title: ddRAD-Seq of Amphiprion: adult fin/gill
design: DNA extractions were performed from fin or gill tissue. Genomic libraries were prepared from 500 ng of DNA per sample. Genomic libraries were prepared from 500 ng of DNA per sample following the ddRAD-Seq protocol described by Peterson et al. (2012) with some modifications. Briefly, genomic DNA was digested using the restriction enzymes SphI and MluCI (NEB) followed by a ligation step, whereby each sample was assigned to one of 16 unique adaptors. Pools of 16 individuals were combined and run on agarose gel, where 300 to 500 bp fragments were manually excised, purified and amplified leading to generation of a single genomic library and sequenced on a HiSeq 2000 Illumina sequencer.