Rodentia_A	ANCESTRAL SPECIES	3	ENSGT00940000155672	ENSGT00390000010722 #8	ENSGT00390000003769 #9	ENSGT00940000155797 #10	ENSGT00940000155690 #11	ENSGT00390000010822 #12	ENSGT00940000157382 #13	ENSGT00390000013520 #14	ENSGT00390000009552 #15	ENSGT00840000129887 #16	ENSGT00390000018761 #17	ENSGT00940000160834 #18	ENSGT00390000000288	ENSGT00940000156706 #20	ENSGT00390000008122 #21	ENSGT00940000156751 #22	ENSGT00940000160675 #23	ENSGT00390000010789 #24	ENSGT00550000074863 #25	ENSGT00940000153818.a.b.a.b #28	ENSGT00390000016675 #29	ENSGT00520000060616	ENSGT00960000187851	ENSGT00940000165476	ENSGT01100000263482.D ##32	ENSGT00390000007247	ENSGT00940000156438	ENSGT00940000159596	ENSGT00390000007830	ENSGT00940000154849.a	ENSGT01060000250264
Sciuridae	ANCESTRAL SPECIES	4	ENSGT00940000155672	ENSGT00390000010722 #8	ENSGT00390000003769 #9	ENSGT00940000155797 #10	ENSGT00940000155690 #11	ENSGT00390000010822 #12	ENSGT00940000157382 #13	ENSGT00390000013520 #14	ENSGT00390000009552 #15	ENSGT00840000129887 #16	ENSGT00390000018761 #17	ENSGT00940000160834 #18	ENSGT00390000000288	ENSGT00940000156706 #20	ENSGT00390000008122 #21	ENSGT00940000156751 #22	ENSGT00940000160675 #23	ENSGT00390000010789 #24	ENSGT00550000074863 #25	ENSGT00940000153818.a.b.a.b #28	ENSGT00390000016675 #29	ENSGT00520000060616	ENSGT00960000187851	ENSGT00940000166945 #31	ENSGT01100000263482.C.c.a #32	ENSGT01100000263482.C.c.b.b.a.b #34	ENSGT00940000165476	ENSGT01100000263482.C.c.b.a.b.a ##32	ENSGT01100000263482.C.c.b.a.b.b ##32	ENSGT01100000263482.B ##32	ENSGT01100000263482.D ##32
Marmotini	ANCESTRAL SPECIES	8	ENSGT00940000153288.a.b.a.a #7	ENSGT00390000010722 #8	ENSGT00390000003769 #9	ENSGT00940000155797 #10	ENSGT00940000155690 #11	ENSGT00390000010822 #12	ENSGT00940000157382 #13	ENSGT00390000013520 #14	ENSGT00390000009552 #15	ENSGT00840000129887 #16	ENSGT00390000018761 #17	ENSGT00940000160834 #18	ENSGT00390000000288	ENSGT00940000156706 #20	ENSGT00390000008122 #21	ENSGT00940000156751 #22	ENSGT00940000160675 #23	ENSGT00390000010789 #24	ENSGT00550000074863 #25	ENSGT00940000153818.a.b.a.b #28	ENSGT00390000016675 #29	ENSGT00520000060616	ENSGT01100000263482.C.c.a #32	ENSGT01100000263482.C.c.b.b.a.b #34	ENSGT00390000010003.ab #37	ENSGT01100000263482.C.c.b.a.b.a ##32	ENSGT01100000263482.C.c.b.a.b.b ##32	ENSGT01100000263482.B ##32	ENSGT01100000263482.D ##32	ENSGT00390000007247	ENSGT00940000156438
