Otomorpha	ANCESTRAL SPECIES	252			ENSGT00670000098179.d.a ##15	ENSGT00390000005102.id.b	ENSGT00940000156471.a	ENSGT00510000047107.B	ENSGT01100000263544.c.a.a.b	ENSGT00390000009453.gb	ENSGT00940000155983.a.b	ENSGT00940000168590	ENSGT00940000159066	ENSGT00940000156161.B	ENSGT00940000159475.c	ENSGT00530000063205.B #20	ENSGT00940000158928 #21	ENSGT00950000183010.a.a.b #22	ENSGT00940000160897 #23	ENSGT01030000234574.B.c.b.a.a.a #24	ENSGT00530000063424.b	ENSGT00940000165965	ENSGT00940000157350	ENSGT00390000004874.a.b	ENSGT00940000163023	ENSGT00940000160508	ENSGT00940000157215	ENSGT00950000182914.a.b	ENSGT01030000234534.B.a.a.a.b	ENSGT00940000161886	ENSGT00940000157400	ENSGT00940000158907.c	ENSGT00390000004624.a.a
Clupeiformes	ANCESTRAL SPECIES	199	ENSGT00940000160353	ENSGT00940000158101	ENSGT00940000162631	ENSGT00940000166787 #7	ENSGT00940000166216 #9	ENSGT00910000144252.d.b #10	ENSGT00950000182904.a.b.a #11	ENSGT00940000153340.B #12	ENSGT00940000157856 #13	ENSGT00390000014879.c.a.a.a #14	ENSGT00390000011206.a #16	ENSGT00390000006707 #18	ENSGT00940000156185 #19	ENSGT00530000063205.B #20	ENSGT00940000158928 #21	ENSGT00950000183010.a.a.b #22	ENSGT00940000160897 #23	ENSGT01030000234574.B.c.b.a.a.a #24	ENSGT00940000156038.a.b.a.a.a.b #25
Denticle herring	DUPLICATION
Denticle herring	MODERN SPECIES	13	slc2a11l (ENSDCDG00000001613) #7	slc2a11l (ENSDCDG00000001609) #8	ska1 (ENSDCDG00000001603) #9	smarcad1b (ENSDCDG00000001560) #10	KCNN2 (ENSDCDG00000001548) #11	drg1 (ENSDCDG00000001546) #12	STARD7 (ENSDCDG00000001529) #13	slc20a1b (ENSDCDG00000001523) #14	ENSDCDG00000001520 #15	pcyox1 (ENSDCDG00000001519) #16	pcyox1 (ENSDCDG00000001517) #17	fam136a (ENSDCDG00000001515) #18	gmcl1 (ENSDCDG00000001513) #19	eri1 (ENSDCDG00000001512) #20	MFHAS1 (ENSDCDG00000001510) #21	rpl17 (ENSDCDG00000001503) #22	nkx6.1 (ENSDCDG00000001501) #23	gpat3 (ENSDCDG00000001496) #24	ENSDCDG00000001489 #25	ENSDCDG00000001470 #26	ENSDCDG00000001459 #27	nfil3-5 (ENSDCDG00000001458) #28	ENSDCDG00000001457 #29	ENSDCDG00000001454 #30	ENSDCDG00000001452 #31	PLPPR2 (ENSDCDG00000001447) #32	myh9a (ENSDCDG00000000630) #33	ENSDCDG00000000275 #34
Denticle herring	MODERN SPECIES	138														eri1 (ENSDCDG00000011248) ##20	MFHAS1 (ENSDCDG00000011276) ##21	rpl17 (ENSDCDG00000011297) ##22	nkx6.1 (ENSDCDG00000011328) ##23
