Charles Robert Darwin (1809–1882) (Fig. XXVIII.6) is certainly the most famous biologist of all time. Even in the absence of his work on the theory of evolution, his other discoveries in various fields of biology would be sufficient to make him renowned. Amongst other things, he discovered the mechanism of formation of corral atolls and the mechanism of the formation of soil through the activities of earthworms, he wrote a number of books, for example books about emotions in animals and about movement in plants, and also compiled an extensive monograph about barnacles. Simultaneously, Darwin had no formal education in biology. According to the wishes of his father, he began to study medicine, but was so bored that he abandoned his studies after one year. In the end, he completed three-year bachelor’s study in theology. During his studies, he was constantly interested in nature, especially geology and biology. He maintained contacts with the best scientists in his surroundings, collected various natural materials and systematically extended his knowledge through his own studies. After completing his studies, he took part in a five-year oceanic expedition, intended for mapping and exploring the shores of South America. Although he was originally accepted on board the research ship Beagle mainly because captain Fritzroy wanted company, he originally unofficially and later officially held the position of natural scientist of the expedition. During the expedition, he collected a great deal of knowledge in the fields of geology and biology, which later substantially affected his scientific ideas, and also gathered a extensive material in his collections, which he regularly sent to England. When he returned to London after the end of the expedition, at the age of 27, he already had the reputation of an important natural scientist. After his return, he married within 2 years and moved to the countryside after three years. He travelled to London only sporadically and travelled around England only to attend scientific meetings. However, he maintained very intense and extensive correspondence with domestic and foreign scientists and carefully followed all the contemporary professional literature. Darwin’s entries in his working daybooks indicate that he began to formulate his theory of evolution around 1837. In 1844, he drew up a 230-page description of his theory of evolution and asked his wife to publish it if he were to die prematurely. Until 1858, he systematically prepared for publication of his theory of evolution and gradually gathered evidence and arguments in its favor and established a sufficiently strong scientific and social position to allow him to publish and defend his ideas. However, he never completed his fundamental and very extensive evolutionary work because, in 1858, a different British biologist, Alfred Russel Wallace (1823–1913) (Fig. XXVIII.7), sent him the manuscript of his work, in which he described his own version of the theory of evolution, asking him to evaluate and potentially publish it. Except for minor details, Wallace’s theory was practically identical with Darwin’s. Darwin’s friends finally arranged for Wallace’s manuscript to be read together with excerpts from Darwin’s manuscript of 1844 at the same meeting of the Linnean Society and both papers were subsequently published in the same edition of the Proceedings. In addition, Darwin interrupted his efforts on his extensive work and, instead, rapidly prepared an abbreviated version of “On the Origin of Species through Natural Selection” for publication.
Darwin’s theory of evolution, published in 1859, actually consists of at least five mutually complementary theories (Mayr 1982). Most of them had already appeared at the very least in intimations in the works of his predecessors; however, Darwin was the first to present them to the public in comprehensive form and to demonstrate their veracity by empirical facts.
The first of Darwin’s theories is the theory of the existence of the evolution of species. According to it, species are not invariant, but vary and can evolve over time. Lamarck propounded the same theory before him, but Darwin was the first to collect sufficient data (and social capital) to convince a large part of the professional public.
The second theory is the theory of the common origin of all species. Darwin postulated that species were formed and are still formed in evolution by divergence from a common ancestor. This theory meant a radical rejection of all the ideas about the independent, either natural or supernatural, creation of the individual species.
The third theory is the theory of the divergence of species in their phenotype traits. Darwin even proposed a mechanism that could lead to the divergence and mutual differentiation of individual species. This mechanism was founded on centrifugal selection and we now know that it is actually not very important in evolution in the suggested form. However, the fact that the organisms that are formed by divergence from a common ancestor can gradually differ more and more through the continuous accumulation of changes over time is more important than the actual mechanism of phenotype divergence. The general acceptance of this fact led to fundamental changes in the concept of systematic biology and in the approach to the creation of a taxonomic system.
The fourth theory is the theory of gradualism. According to it, species gradually evolve and change from one to another through the slow accumulation of minor changes. In his work, Darwin explicitly rejected the opposite possibility, i.e. saltationism, i.e. sudden changes in jumps from one species to a different species.
