Strong Selective Sweeps on the X Chromosome in the Human-Chimpanzee Ancestor Explain Its Low Divergence.

0.00276, Fisher's exact test p-value = 1.34e-05), there is a highly significant excess of sites supporting the species topology (0.00229 vs. 0.00210, Fisher's exact test p-value < 2.2e-16) and deficit of sites in these regions supporting ILS topologies (0.00042 vs. 0.00066, Fisher's exact test p-value < 2.2e-16, Fig 2B and 2C ), which suggests that the observed reduction of ILS is not the result of a lower mutation rate.

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We find a striking correspondence between regions of low ILS and the regions devoid of Neanderthal introgression for European populations (p-value = 0.00021, permutation test) and a marginally significant association with the more introgressed Asian populations (p-value = 0.06721, Fig 5 ).

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