Journal article
Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation
Molecular ecology resources, Vol.17(2), pp.142-152
03/2017
Handle:
https://hdl.handle.net/2376/106230
PMCID: PMC5446919
PMID: 27860289
Abstract
Understanding how and why populations evolve is of fundamental importance to molecular ecology. Restriction site-associated DNA sequencing (RADseq), a popular reduced representation method, has ushered in a new era of genome-scale 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.
Metrics
1 File views/ downloads
9 Record Views
Details
- Title
- Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation
- Creators
- David B Lowry - Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, 48824, USASean Hoban - National Institute for Mathematical and Biological Synthesis (NIMBioS), Knoxville, TN, USAJoanna L Kelley - School of Biological Sciences, Washington State University, Pullman, WA, 99164, USAKatie E Lotterhos - Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, 430 Nahant Rd., Nahant, MA, 01908, USALaura K Reed - Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, 35406, USAMichael F Antolin - Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USAAndrew Storfer - School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
- Publication Details
- Molecular ecology resources, Vol.17(2), pp.142-152
- Academic Unit
- Kelley Lab; Biological Sciences, School of
- Publisher
- Wiley; England
- Number of pages
- 11
- Grant note
- R01 GM098856 / NIGMS NIH HHS
- Identifiers
- 99900547020801842
- Language
- English
- Resource Type
- Journal article