Quantifying how constraints limit the diversity of viable routes to adaptation

PLoS Genet. 2018 Oct 8;14(10):e1007717. doi: 10.1371/journal.pgen.1007717. eCollection 2018 Oct.

Abstract

Convergent adaptation occurs at the genome scale when independently evolving lineages use the same genes to respond to similar selection pressures. These patterns of genetic repeatability provide insights into the factors that facilitate or constrain the diversity of genetic responses that contribute to adaptive evolution. A first step in studying such factors is to quantify the observed amount of repeatability relative to expectations under a null hypothesis. Here, we formulate a novel index to quantify the constraints driving the observed amount of repeated adaptation in pairwise contrasts based on the hypergeometric distribution, and then generalize this for simultaneous analysis of multiple lineages. This index is explicitly based on the probability of observing a given amount of repeatability by chance under a given null hypothesis and is readily compared among different species and types of trait. We also formulate an index to quantify the effective proportion of genes in the genome that have the potential to contribute to adaptation. As an example of how these indices can be used to draw inferences, we assess the amount of repeatability observed in existing datasets on adaptation to stress in yeast and climate in conifers. This approach provides a method to test a wide range of hypotheses about how different kinds of factors can facilitate or constrain the diversity of genetic responses observed during adaptive evolution.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptation, Biological / genetics*
  • Adaptation, Physiological / genetics*
  • Animals
  • Biological Evolution
  • Data Interpretation, Statistical
  • Evolution, Molecular
  • Genome
  • Genomics / methods*
  • Humans
  • Phylogeny
  • Selection, Genetic / genetics

Associated data

  • Dryad/10.5061/dryad.615p248

Grants and funding

SY is funded by grants from the Natural Sciences and Engineering Research Council (RGPIN-2017-03950), Alberta Innovates Health Solutions (20150252), and Genome Canada Large Scale Applied Research Project (M16-00620, F16-02098). ACG is funded by the Natural Sciences and Engineering Research Council, Banting Postdoctoral Fellowship. KAH is funded by grants from the Hermon Slade Foundation (HS17.03) and Australian Research Council (DP180102531). MCW is funded by grants from the Natural Sciences and Engineering Research Council (RGPIN-2016-03779) and Genome Canada Large Scale Applied Research Project (M16-00620, F16-02098). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.