selection

Galtier N 2016 Adaptive protein evolution in animals and the effective population size hypothesis. PLoS Genet 12:e1005774.

  • the proportion of adaptive amino-acid substitution is found to be positively correlated to species effective population size
  • this relationship, however, appears to be primarily driven by a decreased rate of nearly-neutral amino-acid substitution because of more efficient purifying selection in large populations
  • our analysis does not confirm that population size, here approached through species genetic diversity and ecological traits, does influence the rate of adaptive molecular evolution, but points to human and apes as a special case, compared to other animals, in terms of adaptive genomic processes
  • the analysis revealed a pervasive impact of adaptive processes on the evolution of coding sequences in the eight sampled animal phyla, but did not detect any influence of Ne on the rate of adaptive molecular evolution
  • among the newly introduced DFE models, GammaExpo and ScaledBeta were the ones best fitting the data
  • the two DFE models that were suggested from theoretical studies based on Fisher's geometric formalism did not perform well in this analysis
  • observing a high α therefore seems to be the rule, and a low α the exception, making humans and apes a peculiar, intriguing case
  • no effect of Ne on the adaptive rate?
  • proteins in small-Ne species tend to be less adapted (i.e., further away from their fitness optimum), and therefore more prone to adaptation, than in large-Ne species
  • the accumulation of slightly deleterious amino-acid substitutions in small-Ne
  • a positive relationship between ωa and Ne would be expected if the DFE was independent of Ne, i.e., if the adaptive mutation rate was similar in small and large populations
  • our study, if confirmed, would suggest that this hypothesis does not hold
  • adaptive mutations could be more common in small-Ne species
  • this would compensate for their lower fixation probability
  • McDonald-Kreitman-related methods estimate the number of adaptive steps, not the associated fitness effect
  • large populations adapt more efficiently than small populations by making larger steps (on average), not more steps
  • the synonymous diversity, πS, was used as a proxy for Ne
  • this can be problematic