Pseudocrenilabrinae	ANCESTRAL SPECIES	22	ENSGT00940000165979	ENSGT00970000193372.b.a.b	ENSGT00390000010895.a	ENSGT00390000013776 #13	ENSGT00940000155954.b #14	ENSGT00530000063489.a #16	ENSGT00950000183014.f.a	ENSGT00970000193449	ENSGT00940000162403	ENSGT00940000176917 #15	ENSGT00940000159500 #17	ENSGT00940000166595.b #18	ENSGT00940000156504.i.a #19	ENSGT00940000156948.j #20	ENSGT00390000016324 #21	ENSGT00940000154369.g.b #22	ENSGT01030000234629.C.b #23	ENSGT00950000183086.a.a.b.h.a #25	ENSGT00950000183136.b.b.c #26	ENSGT00940000160165.a.b #27	ENSGT00900000141083.c.b #28	ENSGT00390000006095 #29	ENSGT00940000157522 #30	ENSGT00940000156342.d #31	ENSGT00940000161398.e #32	ENSGT00940000164578.a.a #33	ENSGT00390000004360.a.a #34	ENSGT00950000183115.a.a.a #35	ENSGT00950000183136.b.b.d.a.a.a #36	ENSGT00950000183136.b.b.d.a.a.b.b ##26	ENSGT00950000183136.b.b.d.a.a.b.a ##26
Pseudocrenilabrinae_A	ANCESTRAL SPECIES	25	ENSGT00940000165979	ENSGT00970000193372.b.a.b	ENSGT00390000010895.a	ENSGT00390000013776 #13	ENSGT00940000155954.b #14	ENSGT00530000063489.a #16	ENSGT00950000183014.f.a	ENSGT00970000193449	ENSGT00940000162403	ENSGT00940000176917 #15	ENSGT00940000159500 #17	ENSGT00940000166595.b #18	ENSGT00940000156504.i.a #19	ENSGT00940000156948.j #20	ENSGT00390000016324 #21	ENSGT00940000154369.g.b #22	ENSGT01030000234629.C.b #23	ENSGT00950000183086.a.a.b.h.a #25	ENSGT00950000183136.b.b.c #26	ENSGT00940000160165.a.b #27	ENSGT00900000141083.c.b #28	ENSGT00390000006095 #29	ENSGT00940000157522 #30	ENSGT00940000156342.d #31	ENSGT00940000161398.e #32	ENSGT00940000164578.a.a #33	ENSGT00390000004360.a.a #34	ENSGT00950000183115.a.a.a #35	ENSGT00950000183136.b.b.d.a.a.a #36	ENSGT00950000183136.b.b.d.a.a.b.b ##26	ENSGT00950000183136.b.b.d.a.a.b.a ##26
Haplochromini	ANCESTRAL SPECIES	35	ENSGT00390000010895.a	ENSGT00390000013776 #13	ENSGT00940000155954.b #14	ENSGT00530000063489.a #16	ENSGT01100000263520.a.b.a.a.a.b.a.b.c.d.a.a.a	ENSGT00940000154907.a.a.x.b	ENSGT00970000193449	ENSGT00950000183014.f.a	ENSGT00940000162403	ENSGT00940000176917 #15	ENSGT00940000159500 #17	ENSGT00940000166595.b #18	ENSGT00940000156504.i.a #19	ENSGT00940000156948.j #20	ENSGT00390000016324 #21	ENSGT00940000154369.g.b #22	ENSGT01030000234629.C.b #23	ENSGT00950000183086.a.a.b.h.a #25	ENSGT00950000183136.b.b.c #26	ENSGT00940000160165.a.b #27	ENSGT00900000141083.c.b #28	ENSGT00390000006095 #29	ENSGT00940000157522 #30	ENSGT00940000156342.d #31	ENSGT00940000161398.e #32	ENSGT00940000164578.a.a #33	ENSGT00390000004360.a.a #34	ENSGT00950000183115.a.a.a #35	ENSGT00950000183136.b.b.d.a.a.a.a.a ##26	ENSGT00950000183136.b.b.d.a.a.a.a.b #36	ENSGT00950000183136.b.b.d.a.a.a.b #37
