SNP calling
We retained 104,933 SNPs, with a mean depth of 19X, a minor allele
frequency < 0.05, which had been genotyped on at least 80% of
the 79 individuals. Of these SNPs, 1,532 were on scaffolds anchored to
the Z chromosome, 57,913 were on scaffolds anchored to autosomes, and
45,487 were on unplaced scaffolds.