Tests for sex-linked loci in Macquarie perch WGS-derived SNPs
using population-by-sex pools
Cochran-Mantel-Haenszel (CMH) tests applied to four in-silicoMacquarie perch population-by-sex pools tested 1,492,004 SNP loci, of
which 4.1% were differentiated p<1e-5 between male and female
pools (Supplementary Material S3) and 0.25% had sex-specific alleles in
both populations, with a similar number of male- and female-specific
alleles (Table 2). The 274,905-bp long scaffold 633 had the most loci
with male-specific alleles (40 of 1831), two thirds of which clustered
within a ~6.2 Kb region (87120-93327; Appendix B; Table
B2). Of 30 SNP loci most strongly differentiated between male and female
pools (CMH p<1e-20), nine were loci with male-specific alleles
located within a ~3.8-Kb region 90152-94017 of scaffold
633 (Table B1). Of these nine loci, five clustered within a short 146-bp
fragment (93182-93327; hereafter, ‘the 146-bp sexing region ’).
Fifteen additional scaffolds had smaller clusters of 3-6 loci with
male-specific alleles (CMH p<1e-5), and eight scaffolds had
clusters of 3-4 loci with female-specific alleles (Appendix B, Table
B3).