The fifth theory was the theory of natural selection as the main mechanism driving all evolutionary changes, whether the formation of adaptive traits, the formation of complexity or the formation of biological diversity. At the time of its publication, this part of the theory of evolution met the greatest resistance amongst the professional public. Especially paleontologists, but also a great many biologists, including Darwin’s greatest supporters, had serious doubts about the importance of natural selection. In fact, their arguments convinced Darwin to gradually admit the possibility of other mechanisms, including the heritability of acquired traits, in his later editions of the “On the Origin of Species”.
Before he died, Darwin published a number of other extensive works, in which he elaborated his theory of evolution. Of his most important evolutionary discoveries, mention should be made of the discovery of sexual selection as a mechanism acting independently of natural selection. According to Darwin, sexual selection, i.e. selection that occurs in the choice of sexual partners, enables explanation of a number of biological phenomena, including a great many aspects of human evolution. On the other hand, another of Darwin’s theories of evolution, i.e. the theory of inheritability, was erroneous right from the beginning and is currently only of historical importance.
see Rates of anagenetic changes
see Dawkinsian evolution
History of evolutionism – post-neo-Darwinist period
The emergence of amphimixis also brought about the creation of extraordinarily favorable conditions for the spreading of a number of types of ultraselfish genes, i.e. genes that spread in the population even when they simultaneously reduce the fitness of their carriers. While, in asexually reproducing organisms, the fate of the individual gene is permanently connected with the genome in which it occurs, and the gene must thus be more or less loyal to the other genes, in organisms with amphimixis, a gene or, to be more exact, the allele of a certain gene appears in a different genome in every generation. As a consequence, classical Darwinian evolution, in which those alleles that increase the fitness of their carriers are fixed, changes into Dawkinsian evolution (see IV.9.1). During Dawkinsian evolution, preferentially those alleles that are capable of ensuring propagation of their copies at the expense of copies of other alleles in the same locus and sometimes at the expense of the fitness of their carrier are preferentially fixed – see the bluebeard model in Section IV.9.1 (Dawkins 1976; Dawkins 1982). The main driving force for evolution ceased to be competition between individuals within a population and became competition between alleles within the individual loci (Tab. XII.1). The ability of alleles to program the traits or behavior of their hosts so as to gain advantages in intra-species competition became only one of many strategies through which the allele can ensure its preferential spreading within the population.
see History of evolutionism – classical Darwinist period
see Mass extinction, after the end of mass extinction events
see Clonal reproduction in parasitic organisms - role of
see Point mutations and also Mutations at the level of the entire DNA section
The progress of cladogenesis can be depicted in a graphical form, called a tree graph, a dendrogram, by mathematicians, and simply a tree by biologists. It would be logical to call a tree depicting cladogenesis a cladogram. However, at the present time, a large number of authors use the term cladogram to denote the tree formed using cladistic methods, not depicting the progress of cladogenesis but rather the distribution of apomorphies (i.e. new evolutionary features – see below) within studied taxonomical units, most frequently species. Consequently, the tree describing cladogenesis will be denoted in the following text by the rather awkward term scheme of cladogenesis. The tree consists of a system of gradually branching out lines, termed branches, where the order and sites of branching, i.e. distribution of nodes, reflects the time order of the mutual splitting off of the phylogenetic lines (Fig. XXIII.4). Each branch (line joining two nodes) depicts a single species and its final node corresponds to the particular species at the instant of speciation. The branches originate from a particular single node denoting the individual phylogenetic lines of organisms. The phylogenetic line can contain several species or just a single species. For the purposes of phylogenetic studies, the species of a single phylogenetic line form an operational taxonomic unit (OTU). For example, however, in phenetics (see XXV.2.1), OTU need not be formed of species of the same phylogenetic line, but of species that have a certain type of phenotype similarity. In contrast to regular taxa, it is not necessary to name the individual OTU or to find a formal taxonomic level (rank) for them. The root of the tree, i.e. the lowest branch, from which all the other branches split off in a certain order, denotes the common ancestor of all the studied species, and the terminal branches correspond to the individual species that were included in the analysis. The arrangement of the inner branches in the direction from the root to the terminal branches of the tree denotes the order of splitting off of the ancestors of the individual species included in the analysis. As the species last for only a limited period of time and sooner or later die out, most of the inner branches of the tree denote already extinct ancestors of modern species. If the analysis includes only living species of organisms, the ancestors are hypothetical, whose existence has been derived on the basis of the traits of modern, i.e. neontological species. In contrast, if the scheme also includes species living on the Earth in the past and thus known only from the paleontological record, these species can also be placed on one of the inner branches of the graph depicting the cladogenesis scheme. However, even in this case, all the species are again placed on terminal branches on trees if they are created by cladistic methods. The length of the branches on the graph and the angles enclosed by the individual branches do not have any biological meaning. If the length of the branches were to correspond to the duration of the individual species or number of evolutionary changes that occurred in the individual branches, this would no loner be a cladogenesis scheme, but rather a phylogenetic tree, i.e. a phylogram.
