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r - selection

see selection r- and K

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

Ramets

see Genet

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

Range

see Metapopulation

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

Rapoport’s rule

see Gene flow and range of a species

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

Rare male advantage phenomenon

see Selection frequency dependent

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

Rate of evolytion of quantitative traits, units

For quantitative traits, either morphological or other traits, the rate of their evolution can be measured, for example, in units (e.g. in millimetres) by which the particular trait changes for an average member of the particular species over 1 million years. Because, in small structures, growth by 1 millimetre corresponds to a far more substantial evolutionary change than for large structures, it is more common to give the rate of evolution in percentage or in multiples of the standard deviation over a certain time interval. The best known unit used for measuring the rate of evolution of quantitative traits is the Darwin, where a rate of 1 Darwin corresponds to the rate of change of a structure that changed approximately 2.7182 times over 1 million years, i.e. by a multiple of the base of the natural logarithm. The rate of an evolutionary change in Darwins can thus be calculated using the equation
 
v =   (ln X1 – lnX2) / t
 
where X1 is the original size of the structure, X2 is the new size of the structure and t is the time interval (in million years) during which evolution of this structure occurred. As the change is calculated as the difference in natural logarithms, it actually corresponds to the ratio of the original and new sizes of the structure and consequently the calculated rate does not depend on the units employed or on the absolute size of the studied structures. Understandably, a different rate would be measured if we were to monitor the rate of a change in the length of a certain structure, its area or its volume. Thus, if we want to compare the rates of evolution of fleas and elephants, we can employ the Darwin rate unit, but we must be careful and ensure that we do not compare a change in length with a change in volume.
            The Haldane is another well-known unit used to express the rate of evolutionary changes in quantitative traits (Hendry & Kinnison 1999). A rate of 1 Haldane corresponds to a change in the size of the trait by one standard deviation per generation. Rates given in this unit also take into account the variability in the studied trait and the generation time of the studied species, so that they are more useful for comparing the abilities of species to respond to selection with a certain intensity. In addition, Darwins cannot be used to measure the rate of evolution of quantitative traits expressed on an interval scale. If, for example, we measure the rate of evolution of body temperature expressed in degrees Celsius or Kelvins, a different number is obtained in each case. However, if this rate is measured in Haldanes, the same number is obtained for both scales. If we compare the rates of evolution of two species calculated in Darwins and Haldanes, quite the opposite results can frequently be obtained. Consequently, where possible, it is mostly preferable to give the evolutionary rate in both units (Hendry & Kinnison 1999).

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

Rate taxonomic

Important method of measuring the rate of evolution consists in measuring the number of new species or arbitrary higher taxa formed within a certain line or that, on the other hand, disappear over a certain time interval (Simpson 1944). The method is based on the assumption that new species or higher taxa are defined by an expert on the particular group on the basis of a greater number of traits, taking into account the overall intraspecies and interspecies variability within the entire relevant taxon, and of the mutual interconnection or, to the contrary, independence of the changes in the individual traits. The individual traits and thus also evolutionary changes are often mutually dependent and thus a change in a certain trait for functional or ecological reasons can be automatically accompanied by changes in an entire range of other traits. Two forms of an organism that differ in a set of 50 interconnected traits can thus be much closer than two forms that differ in 5 independent traits. The number of new species formed in a certain time interval should thus reflect more accurately the rate of evolution of the given group rather than mechanically correspond to the sum of the number of traits that change in the given period within the particular taxon. The rate measured in terms of changes in the number of species per time interval, most frequently the fraction of species that became extinct in this interval, is termed the taxonomic rate. Once again, it holds that it is necessary to compare taxonomic rates within a single line or at least within related lines. Further, it is necessary to take into consideration changes in the numbers of species within the particular line; it is not possible to mechanically compare the taxonomic rate of a line that is dying out at the particular time with the taxonomic rate of a line that is in equilibrium state or that is growing.

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

Rates of anagenetic changes

There are species and entire phylogenetic lines in which anagenetic changes occur very rapidly during evolution. In contrast, other species and other lines developed very slowly or did not change at all over a long time. In addition, the rate of evolution within a single phylogenetic line can change substantially over time – it can be small initially, can grow many fold within a certain interval and can then remain completely or almost completely unchanged. A sudden increase in evolutionary rate is generally connected with adaptive radiation of the given line; however, in many cases the reasons for the change remain unclear.
Where the evolution occurs at the usual rate, it is termed horotelic evolution. If its rate is less than normal, this is termed bradytelic evolution, while that with unusually high rate is termed tachytelic evolution. It is obvious that there are no absolute borderlines between the individual types of evolution and that inclusion of a certain species in one of these categories also depends on the evolutionary lines within which we attempt to define the individual categories in relation to one another. Bradytelic species within a rapidly evolving line can change faster in evolution than tachytelic species in a line in which most species evolve slowly. Simpson originally introduced these terms to categorize the taxonomic rate (see below) and defined its individual types on the basis of the character of categorization of the rates within a particular taxon (Simpson 1944). He demonstrated, for example, that the histograms of the number of genera evolving at a certain rate are highly unsymmetrical, where most of the species form a single, generally narrow peak on the graph and the numbers of genera evolving at slower or faster rates rapidly decrease on both sides of the graph. Simultaneously, especially on the side of more slowly evolving genera (and also frequently on the side of species evolving very rapidly) there is a statistically significant surplus of species in a great many taxa that evolve at a very slow or very fast rate. Simpson emphasized that, because of the statistical character of the method through which the individual categories of evolutionary rate are defined, we cannot speak about a specific bradytelic or tachytelic species, but only of groups of bradytelic or tachytelic species (Simpson 1961).
These terms are currently very frequently used in a broader sense and are also related to the rate of anagenetic changes. One of the attempts to make the individual categories of evolution more objective is based on comparison of the rate of anagenetic changes in a certain line with the theoretical rate of evolutionary changes occurring through the action of genetic drift. Then changes occurring more slowly than the minimum rate corresponding to genetic drift can be termed bradytelic evolution, while changes occurring at a faster rate that the theoretical rate of genetic drift in a population of the given size can be termed tachytelic. Rates falling in the interval between the theoretically minimum and maximum rates of drift can be termed horotelic. If a certain line evolves at a bradytelic rate, it is apparent that genetic drift is prevented by normalized (centripetal) selection or by evolutionary limitations. On the other hand, in cases of tachytelic evolution, it is apparent that the change is caused by directional selection and not genetic drift. This categorization of rates of evolution has the chief disadvantage that it is rather difficult, in practice, calculate the theoretical rate of genetic drift.
Some authors also mention ultrabradytelic evolution as a separate category. Microscopic organisms evolved at ultrabradytelic rates throughout the entire Paleoproterozoic and Mezoproterozoic, i.e. at least in the period 3.5 to 1.1 billion years ago (Schopf 1980). Some studies state that the period of ultrabradytelic evolution lasted to the beginning of the Phanerozoic, i.e. until 600 million years ago (Schopf 1994). During the Phanerozoic, only asexual organisms evolved at ultrabradytelic rates. For example, it is known that a great many blue-green algae described on the basis of microfossils from the Proterozoic are morphologically almost identical with modern species of blue-green algae (Schopf 1994). It is not clear whether ultrabradytelic evolution is specific for only blue-green algae (which are actually not algae at all, but bacteria) or whether it applies to all organisms living at the time of the Proterozoic and whether faster forms of evolution began only with the establishment of sexual reproduction, which could have occurred somewhere at the borderline between the Mezoproterozoic and Neoproterozoic.

