterogametic sex with a single copy of the X-chromosome, the presence of these mutations is manifested in reduced functioning of the cells and tissues and thus reduced viability of the organism. Similar to the recessive gene hypothesis, the hypothesis of somatic mutations also explains the strong manifestations of this effect in interspecific hybrids by an exponential dependence between the number of mutations and the decrease in the fitness of the individual. In contrast to the recessive gene hypothesis, the reduced average frequency of recessive negative mutations on X-chromosomes, which is necessary consequence of the greater effectiveness of selection acting on the representatives of the heterogametic sex, in which the harmful effect of mutations is not masked by the presence of a functional copy on the second X-chromosome, does not represent a complication here.. The frequency of these mutations in the gene pool is totally irrelevant; the reduced viability of hybrids is a result of somatic mutations occurring during the life of the individual.
The hypothesis of somatic mutations also explains the results of experiments with hybrid drosophila with an “unbalanced” genome (see XXI.4.3.1). It is apparent that, in males, which bear two X-chromosomes from the same species, the effect of recessive somatic mutations on the X-chromosome must be less than in hybrid males with a single X-chromosome, i.e. just that demonstrated by experiments with drosophila, i.e. contrary to expectations following from the dominance hypothesis.
The hypothesis of somatic mutations also offers a simple explanation of why the Haldane rule for viability is basically not valid for mammals. In this taxon, compensation of the genetic dose, i.e. inactivation of one of the X-chromosomes, occurs in the somatic cells. Because of this inactivation, each somatic cell of a female, similar to males, contains only one active copy of the X-chromosome, and the viability of hybrid females is thus reduced here similarly to the viability of hybrid males. However, this effect can analogously also be explained by the dominance hypothesis.
The hypothesis of somatic mutations also explains other phenomena encountered in nature and not directly related to the Haldane rule. It explains why all large fauna are diploid, while small fauna, whose somatic cells undergo only a small number of divisions during ontogenesis and accumulate only a small number of mutations, are sometimes haploid. It also offers an explanation of why male haplodiploid insects are much more sensitive to irradiation in the early stages of ontogenesis, when their cells are haploid, where the differences between the sexes disappear in adulthood, when diploidization or tetraploidization occurs in most of the cells in the somatic tissues of males. This explains why large species have small X-chromosomes, while small species, for example drosophila, can have X-chromosomes that bear up to 40% of all the genes. This also provides an explanation for the fact that, in mammals (with heterogametic males), the males mostly exhibit higher mortality and a shorter average lifetime, while the opposite is true of birds (with heterogametic females) (Promislow 2003).
            The hypothesis of somatic mutations, in itself, cannot explain the existence of all the phenomena described by the Haldane rule. The sterility of the members of the heterogametic sex is a result, to a major degree, of defects in the germinal cells themselves, where the number of cell divisions that occur in the germinal line is low for large organisms. It is thus apparent that a number of mechanisms are responsible for the phenomena described by the Haldane rule; however, they most probably also include the accumulation of somatic mutations in the sex chromosomes.

Spandrels are architectural elements that develop not through the intention of the architect, but as a consequence of objective, e.g. geometric. Pendentives are given as a special case of spandrels in evolutionary literature; these are spherical triangular areas permitting the placing of a circular dome over a square room. The best known case (at least for evolutionary biologists) consists in the pendentives in the Basilica of St. Mark in Venice. At the present time, these pendentives bear pictures of the four evangelists and thus seem to be an essential and intentionally created element of the artistic decoration of the cathedral. In actual fact, they were not created to bear these paintings, but because this was the most rational structural solution for joining a four-walled base with its cupola ceiling. It is typical that the pendentives in the Basilica of St. Mark acquired an adaptive significance, i.e. that mosaics of four evangelists were placed on them later, several centuries after the creation of the basilica. Many biological structures, even highly organized structures with a highly favourable effect for the survival of the organism, are in fact spandrels, not adaptations.

