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Emphasis of the impact of neutral mutations, in combination with genetic drift, on allele frequencies, and this is rather than emphasizing the impact of biased reproductive success.
The non-Darwinian evolutionary mechanisms are mutation, migration, and genetic drift, contrasting Darwinian evolution, which instead places an emphasis on natural selection (i.e., biased reproductive success). Alleles are most affected by genetic drift when they are least affected by natural selection, and this siutation occurs when fitness differences between alleles are small and population sizes are small as well.
The frequencies of neutral alleles by definition are not directly impacted by natural selection and therefore are affected, once formed, solely by random processes such as genetic drift. As genetic drift can be an inefficient mechanism of allele culling, particularly in larger populations, to the extent that neutral mutations occur then they should accumulate within such populations. The result is that successful populations – ones whose numbers have been consistently large over relatively long intervals – should possess a substantial amount of accumulated neutral variation, and indeed that appears to be the case.
Such genetic variation, though invisible to natural selection, can become relevant particularly given environmental change, such that by chance a subset of such once-neutral alleles instead become beneficial. Neutral as well as near-neutral variation within populations thus can contribute to long-term population success, and particularly so given changing environmental conditions. Alternatively, the bottlenecking of populations has the effect of depleting both neutral and beneficial alleles, resulting in a genetic impoverishment that has the effect of increasing the likelihood of population extinction when environments change.
An important means of distinguishing between neutral and non-neutral genetic variation, at least to a first approximation, is achieved by determining ratios of synonymous to nonsynonymous substitutions, that is, mutations that either do not or do, respectively, lead to changes in the amino acid sequence of proteins.
Change in amino acid sequences that accumulate within populations is predominantly associated with natural selection. That is, nonsynonymous substitutions give rise to potential changes in organism phenotype which, if phenotype has indeed been modified, is more likely to have an impact of organism fitness. Furthermore, given their accumulation, such mutations are likely to be beneficial (or, rather, beneficial mutations are more likely to accumulate).
Beneficial changes, like beneficial mutations in general, should be relative rare. Nonsynonymous substitutions that are deleterious, by contrast, should be more common among random mutations, since there are many may ways to "mess" a protein up. Nevertheless, detrimental mutations should be less likely to be retained. That is, such mutations by definition are selected against. The accumulation of non-synonymous substitutions within lineages therefore is indicative both of the impact of natural selection on gene sequences and of the accumulation of beneficial alleles within populations.
Contrasting nonsynonymous substitutions, synonymous substitutions are rarer to begin with (i.e., see redundancy of the genetic code). They are also less likely to have a impact on phenotype and, consequently, are more likely to have an only neutral impact on fitness. The accumulation of the resulting neutral alleles should occur, as noted, only as a consequence of random processes, such as genetic drift. Large numbers of synonymous alleles within populations therefore serve as a handy sequence-based means of judging the role of genetic drift versus natural selection in the evolution of populations and therefore of the impact of non-Darwinian versus Darwinian evolutionary mechanisms (associated predominantly with synonymous versus nonsynonymous substitutions, respectively).
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