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.

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“…Using simulations, Kardos et al [62] showed that tens of thousands of SNP markers may not be adequate to detect genotype-phenotype associations in natural populations, and recommended wholegenome sequencing of extreme phenotypes. Lowry et al [61] argued that most reduced-representation sequencing studies genotype far too few SNPs to find significant associations, given the extent of linkage disequilibrium. However, when linkage disequilibrium is high, such as in hybrid zones (e.g.…”

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“…Association (population-based) or QTL (pedigree-based) mapping could then be used to identify genes that are related to local adaptation, but this is contingent on identification of genetically differentiated populations. Restriction site associated DNA sequencing (RADseq) is an excellent tool for population genetic studies but may provide insufficient genomic coverage to detect regions under local selection (Lowry et al 2017). In the absence of full genomic sequences, transcriptomic or exome capture techniques provide a relatively high coverage of genic regions (Lowry et al 2017).…”

“…Restriction site associated DNA sequencing (RADseq) is an excellent tool for population genetic studies but may provide insufficient genomic coverage to detect regions under local selection (Lowry et al 2017). In the absence of full genomic sequences, transcriptomic or exome capture techniques provide a relatively high coverage of genic regions (Lowry et al 2017). While methods that provide a sampling of loci across the entire genome, such as RADseq, alone are insufficient tests of local adaptation, they are important in identifying patterns potentially associated with adaptation and provide a wealth of valuable information on population structure and allele frequencies.…”