A new species can be most readily formed by gradual evolution outside of direct contact with the parent species, i.e. by allopatric speciation (Fig. XXI.3). If, for example, a geographically isolated population is formed, which branched off from the population of the original species, and this population is reproductively isolated from the parent population for a sufficiently long time, genetic changes can gradually accumulate in its gene pool that finally lead to phenotype and subsequently also ecological differentiation of the two populations. If the two populations come into contact before they are sufficiently differentiated, the two species can again merge into a single species. Otherwise, the two species can exist sympatrically next to one another (if there was differentiation of their niches) or one of the species can force the other species out of the location or even globally.
If an originally uniform population is divided by a barrier (mountain range, river, for aquatic organisms a strip of land) into two comparably large populations and these populations differentiate in time both genetically and phenotypically, then this is called vicariant speciation or dichopatric speciation. On the other hand, if only a very small population splits off from the parent population and then gradually develops into a new species, this is termed peripatric speciation (Mayr 1999) (se Fig. XXI.3). Empirical data and the results of theoretical analyses, for example comparison of the differences in the sizes of the ranges of occurrence of young sister species, indicate that peripatric speciations are apparently more common than vicariant speciations (Barraclough & Nee 2001); however, sometimes quite the opposite is stated {8917}. In addition, it seems that these types of peripatric speciations more frequently lead to the evolution of species that have different phenotypes than the parent species. For example, mutually related species and geographical races of kingfishers of the genus Tanysiptera, which occur on tiny islands in the vicinity of New Guinea and which probably originated by peripatric speciation, differ in their phenotype substantially more than the related species and races occurring on New Guinea (Mayr 1963).
The more frequent occurrence of peripatric speciations can have a quite prosaic cause. The splitting off of small populations, e.g. by introduction outside of the original range of occurrence or splitting off of tiny subpopulations on the fluctuating edge of a range of occurrence can occur far more often than division of the original range by a newly formed barrier. In most cases, these new subpopulations disappear or merge with the main population after some time. However, a certain percentage of them can lead to the formation of a new species.
There can be at least two reasons for greater phenotype differentiation of species formed by peripatric speciation. Populations at the very edge of the range of occurrence and even more so populations formed by introduction outside of this range mostly find themselves in different natural conditions than those in which most of the populations of their species live. Thus there are also different selection pressures acting on them and, as a consequence, their genotype also substantially changes with time. However, if the original range is divided into two parts of approximately the same size, the natural conditions in the two parts will probably be rather similar. Thus, the sister species will be differentiated more by the action of evolutionary drives and genetic drift than by the action of different selection pressures. Thus, the differences between the species will very frequently tend to be selectionally neutral and need not substantially affect the phenotype.
The second reason for the greater differences in species formed by peripatric speciation can lie in the founder effect and following transition of a species from the evolutionary frozen to a plastic state. The existence of the founder effect was derived in the middle of the last century by Ernst Mayr (Mayr 1963). He stated that species cohesion exists in sexually reproducing species because their gene pool represents an integrated whole – an adaptive gene complex, in which approximately constant representation of the individual alleles is spontaneously maintained through a form of genetic homeostasis. If a new allele appears in the gene pool, either by penetration from an external gene flow or formed directly on site through mutation, it will not be capable of functioning as well in the context of the other alleles present in the gene pool of the population as the original alleles, which have been repeatedly tested in all the possible combinations. Thus, it will be eliminated in the population in time. Massive penetration of foreign alleles, e.g. as a consequence of merging of two originally separate populations, can even lead to a drastic reduction in the average fitness of the members of the population. This will be caused both by the fact that migrants coming from different conditions and their progeny will have phenotypes that are poorly adapted to local conditions and also by the fact that crosses that have emerged, bearing untested combinations of local and foreign alleles, can have reduced viability and fertility – alleles derived from distant populations will not be sufficiently mutually compatible. If an originally uniform population divides into two daughter populations, each of them will bear approximately the same gene pool, in which the frequencies of the individual alleles will remain mutually interconnected and the overall composition of the gene pool will thus remain stabilized. Thus, the gene pools will have only limited ability to evolve. The action of strong selection pressures can force the frequencies of the individual alleles to deviate somewhat form the original values; however, the greater this deviation, the greater will be the resistance of the gene pool of the population to the particular selection pressure. Following reduction of the selection pressure, the frequencies of the alleles will return to the original value (see the genetic homeostasis effect, IV.9.2). In contrast, a small population formed by splitting off from the large population will take only a small part of the overall genetic polymorphism with it and, subsequently, they will lose most of the remaining polymorphism through drift. Even if the population rapidly increases in size in the new environment without competitors, a great many alleles will be completely missing in it or will occur randomly, as a consequence of the founder effect, with very unusual frequency. This can completely disturb the homeostatic stabilization of the composition of the gene pool and the population will respond much more readily and willingly (and irreversibly) to selection pressures. In addition, in a population with drastically reduced polymorphism, new alleles, for example formed by mutations, will always find themselves (i.e. in each newly born individual) in the context of an almost identical set of alleles. Thus, their selection coefficients will not change from one generation to the next, i.e. will not, for example, oscillate between positive and negative values. Thus, the selection of new alleles can be far more effective in a non-polymorphic population than in a polymorphic population (Flegr 1998, Flegr 2010) and the newly formed daughter species will be able to differ substantially from the parent species.