Burton s mouthbrooder	MODERN SPECIES	349							kcne4 (ENSHBUG00000022240) #13	ENSHBUG00000022286 #14	ENSHBUG00000022296 #15	farsb (ENSHBUG00000022379) #16	SGPP2 (ENSHBUG00000022394) #17	ENSHBUG00000022407 #18	pax3b (ENSHBUG00000022451) #19	epha4a (ENSHBUG00000022511) #20	pxylp1 (ENSHBUG00000022527) #21	SLC25A36 (ENSHBUG00000022561) #22	spsb4a (ENSHBUG00000022597) #23	ENSHBUG00000022617 #24	CLSTN2 (ENSHBUG00000022673) #25	lpar5b (ENSHBUG00000022688) #26	rbp2a (ENSHBUG00000022702) #27	COPB2 (ENSHBUG00000022803) #28	mrps22 (ENSHBUG00000022826) #29	PIK3CB (ENSHBUG00000023142) #30	PER2 (ENSHBUG00000000709) #31	her13 (ENSHBUG00000023176) #32	her8.2 (ENSHBUG00000023184) #33	ENSHBUG00000023216 #34	ITM2C (ENSHBUG00000023261) #35	lpar5b (ENSHBUG00000023274) #36	lpar5b (ENSHBUG00000023292) #37
Haplochromini_A	ANCESTRAL SPECIES	40	ENSGT00940000164087	ENSGT00940000158424	ENSGT00940000157731	ENSGT00940000165979	ENSGT00970000193372.b.a.b	ENSGT00390000010895.a	ENSGT00390000013776 #13	ENSGT00940000155954.b #14	ENSGT00530000063489.a #16	ENSGT00940000176917 #15	ENSGT00940000159500 #17	ENSGT00940000166595.b #18	ENSGT00940000156504.i.a #19	ENSGT00940000156948.j #20	ENSGT00390000016324 #21	ENSGT00940000154369.g.b #22	ENSGT01030000234629.C.b #23	ENSGT00950000183086.a.a.b.h.a #25	ENSGT00950000183136.b.b.c #26	ENSGT00940000160165.a.b #27	ENSGT00900000141083.c.b #28	ENSGT00390000006095 #29	ENSGT00940000157522 #30	ENSGT00940000156342.d #31	ENSGT00940000161398.e #32	ENSGT00940000164578.a.a #33	ENSGT00390000004360.a.a #34	ENSGT00950000183115.a.a.a #35	ENSGT00950000183136.b.b.d.a.a.a.a.a ##26	ENSGT00950000183136.b.b.d.a.a.b.a ##26	ENSGT00950000183136.b.b.d.b ##26
P. nyererei	MODERN SPECIES	378	wdfy1 (ENSPNYG00000011057)	dhrs12la (ENSPNYG00000011099)	AP1S3 (ENSPNYG00000011149)	ENSPNYG00000011372	kcne4 (ENSPNYG00000011382) #13	acsl3a (ENSPNYG00000011402) #14	farsb (ENSPNYG00000011433) #16	ENSPNYG00000011468	ENSPNYG00000011481 #15	SGPP2 (ENSPNYG00000011492) #17	ENSPNYG00000011511 #18	pax3b (ENSPNYG00000011527) #19	ENSPNYG00000011554	epha4a (ENSPNYG00000011571) #20	pxylp1 (ENSPNYG00000011653) #21	SLC25A36 (ENSPNYG00000011731) #22	spsb4a (ENSPNYG00000011766) #23	CLSTN2 (ENSPNYG00000011806) #25	