Table 1. Synonymous and nonsynonymous variation in D. melanogaster mitochondrial genes and OXPHOS complexes.

Gene/Complexa	Synonymous Sitesb					Nonsynonymous Sites
	n (bp)	S	π	ӨW	D	n (bp)	S	π	ӨW	D
COI	347	16	1.57	3.81	−1.91	1183	0	0	0	Undef
COII	142	5	0.31	1.19	−1.90	539	1	0.05	0.24	−1.13
COIII	169.33	9	0.72	2.14	−1.96	613.67	1	0.05	0.24	−1.13
ND1	194	3	0.16	0.71	−1.72	739	3	0.16	0.71	−1.72
ND2	198	5	0.41	1.19	−1.69	822	6	0.34	1.43	−2.07
ND3	68	1	0.05	0.24	−1.12	280	1	0.05	0.24	−1.12
ND4	273.33	7	0.51	1.67	−1.95	1061.67	7	0.38	1.67	−2.17
ND4L	56	1	0.05	0.24	−1.13	229	2	0.11	0.48	−1.49
ND5	351	10	0.68	2.38	−2.16	1365	4	0.21	0.95	−1.88
ND6	103.33	4	0.26	0.95	−1.75	415.67	2	0.11	0.48	−1.49
Complex I	1243.66	31	2.12	7.38	−2.48	4912.34	25	1.35	5.95	−2.64
Complex III	239	5	0.55	1.19	−1.38	892	2	0.16	0.48	−1.29
Complex IV	658.33	30	2.60	7.14	−2.21	2335.67	2	0.11	0.48	−1.49
Complex V	174.67	2	0.16	0.71	−1.72	650.33	6	0.32	1.43	−2.10
Total	2315.66	68	5.43	16.42	−2.44	8790.34	35	1.93	8.33	−2.70

OXPHOS, oxidative phosphorylation; Undef, undefined; CO, cytochrome c oxidase; ND, NADH dehydrogenase; ATPase, ATP synthase.

^aComplex I (ND), 7 loci; Complex III (Cytochrome B), 1 locus; Complex IV (CO), 3 loci; Complex V (ATPase), 2 overlapping loci.

^bFor synonymous and nonsynonymous sites, we calculated the number of segregating sites (S), heterozygosity (π), Watterson’s Ө_W, and Tajima’s D. The heterogeneity test for differences between synonymous and nonsynonymous D was never significant (P > 0.35 for all comparisons).