- Sexual selection can basically occur through two different mechanisms. The members of a certain sex, in the vast majority of cases males, can do battle for access to sexual partners or they can be selected as their sexual partners by the members of the opposite sex on the basis of more or less arbitrary criteria.
In the latter case, objective preconditions are formed for the manifestation of a continuously acting tendency towards the creation of new kinds of species by the coevolutionary lift mechanism (autoelection). Amongst females, there is a certain constant variability in the genes determining the traits according to which they will select their sexual partners. As soon as a new trait appears in the population and, simultaneously, in the population of females a gene for preference for this trait emerges, favorable conditions are formed for positive assortative mating of the bearers of this trait and the bearers of the genes for its preference, and thus for branching off and partial reproductive isolation of a certain part of the population. If the presence of the new trait were to reduce the attractiveness of the particular male for the other females and increase his attractiveness only for the subpopulation of females bearing the gene for its preference, the presence of the two complementary genes will constantly increase in the population. The reasons for the increase in the frequency of genes for preferred trait in the population are obvious. However, the genes for preference for the particular trait are also at an advantage. A bearer of the trait (male) is most probably also simultaneously a latent bearer of the gene for preference for this trait. His father was most probably a male who was also a bearer of this trait and therefore his mother was a female that most probably preferred this trait, as she selected a bearer of this trait as her sexual partner. The genes that cause that the female prefer the bearer of a certain trait thus also assist in its preferential spreading, to be more exact spreading of its own copies, which are most probably contained in the genotype of preferred individuals. The fact that there is a simultaneous increase in the frequency of both traits in the population accelerates the coevolutionary lift process because of positive feedback and the gene for the new trait and the gene for its preference are fixed in the population.
            The evolution of the system does not end with fixation of the two complementary genes. As soon as all the males in the local population carry the new trait, females that lose the ability to recognize the presence or absence of this trait in their sexual partners cease to be “penalized”. Thus, the gene for preference for the particular trait can gradually disappear from the population. In contrast, males that would lose the particular trait will be selectionally “penalized” as long as at least some females remain in the population that bear a functional gene for preference for the relevant trait. Consequently, males will have a tendency during evolution to gradually accumulate and fix genes for marked secondary sexual traits, while in females the genes for preference for certain sexual traits will tend to periodically fluctuate and accumulate in the population maximally in the form of more or less selectionally neutral polymorphism.
The evolution of male secondary sexual traits and female preference traits can be important from the viewpoint of speciation, for example, when the species has a discontinuous range of occurrence and a number of various traits, according to which the females select their sexual partners, are gradually independently fixed in each individual population. As these traits are fixed in separated populations, some of them can be mutually exclusive or the differences between the males in two populations can be so great that the males of one population can become completely unattractive for the females of the other population. Thus, internal prezygotic reproduction barriers can be created as a consequence of the action of sexual selection through female choice.
If two new sexual traits spread simultaneously in a single population, which can occur quite frequently in species with large unstructured populations, three basic alternatives can occur. If these are traits whose expression in a single individual is mutually excluded, and if the population is otherwise panmictic, it is highly probable that the trait that is preferred by a greater percentage of females will predominate in the population. The bearers of this trait have a greater chance of reproducing than the bearers of the alternative trait. However, the suppression of one of the traits does not mean that its bearers and their progeny, i.e. all its alleles located in other loci, would be eliminated from the population by selection. As the gene flow barriers formed by preference for sexual partners are mostly permeable, i.e. individuals sometimes make a mistake in selection of the right sexual partner, and the individual genes can “move” between the chromosomes bearing various alleles for the preferential and preferred genes through genetic recombination, probably only the genes for the particular trait, genes for its preference and also alleles in immediately neighboring loci will be eliminated.
The second possibility occurs if the traits are also mutually exclusive, but the population is spatially structured and new traits spread towards one another from two different areas. A more or less sharp boundary in male phenotypes will tend to exist at places where the two populations meet. If a male passes into the territory in which females preferring bearers of the opposite trait predominate, he will be at a disadvantage in sexual selection and will leave fewer progeny. Simultaneously, there need not be practically any barrier between the two forms for the passage of other genes than genes for the sexual trait and genes for its preference. As soon as a male in the territory of the other form crosses with the local female form, some of its sons will inherit from the female the genes for the alternative form of the sexual trait and some of his daughters will inherit the gene for preference for this trait, so that they will not be at a disadvantage in competition with the other members of the population and will be able to freely pass their genes down in the second part of the population.
The third possibility occurs when the expression of both traits is not mutually exclusive. In this case, both traits will probably be fixed.
The importance of sexual selection in speciation is not entirely clear at the present time. However, meta-studies have indicated that, of 15 formerly published comparative studies, twelve demonstrated a positive correlation between the level of sexual dimorphism and species diversity in the relevant taxon (Panhuis et al. 2001). This could mean that species in which this mechanism is important also actually exhibit a greater rate of speciation. On the other hand, from the viewpoint of anagenesis, the coevolutionary lift mechanism could explain the fact that there are very great differences between related species in traits visible on the surface, i.e. in coloration, patterns or structure of the surface. This mechanism could, in fact, be responsible for “address phenomena”, whose existence was pointed out in the mid-twentieth century by A. Portmann (Portmann 1960). It is very striking that most organisms have a tendency towards “self presentation”, i.e. have various ornaments, bright colors or structures on their surfaces. In contrast, most internal organs are usually uniform in color, aesthetically uninteresting or even ugly. It is frequently very difficult to imagine a biological function that these surface structures, which are part of the self presentation of the members of a certain species, could fulfill for their bearers, e.g. some marine turbellarians or opistobrancial gastropods. It is quite possible that, in actual fact, these traits do not provide any advantage for their bearers, but only provide an advantage for those genes that encode their formation, and the genes that enable the members of the other sex to recognize these traits. Any mutation can be fixed by genetic drift. However, the probability of fixation of a new mutation by drift is very low. Mutations advantageous for the aspect of survival can become fixed by natural selection; however, this mechanism is also not very efficient in polymorphous populations of species with sexual reproduction (see IV.9). In contrast, practically any mutation that is capable of sufficiently obvious manifestation in the appearance of its bearer can be very efficiently fixed in sexually reproducing species through the coevolutionary lift mechanism. Thus, coevolutionary lift could be responsible for a large portion of self-presentation phenomena manifested in living organisms and thus for a large part of the aesthetics of living nature.

see Speciation branching

Ecological speciation is a form of speciation that has come into and fallen out of favor (Via 2001). Ecological speciation is generally termed sympatric speciation in discussions related to this subject. As sympatric speciation also includes a number of types of instant speciation which, understandably, have completely different mechanisms, this established terminology is not really appropriate. Ecological speciation very frequently has the character of parapatric speciation. A great many species of organisms have a rather broad ecological valence, while the environment in which they occur has a heterogeneous and discontinuous character from the viewpoint of the prevailing conditions. Thus, it is advantageous for the population to specialize on various local environmental conditions by evolving various ecological forms, each of which is adapted to a certain type of environment or certain strategy for utilization of these conditions. The numbers of the individual ecological forms can fluctuate in the population in dependence on the character of the environment in which they occur. If the individual types of environment are also separated spatially and the organisms are not very mobile, there is a greater chance that the members of a single ecological form will preferentially reproduce together and will only occasionally cross with members of the opposite form.
 The existence of large phenotype differences between the members of the two forms, as a result of which they need not recognize one another as members of the same species, can have similar consequences. In some cases, such a situation can even lead to differentiation of the parent species into two daughter species, which divide up the original ecological niche and then each of them will have lower ecological valence than the original species. The effect of disruptive natural selection, caused by the original differentiation into two ecological forms, is frequently further reinforced by the fact that the crosses of the two forms have a transition phenotype, which is suboptimal in both types of environment. This creates a selection pressure on the creation of further, this time prezygotic (for example ethological) mechanisms that could reduce the probability of crossing between the members of the two ecological forms. The main problem in functioning of ecological speciation is the necessity of preventing recombination, which would break the connection between the genes responsible for the ecological differentiation between the two forms and the genes responsible for their prezygotic reproductive isolation. Mathematical models have shown that the formation of a new species is favored by a situation in which only a small number of genes is responsible for prezygotic isolation and a medium number of genes is responsible for ecological differentiation (Kondrashov & Kondrashov 1999; Via 2001).
 To the present day, only a few systems have been described in which the mechanism of ecological speciation is assumed to play a role. Primarily, this applies to the historically documented case of speciation of the apple maggot fly Rhagoletis pomonella in America, which moved from the hawthorn to apple trees in the middle of the nineteenth century (Bush 1969). Other probable candidates for ecological speciation include cichlids in one of the African crater lakes {12524}, palms in Lord Howe Island {12340} and possibly also American freshwater sticklebacks.

