Dataset Information

Rapid Adaptation of a Polygenic Trait After a Sudden Environmental Shift.

ABSTRACT: Although a number of studies have shown that natural and laboratory populations initially well adapted to their environment can evolve rapidly when conditions suddenly change, the dynamics of rapid adaptation are not well understood. Here a population genetic model of polygenic selection is analyzed to describe the short-term response of a quantitative trait after a sudden shift of the phenotypic optimum. We provide explicit analytical expressions for the timescales over which the trait mean approaches the new optimum. We find that when the effect sizes are small relative to a scaled mutation rate, small to moderate allele frequency changes occur in the short-term phase in a synergistic fashion. In contrast, selective sweeps, i.e., dramatic changes in the allele frequency, may occur provided the size of the effect is sufficiently large. Applications of our theoretical results to the relationship between QTL and selective sweep mapping and to tests of fast polygenic adaptation are discussed.

SUBMITTER: Jain K

PROVIDER: S-EPMC5419483 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature

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Rapid Adaptation of a Polygenic Trait After a Sudden Environmental Shift.

Jain Kavita K Stephan Wolfgang W

Genetics 20170324 1

Although a number of studies have shown that natural and laboratory populations initially well adapted to their environment can evolve rapidly when conditions suddenly change, the dynamics of rapid adaptation are not well understood. Here a population genetic model of polygenic selection is analyzed to describe the short-term response of a quantitative trait after a sudden shift of the phenotypic optimum. We provide explicit analytical expressions for the timescales over which the trait mean app ...[more]

PMID: 28341654

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Project description:Understanding the genetic basis of phenotypic adaptation to changing environments is an essential goal of population and quantitative genetics. While technological advances now allow interrogation of genome-wide genotyping data in large panels, our understanding of the process of polygenic adaptation is still limited. To address this limitation, we use extensive forward-time simulation to explore the impacts of variation in demography, trait genetics, and selection on the rate and mode of adaptation and the resulting genetic architecture. We simulate a population adapting to an optimum shift, modeling sequence variation for 20 QTL for each of 12 different demographies for 100 different traits varying in the effect size distribution of new mutations, the strength of stabilizing selection, and the contribution of the genomic background. We then use random forest regression approaches to learn the relative importance of input parameters in determining a number of aspects of the process of adaptation, including the speed of adaptation, the relative frequency of hard sweeps and sweeps from standing variation, or the final genetic architecture of the trait. We find that selective sweeps occur even for traits under relatively weak selection and where the genetic background explains most of the variation. Though most sweeps occur from variation segregating in the ancestral population, new mutations can be important for traits under strong stabilizing selection that undergo a large optimum shift. We also show that population bottlenecks and expansion impact overall genetic variation as well as the relative importance of sweeps from standing variation and the speed with which adaptation can occur. We then compare our results to two traits under selection during maize domestication, showing that our simulations qualitatively recapitulate differences between them. Overall, our results underscore the complex population genetics of individual loci in even relatively simple quantitative trait models, but provide a glimpse into the factors that drive this complexity and the potential of these approaches for understanding polygenic adaptation.

Dataset Information

Rapid Adaptation of a Polygenic Trait After a Sudden Environmental Shift.

Publications

Rapid Adaptation of a Polygenic Trait After a Sudden Environmental Shift.

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