Table S6. Transcription factor motif enrichments among genes under positive selection in N. melanderi.							
							
Motif name	D. melanogaster TF symbol	D. melanogaster TF gene ID	N. melanderi gene	Motif set size	Normalization method	Gene regulatory region	Adjusted p
bab1_SOLEXA	bab1	FBgn0004870	Nmel06448	800	Rank	Enhancer-containing	8.00E-06
pros_SELEX	pros	FBgn0004595	Nmel00241	800	GC	Enhancer-containing	2.00E-04
mef2_compiled	mef2	FBgn0011656	Nmel09954	800	Rank	Core promoter	2.00E-05
fkh_NAR	"bin, fkh"	"FBgn0045759, FBgn0000659"	"Nmel08257, Nmel10390"	100	Rank	Enhancer-containing	1.00E-04
nub_SOLEXA	"nub, pdm2"	"FBgn0085424, FBgn0004394"	Nmel10831	800	Rank	Core promoter	2.00E-04
vfl_SOLEXA_5	Vfl	FBgn0259789	Nmel04616	800	GC	Core promoter	2.00E-04
toy_SOLEXA	"sv, toy"	"FBgn0005561, FBgn0019650"	Nmel00775	800	GC	Core promoter	2.00E-04
Poxm_SOLEXA	Poxm	FBgn0003129	Nmel01403	800	GC	Enhancer-containing	4.00E-04
Aef1_SOLEXA_5	Aef1	FBgn0005694	Nmel00333	800	GC	Enhancer-containing	4.00E-04
dimm_da_SOLEXA_5	Dim	FBgn0023091	Nmel05042	800	Rank	Enhancer-containing	6.00E-04
CG17181_SOLEXA_5	"CG17181, sna, wor"	"FBgn0035144, FBgn0003448, FBgn0001983"	"Nmel05473, Nmel08919"	800	GC	Enhancer-containing	6.00E-04