Table 6 Genetic diversity and results of selective neutrality tests for the three NAT gene paralogs in the different species and sub-species of the genus Pan, with equivalent estimates in human populations shown in the last column.
Pan species and sub-species
P. t. verus (Western chimpanzee)Homo sapiens
San Diego sampleaBPRC sampleP. t. ellioti (Nigeria-Cameroon)P. t. troglodytes (Central)P. t. schweinfurthii (Eastern)P. paniscus (Bonobo)(human populations average)b
Pan NAT1
Total (2N chromosomes)364620101228119.7
Number of usable positions903903898898898898903
Number of segregating sites (S)3.57 (0.5)334523.75
Number of haplotypes (k)4.57 (0.5)444533.5
Expected heterozygosity (h)0.37 (0.03)0.340.550.530.580.630.095
Nucleotide diversity (π) x 10−30.58 (0.03)0.631.020.891.080.960.187
Ewens-Watterson testc:
Fo0.64 (0.026)0.670.480.520.470.400.902
Fe0.45 (0.041)0.520.440.370.300.590.618
P-value∈ [0.84 ; 0.95]0.82 (0.18)0.70 (0.10)> 0.99 (>0.99)> 0.99 (>0.99)0.09 (0.25)9 (8)/19
Tajima’s D testd:
D−0.91 (0.17)−0.350.24−1.67−1.531.43−1.475
P-value∈ [0.112 ; 0.282]0.398 (0.642)0.642 (0.099)0.031 (0.061)0.056 (0.056)0.917 (0.752)11 (1) / 18
Fu’s FS teste:
FS−1.64 (0.47)−0.59−0.20−1.35−1.981.19−2.849
P-value∈ [0.038 ; 0.197]0.321 (0.642)0.399 (0.901)0.043 (0.061)0.024 (0.048)0.742 (0.742)8 (3) / 18
Pan NAT2
Total (2N chromosomes)364620101228137.8
Number of usable positions1’1151’1151’0911’0911’0911’1121'115
Number of segregating sites (S)1.87 (0.34)322329.78
Number of haplotypes (k)2.87 (0.34)4332310.7
Expected heterozygosity (h)0.15 (0.02)0.170.280.380.170.200.761
Nucleotide diversity (π) x 10−30.13 (0.02)0.150.410.500.450.192.041
Ewens-Watterson testc:
Fo0.86 (0.02)0.840.740.660.850.800.249
Fe0.63 (0.05)0.520.560.490.700.590.291
P-value∈ [0.75 ; > 0.99]f0.98 (0.96)0.90 (0.69)> 0.99 (>0.99)> 0.99 (>0.99)0.92 (0.92)0 / 18
Tajima’s D testd:
D−1.26 (0.19)−1.58−0.44−0.69−1.63−1.240.639
P-value∈ [0.034 ; 0.158]0.020 (0.040)0.337 (0.521)0.237 (0.246)0.019 (0.039)0.076 (0.076)2 (0) / 18
Fu’s FS teste:
FS−1.84 (0.55)−3.43−0.377−0.591.054−1.59−0.765
P-value∈ [0.004 ; 0.129]g0.001 (0.003)0.260 (0.521)0.123 (0.246)0.595 (0.595)0.015 (0.015)2 (0) / 18
Pan NATP
Total (2N chromosomes)365020101228128.8
Number of usable positions1’0001’0009369379369751'002.61
Number of segregating sites (S)3.51 (0.62)478619.22
Number of haplotypes (k)4.41 (0.61)5665210.6
Expected heterozygosity (h)0.65 (0.01)0.640.780.890.670.070.755
Nucleotide diversity (π) x 10−30.81 (0.05)0.772.602.751.740.071.804
Ewens-Watterson testc:
Fo0.37 (0.01)0.380.260.200.390.930.255
Fe0.46 (0.06)0.440.290.220.300.750.269
P-value∈ [0.07 ; 0.51]0.40 (0.93)0.43 (0.86)0.48 (0.95)0.95 (0.83)> 0.99 (>0.99)1 (0) / 18
Tajima’s D testd:
D−0.06 (0.36)−0.301.04−0.11−0.47−1.150.018
P-value∈ [0.383 ; 0.849]0.424 (0.935)0.865 (0.594)0.483 (0.947)0.338 (0.637)0.138 (0.138)0 / 18
Fu’s FS teste:
FS−0.37 (0.55)−0.810.48−1.02−0.55−1.15−1.771
P-value∈ [0.245 ; 0.706]0.312 (0.935)0.623 (0.863)0.222 (0.667)0.318 (0.637)0.005 (0.010)3 (1) / 18
  • a Average over the 122 samples, standard deviation in brackets.

  • b Average values for 18 to 20 human populations from four continents; single population values are reported in Supplementary Tables S7 and S12.

  • c Ewens-Watterson test for departure from selective neutrality and demographic equilibrium; Fo: observed homozygosity, Fe: expected homozygosity; the P-value is given as the proportion of random Fe values generated under the neutral equilibrium model that are smaller than, or equal to the observed Fo value. Significant deviations (P-value < 0.025 or > 0.975) are shown in bold, and after correction for multiple testing in brackets; for humans, we report the number of population samples associated with a significant deviation (before slash, and significant after correction for multiple testing in bold and brackets) on the total number of population samples tested (after slash, see Supplementary Table S12).

  • d Tajima’s D test for departure from selective neutrality and demographic equilibrium; the P-value is given as the proportion of random D values generated under the neutral equilibrium model that are smaller than, or equal to the observed D value. Significant deviations (P-value < 0.025 or > 0.975) are shown in bold, and after correction for multiple testing in brackets; for humans, we report the number of population samples associated with a significant deviation (before slash, and significant after correction for multiple testing in bold and brackets) on the total number of population samples tested (after slash, see Supplementary Table S12).

  • e Fu’s FS test for departure from selective neutrality and demographic equilibrium; the P-value is given as the proportion of random FS values generated under the neutral equilibrium model that are smaller than, or equal to the observed FS value. Significant deviations (P-value < 0.02) are shown in bold, and after correction for multiple testing in brackets; for humans, we report the number of population samples associated with a significant deviation (before slash, and significant after correction for multiple testing in bold and brackets) on the total number of population samples tested (after slash, see Supplementary Table S12).

  • f Twenty tests out of 122 (16%) indicated significant homozygosity excess (P-value > 0.975), thus exceeding by 13 tests the expected proportion of 5% (6.1 out of 122) false positives.

  • g One hundred and six tests out of 122 (87%) indicated significant deviation from neutral expectation (P-value < 0.02), thus exceeding by 103 tests the expected proportion of 2% (2.44 out of 122) false positives.