Atlantic herring	MODERN SPECIES	3	hint1 (ENSCHAG00000012294)	ENSCHAG00000012287	ttll11 (ENSCHAG00000012269)	ENSCHAG00000012223	dab2ipb (ENSCHAG00000011875)	zgc:63972 (ENSCHAG00000011860)	fibcd1b (ENSCHAG00000011845)	ENSCHAG00000011841	aif1l (ENSCHAG00000011793)	gfm2 (ENSCHAG00000011498)	hexb (ENSCHAG00000011143)	fam136a (ENSCHAG00000011118) #18	gmcl1 (ENSCHAG00000010832) #19	eri1 (ENSCHAG00000010804) #20	MFHAS1 (ENSCHAG00000010800) #21	rpl17 (ENSCHAG00000010742) #22	mef2ca (ENSCHAG00000010634)	cetn3 (ENSCHAG00000010592)	arrdc3b (ENSCHAG00000010510)	nr2f1b (ENSCHAG00000010335)	TLR8 (ENSCHAG00000010070)	MCTP1 (ENSCHAG00000009821)	ENSCHAG00000009797	septin5b (ENSCHAG00000009078)	cldn5b (ENSCHAG00000009062)	acads (ENSCHAG00000008810)	crybb1 (ENSCHAG00000008790)	cryba4 (ENSCHAG00000008761)	ENSCHAG00000008281	npm2b (ENSCHAG00000008262)	SEZ6L (ENSCHAG00000004829)
Otophysi	ANCESTRAL SPECIES	37				ENSGT01030000234627.a.b.a.b.b	ENSGT00950000183203.c.a	ENSGT00940000166762	ENSGT00940000154702.a.b	ENSGT00390000006044	ENSGT00940000167368	ENSGT00730000111140	ENSGT00820000127055.b	ENSGT00940000164254.a.b	ENSGT00950000182926.b.c	ENSGT00940000156208.i.e	ENSGT00940000161685.A.a.d	ENSGT00950000183010.a.a.b #22	ENSGT00940000160897 #23	ENSGT01030000234574.B.c.b.a.a.a #24	ENSGT00530000063424.b	ENSGT00940000165965	ENSGT00940000157350	ENSGT00390000004874.a.b	ENSGT00940000163023	ENSGT00940000160508	ENSGT00940000157215	ENSGT00950000182914.a.b	ENSGT01030000234534.B.a.a.a.b	ENSGT00940000161886	ENSGT00940000157400	ENSGT00940000158907.c	ENSGT00390000004624.a.a
Characiphysae	ANCESTRAL SPECIES	23	ENSGT00940000156662.d	ENSGT00940000181939	ENSGT00530000063497.a.a	ENSGT00950000183203.c.a	ENSGT00940000166762	ENSGT00940000154702.a.b	ENSGT00390000003581	ENSGT00390000006044	ENSGT00940000167368	ENSGT00730000111140	ENSGT00820000127055.b	ENSGT00940000164254.a.b	ENSGT00950000182926.b.c	ENSGT00940000156208.i.e	ENSGT00940000161685.A.a.d	ENSGT00950000183010.a.a.b #22	ENSGT00940000160897 #23	ENSGT01030000234574.B.c.b.a.a.a #24	ENSGT00530000063424.b	ENSGT00940000165965	ENSGT00940000157350	ENSGT00390000004874.a.b	ENSGT00940000163023	ENSGT00940000160508	ENSGT00940000157215	ENSGT00950000182914.a.b	ENSGT01030000234534.B.a.a.a.b	ENSGT00940000161886	ENSGT00940000157400	ENSGT00940000158907.c	ENSGT00390000004624.a.a
Characiphysae_b	ANCESTRAL SPECIES	21	ENSGT00940000156662.d	ENSGT00940000181939	ENSGT00530000063497.a.a	ENSGT00950000183203.c.a	ENSGT00940000166762	ENSGT00940000154702.a.b	ENSGT00390000003581	ENSGT00390000006044	ENSGT00940000167368	ENSGT00730000111140	ENSGT00820000127055.b	ENSGT00940000164254.a.b	ENSGT00950000182926.b.c	ENSGT00940000156208.i.e	ENSGT00940000161685.A.a.d	ENSGT00950000183010.a.a.b #22	ENSGT00940000160897 #23	ENSGT01030000234574.B.c.b.a.a.a #24	ENSGT00530000063424.b	ENSGT00940000165965	ENSGT00940000157350	ENSGT00390000004874.a.b	ENSGT00940000163023	ENSGT00940000160508	ENSGT00940000157215	ENSGT00950000182914.a.b	ENSGT01030000234534.B.a.a.a.b	ENSGT00940000161886	ENSGT00940000157400	ENSGT00940000158907.c	ENSGT00390000004624.a.a
