Rodentia_A	ANCESTRAL SPECIES	6	ENSGT00940000160506	ENSGT00940000162766	ENSGT00940000163003	ENSGT00940000154432.n #7	ENSGT00940000163805 #12	ENSGT00940000154432.m.a ##7	ENSGT00940000161634 #13	ENSGT00940000161069 #14	ENSGT00390000017267 #15	ENSGT00940000159256 #16	ENSGT00940000159112.b #17	ENSGT00940000160330 #18	ENSGT00390000005826.a.a #19	ENSGT00390000002548 #20	ENSGT00940000158344.b #21	ENSGT00940000161057 #22	ENSGT00940000158721 #23	ENSGT01100000263564.a.h #24	ENSGT01100000263564.a.g #25	ENSGT00550000076229	ENSGT00530000063950.a.b #27	ENSGT00390000002767 #28	ENSGT00550000075007 #29	ENSGT00940000160011 #30	ENSGT00390000012863 #31	ENSGT00940000161295 #32	ENSGT01030000234635.a.b.a.b.b.a.b #33	ENSGT00970000193421.A #34	ENSGT00940000159485 #36	ENSGT00390000017583 #37	ENSGT00950000183095.a.b.a.b.a
Sciuridae	ANCESTRAL SPECIES	5			ENSGT00940000163805 #12	ENSGT00940000162766	ENSGT00940000163003	ENSGT00940000154432.n #7	ENSGT00940000161634 #13	ENSGT00940000161069 #14	ENSGT00390000017267 #15	ENSGT00940000159256 #16	ENSGT00940000159112.b #17	ENSGT00940000160330 #18	ENSGT00390000005826.a.a #19	ENSGT00390000002548 #20	ENSGT00940000158344.b #21	ENSGT00940000161057 #22	ENSGT00940000158721 #23	ENSGT01100000263564.a.h #24	ENSGT01100000263564.a.g #25	ENSGT00550000076229	ENSGT00530000063950.a.b #27	ENSGT00390000002767 #28	ENSGT00550000075007 #29	ENSGT00940000160011 #30	ENSGT00390000012863 #31	ENSGT00940000161295 #32	ENSGT01030000234635.a.b.a.b.b.a.b #33	ENSGT00970000193421.A #34	ENSGT00940000159485 #36	ENSGT00390000017583 #37	ENSGT00950000183095.a.b.a.b.a.j
Eurasian red squirrel	MODERN SPECIES	8	ENSSVLG00005015636 #7	ENSSVLG00005015448 #8	ENSSVLG00005014930 #9	ENSSVLG00005014859 #10	ENSSVLG00005014702 #11	ENSSVLG00005014636 #12	CRX (ENSSVLG00005014575) #13	SELENOW (ENSSVLG00005014510) #14	NOP53 (ENSSVLG00005014437) #15	EHD2 (ENSSVLG00005014364) #16	BICRA (ENSSVLG00005013976) #17	ZNF541 (ENSSVLG00005013491) #18	NAPA (ENSSVLG00005012991) #19	KPTN (ENSSVLG00005012899) #20	SLC8A2 (ENSSVLG00005012674) #21	MEIS3 (ENSSVLG00005012542) #22	DHX34 (ENSSVLG00005012498) #23	C5AR2 (ENSSVLG00005012478) #24	C5AR1 (ENSSVLG00005012437) #25	ENSSVLG00005012324 #26	CCDC9 (ENSSVLG00005012213) #27	BBC3 (ENSSVLG00005012098) #28	SAE1 (ENSSVLG00005011951) #29	ZC3H4 (ENSSVLG00005011727) #30	TMEM160 (ENSSVLG00005011672) #31	NPAS1 (ENSSVLG00005011606) #32	ARHGAP35 (ENSSVLG00005011555) #33	AP2S1 (ENSSVLG00005011272) #34	ENSSVLG00005011219 #35	SLC1A5 (ENSSVLG00005010966) #36	FKRP (ENSSVLG00005010926) #37
