Adaptive evolution in the human genome

Adaptive evolution results from the propagation of advantageous mutations through positive selection. This is the modern synthesis of the process which Darwin and Wallace originally identified as the mechanism of evolution. However, in the last half century there has been considerable debate as to whether evolutionary changes at the molecular level are largely driven by natural selection or random genetic drift. Unsurprisingly, the forces which drive evolutionary changes in our own species’ lineage have been of particular interest. Quantifying adaptive evolution in the human genome gives insights into our own evolutionary history and helps to resolve this neutralist-selectionist debate. Identifying specific regions of the human genome that show evidence of adaptive evolution helps us find functionally significant genes, including genes important for human health, such as those associated with diseases.

The methods used to identify adaptive evolution are generally devised to test the null hypothesis of neutral evolution, which, if rejected, provides evidence of adaptive evolution. These tests can be broadly divided into two categories.

Firstly, there are methods that use a comparative approach to search for evidence of function altering mutations. The dN/dS rates-ratio test estimates ω, the rates at which nonsynonymous ('dN') and synonymous ('dS') nucleotide substitutions occur ('synonymous' nucleotide substitutions do not lead to a change in the coding amino acid, while 'nonsynonymous' ones do). In this model, neutral evolution is considered the null hypothesis, in which dN and dS approximately balance so that ω ≈ 1. The two alternative hypotheses are a relative absence of nonsynonymous substitutions (dN < dS; ω < 1), suggesting the effect on fitness ('fitness effect', or 'selection pressure') of such mutations is negative (purifying selection has operated over time; or a relative excess of nonsynonymous substitutions (dN > dS; ω > 1), indicating positive effect on fitness, i.e. diversifying selection (Yang and Bielawski 2000).

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