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Fig. S1 Frequency distribution of random Rst vs observed Rst for 10 000 permutations for P52, P50 and P80 loci.

Fig. S2 Loci duplication on P50 and P52 loci.

Fig. S3 Haplogroups distribution.

Table S1 Sampling distribution according to origin and gender

Table S2 Main features of microsatellite loci belonging to scaffolds linked to gender and diversity microsatellite loci

Table S3 Allele sizes and frequencies in male and female subgroups

Table S4 Estimation of exact P-values by the Markov chain method

Table S5 Comparison of genetic diversity between X and Y chromosomes generated by the sex-linked loci

Table S6 Frequencies of X and Y alleles within male and female geographic subgroups

Table S7 Summary of sizes of Y-linked male-specific alleles and X-linked alleles shared by males and females, for each sex-linked locus

Table S8 Haplotype frequencies in male and female individuals computed with the EM algorithm

Table S9 Summary statistics of the haplotype frequencies in male and female individuals computed

Notes S1 The EM algorithm.

Notes S2 Frequencies of X-linked and Y-linked alleles and genetic diversity.