Pan species and sub-species | |||||||
---|---|---|---|---|---|---|---|

P. t. verus (Western chimpanzee) | Homo sapiens | ||||||

San Diego sample^{a} | BPRC sample | P. t. ellioti (Nigeria-Cameroon) | P. t. troglodytes (Central) | P. t. schweinfurthii (Eastern) | P. paniscus (Bonobo) | (human populations average)^{b} | |

Pan NAT1 | |||||||

Total (2N chromosomes) | 36 | 46 | 20 | 10 | 12 | 28 | 119.7 |

Number of usable positions | 903 | 903 | 898 | 898 | 898 | 898 | 903 |

Number of segregating sites (S) | 3.57 (0.5) | 3 | 3 | 4 | 5 | 2 | 3.75 |

Number of haplotypes (k) | 4.57 (0.5) | 4 | 4 | 4 | 5 | 3 | 3.5 |

Expected heterozygosity (h) | 0.37 (0.03) | 0.34 | 0.55 | 0.53 | 0.58 | 0.63 | 0.095 |

Nucleotide diversity (π) x 10^{−3} | 0.58 (0.03) | 0.63 | 1.02 | 0.89 | 1.08 | 0.96 | 0.187 |

Ewens-Watterson test^{c}: | |||||||

Fo | 0.64 (0.026) | 0.67 | 0.48 | 0.52 | 0.47 | 0.40 | 0.902 |

Fe | 0.45 (0.041) | 0.52 | 0.44 | 0.37 | 0.30 | 0.59 | 0.618 |

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 test^{d}: | |||||||

D | −0.91 (0.17) | −0.35 | 0.24 | −1.67 | −1.53 | 1.43 | −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 F_{S} test^{e}: | |||||||

F_{S} | −1.64 (0.47) | −0.59 | −0.20 | −1.35 | −1.98 | 1.19 | −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) | 36 | 46 | 20 | 10 | 12 | 28 | 137.8 |

Number of usable positions | 1’115 | 1’115 | 1’091 | 1’091 | 1’091 | 1’112 | 1'115 |

Number of segregating sites (S) | 1.87 (0.34) | 3 | 2 | 2 | 3 | 2 | 9.78 |

Number of haplotypes (k) | 2.87 (0.34) | 4 | 3 | 3 | 2 | 3 | 10.7 |

Expected heterozygosity (h) | 0.15 (0.02) | 0.17 | 0.28 | 0.38 | 0.17 | 0.20 | 0.761 |

Nucleotide diversity (π) x 10^{−3} | 0.13 (0.02) | 0.15 | 0.41 | 0.50 | 0.45 | 0.19 | 2.041 |

Ewens-Watterson test^{c}: | |||||||

Fo | 0.86 (0.02) | 0.84 | 0.74 | 0.66 | 0.85 | 0.80 | 0.249 |

Fe | 0.63 (0.05) | 0.52 | 0.56 | 0.49 | 0.70 | 0.59 | 0.291 |

P-value | ∈ [0.75 ; > 0.99]^{f} | 0.98 (0.96) | 0.90 (0.69) | > 0.99 (>0.99) | > 0.99 (>0.99) | 0.92 (0.92) | 0 / 18 |

Tajima’s D test^{d}: | |||||||

D | −1.26 (0.19) | −1.58 | −0.44 | −0.69 | −1.63 | −1.24 | 0.639 |

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 F_{S} test^{e}: | |||||||

F_{S} | −1.84 (0.55) | −3.43 | −0.377 | −0.59 | 1.054 | −1.59 | −0.765 |

P-value | ∈ [0.004 ; 0.129]^{g} | 0.001 (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) | 36 | 50 | 20 | 10 | 12 | 28 | 128.8 |

Number of usable positions | 1’000 | 1’000 | 936 | 937 | 936 | 975 | 1'002.61 |

Number of segregating sites (S) | 3.51 (0.62) | 4 | 7 | 8 | 6 | 1 | 9.22 |

Number of haplotypes (k) | 4.41 (0.61) | 5 | 6 | 6 | 5 | 2 | 10.6 |

Expected heterozygosity (h) | 0.65 (0.01) | 0.64 | 0.78 | 0.89 | 0.67 | 0.07 | 0.755 |

Nucleotide diversity (π) x 10^{−3} | 0.81 (0.05) | 0.77 | 2.60 | 2.75 | 1.74 | 0.07 | 1.804 |

Ewens-Watterson test^{c}: | |||||||

Fo | 0.37 (0.01) | 0.38 | 0.26 | 0.20 | 0.39 | 0.93 | 0.255 |

Fe | 0.46 (0.06) | 0.44 | 0.29 | 0.22 | 0.30 | 0.75 | 0.269 |

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 test^{d}: | |||||||

D | −0.06 (0.36) | −0.30 | 1.04 | −0.11 | −0.47 | −1.15 | 0.018 |

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 F_{S} test^{e}: | |||||||

F_{S} | −0.37 (0.55) | −0.81 | 0.48 | −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;

*F*o: observed homozygosity,*F*e: expected homozygosity; the*P*-value is given as the proportion of random*F*e values generated under the neutral equilibrium model that are smaller than, or equal to the observed*F*o 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

*F*_{S}test for departure from selective neutrality and demographic equilibrium; the*P*-value is given as the proportion of random*F*_{S}values generated under the neutral equilibrium model that are smaller than, or equal to the observed*F*_{S}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.