TABLE 3.

Synonymous (K_s), silent (K_silent), and nonsynonymous (K_a) divergence betweenD. miranda, D. pseudoobscura, andD. affinis, expressed as percentages

	D. miranda vs. D. pseudoobscura				D. miranda vs. D. affinis				D. pseudoobscura vs. D. affinis
Gene	Ks	Ksilent	Ka	Ka/Ks	Ks	Ksilent	Ka	Ka/Ks	Ks	Ksilent	Ka	Ka/Ks
bcd	4.13	3.58	0.14	0.03	22.32	21.32	0.91	0.04	20.89	19.78	1.02	0.05
Bruce	6.55	6.35	0.23	0.03	39.01	29.57	0.86	0.02	41.59	31.68	0.63	0.02
ftz	6.05	5.39	0.96	0.16	20.83	19.52	3.51	0.17	19.75	18.02	3.36	0.17
Gld	4.16	4.16	0.01	0.00	20.96	20.96	0.40	0.02	20.07	20.07	0.39	0.02
hb	3.77	3.75	0.32	0.09	23.87	23.74	0.93	0.04	22.96	22.83	1.06	0.05
hyd	2.50	2.37	0.60	0.24	20.42	18.35	0.87	0.04	21.78	18.85	0.72	0.03
ninaE	3.73	3.81	0.00	0.00	23.23	32.53	0.84	0.04	23.78	33.81	0.84	0.04
nop56	4.11	3.97	0.31	0.08	17.15	19.14	0.52	0.03	18.82	20.20	0.62	0.03
RpL32	3.21	2.15	0.00	0.00	13.68	13.16	0.00	0.00	17.59	13.71	0.00	0.00
rosy	6.03	5.81	0.52	0.09	28.40	27.00	2.19	0.08	30.66	28.93	2.22	0.07
sry-alpha	2.75	2.75	0.62	0.23	35.60	35.60	11.23	0.32	34.46	34.46	10.80	0.31
Tl	6.92	6.65	0.42	0.06	26.53	25.22	5.94	0.22	24.89	24.29	5.74	0.23
ade3	5.27	5.91	0.83	0.16	22.34	27.16	1.18	0.05	25.49	29.10	0.68	0.03
Adh	4.49	3.21	1.06	0.24	20.34	26.41	1.78	0.09	20.07	25.94	2.14	0.11
Adh-dup	3.87	4.76	0.97	0.25	33.31	33.80	2.64	0.08	35.24	35.22	2.84	0.08
amd	2.30	2.83	0.30	0.13	22.92	16.54	1.47	0.06	23.03	17.54	1.45	0.06
Ddc	6.01	6.01	0.29	0.05	26.99	26.99	1.28	0.05	32.30	32.30	1.01	0.03
dpp	3.26	4.45	1.07	0.33	12.86	18.91	2.14	0.17	11.81	18.92	1.99	0.17
Eno	2.67	2.41	0.01	0.00	12.12	11.20	1.08	0.09	12.77	12.08	1.07	0.08
Gpdh	3.25	3.32	0.00	0.00	7.81	16.09	0.00	0.00	11.43	14.98	0.00	0.00
Lam	3.03	2.40	0.64	0.21	25.10	22.77	3.97	0.16	26.25	23.70	4.23	0.16
smo	3.74	2.80	0.10	0.03	14.41	17.06	0.56	0.04	13.41	16.30	0.41	0.03
Uro	6.96	5.82	0.31	0.04	25.50	23.84	1.23	0.05	26.41	25.04	1.23	0.05
AnnX	8.96	9.55	0.02	0.00	22.87	25.47	0.66	0.03	25.73	30.98	0.64	0.02
Cyp1	—	2.11	—	—	—	14.48	—	—	—	14.04	—	—
Est-5B	5.78	4.79	0.96	0.17	31.82	24.20	4.47	0.14	31.35	24.17	4.47	0.14
Gapdh2	3.22	3.22	0.00	0.00	15.07	15.07	0.35	0.02	17.02	17.02	0.35	0.02
Hsp83	4.18	4.18	0.00	0.00	17.60	17.60	0.16	0.01	16.77	16.77	0.16	0.01
scute	2.13	3.98	0.26	0.12	23.18	13.84	2.08	0.09	24.63	16.55	2.22	0.09
sesB	2.44	3.83	0.37	0.15	7.15	16.42	0.65	0.09	7.11	15.63	1.02	0.14
sisA	3.91	3.50	1.16	0.30	29.73	25.09	10.56	0.36	31.97	27.40	9.33	0.29
Sod	5.60	1.79	0.41	0.07	16.55	9.55	1.66	0.10	16.57	9.81	1.24	0.07
swallow	4.64	3.70	1.11	0.24	34.64	29.59	8.07	0.23	37.21	30.18	7.71	0.21
Average	4.36	4.10	0.44	0.11	22.32	21.76	2.32	0.09	23.24	22.43	2.24	0.09
SE	0.284	0.287	0.068	0.017	1.359	1.146	0.498	0.015	1.422	1.241	0.469	0.015

Silent (K_silent), synonymous (K_s), and nonsynonymous (K_a) divergence was estimated by the Jukes-Cantor correction for multiple hits. The data shown in this table are not corrected for within-species diversity.