Journal article
Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions
The American naturalist, Vol.188(4), pp.379-397
10/2016
Handle:
https://hdl.handle.net/2376/111995
PMCID: PMC5457800
PMID: 27622873
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 genome-scale 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 outlier methods) 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 scan methods, 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.
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Details
- Title
- Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions
- Creators
- Sean Hoban - Morton Arboretum, Lisle, Illinois 60532; and National Institute for Mathematical and Biological Synthesis (NIMBioS), Knoxville, Tennessee 37966Joanna L Kelley - School of Biological Sciences, Washington State University, Pullman, Washington 99164Katie E Lotterhos - Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, Massachusetts 01908Michael F Antolin - Department of Biology, Colorado State University, Fort Collins, Colorado 80523Gideon Bradburd - Museum of Vertebrate Zoology and Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720David B Lowry - Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824Mary L Poss - Department of Biology and Veterinary and Biomedical Sciences, Penn State University, University Park, Pennsylvania 16802Laura K Reed - Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35406Andrew Storfer - School of Biological Sciences, Washington State University, Pullman, Washington 99164Michael C Whitlock - Department of Zoology, University of British Columbia, Vancouver, Canada
- Publication Details
- The American naturalist, Vol.188(4), pp.379-397
- Academic Unit
- Biological Sciences, School of
- Identifiers
- 99900547329801842
- Language
- English
- Resource Type
- Journal article