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

Recessive gene hypothesis

The recessive gene hypothesis is another hypothesis explaining Haldane’s rule. It should be pointed out that the simple explanation offered by this hypothesis is not currently considered to be correct. In contrast to the dominance hypothesis, which assumes recessivity of genetic interactions, i.e. recessivity of phenotype manifestations of the joint products of at least pairs of genes, of which one is located, for example, on the sex chromosome and the other on the autosome, the recessive gene hypothesis directly considered the effect of the individual recessive genes without interactions. The X-chromosome is present in the hemizygous state in the cells of the heterogametic sex, i.e. is present in only a single copy, while it is present in the cells of the homogametic sex in two copies. The occurrence of any recessive mutation on the X-chromosome is thus necessarily manifested to a greater degree in the members of the heterogametic sex than in the members of the homogametic sex.
This model has two main inadequacies. The first problem consists in the fact that the effect of reduced fitness of the members of the heteogametic sex should be manifested in both hybrid and nonhybrid individuals. It is, of course, possible to argue that this effect is actually manifested in many species. For example in an ageing population, a gradual shift in the sex index in favor of members of the homogametic sex is often observed. It can be further objected that the negative effects need not be simply additive, but can grow at an faster rate (e.g. exponentially) with an increasing number of participating genes. Thus, the same number of recessive negative mutations can have a much greater effect in hybrids that have reduced fitness for a great many other reasons than in nonhybrid individuals. The existence of this nonlinearity, i.e. the snowball effect, is actually very probable. The individual genes can replace one another in their function. The probability that all mutually replaceable genes will be inactivated by mutations increases exponentially with the number of mutations in the genome (Orr & Turelli 2001).
A second, this time very substantial objection against the recessive gene hypothesis is that the number of recessive mutations on the X-chromosome should apparently be, on an average, much lower than in the genes on autosomes. While recessive negative mutations on autosomes can survive for a long time in the population, X-chromosomes with these mutations are constantly removed from the gene pool of the population by selection that acts on the members of the heterogametic sex. I am of the opinion that these objections were satisfied only by the hypothesis of somatic mutations (Gorshkov & Makar'eva 1999) (XXI.4.3.5), which can be considered to be a certain variation of the recessive gene hypothesis.

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

Reciprocal altruism

see Altruistic behavior evolution of

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

Reciprocal translocation

see Mutations at the level of the entire DNA section

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

Recombination

Recombination entails the exchange of a DNA section between two chromosomes or between two chromatids of a single chromosome. The actual mechanism of recombination is, in fact, far more complicated and includes, amongst other things, also synthesis of a new DNA chain and degradation of parts of the older chains. Recombination takes place primarily during meoisis and, less frequently, also during mitosis.

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

Red queen hypothesis in macroevolution

– see Extinctions, macroevolutionary trends

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

Red Queen principle

- Only those species that were capable of coming to terms with the fact that their environment constantly undergoes irreversible changes are encountered in nature. This means that these must always be species that are capable of evolution, i.e. those that are capable of forming new organs or patterns of behavior, through which they are able to effectively react to changes in the environment, especially to new evolutionary adaptation of the species with which they interact. As soon as a species is incapable of maintaining a sufficient tempo in this evolutionary race, it is eliminated, without regard as to whether it could be otherwise very well adapted to the abiotic conditions of its environment. This phenomenon is described by the Red Queen principle. This principle, named after the characters in Lewis Carroll’s book “Through the Looking Glass”, roughly states in its commonest form that “in nature, it is necessary to run as fast as possible to at least stay in the same place”. It follows from the Red Queen principle, specifically from the necessity of keeping pace with the evolution of the other species in the biosphere, for example that species with a mutation rate reduced to zero cannot exist in nature. From a short-term perspective, such a reduced mutation rate could be advantageous for the species, as most mutations are detrimental for their bearers and reduce the average viability and fertility of the population. However, from the long-term point of view, a reduction in the mutation rate in the population is destructive, because a species that mutates slowly is not capable of sufficiently rapidly and effectively reacting evolutionarily to emerging new evolutionary features in the species with which it interacts in its environment. The necessity of adapting the tempo of one’s own evolution to the tempo of evolution of other species is apparently the reason why very varied species of organisms have very similar mutation rates measured in the number of mutations per generation without regard to their complexity, the lengths of their life cycles or the size of their genomes (Drake 1999).
The Red Queen principle was first described and employed to explain macroevolutionary processes (van Valen 1973), but is also applied at least to the same degree for cyclic and acyclic microevolutionary processes (Grant & Grant 1995). Sexually reproducing species are capable of reacting to short-term, frequently cyclically repeated changes in the environment through a shift in the frequencies of the individual alleles in the population. These shifts are simultaneously adaptive, i.e. they assist the population to better survive under the altered conditions, and also reversible, as the frequency of the alleles more or less flexibly returns to its original value on a reverse change in the conditions. In contrast, asexually reproducing species are evolutionarily plastic, react more slowly but more intensively to selection pressures, but changes in the composition of the gene pool are usually irreversible and thus primarily consist in complete loss or, to the contrary, fixation of certain alleles (Flegr 1998). Consequently, when the conditions again change, they can easily be stranded in a valley of the adaptive landscape and are not capable of sufficiently rapidly returning to the originally occupied adaptive peak. This could be the cause of the lack of success of parthenogenetic species. While sexually reproducing species can adapt in microevolution to regular fluctuations in the natural conditions and simultaneously constantly remain close to a once-occupied adaptive peak, parthenogenetic species are not capable of sufficiently rapidly following changes in the position of their adaptive peaks, so the average fitness of their individuals in the population under unpredictably changing conditions is lower than that for sexually reproducing species.

