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 (RAD seq), 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. RAD seq 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 RAD seq‐based genome scan studies to detect loci involved in local adaptation. To understand what proportion of the genome is missed by RAD seq 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 RAD seq 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 RAD seq 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 RAD seq study. Thus, we conclude that genome scans based on RAD seq 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.