Rodentia_A	ANCESTRAL SPECIES	1	ENSGT00940000161414	ENSGT00940000161889 #36	ENSGT00940000161029 #35	ENSGT00390000017536	ENSGT00950000183012.A.b	ENSGT00940000153747	ENSGT00940000161089 #14	ENSGT00950000183151.a.a.a #15	ENSGT00390000015415 #16	ENSGT00950000183197.b.a #17	ENSGT00390000018587 #18	ENSGT00940000153899.a.a #19	ENSGT00730000110905.a #20	ENSGT00390000001149 #21	ENSGT00390000003127	ENSGT00940000155040.a #22	ENSGT00940000157180 #23	ENSGT00940000161192 #24	ENSGT00530000063626.a	ENSGT00390000010089.f #25	ENSGT00940000155807.a #26	ENSGT00520000061410	ENSGT00950000182990.a.a.b.b #27	ENSGT00950000182990.a.a.a.b.u.a #29	ENSGT00950000182990.a.a.a.b.u.b #30	ENSGT00940000159102 #31	ENSGT00940000158650 #32	ENSGT00950000182841.b.a.a.b.b.p ##33	ENSGT00730000111073	ENSGT00530000063866.f.b ##12	ENSGT00390000013802.v.b
Hystricomorpha	ANCESTRAL SPECIES	37	ENSGT00940000159914	ENSGT00390000007552.f	ENSGT00940000154902.bb.a ##8	ENSGT00940000154902.bb.b #8	ENSGT00950000183045.A.a.a #10	ENSGT00530000063866.e #12	ENSGT00940000161089 #14	ENSGT00950000183151.a.a.a #15	ENSGT00390000015415 #16	ENSGT00950000183197.b.a #17	ENSGT00390000018587 #18	ENSGT00940000153899.a.a #19	ENSGT00730000110905.a #20	ENSGT00390000001149 #21	ENSGT00390000003127	ENSGT00940000155040.a #22	ENSGT00940000157180 #23	ENSGT00940000161192 #24	ENSGT00530000063626.a	ENSGT00390000010089.f #25	ENSGT00940000155807.a #26	ENSGT00950000182990.a.a.b.b #27	ENSGT00950000182990.a.a.a.b.u.a #29	ENSGT00950000182990.a.a.a.b.u.b #30	ENSGT00940000159102 #31	ENSGT00940000158650 #32	ENSGT00950000182841.b.a.a.b.b.p.d ##33	ENSGT00730000111073	ENSGT00940000153747	ENSGT00950000183012.A.b	ENSGT00390000017536
Naked mole-rat female	MODERN SPECIES	14	ENSHGLG00000034389 #7	ENSHGLG00000037481 #8	ENSHGLG00000035437 #9	ENSHGLG00000038948 #10	ENSHGLG00000029155 #11	ENSHGLG00000046269 #12	ENSHGLG00000033722 #13	ENSHGLG00000002837 #14	ENSHGLG00000046341 #15	TKFC (ENSHGLG00000018883) #16	CYB561A3 (ENSHGLG00000013997) #17	ENSHGLG00000034372 #18	ENSHGLG00000038968 #19	ENSHGLG00000019090 #20	ENSHGLG00000032097 #21	LRRC10B (ENSHGLG00000020706) #22	SYT7 (ENSHGLG00000004485) #23	DAGLA (ENSHGLG00000003887) #24	ENSHGLG00000049174 #25	FEN1 (ENSHGLG00000002899) #26	ENSHGLG00000002762 #27	ENSHGLG00000048948 #28	ENSHGLG00000039242 #29	ENSHGLG00000006364 #30	ENSHGLG00000047074 #31	ENSHGLG00000004202 #32	ENSHGLG00000034974 #33	ENSHGLG00000048559 #34	ENSHGLG00000013374 #35	ENSHGLG00000013265 #36	ENSHGLG00000048282 #37