Alpin marmot	MODERN SPECIES	42	ENSMMMG00000019748 #7	APPBP2 (ENSMMMG00000019739) #8	CHCT1 (ENSMMMG00000019735) #9	ENSMMMG00000019716 #10	ENSMMMG00000019712 #11	ZNHIT3 (ENSMMMG00000019709) #12	MYO19 (ENSMMMG00000019686) #13	PIGW (ENSMMMG00000019680) #14	GGNBP2 (ENSMMMG00000019594) #15	DHRS11 (ENSMMMG00000019586) #16	MRM1 (ENSMMMG00000019574) #17	LHX1 (ENSMMMG00000019565) #18	ENSMMMG00000019558 #19	ACACA (ENSMMMG00000019480) #20	C17orf78 (ENSMMMG00000019471) #21	TADA2A (ENSMMMG00000019464) #22	DUSP14 (ENSMMMG00000019458) #23	SYNRG (ENSMMMG00000019201) #24	DDX52 (ENSMMMG00000019175) #25	ENSMMMG00000019174 #26	ENSMMMG00000019173 #27	HNF1B (ENSMMMG00000019142) #28	HEATR6 (ENSMMMG00000019131) #29	ENSMMMG00000019129 #30	ENSMMMG00000019125 #31	ENSMMMG00000019119 #32	ENSMMMG00000019116 #33	ENSMMMG00000019105 #34	ENSMMMG00000019093 #35	ENSMMMG00000019090 #36	ENSMMMG00000019088 #37
Marmotini_b	ANCESTRAL SPECIES	5	ENSGT00940000153288.a.b.a.a #7	ENSGT00390000010722 #8	ENSGT00390000003769 #9	ENSGT00940000155797 #10	ENSGT00940000155690 #11	ENSGT00390000010822 #12	ENSGT00940000157382 #13	ENSGT00390000013520 #14	ENSGT00390000009552 #15	ENSGT00840000129887 #16	ENSGT00390000018761 #17	ENSGT00940000160834 #18	ENSGT00390000000288	ENSGT00940000156706 #20	ENSGT00390000008122 #21	ENSGT00940000156751 #22	ENSGT00940000160675 #23	ENSGT00390000010789 #24	ENSGT00550000074863 #25	ENSGT00940000153818.a.b.a.b #28	ENSGT00390000016675 #29	ENSGT00520000060616	ENSGT01100000263482.C.c.a #32	ENSGT01100000263482.C.c.b.b.a.b #34	ENSGT00390000010003.ab #37	ENSGT01100000263482.C.c.b.a.b.a ##32	ENSGT01100000263482.C.c.b.a.b.b ##32	ENSGT01100000263482.B ##32	ENSGT01100000263482.D ##32	ENSGT00390000007247	ENSGT00940000156438
Squirrel	MODERN SPECIES	90	PPM1D (ENSSTOG00000021256)	APPBP2 (ENSSTOG00000011350) #8	CHCT1 (ENSSTOG00000003182) #9	ENSSTOG00000029070 #10	CA4 (ENSSTOG00000010432) #11	ZNHIT3 (ENSSTOG00000013559) #12	MYO19 (ENSSTOG00000013563) #13	PIGW (ENSSTOG00000034045) #14	GGNBP2 (ENSSTOG00000002398) #15	DHRS11 (ENSSTOG00000002410) #16	MRM1 (ENSSTOG00000002422) #17	LHX1 (ENSSTOG00000022593) #18	AATF (ENSSTOG00000002458)	C17orf78 (ENSSTOG00000002508) #21	ACACA (ENSSTOG00000002468) #20	TADA2A (ENSSTOG00000002518) #22	DUSP14 (ENSSTOG00000002528) #23	SYNRG (ENSSTOG00000002530) #24	DDX52 (ENSSTOG00000002550) #25	HNF1B (ENSSTOG00000012440) #28	HEATR6 (ENSSTOG00000026901) #29	ENSSTOG00000032858	ENSSTOG00000013313 #32	ENSSTOG00000027458 #34	ENSSTOG00000031610 #37	ENSSTOG00000027899 #34	ENSSTOG00000034887 ##32	CCL14 (ENSSTOG00000033490) ##32	ENSSTOG00000015833 ##32	HEATR9 (ENSSTOG00000028751)	TAF15 (ENSSTOG00000002081)
