1

Appendix

The number of amino acid (A) and synonymous (S) polymorphic sites within D. melanogaster and between D. melanogaster and D. simulans

Sample size / Gene / Polymorphism / Divergence / Reference
Rare / Common
African / non-African / A / S / A / S / A / S / Ka / Ks
2 / 4 / eve / 0 / 0 / 0 / 1 / 0.0 / 1.5 / 0.000 / 0.034 / 1
4 / 23 / Ras1 / 0 / 1 / 0 / 0 / 0.0 / 4.7 / 0.000 / 0.033 / 2
4 / 23 / Ras2 / 0 / 2 / 0 / 2 / 0.0 / 2.1 / 0.000 / 0.018 / 2
4 / 23 / Ras3 / 0 / 2 / 0 / 2 / 0.0 / 2.9 / 0.000 / 0.021 / 2
8 / 17 / Tpi / 1 / 21 / 0 / 6 / 0.0 / 10.8 / 0.000 / 0.057 / 3
11 / 10 / Pgi / 2 / 3 / 1 / 2 / 1.2 / 28.4 / 0.001 / 0.067 / 4
20 / 51 / v* / 1 / 31 / 0 / 12 / 0.8 / 41.4 / 0.001 / 0.142 / 5
2 / 4 / per* / 0 / 0 / 1 / 19 / 2.4 / 48.7 / 0.002 / 0.118 / 6
2 / 3 / Rh3 / 0 / 0 / 0 / 2 / 1.7 / 27.1 / 0.002 / 0.094 / 7
2 / 9 / Adh / 0 / 9 / 1 / 9 / 1.7 / 10.9 / 0.003 / 0.053 / 8,9
0 / 21 / sod / 0 / 3 / 1 / 3 / 1.0 / 12.8 / 0.003 / 0.113 / 10,11
2 / 4 / z* / 0 / 0 / 0 / 6 / 1.8 / 17.9 / 0.003 / 0.097 / 12
10 / 45 / gld / 4 / 2 / 1 / 2 / 5.0 / 52.7 / 0.004 / 0.111 / 13
2 / 3 / boss / 0 / 0 / 2 / 15 / 4.6 / 37.6 / 0.004 / 0.096 / 14
0 / 18 / dpp / 1 / 9 / 1 / 12 / 5.2 / 16.8 / 0.004 / 0.036 / 15
11 / 0 / run* / 1 / 6 / 2 / 14 / 2.1 / 9.2 / 0.004 / 0.049 / 16
0 / 15 / w* / 0 / 6 / 2 / 5 / 7.0 / 52.0 / 0.005 / 0.099 / 17
2 / 4 / yp2* / 0 / 0 / 2 / 7 / 4.7 / 14.7 / 0.006 / 0.055 / 12
5 / 7 / cecA1 / 2 / 2 / 0 / 1 / 1.1 / 4.8 / 0.008 / 0.096 / 18
10 / 0 / fbp2 / 4 / 0 / 1 / 13 / 4.9 / 18.8 / 0.008 / 0.124 / 19
0 / 16 / mlc1 / 0 / 0 / 0 / 0 / 1.7 / 2.1 / 0.008 / 0.032 / 20
0 / 13 / Pgd* / 0 / 0 / 1 / 3 / 8.6 / 42.4 / 0.008 / 0.114 / 21
12 / 9 / Adhr / 1 / 4 / 0 / 0 / 6.0 / 26.2 / 0.010 / 0.133 / 8
2 / 7 / cta / 0 / 0 / 0 / 0 / 8.1 / 13.6 / 0.011 / 0.063 / 22
3 / 12 / hsp83 / 0 / 3 / 0 / 4 / 3.6 / 12.8 / 0.012 / 0.116 / 23
0 / 5 / pn* / 0 / 0 / 1 / 0 / 10.3 / 27.4 / 0.012 / 0.088 / 24
4 / 9 / cecB / 2 / 3 / 1 / 3 / 1.8 / 4.0 / 0.013 / 0.081 / 18
52 / 49 / Acp26Ab / 3 / 13 / 2 / 3 / 2.9 / 2.0 / 0.014 / 0.034 / 25,26,27
3 / 13 / Dpt / 4 / 7 / 2 / 1 / 3.6 / 10.8 / 0.015 / 0.139 / 18
2 / 4 / ase* / 0 / 0 / 3 / 3 / 13.5 / 10.1 / 0.017 / 0.037 / 28
14 / 32 / Zw^* / 2 / 24 / 1 / 12 / 23.4 / 44.4 / 0.020 / 0.116 / 29,30
0 / 9 / Acp70A / 0 / 2 / 1 / 2 / 2.7 / 4.1 / 0.022 / 0.099 / 31
2 / 12 / est-6^ / 4 / 2 / 7 / 23 / 28.0 / 51.4 / 0.023 / 0.126 / 23
5 / 8 / cecC / 4 / 1 / 4 / 3 / 2.7 / 4.2 / 0.025 / 0.108 / 18
2 / 8 / ref(2)P^ / 6 / 3 / 4 / 1 / 37.5 / 30.6 / 0.028 / 0.067 / 32
0 / 10 / ci^ / 0 / 0 / 0 / 0 / 20.9 / 23.9 / 0.029 / 0.101 / 33
20 / 0 / su(H) / 0 / 1 / 0 / 1 / 7.4 / 0.0 / 0.035 / 0.000 / 34
0 / 10 / tra^ / 0 / 1 / 0 / 1 / 16.6 / 22.2 / 0.041 / 0.151 / 35
4 / 5 / Anp / 3 / 2 / 0 / 0 / 4.1 / 1.6 / 0.042 / 0.048 / 18
3 / 23 / anon1A3^ / 9 / 3 / 1 / 2 / 30.4 / 23.3 / 0.044 / 0.100 / 36
3 / 12 / anon1E9^ / 4 / 2 / 0 / 0 / 58.2 / 34.7 / 0.044 / 0.083 / 36
2 / 14 / anon1G5^ / 2 / 1 / 2 / 5 / 30.5 / 13.0 / 0.053 / 0.071 / 36
6 / 0 / Rel^ / 0 / 0 / 6 / 7 / 96.4 / 55.0 / 0.053 / 0.091 / 37
27 / 12 / Acp29Ab^ / 3 / 4 / 3 / 11 / 40.6 / 41.5 / 0.075 / 0.258 / 38
52 / 49 / Acp26Aa^ / 20 / 20 / 11 / 6 / 93.4 / 33.1 / 0.165 / 0.174 / 25,26,27
^adaptive genes
*X-linked genes

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