lpar5b (ENSPNYG00000011904) #26	rbp2a (ENSPNYG00000011924) #27	COPB2 (ENSPNYG00000011944) #28	mrps22 (ENSPNYG00000011985) #29	foxl2b (ENSPNYG00000012072)	PIK3CB (ENSPNYG00000012104) #30	PER2 (ENSPNYG00000012204) #31	her13 (ENSPNYG00000012240) #32	her8.2 (ENSPNYG00000012263) #33	ENSPNYG00000012316 #34	ITM2C (ENSPNYG00000012355) #35	lpar5b (ENSPNYG00000012388) ##26
Haplochromini_B	ANCESTRAL SPECIES	9	ENSGT00940000164087	ENSGT00940000158424	ENSGT00940000157731	ENSGT00940000165979	ENSGT00970000193372.b.a.b	ENSGT00390000010895.a	ENSGT00390000013776 #13	ENSGT00940000155954.b #14	ENSGT00530000063489.a #16	ENSGT00940000176917 #15	ENSGT00940000159500 #17	ENSGT00940000166595.b #18	ENSGT00940000156504.i.a #19	ENSGT00940000156948.j #20	ENSGT00390000016324 #21	ENSGT00940000154369.g.b #22	ENSGT01030000234629.C.b #23	ENSGT00950000183086.a.a.b.h.a #25	ENSGT00950000183136.b.b.c #26	ENSGT00940000160165.a.b #27	ENSGT00900000141083.c.b #28	ENSGT00390000006095 #29	ENSGT00940000157522 #30	ENSGT00940000156342.d #31	ENSGT00940000161398.e #32	ENSGT00940000164578.a.a #33	ENSGT00390000004360.a.a #34	ENSGT00950000183115.a.a.a #35	ENSGT00950000183136.b.b.d.a.a.a.a.a ##26	ENSGT00950000183136.b.b.d.a.a.b.a ##26	ENSGT00950000183136.b.b.d.b.a.a ##26
Eastern happy	MODERN SPECIES	5	dhrs12la (ENSACLG00000014210)	ENSACLG00000014191	AP1S3 (ENSACLG00000014183)	kcne4 (ENSACLG00000014128) #13	acsl3a (ENSACLG00000014060) #14	ENSACLG00000014051 #15	farsb (ENSACLG00000013951) #16	SGPP2 (ENSACLG00000013928) #17	ENSACLG00000013923 #18	pax3b (ENSACLG00000013881) #19	ENSACLG00000013809	epha4a (ENSACLG00000013751) #20	ENSACLG00000013740	ENSACLG00000013580	pxylp1 (ENSACLG00000013559) #21	SLC25A36 (ENSACLG00000013526) #22	spsb4a (ENSACLG00000013515) #23	ENSACLG00000013213	ENSACLG00000013208	ENSACLG00000013193	CLSTN2 (ENSACLG00000013110) #25	lpar5b (ENSACLG00000012853) #26	rbp2a (ENSACLG00000012843) #27	COPB2 (ENSACLG00000012761) #28	mrps22 (ENSACLG00000012727) #29	PIK3CB (ENSACLG00000012502) #30	PER2 (ENSACLG00000012344) #31	her13 (ENSACLG00000012297) #32	her8.2 (ENSACLG00000012275) #33	ENSACLG00000012262 #34	ITM2C (ENSACLG00000012210) #35