Arctic ground squirrel	MODERN SPECIES	193	PPM1D (ENSUPAG00010011169)	ENSUPAG00010011175 #7	APPBP2 (ENSUPAG00010011180) #8	CHCT1 (ENSUPAG00010011193) #9	ENSUPAG00010011211 #10	CA4 (ENSUPAG00010011234) #11	ENSUPAG00010011238 #14	MYO19 (ENSUPAG00010011260) #13	GGNBP2 (ENSUPAG00010011289) #15	DHRS11 (ENSUPAG00010011375) #16	MRM1 (ENSUPAG00010011380) #17	LHX1 (ENSUPAG00010011394) #18	AATF (ENSUPAG00010011404)	ACACA (ENSUPAG00010011440) #20	C17orf78 (ENSUPAG00010011568) #21	TADA2A (ENSUPAG00010011582) #22	DUSP14 (ENSUPAG00010011617) #23	SYNRG (ENSUPAG00010011623) #24	DDX52 (ENSUPAG00010012034) #25	HNF1B (ENSUPAG00010012073) #28	HEATR6 (ENSUPAG00010012102) #29	ENSUPAG00010012127
Eurasian red squirrel	MODERN SPECIES	12	APPBP2 (ENSSVLG00005007432) #8	CHCT1 (ENSSVLG00005007474) #9	ENSSVLG00005007515 #10	CA4 (ENSSVLG00005007650) #11	ZNHIT3 (ENSSVLG00005007716) #12	ENSSVLG00005007764 #13	PIGW (ENSSVLG00005007830) #14	GGNBP2 (ENSSVLG00005007850) #15	DHRS11 (ENSSVLG00005007894) #16	MRM1 (ENSSVLG00005007932) #17	LHX1 (ENSSVLG00005007965) #18	AATF (ENSSVLG00005008003)	ACACA (ENSSVLG00005008078) #20	ENSSVLG00005008470 #21	ENSSVLG00005008508	TADA2A (ENSSVLG00005008528) #22	ENSSVLG00005008610	SYNRG (ENSSVLG00005008671) #24	DDX52 (ENSSVLG00005008941) #25	HNF1B (ENSSVLG00005008984) #28	HEATR6 (ENSSVLG00005009203) #29	ENSSVLG00005009414	ENSSVLG00005009438	ENSSVLG00005009477 #32	ENSSVLG00005009573 #34	ENSSVLG00005009611 #34	ENSSVLG00005009720	ENSSVLG00005009747 ##32	CCL14 (ENSSVLG00005009782) ##32	CCL16 (ENSSVLG00005009830) ##32	ENSSVLG00005009862 ##32
Hystricomorpha	ANCESTRAL SPECIES	3	ENSGT00940000155672	ENSGT00390000010722 #8	ENSGT00390000003769 #9	ENSGT00940000155797 #10	ENSGT00940000155690 #11	ENSGT00390000010822 #12	ENSGT00940000157382 #13	ENSGT00390000013520 #14	ENSGT00390000009552 #15	ENSGT00840000129887 #16	ENSGT00390000018761 #17	ENSGT00940000160834 #18	ENSGT00390000000288	ENSGT00940000156706 #20	ENSGT00390000008122 #21	ENSGT00940000156751 #22	ENSGT00940000160675 #23	ENSGT00390000010789 #24	ENSGT00550000074863 #25	ENSGT00940000153818.a.b.a.b #28	ENSGT00390000016675 #29	ENSGT00520000060616	ENSGT00940000166945 #31	ENSGT01100000263482.C.c.a #32	ENSGT01100000263482.C.c.b.b.b ##32	ENSGT01100000263482.C.c.b.b.a.b #34	ENSGT01100000263482.C.c.b.a.a ##32	ENSGT01100000263482.C.c.b.a.b.a ##32	ENSGT01100000263482.C.c.b.a.b.b ##32	ENSGT01100000263482.B ##32	ENSGT01100000263482.D ##32
