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      The probability of genetic parallelism and convergence in natural populations

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          Abstract

          Genomic and genetic methods allow investigation of how frequently the same genes are used by different populations during adaptive evolution, yielding insights into the predictability of evolution at the genetic level. We estimated the probability of gene reuse in parallel and convergent phenotypic evolution in nature using data from published studies. The estimates are surprisingly high, with mean probabilities of 0.32 for genetic mapping studies and 0.55 for candidate gene studies. The probability declines with increasing age of the common ancestor of compared taxa, from about 0.8 for young nodes to 0.1–0.4 for the oldest nodes in our study. Probability of gene reuse is higher when populations begin from the same ancestor (genetic parallelism) than when they begin from divergent ancestors (genetic convergence). Our estimates are broadly consistent with genomic estimates of gene reuse during repeated adaptation to similar environments, but most genomic studies lack data on phenotypic traits affected. Frequent reuse of the same genes during repeated phenotypic evolution suggests that strong biases and constraints affect adaptive evolution, resulting in changes at a relatively small subset of available genes. Declines in the probability of gene reuse with increasing age suggest that these biases diverge with time.

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          The genomic basis of adaptive evolution in threespine sticklebacks

          Summary Marine stickleback fish have colonized and adapted to innumerable streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of 20 additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results suggest that reuse of globally-shared standing genetic variation, including chromosomal inversions, plays an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, with regulatory changes likely predominating in this classic example of repeated adaptive evolution in nature.
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            The Structure of Lizard Communities

             E Pianka (1973)
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              Adaptation from standing genetic variation.

              Populations adapt to novel environments in two distinct ways: selection on pre-existing genetic variation and selection on new mutations. These alternative sources of beneficial alleles can result in different evolutionary dynamics and distinct genetic outcomes. Compared with new mutations, adaptation from standing genetic variation is likely to lead to faster evolution, the fixation of more alleles of small effect and the spread of more recessive alleles. There is potential to distinguish between adaptation from standing variation and that from new mutations by differences in the genomic signature of selection. Here we review these approaches and possible examples of adaptation from standing variation in natural populations. Understanding how the source of genetic variation affects adaptation will be integral for predicting how populations will respond to changing environments.
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                Author and article information

                Journal
                Proc Biol Sci
                Proc. Biol. Sci
                RSPB
                royprsb
                Proceedings of the Royal Society B: Biological Sciences
                The Royal Society
                0962-8452
                1471-2954
                22 December 2012
                17 October 2012
                17 October 2012
                : 279
                : 1749
                : 5039-5047
                Affiliations
                [1 ]Biodiversity Research Centre and Zoology Department, University of British Columbia , Vancouver, British Columbia, CanadaV6T 1Z4
                [2 ]Division of Human Biology, Fred Hutchinson Cancer Research Center , Seattle, WA 98109, USA
                Author notes
                [* ]Author for correspondence ( conte@ 123456zoology.ubc.ca ).

                One contribution to a Special Feature ‘Genomics of adaptation’.

                Article
                rspb20122146
                10.1098/rspb.2012.2146
                3497250
                23075840
                This Journal is © 2012 The Royal Society

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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