Hystricomorpha_a	ANCESTRAL SPECIES	44	ENSGT01030000234573.B.c.b.b	ENSGT00940000159914	ENSGT00390000007552.f	ENSGT00940000154902.bb.a ##8	ENSGT00950000183045.A.a.a #10	ENSGT00390000013802.u	ENSGT00940000161089 #14	ENSGT00950000183151.a.a.a #15	ENSGT00390000015415 #16	ENSGT00950000183197.b.a #17	ENSGT00390000018587 #18	ENSGT00940000153899.a.a #19	ENSGT00730000110905.a #20	ENSGT00390000001149 #21	ENSGT00390000003127	ENSGT00940000155040.a #22	ENSGT00940000157180 #23	ENSGT00940000161192 #24	ENSGT00530000063626.a	ENSGT00390000010089.f #25	ENSGT00940000155807.a #26	ENSGT00950000182990.a.a.b.b #27	ENSGT00950000182990.a.a.a.b.u.a #29	ENSGT00950000182990.a.a.a.b.u.b #30	ENSGT00940000159102 #31	ENSGT00940000158650 #32	ENSGT00950000182841.b.a.a.b.b.p.d ##33	ENSGT00730000111073	ENSGT00940000153747	ENSGT00950000183012.A.b	ENSGT00390000017536
Hystricomorpha_b	ANCESTRAL SPECIES	80	ENSGT00940000159589	ENSGT01030000234573.B.c.b.b	ENSGT00940000159914	ENSGT00390000007552.f	ENSGT00940000154902.bb.a ##8	ENSGT00950000183045.A.a.a #10	ENSGT00940000161089 #14	ENSGT00950000183151.a.a.a #15	ENSGT00390000015415 #16	ENSGT00950000183197.b.a #17	ENSGT00390000018587 #18	ENSGT00940000153899.a.a #19	ENSGT00730000110905.a #20	ENSGT00390000001149 #21	ENSGT00390000003127	ENSGT00940000155040.a #22	ENSGT00940000157180 #23	ENSGT00940000161192 #24	ENSGT00530000063626.a	ENSGT00390000010089.f #25	ENSGT00940000155807.a #26	ENSGT00950000182990.a.a.b.b #27	ENSGT00950000182990.a.a.a.b.u.a #29	ENSGT00950000182990.a.a.a.b.u.b #30	ENSGT00940000159102 #31	ENSGT00940000158650 #32	ENSGT00950000182841.b.a.a.b.b.p.d ##33	ENSGT00730000111073	ENSGT00950000183012.A.b	ENSGT00390000017536	ENSGT00940000161029 #35
Long-tailed chinchilla	MODERN SPECIES	218						ENSCLAG00000003953 #12	VWCE (ENSCLAG00000003291) #14	DDB1 (ENSCLAG00000004126) #15	TKFC (ENSCLAG00000003740) #16	CYB561A3 (ENSCLAG00000003653) #17	TMEM138 (ENSCLAG00000003609) #18	TMEM216 (ENSCLAG00000003298) #19	CPSF7 (ENSCLAG00000003174) #20	SDHAF2 (ENSCLAG00000013117) #21	PPP1R32 (ENSCLAG00000011656)	LRRC10B (ENSCLAG00000018115) #22	SYT7 (ENSCLAG00000009934) #23	DAGLA (ENSCLAG00000008252) #24	MYRF (ENSCLAG00000007140)	ENSCLAG00000006661 #25	FEN1 (ENSCLAG00000008656) #26	FADS1 (ENSCLAG00000008455) #27	FADS2 (ENSCLAG00000008171) #29	FADS3 (ENSCLAG00000008335) #30	RAB3IL1 (ENSCLAG00000007706) #31	BEST1 (ENSCLAG00000006972) #32	ENSCLAG00000006041 ##33	INCENP (ENSCLAG00000005037)	VPS37C (ENSCLAG00000005309)	CD5 (ENSCLAG00000004976)	SLC15A3 (ENSCLAG00000004538) #36
Guinea pig	MODERN SPECIES	65								DDB1 (ENSCPOG00000009956) #15	TKFC (ENSCPOG00000009973) #16	CYB561A3 (ENSCPOG00000019892) #17	TMEM138 (ENSCPOG00000033021) #18	TMEM216 (ENSCPOG00000009977) #19	CPSF7 (ENSCPOG00000009980) #20	SDHAF2 (ENSCPOG00000010348) #21	PPP1R32 (ENSCPOG00000012220)	LRRC10B (ENSCPOG00000014403) #22	SYT7 (ENSCPOG00000019369) #23	DAGLA (ENSCPOG00000012891) #24	MYRF (ENSCPOG00000013543)	TMEM258 (ENSCPOG00000013553) #25	FEN1 (ENSCPOG00000038134) #26	FADS1 (ENSCPOG00000037066) #27	FADS2 (ENSCPOG00000025656) #29	FADS3 (ENSCPOG00000026811) #30	RAB3IL1 (ENSCPOG00000012622) #31	BEST1 (ENSCPOG00000006105) #32	ENSCPOG00000031917 ##33	INCENP (ENSCPOG00000005701)	ENSCPOG00000023404	VPS37C (ENSCPOG00000035274)	CD5 (ENSCPOG00000025895)