Naked mole-rat female	MODERN SPECIES	12	ENSHGLG00000008032	ENSHGLG00000045654	ENSHGLG00000050018	ENSHGLG00000009096 #10	ENSHGLG00000010334 #11	ENSHGLG00000034474 #12	ENSHGLG00000011039 #13	PIGW (ENSHGLG00000012822) #14	GGNBP2 (ENSHGLG00000013148) #15	DHRS11 (ENSHGLG00000035143) #16	MRM1 (ENSHGLG00000008701) #17	LHX1 (ENSHGLG00000042105) #18	AATF (ENSHGLG00000009510)	ENSHGLG00000038049	ACACA (ENSHGLG00000011781) #20	TADA2A (ENSHGLG00000003972) #22	DUSP14 (ENSHGLG00000033195) #23	ENSHGLG00000047903	SYNRG (ENSHGLG00000004431) #24	DDX52 (ENSHGLG00000006235) #25	ENSHGLG00000007638 #28	ENSHGLG00000001663	ENSHGLG00000001698	POLG2 (ENSHGLG00000037428)	DDX5 (ENSHGLG00000001771)	ENSHGLG00000044021	ENSHGLG00000001847	ENSHGLG00000001992	ENSHGLG00000002095	ENSHGLG00000002130	ENSHGLG00000047592
Hystricomorpha_a	ANCESTRAL SPECIES		ENSGT00940000155672	ENSGT00390000010722 #8	ENSGT00390000003769 #9	ENSGT00940000155797 #10	ENSGT00940000155690 #11	ENSGT00390000010822 #12	ENSGT00940000157382 #13	ENSGT00390000013520 #14	ENSGT00390000009552 #15	ENSGT00840000129887 #16	ENSGT00390000018761 #17	ENSGT00940000160834 #18	ENSGT00390000000288	ENSGT00940000156706 #20	ENSGT00390000008122 #21	ENSGT00940000156751 #22	ENSGT00940000160675 #23	ENSGT00390000010789 #24	ENSGT00550000074863 #25	ENSGT00940000153818.a.b.a.b #28	ENSGT00390000016675 #29	ENSGT00520000060616	ENSGT00940000166945 #31	ENSGT01100000263482.C.c.a #32	ENSGT01100000263482.C.c.b.b.b ##32	ENSGT00940000165476	ENSGT01100000263482.D ##32	ENSGT00390000007247	ENSGT00940000156438	ENSGT00940000159596	ENSGT00390000007830
Hystricomorpha_b	ANCESTRAL SPECIES		ENSGT00940000155672	ENSGT00390000010722 #8	ENSGT00390000003769 #9	ENSGT00940000155797 #10	ENSGT00940000155690 #11	ENSGT00390000010822 #12	ENSGT00940000157382 #13	ENSGT00390000013520 #14	ENSGT00390000009552 #15	ENSGT00840000129887 #16	ENSGT00390000018761 #17	ENSGT00940000160834 #18	ENSGT00390000000288	ENSGT00940000156706 #20	ENSGT00390000008122 #21	ENSGT00940000156751 #22	ENSGT00940000160675 #23	ENSGT00390000010789 #24	ENSGT00550000074863 #25	ENSGT00940000153818.a.b.a.b #28	ENSGT00390000016675 #29	ENSGT00520000060616	ENSGT00940000166945 #31	ENSGT01100000263482.C.c.a #32	ENSGT01100000263482.C.c.b.b.b ##32	ENSGT01100000263482.C.c.b.a.a ##32	ENSGT01100000263482.C.c.b.a.b.a ##32	ENSGT00940000165476	ENSGT01100000263482.D ##32	ENSGT00390000007247	ENSGT00940000156438