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

Redeposition

see Fossils age of

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

Reinforcement

 

- As soon as postzygotic reproductive isolation barriers are formed for some reason between various forms in a single population, selection pressure immediately appears for the formation of prezygotic barriers, for example ethological barriers. If a particular mutant gains the ability to recognize whether or not its potential sexual partner is reproductively compatible with it and is capable of preferentially reproducing with compatible individuals, it immediately gains a selection advantage over the other members of the population.
The model of reinforcement of reproduction barriers through such selection (the reinforcement model) is frequently successfully applied to explaining processes occurring during secondary encounter of two populations that developed separately for a longer period of time and between whose members postzygotic reproductive isolation barriers have at least partially formed (Butlin & Tregenza 1997). If genetic variability exists in these populations in preference for sexual partners, the reinforcement mechanism can rapidly complete the formation of interspecific barriers. This mechanism has lower effectiveness for speciation that runs sympatrically from the very beginning. In these cases, the fitness of the less numerous form is fundamentally lower than that of the more numerous form, as its members more frequently encounter genetically incompatible sexual partners. The tendency to reproduce exclusively with the members of one’s own form can, in addition, substantially reduce the choice of potential sexual partners and thus even further reduce the chance of reproduction of individuals with emerging prezygotic isolation mechanisms. The ability to differ between the two forms is understandably also advantageous for the members of the less common form. A weak point of the reinforcement model lies in the risk that, before the reinforcement creates an impermeable reproductive barrier between the two species, the individual genes causing both postzygotic isolation and prezygotic preference for the members of a certain form as a consequence of genetic recombination will end up in the wrong gene pool and will thus reduce the chance of fixation of the genes for preference for one’s own form. However, experiments with artificial selection in favor of drosophila capable of discriminating between their own and foreign forms indicated that the isolation reinforcement mechanism is quite realistic and that sufficiently strong prezygotic isolation barriers can emerge within just a few generations (Rice & Hostert 1993).
The effectiveness of this mechanism has also been confirmed by observations of natural populations. While postzygotic reproduction barriers are equally strong between allopatric and sympatric pairs of drosophila species, prezygotic (ethological) barriers are much stronger for sympatric pairs and are formed in them much faster than for allopatric species (Coyne & Orr 1989). An old species of Galapagan finches, Certhidea fusca, which lives alone on the island, did not form a sufficiently strong ethological prezygotic reproductive isolation barrier even over 1.5 – 2 million years, while much younger species, occurring sympatrically on other islands, formed these barriers (recognition of species-specific song) over a much shorter time (Grant & Grant 2002). Similarly, a meta-study, i.e. a study performed by the methods of statistical meta-analysis on the basis of a great many formerly published works indicated that it holds for the most varied taxons that sympatric species have better developed traits according to which the members of a single species recognize one another and thus better developed prezygotic reproduction barriers than allopatric species (Noor 1999).
It can be objected that the cause of the stronger reproduction barriers in sympatric species does not lie in reinforcement but simply in the fact that species that did not have these barriers fused together and thus disappeared. This explanation is apparently erroneous as, in this case, the differences between sympatric and allopatric species would apply to both prezygotic and postzygotic barriers (Noor 1999).
            The mechanism of the reinforcement model is similar to the character displacement model (Schluter 2000). This describes the situation where two species with partly overlapping niches occur together at some places and independently at other places. In these cases, the ecological valence of the two species frequently differs between the two types. At places where the two species occur together and where they thus compete, ecological specialization and thus greater phenotype differentiation occur. In contrast, at places where only one species occurs, they have broader ecological valence and each species utilizes more resources from the environment and their phenotypes are more similar. The character displacement model differs from the reinforcement model primarily in that it can be valid only for reproductively isolated species. Moreover, the reinforcement model concerns the formation of reproduction barriers and not ecological specialization. Last but not least, the two models are based on somewhat different mechanisms (Schilthuizen 2000). While, in the case of reinforcement, individuals with imperfectly developed ability to discriminate between members of their own and a foreign species have lower fertility (because they produce more unviable crosses), in the case of displacement, unspecialized individuals have lower viability, because they attempt to utilize the resources for which the members of another species have specialized and are better adapted.

