Inferring phylogenetic history from restriction site associated DNA (RADseq)

Next-generation sequencing of restriction site associated DNA, or RADseq, was introduced in 2008 as a rapid genotyping method that does not require prior marker development. Developed for linkage mapping, genome-wide association, and population genetic studies, RADseq was initially viewed as ill-suited to interspecific phylogenetic questions. However, since 2012, approximately a dozen RADseq phylogenetic studies have been published. These studies utilize a variety of bioinformatic methods to identify loci, estimate orthology, and assemble phylogenetic matrices, and software pipelines customized for phylogenetic analyses are being rapidly developed. The resulting data matrices tend to be large (sometimes megabases in total aligned length) but relatively incomplete, presenting analytical challenges. Empirical and simulated RADseq studies have demonstrated that RADseq is suitable for phylogenetic inquiries at relatively deep scales, in some cases at least 60 million years. Yet its real strengths may show up at the boundary between withinand among-species inquiries. As sequence-based data, RADseq can be mapped to genomic resources for purposes of alignment, gene identification, and investigating the genomic architecture of introgression and differentiation. Given the ease with which RADseq data can be generated, particularly in comparison to targeted enrichment methods that require prior identification of candidate loci, in the coming years we anticipate greater use of RADseq for phylogenetic inference and predict that methods of species-tree estimation and genomic analysis will increasingly accommodate its characteristically large, incomplete, genome-scale data matrices.