TABLE 2.

Polymorphism data summary

Locus	Species	na	Sb	Sync	Repc	θtd	θsd	De	L (bp)f
A. Regions of reduced frequency of crossing over
ND5–ND4	D. yakuba	11	8	6	2	0.0016	0.0046	−1.27	1657
D. santomea	10	4	4	0	0.00085	0.0032	−0.52
Dhc-Yh3	D. yakuba	11	0	0	0	0	0	—	1219
D. santomea	10	0	0	0	0	0	—
CG17629	D. yakuba	11	1	1	0	0.0004	0.0016	0.67	936
D. santomea	10	3	1	2	0.0011	0.001	−1.03
Pp1Y1	D. yakuba	11	1	0	1	0.0007	0	−1.13	490
D. santomea	10	0	0	0	0	0	—
y	D. yakuba	16	6	6	0	0.0019	0.0078	−1.17	965
D. santomea	16	0	0	0	0	0	—
su(f)	D. yakuba	16	1	0	0	0.0005	0.0008	0.15	607
D. santomea	16	0	0	0	0	0	—
l(2)gl	D. yakuba	16	1	1	0	0.0005	0.0021	1.03	608
D. santomea	16	3	2	1	0.0015	0.0042	0.17
His3	D. yakuba	16	3	0	0	0.0018	0.0022	−0.65	496
D. santomea	16	0	0	0	0	0	—
Kr	D. yakuba	16	3	3	0	0.002	0.0086	0.01	456
D. santomea	16	0	0	0	0	0	—
Lsp1-γ	D. yakuba	16	3	2	0	0.0018	0.006	−0.41	508
D. santomea	16	4	0	3	0.0024	0.002	−1.55*
Ssl1	D. yakuba	16	2	2	0	0.0012	0.0051	−0.58	501
D. santomea	16	1	1	0	0.0006	0.0025	0.15
krzg	D. yakuba	16	0	—	—	0	0	—	165
D. santomea	16	2	—	—	0.0036	0.0036	−1.50*
B. Regions of nonreduced frequency of crossing over
rux	D. yakuba	16	28	20	7	0.0090	0.023	−1.62*	940
D. santomea	16	21	17	3	0.0067	0.02	−1.42
per	D. yakuba	16	3	0	0	0.001	0.0013	−1.35	905
D. santomea	14	5	0	1	0.0017	0.0019	−1.36
sog	D. yakuba	16	25	23	2	0.007	0.024	−0.63	1100
D. santomea	16	18	17	1	0.0049	0.018	−0.59
bnb	D. yakuba	14	33	24	9	0.012	0.037	−0.86	837
D. santomea	16	25	18	7	0.009	0.026	−0.97
Hex-A	D. yakuba	16	3	3	0	0.0014	0.058	−0.63	639
D. santomea	16	9	8	1	0.0042	0.016	−0.67
Rad1	D. yakuba	16	16	14	1	0.011	0.04	−1.45	428
D. santomea	16	10	8	1	0.007	0.024	−1.48*
RpL27A	D. yakuba	14	20	2	1	0.0076	0.01	0.13	822
D. santomea	14	19	2	1	0.0073	0.0099	−1.17
salr	D. yakuba	16	28	25	2	0.0086	0.038	−0.72	869
D. santomea	16	26	22	3	0.0090	0.033	−0.58
Rep4	D. yakuba	16	25	19	6	0.0093	0.032	−0.76	808
D. santomea	16	14	11	3	0.0052	0.019	−1.61*
Sara	D. yakuba	16	21	13	7	0.0068	0.02	−0.26	887
D. santomea	16	12	8	4	0.0040	0.012	0.52
Hex-C	D. yakuba	16	21	19	2	0.011	0.04	0.65	552
D. santomea	16	13	12	1	0.0071	0.021	−0.73
Ngp	D. yakuba	16	3	3	0	0.0012	0.005	0.47	767
D. santomea	16	5	4	1	0.0020	0.0067	−0.32
sfl	D. yakuba	16	40	40	0	0.014	0.058	−0.86	867
D. santomea	16	37	37	0	0.013	0.053	−0.59
Est6	D. yakuba	16	37	22	8	0.016	0.043	0.17	687
D. santomea	16	27	15	9	0.012	0.027	0.12
Xdh	D. yakuba	16	32	23	9	0.012	0.036	−0.14	782
D. santomea	16	24	18	6	0.0092	0.028	−1.95**
AP-50	D. yakuba	16	35	25	2	0.01	0.035	−0.63	1025
D. santomea	16	29	22	1	0.0085	0.029	−1.84*
Mlc1	D. yakuba	16	7	0	0	0.0059	0.0071	−1.52	359
	D. santomea	16	10	0	0	0.0084	0.01	−1.54*

^*P < 0.05,

^**P < 0.01. —, values could not be estimated because of lack of informative sites.

^aSample size.

^bNumber of polymorphic sites.

^cNumber of synonymous (syn) and nonsynonymous (rep) polymorphic sites estimated using Nei and Gojobori (1986).

^dWatterson's (1975) estimate of total and silent (synonymous and noncoding) heterozygosity.

^eTajima's (1989b) D-statistic. Significance was calculated with coalescent simulations without recombination.

^fSize of the sequenced region.

^gThis locus does not include the coding region sequence.