Natural selection
Natural selection is the process of uneven transfer of alleles derived from particular individuals to the gene pool of the following generations through their progeny.This process is fully responsible for the origin of evolutionary adaptations and partly responsible for increase of disparity during evolution. It can occur in a number of quite different ways, and thus it is possible to differentiate several basic types of natural selection and also their combinations.The individual types of selection can be studied from the standpoint of their impact on the course of evolution, i.e. on the speed and direction of changes that they cause in the gene pool of the population, and from the standpoint of the level at which the selection acts (alleles, individuals, populations, etc.). We can recognize for example environmental selection, sexual selection, parental selection, hard selection, soft selection, r-selection, K-selection, random selection, turbidostatic selection, chemostatic selection, frequency-dependent selection, apostatic selection, stabilizing selection, disruptive selection, directional selection, individual selection, group selection, kin selection, interspecies selection, intercommunity selection, interallele selection.
Nearly neutral theory of molecular evolution
suggests that most mutations observed on DNA level have slightly negative effect on fitness– see the Effective neutral mutations. The nearly neutral theory of molecular evolution provides a potential explanation of the causes of the existence of the effect of generation time of organism on the rate of the molecular clock for synonymous but not for nonsynonymous mutations (Ohta 1993; Ohta 1996) (see V.5). This explanation is based on the more or less reasonable assumption that a large portion of nonsynonymous mutations is slightly detrimental for their bearers. The rate of fixation of slightly negative mutations (k) or, to be more exact, the percentage of negative mutations that fall in the category of slightly negative mutations acting as effectively neutral mutations, is inversely proportional to the effective size of the population. Organisms with a long generation time, i.e. in general large organisms, mostly have a substantially smaller effective population size than organisms with a short generation time. Consequently, a greater fraction of nonsynonymous mutations fall in the category of selectively neutral for them and thus they have an overall larger fixation rate. As a consequence, the effect of the generation time on the number of mutations formed per year (negative) and the effect of the generation time on the rate of their fixation (positive) are mutually cancelled out for mutations in the coding region.
Negative heritability of fitness model of advantage of sexuality
The negative heritability of fitness model is basically a sort of application of the Red Queen evolutionary principle (van Valen 1973; Bell 1982). This principle, named after the Red Queen’s Race in Lewis Carroll’s “Through the Looking Glass”, states that, in some situations, it is necessary to run as fast as you can to stay in the same place. In order to move forward, it is not enough to just run, but it is necessary to run faster than the others. The hypothesis takes into consideration the fact that, in an environment in which biotic factors, especially parasites and predators, are responsible for most of the selection pressure, it is frequently advantageous to differ from one’s parents and from most of the other individuals of the same species. Experimentally, it has been repeatedly confirmed that genetically more diverse sexually reproducing organism are much more resistant to parasites than their asexually reproducing competitors (Fig. XIII.10 and Fig. XIII.11).
Extremely high pressure of this kind is exerted by parasitic organisms, bacteria, viruses and eukaryotic parasites (Hamilton, Axelrod, & Tanese 1990). It has been documented that a population of host organisms can be decimated by its parasite and only a few resistant individuals can survive the epidemic. In the following generation, they lead to the establishment of a new population of individuals that are resistant to the original strain of the parasite but, because of their uniformity (they come from only a few ancestors) can easily become the victims of another epidemic wave of a mutated parasite. Simultaneously, compared to their hosts, parasites are exposed to much stronger selection pressure on a change in their properties, for example, a change in the antigen properties of the proteins that are the target of the immune response of the host. In addition, they almost always have a shorter generation time than the host, so that their microevolution usually proceeds faster than evolution of the host. Thus, the parasite constantly maintains an advantage over its host in the co-evolutionary battle. This is manifested, for example, in that a host can be most readily infected by parasites derived from the same location (Fig. XIII.12). The only effective counter-strategy of the host consists in the production of diverse progeny, as this is the only way to ensure that at least some individuals survive the succession of waves of the epidemic. Simultaneously, resistance to epidemics exhibits marked negative heritability. Parasites in the new wave of the epidemic are generally better adapted to the most common variant of the host, i.e. the one that was most resistant in the last epidemic (Fig. XIII.13).
Negative mutations
see Mutations
Neoteny
Neoteny is apparently the best known heterochrony. Neoteny consists in delay of the development of some body organs compared to development of the sex organs (Wakahara 1996). Most authors now distinguish progenesis as special type of heterochrony, during which premature development occurs of the sexual organs without delay in the development of the somatic organs. An adult organism capable of reproduction thus frequently bears a number of traits characteristic for younger developmental stages, juveniles or larva of a related species of organisms. The best known example of a neotenic animal is the Mexican axolotl, a tailed amphibian, whose body structure differs drastically from related species and is remarkably similar to their larvae. Experimental intervention, specifically administration of a hormone, can induce metamorphosis in this species and the resultant organisms do not differ much from related species in which neoteny does not occur. Neoteny most probably played an important role in the anagenesis of humans (Gould 1978). A number of our body and other traits, e.g. the size of the cerebral cavity, shape of the facial part of the skull and, of nonanatomical traits, e.g. playfulness, are remarkably reminiscent of the traits of immature individuals of related species of anthropoids.
