polygenic adaptation

Radwan J & Babik W 2012 The genomics of adaptation. Proc R Soc Lond B 279:5024-5028.

  • models of adaptive evolution have traditionally assumed adaptation from de novo mutations
  • such scenarios seem to fit the evolution of microorganisms reasonably well
  • in larger organisms, which typically have smaller effective population sizes, adaptation from standing variation may be commonplace
  • soft sweeps [29,35], in which beneficial QTNs occur in variable genetic backgrounds, may explain why clear genomic signatures of the fixation of newly arisen beneficial mutations are often not observed in obvious cases of adaptive evolution
  • the long-term effective size of the human population seems comparable to those used in experimental evolution studies on non-microbial organisms
  • complete selective sweeps are rarely observed in such experiments
  • Burke [29] discusses how the complex genomic landscape of adaptive changes revealed by the genomic analyses of selection experiments may be explained by a combination of soft, incomplete sweeps and subtle changes in allele frequencies that generate dramatic phenotypic changes in highly polygenic complex traits
  • if genetic variation in certain traits is maintained by some form of balancing selection, or many polymorphisms exhibit conditional neutrality, repeated adaptation from standing genetic variation may result in parallel evolution
  • the genetic basis of parallel adaptations has intrigued researchers for years
  • its understanding may help answer questions about repeatability of evolution
  • it appears that multiple outcomes are possible:
  • identical polymorphisms repeatedly recruited from standing variation
  • independent adaptive mutations in a single gene
  • changes in various genes involved in particular pathways
  • Conte et al. (this issue [41]) provide the first systematic assessment of the probability of the same gene being used by convergent or parallel evolutionary processes
  • the numbers are surprisingly high, with probability estimates of gene reuse ranging from 0.32 (based on genome-wide linkage studies) to 0.55 (based on candidate gene data)
  • the effective number of genes available to adaptive evolution in such cases may typically be as small as two or three
  • apart from the recruitment of genes from standing genetic variation, which may increase the probability of gene reuse in closely related populations or taxa, other factors that limit the effective number of genes available for adaptation require further study
  • the accumulating empirical evidence has led to renewed interest in population genetics models of adaptation from standing genetic variation, including soft sweeps [35], as well as an appreciation of the highly polygenic nature of most adaptations in humans