Characoidei	ANCESTRAL SPECIES	31	ENSGT00940000156662.d	ENSGT00940000181939	ENSGT00530000063497.a.a	ENSGT00950000183203.c.a	ENSGT00940000166762	ENSGT00940000154702.a.b	ENSGT00390000003581	ENSGT00390000006044	ENSGT00940000167368	ENSGT00730000111140	ENSGT00820000127055.b	ENSGT00940000164254.a.b	ENSGT00950000182926.b.c	ENSGT00940000156208.i.e	ENSGT00940000161685.A.a.d	ENSGT00950000183010.a.a.b #22	ENSGT00940000160897 #23	ENSGT01030000234574.B.c.b.a.a.a #24	ENSGT00530000063424.b	ENSGT00940000165965	ENSGT00940000157350	ENSGT00390000004874.a.b	ENSGT00940000163023	ENSGT00940000160508	ENSGT00940000157215	ENSGT00950000182914.a.b	ENSGT01030000234534.B.a.a.a.b	ENSGT00940000161886	ENSGT00940000157400	ENSGT00940000158907.c	ENSGT00390000004624.a.a
Mexicana tetra	MODERN SPECIES	66	ENSAMXG00000031269	ENSAMXG00000031686	ENSAMXG00000038695	TMEM132C (ENSAMXG00000002738)	ENSAMXG00000031497	ENSAMXG00000026016	smpd4 (ENSAMXG00000031407)	si:ch211-222n4.2 (ENSAMXG00000031218)	med15 (ENSAMXG00000040274)	ENSAMXG00000037233	crkl (ENSAMXG00000041556)	neflb (ENSAMXG00000001050)	ENSAMXG00000001033	pgam2 (ENSAMXG00000030317)	nefma (ENSAMXG00000040032)	rpl17 (ENSAMXG00000001082) #22	nkx6.1 (ENSAMXG00000001095) #23	gpat3 (ENSAMXG00000012191) #24	abraxas1 (ENSAMXG00000038713)	ENSAMXG00000029786	mrps18c (ENSAMXG00000012238)	HELQ (ENSAMXG00000012252)	hpse (ENSAMXG00000032004)	MYL5 (ENSAMXG00000034506)	btc (ENSAMXG00000037033)	amacr (ENSAMXG00000029907)	slc45a2 (ENSAMXG00000011270)	rxfp3 (ENSAMXG00000025441)	ENSAMXG00000034072	rai14 (ENSAMXG00000011402)	fgf10a (ENSAMXG00000043492)
Channel catfish	MODERN SPECIES	9	wdr34 (ENSIPUG00000003139)	sptan1 (ENSIPUG00000003170)	smpd4 (ENSIPUG00000003269)	ENSIPUG00000003370	TMEM132C (ENSIPUG00000003376)	ENSIPUG00000003418	RIMBP2 (ENSIPUG00000003435)	odf2 (ENSIPUG00000003472)	cp080 (ENSIPUG00000003491)	med15 (ENSIPUG00000003511)	crkl (ENSIPUG00000003533)	ENSIPUG00000003546	pgam2 (ENSIPUG00000003558)	neflb (ENSIPUG00000003563)	nefm (ENSIPUG00000003572)	rpl17 (ENSIPUG00000003599) #22	nkx6.1 (ENSIPUG00000003661) #23	agpat9 (ENSIPUG00000003715) #24	fam175a (ENSIPUG00000003772)	mrps18c (ENSIPUG00000003783)	helq (ENSIPUG00000003800)	hpse (ENSIPUG00000003847)	myl5 (ENSIPUG00000003872)	btc (ENSIPUG00000003972)	AMACR (ENSIPUG00000003980)	slc45a2 (ENSIPUG00000003993)	rxfp3 (ENSIPUG00000004003)	gzmk (ENSIPUG00000004016)	rai14 (ENSIPUG00000004046)	fgf10a (ENSIPUG00000004119)	nnt (ENSIPUG00000004138)
