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. 2010 Oct 26;28(2):1043–1056. doi: 10.1093/molbev/msq280

Table 3.

Interspecific Divergence and McDonald–Kreitman Analysis.

n Ln Ls KA KS KA/KS Ds Ps Dn Pn a a/bp
Drosophila melanogaster
    CG7275 12 941 280 0.002 0.054 0.042 9 21 2 1 0 0.000
    yellow-k 12 882 252 0.005 0.059 0.082 9 16 3 6 −6 −0.007
    CrebA 12 761 247 0.003 0.04 0.079 8 8 2 3 −3 −0.004
    AGO2 12 1884 567 0.032 0.068 0.476 34 5 54 4 48 0.025
    CG7739 12 1055 322 0.009 0.082 0.11 23 7 9 3 4 0.004
    CG6498 12 1074 336 0.004 0.038 0.103 11 6 4 2 1 0.001
    CG12301 12 1064 275 0.022 0.027 0.819 7 5 21 8 8 0.008
    RhoGAP71E 12 537 171 0.001 0.062 0.017 8 6 0 2 −3 −0.006
    CG7372 12 974 265 0.017 0.065 0.263 15 5 14 11 −3 −0.003
D. simulans
    CG7275 21 941 280 0.005 0.081 0.061 8 56 4 7 2 0.002
    yellow-k 21 883 251 0.008 0.071 0.11 7 43 3 17 −3 −0.003
    CrebA 21 761 247 0.001 0.031 0.018 6 8 0 2 −1 −0.001
    AGO2 21 1889 565 0.041 0.067 0.632 37 6 75 1 75 0.040
    CG7739 21 1058 328 0.011 0.04 0.27 11 10 11 3 10 0.009
    CG6498 21 1072 338 0.002 0.033 0.064 6 26 2 6 0 0.000
    CG12301 21 1121 295 0.009 0.051 0.179 10 36 4 33 −7 −0.006
    RhoGAP71E 21 531 171 0.007 0.046 0.162 2 28 1 15 −4 −0.008
    CG7372 21 948 258 0.028 0.077 0.359 7 64 6 94 −26 −0.027
D. yakuba
    CG7275 7 939 282 0.014 0.149 0.091 29 37 11 3 4 0.005
    yellow-k 8 880 254 0.019 0.166 0.113 34 13 14 9 −5 −0.006
    CrebA 7 759 249 0.017 0.091 0.183 21 4 12 2 7 0.010
    AGO2 11 1882 566 0.04 0.215 0.186 11 8 70 4 63 0.033
    CG7739 8 1056 327 0.015 0.19 0.079 52 12 15 1 13 0.012
    CG6498 8 1009 323 0.01 0.15 0.068 37 19 10 1 8 0.008
    RhoGAP71E 7 557 178 0.015 0.184 0.079 26 12 8 0 8 0.014
    CG7372 7 1034 283 0.112 0.245 0.458 59 22 96 17 58 0.056

Note.—n is the number of alleles sampled; Ln and Ls the number of nonsynonymous and synonymous sites, respectively; KA and KS are the nonsynonymous and synonymous divergence; Ds, Ps, Dn, and Pn are counts of fixed differences (D) and polymorphisms (P) at synonymous and nonsynonymous sites; and “a” is the maximum-likelihood estimate of the number of nonsynonymous adaptive substitutions per gene under the model described in Obbard, Welch, et al. (2009) and Materials and Methods (above). Divergence is measured from their common ancestor in the case of D. melanogaster and D. simulans and from D. erecta in the case of D. yakuba.