HKA test comparing intraspecific polymorphism within or to interspecific divergence among D. simulans and D. melanogaster using silent and synonymous sites

siIIsiIII: (pooled)
MwanzaDar es SalaamMalindiNairobi
Intraspecific polymorphisma
    Sample size11/211/29/29/29/29/211/211/237/237/2
    No. of segregating sites (obs)0/546/55/539/58/536/56/546/50/587/5
    No. of segregating sites (exp)12.13/2.6433.87/7.3612.71/2.8931.29/7.1113.76/3.1330.24/6.8715.92/3.0636.08/6.9418.71/2.1568.29/7.85
    Total no. of sites352.33335.95352.18335.93352.33337.06352.33336.90354.60332.82
Interspecific divergence
    Mean no. of differences (obs)52.0035.8649.4436.5650.5636.2850.2735.6852.5036.77
    Mean no. of differences (exp)42.2345.6343.8442.1646.6740.1749.2943.6636.6452.63
    Total no. of sites352.33335.95352.18335.95352.33337.06352.33336.91354.60332.82
Sum of deviations (P)b
    MtDNA = 1/3 perc7.56 (0.03)2.80 (0.25)1.48 (0.48)3.74 (0.14)15.40 (0.004)
    MtDNA = 1/6 perdNAe2.17 (0.36)1.19 (0.57)2.35 (0.33)12.17 (0.03)

obs, observed; exp, expected.

  • a Values within each cell are reported for D. simulans/D. melanogaster, respectively.

  • b P, proportion of simulated values that were greater than the observed sum of deviations.

  • c The effective population size of mtDNA was corrected to be one-third that of per, which occurs on the X chromosome.

  • d It may be argued that the effective population size of D. simulans mtDNA in populations containing both siII and siIII should be one-sixth that of per to accommodate sympatry (see text for details).

  • e NA, not applicable, since Mwanza contained only siII flies.