Table 3 Site frequency tests of departures from neutral models for eight GSC genes in D. melanogaster and D. simulans

Test Details	SweeD Test of Recent Selection				OmegaPlus Test of Recent Selection
	D. melanogaster		D. simulans		D. melanogaster		D. simulans
	Orig P-value	FDR adj P-Value	Orig P-Value	FDR adj P-Value	Orig P-Value	FDR adj P-Value	Orig P-Value	FDR adj P-Value
CycA1.SN	0.0007	0.0023	0.0015	0.0032	0.367	0.4037	0.4756	0.4756
CycA1.Ex	0.0007	0.0023	0.0009	0.0023	0.4323	0.4390	0.4049	0.4711
CycA1.3Ep	0.0007	0.0023	0.0012	0.0027	0.439	0.4390	0.4094	0.4711
CycA2.SN	0.6203	0.7030	0.9933	0.9933	0.3726	0.4037	0.2594	0.4214
CycA2.Ex	0.3460	0.4334	0.7363	0.8024	0.2809	0.3894	0.2622	0.4214
CycA2.3Ep	0.3467	0.4334	0.7863	0.8460	0.2866	0.3894	0.2595	0.4214
meiP26.SN	0.0010	0.0023	0.0009	0.0023	0.1894	0.3894	0.0333	0.4214
meiP26.Ex	0.0008	0.0023	0.0010	0.0023	0.2081	0.3894	0.0999	0.4214
meiP26.3Ep	0.0008	0.0023	0.0006	0.0023	0.2108	0.3894	0.0648	0.4214
nano.SN	0.0090	0.0150	0.0008	0.0023	0.4055	0.4274	0.2278	0.4214
nano.Ex	0.0020	0.0040	0.0010	0.0023	0.2560	0.3894	0.2329	0.4214
nano.3Ep	0.0050	0.0092	0.0009	0.0023	0.3403	0.4037	0.2204	0.4214
piwi.SN	0.0009	0.0023	0.9680	0.9795	0.1267	0.3894	0.1899	0.4214
piwi.Ex	0.0070	0.0124	0.9370	0.9713	0.1096	0.3894	0.3899	0.4711
piwi.3Ep	0.0010	0.0023	0.9500	0.9729	0.1030	0.3894	0.3909	0.4711
pum1.SN	0.0008	0.0023	0.4174	0.4997	0.2302	0.3894	0.2198	0.4214
pum1.Ex	0.0009	0.0023	0.1640	0.2213	0.2537	0.3894	0.2126	0.4214
pum1.3Ep	0.0009	0.0023	0.1736	0.2306	0.2532	0.3894	0.2293	0.4214
pum2.SN	0.0008	0.0023	0.0919	0.1281	0.3631	0.4037	0.2649	0.4214
pum2.Ex	0.0009	0.0023	0.0278	0.0407	0.3630	0.4037	0.2599	0.4214
pum2.3Ep	0.0008	0.0023	0.0227	0.0339	0.3389	0.4037	0.2605	0.4214
pum3.SN	0.2073	0.2711	0.0153	0.0245	0.1728	0.3894	0.1664	0.4214
pum3.Ex	0.1633	0.2213	0.0010	0.0023	0.0612	0.3894	0.2701	0.4214
pum3.3Ep	0.0800	0.1133	0.0019	0.0039	0.0800	0.3894	0.2131	0.4214
pum4.SN	0.0186	0.0287	0.8249	0.8765	0.2995	0.3894	0.4296	0.4711
pum4.Ex	0.0067	0.0121	0.7174	0.7919	0.2694	0.3894	0.3909	0.4711
pum4.3Ep	0.0080	0.0139	0.6710	0.7505	0.2690	0.3894	0.3414	0.4711
stwlReg1.SN	0.0159	0.0250	0.0219	0.0332	0.0885	0.3894	0.0444	0.4214
stwlReg1.Ex	0.0009	0.0023	0.0021	0.0042	0.0630	0.3894	0.1062	0.4214
stwlReg1.3Ep	0.0043	0.0081	0.0010	0.0023	0.0516	0.3894	0.0827	0.4214
stwlReg2.SN	0.0010	0.0023	0.8780	0.9214	0.2987	0.3894	0.4099	0.4711
stwlReg2.Ex	0.0006	0.0023	0.4943	0.5756	0.2851	0.3894	0.4637	0.4756
stwlReg2.3Ep	0.0007	0.0023	0.4688	0.5534	0.2869	0.3894	0.4349	0.4711
yb.SN	0.0009	0.0023	0.0014	0.0031	0.0009	0.0351	0.4469	0.4711
yb.Ex	0.0006	0.0023	0.0040	0.0077	0.0059	0.0767	0.4212	0.4711
yb.3Ep	0.0008	0.0023	0.0007	0.0023	0.0033	0.0644	0.3702	0.4711
zpg.SN	0.0008	0.0023	0.0009	0.0023	0.2129	0.3894	0.2093	0.4214
zpg.Ex	0.0090	0.0150	0.0006	0.0023	0.2991	0.3894	0.1461	0.4214
zpg.3Ep	0.0010	0.0023	0.0009	0.0023	0.2807	0.3894	0.1692	0.4214

Simulations to establish P-values were from the standard neutral model (SN), exponential growth model (Ex), or a 3-epoch model (3Ep; large, small, large population size) as described in the section Materials and Methods. FDR-adjusted P-values were determined as described in text. Significant results (P < 0.05) are in bold. FDR, false-discovery rate.