Table 13 . Named genes in the golden set with two or more nonsynonymous shared polymorphisms in D. melanogaster and D. simulans (see text).

FBgn	Gene name	No. shared nonsynonymous polymorphisms	No. shared nonsingleton nonsynymous polymorphisms	No. synonymous polymorphisms	Shared amino acid coded with different codon	One of the shared nonsynonymous states present in yakuba and/or erecta	Alternative shared nonsynonymous states present in yakuba and erecta	FET P-value for nonsynonymous polymorphisms	FET P-value for synonymous polymorphisms
FBgn0040102	Lectin-24Db	4	2	3	1	3	0	0.001	0.080
FBgn0261714	Cpn	4	3	1	1	3	1	0.002	1
FBgn0043841	vir-1	3	3	1	0	2	1	0.0001	0.583
FBgn0050169	Brca2	3	2	0	1	0	0	0.024	0.652
FBgn0000928	fs(1)Yb	3	1	2	0	0	0	0.019	0.655
FBgn0015663	Dot	2	2	6	0	0	0	0.005	0.001
FBgn0052656	Muc11A	2	1	3	0	0	0	0.009	0.019
FBgn0036463	Reck	2	2	6	0	0	0	0.008	0.030
FBgn0031592	Art2	2	2	2	0	0	0	0.006	0.166
FBgn0032728	Tango	2	2	0	1	2	0	0.026	0.412
FBgn0040262	Ugt36Ba	2	2	0	0	2	0	0.007	0.631
FBgn0004400	rhi	2	1	0	0	0	0	0.040	1
FBgn0032840	sNPF	2	1	0	0	1	0	0.001	1
FBgn0036032	Ino80	2	1	1	0	1	0	0.014	1
FBgn0011297	l(2)not	2	2	1	1	2	0	0.002	1
FBgn0000140	asp	2	1	2	0	2	0	0.043	1