TABLE 3

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

	siII								siIII: (pooled)
	Mwanza		Dar es Salaam		Malindi		Nairobi		siIII: (pooled)
	mtDNA	per	mtDNA	per	mtDNA	per	mtDNA	per	mtDNA	per
Intraspecific polymorphism^{^a}
Sample size	11/2	11/2	9/2	9/2	9/2	9/2	11/2	11/2	37/2	37/2
No. of segregating sites (obs)	0/5	46/5	5/5	39/5	8/5	36/5	6/5	46/5	0/5	87/5
No. of segregating sites (exp)	12.13/2.64	33.87/7.36	12.71/2.89	31.29/7.11	13.76/3.13	30.24/6.87	15.92/3.06	36.08/6.94	18.71/2.15	68.29/7.85
Total no. of sites	352.33	335.95	352.18	335.93	352.33	337.06	352.33	336.90	354.60	332.82
Interspecific divergence
Mean no. of differences (obs)	52.00	35.86	49.44	36.56	50.56	36.28	50.27	35.68	52.50	36.77
Mean no. of differences (exp)	42.23	45.63	43.84	42.16	46.67	40.17	49.29	43.66	36.64	52.63
Total no. of sites	352.33	335.95	352.18	335.95	352.33	337.06	352.33	336.91	354.60	332.82
Sum of deviations (P)^{^b}
MtDNA = 1/3 per^{^c}	7.56 (0.03)		2.80 (0.25)		1.48 (0.48)		3.74 (0.14)		15.40 (0.004)
MtDNA = 1/6 per^{^d}	NA^{^e}		2.17 (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.