Extinction speciation is another example of instant speciation (Fig. XXI.2). A great many species form an extended linear series of individual populations in their area of occurrence, where exchange of genetic material (sexual reproduction) occurs solely or almost solely between neighboring populations. Geographically more distant populations can thus be so phenotypically and genetically different that their members are not capable of fertile crossing and can occupy different ecological niches in nature. Nonetheless, they must be considered to be the members of a single species, as exchange of genetic material is mediated by a number of mutually neighboring populations, which geographically connect them. Ring species are an interesting example of species with this type of population structure. Their range of occurrence frequently forms a relatively narrow line of mutually neighboring populations that, for example, encircle a certain geographic obstacle (Californian salamanders of the Ensatina genus) or that even extend in a strip around the entire Earth (the lesser black-backed gull (Larus fuscus) and the herring gull (Larus argentatus)). These species spread in the past in one or both directions from the place of their original occurrence until their populations met secondarily in a certain area and closed the range of occurrence to form its present-day ring shape. Thus the phenotypically and genetically most distant populations met at the site of encounter and their members act as well defined species; in the ideal case, they do not cross and even do not compete much. Extinction speciation occurs when one of the inner populations becomes extinct, interrupting the gene flow from one end of the range to the other.

The hybridization of two different species frequently yields crosses that have phenotype traits different from both the original species and even exhibit better viability in some habitats. If crossing occurs repeatedly between these species, interspecific crosses can have great importance in the particular ecosystems. In subsequent filial generations or on recrossing with the parent species, however, both their viability and their fertility are reduced as a result of irregularity in the separation of chromosomes derived from two different species. If we ignore the possibility of transition to a purely asexual means of reproduction, there are two basic ways in which hybridization can lead to the formation of a new fully fledged species.
_{The first means of hybridization speciationis called recombination speciation. The individual recombinants derived from crossing of hybrids of the F1-generation may occasionally contain individuals that are normally fertile and have different ecological requirements than the original species. If sufficiently strong reproduction barriers are also created between these individuals and the original species, they can form the basis for the emergence of a new species.
Hybrid polyploidization is another means of hybridization speciation. The emergence of fertile individuals through hybrid polyploidization, i.e. the emergence of a fertile alopolyploid, is even easier than its formation by polyploidization of a nonhybrid individual, i.e. than the formation of a fertile autopolyploid. In autopolyploids, the double chromosome set is derived from a single species. For example, in autotetraploids, all the chromosomes are present in the cell in four copies and, in meiosis, tetravalents can be formed instead of bivalents. The presence of these structures can seriously disturb the progress of meiosis and thus reduce the fertility of the polyploid. In contrast, with alopolyploids, the two original sets are derived from two different species so that the relevant homeological chromosomes mostly do not pair together and, rather than tetravalents, twice as many regular bivalents are formed during meiosis. As a result, alopolyploids can be fully fertile.
Polyploidization mostly occurs in that the first (reduction) division does not occur during meiosis, yielding diploid gametes. Tetraploids are only rarely formed by the meeting of two rare diploid gametes. Mostly a diploid gamete first encounters a haploid gamete and a triploid is formed. This then forms a triploid gamete as a consequence of a disorder in reduction division. A tetraploid individual is formed only by fusion of a triploid gamete with a haploid gamete. Thus, the triploid stage is a frequent intermediate step in the evolution of a new species by polyploidization; this has two haploid chromosome sets from one species and the third from the other species. Once again, it is necessary to bear in mind that this type of speciation comes into consideration primarily for species without chromosomal sex determination through differentiated sex chromosomes, where the ratio of the gene dose located on the sex chromosomes and on the autosomes must be retained, and thus primarily for some taxons of plants and fish. Hybridization speciation can be of relatively great importance for these taxons. According to some estimates, up to 11% of all species diversity in plants exists as a result of hybridization (Barraclough & Nee 2001).}

see see Speciation sympatric

Postzygotic reproductive isolation barriers can be a direct product of the activity of some parasitic microorganisms (Breeuwer & Werren 1995). The best known and apparently the most widely spread such parasites are bacteria of the Wolbachia genus, which parasitize in the cells of a large number of species of arthropods, especially insects, and in nematodes. It has been estimated that up to 75% of all species of arthropods are infected by them (Stevens, Giordano, & Fialho 2002). One of the many manifestations of the presence of parasites is the formation of reproductive incompatibility between infected males and uninfected females of the host species. Wolbachia cannot be transmitted by male sex cells. Thus, if this parasite finds itself in the body of a male, it has only a very few ways of increasing its inclusive fitness. One of these is induction of reproductive incompatibility between infected males and uninfected females. If an infected male copulates with both infected and uninfected females, only the infected ones produce viable (and infected) progeny and their percentage in the population and thus also the total number of parasites (potential relatives of the parasite that induced the reproductive incompatibility in the male) will increase (Fig. XXI.13). The mechanism of induction of incompatibility is not known in detail. It was originally supposed that the sperm of infected males contain a toxin that, after fertilization, destroys the zygote formed from eggs that do not contain the antitoxin formed by Wolbachia in infected females. The new results, however, suggest that Wolbachia changes the timing of certain steps in the division of the male cell nucleus, which may lead to desynchronization of divisions of pronuclei of male and female origin in a fertilized ovum and therefore disruption of division of the zygote {10891}.
Various strains or various species of Wolbachia frequently exist in the host population and their toxins and antitoxins (or their desynchronization mechanisms) need not be compatible. Thus, if one Wolbachia variant spreads in part of the population and a different one in another part of the population, the incompatibility of their toxins and antitoxins may lead to an impermeable reproductive barrier between the two subpopulations and can facilitate speciation. The fact that Wolbachia is really responsible for the existence of reproduction barriers can be verified by “curing” the relevant host species by administration of antibiotics (Fig. XXI.14). Following this procedure, the mutual reproductive incompatibility of the members of the two populations generally disappears (Mandel, Ross, & Harrison 2001). According to some theories, Wolbachia are the main motor for speciation in insects and also the reason why a great many of its taxa are extremely rich in species (Rokas 2000).

