Genomic Studies of Adaptation in Natural Populations

Abstract

Understanding the genetic basis of adaptive evolution is a problem almost as old as evolutionary biology itself. Recent advances in genome sequencing and the ability to generate genomic samples from natural populations promises to provide answers to many long‐standing questions. The recent surge in genomic studies of adaptation has been accompanied by the development of numerous powerful techniques to analyse these enormous data sets. The state of the field is reviewed in this article, with an emphasis on the various approaches used. This article covers both ‘top‐down’, used to identify the genetic basis of a known trait, and ‘bottom‐up’ approaches, used to identify the footprints of selection on the genome. It shows how recent studies highlight the benefits of combining multiple methods and also discusses important goals for the future of the field.

Key Concepts:

  • Association mapping is used to identify genomic loci that control a trait of interest, by identifying molecular markers that display genotype‐by‐phenotype associations.

  • Either offspring from controlled crosses or population samples can be used as the recombinant ‘mapping population’.

  • Numerous loci underlying important adaptive traits have been identified using association mapping; however, this approach is biased towards loci of large effect and may not accurately capture the true genetic architecture of a trait.

  • Genome‐wide scans for the footprints of selection are less sensitive to effect‐size biases but are naive with regard to the trait(s) under selection.

  • Selective sweeps can be identified by the presence of reduced variation, enhanced linkage disequilibrium and a shift in the ‘site frequency spectrum’.

  • Loci under divergent selection between populations can be identified as outliers displaying greater differentiation between populations than expected under neutral evolution.

  • By comparing between‐species divergence with within‐species polymorphism at synonymous and nonsynonymous sites, it has been estimated that a large proportion of the genome is involved in adaptive evolution.

Keywords: QTL; association mapping; effect size; positive selection; selective sweep; genome scan

Figure 1.

Pedigree‐ and population‐based mapping. Recombinant mapping populations can be obtained by controlled crosses (a) or by sampling an out‐breeding population (b). Successive generations of inbreeding can then be implemented to generate recombinant inbred (homozygous) lines (RILs).

Figure 2.

Genomic signatures of a selective sweep. (a) A recent selective sweep would have caused a reduction in diversity at the selected locus. The depth of the trough and the size of the affected region depend on the strength of selection. (b) After a selective sweep, the site frequency spectrum (SFS) will be skewed relative to neutral expectations, with excesses of both rare and common derived (new) alleles.

Figure 3.

Identifying selected loci from genome scans. Strongly selected loci will appear as FST outliers, indicating enhanced differentiation between populations. Typically, loci above a chosen threshold (dashed line) are accepted as showing greater differentiation than would be expected under neutral evolution. This subset (shaded area) is, by definition, a small fraction of loci.

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Martin, Simon H, and Jiggins, Chris D(Sep 2013) Genomic Studies of Adaptation in Natural Populations. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0024613]