 

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Religions and to attacks on evolutionary theories

- The first and probably the most frequent reason for attack on the theory of evolution is its actual or apparent inconsistency of its conclusions with the ideological model of the world that is held by a certain person or, more frequently, group of persons. This model most frequently has the form of a religious or ideological system. The objective cause of the existence of attacks of this kind is quite apparent from the viewpoint of an evolutionary biologist. As pointed out in the chapter concerned with cultural evolution (XVII.4), long-term existence of ideological systems in society is possible only for those that have created internal or external mechanisms that ensure them this long survival and potential spreading at the expense of other ideological systems. Just such a very effective mechanism consists in intolerance of other ideological systems, organized or unorganized attempts of proponents of the particular system to eliminate, in the better case ideologically, in the worst case physically, the proponents of other systems or, even better, convert them to one’s own faith. If two religious systems exist next to one another, differing only in that one of them will require that its proponents acquire new members, it is quite obvious that it will predominate after a certain period of time. Understandably, some mechanisms permitting long-term survival or successful spreading of a certain ideological system can also be based on preferential biological survival and multiplication of the proponents of the particular system. From the point of view of the success of this ideological system, it makes no difference whether the greater fitness its proponents will be ensured by promotion of behavior amongst its bearers that increases the probability that they will survive to reproductive age in good health and economic condition, or simply by the fact that they will be prohibited to perform abortions and use contraception. I am not attempting to prove whether the theory of evolution is or is not compatible with a particular religious or ideological system. I am simply pointing out that, in my opinion, the theory of evolution is quite compatible, for example, with a Christian view of the word, in spite of the fact that the theory of evolution is very frequently attacked from this point of view at the present time.

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

Rensch

see History of evolutionism - neo-Darwinist period

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

Repairing mutations hypothesis of advantage of sexuality

In most species whose members can reproduce asexually, the series of asexual reproductions must be interrupted from time to time by sexual reproduction; otherwise the population gradually degenerates, reproduces ever more slowly and finally completely dies out. A single cycle of sexual reproduction is then capable of genetically rejuvenating the particular population, of renewing its reproductive potential and permitting its further existence. A number of authors assume that, during sexual reproduction, some so-far obscure mechanism repairs the mutations and damaged genetic material that have accumulated during the time of asexual reproduction (Bernstein et al. 1985; Avise 1993). If a point mutation occurs in the DNA, in which, for example, one nucleotide is replaced by another nucleotide, the enzymes of the reparation apparatus can find the place where this mutation occurred, as here the bases in the helix do not pair together; however, they cannot determine in which chain a nucleotide exchange occurred. If the cell contains a second copy of the given DNA section, e.g. if a normally haploid organism is passing through its diploid phase during sexual reproduction, the situation is far more favourable. The site where the bases do not pair can be repaired according to the sequence in the second copy of the given DNA section. If DNA replication occurs at the given site without previous reparation of nonpairing bases, the regular DNA structure is renewed and it is then more difficult to recognize the presence of a mutation. However, repair is possible even in this case (see XII.3 and Fig. XII.2). As even neutral mutations can be repaired in this way, this mechanism combined with sexual reproduction appears to be a powerful means of stopping Muller’s ratchet. On the other hand, in a changing environment, the repair of mutations can be disadvantageous in the long term, as it could prevent the particular species from adapting evolutionarily to on-going changes. It is possible that only certain gene sections in the genome could be protected in this way. This possibility is supported, for example, by the results of an in vitro study of the mutagenesis of the gene for DNA polymerase. The results indicated that a number of aminoacid substitutions can be created artificially at a critical site in the enzyme, while the activity or specificity of the mutated enzyme does not change fundamentally and even increases in some cases. Nonetheless, the vast majority of the so-far sequenced DNA polymerases from mutually unrelated organisms have identical or very similar sequences in the given section (Patel & Loeb 2000).

            While the advantageousness of the ability to repair mutations in the germinal line is somewhat doubtful, a similar ability to repair mutations in the somatic cell line is unambiguously advantageous.  According to some authors, diploidy, permitting repair of somatic mutations, is an essential condition for the existence of multicellular organisms (Gorshkov & Makar'eva 1999).

 

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

Reparation drive

It is frequently difficult to draw a sharp boundary line between mutation bias and reparation drive. Both processes have very similar external manifestations and similar or even identical molecular processes are responsible for them both. Nonetheless, it is apparently advantageous to differentiate between these closely related processes. While only the chemical-physical properties of nucleic acids or molecules that interact with the nucleic acids are responsible for mutation bias, reparation drive is a process whose manifestations are, at the very least, partly tuned, i.e. from a functional standpoint more or less optimized through natural selection. As a consequence of this tuning, mutation bias and reparation drive frequently act in opposite directions and neutralize one another in their effects. For example, methylated dinucleotides CG frequently mutate to TG, as deamination of methylated cytosine yields thymine. Consequently, the cell nucleus contains molecular repair systems that preferentially replace nucleotide T by nucleotide C at sites where the G-T pair is present instead of the G-C  pair in opposing positions on the DNA (Brown & Jiricny 1988). Where the mutation actually occurred through deamination of methylated cytosine, the repair system renews the original DNA sequence (Fig. VI.1a). Where the mutation occurred through some other mechanism and, on the other hand, the incorrect nucleotide is G in the opposing strand, the repair mechanism conserves the mutation (Fig. VI.1b). In DNA segments where deamination occurs very frequently, i.e. mutation bias leads to replacement of nucleotide C by nucleotide T, in segments where these mutations do not occur, in contrast, nucleotide T is replaced by nucleotide C through reparation drive.

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

Replica plating test

The best known experiments that tested whether mutations are random or environmentally directed consist in replica plating tests (Ledeberg & Ledeberg 1952)and also various variants of the fluctuation test (Luria & Delbruck 1943). In the replica plating test (Fig. III.6), a bacteria suspension is seeded on a Petri dish and, after small colonies are formed, they are imprinted using a large round stamp on a dish whose agar contains a suitable selection agent (e.g. a certain antiobiotic) and also on a dish without the antibiotic. Only colonies of mutated cells grow in the dish with the antibiotic. In the next phase, samples of the colonies are taken corresponding to the positions of the colonies of mutated cells in the dish without the antibiotic, i.e. samples of bacteria that never came into contact with this antibiotic, and their resistance is tested. If the mutations occurred only as a consequence of the action of the selection agent, the bacteria from these colonies should not be resistant. In contrast, if the mutations occurred randomly, bacteria from the original colonies should be resistant. The results of replica plating tests demonstrated that bacteria on the original dish are already resistant and thus that they mutated randomly.

