Journal
MOLECULAR ECOLOGY RESOURCES
Volume 17, Issue 2, Pages 142-152Publisher
WILEY
DOI: 10.1111/1755-0998.12635
Keywords
F-ST; genome scan; genome-environment association; genotyping by sequencing; local adaptation; outlier analysis
Funding
- National Science Foundation through NSF Award [DBI-1300426]
- University of Tennessee, Knoxville
- NSF [DEB-1316549, IOS-1557795]
- NIH [R01GM098856]
- Washington State University, Army Research Office [W911NF-15-1-0175]
- Michigan State University
- Northeastern University
- Direct For Biological Sciences
- Div Of Biological Infrastructure [1300426] Funding Source: National Science Foundation
- Division Of Environmental Biology
- Direct For Biological Sciences [1316549] Funding Source: National Science Foundation
- Div Of Biological Infrastructure
- Direct For Biological Sciences [GRANTS:13718161] Funding Source: National Science Foundation
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Understanding how and why populations evolve is of fundamental importance to molecular ecology. Restriction siteassociated DNA sequencing (RADseq), a popular reduced representation method, has ushered in a new era of genomescale research for assessing population structure, hybridization, demographic history, phylogeography and migration. RADseq has also been widely used to conduct genome scans to detect loci involved in adaptive divergence among natural populations. Here, we examine the capacity of those RADseq-based genome scan studies to detect loci involved in local adaptation. To understand what proportion of the genome is missed by RADseq studies, we developed a simple model using different numbers of RAD-tags, genome sizes and extents of linkage disequilibrium (length of haplotype blocks). Under the best-case modelling scenario, we found that RADseq using six-or eight-base pair cutting restriction enzymes would fail to sample many regions of the genome, especially for species with short linkage disequilibrium. We then surveyed recent studies that have used RADseq for genome scans and found that the median density of markers across these studies was 4.08 RAD-tag markers per megabase (one marker per 245 kb). The length of linkage disequilibrium for many species is one to three orders of magnitude less than density of the typical recent RADseq study. Thus, we conclude that genome scans based on RADseq data alone, while useful for studies of neutral genetic variation and genetic population structure, will likely miss many loci under selection in studies of local adaptation.
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