Polyploid individuals are readily formed in some taxons and a new species can be formed by polyploidization speciation from these individuals under favorable circumstances. In species with differentiated sex chromosomes, the balance between autosomes and the sex chromosomes is frequently disturbed in polyploid individuals, so that polyploidization, for example by doubling of a chromosome set, yields individuals with serious disorders in the development of the sex organs and thus reduced or even zero fitness. In species without differentiated sex chromosomes, especially in plants, these individuals are frequently fertile and can lead to the emergence of a new species (Rieseberg 2001). It has been estimated that polyploidization speciation is responsible for 2-4% of all speciation in vascular plants (about 7% amongst ferns) (Otto & Whitton 2000).
Crossing between tetraploid and diploid individuals then yields triploid individuals, which are often infertile. During meiosis, part of the chromosomes do not find unoccupied homologous partners with which they could form bivalents during meiosis and thus participate in the formation of trivalents or even remain unpaired as free univalents. Especially univalents are unevenly distributed amongst the daughter cells or their presence can completely block the completion of meiosis. Thus, reproductive barriers exist between polyploids and diploids, which can lead to the emergence of a new species under favorable circumstances. This speciation is greatly assisted by the fact that, due to the larger size of cells of polyploidy plants, the phenotype traits of polyploids and diploids can differ substantially (Otto & Whitton 2000). This can contribute to differentiation of the ecological niches of the two forms and facilitate their prolonged or even permanent sympatric or microallopatric coexistence in a single territory.
 see also Speciation gradual

see Speciation chromosomal

see Speciation alopatric

Within some taxons, the species differ primarily in the type of biotope that they chose for the lives of their members in the typical case. For example, it is known that individual species of birds divide up the landscape that they inhabit in great detail. For example, some species are strictly bound to the lower level of forest stands, while others are linked to the middle level and others, for example, to isolated bushes outside of continuous forest stands. Simultaneously, it is not very probable that such a detailed division of the biotope would be a consequence of disruptive selection, possibly supplemented by evolutionary character displacement (see XXI.4.4). For example, bird species bound to the lower level of a forest stand could probably inhabit isolated bushes just as well, but are not encountered there under normal circumstances, even when potential competitors bound to this type of biotype are missing.
            Some authors are of the opinion that this speciation of individual species and thus their primary mutual limitations are a result of differences in the characteristics according to which the members of the individual species recognize their normal biotope (Storch & Frynta 1999). These characteristics were chosen more or less at random in the evolution of the particular evolutionary line and basically only very loosely reflect the suitability of the particular biotope for the life of the given species. As indicated by the relevant models, the evolution of characteristics employed by the individual species for choice of a suitable biotope is a cumulative process and is, to a substantial degree, a one-way process – characteristics gradually accumulate during the evolution of a particular developmental line rather than some of them being ignored by younger species. This necessarily leads to a situation where the species gradually divide up the available biotopes in great detail. Thus, specialization of the individual species is not primarily related to the diversification of their phenotypes as a consequence of diversification of natural selection, but rather to more or less autonomous diversification of their cognitive apparatus and the relevant concept of a species can be denoted as the biotope recognition concept.

Buffon’s concept of a species is apparently the oldest definition of a species as a natural taxon (Mayr 1982). According to this concept, the criterion of belonging to the same species is the ability to productively reproduce, i.e. the ability of a pair of individuals of the opposite sex to produce fertile progeny. As soon as the members of two different forms become capable of fertile reproduction, it is necessary to consider them to be members of the same species, even if their phenotypes are very different and they do not cross in nature – for example because their areas of occurrence do not meet. It is apparent that this method of distinguishing species can be employed only for sexually reproducing organisms.

Variability is constantly generated within any species through random mutations. The genotype and thus also the phenotype spectrum of each species should be constantly expanding, which should also lead to gradual reduction of phenetic distances and thus to obscuring of the boundaries between different species. However, such processes do not seem to occur in nature. So far, no example is known where two phenotypically identical species would be formed by gradual convergence of two phylogenetically unrelated species. One of the possible explanations could be that mechanisms of species cohesion exist for the individual species, i.e. mechanisms that act against the broadening of the phenotype and apparently also the genotype spectra of the relevant species and that prevent the fusion and merging of two species (Templeton 1989; Templeton 2001). Several possible mechanisms of species cohesion have been proposed up to the present time. They have the common property that they are responsible for the active process of maintenance of the similarity between the members of a single species and simultaneously indirectly for the existence of differences between the members of different species.

The basic mechanism of species cohesion, sexual reproduction, cannot function in asexually reproducing organism; however, simultaneously, a different process that is capable of ensuring species cohesion can exist here, i.e. genetic draft (Gillespie 2000; Gillespie 2001). Genetic draft, which is also known under the older name hitchhiking, consists in elimination of genetic (and thus also phenotype) polymorphism from the gene pool together with an allele that is subject to selection (see IX.4.4.1). The effects of this process are very limited amongst sexually reproducing organisms. They are related only to elimination of polymorphism in genes in close genetic linkage with a gene that is the actual object of selection. The effect of draft is manifested most strongly here in the sections of the genome in which genetic recombination does not occur, for example, in the non-recombining parts of the sex chromosomes. It is assumed that genetic draft is responsible for the absence of intraspecific polymorphism, which is typical for these genome sections. The importance of genetic draft is much greater in asexually reproducing species, as all the genes of the individual are in absolute genetic linkage. Thus, if a single advantageous mutation appears in the population at a certain moment, that has a sufficiently large selection coefficient and sufficient luck to become fixed, the alleles of all the genes that occurred in the genome of the mutant are also fixed. All the other alleles occurring in the population at the given moment are, on the other hand, eliminated (Fig. XX.4). If the fixation of the new alleles is so fast that there is no time for the formation of new genetic variability in the progeny of the particular mutant, the entire species can become genetically and, to a considerable degree, also phenotypically uniform. Over time, new mutations will accumulate in the gene pool of the species and genotype and phenotype polymorphism will be renewed. However, over shorter or longer intervals, new, advantageous mutations will repeatedly “sweep out” this polymorphism and thus renew the gene and phenotype uniformity of the species.
Continuous elimination of negative mutations will understandably contribute to the maintenance of the uniformity of members of an asexual species. As soon as negative mutations appear in the genome of an individual and become an object of gradual elimination through the action of negative (purifying) selection, all the copies of alleles occurring in the genome of the individual are also fated to disappear. Of course, this disappearance occurs only for copies occurring in the particular individual, so that the final effect on the overall polymorphism of the species or population will be less than for positive mutations. However, because negative mutations occur far more often than positive mutations, their overall importance for maintenance of species cohesion can actually be greater than the effect of positive mutations.