Cyprinoidei	ANCESTRAL SPECIES	54					ENSGT01030000234627.a.b.a.b.b	ENSGT00950000183203.c.a	ENSGT00940000166762	ENSGT00940000154702.a.b	ENSGT00390000006044	ENSGT00940000167368	ENSGT00730000111140	ENSGT00820000127055.b	ENSGT00950000182926.b.c	ENSGT00940000156208.i.e	ENSGT00940000161685.A.a.d	ENSGT00950000183010.a.a.b #22	ENSGT00940000160897 #23	ENSGT01030000234574.B.c.b.a.a.a #24	ENSGT00530000063424.b	ENSGT00940000165965	ENSGT00940000157350	ENSGT00390000004874.a.b	ENSGT00940000160508	ENSGT00940000157215	ENSGT00950000182914.a.b	ENSGT01030000234534.B.a.a.a.b	ENSGT00940000163160.a	ENSGT00940000157400	ENSGT00940000158907.c	ENSGT00390000004624.a.a	ENSGT00940000166240
Cyprininae	DUPLICATION
Cyprininae	ANCESTRAL SPECIES	85	ENSGT00940000159721.h.i.b	ENSGT00940000159721.h.j.a	ENSGT00940000166328.b	ENSGT00390000014845.ab	ENSGT00940000156436.w.a	ENSGT01030000234627.a.b.a.b.b.b	ENSGT00950000183203.c.a.b	ENSGT00940000166762.c	ENSGT00940000154702.a.b.a	ENSGT00390000006044.l	ENSGT00730000111140	ENSGT00820000127055.b.d	ENSGT00950000182926.b.c.l	ENSGT00940000156208.i.e.b	ENSGT00940000161685.A.a.d.a	ENSGT00950000183010.a.a.b.e #22	ENSGT00940000160897.g #23	ENSGT01030000234574.B.c.b.a.a.a.b #24	ENSGT00530000063424.b.x	ENSGT00940000165965.a.a	ENSGT00940000157350.o	ENSGT00940000165965.b	ENSGT00390000004874.a.b.c	ENSGT00940000160508.b	ENSGT00940000157215.d	ENSGT00950000182914.a.b.f	ENSGT01030000234534.B.a.a.a.b.d	ENSGT00940000163160.a.d.a	ENSGT00940000157400.c	ENSGT00940000158907.c.a	ENSGT00390000004624.a.a.d
Cyprininae_a	ANCESTRAL SPECIES	44	ENSGT00940000154143.d.d	ENSGT00940000162790.b.c.a	ENSGT00940000159718.o.b	ENSGT01040000240817.b	ENSGT00940000156436.w.a	ENSGT01030000234627.a.b.a.b.b.b	ENSGT00950000183203.c.a.b	ENSGT00940000166762.c	ENSGT00940000154702.a.b.a	ENSGT00390000006044.l	ENSGT00730000111140.ec	ENSGT00820000127055.b.d	ENSGT00950000182926.b.c.l	ENSGT00940000165501.d	ENSGT00940000161685.A.a.d.a	ENSGT00950000183010.a.a.b.e #22	ENSGT00940000160897.g #23	ENSGT01030000234574.B.c.b.a.a.a.b #24	ENSGT00530000063424.b.x	ENSGT00940000165965.a.a	ENSGT00940000157350.o	ENSGT00940000165965.b	ENSGT00390000004874.a.b.c	ENSGT00940000160508.b	ENSGT00940000157215.d.a	ENSGT00940000163160.a.d.a	ENSGT00940000157400.c	ENSGT00940000158907.c.a	ENSGT00390000004624.a.a.d	ENSGT00940000166240	ENSGT00530000063460.A.b.f.a.a