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

Replicator

In classical Darwinian evolution, organisms have two functions. These are the replicator function, i.e. carriers of genetic information that enable transfer of information to further generations in more or less unaltered form, and also the interactor function, which enables the relevant genetic information to be manifested externally and to become a subject of natural selection (Dawkins 1976). Separation of the function of replicator and interactor, leading in sexually reproducing organisms to a substantial reduction in the heritability of fitness, probably has a fundamental impact on the character of the biological evolution of these organisms (see IV.9.2). While the properties of asexually reproducing organisms can evolve through natural selection for the whole term of existence of the species, the effectiveness of natural selection is very small under normal circumstances in sexually reproducing organisms because of the limited heritability of traits and the very limited heredity of fitness. Of course, this effectiveness increases very substantially in situations where the natural genetic polymorphism in the population is substantially limited and where a new mutation appears in each generation in the context of the same alleles and has the same effect on the fitness of its carriers. Under normal circumstances, this occurs primarily after a drastic reduction in the size of the population, which accompanies most types of speciation and the period immediately after speciation. While the properties of asexually reproducing species can change constantly through the effect of natural selection, in sexually reproducing species the periods of changes in properties are coincident with the moments of speciation, so that anagenesis is frequently temporally coincident with cladogenesis. Classical Darwinian gradualistic evolution can occur in nonsexually reproducing organisms while, in sexually reproducing organisms, evolution must have the character of punctuated evolution in the typical case (see XXVI.5.3).

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

Reproduction

Only systems containing elements or subsystems capable or propagation, reproduction can undergo natural selection and thereforebiological evolution. The reproduction mechanism can differ. Growth followed, after a certain period of time or after achieving a certain size, by division into two or more daughter individuals probably seems most natural to us. However, it should be emphasized that this is a highly “biocentric” point of view and, in actual fact, reproduction can occur through a quite different mechanism. Some transposons or viruses are actually copied and inserted to a new site on the genome, while others only rewrite a certain section of the DNA according to their own sequence in a process of gene conversion.  Thus physical reproduction does not actually occur at all; what is reproduced is the number of copies of certain information.

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

Reproductive isolation barriers

While, in species without sexual reproduction, the most important and critical step in speciation is differentiation of the niches of the parent and daughter species, amongst sexually reproducing species the most critical and apparently the first step in speciation consists in reproductive separation of part of the population. In the absence of this separation, crossing between members of the older and newer forms constantly blurs the phenotype differences, so that differentiation of niches cannot occur. However, if reproductive separation occurs, and this need not be initially accompanied by the existence of phenotype differences, preconditions are created for the emergence of these differences in the future. Mechanisms facilitating reproductive separation of part of the population can basically be divided into external and internal reproductive isolation mechanisms (RIM) (Fig. XXI.5). External reproductive isolation barriers exist in the environment independent of the existence and biological traits of organisms. In contrast, internal barriers are directly or indirectly determined by the genotype of the organism and emerge and disappear as a result of genetic processes, most frequently as a consequence of mutations or recombinations.

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

Reproductive isolation barriers external

- The environment of most species of organisms has a more or less heterogeneous character in space and time. The boundaries between the individual types of environment are usually sharply defined and can constitute important barriers preventing free movement of the members of a particular species from one side of the barrier to the other, or can at least retard this movement. This limits ecological and genetic interactions between the individual parts of the population, which can lead to phenotype and genetic differentiation of their members and to subsequent speciation.
Geographic isolation was discussed in Chap. XXI.3. Temporal isolation can occur, for example in species with a multi-year life cycle. In this case, the individual temporal cohorts of individuals that hatch and reproduce in individual years can be strictly separated. As a consequence, the adult members of the different cohorts never meet under normal conditions and thus gene flow cannot occur between the cohorts. If the spatial or temporal separation of populations lasts sufficiently long, this will most probably lead to allopatric speciation - the formation of internal reproductive isolation mechanisms that are capable of preventing crossing between the members of the two populations even after the external spatial or temporal barriers disappear. If the conditions of the environment at places occupied by the original and new populations differ substantially, then selection participates in the evolution of the species, in addition to evolutionary drives and genetic drift. This substantially accelerates the phenotype and genetic diversification of the populations. Genetic diversification also leads to faster establishment of reproductive barriers. For example, when trout were exposed to divergent selection in two different environments, a reproductive barrier developed within 13 generations (Hendry et al. 2000). Similarly, reproductive barriers evolved in lines of drosophila bred under different conditions, while these barriers were not formed between lines bred under identical conditions (Schluter 2001). Similar results were also obtained in studies of natural populations. For example, it was found for sticklebacks (Gasterosteus) that reproductive barriers are much stronger between allopatric species living in different types of environment, specifically between benetic species (bottom-dwelling species) and limnetic species (living in open water) than between allopatric species living in similar environments (Orr & Smith 1998).

