title: RADseq provides unprecedented insights into molecular ecology and evolutionary genetics: comment on Breaking RAD by Lowry et al. (2016).
abstract: In their recently corrected manuscript, "Breaking RAD: An evaluation of the utility of restriction site associated DNA sequencing for genome scans of adaptation", Lowry et al. argue that genome scans using RADseq will miss many loci under selection due to a combination of sparse marker density and low levels of linkage disequilibrium in most species. We agree that marker density and levels of LD are important considerations when designing a RADseq study; however, we dispute that RAD-based genome scans are as prone to failure as Lowry et al. suggest. Their arguments ignore the flexible nature of RADseq; the availability of different restriction enzymes and capacity for combining restriction enzymes ensures that a well-designed study should be able to generate enough markers for efficient genome coverage. We further believe that simplifying assumptions about linkage disequilibrium in their simulations are invalid in many species. Finally, it is important to note that the alternative methods proposed by Lowry et al. have limitations equal to or greater than RADseq. The wealth of studies with positive impactful findings that have used RAD genome scans instead supports the argument that properly conducted RAD genome scans are an effective method for gaining insight into ecology and evolution, particularly for non-model organisms and those with large or complex genomes.
authors.affiliation: School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195-5020, USA.
authors.forename: Garrett J
authors.identifier: 0000-0002-6267-2203
authors.initials: GJ
authors.lastname: McKinney
authors.affiliation: U.S. Geological Survey, Wisconsin Cooperative Fishery Research Unit, College of Natural Resources, University of Wisconsin-Stevens Point, 800 Reserve St., Stevens Point, WI, 54481, USA.
authors.forename: Wesley A
authors.initials: WA
authors.lastname: Larson
authors.affiliation: School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195-5020, USA.
authors.forename: Lisa W
authors.initials: LW
authors.lastname: Seeb
authors.affiliation: School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195-5020, USA.
authors.forename: James E
authors.initials: JE
authors.lastname: Seeb
mesh_terms: D001483:Base Sequence; D004262:DNA Restriction Enzymes; D016678:Genome; D015810:Linkage Disequilibrium; D017422:Sequence Analysis, DNA
chemical_list: D004262:DNA Restriction Enzymes
keywords: RADseq; adaptation; genome scan; linkage disequilibrium