see Taxonomic system types
It is quite clear that the process of evolutionary biology is a stochastic process. Living organisms and their environment, i.e. the system in which the process occurs, contain an enormous number of elements whose behaviour is determined to a greater or lesser degree by chance.
If an advantageous new mutation appears in the DNA of an individual, that brings its bearer increased resistance to a certain disease, we could theoretically expect that the descendants of this mutant will gradually become predominant in the population, i.e. that the particular mutation will become fixed. In actual fact, this need not occur. The resistant mutant could be killed while still young by a falling tree, could be eaten by a predator, or the particular population need not necessarily encounter the relevant disease for a long time. Thus, the potentially advantageous mutation will most probably be eliminated by genetic drift.
Mutations themselves occur more or less by chance, so that the character and order in time of their occurrence cannot be in any way predicted. On the other hand, it must be admitted that some micro-evolutionary processes are highly deterministic, such as natural selection, molecular drive, meiotic drive. This means that, in short experiments, we are frequently capable of predicting the course of the relevant micro-evolutionary changes on the basis of the properties of the individual organisms. When several islands in the Greater Antilles were experimentally colonized by populations of small lizards of the Anolis genus, it could be observed that genetic fixation of very similar morphological changes occurred in all the populations after several years. In contrast, as a consequence of participation in the random process of mutagenesis, the results of repeated laboratory experiments, in which the microevolution of bacterial populations is modelled under strictly controlled conditions of continuous cultivation, are frequently quite different.
Biological evolution as a whole, i.e. encompassing both microevolutionary and macroevolutionary processes, is a very long-term process. Simultaneously, organisms are systems with a memory, whose future development depends on the development that they underwent in the past. The effects of random processes also logically accumulate andare amplified. If it were possible to perform a long-term evolutionary experiment consisting, for example, in colonizing completely identical islands with completely identical species of organisms and subsequent long-term observation of the evolution of these species on the individual islands, it is quite certain that the flora and fauna of the individual islands would gradually become different through the effect of random processes.
Evolutionary processes are governed by their own laws. As we gradually come to understand these laws, we are increasingly capable of predicting the course of evolutionary processes. As the element of chance plays a role in evolutionary processes in many respects, it is quite impossible that we would be able, sometime in the future, to specifically (and thus not statistically) predict the course of biological evolution of some species of organism. The influence of chance similarly excludes the possibility that evolution could occur in exactly the same way at two places in the universe, i.e. that the same kinds of organisms could develop on two different planets.
The role of epigenetic processes is of fundamental importance for the development of multicellular organisms. If these processes did not participate, the results of individual development would be extremely sensitive to various random internal and external disturbances. For example, if the length of a vein that is intended to supply the brain with blood were determined by the number of times that its cells divided during embryogenesis, where the number of cell divisions would be determined genetically, any mutation or intervention from the environment affecting the length of the individual would have catastrophic consequences for the viability of the organism. In such a case, the relevant vein would not reach to the brain or it would be narrowed or interrupted, the brain would not be supplied with blood and its tissues would die. In contrast, if the length of the vein is determined epigenetically, for example, by the fact that its cells should renew division when the mechanical strain on a forming vein, fixed at one end to the heart and at the other to the head part of the embryo, exceeds a certain value, it will be ensured that the vein will always reach from the heart to the brain regardless of whether, under the effect of a mutation or unusual external conditions, a very short or long neck were to form in the particular embryo. The existence of self-regulation epigenetic processes is probably the most important source of developmental canalization (directing), i.e. the resistance of developmental processes to the action of genetic and environmental disturbances (Wilkins 1997; Wagner 1996; Hartman, Garvik, & Hartwell 2001). The term developmental canalization is understood by various authors as both the actual resistance of developmental processes against disturbances and also the process of evolutionary accumulation of alleles that determine this resistance through their effects. C.H. Waddington studied canalization by genetic methods in the 1950’s and 1960’s. At the present time, this phenomenon is also being studied at a molecular level primarily on organisms into whose genome a certain gene has been inserted (transgenic organisms) or on organisms with targeted removal or inactivation of genes (knock-out organisms). It was found that similar interventions frequently have only a surprisingly small effect on the phenotype of the organism. Thus, development is generally well buffered against drastic changes in the external environment. If, on the other hand, the phenotype of organisms differs substantially according to the conditions under which they developed, which frequently occurs especially in plants (Pigliucci 1998) and somewhat less frequently in some animals (Gotthard & Nylin 1995; Brönmark & Miner 1992), then this developmental plasticity is mostly genetically programmed in advance; from the standpoint of the viability of the organisms in the particular environment, it is usually useful and the relevant mechanisms of its formation and functioning arose in the course of evolution through natural selection.
