Fig. 2
Reduced X-linked region nucleotide diversity compared to that of homologous Y-linked genes. The percentage differences in synonymous site nucleotide diversity between X and Y gene copies, relative to the diversity estimates for the Y-linked copies, are plotted for each gene with non-zero diversity in the Y-linked copy in the old stratum (Region 1), young stratum (Region 2) and the Collinear region. The names of the genes are shown on the x-axes of the plots. Four genes with one or more variants in the X-linked copy but none in the Y-linked copy were excluded from the figure, one in region 2 and three in the collinear region; the diversity among the X-linked copies of all these genes was very low (the highest value was 5 × 10−4 for one of the collinear region genes, about 100 times less than the average for alleles inferred to be associated with the corresponding Y-linked region)