Neutral evolution
When it was realized that the effectiveness of natural selection can be very low in small populations, suggestions began to arise as to the degree to which this basic pillar of Darwinism can play a role in biological evolution. Some authors concluded that the effective size of real populations is so small that natural selection cannot basically play any role here. With reference to the relationships mostly derived by Kimura, they argued that most traits were fixed during evolution by genetic drift, so that biological evolution basically did not occur as Darwinist evolution, but rather as neutral evolution.
This conclusion was rejected by most evolutionary biologists, including M. Kimura. Primarily, it was found that mutations with selection coefficients so large that they cannot act as selectionally neutral even in a relatively small population occur in nature with a non-negligible frequency . At the present time, it has even been found that the populations of a great many species are apparently so large that even a prototype of neutral mutation, i.e. a synonymous mutation, can act as a selectionally significant mutation in at least some phases of evolution (Akashi 1995; Berg 1996). Primarily, however, a great many authors have repeatedly emphasized that the nature of evolution is not so much determined by how many mutations are fixed by a particular mechanism, but rather primarily through which mutations become fixed. The number of mutations fixed by selection can be incomparably fewer than the number of mutations fixed by genetic drift or genetic draft. However, because primarily those rare mutations that fundamentally affect the phenotype of organisms will be preferentially fixed by selection, it will be selection that plays a major role in determining the nature of biological evolution.
Regardless of the basic evolutionary importance of mutations affected by selection, it must be borne in mind that there is an extremely large class of mutations that act as effectively neutral in populations of normal size. These are mostly synonymous point mutations and also mutations in those parts of the DNA that do not code a functional protein or RNA and do not even participate in the regulation of biological processes. Simultaneously, it is probable that most other mutations that are not synonymous and that can thus be manifested in the structure of coded proteins or in the regulation of their synthesis have such a small effect on the overall fitness of the organism that they act as neutral mutations in populations of normal size. When molecular biologists study a sequence of nucleic acids or proteins, the vast majority of the differences between the individual sequences, from a practical standpoint almost all that they encounter, tend to fall into the category of effectively neutral mutations.
In Chapter IX (DNA Sequence Evolution), it will be shown that the study of neutral mutations is of substantial importance for the evolutionary biologist when he attempts to reconstruct the progress of cladogenesis of a certain taxon. Determination of the molecular traits that are shared by the individual species permits determination, with well-quantifiable probability, of the order in which the individual species branched off from their common developmental base. The number of fixed mutations in the gene pools of the individual species also permits dating of the instances of splitting off of the individual phylogenetic branches.
However, these neutral mutations are insignificant and play no role in the formation of adaptive structures or in increasing the complexity of organisms, i.e. in anagenesis. Natural selection plays an exclusive and irreplaceable role in the anagenesis of organisms.
Neutral mutations
see Mutations
Nidocolous parasites
see Anagenesis in parasites
Nonsense mutations
see Point mutations in the protein-encoding DNA
Nonsynonymous mutations
see Point mutations in the protein-encoding DNA
Numerical taxonomy
The multidimensional statistical method of cluster analysis permits the creation of clusters of objects on the basis of the similarity of the individual objects, where the distance between these clusters and the manner in which they are gradually immersed in one another express the degree and character of mutual similarity amongst the classified objects. If these objects are individual species of organisms and the degree of mutual similarity consists, for example, in the number of shared traits, then the created system of clusters can be used as a taxonomic system for this group. More serious attempts to create systems of some organisms using the methods of cluster analysis were made only in the middle of the last century (Michner & Sokal 1957). The usefulness of the relevant methods in biology was dependent on the existence of computers, as it required the processing of a large amount of data. This procedure came to be called numerical taxonomy or numerical phenetics. Numerical taxonomists assumed that, if the initial data set contains information on the maximum number of traits for all the studied species, the outputs of the relevant programs would be a hierarchically ordered system of clusters, objectively expressing the existing relationships amongst the studied organisms. Such a system could form a good basis for taxonomic classification of organisms. Experience in the use of the methods of numerical taxonomy has shown that, for a sufficiently large number of traits and using the same methods of cluster analysis, the results obtained are truly objective, i.e. individual taxonomists processing the same group of organisms come to more or less the same results. However, the choice of suitable methods of cluster analysis remains a problem. There are a great many ways of calculating the phenetic distances (or similarities) amongst the classified species on the basis of the individual traits and also a great many methods that can be used to form clusters on the basis of the phenetic distances, where each method usually provides qualitatively different results. Simultaneously, it cannot be stated that one method is the right one and the others are wrong. The choice of methods is a matter for the subjective decision of each taxonomist and thus the consequent taxonomic system is subjective.
When any phenetic taxonomic system is used, it must be constantly borne in mind that the system expresses only the similarity but not the relatedness of the organisms. In a great many systems this does not matter much, for example, if it is necessary to classify species that diverged apart at a single moment a long time ago. At other times, the use of a phenetic approach seems more like the only solution in a bad situation. If no traits are available, on the basis of which we could reconstruct the cladogenesis of the particular group, we will have no choice but to use phenetic classification. Finally, it should be pointed out that, where the input data consisted in selectively neutral traits, which changed during evolution at roughly a constant rate in all the species in the studied line, the obtained phenogram should be identical with the cladogenesis scheme and should allow us to reconstruct the relationships amongst the species of the particular phylogenetic line (see XXIV.6).