It is advantageous for organisms if they are able to modify their ontogenesis in dependence on the local conditions in which they find themselves. This ability is especially advantageous for immobile organisms that are bound all their lives to the place where they were born and grew up. It is thus encountered primarily in plants (Pigliucci 1998) and to a lesser degree in other organisms (Gotthard & Nylin 1995; Brönmark & Miner 1992). In a great many species of plants, the phenotype of individuals growing at relatively dry sites differs from the phenotype of individuals at damp sites; however, frequently even the phenotype of separate parts of a single individual differs in dependence on the local conditions (Fig. XII.12). The phenotype of water plants differs according to the speed of water flow at the particular sites. In a great many species of plants, preference is given to the phase formed by the vegetative or by the reproductive organs, in dependence on the amount of resources available to the particular individual. Development of the organism is thus programmed so that it occurs in dependence on the external conditions and so that it results in an individual with the phenotype that is best adapted to these local conditions. The ability to purposefully modify ontogenesis in dependence on the external conditions is called developmental plasticity. From the viewpoint of the individual, it is advantageous if its phenotype corresponds best to the local conditions of the environment in which it finds itself. However, from the standpoint of the existence of the species, adaptive developmental plasticity reduces the ability of the species to submit to the action of selection pressure in the environment, and thus to evolutionarily adapt to changing conditions. If the environment undergoes cyclic changes, i.e. oscillates between several different states at regular or irregular intervals, this evolutionary stability of the species can be advantageous, as it reduces the substitution burden to which the species would otherwise be exposed. In contrast, if the changes are acyclic and irreversible or cyclic, but with a periodicity that is comparable with the usual length of existence of the species, developmental plasticity and the related reduced evolutionary plasticity will decrease the chance of long-term survival of the particular species. While species without developmental plasticity have a chance to gradually adapt to the particular changes in the environment as a consequence of the action of selection, a developmentally plastic species only avoids the relevant selection pressure temporarily and frequently imperfectly within the limits of its developmental plasticity. Whether and how much developmental plasticity actually reduces the evolutionary potential of a species is still a subject of discussion. The fact that, on a drastic change in the conditions in the external environment, it partly protects the species against the action of selection, simultaneously provides the species with time to accumulate mutations that gradually lead to the formation of adaptive adjustment to the new conditions (see XVI.3.1). See also developmental canalization.
A typological species can be defined on the basis of any trait occurring in at least some life stage of a member of the given species, where possible in all the individuals in the population. Simultaneously, theoretically any trait that can form the basis for differentiation of the members of a certain species from other species can be used as a diagnostic trait, i.e. a trait according to which membership in a particular species is recognized. The main criterion for a trait designated for definition of a typological species is its presence in the greatest possible number of individuals in the largest possible number of individuals. An ideal trait would occur in all the individuals in all the populations; however, it is frequently not an easy matter to find such a trait (Wiens & Servedio 2000). In contrast, the choice of a diagnostic trait is governed mainly by pragmatic considerations. Primarily a trait for which there is the lowest risk of a mistake in determining the species is chosen as a diagnostic trait. If, for example, it were necessary to decide whether to chose as the diagnostic trait morphological structure A, occurring only in the given species, in all the individuals, but which is difficult to distinguish, so that its presence is not found in 80% of individuals, or whether to chose morphological structure B, which occurs in only 90% of individuals, but whose presence or absence can be determined with 100% certainty, then obviously structure B is preferable. A side effect of the application of the definition of diagnostic traits is also that traits that do not have any relationship to the causes or mechanisms of evolutionary differentiation of the given species are employed as traits to differentiate the individual species in the vast majority of cases. If, for example, speciation occurred in a certain plant pest as a consequence of reorientation of part of the population to a new species of plant food, then the diagnostic trait could be chosen as the presence of a structure that is not in any way connected with the move to the new host species, for example a trait on the genitals rather than the ability to decompose a secondary metabolite of the new host species.
