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The Linked Selection Signature of Rapid Adaptation in Temporal Genomic Data

View ORCID ProfileVince Buffalo, View ORCID ProfileGraham Coop
doi: https://doi.org/10.1101/559419
Vince Buffalo
Population Biology Graduate GroupCenter for Population Biology, Department of Evolution and Ecology, University of California, Davis, CA 95616
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  • For correspondence: vsbuffalo@ucdavis.edu
Graham Coop
Center for Population Biology, Department of Evolution and Ecology, University of California, Davis, CA 95616
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Abstract

Populations can adapt over short, ecological timescales via standing genetic variation. Genomic data collected over tens of generations in both natural and lab populations is increasingly used to find selected loci underpinning such rapid adaptation. Although selection on large effect loci may be detectable in such data, often the fitness differences between individuals have a polygenic architecture, such that selection at any one locus leads to allele frequency changes that are too subtle to distinguish from genetic drift. However, one promising signal comes from the fact that selection on polygenic traits leads to heritable fitness backgrounds that neutral alleles can become stochastically associated with. These associations perturb neutral allele frequency trajectories, creating autocovariance across generations that can be directly measured from temporal genomic data. We develop theory that predicts the magnitude of these temporal autocovariances, showing that it is determined by the level of additive genetic variation, recombination, and linkage disequilibria in a region. Furthermore, by using analytic expressions for the temporal variances and autocovariances in allele frequency, we demonstrate one can estimate the additive genetic variation for fitness and the drift-effective population size from temporal genomic data. Finally, we also show how the proportion of total variation in allele frequency change due to linked selection can be estimated from temporal data. Temporal genomic data offers strong opportunities to identify the role linked selection has on genome-wide diversity over short timescales, and can help bridge population genetic and quantitative genetic studies of adaptation.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted February 24, 2019.
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The Linked Selection Signature of Rapid Adaptation in Temporal Genomic Data
Vince Buffalo, Graham Coop
bioRxiv 559419; doi: https://doi.org/10.1101/559419
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The Linked Selection Signature of Rapid Adaptation in Temporal Genomic Data
Vince Buffalo, Graham Coop
bioRxiv 559419; doi: https://doi.org/10.1101/559419

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