Table 1. Observed and mean modeled estimates of neutral diversity.

	Diversity
	African			European
chr	Observed			Observed
	π	πFar	Modeled	π	πFar	Modeled
A	0.0739	0.0804	0.0733	0.0563	0.0615	0.0561
X	0.0601	0.0723	0.0565	0.0365	0.0459	0.0403
Y	0.0018	0.0019	0.0223	0.0024	0.0027	0.0100
M	0.0235	0.0235*	0.0222	0.0147	0.0147*	0.0101

For Africans, the neutral model is of an expansion from 10,000 individuals to 20,000 individuals 4,000 generations ago. For Europeans the neutral model includes a bottleneck from 10,000 individuals to 1000 individuals 1,500 generations ago, followed by an expansion to 10,000 individuals 1,100 generations ago. Expected values assume the null model of equal numbers of breeding males and females (N _m/N _f = 1). Diversity is normalized by human-chimpanzee divergence, to correct for different mutation rates for each class of sequence. Diversity is additionally calculated far from genes (100 kb away), except for on the mtDNA, where doing so would eliminate all sequence from analysis.

If the “far from genes” filter were applied to the mtDNA, there would be no sequence left to analyze.