We then followed quality control procedures recommended for the chip-based genomic data (Anderson et al., 2010; Turner et al., 2011). Each of the six plates contained a standard sample, and seven samples were run as duplicates on separate plates. Identity by descent (IBD) analysis conducted in PLINK (Purcell et al., 2007) showed high quality duplication of genotyping results (pi-hat = 1.0 for all duplicate pairs and standard pairs). Sex check analysis of X chromosome heterozygosity identified 6 individuals with sexes inconsistent with their self-reported sexes, likely an indication of a plating error. Inbreeding coefficients and IBD analyses identified four samples that were likely contaminated, and one that was erroneously duplicated. After removing these samples, no sample pairs showed IBD relatedness values greater than 0.1875 (Anderson et al., 2010), and all self-reported sexes were consistent with X chromosome heterozygosity. One further sample was removed from analyses due to low genotyping efficiency (genome-wide missingness greater than 10%).