Common carp reference	MODERN SPECIES	45	brd3a (ENSCCRG00000051597)	ENSCCRG00000048535	ENSCCRG00000030916	dnai1.2 (ENSCCRG00000047227)	stx2a (ENSCCRG00000048584)	ENSCCRG00000023964	ENSCCRG00000023977	ENSCCRG00000062413	smpd4 (ENSCCRG00000030618)	med15 (ENSCCRG00000069677)	ENSCCRG00000072989	ENSCCRG00000045323	ENSCCRG00000045333	pgam2 (ENSCCRG00000076384)	nefma (ENSCCRG00000053665)	rpl17 (ENSCCRG00000025631) #22	nkx6.1 (ENSCCRG00000077610) #23	gpat3 (ENSCCRG00000049286) #24	abraxas1 (ENSCCRG00000022204)	mrps18c (ENSCCRG00000049341)	HELQ (ENSCCRG00000049351)	hpse (ENSCCRG00000018956)	btc (ENSCCRG00000070380)	amacr (ENSCCRG00000021193)	ENSCCRG00000021186	rai14 (ENSCCRG00000020713)	fgf10a (ENSCCRG00000020695)	nnt (ENSCCRG00000057395)	ENSCCRG00000019874	ENSCCRG00000061180	ENSCCRG00000075254 #21
Goldfish	MODERN SPECIES	13	GCNT4 (ENSCARG00000012190)	lhx5 (ENSCARG00000012184)	ENSCARG00000012130	VAV2 (ENSCARG00000010911)	ENSCARG00000010865	dnai1.2 (ENSCARG00000010308)	stx2a (ENSCARG00000010257)	RIMBP2 (ENSCARG00000010157)	ENSCARG00000010135	TMEM132C (ENSCARG00000010129)	smpd4 (ENSCARG00000008444)	crkl (ENSCARG00000008369)	pgam2 (ENSCARG00000008359)	NEFL (ENSCARG00000008349)	nefma (ENSCARG00000008332)	rpl17 (ENSCARG00000008315) #22	nkx6.1 (ENSCARG00000008308) #23	gpat3 (ENSCARG00000007805) #24	abraxas1 (ENSCARG00000007783)	mrps18c (ENSCARG00000007773)	HELQ (ENSCARG00000007636)	hpse (ENSCARG00000007573)	ENSCARG00000007546	ENSCARG00000007539	atp5mea (ENSCARG00000007526)	PDE6B (ENSCARG00000007078)	rbp4l (ENSCARG00000007026)	slc26a1 (ENSCARG00000007013)	zgc:86764 (ENSCARG00000006976)	ENSCARG00000006960	dusp4 (ENSCARG00000006954)
Cyprininae	ANCESTRAL SPECIES	141	ENSGT00940000159789.r.b	ENSGT00940000154143.d.c	ENSGT00940000162790.b.c.b	ENSGT00940000159718.o.a	ENSGT01040000240817.a	ENSGT00940000156436.w.b	ENSGT01030000234627.a.b.a.b.b.a	ENSGT00950000183203.c.a.a	ENSGT00940000166762.d	ENSGT00940000154702.a.b.b	ENSGT00390000006044.k	ENSGT00820000127055.b.c	ENSGT00950000182926.b.c.k	ENSGT00940000156208.i.e.a	ENSGT00940000161685.A.a.d.b	ENSGT00950000183010.a.a.b.f #22	ENSGT00940000160897.h #23
Goldfish	MODERN SPECIES	40	slc45a2 (ENSCARG00000025889)	amacr (ENSCARG00000025874)	btc (ENSCARG00000025870)	hpse (ENSCARG00000025811)	mrps18c (ENSCARG00000025796)	abraxas1 (ENSCARG00000025778)	gpat3 (ENSCARG00000025669) #24	ENSCARG00000025650	ENSCARG00000025638	smpd4 (ENSCARG00000024004)	med15 (ENSCARG00000023896)	crkl (ENSCARG00000023888)	pgam2 (ENSCARG00000023868)	NEFL (ENSCARG00000023860)	nefma (ENSCARG00000023855)	rpl17 (ENSCARG00000023847) #22	nkx6.1 (ENSCARG00000023839) #23	nipal4 (ENSCARG00000023829)	tlcd1 (ENSCARG00000023822)	rpl23a (ENSCARG00000023797)	ENSCARG00000069899	supt6h (ENSCARG00000069868)	sdf2 (ENSCARG00000069856)	ENSCARG00000069853	nf2b (ENSCARG00000069851)	ENSCARG00000069850	RBFOX3 (ENSCARG00000069848)	c1qtnf1 (ENSCARG00000069846)	csnk1db (ENSCARG00000069829)	slc16a3b (ENSCARG00000069821)	ccdc57 (ENSCARG00000069769)
