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

denotes  removing from the population mutations that reduce the fitness of their bearers. The vast majority of all mutations fall in this category in a sufficiently large population. Some genes are capable of tolerating a large number of changes without greatly affecting the functioning of the relevant protein. These proteins change very rapidly in evolution. On the other hand, other genes are very conservative and any change in their sequence is greatly manifested in the functioning of the protein and thus in the fitness of the particular individual (Fig. IX.3).

            If the intensity and character of selection pressures, to which its representatives are exposed, change during the evolutionary history of a certain taxon, then the intensity of selection acting on the individual genes also changes. If a gene is exposed to more intense selection in a certain period, this is generally manifested by a reduction in the substitution rate for selectively significant mutations. In this case, at a molecular level, a reduction in the overall substitution rate and also a reduction in the ratio of the number of nonsynonymous mutations to the number of synonymous mutations are observed. In both cases, we must relate the numbers of synonymous and nonsynomous mutations to the numbers of positions in which synonymous or nonsynonymous mutations can occur in the given gene. In highly conservative genes exposed to intense negative selection, synonymous mutations substantially predominate and this ratio is thus much lower than 1. From an evolutionary standpoint, the genes for proteins that have a great many functions and that, e.g., interact physically with a large number of other proteins, are very conservative (Fraser et al. 2002). This ratio approaches a value of 1 in DNA sections that usually do not have any function, e.g. in pseudogenes, i.e. in unused and usually incomplete or otherwise damaged copies of genes. In contrast, in genes that are, or were in the past, exposed to intense positive selection, i.e. selection for evolutionary change, nonsynonymous mutations can predominate and this ratio can substantially exceed a value of 1. Genes participating in some way in the co-evolutionary battle amongst parasites and hosts, for example the genes for the components of the immune system, change especially rapidly (Endo, Ikeo, & Gojobori 1996) (Fig. IX.4). Genes that participate in interactions between members of the same species during reproduction, for example receptors on the surface of gametes, proteins expressed in the somatic tissues of the reproductive organs, etc. also develop rapidly (Lee, Ota, & Vacquier 1995; Vacquier 1998; Singh & Kulathinal 2000). This trend is especially important in taxa with polyandrous species in which both intense competition amongst sperms and also stronger genetic conflict between males and females occurs (Panhuis et al. 2001). The ratio of fixed nonsynonymous and synonymous mutations is usually greater than one in these proteins. This situation is encountered in approximately 0.5% of all the proteins that have so far been sequenced.