soft sweep

Cutter AD, Jovelin R & Dey A 2013 Molecular hyperdiversity and evolution in very large populations. Mol Ecol, in press.
doi:10.1111/mec.12281

  • hyperdiverse species are particularly well suited for studying how compensatory mutation can mediate divergence under stabilizing selection
  • developmental system drift (DSD) ... involves the dissociation between homology at the phenotypic and molecular levels
  • mutations at a locus for the trait that experiences stabilizing selection can compensate for divergence at a pleiotropic locus
  • the result is trait conservation at the phenotypic level despite divergence amongst species in its genetic underpinnings
  • systems drift
  • hyperdiversity complicates the inference of ancestral states for individual nucleotide sites
  • typically, a single copy of an outgroup reference sequence is used, or sometimes a single copy from each of several outgroups, for comparison with the multiple sequences from the focal species' population
  • this approach neglects polymorphism within the outgroup taxa, which will underestimate the uncertainty in ancestral states, and potentially prove egregious, particularly if both focal and outgroup species are hyperdiverse
  • what is the relative incidence of 'hard sweeps,' 'soft sweeps' and partial sweeps involving polygenic selection on traits (Pritchard et al. 2010)?
  • our expectations also depend on whether we conceive of adaptation as any form of positive selection, including compensatory evolution and genomic conflict, or in the more restrictive sense as a response to extrinsic ecological and/or environmental changes
  • when selection is strong and the population mutation rate is low, then a selectively favoured allele most likely has a single mutational origin
  • hyperdiverse organisms, however, are unlikely to conform neatly to this scenario—regardless of whether the hyperdiversity results from large Ne or high mutation rate
  • adaptation in such species often will not be mutation-limited
  • selection via soft sweeps involving multiple allelic origins might be particularly important
  • if hyperdiverse organisms provide greater power than low-diversity species to identify soft sweeps by virtue of the greater density of polymorphic sites, then they may nevertheless prove valuable in testing theory related to dominance, epistasis and the distribution of selective effects