Zebra mbuna	MODERN SPECIES	1096	ENSMZEG00005004351	gemin4 (ENSMZEG00005004438)	TLCD3A (ENSMZEG00005004444)	usp2a (ENSMZEG00005004453)	TBCEL (ENSMZEG00005004478)	kcne4 (ENSMZEG00005004495) #13	ENSMZEG00005004509 #14	farsb (ENSMZEG00005004544) #16	ENSMZEG00005004588	ENSMZEG00005004594 #15	SGPP2 (ENSMZEG00005004600) #17	ENSMZEG00005004622 #18	pax3b (ENSMZEG00005004628) #19	epha4a (ENSMZEG00005004684) #20	pxylp1 (ENSMZEG00005004789) #21	SLC25A36 (ENSMZEG00005004803) #22	spsb4a (ENSMZEG00005004837) #23	ENSMZEG00005004855	CLSTN2 (ENSMZEG00005004867) #25	ENSMZEG00005004907 #26	rbp2a (ENSMZEG00005004916) #27	COPB2 (ENSMZEG00005004942) #28	mrps22 (ENSMZEG00005005002) #29	foxl2a (ENSMZEG00005005026)	nop53 (ENSMZEG00005005033)	ENSMZEG00005005051	ENSMZEG00005005059	psma6l (ENSMZEG00005005071)	ENSMZEG00005005107	sars2 (ENSMZEG00005005189)	si:dkey-260j18.2 (ENSMZEG00005005293)
Lyretail cichlid	MODERN SPECIES	367	prss16 (ENSNBRG00000003861)	serpine2 (ENSNBRG00000003846)	wdfy1 (ENSNBRG00000003804)	AP1S3 (ENSNBRG00000003658)	ENSNBRG00000003634	kcne4 (ENSNBRG00000003631) #13	acsl3a (ENSNBRG00000003327) #14	ENSNBRG00000003270 #15	farsb (ENSNBRG00000003198) #16	SGPP2 (ENSNBRG00000003149) #17	ENSNBRG00000003132 #18	pax3b (ENSNBRG00000003096) #19	epha4a (ENSNBRG00000003033) #20	pxylp1 (ENSNBRG00000002984) #21	ENSNBRG00000002963	SLC25A36 (ENSNBRG00000002942) #22	CLSTN2 (ENSNBRG00000002891) #25	lpar5b (ENSNBRG00000002874) #26	rbp2a (ENSNBRG00000002854) #27	COPB2 (ENSNBRG00000002788) #28	mrps22 (ENSNBRG00000002593) #29	PIK3CB (ENSNBRG00000002386) #30	PER2 (ENSNBRG00000002361) #31	her13 (ENSNBRG00000002345) #32	her8.2 (ENSNBRG00000002319) #33	ENSNBRG00000002297 #34	ITM2C (ENSNBRG00000002259) #35	lpar5b (ENSNBRG00000002226) ##26	lpar5b (ENSNBRG00000002212) ##26	ENSNBRG00000002192	meis3 (ENSNBRG00000002156)
Nile tilapia	MODERN SPECIES	5	psmd2 (ENSONIG00000010770)	prss16 (ENSONIG00000010768)	serpine2 (ENSONIG00000010765)	wdfy1 (ENSONIG00000014648)	dhrs12la (ENSONIG00000014649)	ENSONIG00000014647	kcne4 (ENSONIG00000014646) #13	acsl3a (ENSONIG00000014644) #14	farsb (ENSONIG00000014639) #16	ENSONIG00000036757 #15	SGPP2 (ENSONIG00000014638) #17	ENSONIG00000037185 #18	pax3b (ENSONIG00000014632) #19	epha4a (ENSONIG00000014623) #20	pxylp1 (ENSONIG00000030369) #21	SLC25A36 (ENSONIG00000014617) #22	spsb4a (ENSONIG00000014616) #23	CLSTN2 (ENSONIG00000014608) #25	ENSONIG00000034460	lpar5b (ENSONIG00000020974) #26	rbp2a (ENSONIG00000014606) #27	COPB2 (ENSONIG00000014597) #28	mrps22 (ENSONIG00000014596) #29	ENSONIG00000033377	PIK3CB (ENSONIG00000007924) #30	PER2 (ENSONIG00000007937) #31	ENSONIG00000039254	her13 (ENSONIG00000035460) #32	her8.2 (ENSONIG00000007948) #33	ENSONIG00000007949 #34	ITM2C (ENSONIG00000007951) #35