RAD library sequences for C. caeruleus satunini, sample JDI2 (sorted per sample, MID removed, PCR duplicates removed)
We prepared paired-end restriction site-associated DNA (RAD) libraries following Baird et al. (2008) and Etter et al. (2011) with the following modifications. We considered no RNase A treatment necessary; DNA fragments were sheared with a Bioruptor Standard UCD-200 (Diagenode) and selected to a size range comprising 150–750 bp (length excluding adapters); PCR reactions were set up at 50 μl with 16 μl RAD library template running 16 cycles. Such protocol, with more library template and fewer cycles, leads to more P2–P2 fragments but fewer PCR clones. We used the restriction enzyme SbfI and multiplexed 16 samples per library; each library was then sequenced on one HiSeq 2000 (Illumina) channel at BGI, Hong Kong.