RAD Sequencing for Conservation Genomics: Lessons from Threespine Stickleback

Next-generation sequencing technology provides vastly increased power to address existing issues as well as the possibility to answer entirely new questions in conservation genetics.  Restriction-site Associated DNA (RAD) sequencing is one next-generation technique that is particularly well-suited to species of conservation concern, where little or no prior genetic resources exist.  However, to best apply such novel techniques in conservation, it is useful to fully understand their power and limitations using a well-studied system.  RAD sequencing has been applied successfully in threespine stickleback to identify genomic regions underlying parallel adaptation, map genomic regions linked to phenotypes, and understand the genomic architecture of rapid adaptation.  I will draw on this experience to explore basic issues for applying RAD sequencing in populations of less-studied organisms.  Key requirements for experimental design include sample size of individuals, marker density across the genome, and average depth of sequencing coverage.  In particular, in many fish taxa, a critical issue is how to avoid the pitfalls of repetitive and duplicate genomic sequence in identifying and genotyping genetic markers.