Fig 1.
The geographic distribution and population history of chimpanzees.
A, The ranges of each chimpanzee subspecies within western and central Africa. Range data extracted from the map of chimpanzee geographic range from [21]. Map of Africa modified from public domain source [88]. B, Phylogenetic relationships amongst chimpanzees and the timing of their population divergence, modified from [20]. 1 kya: Long term effective population sizes until 1 kya; present: effective population sizes from 1 kya to present. C, Heterozygosity, reflective of relative differences in effective population sizes. Box plots show median central interquartile range, whiskers the upper and lower interquartile range. Points show individual heterozygosity. For all panels, colour designates subspecies: Blue = western, red = Nigeria-Cameroon, green = central, orange = eastern.
Fig 2.
Genic enrichment in bins of signed difference in derived allele frequency (δ).
A, X-axis: δ is computed as the difference in derived allele frequency, for each pair of chimpanzee subspecies. Tail bins (the last bin in either end of δ) contain those SNPs with the largest allele frequency differences. Numbers are of the genic SNPs in each tail bin. Y-axis: genic enrichment in each δ bin (Methods). B, Genic enrichment eastern and central chimpanzee δ, plotted separately due to a different Y-axis limit. NC = Nigeria-Cameroon. The asterisk shows significance of the asymmetry in the genic enrichment (* = 0.01). Shading represents the 95% CI (i.e. alpha = 0.05 for a two-tailed test) estimated by 200kb weighted block jackknife. Grey dashed lines represent simulations under increasing levels of background selection that best match different aspects of the data: lightest to darkest shades: B = 0.93 (excluding δ tail bins), 0.92 (all δ bins), and 0.88 (unmodified genic B values form McVicker et. al. 2009 [34]).
Fig 3.
Direct quantification of δ tail bin genic enrichment asymmetry.
The asymmetry of the genic enrichments in the δ tails is measured by taking their log2 ratio, thus 0 indicates a symmetric enrichment (equal enrichment in both δ tails). NC = Nigeria-Cameroon. Dot = observed asymmetry. Horizontal lines represent confidence intervals estimated by 200kb weighted block jackknife (light = 95%, i.e. alpha = 0.05 for a two-tailed test). Grey vertical marks represent the δ tail asymmetry in simulations, under increasing levels of background selection that best match different aspects of the data: lightest to darkest shades: B = 0.93 (excluding δ tail bins), 0.92 (all δ bins), and 0.88 (unmodified genic B values form McVicker et. al. 2009 [34]).
Fig 4.
Genic enrichment in bins of PBSnj in eastern and central chimpanzees. A X-axes: PBS scaled to take values in the range 0–1. Y-axes: Genic enrichment computed as described in Fig 2. Shading represents the 95% CI (i.e. alpha = 0.05 for a two-tailed test) estimated by 200kb weighted block jackknife. B: log2 ratio of the eastern and central PBSnj tail (PBS > = 0.8) genic enrichment. A,B Grey dashed (A) or vertical (B) lines represent the PBSnj genic enrichment in simulations, under increasing levels of background selection that best match different aspects of δ, as described in Figs 2 and 3: lightest to darkest shades: B = 0.93 (excluding δ tail bins), 0.92 (all δ bins), and 0.88 (unmodified genic B values form McVicker).
Table 1.
VIP gene enrichment in the PBSnj eastern tail.
Table 2.
SIV responsive gene enrichment in subspecies PBSnj tails.