see species morphological

see Species recognition concept of species

It has been found for a number of morphological species that they actually consist of a complex of two or more species that can fundamentally not be differentiated on the basis of morphological traits. In some cases, they can be differentiated on the basis of ethological and ecological traits and in some cases on the basis of the geographic occurrence. However, sometimes the main or only indication of the existence of cryptic species (sibling species) is the existence of a reproduction barrier between their members. This can be manifested either in direct study of reproduction of the members of the particular “species” or in study of the genotype composition of the population. In the latter case, a certain combination of alleles does not occur in the population, although its occurrence would have been expected on the basis of the frequency of the individual alleles in the gene pool of the population. It is understandable that the absence, for example, of heterozygotes in a particular locus does not necessarily indicate the existence of cryptic species. Some heterozygotes could, for some reason, not be viable and there could be a strong selection pressure against them in natural populations. However, if the absence is related to a greater number of genotypes and a greater number of loci, the existence of cryptic species becomes a very probable explanation of the given phenomenon.
            The existence of cryptic species constitutes a complication, not only from the viewpoint of the theoretical definition of a species, but from a factual standpoint. Cryptic species generally have overlapping ecological niches, so that it is a mystery how they can occur in nature over prolonged periods and with such a high frequency. It is quite possible that they could correspond to newly emerging species that will also differ morphologically in the future. However, it is also possible that this is only a transitory state that will end either with the disappearance of one of the almost identical species or renewal of gene flow between the given species.

A phylogenetic species is most frequently defined as the basic (smallest possible) set of a population between which the ancestor – progeny relationship exists and which can be distinguished from other such sets on the basis of a diagnostic trait (Nixon & Wheller 1990). This definition encompasses both the requirement on monophyly of the given set in the population (otherwise some of them would have ancestors outside of the population set) and also the requirement on the presence of a phenotypic trait, on the basis of which it is possible to differentiate its members from the members of other species. This trait can, of course, be a certain combination of individual traits that, in themselves, i.e. in other combinations, can also exist in other species. Simultaneously, the trait need not be present in all the individuals in the population and can occur, for example, only in the members of one sex or only at a certain stage in development, e.g. in larvae or in adults. The definition of a phylogenetic species does not permit a decision to be made on whether a certain population is a species. The main contribution of the concept of a phylogenetic species is, however, that it allows delimitation of what is certainly not a species. Thus, higher taxons cannot be species as this is not the smallest possible set in the population fulfilling both criteria, and even a certain phenotype variant cannot be a species, for example all albino individuals, because they split off repeatedly, independently of mutual relatedness and do not, together, form a monophyly. Even a monophyletic group in the population, which would not differ in any trait from other similar groups in the population, cannot be a phylogenetic species. Thus, according to the concept of a phylogenetic species, the formation of a new species requires anagenesis – an evolutionary change in phenotype.

- The typological definition of species is not easy to defend theoretically but nonetheless is used most frequently in practice. This is primarily a result of the fact that the commonest task faced by the taxonomist is that of determining the species of a particular individual, i.e. deciding whether a certain individual belongs in a particular predefined species. Even in cases when the goal of the taxonomist at the particular moment is not to assign an individual to a known species, but to define the boundaries of new species, an attempt to assign all the studied individuals to known species is the first and an absolutely necessary step.
Most species are defined as typological species, i.e. on the basis of phenotype traits characteristic for their members, i.e. on the basis of properties that occur in the members of the given species and simultaneously are not present in the members of other species. In species with separate sexes and sexual dimorphism, with several developmental stages in their life cycles or with phenotype-differentiated casts, traits occurring in any of the life forms of this species can be used. Both morphological traits and physiological, biochemical and ethological traits can be used to define the boundaries between species. However, morphological traits are used most frequently to define species and, in these cases, they are designated as morphological species. If a large number of mostly mutually interchangeable traits are used to define species rather than a small number of key traits and the species are delimited by the exact methods of numerical phenetics, then the species are sometimes designated as phenetic species.
Some species are monotypical, i.e. they are represented by a single form in their entire area of occurrence. Other species are polytypical; they occur in several and frequently a great many phenotypically different forms within their area of occurrence or at a single site. In the first case, the species can be defined by a list of the traits that its members must have; in the second case, however, the individual traits are usually mutually interchangeable, so that membership in a certain species tends to be determined by the presence of a certain combination of traits and not the simple presence or absence of one particular trait or a single combination of traits. In the most complicated cases, a decision cannot be made on the membership of an individual in a particular species on the basis of its phenotype, as the presence of a certain combination of traits simply determines the probability with which a particular individual will belong to a certain species. If, for example, an individual bears a combination of alleles that occur only very rarely in one species and, on the other hand, relatively frequently in another species, it can be assumed that it will more probably be a member of the latter species. If a larger number of individuals from the same population is available, the frequency of the occurrence of the individual forms of various traits can be found and thus the species membership of these individuals can be determined with greater certainty (Ayala 1983) (Fig. XX.5).
            Typological definition of species should not be confused with definition of species using type specimens. In the description of a new species, it is extremely important to place type specimens in a collection, i.e. specific individuals (for microorganisms a specific culture), to which a description, and thus also the naming of the particular new species, is related. If it is found in the future that the description was ambiguous and that it can actually apply to two or more species, the existence of the type specimen allows us to decide which of the original species is described by the original description and thus which of the species should continue to bear the relevant name. The possibility of using type specimens follows directly from the manner of definition of typological species. Nonetheless, the typological definition of species need not always be related to the existence of a type specimen; in a great many cases only a description of its traits forms the basis for definition of a species.

