hyRAD of Dasypus novemcinctus: museum skin subsample
hyRAD library preparation: Libraries were prepared for sequencing following the hybridization restriction site-associated DNA sequencing method (hyRAD) of Suchan et al. (2016) with the following modifications.1)Genomic libraries of target samples: Genomic libraries for DNA from study skins were prepared using a UCB Evolutionary Genetics Laboratory (EGL) protocol, with a preliminary step that removes uracil residues resulting from the deamination of cytosine (Briggs et al. 2010). Genomic libraries for DNA from tissue samples were prepared with modifications of the Meyer and Kircher (2010) protocol. Both the skin and tissue-derived genomic libraries were dual indexed with TruSeq-style 7bp indexes based on Meyer and Kircher (2010).2)Construction of ddRAD probes: Probes for targeted capture were constructed following a modified double digest restriction-site associated DNA sequencing (ddRAD) protocol (Peterson et al. 2012, Shultz et al. 2016). High-fidelity versions of two restriction enzymes, EcoRI and PstI, were used to subsample the genomes. Size selection products from Pippin Prep were cleaned using Dynabeads M-270 Streptavidin beads (Thermo Fisher Scientific). The resultant ddRAD libraries were amplified following the protocol of Linck et al. (2017) with modifications, deadapterized, and biotinylated.3)Hybridization of ddRAD probes to target genomic libraries: Hybridization reactions of the genomic libraries with the biotinylated ddRAD probes were carried out following the protocol of Linck et al. (2017) with modifications. Eight hybridization reactions were performed using capture pools composed of samples from different geographic regions, each pool consisting of only libraries derived from skin or tissue samples. The performance of the reactions was assessed by testing for enrichment of targeted regions using quantitative PCR. Bioanalyzer assays were used to assess the final size distributions of the hybridization products, which were cleaned up using Streptavidin beads.DNA sequencing: The cleaned hybridization products were sequenced on an Illumina HiSeq 4000 at the UCB Vincent J. Coates Genomics Sequencing Laboratory to generate 150bp paired-end reads. These products were sequenced in two separate runs.