Demystifying the RAD fad

We are writing in response to the population and phylogenomics meeting review by Andrews & Luikart () entitled Recent novel approaches for population genomics data analysis'. Restriction-site-associated DNA (RAD) sequencing has become a powerful and useful approach in molecular ecology, with several different published methods now available to molecular ecologists, none of which can be considered the best option in all situations. A&L report that the original RAD protocol of Miller etal. () and Baird etal. () is superior to all other RAD variants because putative PCR duplicates can be identified (see Baxter etal. ), thereby reducing the impact of PCR artefacts on allele frequency estimates (Andrews & Luikart ). In response, we (i) challenge the assertion that the original RAD protocol minimizes the impact of PCR artefacts relative to that of other RAD protocols, (ii) present additional biases in RADseq that are at least as important as PCR artefacts in selecting a RAD protocol and (iii) highlight the strengths and weaknesses of four different approaches to RADseq which are a representative sample of all RAD variants: the original RAD protocol (mbRAD, Miller etal. ; Baird etal. ), double digest RAD (ddRAD, Peterson etal. ), ezRAD (Toonen etal. ) and 2bRAD (Wang etal. ). With an understanding of the strengths and weaknesses of different RAD protocols, researchers can make a more informed decision when selecting a RAD protocol.