Hybridization capture using RAD probes (hyRAD), a new tool for performing genomic analyses on museum collection specimens.
In the recent years, many protocols aimed at reproducibly sequencing reduced-genome subsets in non-model organisms have been published. Among them, RAD-sequencing is one of the most widely used. It relies on digesting DNA with specific restriction enzymes and performing size selection on the resulting fragments. Despite its utility, this method is of a limited use with degraded DNA samples, such as those isolated from museum specimens, as these are either less likely to harbor fragments long enough to comprise two restriction sites making possible ligation of the technical sequences required or performing size selection of the resulting fragments. In addition, RAD-sequencing also reveals a suboptimal technique when applied to an evolutionary scale larger than the intra-specific level, as polymophisms in the restriction sites cause loci dropout. Here, we address both of these limitations by a novel method called hybridization RAD (hyRAD). In this method, biotinylated RAD fragments, covering a random fraction of the genome, are used as baits for capturing homologous fragments from samples processed through a classical genomic shotgun sequencing protocol. This simple and cost- effective approach allows sequencing orthologous sequences even from highly degraded DNA samples, opening new avenues of research in the field of museum genomics. Not relying on the restriction site presence, it improves among-sample loci coverage, and can be applied to broader phylogenetic scales. In a trial study, hyRAD allowed us to obtain a large set of orthologous loci from fresh and museum samples from a non-model butterfly species, with over 10.000 single nucleotide polymorphisms present in all eight analyzed specimens, including 58 years old museum samples.