title: Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation.
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.
authors.affiliation: Plant Biology Laboratories, Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 166, East Lansing, MI, 48824, USA.|Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, 48824, USA.
authors.forename: David B
authors.initials: DB
authors.lastname: Lowry
authors.affiliation: The Morton Arboretum, Lisle, IL, USA.|National Institute for Mathematical and Biological Synthesis (NIMBioS), Knoxville, TN, USA.
authors.forename: Sean
authors.initials: S
authors.lastname: Hoban
authors.affiliation: School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA.
authors.forename: Joanna L
authors.initials: JL
authors.lastname: Kelley
authors.affiliation: Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, 430 Nahant Rd., Nahant, MA, 01908, USA.
authors.forename: Katie E
authors.initials: KE
authors.lastname: Lotterhos
authors.affiliation: Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, 35406, USA.
authors.forename: Laura K
authors.initials: LK
authors.lastname: Reed
authors.affiliation: Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USA.
authors.forename: Michael F
authors.initials: MF
authors.lastname: Antolin
authors.affiliation: School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Storfer
mesh_terms: D000220:Adaptation, Biological; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004262:DNA Restriction Enzymes / Q000378:metabolism*; D014644:Genetic Variation; D005828:Genetics, Population / Q000379:methods*; D023281:Genomics / Q000379:methods*; D015810:Linkage Disequilibrium; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA; D004262:DNA Restriction Enzymes
keywords: 
  
  F
  ST
  
  ; genome scan; genome-environment association; genotyping by sequencing; local adaptation; outlier analysis