Cyprininae_a	ANCESTRAL SPECIES	89	ENSGT00940000162790.b.c.b	ENSGT00940000159718.o.a	ENSGT01040000240817.a	ENSGT00940000156436.w.b	ENSGT01030000234627.a.b.a.b.b.a	ENSGT00950000183203.c.a.a	ENSGT00940000166762.d	ENSGT00940000154702.a.b.b	ENSGT00390000006044.k	ENSGT00940000167368	ENSGT00730000111140.dc	ENSGT00820000127055.b.c	ENSGT00950000182926.b.c.k	ENSGT00940000156208.i.e.a	ENSGT00940000161685.A.a.d.b	ENSGT00950000183010.a.a.b.f #22	ENSGT00940000160897.h #23	ENSGT01030000234574.B.c.b.a.a.a.a #24	ENSGT00530000063424.b.w	ENSGT00940000165965.a.b	ENSGT00940000157350.p	ENSGT00390000004874.a.b.d	ENSGT00940000160508.a	ENSGT00940000157215.c	ENSGT00950000182914.a.b.e	ENSGT01030000234534.B.a.a.a.b.d	ENSGT00940000157400.d	ENSGT00940000158907.c.b	ENSGT00390000004624.a.a.c	ENSGT00940000173711	ENSGT00530000063460.A.b.f.a.b
Common carp reference	MODERN SPECIES	38	rxraa (ENSCCRG00000011147)	wdr5 (ENSCCRG00000067522)	brd3a (ENSCCRG00000049737)	ENSCCRG00000029921	stx2a (ENSCCRG00000010609)	ENSCCRG00000078045	ENSCCRG00000024984	ENSCCRG00000058288	ENSCCRG00000064563	smpd4 (ENSCCRG00000048346)	med15 (ENSCCRG00000081800)	crkl (ENSCCRG00000034747)	ENSCCRG00000034745	ENSCCRG00000055031	nefma (ENSCCRG00000055322)	ENSCCRG00000009887 #22	ENSCCRG00000069417	nkx6.1 (ENSCCRG00000009898) #23	gpat3 (ENSCCRG00000029084) #24	abraxas1 (ENSCCRG00000074286)	mrps18c (ENSCCRG00000056607)	HELQ (ENSCCRG00000022228)	hpse (ENSCCRG00000049378)	btc (ENSCCRG00000072417)	amacr (ENSCCRG00000073501)	slc45a2 (ENSCCRG00000024947)	rai14 (ENSCCRG00000041158)	fgf10a (ENSCCRG00000041138)	nnt (ENSCCRG00000077664)	ENSCCRG00000019866	ENSCCRG00000070694 #21
Zebrafish	MODERN SPECIES	13	dnai1.2 (ENSDARG00000038788)	VAV2 (ENSDARG00000044718)	brd3a (ENSDARG00000006527)	wdr5 (ENSDARG00000016903)	DNAI1 (ENSDARG00000100081)	RIMBP2 (ENSDARG00000104101)	ENSDARG00000075837	TMEM132C (ENSDARG00000074863)	si:dkey-65l23.2 (ENSDARG00000093234)	smpd4 (ENSDARG00000020730)	si:ch211-222n4.2 (ENSDARG00000093026)	med15 (ENSDARG00000014292)	crkl (ENSDARG00000028699)	ENSDARG00000058477	MPP4 (ENSDARG00000009386)	rpl17 (ENSDARG00000057556) #22	pgam2 (ENSDARG00000057571)	ENSDARG00000057568	nefma (ENSDARG00000021351)	nkx6.1 (ENSDARG00000022569) #23	gpat3 (ENSDARG00000016048) #24	abraxas1 (ENSDARG00000043339)	mrps18c (ENSDARG00000069624)	helq (ENSDARG00000079818)	hpse (ENSDARG00000063634)	btc (ENSDARG00000098112)	amacr (ENSDARG00000057435)	slc45a2 (ENSDARG00000002593)	rxfp3 (ENSDARG00000057410)	ENSDARG00000028780	ENSDARG00000090380