Table 1 Diversity across regions of the human X chromosome
Human-chimpanzeeHuman-macaqueHuman-dogHuman-mouse
RegionUncorrected πDivergenceπDivergenceπDivergenceπDivergenceπ
nonPAR0.0006020.0098140.0628650.0497020.0122740.2344230.0025660.3050700.001972
nonPARminus_XTR0.0005950.0097820.0624340.0495120.0121940.2343720.0025390.3044600.001954
PAR10.0015050.0226430.0664820.0998920.0150700.3377170.004457NA0.000000
P vs. nonPAR0.00000.34460.00700.0000NA
P vs. nonPARminus_XTR0.00000.40070.00770.0000NA
PAR20.0006780.0087200.0777940.0409670.0165590.2187710.0031010.2576090.002633
P vs. nonPAR0.30940.51050.48040.48520.5547
P vs. nonPARminus_XTR0.33800.52680.48960.48140.5824
XTR0.0007470.0109370.0682560.0569530.0131080.2457170.0030380.3367250.002217
P vs. nonPAR0.00040.00380.02230.01480.0007
  • Diversity, measured as the average number of pairwise differences per site (π) between the X chromosomes of 26 unrelated genetic females, in each region of the human X chromosome is presented first unnormalized for mutation-rate variation, then normalized using human-chimpanzee (hg19-panTro4) divergence, and then separately normalized for human-macaque (hg19-rheMac3), human-dog (hg19-canFam3), and human-mouse (hg19-mm10) divergence. The regions analyzed include the PAR1, PAR2, the XTR, and the nonPARs either including the XTR (nonPAR) or excluding the XTR (nonPARminus_XTR). The ampliconic and low-diversity regions have been filtered out. P-values from permutation tests with 10,000 replicates are shown between each recombining region and the nonPARs. All P-values are indicated in italics while bold corresponds to significant P-values.