polygenic adaptation
Hernandez RD, Kelley JL, Melton SC, Auton A, McVean G, 1000 Genomes Project, Sella G & Przeworski M 2011 Classic selective sweeps were rare in recent human evolution. Science 331:920-924.
- two main lines of evidence have been advanced in support of the hypothesis that classic selective sweeps were common
- these patterns are informative but are only indirectly related to theoretical predictions
- some―possibly all―of these patterns may instead result from purifying selection acting on deleterious mutations at linked sites ("background selection")
- in the fly Drosophila simulans, diversity levels ... suggest that ~13% of amino acid substitutions involved classic sweeps
- human diversity levels around amino acid substitutions are not lower than around synonymous substitutions
- the similar troughs indicate ..., more plausibly, that few amino acid substitutions resulted from classic sweeps
- simulations suggest that even if only 10% of human-specific amino acid substitutions were strongly favored or if 25% of amino acid fixations were favored with weak effects, there should be a significant decrease in the diversity levels relative to what would be expected if all fixations were neutral
- amino acid substitutions are more clustered with one another than with synonymous substitutions
- patterns of diversity around genic substitutions and of highly differentiated alleles are inconsistent with the expectation for frequent classic sweeps, but could result, at least in part, from background selection
- although some substitutions in proteins and regulatory positions undoubtedly involved classic sweeps, they were too infrequent within the past 250,000 years to have had discernible effects on genomic diversity
- this conclusion does not imply that humans have experienced few phenotypic adaptations, or that adaptations have not shaped genomic patterns of diversity
- comparisons of diversity and divergence levels at putatively functional versus neutral sites, for example, suggest that 10 to 15% [and possibly as many as 40% (29)] of amino acid differences between humans and chimpanzees were adaptive [e.g., (30)], as were 5% of substitutions in conserved noncoding regions (22, 29) and ~20% in UTRs (22)
- an excess of functional divergence would point to the importance of other modes of adaptation
- classic sweeps bring new alleles to fixation
- selection on standing variation or on multiple beneficial alleles brings rare or intermediate frequency alleles to fixation
- other forms of adaptation, such as selection on polygenic traits, increase or decrease allele frequencies to a lesser extent