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

Reproductive isolation barriers internal

- If new species evolve in the same territory or in neighboring territories, crossing can normally occur between their members and the occurrence of interspecific crosses would blur the boundaries between the species. This process can be prevented by various internal prezygotic and postzygotic reproductive isolation mechanisms.As a consequence of these mechanisms, internal postzygotic and prezygotic reproductive barriers exist between emerging species. Any ecological, ethological, physiological or biochemical factor reducing the probability of the formation of a hybrid zygote can be considered to be a prezygotic barrier. Any such factor that reduces the probability of development of these zygotes into adults capable of reproduction is considered to be a postzygotic barrier.
Spatial isolation of a sympatric species is an important prezygotic reproductive isolation mechanism (RIM). If two species inhabit different biotopes in a common range or utilize different plants for food within a single biotope, their members will encounter one another (and thus reproduce) far less frequently than members of the same species. Temporal isolation functions similarly. If two species occur in the same territory but are active at different times of the day, they need never meet. Temporal and spatial isolation can be included amongst both external and internal prezygotic reproductive barriers, as they can be substantially affected both by external factors and by genetically determined differences in the behavior of individuals in the two differentiating species.
Internal prezygotic RIM include ethological isolation mechanisms, which encompass specific patterns of behavior, through which the members of a single species communicate prior to reproduction or during its progress. Even very close species can differ substantially in the character and timing of these patterns of behavior, where differences in behavior can very effectively prevent interspecific crossing. Mutual seeking out of the members of the opposite sex for the purpose of reproduction is very frequently accompanied by unilateral or bilateral exchange of acoustic, chemical and/or mechanical signals. The receptors of these signals are generally very specific. For example, the receptors of acoustic signals do not register sounds whose frequency differs only slightly from that of the species-specific signal. Ethological isolation mechanisms can also be important for flowering plants. In this case, pollinators also participate in these mechanisms. The flower sends out species-specific optical or chemical signals, attracting certain species of pollinators. If two close species of plants differ in their signals, they can also differ in their spectra of pollinators. This can substantially reduce pollination of the oocytes by the pollen of a foreign species.
Morphological isolation is another type of prezygotic isolation mechanism. Put simply, the male and female sex organs of two individuals need not fit together (Sota & Kubota 1998). Great importance was attributed to morphological isolation in the past, especially amongst arthropods. It is known that even very closely related species of arthropods have very different shapes of their copulation organs. In a great many cases, related species can be differentiated only on the basis of the morphology of these organs. Frequently various complicated protrusions are formed on the copulation organs, so that they naturally evoke the idea of a sort of lock and key capable of ensuring an effective interspecific reproductive isolation barrier. However, at the present time, it seems that the evolutionary reasons for the formation and rapid development of complicated copulation organs in insects will lie elsewhere. Mechanical reproduction barriers are mostly rather ineffective and, in addition, the copulation organs also rapidly diverge in allopatric species {11021}. It is highly probable that this could entail a co-evolutionary battle between males and females over control of the fate of the ejaculate inside the female body. The female frequently has quite different biological interests in how to manage the sperm than those of the male that mated with her. While the female attempts within the context of cryptic female choice to select, from the sperm obtained from various males, that from the best-quality male, or attempts to ensure that the individual oocytes are fertilized by the sperm of different males, it is, to the contrary, advantageous for the male if the female employs his sperm to fertilize the greatest number of oocytes, regardless of his own genetic quality or the genetic quality of the female. In this co-evolutionary battle, the two sexes employ various ethological, chemical and mechanical weapons and counter-weapons, through which both sexes attempt to achieve their contradictory goals. Because of the co-evolutionary character of this battle, the evolution of the individual mechanisms and thus of the corresponding morphological structures is extremely fast. If, in the experiment, we prevent the males or females from responding to the evolutionary moves of the members of the opposite sex, they lose the co-evolutionary battle in a few generations and the results of copulation begin to be unilaterally advantageous for the members of the other sex (Fig. XXI.6). For example, in experiments, the males of drosophila were kept for long periods of time in the cultivation vessel, while the females were removed in each generation and replaced by “naive” females (i.e. females obtained from a different breeding). Within 30 generations, the experimental males already had 24% greater fitness compared with the control males. This was caused primarily by the fact that they were capable of copulating more frequently with females that formerly copulated with a different male and also by the fact that the females that copulated with them did not subsequently copulate with a different male. The means, or rather the chemical instruments, through which the males achieved this, simultaneously damaged the females in some way. Females that copulated with the experimental males exhibited substantially higher mortality than females that copulated with control males (Rice 1996). It is highly probable that the present-day complicated morphology of copulation organs is a result of just such a co-evolutionary battle and its interspecific differences are only a side effect of the accelerated evolution of these structures. 
            Gamete incompatibility represents another barrier preventing interspecific crossing. This barrier is especially important in species whose members release their gametes into the open environment, where they actively seek out one another. In many cases, the gametes seek one another through species-specific chemical attractants. It very often happens that the microgametes require specific molecules that enable them to penetrate into the macrogametes of their own species. It is significant that the surface proteins of a gamete are amongst the molecules with the greatest rate of evolutionary accumulation of nonsynonymous changes. Gamete incompatibility is very important in plants. The pollen of foreign species very frequently reaches the stigma of flowers. The pollen mostly germinates, but the growth of the pollen tubes is mostly slow and the tubes mostly do not reach the oocytes.