Marmotini	ANCESTRAL SPECIES	7	ENSGT00940000154432.n.h.a.b.a.b.a #7	ENSGT00940000163003	ENSGT00940000154432.n.h.a.b.b #7	ENSGT00940000154432.n.h.a.a #7	ENSGT00940000163805 #12	ENSGT00940000154432.n.g #7	ENSGT00940000161634 #13	ENSGT00940000161069 #14	ENSGT00390000017267 #15	ENSGT00940000159256 #16	ENSGT00940000159112.b #17	ENSGT00940000160330 #18	ENSGT00390000005826.a.a #19	ENSGT00390000002548 #20	ENSGT00940000158344.b #21	ENSGT00940000161057 #22	ENSGT00940000158721 #23	ENSGT01100000263564.a.h #24	ENSGT01100000263564.a.g #25	ENSGT00550000076229	ENSGT00530000063950.a.b #27	ENSGT00390000002767 #28	ENSGT00550000075007 #29	ENSGT00940000160011 #30	ENSGT00390000012863 #31	ENSGT00940000161295 #32	ENSGT01030000234635.a.b.a.b.b.a.b #33	ENSGT00970000193421.A #34	ENSGT00940000159485 #36	ENSGT00390000017583 #37	ENSGT00950000183095.a.b.a.b.a.j
Marmotini_b	ANCESTRAL SPECIES	22	ENSGT00940000154432.n.h.a.b.a.b.a #7	ENSGT00940000154432.n.h.a.b.a.a #7	ENSGT00940000163003	ENSGT00940000154432.n.h.a.b.b #7	ENSGT00940000154432.n.h.a.a #7	ENSGT00940000163805 #12	ENSGT00940000161634 #13	ENSGT00940000161069 #14	ENSGT00390000017267 #15	ENSGT00940000159256 #16	ENSGT00940000159112.b #17	ENSGT00940000160330 #18	ENSGT00390000005826.a.a #19	ENSGT00390000002548 #20	ENSGT00940000158344.b #21	ENSGT00940000161057 #22	ENSGT00940000158721 #23	ENSGT01100000263564.a.h #24	ENSGT01100000263564.a.g #25	ENSGT00550000076229	ENSGT00530000063950.a.b #27	ENSGT00390000002767 #28	ENSGT00550000075007 #29	ENSGT00940000160011 #30	ENSGT00390000012863 #31	ENSGT00940000161295 #32	ENSGT01030000234635.a.b.a.b.b.a.b #33	ENSGT00970000193421.A #34	ENSGT00940000159485 #36	ENSGT00390000017583 #37	ENSGT00950000183095.a.b.a.b.a.j
Squirrel	MODERN SPECIES	264	ENSSTOG00000020452 #7	ENSSTOG00000023396 #7	ENSSTOG00000020676 #7	BSPH1 (ENSSTOG00000034649)	ENSSTOG00000025647 #7	ENSSTOG00000022010 #7	ENSSTOG00000021552 #12	CRX (ENSSTOG00000024356) #13	NOP53 (ENSSTOG00000022092) #15	ENSSTOG00000011087 #16	BICRA (ENSSTOG00000028398) #17	ZNF541 (ENSSTOG00000026879) #18	NAPA (ENSSTOG00000006983) #19	KPTN (ENSSTOG00000006963) #20	SLC8A2 (ENSSTOG00000020165) #21	MEIS3 (ENSSTOG00000028182) #22	DHX34 (ENSSTOG00000015831) #23	C5AR2 (ENSSTOG00000023346) #24	C5AR1 (ENSSTOG00000026678) #25	ENSSTOG00000005813 #27	SAE1 (ENSSTOG00000016251) #29	ZC3H4 (ENSSTOG00000016249) #30	TMEM160 (ENSSTOG00000024623) #31	NPAS1 (ENSSTOG00000003396) #32	ARHGAP35 (ENSSTOG00000011409) #33	SLC1A5 (ENSSTOG00000028576) #36	FKRP (ENSSTOG00000027896) #37	STRN4 (ENSSTOG00000025660)	PRKD2 (ENSSTOG00000026693)	ENSSTOG00000028905	GNG8 (ENSSTOG00000024152)