It could be expected that spiteful behavioral patterns will become fixed in evolution in the same way as selfish behavioral patterns because, in sexually reproducing species, the spreading of a biological trait in the population is determined by how much it increases the effectiveness of spreading the allele responsible for this trait  (compared to the other alleles of the same gene) and, in asexually reproducing organisms, it is decided by how much the trait  heightens the individual fitness of the carrier of a particular allele (compared to the average carriers of other alleles in the population) (Hamilton 1970). At first sight, it seems that it does not matter whether the individual achieves an increase in its relative fitness by increasing its absolute fitness or by lowering the absolute fitness of its competitors, other individuals in the population. Nonetheless, observations in nature show that spiteful behavioral patterns are quite rare (Dobson, Chesser, & Zinner 2000; Foster, Wenseleers, & Ratnieks 2001).  I will intentionally ignore the most trivial explanation that the individuals “selflessly harm” other members of the population so skillfully and inconspicuously that, in most cases, a naive and idealistic biologist cannot observe it.  In any case, it would be appropriate to mention that our shared experience with the behavior of the representatives of a certain well-studied primate species indicate that this possibility should not be ignored.
            The simplest explanation of the evident absence of spiteful behavior is that all three mechanisms of the evolution of altruistic behavior mentioned in the previous section, i.e. group selection, kin selection and reciprocal behavior, simultaneously act as a barrier against the egression and spreading of spiteful behavioral patterns. A technically different, but at least equally important, reason for the absence of these behavioral patterns is that, in consequence, not only the bearer of the trait, the Vandal, but also other individuals in the population (more specifically those who are at the particular moment not directly affected by the spiteful behavior) profit from it.   These “innocent bystanders”, whose relative fitness increases thanks to lowering the absolute fitness of the individual affected by vandalism, are moreover at an advantage in relation to the bearer of spiteful behavior. They do not have to expend any strength on spiteful behavior and do not expose themselves to the risk of possible revenge from the vandalized victims.
            Theoretic models show that spiteful behavior can spread in a population mainly when vandals can recognize the degree of their genetic affinity to the victims and direct the spiteful behavior primarily towards unrelated individuals. In this context, it is sometimes discussed whether certain elements of behavior of individuals infected by some parasites could be interpreted and their origin be explained as spiteful behavior of the infected host (Rozsa 1999; Rozsa 2000). If the individual’s fitness is lowered, because it has been infected  with a parasite, then the best thing it can do is to infect other individuals in the population. Theoretical models show that, if it infects other individuals in the population regardless of the degree of their genetic relationship, i.e. regardless of the probability of their sharing the copies of the same alleles, this behavior will be selectively neutral, i.e. it will not lead to any change in the inclusive fitness of the individual.  If the infected organism preferentially harms the individuals that are not related to it, the gene for this behavior may spread in the population.
It is well known that individuals infected by certain kinds of parasites have higher motility and are able to migrate over longer distances (Poulin 1994a). According to some concepts, this may be a result of manipulative activity of the parasite, which is favored by higher motility of the infected individuals, because motile hosts can infect more so-far healthy organisms (Randolph 1998). According to another hypothesis, it can be an expression of spiteful behavior of the infected host, which is trying to infect as many still healthy non-relatives in the population as it can, thus heightening its own inclusive fitness.

Spontaneousand induced mutations can be differentiated according to the causes of their formation.The existence of induced mutations was already demonstrated in the 1920’s, when the effect of radiation on organisms was first studied.Since then, it has been shown that a great many physical and especially chemical factors can cause the formation of mutations in organisms.The exact mechanisms of their action are known for a great many factors, i.e. the specific course of the chemical reaction that leads to replacement of one nucleotide by another, to insertion, deletion or fission.

In fact, the existence of spontaneous mutations was doubted for some time.Some biologists assumed that all mutations are actually caused by external effects, mutagens, occurring in the environment.However, it was gradually demonstrated that there are some categories of mutations that are actually spontaneous.The most typical example consists in mutations that occur through inclusion of the incorrect nucleotide during DNA replication as a consequence of statistically random transitions of individual bases to less common structural forms, i.e. tautomeric transitions (Cox 1976).The individual bases are present in these forms for only a short time (10^–5–10^–4 s), after which they spontaneously return to the usual form (Fersht 1980).Bases in the unusual forms can form hydrogen bonds with the wrong nucleotides so that, during replication, the wrong nucleotide is included in the synthesized  chain with a certain, non-zero probability.For example, the enol form of T pairs with C (instead of with A) and the imino-form of C pairs with A (instead of with G) (Fig. III.5).The enzyme DNA-polymerase exhibits 3’-5’-nuclease activity, so that it is mostly capable of eliminating these mutations; a large part of the remaining mutations are repaired by subsequently acting  specialized repair systems, which are capable of differentiating which of the unpaired nucleotides is located in the newly synthesized chain and thus which must be repaired.However, some mutations are not repaired and remain a permanent part of the DNA.It is assumed that the frequency of mutations in human beings is 10^–10 /nucleotide/cell cycle.During a human lifetime, mutation affects each 4^th base in the DNA of brain cells and each base is replaced on an average of 5x as a result of repair processes (Holmquist & Filipski 1994).s

of the origin of genetic code From the viewpoint of discussion of the evolution of the genetic code, it could also be important that a correlation exists between certain properties of aminoacids and the corresponding triplets of the genetic code (Tolstrup et al. 1994). At random, we can, for example, mention the high positive correlation of the index of hydrophobicity of aminoacids and the 3’-dinucleotides of the corresponding anti-codons, or the negative correlation of the chemical reactivity of aminoacids in the formation of peptide bonds and the content of nucleotides G and C in the corresponding codon. According to some authors, these correlations indicate that, at the beginning of the evolution of the genetic code, direct stereochemical interactions between the aminoacids and the corresponding codons and anticodons also participated in assigning of codons to the individual aminoacids (Woese 1965; Shimizu 1982). The original stereochemical hypothesis of the formation of the genetic code tends, however, to be gradually abandoned at the present time or has undergone substantial changes (Alberti 1999; Di Giulio 2001).