see History of evolutionism - pre-Darwinist period
See inclusive fitness.
see Environmentally directed mutations
Sharp discontinuities exist in the paleontological record, where the species composition of the leading (i.e. most frequent) fossils suddenly changed in certain neighboring layers. Today, it is apparent that these discontinuities were caused by mass extinction, during which the rate of extinction increased many fold. In the periods following mass extinction, the number of species and the sizes of their populations were renewed with a certain delay; however, in a number of cases, the species composition of the renewed communities changed drastically. While the members of a certain taxon dominated in the individual communities in the period that preceded the mass extinction, in the following period the members of this taxon were of only marginal importance and their place could be occupied by the members of some other taxon. On the basis of the existence of a great many more or less marked periods of extinction that affected communities over a wide territory or even life on a global scale, the history of evolution during the Phanerozoic eon, i.e. the period from which numerous fossils of multi-celled organisms with hard skeletons or shells are available, can be divided into time zones: eras (e.g. Palaeozoic), periods (e.g. Permian), epochs (e.g. the Early Devonian) and ages (e.g. Lochkov), see the Fig. XXII.4 . Simultaneously, the individual time zones differ in the compositions of their fauna and flora.
Dissipation systems are systemscapable of spontaneously adopting a state of relatively greater organization and of remaining in this state at the expense of the energy that flows through them.
Mutationsin the narrow sense of the word refer to changes in the structure of the genetic material, i.e. in the DNA for most organisms, in which the sense of the genetic information is changed, without violating the syntactic rules of its writing.If the change violates these rules, for example, if depurination of certain nucleotides (or whole DNA sections) occurs or if a single-strand or double-strand break occurs, then this is termed DNA damage.The cell contains a number of enzyme systems capable of recognizing and repairing damaged sites.In some cases, the repair can be perfect and can renew the original information sense of the given DNA section.However, sometimes, repair is not possible and the cell can thus be permanently prevented from undergoing DNA replication and division.The repair very frequently renews the physical intactness of the DNA; however, it does not renew the original information content – mutations occur.Repair processes are apparently amongst the most important sources of mutations.
see History of evolutionism - neo-Darwinist period
Reproductive isolation postzygotic
The heterogametic sex differs from the homogametic sex in that the pair sex chromosome (X or Z) is contained in its cells in only a single copy. While, for autosomes, the F1-hybrids of both sexes contain the complete chromosomal set from each species; for the X-chromosome this is true only for females. In the first half of the 20th century, Dobzhansky and Muller (Dobzhansky 1936; Muller 1940) pointed out that, in cases where some of the genes on the autosomes derived from a species from which an allosome is derived, i.e. an unpaired sex chromosome (Y or W), are not sufficiently compatible with the corresponding genes on the X-chromosome (Z-chromosome) derived from the second species, the hybrid members of the heterogametic sex will probably have reduced fitness (Fig. XXI.9). It is apparent that a second necessary precondition for the reduced fitness of these hybrids lies in the highly recessive nature of the interactions between the participating alleles. The term dominance hypothesis is derived from this; the designation began to be used for the Dobzhansky - Muller hypothesis after H.A. Orr demonstrated, on the basis of analysis of a mathematical model of this phenomenon, that key importance in the formation of phenomena responsible for the Haldane rule lies in the average degree of dominance of phenotype manifestations of the relevant interactions (Orr 1993). If the functions of the given genes were ensured by the products of mutually interacting genes from the chromosome set of the species from which the X-chromosome was derived, the incompatibility of the autosomes of one species with the X-chromosome of the other species should not be manifested in the phenotype. If the average degree of dominance of the negative effects of the products of interacting genes were greater than 0.5, the homogametic sex would be affected more. As females have two X-chromosomes, they should have twice as many incompatible genes. The requirement of low dominance of negative manifestations of common products of incompatible genes will apparently not be very restrictive. The commonest type of disorder will tend to be loss of functioning of a certain molecular complex, i.e. an effect that is, in its nature, usually recessive.