Sciuridae	ANCESTRAL SPECIES	40	ENSGT00940000161414	ENSGT00940000161889 #36	ENSGT00940000161029 #35	ENSGT00390000017536	ENSGT00950000183012.A.b	ENSGT00940000153747	ENSGT00940000161089 #14	ENSGT00950000183151.a.a.a #15	ENSGT00390000015415 #16	ENSGT00950000183197.b.a #17	ENSGT00390000018587 #18	ENSGT00940000153899.a.a #19	ENSGT00730000110905.a #20	ENSGT00390000001149 #21	ENSGT00390000003127	ENSGT00940000155040.a #22	ENSGT00940000157180 #23	ENSGT00940000161192 #24	ENSGT00530000063626.a	ENSGT00390000010089.f #25	ENSGT00940000155807.a #26	ENSGT00520000061410	ENSGT00950000182990.a.a.b.b #27	ENSGT00950000182990.a.a.a.b.u.a #29	ENSGT00950000182990.a.a.a.b.u.b #30	ENSGT00940000159102 #31	ENSGT00940000158650 #32	ENSGT00950000182841.b.a.a.b.b.o.b ##33	ENSGT00950000182841.b.a.a.b.a.a.b.a ##33	ENSGT00730000111073	ENSGT00530000063866.f.b ##12
Marmotini	ANCESTRAL SPECIES	6	ENSGT00940000161414	ENSGT00940000161889 #36	ENSGT00940000161029 #35	ENSGT00390000017536	ENSGT00950000183012.A.b	ENSGT00940000153747	ENSGT00940000161089 #14	ENSGT00950000183151.a.a.a #15	ENSGT00390000015415 #16	ENSGT00950000183197.b.a #17	ENSGT00390000018587 #18	ENSGT00940000153899.a.a #19	ENSGT00730000110905.a #20	ENSGT00390000001149 #21	ENSGT00390000003127	ENSGT00940000155040.a #22	ENSGT00940000157180 #23	ENSGT00940000161192 #24	ENSGT00530000063626.a	ENSGT00390000010089.f #25	ENSGT00940000155807.a #26	ENSGT00520000061410	ENSGT00950000182990.a.a.b.b #27	ENSGT00950000182990.a.a.a.b.u.a #29	ENSGT00950000182990.a.a.a.b.u.b #30	ENSGT00940000159102 #31	ENSGT00940000158650 #32	ENSGT00950000182841.b.a.a.b.b.o.b ##33	ENSGT00950000182841.b.a.a.b.a.a.b.a ##33	ENSGT00730000111073	ENSGT00390000013802.v.b.b
Marmotini_b	ANCESTRAL SPECIES	21	ENSGT00940000161414	ENSGT00940000161889 #36	ENSGT00940000161029 #35	ENSGT00390000017536	ENSGT00950000183012.A.b	ENSGT00940000153747	ENSGT00940000161089 #14	ENSGT00950000183151.a.a.a #15	ENSGT00390000015415 #16	ENSGT00950000183197.b.a #17	ENSGT00390000018587 #18	ENSGT00940000153899.a.a #19	ENSGT00730000110905.a #20	ENSGT00390000001149 #21	ENSGT00390000003127	ENSGT00940000155040.a #22	ENSGT00940000157180 #23	ENSGT00940000161192 #24	ENSGT00530000063626.a	ENSGT00390000010089.f #25	ENSGT00940000155807.a #26	ENSGT00520000061410	ENSGT00950000182990.a.a.b.b #27	ENSGT00950000182990.a.a.a.b.u.a #29	ENSGT00950000182990.a.a.a.b.u.b #30	ENSGT00940000159102 #31	ENSGT00940000158650 #32	ENSGT00950000182841.b.a.a.b.b.o.b ##33	ENSGT00950000182841.b.a.a.b.a.a.b.a ##33	ENSGT00730000111073	ENSGT00390000013802.v.b.b
