polygenic adaptation

Sattath S, Elyashiv E, Kolodny O, Rinott Y & Sella G 2011 Pervasive adaptive protein evolution apparent in diversity patterns around amino acid substitutions in Drosophila simulans. PLoS Genet 7:e1001302.

  • approximately 13% of amino acid substitutions were beneficial
  • a minority of which (3%) conferred a large selective advantage of nearly 0.5%
  • the majority of which (10%) conferred a much smaller advantage of about 0.01%
  • these findings ... suggest how the widely varying estimates obtained in previous studies of Drosophila may be reconciled
  • our estimates of the fraction of beneficial amino acid substitutions (~13%) are on the same order of magnitude but lower than previous McDonald-Kreitman based estimates (~50%; cf. [7])
  • some of this difference might arise from violations of the assumptions
  • an intriguing alternative is that the two approaches are actually estimating parameters of somewhat different modes of adaptation
  • our inference is based on the effects of beneficial substitutions that arise from new mutations and likely misses some contribution of adaptation from standing variation
  • a subset of beneficial substitutions could stem from previously neutral or deleterious alleles that were segregating in the population before a change in the environment rendered them beneficial
  • they would lead to a negligible effect on diversity and would therefore not contribute to the signature on which our inference relies
  • these beneficial substitutions would nonetheless contribute to an excess of non-synonymous divergence compared to the neutral expectation, and should therefore be picked by the McDonald-Kreitman based inferences, leading to higher estimates of adaptive substitutions than obtained by our approach
  • other modes of adaptation, such as polygenic selection, may also contribute differentially to the two inference methodologies
  • a current limitation of our inference is its reliance on rough estimates of the recombination rate, and its assumption of a constant rate per base
  • we therefore consider our estimates of selection coefficients to be rough approximations