For a long time, the most serious obstacle in accepting the dominance hypothesis came from the results of genetic experiments in which female drosophila with an “unbalanced” genome were prepared by an ingenious procedure, i.e. with a genome containing one complete set of autosomes from each parent species, and simultaneously both X-chromosomes derived from the same species (Coyne 1985a). On the basis of the dominance hypothesis, we would expect that these females would have viability and fertility reduced to the same degree as hybrid males. However, it was found that this assumption is valid only for their viability; they have the same fertility as normal hybrid females, i.e. substantially greater than hybrid males. Several possible explanations of these experiments have been proposed to date (Turelli & Orr 1995; Orr & Turelli 1996; Gorshkov & Makarieva 1999); a frequently accepted explanation consists in the faster male hypothesis (XXI.4.3.2) and another very probable explanation will be discussed in the section concerned with the somatic mutation hypothesis (XXI.4.3.5).
The fact that X-chromosomes are important for existence of the Haldane rule for sterility is confirmed by comparison of species in which the X-chromosomes are large with species in which the X-chromosomes are small and thus contain a smaller number of all genes. Such a comparison can be performed for the Drosophila genus, where there are groups of species whose X-chromosomes bear approximately 20% of the genes and groups of species whose large X-chromosomes bear approximately 40% of all the genes present in the genome of the particular species. A study encompassing 81 interspecific hybridizations of Drosophila with smaller X-chromosomes and 44 interspecific hybridizations of Drosophila with large X-chromosomes indicated that the F1-males of species with large X-chromosomes have relatively more reduced fitness than the F1-males of species with smaller X-chromosomes (Turelli & Begun 1997).
The major effect of the X-chromosome on the fertility of hybrids is sometimes explained not only in that they are present in only one copy in the genome of the males, but also its anticipated greater content of genes responsible for interspecific incompatibility. This effect, in itself, has become the subject of a great many discussions and independent studies. Usually, the possible greater content of incompatible genes is explained as a result of faster fixation of recessive adaptive mutations on this chromosome and thus greater interspecific divergence of the X-chromosomes compared with the divergence of the autosomes (Charlesworth, Coyne, & Barton 1987). While the presence of recessive mutations is not manifested on the autosomes, as its effect is masked by the standard allele on the other chromosome, the presence of a recessive mutation on the X-chromosome of males is manifested in males and can immediately be an object of selection. Negative mutations are understandably eliminated faster on X-chromosomes than on autosomes; however, these mutations are rarely fixed and thus mostly do not contribute to interspecific genetic divergence.
However, it should be pointed out that the very existence of this phenomenon, i.e. of a large content of genes responsible for the sterility of hybrids on the X-chromosome, is occasionally thrown into doubt. For example, experiments have been performed in which the methods of classical genetics were employed to introduce, into the genome of an individual of one species, in place of its own chromosome sections, the corresponding sections from a foreign species. In some cases, it was demonstrated, and in others not demonstrated (Hollocher & Wu 1996; True, Weir, & Laurie 1996; Jiggins et al. 2001) that there is a substantial difference between situations when a DNA section was inserted into the X-chromosome of a male and when an identically long homological section of foreign DNA was inserted into both its autosomes.
The dominance hypothesis is not relevant only for the interactions of autosomes and X-chromosomes, but can also be applied to other types of interactions leading to manifestation of the Haldane rule. It has been found that interactions between X- and Y-chromosomes, Y-chromosomes and autosomes and between chromosomes, especially an X-chromosome and cytoplasm, can be very important here (Turelli & Orr 2000). Interactions involving the Y-chromosome increase manifestations of the Haldane rule on the sterility of members of the relevant heterogamete sex in all species. However, from the viewpoint of viability, because of the low number of functional genes on the usual, i.e. differentiated type of Y-chromosome, they are apparently of very little importance. Interactions with participation by the cytoplasm, include both interactions between genetic elements in the cytoplasm derived from one and from the other species, i.e., for example between proteins synthesized in the zygote and in the parent cell. Interactions between the cytoplasm and genes on the sex chromosomes weaken the manifestations of the Haldane rule in species with heterogametic males. The cytoplasm and the X-heterochromosome of hybrids of male sex are derived from the same species here. In species with heterogametic females, to the contrary, these interactions increase the manifestations of the Haldane rule, as here the cytoplasm and Y (in fact W) chromosome are derived from different species.