Squirrel	MODERN SPECIES	181	TMEM132A (ENSSTOG00000007846)	SLC15A3 (ENSSTOG00000007862) #36	CD6 (ENSSTOG00000007470) #35	CD5 (ENSSTOG00000026365)	VPS37C (ENSSTOG00000007504)	ENSSTOG00000023073	ENSSTOG00000007513 #14	DDB1 (ENSSTOG00000007552) #15	TKFC (ENSSTOG00000007623) #16	CYB561A3 (ENSSTOG00000007652) #17	TMEM138 (ENSSTOG00000007669) #18	TMEM216 (ENSSTOG00000020858) #19	CPSF7 (ENSSTOG00000007708) #20	SDHAF2 (ENSSTOG00000007755) #21	PPP1R32 (ENSSTOG00000007762)	LRRC10B (ENSSTOG00000032386) #22	SYT7 (ENSSTOG00000008542) #23	DAGLA (ENSSTOG00000013182) #24	MYRF (ENSSTOG00000000529)	TMEM258 (ENSSTOG00000003383) #25	ENSSTOG00000031633	FEN1 (ENSSTOG00000003387) #26	FADS1 (ENSSTOG00000003391) #27	FADS2 (ENSSTOG00000014489) #29	FADS3 (ENSSTOG00000019661) #30	RAB3IL1 (ENSSTOG00000014496) #31	BEST1 (ENSSTOG00000014508) #32	ENSSTOG00000014521 ##33	ENSSTOG00000034070	INCENP (ENSSTOG00000014541)	ENSSTOG00000033144 ##12
Arctic ground squirrel	MODERN SPECIES	366	TMEM132A (ENSUPAG00010004114)	SLC15A3 (ENSUPAG00010004134) #36	CD6 (ENSUPAG00010004151) #35	CD5 (ENSUPAG00010004200)	VPS37C (ENSUPAG00010004210)	ENSUPAG00010004227	VWCE (ENSUPAG00010004250) #14	DDB1 (ENSUPAG00010004285) #15	TKFC (ENSUPAG00010004335) #16	CYB561A3 (ENSUPAG00010004371) #17	TMEM138 (ENSUPAG00010004380) #18	TMEM216 (ENSUPAG00010004393) #19	CPSF7 (ENSUPAG00010004406) #20	ENSUPAG00010004422 #21	PPP1R32 (ENSUPAG00010004440)	LRRC10B (ENSUPAG00010004468) #22	SYT7 (ENSUPAG00010004474) #23	ENSUPAG00010004590	DAGLA (ENSUPAG00010004596) #24	MYRF (ENSUPAG00010004659)	ENSUPAG00010004772 #25	FEN1 (ENSUPAG00010004780) #26	ENSUPAG00010004784	FADS1 (ENSUPAG00010004789) #27	FADS2 (ENSUPAG00010004799) #29	ENSUPAG00010004814 #31	BEST1 (ENSUPAG00010004888) #32	ENSUPAG00010004905 ##33	INCENP (ENSUPAG00010004917)	ENSUPAG00010004941	ENSUPAG00010004946 ##12
Eurasian red squirrel	MODERN SPECIES	2	TMEM132A (ENSSVLG00005010099)	SLC15A3 (ENSSVLG00005010014) #36	CD6 (ENSSVLG00005009750) #35	CD5 (ENSSVLG00005009586)	VPS37C (ENSSVLG00005009545)	ENSSVLG00005009304	VWCE (ENSSVLG00005009126) #14	DDB1 (ENSSVLG00005009066) #15	TKFC (ENSSVLG00005009023) #16	CYB561A3 (ENSSVLG00005008965) #17	TMEM138 (ENSSVLG00005008948) #18	TMEM216 (ENSSVLG00005008859) #19	CPSF7 (ENSSVLG00005008784) #20	SDHAF2 (ENSSVLG00005008680) #21	PPP1R32 (ENSSVLG00005008524)	LRRC10B (ENSSVLG00005008474) #22	SYT7 (ENSSVLG00005007921) #23	DAGLA (ENSSVLG00005007644) #24	MYRF (ENSSVLG00005007408)	TMEM258 (ENSSVLG00005007336) #25	FEN1 (ENSSVLG00005007324) #26	ENSSVLG00005007308	FADS1 (ENSSVLG00005007252) #27	FADS2 (ENSSVLG00005007178) #29	FADS3 (ENSSVLG00005007116) #30	RAB3IL1 (ENSSVLG00005006928) #31	BEST1 (ENSSVLG00005006784) #32	ENSSVLG00005006740 ##33	ENSSVLG00005006675	ENSSVLG00005006645	ASRGL1 (ENSSVLG00005006616) #10