Sampling, DNA extraction, library preparation, sequencing
Individual larvae were genotyped (total n = 68) across five families representing three population crosses (n = WW: 34, WC: 15, CW: 19). All samples were sequenced on the Illumina HiSeq2500 and genotyped using proprietary DArT-seqTM technology at Diversity Arrays Technology (Canberra, Australia). Digestion and ligation reactions were carried out with the PstI and HpaII restriction enzymes following (Jaccoud, Peng, Feinstein, & Kilian, 2001; Kilian et al., 2012). DNA purification and library preparation followed DArT proprietary methods (Kilian et al., 2012). As part of the DArT pipeline, raw sequence data was filtered based on Q-scores and filtered against viral and bacterial databases to remove contamination. The restriction site fragments generated were used to call single nucleotide polymorphisms (SNPs) with the KDCompute pipeline and DArTsoft14 algorithm (Diversity Arrays Technology, http://www.kddart.org/kdcompute.html). SNPs were referenced against the Acropora digitifera genome (Shinzato et al., 2011) and further quality controlled and filtered to produce a reduced dataset of only high quality loci using both proprietary DART software and the following criteria, which included filtering loci for average repeatability of alleles at the locus (‘filter.repavg’, >99%), collapsing duplicated sequences (‘keep monomorphs’), individuals with missing data (‘filter.callrate’, >25%), filtering by Minor Allele Frequencies (< 0.02), coverage (< 8 read depth), and filtering loci out of Hardy-Weinberg Equilibrium.