Arctic ground squirrel	MODERN SPECIES	455							CRX (ENSUPAG00010010106) #13	ENSUPAG00010010102 #14	NOP53 (ENSUPAG00010010094) #15	EHD2 (ENSUPAG00010010085) #16	BICRA (ENSUPAG00010010059) #17	ZNF541 (ENSUPAG00010010048) #18	NAPA (ENSUPAG00010010015) #19	KPTN (ENSUPAG00010010006) #20	SLC8A2 (ENSUPAG00010009969) #21	MEIS3 (ENSUPAG00010009940) #22	DHX34 (ENSUPAG00010009871) #23	C5AR2 (ENSUPAG00010009867) #24	C5AR1 (ENSUPAG00010009863) #25	INAFM1 (ENSUPAG00010009857)	CCDC9 (ENSUPAG00010009846) #27	BBC3 (ENSUPAG00010009844) #28	SAE1 (ENSUPAG00010009824) #29	ZC3H4 (ENSUPAG00010009793) #30	TMEM160 (ENSUPAG00010009790) #31	NPAS1 (ENSUPAG00010009764) #32	ARHGAP35 (ENSUPAG00010009739) #33	AP2S1 (ENSUPAG00010009722) #34	SLC1A5 (ENSUPAG00010009701) #36	STRN4 (ENSUPAG00010009670)	PRKD2 (ENSUPAG00010009657)
Alpin marmot	MODERN SPECIES	45	ENSMMMG00000012846 #7	ENSMMMG00000012847 #7	ENSMMMG00000012878 #7	ENSMMMG00000013050 #7	ENSMMMG00000013103 #12	ENSMMMG00000013119 #7	CRX (ENSMMMG00000013129) #13	SELENOW (ENSMMMG00000013140) #14	ENSMMMG00000013145 #15	EHD2 (ENSMMMG00000013147) #16	BICRA (ENSMMMG00000013156) #17	ZNF541 (ENSMMMG00000013251) #18	NAPA (ENSMMMG00000013273) #19	KPTN (ENSMMMG00000013277) #20	SLC8A2 (ENSMMMG00000013339) #21	MEIS3 (ENSMMMG00000013369) #22	DHX34 (ENSMMMG00000013402) #23	C5AR2 (ENSMMMG00000013488) #24	C5AR1 (ENSMMMG00000013493) #25	CCDC9 (ENSMMMG00000013499) #27	SAE1 (ENSMMMG00000013566) #29	ZC3H4 (ENSMMMG00000013587) #30	ENSMMMG00000013602 ##35	NPAS1 (ENSMMMG00000013606) #32	ARHGAP35 (ENSMMMG00000013646) #33	AP2S1 (ENSMMMG00000013659) #34	SLC1A5 (ENSMMMG00000013678) #36	FKRP (ENSMMMG00000013696) #37	STRN4 (ENSMMMG00000013698)	PRKD2 (ENSMMMG00000013741)	ENSMMMG00000013782
Hystricomorpha	ANCESTRAL SPECIES	2	ENSGT01030000234606.a.b.d	ENSGT00940000160506	ENSGT00940000162766	ENSGT00940000163805 #12	ENSGT00940000154432.m.a.b ##7	ENSGT00940000154432.m.a.a ##7	ENSGT00940000161634 #13	ENSGT00940000161069 #14	ENSGT00390000017267 #15	ENSGT00940000159256 #16	ENSGT00940000159112.b #17	ENSGT00940000160330 #18	ENSGT00390000005826.a.a #19	ENSGT00390000002548 #20	ENSGT00940000158344.b #21	ENSGT00940000161057 #22	ENSGT00940000158721 #23	ENSGT01100000263564.a.h #24	ENSGT01100000263564.a.g #25	ENSGT00530000063950.a.b #27	ENSGT00390000002767 #28	ENSGT00550000075007 #29	ENSGT00940000160011 #30	ENSGT00390000012863 #31	ENSGT00940000161295 #32	ENSGT01030000234635.a.b.a.b.b.a.b #33	ENSGT00970000193421.A #34	ENSGT00940000159485 #36	ENSGT00390000017583 #37	ENSGT00950000183095.a.b.a.b.a	ENSGT00950000183024.a.b.b