Dominant and recessive relationships are the best known forms of gene interaction between alleles within a single locus. (See also Gene interactions). Diploid organisms have two alleles from each gene. If both alleles at a given locus are the same, then (from the standpoint of the particular gene) this is termed a homozygote individual, a homozygote. If the two alleles differ, then this is a heterozygote individual, a heterozygote. The manifestation of each allele can depend on the second allele in the given locus for the particular individual. It very often happens that a particular allele is recessive, i.e. it is manifested in the phenotype only when present in two copies in the given individual, i.e. in a recessive homozygote. A dominant allele is the opposite of a recessive allele. Its presence is manifested in the same way both in a carrier of two copies of the given allele, i.e. in a dominant homozygote, and in a heterozygote, i.e. in an individual in which it is present in only one copy. The degree to which semi-dominant alleles, i.e. alleles with partial dominance, are manifested in the phenotype of an individual depends on whether they occur in the genotype of the given individual in one or both copies. In co-dominance, the two alleles present are manifested to the same degree to which they would be manifested in the relevant homozygotes. While, in partial dominance, the degree of manifestation of the two alleles in a heterozygote is less than for one or the other homozygote, in super-dominance, the expression of the given trait is greater in a heterozygote than in either of the two homozygotes. Interactions between alleles of a single locus can be divided schematically only if these alleles are manifested in the degree of the phenotype expression of a simple quantitative trait. For traits of qualitative character, it is mostly possible to differentiate only between dominant and recessive alleles; mutual differentiation of alleles with partial dominance, super-dominance and co-dominance is usually rather difficult or even impossible.
The picture is further complicated by the fact that that there are usually more than two alleles of a single gene and also by the fact that dominance is a relative matter, i.e. the matter of the relationship between two specific alleles of a given gene, rather than an absolute property of a particular allele. Allele a1 can act as dominant in relation to allele a2, allele a2 as dominant in relation to allele a3 and simultaneously allele a3 as dominant in relation to allele a1. So that the subject of dominance and recessivity is even more complicated, it is necessary to point out the fact that a particular relationship between two particular alleles can also depend on the context, i.e. the effects of genes present at other loci can also be important. In the presence of a particular allele at locus B, allele a1of locus A can be dominant in relation to allele a2; in the context of a different allele at locus B, allele a1can, on the other hand, act as recessive towards allele a2
A certain amount of direct and indirect evidence demonstrates that the dominance of alleles is actually a more complex phenomenon that is, itself, the subject of biological evolution (Bourguet 2001). For example, it was repeatedly found that, in the natural population, the most common alleles are usually dominant and, on the other hand, minority alleles are frequently recessive. If, on the other hand, we isolate individuals in the laboratory that bear two newly formed mutated alleles, or if we obtain individuals bearing minority alleles in mutually isolated natural populations, then the relationship of partial dominance is mostly found between their alleles. For different explanation of the phenomenon see also Haldane’s sieve.
Certain types of organisms produce dormant (i.e. idle) stages that can remain in the environment for a very long time. Spores of many microorganisms or the seeds of some plants are typical examples of these dormant stages. It is known that the seeds of many plant species accumulate in the soil for long periods of time and sprout only when the particular location offers convenient conditions, for example after the forest in that location has been destroyed by fire. Just as migrants can transfer genes in space from one local population to others, even very distant ones, dormant stages can transfer genes from one generation to others, also very distant ones, in time. In a similar way as the heterogeneity of the environment and the ensuing heterogeneity of selection pressures can lead to differences in the gene pools of two distant populations, the gene pool of a local population can also gradually change as a result of changing local conditions. Migrants in space and migrants in time can thus introduce alleles into the gene pool of the local population, which are no longer present there or which occur with low frequency. In this way, gene flow in time facilitated by dormant stages can enhance the genetic polymorphism of populations or hinder their optimal adaptation to local conditions (see below).
see Evolutionarily stable strategy
see vertical transmission of parasites and virulence