Figure 1.
Observed and expected ratios of normalized X/Autosome, Y/Autosome, and mtDNA/Autosome nucleotide diversities.
The expected values under an equal male/female ratio for X/Autosome ratio (0.75) and for Y/Autosome and mtDNA/Autosome (0.25) are plotted for reference. Twice the standard error is plotted for each model, computed from the ratios of 10,000 replicates per chromosome comparison. Expected values were computed from simulations using different demographic histories for Africans and Europeans (Tables 1, S4 and S5), first assuming equal numbers of males and females (Nm/Nf = 1), then successively skewing the effective number of males relative to females in each population (e.g. Nm/Nf = 0.75 implies three males for every four females in the population). All chromosomes were normalized for chromosome-specific mutation rates using divergence from chimpanzee.
Table 1.
Observed and mean modeled estimates of neutral diversity.
Table 2.
Estimates of Nm/Nf using X and autosomal genetic diversity far from genes.
Figure 2.
Estimates of the number of sites affected by purifying selection (L) on chromosome Y.
The maximum likelihood estimates (MLEs) and 95% confidence intervals of the number of sites affected by purifying selection on the Y chromosome are plotted for Africans (red) and Europeans (blue). Assuming no sex-biased demography, the MLE for Africans is 5 Mb (95% CI: 1.36–6 Mb) and for Europeans it is 3 Mb (95% CI: 0.798–6 Mb). Estimates were made assuming an equal sex ratio (Nm/Nf = 1), and assuming a highly skewed sex ratio (Nm/Nf = 0.38). Assuming this sex-biased demography, the MLE for Africans is 5 Mb (95% CI: 1.85–6 Mb), and for Europeans it is 2 Mb (95% CI: 0.18–4.2 Mb). The number of ampliconic and coding sites on the Y chromosome are plotted in horizontal dotted lines.