TABLE 3

Ratios of numbers and rates of nonsynonymous over synonymous sites, nucleotide diversity, Tajima's D, Fu and Li's D and F, and number of changes from and to valine and threonine for the 13 protein-coding mitochondrial genes according to continental affiliation

Continent
AfricaSouth AfricaWest AfricaBurkina FasoaDominican RepublicbPygmyEast AfricaNon-AfricanSouthwest AsiaOceaniaEast AsiaAmericaSouthern EuropeNorthern EuropeGlobal
GeneNo. of samples:129167033372515148231218152038277
ND1
    MN/MS13/463/1411/265/158/201/91/1115/393/82/62/94/42/53/819/74
    dN/(dS + const.)0.0580.0520.0730.0730.0710.0370.0140.1160.1020.0800.0280.1930.0890.1190.074
ND2
    MN/MS17/422/1013/256/1211/203/103/1319/538/104/55/163/61/84/1630/84
    dN/(dS + const.)0.1290.0790.1180.0860.1400.1080.0640.138c0.1960.2390.1070.0790.0560.1210.136
COI
    MN/MS11/583/149/374/158/332/193/1510/602/170/40/111/71/95/1518/100
    dN/(dS + const.)0.0220.0500.0600.0600.0600.0420.0550.028c0.030000.0180.0240.060.043
COII
    MN/MS7/310/104/161/83/153/90/56/270/51/42/52/21/30/910/49
    dN/(dS + const.)0.04500.0350.0080.0530.09300.025c00.0440.0700.0800.03000.073
ATP8
    MN/MS8/95/64/80/54/71/31/56/82/10/11/11/00/01/212/14
    dN/(dS + const.)0.0500.1020.04900.0140.0390.0200.061c0.05500.1010.16800.0080.054
ATP6
    MN/MS25/235/415/169/510/134/97/323/238/63/77/54/02/26/642/39
    dN/(dS + const.)0.1740.1910.1870.2120.1680.0790.3000.236c0.2450.1340.3520.3670.0660.1480.259
COIII
    MN/MS8/382/103/200/113/183/142/1411/372/90/82/100/32/63/1116/59
    dN/(dS + const.)0.0240.0550.01400.0250.0270.0190.062c0.03300.03700.0570.1240.037
ND3
    MN/MS5/91/13/62/43/42/22/25/101/31/31/52/11/12/17/18
    dN/(dS + const.)0.1180.0370.0750.0580.0880.1970.1030.109c0.0870.0550.0450.1030.0450.1080.157
ND4L
    MN/MS1/100/31/90/61/70/40/41/100/10/10/30/00/21/32/16
    dN/(dS + const.)0.00400.00900.015000.005000000.0180.005
ND4
    MN/MS9/672/146/460/206/383/190/2014/564/152/83/133/51/122/1621/103
    dN/(dS + const.)0.0230.0300.01500.0260.03400.029c0.0490.0410.0370.1010.0270.0160.024
ND5
    MN/MS35/755/1725/3812/2121/269/2311/2538/608/187/68/104/103/128/1756/112
    dN/(dS + const.)0.1810.1540.1930.1610.2200.1060.2200.098c0.0940.1710.1350.0840.0460.0860.145
ND6
    MN/MS9/262/77/165/83/161/70/87/231/71/22/71/41/41/414/42
    dN/(dS + const.)0.0590.0600.0610.0790.0470.05400.033c0.0140.0480.0670.0640.0310.0150.047
Cytb
    MN/MS31/415/1218/3112/1412/263/88/829/415/111/108/112/95/48/1047/65
    dN/(dS + const.)0.1450.0800.1630.2130.1260.1110.1930.199c0.1380.0350.1270.0540.2400.3510.166
No. of recurrent synonymous sites812285144271834211241
No. of recurrent nonsynonymous sites35214561330302003106
π (×10−3)3.793.593.222.693.684.263.161.851.781.931.991.661.011.413.06
±SD±0.12±0.23±0.17±0.18±0.23±0.16±0.37±0.08±0.14±0.23±0.15±0.19±0.18±0.09±0.10
θ (×10−3)10.554.127.544.347.013.994.6110.023.752.543.792.112.243.4415.36
±SD±2.45±1.49±1.96±1.31±2.08±1.30±1.69±2.28±1.25±1.00±1.34±0.79±0.78±1.03±3.14
Tajima's D−2.139*−0.552−2.014*−1.455−1.806*0.265−1.385−2.681****−2.117*−1.121−2.012*−0.933−2.249**−2.198**−2.528****
Fu and Li's D−4.203***−0.668−4.186***−2.524*−2.744*0.963−1.015−8.572***−3.300***−1.407−2.847***−1.272−3.138***−4.440***−7.738***
Fu and Li's F−3.883***−0.735−3.956***−2.560*−2.871*0.870−1.291−6.894***−3.437***−1.519−3.024***−1.357−3.349***−4.339***−5.872***
To threonine and valine781036132071274106149314158
From threonine and valine47234102223529213351199
  • *P < 0.05; **P < 0.01; ***P < 0.02; ****P < 0.001.

  • a Rimaibe (N = 10), Foulbe (10), Mossi (10), all from Burkina Faso, plus 2 Mandenka and 1 Ghanan (subset of West Africa).

  • b Individuals of African descent from the Dominican Republic (subset of West Africa).

  • c Significant (P < 0.0001) difference between African and non-African distribution of dN/(dS + constant) values.