Degu	MODERN SPECIES	205	CHCT1 (ENSODEG00000013458) #9	ENSODEG00000012951	ENSODEG00000013719	ENSODEG00000015311 #10	ENSODEG00000012868 #12	MYO19 (ENSODEG00000013791) #13	GGNBP2 (ENSODEG00000012950) #15	ENSODEG00000012529 #16	ENSODEG00000013042 #17	ENSODEG00000012953 #17	ENSODEG00000013680	LHX1 (ENSODEG00000012895) #18	AATF (ENSODEG00000013074)	ENSODEG00000013269	ACACA (ENSODEG00000014030) #20	TADA2A (ENSODEG00000014579) #22	DUSP14 (ENSODEG00000020057) #23	SYNRG (ENSODEG00000013858) #24	ENSODEG00000012814 #25	ENSODEG00000012382	HNF1B (ENSODEG00000012709) #28	HEATR6 (ENSODEG00000013428) #29	ENSODEG00000013109 #31	ENSODEG00000013480 #32	ENSODEG00000013198 ##32	ENSODEG00000013395 #32	ENSODEG00000013298	ENSODEG00000012792 ##32	HEATR9 (ENSODEG00000012621)	ENSODEG00000012915	MMP28 (ENSODEG00000016303)
Long-tailed chinchilla	MODERN SPECIES	158	PPM1D (ENSCLAG00000010623)	APPBP2 (ENSCLAG00000014528) #8	CHCT1 (ENSCLAG00000015267) #9	ENSCLAG00000012909 #10	CA4 (ENSCLAG00000014926) #11	ZNHIT3 (ENSCLAG00000013180) #12	MYO19 (ENSCLAG00000011498) #13	PIGW (ENSCLAG00000010868) #14	GGNBP2 (ENSCLAG00000015068) #15	DHRS11 (ENSCLAG00000012667) #16	MRM1 (ENSCLAG00000010960) #17	LHX1 (ENSCLAG00000014662) #18	AATF (ENSCLAG00000014631)	C17orf78 (ENSCLAG00000013611) #21	ACACA (ENSCLAG00000015071) #20	TADA2A (ENSCLAG00000016976) #22	DUSP14 (ENSCLAG00000012666) #23	SYNRG (ENSCLAG00000013031) #24	DDX52 (ENSCLAG00000016292) #25	HNF1B (ENSCLAG00000016506) #28	HEATR6 (ENSCLAG00000010390) #29	ENSCLAG00000012435	ENSCLAG00000011924	ENSCLAG00000016754 #31	ENSCLAG00000012634 #32	ENSCLAG00000014501 ##32
Guinea pig	MODERN SPECIES	32	BCAS3 (ENSCPOG00000001933)	PPM1D (ENSCPOG00000000343)	APPBP2 (ENSCPOG00000033874) #8	CHCT1 (ENSCPOG00000005521) #9	ENSCPOG00000005504 #10	CA4 (ENSCPOG00000026479) #11	ZNHIT3 (ENSCPOG00000031447) #12	MYO19 (ENSCPOG00000004270) #13	PIGW (ENSCPOG00000004275) #14	GGNBP2 (ENSCPOG00000004278) #15	DHRS11 (ENSCPOG00000036629) #16	MRM1 (ENSCPOG00000004283) #17	LHX1 (ENSCPOG00000027154) #18	AATF (ENSCPOG00000006037)	ACACA (ENSCPOG00000006043) #20	TADA2A (ENSCPOG00000001869) #22	DUSP14 (ENSCPOG00000032995) #23	SYNRG (ENSCPOG00000004643) #24	DDX52 (ENSCPOG00000001232) #25	HNF1B (ENSCPOG00000001234) #28	HEATR6 (ENSCPOG00000015165) #29	ENSCPOG00000036860	ENSCPOG00000035230 #31	ENSCPOG00000032867 #32	ENSCPOG00000033663 ##32	ENSCPOG00000037138 ##32	ENSCPOG00000026400 #34	ENSCPOG00000039417 ##32	CCL14 (ENSCPOG00000035450) ##32	ENSCPOG00000008852 ##32	HEATR9 (ENSCPOG00000010117)