Sequence capture for R. affinis
for each sample DNA libraries (~300 bp insert fragments) were constructed individually using the NEB Next Ultra DNA Library Prep kit (New England Biosciences). Hybridization of the baits with libraries was performed as per the standard protocol for the MYbaits kit (MYcroarray, now called Arbor Biosciences). Then, the baited libraries are obtained with Streptavidin C1 magnetic beads and are cleaned to keep only the target sequences in the final solution. Samples are indexed during the post-hybridization amplification using the Agilent SureSelectXT 96 index primers. Finally, all libraries were pooled and sequenced on the Hiseq2500 fast mode (Illumina, 150 bp paired-end).