title: Responsible RAD: Striving for best practices in population genomic studies of adaptation.
abstract: Two recent articles were written in response to our paper "Breaking RAD: An evaluation of the utility of restriction site associated DNA sequencing scans of adaptation." While we agree with some of the comments made by the authors of these two response papers, we still believe caution should be employed in RADseq studies that aim to detect loci that contribute to adaptation. In this rebuttal, we evaluate the key points made in these papers, attempt to identify a middle ground and make suggestions for responsibly conducting future studies to understand the genomewide mechanisms of adaptation.
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, MI, USA.|Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, USA.
authors.forename: David B
authors.identifier: 0000-0002-8182-1059
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, USA.
authors.forename: Joanna L
authors.identifier: 0000-0002-7731-605X
authors.initials: JL
authors.lastname: Kelley
authors.affiliation: Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA, USA.
authors.forename: Katie E
authors.initials: KE
authors.lastname: Lotterhos
authors.affiliation: Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA.
authors.forename: Laura K
authors.initials: LK
authors.lastname: Reed
authors.affiliation: Department of Biology, Colorado State University, Fort Collins, CO, USA.
authors.forename: Michael F
authors.initials: MF
authors.lastname: Antolin
authors.affiliation: School of Biological Sciences, Washington State University, Pullman, WA, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Storfer
mesh_terms: D001483:Base Sequence; D016678:Genome; D023281:Genomics; D056186:Metagenomics; D017422:Sequence Analysis, DNA
keywords: genome scan; genome-environment association; genotyping by sequencing; local adaptation; outlier analysis