see Reproductive isolation postzygotic

See Determinism and stochasticity of evolution.

see Fossils

The frequency with which mutations are fixed in a certain position or in a given DNA section per time unit in evolution is called the substitution rate. This rate is generally expressed as the number of fixed mutations in the given position per year. The substitution rate must not be confused with the mutation rate; however, it can be concluded that these two rates are numerically equal for neutral mutations (see V.3.3). The mutation rate, i.e. the number of mutations occurring in the given position per time unit for all the members of the population, depends primarily on the accuracy of replication, the efficiency of reparation processes, the intensity of the action of mutagens and the mutability of the sequential motif in the given position of the DNA chain. In contrast, the substitution rate depends not only on the mutation rate at the given site, but also on the intensity and direction of selection that act on the mutation in the given position and in its vicinity. Simultaneously, the substitution rate for selectively neutral mutations does not depend on the size of the population (see V.3.3) (which suggests that genetic drift rather than genetic draft drives the DNA evolution in the studied populations). With growing population size, the number of newly formed mutations in a given position in the population increases linearly, i.e. the mutation rate linearly increases; however, simultaneously, there is a linear decrease in the probability that the newly formed mutation will be fixed by genetic drift.

It must be, however, emphasized that the percentage of mutations that fall in the category of selectively neutral does depend on the size of the population. It is not possible to draw a sharp line between selectively significant and selectively neutral mutations. Basically, only a minimum of them has a selection coefficient equal to zero; most mutations have a negative or positive selection coefficient. It is generally accepted that those mutations whose absolute selection coefficient value is less than 1/N_e, where N_e  is the effective size of the given population, act as effectively neutral in the given population. This means that a greater percentage of mutations fall in the category of effectively neutral mutations in a small population than in a large population. As most mutations have a negative selection coefficient and only a minority have a positive selection coefficient and because the probability of fixation of negative mutations is substantially smaller than the probability of fixation of positive or selectively neutral mutations, the total number of mutations fixed by drift over a time unit, i.e. the substitution rate, is greater in a small population than in a large population (see also V.5).

If a group of genes is located next to one another on the chromosome then, in a short time scale, they act as a single gene during genetic processes. This is advantageous in cases when the relevant gene participates in the formation of traits that exist in two or more forms that are advantageous for their carrier, where other forms of the trait that could be formed by random combination of the alleles in the relevant loci would be disadvantageous for their carrier. The occurrence of genes in closely neighbouring loci is then denoted as a supergene.

The best known cases of supergenes were described in study of mimesis in butterflies. Sometimes, a certain type of butterfly imitates several various kinds of poisonous or bad-tasting butterflies. A number of genes affecting the individual traits of the pattern are required for the creation of the relevant pattern on its wings. These genes are located close to one another on the chromosome, so that the parent passes on the relevant combination of alleles to its progeny together. Thus, the progeny consist almost entirely of individuals that inherit the relevant supergene from the father (and imitate one bad-tasting species of butterfly) or who inherited this supergene from the mother (and imitate another species of bad-tasting of butterfly). Individuals that inherited the recombined genotype, whose phenotype would thus not be similar to either of the imitated species and whose mimetic defense against predators would thus be reduced, occur in the progeny of the particular species only rarely.

see Condensed tree

In the reconstruction of cladogenesis, all the homologous traits are not similarly useful. Systematic biologists have intuitively known these facts and have respected them for ages. However, it wasn’t until 1950 that Willi Hennig in his book “Grundzüge einer Theorie der phylogenetischen Systematik” explicitly stated the requirements that cladogenesis be reconstructed exclusively on the basis of a single category of homologous traits – termed synapomorphies. A trait is understood to refer to any structure, function or behavior that occurs in various species in at least two different forms. From an evolutionary standpoint, the individual forms of a certain traits are not equivalent; one of them, the plesiomorphic form, for short plesiomorphy, is evolutionarily older in the particular phylogenetic line and the other forms were formed secondarily all at once or in a certain order as a consequence of anagenetic changes in the original form of the trait. These evolutionarily derived forms are termed apomorphic forms, abbreviated apomorphies. If several species (or higher taxa) within the studied phylogenetic line inherited certain apomorphies from their common ancestor, this apomorphy is termed a synapomorphy; in contrast an autapomorphy is an apomorphy that no other species shares with the given species. The distribution of synapomorphies within the given set of studied species is the best guide for reconstruction of cladogenesis. Even if two species share a large number of plesiomorphies, they need not be closely related in the particular line (Fig. XXIII.6). This could be only a consequence of the fact that the particular species did not change much during evolution, in contrast to other species, for example because it lives in the same environment as the common ancestor of the given line. In contrast, if two species share a large number of synapomorphies, this is most probably a result of the fact that they have a common ancestor that is simultaneously not the common ancestor of any of other studied species.

At a certain stage in sexual reproduction, fusion, i.e. syngamy, occurs of two sex cells bearing a single copy of the genome, i.e. two haploid gametes. The newly formed zygote is then necessarily diploid and, prior to entering the normal asexual cell cycle, can either renew its haploid state and further cyclically alternate between the haploid (in the G₁-phase) and diploid (in the G₂-phase) states, or can remain diploid and alternate between the diploid state (in the G₁-phase) and the tetraploid state (in the G₂-phase) for the time of its sexual reproduction. It is necessary to state that the ploidy of the cells is even greater in a great many differentiated tissues of multicellular organisms.

- see hybridogenesis