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.