Hystricomorpha_a	ANCESTRAL SPECIES	39							ENSGT00940000154432.m.a.a ##7	ENSGT00940000161634 #13	ENSGT00390000017267 #15	ENSGT00940000159256 #16	ENSGT00940000159112.b #17	ENSGT00940000160330 #18	ENSGT00390000005826.a.a #19	ENSGT00390000002548 #20	ENSGT00940000158344.b #21	ENSGT00940000161057 #22	ENSGT00940000158721 #23	ENSGT01100000263564.a.h #24	ENSGT01100000263564.a.g #25	ENSGT00550000076229	ENSGT00940000167173	ENSGT00390000002767 #28	ENSGT00550000075007 #29	ENSGT00940000160011 #30	ENSGT00390000012863 #31	ENSGT00940000161295 #32	ENSGT01030000234635.a.b.a.b.b.a.b #33	ENSGT00970000193421.A #34	ENSGT00940000159485 #36	ENSGT00390000017583 #37	ENSGT00950000183095.a.b.a.b.a
Guinea pig	MODERN SPECIES	80					Std1 (ENSCPOG00000003036) ##7	Std2 (ENSCPOG00000034234) ##7	ENSCPOG00000034667 ##7	CRX (ENSCPOG00000036687) #13	NOP53 (ENSCPOG00000015665) #15	EHD2 (ENSCPOG00000026417) #16	BICRA (ENSCPOG00000015610) #17	ZNF541 (ENSCPOG00000020622) #18	NAPA (ENSCPOG00000010617) #19	KPTN (ENSCPOG00000010615) #20	SLC8A2 (ENSCPOG00000010035) #21	MEIS3 (ENSCPOG00000026589) #22	DHX34 (ENSCPOG00000006510) #23	C5AR2 (ENSCPOG00000010536) #24	C5AR1 (ENSCPOG00000030913) #25	INAFM1 (ENSCPOG00000034661)	ENSCPOG00000008209	SAE1 (ENSCPOG00000021581) #29	ZC3H4 (ENSCPOG00000036659) #30	TMEM160 (ENSCPOG00000015280) #31	NPAS1 (ENSCPOG00000023069) #32	ARHGAP35 (ENSCPOG00000013236) #33	AP2S1 (ENSCPOG00000026801) #34	SLC1A5 (ENSCPOG00000004326) #36	FKRP (ENSCPOG00000036590) #37	STRN4 (ENSCPOG00000001053)	PRKD2 (ENSCPOG00000003294)
Hystricomorpha_b	ANCESTRAL SPECIES	49								ENSGT00940000161634 #13	ENSGT00390000017267 #15	ENSGT00940000159256 #16	ENSGT00940000159112.b #17	ENSGT00940000160330 #18	ENSGT00390000005826.a.a #19	ENSGT00390000002548 #20	ENSGT00940000158344.b #21	ENSGT00940000161057 #22	ENSGT00940000158721 #23	ENSGT01100000263564.a.g #25	ENSGT00940000167173	ENSGT00390000002767 #28	ENSGT00550000075007 #29	ENSGT00940000160011 #30	ENSGT00390000012863 #31	ENSGT00940000161295 #32	ENSGT01030000234635.a.b.a.b.b.a.b #33	ENSGT00970000193421.A #34	ENSGT00940000159485 #36	ENSGT00390000017583 #37	ENSGT00950000183095.a.b.a.b.a	ENSGT00950000183024.a.b.b	ENSGT00950000183181.B.b
