Finding the genomic basis of local adaptation: Pitfalls, practical solutions, and future directions

Sean Hoban, Joanna L. Kelley, Katie E. Lotterhos, Michael F. Antolin, Gideon Bradburd, David B. Lowry, Mary L. Poss, Laura K. Reed, Andrew Storfer, Michael C. Whitlock

Research output: Contribution to journalArticle

212 Scopus citations

Abstract

Uncovering the genetic and evolutionary basis of local adaptation is a major focus of evolutionary biology. The recent development of cost-effective methods for obtaining high-quality genomescale data makes it possible to identify some of the loci responsible for adaptive differences among populations. Two basic approaches for identifying putatively locally adaptive loci have been developed and are broadly used: one that identifies loci with unusually high genetic differentiation among populations (differentiation outliermethods) and one that searches for correlations between local population allele frequencies and local environments (genetic-environment association methods). Here, we review the promises and challenges of these genome scanmethods, including correcting for the confounding influence of a species’ demographic history, biases caused by missing aspects of the genome, matching scales of environmental data with population structure, and other statistical considerations. In each case, we make suggestions for best practices for maximizing the accuracy and efficiency of genome scans to detect the underlying genetic basis of local adaptation. With attention to their current limitations, genome scan methods can be an important tool in finding the genetic basis of adaptive evolutionary change.

Original languageEnglish (US)
Pages (from-to)379-397
Number of pages19
JournalAmerican Naturalist
Volume188
Issue number4
DOIs
StatePublished - Oct 2016

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics

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    Hoban, S., Kelley, J. L., Lotterhos, K. E., Antolin, M. F., Bradburd, G., Lowry, D. B., Poss, M. L., Reed, L. K., Storfer, A., & Whitlock, M. C. (2016). Finding the genomic basis of local adaptation: Pitfalls, practical solutions, and future directions. American Naturalist, 188(4), 379-397. https://doi.org/10.1086/688018