soft sweep

Messer PW, Ellner SP & Hairston NG Jr 2016 Can population genetics adapt to rapid evolution? Trends Genet 32:408-418.

  • recent estimates suggest that on the order of 10 000 adaptive amino acid changes have occurred between humans and chimpanzees
  • –about one adaptive amino acid substitution every 50 generations
  • molecular adaptation could be abundant despite a slow rate of phenotypic changes if molecular changes occur to maintain a relatively constant phenotype in the face of frequent environmental change
  • without better knowledge about the actual rates of phenotypic change and how this affects the trajectories of genetic variation in a population, it is difficult to say whether the standard model is still appropriate
  • in the ecological literature, temporally fluctuating selection on phenotypic traits is generally assumed to be common and has been invoked to explain the discrepancy between long-term and short-term rates of phenotypic evolution
  • there is accumulating experimental evidence that balancing and fluctuating selection on the molecular level may be more widespread than currently accommodated in our population genomic models
  • the assumption that each mutation can be assigned a fixed selection coefficient lies at the foundation of many key concepts in population genetics, including mutation-selection balance and the Poisson random field
  • these concepts, in turn, form the basis for approaches widely used to infer evolutionary parameters from population genomics data
  • it is unclear to what extent these approaches would be affected by frequent fluctuating selection
  • they would almost certainly underestimate the prevalence and strength of selection
  • if linked selection plays an important role in the dynamics of neutral polymorphism, this could have profound implications on population genetic inferences, given that basically all of our methods for inferring demography and population structure from population genomics data are based on the drift-dominant paradigm
  • we already know that genetic draft can severely mislead these approaches
  • it is reasonable to assume that linked selection from incomplete and soft sweeps will cause similar problems
  • the time-rate scaling of phenotypic evolution strongly suggests that the selection driving these phenotypic changes is fluctuating
  • rapid short-term changes do not accumulate into large long-term changes