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

Reproductive isolation mechanisms

see Reproductive isolation barriers

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

Reproductive isolation postzygotic

- Postzygotic mechanisms represent a very important category of reproductive isolation mechanisms, i.e. mechanisms that are active after fertilization of the oocyte by the microgamete of a foreign species. Compared to prezygotic mechanisms, they have the disadvantage from the viewpoint of the species that they simultaneously reduce the fitness of the reproducing individual. In case of mortality of the zygote, the individual must invest energy and time into the actual act of copulation and production of gametes. The investments into production of imperfect progeny can be even greater for the other types of postzygotic barriers. In the extreme case, the abortive development of hybrid zygotes may even kill the maternal organism. Although the action of normal mutagens leads much more frequently to mutations causing inviability or sterility, in contrast the sterility of hybrids or their progeny is far more common in nature than their inviability (Johnson & Kliman 2002). This is apparently a consequence of the fact that the sterility of hybrids is frequently caused by defects that occur during segregation of chromosomes during meiosis. This incompatibility at the chromosome level evidently often occurs as a consequence of the existence of mutually incompatible changes in the chromosome morphology that were rapidly fixed by evolutionary drive after splitting off from the common ancestor (see VI.3.5.1).
Incompatibility at the chromosome level seems to constitute a very important postzygotic reproduction barrier and its formation as a consequence of chromosome mutation can substantially affect the evolution of a new species. On the other hand, it should be recalled that the reduction in the fertility of hybrids of two species with partly incompatible karyotype cannot, in itself, prevent the flow of the individual genes between two populations or related species. As soon as at least some of the hybrid progeny are fertile, recombination will occur in their genomes. Recombined chromosome with the morphology of species A but bearing genes of type B will subsequently introduce foreign genes into the gene pool of both species.
Incompatibility at the gene level is another source of incompatibility of foreign genomes. The products of some genes of one species cannot properly cooperate with the products of the genes of the other species, so that they form dysfunctional molecular complexes and, at the level of the organism, dysfunctional organs, in crosses. The Dobzhansky and Muller model describes the evolutionary formation of this gene incompatibility (Muller 1939; Dobzhansky 1936) (Fig. XXI.7). At the instant when the gene pools of two populations of one original species are separated (for example, through the effect of spatial isolation), new alleles can be accumulated in the individual loci of one or the other population. The new alleles are always compatible with the alleles originally present in the gene pool of the population (alleles occurring in the same locus and alleles occurring in different loci); otherwise the individuals with the new allele would have reduced fitness and a substantial increase in the frequency or even fixation of the new alleles could not occur. However, the new alleles present in one and the other population need not be mutually compatible, as they never occurred in the same individual during evolution, and their mutual compatibility was thus never tested by natural selection. If the two populations are separated for a sufficiently long time, such a large number of mutually incompatible alleles accumulate in their gene pools that very effective postzygotic reproductive barriers are formed. If the new alleles are evolutionarily fixed in both species, all the hybrids would have approximately the same reduced fertility and viability. In actual fact, a great many new alleles do survive simultaneously in the population together with the old alleles for a long time, most frequently as a substantial component of neutral polymorphism. Consequently, hybrid individuals can differ considerably, even in a single family, in the degree of reduction of their fitness. The existence of postzygotic barriers is thus very often manifested both in reduced fitness of hybrids and in reduced percent of viable progeny formed by hybridization.
 Also in the case of genetic incompatibility, functions connected with reproduction, i.e. the fertility of crosses, are usually affected first. This is apparently a result of the fact that the genes participating in these processes undergo very rapid evolution as a result of the co-evolutionary battle between males and females and partly also as a result of intrasexual competition, especially in males, i.e. the effects of sexual selection.
            Genetic incompatibility need not necessarily be manifested in the F1-generation, but can appear in later generations. This is a result of the fact that the genome of crosses in the F1-generation contains the full chromosome set of both participating species. Thus, together with dysfunctional molecular complexes, composed of the products of both species, also fully functional complexes, composed of the molecules of one or the other species, can be formed in the cells of crosses. However, if, in further generations, the hybrids cross together, hybrid breakdownoccurs (Fig. XXI.8). The genome of the crosses no longer contains the complete chromosome sets of both species, but rather a set of chromosomes some of whose chromosome pairs are from the first and others from the second species. Only then can some cases of genetic incompatibility be manifested (Davies et al. 1997; Turelli & Orr 2000).
            A frequent reason for genome incompatibility consists in inactivation of a nonidentical copy of a gene that multiplied in the genome by gene duplication (Taylor, Van de Peer, & Meyer 2001). Inactivation and subsequent deletion of one of the two copies is the most frequent fate of duplicated genes. In one species, for example, a copy of a gene located on chromosome 1 can be inactivated, while inactivation of a copy of a gene on chromosome 3 occurs in the other species. If the F2-hybrid obtains both copies of the gene on chromosome 1 from the first species and both copies of the gene on chromosome 3 from the other species, it will not have a functional copy of this gene and thus will frequently be unviable.

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

Revealing hidden genetic variability in unfavourable conditions

Several mechanisms are active in a number of organisms, including multicellular animals and plants, that enable them to accelerate evolution when they find themselves in unfavourable circumstances. In some cases, heat shock proteins (Hsp) are of key importance; this is apparently primarily HSP90 in metazoa (Rutherford & Lindquist 1998; Rutherford 2000; Rutherford 2003). Heat shock proteins allow folding of newly synthesized (linear) proteins into the correct spatial shape and can also “repair” proteins, whose shape was damaged by external effects, such as a thermal shock. The activity of some Hsp is of key importance, especially for proteins, whose primary structure is already affected by the mutations present. Under normal circumstances, Hsp are apparently capable of neutralizing the effect of a substantial percentage of these mutations and are able to ensure that a great many abnormal proteins form a normal and completely functional tertiary structure – a three-dimensional shape. If the organism finds itself under abnormal conditions, the Hsp are mobilized for other functions and there begins to be an acute lack of them in the cell. In this case, the presence of the already present mutations begins to be manifested in the tertiary structure of the proteins and subsequently in the phenotype of the organisms. Thus, under abnormally unfavourable conditions, so far unrevealed genetic variability begins to be manifested in the phenotype of the individual organisms in the population and this variability can become material for natural selection and thus also for adaptive evolutionary changes. Populations and species can thus react rapidly to drastic changes in their environments.

