A genomic library was prepared following the double-digest Restriction-Associated DNA (ddRAD) protocol of Brelsford et al. (2016a (link)). Briefly, it consisted of enzyme digestion by SbfI and MseI, ligation of barcoded adapters, PCR-amplification of the resulting fragments and size-selection of PCR products between 400 and 500 bp, and was sequenced on a single Illumina HiSeq 2000 lane.
Raw reads were demultiplexed using the process_radtags module of Stacks v. 1.24 (Catchen et al. 2013 (link)) and loci were built with the denovo_map.pl pipeline, run separately for each species, with –bound_high 0.05 and other parameters left with default values. The resulting variants were then split into separate files for mapping crosses and unrelated adults. Variants were filtered with VCFtools v0.1.10 (Danecek et al. 2011 (link)), retaining genotypes with minimum read depth of 7, and retaining loci genotyped in at least 80% of individuals. We excluded the loci with minor allele frequencies below 0.1 for unrelated adults and below 0.15 for mapping cross parents and offspring. These filters resulted in data sets of 13,622 and 16,024 SNPs for unrelated adults in H. sarda and H. savignyi, respectively, and 12,509 and 11,064 SNPs for mapping crosses in H. sarda and H. savignyi, respectively.
Raw reads were demultiplexed using the process_radtags module of Stacks v. 1.24 (Catchen et al. 2013 (link)) and loci were built with the denovo_map.pl pipeline, run separately for each species, with –bound_high 0.05 and other parameters left with default values. The resulting variants were then split into separate files for mapping crosses and unrelated adults. Variants were filtered with VCFtools v0.1.10 (Danecek et al. 2011 (link)), retaining genotypes with minimum read depth of 7, and retaining loci genotyped in at least 80% of individuals. We excluded the loci with minor allele frequencies below 0.1 for unrelated adults and below 0.15 for mapping cross parents and offspring. These filters resulted in data sets of 13,622 and 16,024 SNPs for unrelated adults in H. sarda and H. savignyi, respectively, and 12,509 and 11,064 SNPs for mapping crosses in H. sarda and H. savignyi, respectively.
