hemiplasy

Lee KM & Coop G 2019 Population genomics perspectives on convergent adaptation. Phil Trans R Soc B 374:20180236.

  • the sharing of traits or alleles incongruent with the population or species tree owing to ancestral variation (i.e. ILS shown in figure 1a) has been termed hemiplasy
  • the key question is whether selection has independently increased the allele to fixation multiple times
  • taxa sharing the same substitution owing to ILS or gene flow means there has not been independence at the level of the mutational change
  • the allele frequency change at the locus can still be independent, that is convergent, across populations
  • even if an allele was shared owing to ILS, selection may have repeatedly driven up the allele in each population separately
  • regardless of the precise terminology we use, it is important to keep clear statements about the level of independence and the role selection has played in these changes
  • we introduce a conceptual framework to quantify the degree to which allele frequency shifts have been independent
  • we should be much more impressed by selection that repeatedly moves an allele from 10−4 to 50% than 50% to 100%, despite being comparable frequency changes and taking roughly the same time under an additive model
  • we should be much more impressed by repeated adaptation from very rare standing variation than common variation
  • we cannot simply sum the work done by selection (i.e. selective deaths) across multiple loci, unless the loci contribute multiplicatively to fitness
  • this argument forms the basis of the rejection of Haldane's substitution load argument, and Kimura's gain of information extension, as a limit on the rate of evolution
  • combining information over loci additively, that is assuming multiplicative epistasis, seems a fine first approximation
  • this limitation should be borne in mind
  • convergent adaptation, at the genetic or phenotypic level, can potentially be conceptualized in this way as the independent gain of information owing to selection
  • dissecting whether the same or different mutations gave rise to the adaptive alleles will help us gain insights into questions related to mutational target size or epistatic constraints
  • these questions can be somewhat orthogonal to more basic questions about adaptation
  • human populations have repeatedly adapted to different environments through changes in skin pigmentation
  • this convergent adaptation on the level of the phenotype comes from a mixture of selection on old standing variation, both derived and ancestral variants, and recent mutations
  • in information theory, the negative log probability of an outcome under a particular model is called the surprise (or the self information)