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

Revolt of ultraselfish genes

The hypothesis of revolt of ultraselfish genes is based on the idea that, in the area of the genome in which recombination does not occur, ultraselfish genetic elements can accumulate and spread in the population by one of the mechanisms of evolutionary drive (see Chap. VI). Generally, the cooperation of several genes is required for their spreading, say gene A, whose product would damage the chromosomes derived from the other parent, and gene B, whose products would protect the chromosomes from the same gene set and thus from the same parent, against the action of the product of gene A (Fig. XXI.11). If both genes are located on an autosome, they can be separated in the progeny as a result of genetic recombination, understandably with catastrophic results for spreading of gene A – in the next generation, it will damage the chromosomes of both chromosome sets and thus basically commit genetic suicide. In contrast, the genes in the nonrecombining DNA sections, i.e. particularly in unpaired sex chromosomes (allosomes) Y and W, are always transferred together and thus form a sort of supergene. They can form coalitions and spread in the gene pool of the population even at the expense of the average viability of its members.
The parliament of genes model (Leigh 1972) assumes that the spreading of such ultraselfish genes in the population is very rapidly prevented by the spreading of some other gene, to be precise some alleles of some other gene, which are capable of neutralizing the function of the ultraselfish gene. Genes on chromosome Y can be readily inactivated, for example by integration of a transposon or retrotransposon. This could be connected with observed accumulation of transposons, in humans primarily retrotransposons, in nonrecombining Y-chromosome areas (Erlandsson, Wilson, & Paabo 2000). Within a species, ultraselfish genes that are located on allosomes are not greatly manifested as they are “held in check” by the appropriate neutralizer genes, located on the other chromosomes. However, as soon as an allosome in a hybrid finds itself in the presence of a foreign gene set, the ultraselfish genes can begin to act and damage both the fertility and viability of their bearers (Tao, Hartl, & Laurie 2001). The presence of its own chromosome set with the relevant neutralizer genes need not necessarily protect a hybrid against the action of an ultraselfish gene, as neutralizer genes can, for example, be capable of protecting only their own chromosome. For example, these can be alleles that have lost the target site for the product of the ultraselfish gene. Another possibility is that the neutralizer can act (for example by protecting the target sites on the chromosome of their own chromosome set by methylation) during the progress of gametogenesis, i.e. sooner than the chromosomes in the zygote come into interaction with the products of the ultraselfish gene.
            The results of some experiments and a number of observations in nature support the action of ultraselfish genes in the formation of postzygotic interspecific barriers (Orr & Presgraves 2000). It has been found primarily in flora that one of the potential consequences of interspecific hybridization and also, e.g., polyploidization (Wendel 2000) consists in the activation of genetic elements of the transposon type, their cutting out and insertion into new sites (Comai 2000). Compared to animals, plants have a far more dynamic genome and are frequently capable of repairing damage to their DNA occurring as a consequence of increased transposon activity. Reparation is frequently accompanied by fundamental restructuring of the genome and this restructuring can also be substantially manifested in the phenotype of hybrid flora and their progeny. It is probable that the passivity of transposons in normal plants is a result of neutralizer genes that are gradually fixed in the gene pool of the plant as a result of transposone selection pressure. Neutralizer genes need not occur in the genome of a foreign species or their functioning in a genome containing the chromosomes of a foreign species are greatly limited so that they are not capable of completely controlling the transposons activity.

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

RHD-gene

see Origin of Rh-blood group polymorphism

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Ribozymes

Some oligonucleotides, alone or in association with other molecules, can exhibit enzymatic activity, which could have placed them at an advantage in competition for the most effective self-replication. Information gained by studying ribozymes, i.e. RNA molecules exhibiting enzymatic activity (Orgel 1986) is certainly very interesting in this respect. Most of the originally studied ribozymes are active in some area of processing RNA (Orgel 1986); nonetheless, at the present time, a great many ribozymes with a broad range of enzymatic activity are known (Connell & Christian 1993).

            For example, the intron contained in the precursor of ribosomal RNA of the protozoa Tetrahymena thermophila is a typical ribozyme. This ribozyme is capable both of hydrolyzing various RNA-substrates, including its own pre-rRNA, and also of catalyzing the transfer of nucleotides from one nucleotide chain to another, i.e., reactions of the type

 

CpU + pGpN--> CpUpN + pG

 

where pU, pG and pN denote the 5’-monophosphate of the relevant nucleotide (N = U, C, A, G). In these reactions, the length of one nucleotide chain increases at the expense of another chain, so that they could be very useful in an environment in which competition occurs between various oligonucleotides. Ribozymes are considered by some biologists to be molecular relics of the time when there was, as yet, no division of functions between nucleic acids and proteins and when nucleic acids also performed all the functions that have been taken over by proteins in modern organisms.

 

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

RIM

seeReproductive isolation barriers

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

Ring species

see Speciation extinction

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Rise and fall of phylogenetic lines

Repeated rise and fall of entire phylogenetic lines (clades) are a characteristic and very conspicuous feature of the evolution of fauna and flora over long periods of time. Lines whose members completely dominated both in the number of species and in the sizes of populations in various environments and occupied diverse niches in various ecosystems in a certain period either completely died out in the subsequent period or left only a very few highly specialized species. Their key positions in the ecosystems were then occupied by other phylogenetic lines, whose members had been of only marginal importance until that time. Typical or, at the very least, the best known examples consist in the rise and fall or trilobites or the rise and fall of the dinosaurs in the terrestrial ecosystem of mammals. 
            In studying these processes of the “rise and fall” of dynasties, an explanation is mostly sought on the basis of differences in the adaptation of the members of the individual phylogenetic lines to certain factors in the environment and also of the differences in the ability to adapt to changes in these factors. The first explanation, that the members of one line force out, in competition, the members of another line, does not seem very probable. In most well-documented cases, the fall of the original dynasty occurs before the rise of the new dynasty (Benton 1996). The alternative that the rise and fall of the dynasties is caused by the inability of a certain line to adapt to a change in the environment is supported particularly by the fact that the rise and fall of dynasties occurs at times of mass extinction and thus at a time of major changes in the environment, which are currently mostly considered to have been caused by an environmental catastrophe of major extent (see XXII.5.3.1). However, the fact that the extinction frequently mostly affects the members of environmentally diversified lines makes this common explanation less credible. It is understandably possible that, following a major change in the environment, the members of an originally not very important line gain competitive advantage in some types of environments. However, it is not very probable that they would gain a similar advantage in all types of environments and while utilizing all possible environmental niches. It seems more probable (at least to me personally) that the temporary victory of a certain line over other lines is a result of species selection. The temporal connection between the rise and fall of dynasties and periods of mass extinction can most readily be explained in that, in the period following a period of mass extinction, the ability of the members of a certain phylogenetic line to rapidly undergo speciation and thus fill all the empty or newly formed niches is of key importance for survival. There are, of course, also other possible explanations, such as the one suggested by the viral theory of background extinction (XII.6.5).

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

RNA world hypothesis

see Gene hypothesis of the origin of life

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

Robertson transloction

see Mutations at the level of the entire chromosomes and Meoitic drive

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

Rudimentary organs

see Haeckel’s recapitulation theory

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Rudiments

see How comparative anatomy and embryology finds proof evolution theory?

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