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. 2006 Jan;172(1):373–387. doi: 10.1534/genetics.105.043901

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
Africa South Africa West Africa Burkina Fasoa Dominican Republicb Pygmy East Africa Non-African Southwest Asia Oceania East Asia America Southern Europe Northern Europe Global
Gene No. of samples: 129 16 70 33 37 25 15 148 23 12 18 15 20 38 277
ND1
    MN/MS 13/46 3/14 11/26 5/15 8/20 1/9 1/11 15/39 3/8 2/6 2/9 4/4 2/5 3/8 19/74
    dN/(dS+ const.) 0.058 0.052 0.073 0.073 0.071 0.037 0.014 0.116 0.102 0.080 0.028 0.193 0.089 0.119 0.074
ND2
    MN/MS 17/42 2/10 13/25 6/12 11/20 3/10 3/13 19/53 8/10 4/5 5/16 3/6 1/8 4/16 30/84
    dN/(dS+ const.) 0.129 0.079 0.118 0.086 0.140 0.108 0.064 0.138c 0.196 0.239 0.107 0.079 0.056 0.121 0.136
COI
    MN/MS 11/58 3/14 9/37 4/15 8/33 2/19 3/15 10/60 2/17 0/4 0/11 1/7 1/9 5/15 18/100
    dN/(dS+ const.) 0.022 0.050 0.060 0.060 0.060 0.042 0.055 0.028c 0.030 0 0 0.018 0.024 0.06 0.043
COII
    MN/MS 7/31 0/10 4/16 1/8 3/15 3/9 0/5 6/27 0/5 1/4 2/5 2/2 1/3 0/9 10/49
    dN/(dS+ const.) 0.045 0 0.035 0.008 0.053 0.093 0 0.025c 0 0.044 0.070 0.080 0.030 0 0.073
ATP8
    MN/MS 8/9 5/6 4/8 0/5 4/7 1/3 1/5 6/8 2/1 0/1 1/1 1/0 0/0 1/2 12/14
    dN/(dS+ const.) 0.050 0.102 0.049 0 0.014 0.039 0.020 0.061c 0.055 0 0.101 0.168 0 0.008 0.054
ATP6
    MN/MS 25/23 5/4 15/16 9/5 10/13 4/9 7/3 23/23 8/6 3/7 7/5 4/0 2/2 6/6 42/39
    dN/(dS+ const.) 0.174 0.191 0.187 0.212 0.168 0.079 0.300 0.236c 0.245 0.134 0.352 0.367 0.066 0.148 0.259
COIII
    MN/MS 8/38 2/10 3/20 0/11 3/18 3/14 2/14 11/37 2/9 0/8 2/10 0/3 2/6 3/11 16/59
    dN/(dS+ const.) 0.024 0.055 0.014 0 0.025 0.027 0.019 0.062c 0.033 0 0.037 0 0.057 0.124 0.037
ND3
    MN/MS 5/9 1/1 3/6 2/4 3/4 2/2 2/2 5/10 1/3 1/3 1/5 2/1 1/1 2/1 7/18
    dN/(dS+ const.) 0.118 0.037 0.075 0.058 0.088 0.197 0.103 0.109c 0.087 0.055 0.045 0.103 0.045 0.108 0.157
ND4L
    MN/MS 1/10 0/3 1/9 0/6 1/7 0/4 0/4 1/10 0/1 0/1 0/3 0/0 0/2 1/3 2/16
    dN/(dS+ const.) 0.004 0 0.009 0 0.015 0 0 0.005 0 0 0 0 0 0.018 0.005
ND4
    MN/MS 9/67 2/14 6/46 0/20 6/38 3/19 0/20 14/56 4/15 2/8 3/13 3/5 1/12 2/16 21/103
    dN/(dS+ const.) 0.023 0.030 0.015 0 0.026 0.034 0 0.029c 0.049 0.041 0.037 0.101 0.027 0.016 0.024
ND5
    MN/MS 35/75 5/17 25/38 12/21 21/26 9/23 11/25 38/60 8/18 7/6 8/10 4/10 3/12 8/17 56/112
    dN/(dS+ const.) 0.181 0.154 0.193 0.161 0.220 0.106 0.220 0.098c 0.094 0.171 0.135 0.084 0.046 0.086 0.145
ND6
    MN/MS 9/26 2/7 7/16 5/8 3/16 1/7 0/8 7/23 1/7 1/2 2/7 1/4 1/4 1/4 14/42
    dN/(dS+ const.) 0.059 0.060 0.061 0.079 0.047 0.054 0 0.033c 0.014 0.048 0.067 0.064 0.031 0.015 0.047
Cytb
    MN/MS 31/41 5/12 18/31 12/14 12/26 3/8 8/8 29/41 5/11 1/10 8/11 2/9 5/4 8/10 47/65
    dN/(dS+ const.) 0.145 0.080 0.163 0.213 0.126 0.111 0.193 0.199c 0.138 0.035 0.127 0.054 0.240 0.351 0.166
No. of recurrent synonymous sites 81 2 28 5 14 4 2 71 8 3 4 2 1 1 241
No. of recurrent nonsynonymous sites 35 2 14 5 6 1 3 30 3 0 2 0 0 3 106
π (×10−3) 3.79 3.59 3.22 2.69 3.68 4.26 3.16 1.85 1.78 1.93 1.99 1.66 1.01 1.41 3.06
±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) 10.55 4.12 7.54 4.34 7.01 3.99 4.61 10.02 3.75 2.54 3.79 2.11 2.24 3.44 15.36
±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 valine 78 10 36 13 20 7 12 74 10 6 14 9 3 14 158
From threonine and valine 47 2 34 10 22 2 3 52 9 2 13 3 5 11 99

*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.