Long-tailed chinchilla	MODERN SPECIES	281								CRX (ENSCLAG00000001963) #13	NOP53 (ENSCLAG00000001860) #15	EHD2 (ENSCLAG00000001756) #16	BICRA (ENSCLAG00000000673) #17	ZNF541 (ENSCLAG00000001489) #18	NAPA (ENSCLAG00000001379) #19	KPTN (ENSCLAG00000001346) #20	SLC8A2 (ENSCLAG00000000972) #21	MEIS3 (ENSCLAG00000000719) #22	DHX34 (ENSCLAG00000000906) #23	C5AR1 (ENSCLAG00000001064) #25	ENSCLAG00000000680	BBC3 (ENSCLAG00000000578) #28	SAE1 (ENSCLAG00000000507) #29	ENSCLAG00000000483	ZC3H4 (ENSCLAG00000001032) #30	TMEM160 (ENSCLAG00000000918) #31	NPAS1 (ENSCLAG00000000717) #32	ARHGAP35 (ENSCLAG00000002385) #33	AP2S1 (ENSCLAG00000002250) #34	ENSCLAG00000002077 #36	FKRP (ENSCLAG00000001845) #37	STRN4 (ENSCLAG00000001542)	PRKD2 (ENSCLAG00000001395)
Degu	MODERN SPECIES	238								CRX (ENSODEG00000006452) #13	NOP53 (ENSODEG00000006707) #15	EHD2 (ENSODEG00000006641) #16	BICRA (ENSODEG00000009243) #17	ZNF541 (ENSODEG00000005850) #18	NAPA (ENSODEG00000008511) #19	ENSODEG00000009127 #20	SLC8A2 (ENSODEG00000007313) #21	MEIS3 (ENSODEG00000006485) #22	DHX34 (ENSODEG00000006333) #23	ENSODEG00000008542	ENSODEG00000009476	BBC3 (ENSODEG00000006470) #28	ENSODEG00000006581 #29	ZC3H4 (ENSODEG00000008320) #30	TMEM160 (ENSODEG00000009538) #31	NPAS1 (ENSODEG00000006878) #32	ARHGAP35 (ENSODEG00000007178) #33	AP2S1 (ENSODEG00000006649) #34	SLC1A5 (ENSODEG00000007341) #36	FKRP (ENSODEG00000019605) #37	STRN4 (ENSODEG00000009103)	PRKD2 (ENSODEG00000006559)	ENSODEG00000006767
Naked mole-rat female	MODERN SPECIES	21	ENSHGLG00000015393	ELSPBP1 (ENSHGLG00000015441)	ENSHGLG00000015622 #12	ENSHGLG00000018150 ##7	SULT2A1 (ENSHGLG00000013462) ##7	ENSHGLG00000034800	ENSHGLG00000048960 ##7	CRX (ENSHGLG00000013944) #13	ENSHGLG00000037909 #14	NOP53 (ENSHGLG00000018240) #15	EHD2 (ENSHGLG00000017825) #16	ZNF541 (ENSHGLG00000017589) #18	NAPA (ENSHGLG00000017294) #19	KPTN (ENSHGLG00000013757) #20	SLC8A2 (ENSHGLG00000017722) #21	MEIS3 (ENSHGLG00000018600) #22	DHX34 (ENSHGLG00000004917) #23	C5AR2 (ENSHGLG00000045362) #24	C5AR1 (ENSHGLG00000005545) #25	CCDC9 (ENSHGLG00000006240) #27	BBC3 (ENSHGLG00000050947) #28	SAE1 (ENSHGLG00000007950) #29	ZC3H4 (ENSHGLG00000008600) #30	TMEM160 (ENSHGLG00000009284) #31	NPAS1 (ENSHGLG00000009357) #32	ARHGAP35 (ENSHGLG00000010970) #33	AP2S1 (ENSHGLG00000018471) #34	SLC1A5 (ENSHGLG00000013744) #36	FKRP (ENSHGLG00000017783) #37	STRN4 (ENSHGLG00000015771)	PRKD2 (ENSHGLG00000017425)