Rodentia_A	ANCESTRAL SPECIES	13	ENSGT01100000263532.A.a.a.b.b.a.a	ENSGT01100000263532.A.a.a.a.b.c.a	ENSGT00900000143154	ENSGT01100000263523.B	ENSGT01100000263532.C.c.b	ENSGT00940000155850	ENSGT00940000159964	ENSGT00950000183140.a.b	ENSGT00940000157618	ENSGT00940000156791	ENSGT00680000100059	ENSGT00940000157883.a.b.e.a	ENSGT00940000162151	ENSGT00390000010116	ENSGT00940000156112 #21	ENSGT00950000182892.a.a.b #22	ENSGT00940000153147.m.a.a.a.b.a.b	ENSGT00950000182919.C #23	ENSGT00940000161892	ENSGT00940000160027 #24	ENSGT00940000157270 #25	ENSGT00940000161653 #26	ENSGT00940000161503 #27	ENSGT00940000158266 #28	ENSGT00940000161308 #29	ENSGT00940000159938 #30	ENSGT00940000161457 #31	ENSGT00940000161025	ENSGT00390000001859 #32	ENSGT00940000154298.a.a #33	ENSGT00940000156582 #34
Sciuridae	ANCESTRAL SPECIES	10	ENSGT01100000263532.A.a.a.b.b.a.a	ENSGT01100000263532.A.a.a.a.b.c.a	ENSGT00900000143154	ENSGT01100000263523.B	ENSGT01100000263532.C.c.b	ENSGT00940000155850	ENSGT00940000159964	ENSGT00950000183140.a.b	ENSGT00940000157618	ENSGT00940000156791	ENSGT00680000100059	ENSGT00940000157883.a.b.e.a	ENSGT00940000162151	ENSGT00390000010116	ENSGT00940000156112 #21	ENSGT00950000182892.a.a.b #22	ENSGT00940000153147.m.a.a.a.b.a.b	ENSGT00950000182919.C #23	ENSGT00940000161892	ENSGT00940000160027 #24	ENSGT00940000157270 #25	ENSGT00940000161653 #26	ENSGT00940000161503 #27	ENSGT00940000158266 #28	ENSGT00940000161308 #29	ENSGT00940000159938 #30	ENSGT00940000161457 #31	ENSGT00940000161025	ENSGT00390000001859 #32	ENSGT00940000154298.a.a.xb #33	ENSGT00940000156582 #34
Marmotini	ANCESTRAL SPECIES	2	ENSGT01100000263532.A.a.a.b.b.a.a	ENSGT01100000263532.A.a.a.a.b.c.a	ENSGT00900000143154	ENSGT01100000263523.B	ENSGT01100000263532.C.c.b	ENSGT00940000155850	ENSGT00940000159964	ENSGT00950000183140.a.b	ENSGT00940000157618	ENSGT00940000156791	ENSGT00680000100059	ENSGT00940000157883.a.b.e.a	ENSGT00940000162151	ENSGT00390000010116.gb	ENSGT00940000156112 #21	ENSGT00950000182892.a.a.b #22	ENSGT00940000153147.m.a.a.a.b.a.b	ENSGT00950000182919.C #23	ENSGT00940000161892	ENSGT00940000160027 #24	ENSGT00940000157270 #25	ENSGT00940000161653 #26	ENSGT00940000161503 #27	ENSGT00940000158266 #28	ENSGT00940000161308 #29	ENSGT00940000159938 #30	ENSGT00940000161457 #31	ENSGT00940000161025	ENSGT00390000001859 #32	ENSGT00940000154298.a.a.xb.a #33	ENSGT00940000156582 #34
Alpin marmot	MODERN SPECIES	5															AGPS (ENSMMMG00000023778) #21	NFE2L2 (ENSMMMG00000023776) #22	MTX2 (ENSMMMG00000023772) #23	HOXD3 (ENSMMMG00000023768) #24	HOXD4 (ENSMMMG00000023767) #25	ENSMMMG00000023765 #26	HOXD9 (ENSMMMG00000023764) #27	HOXD10 (ENSMMMG00000023763) #28	ENSMMMG00000023762 #29	HOXD12 (ENSMMMG00000023760) #30	HOXD13 (ENSMMMG00000023759) #31	LNPK (ENSMMMG00000023755) #32	ENSMMMG00000023748 #33	ATF2 (ENSMMMG00000023733) #34	ENSMMMG00000023730 #35	CHN1 (ENSMMMG00000023718) #36	CHRNA1 (ENSMMMG00000023717) #37
Marmotini_b	ANCESTRAL SPECIES	10	ENSGT01100000263532.A.a.a.b.b.a.a	ENSGT01100000263532.A.a.a.a.b.c.a	ENSGT00900000143154	ENSGT01100000263523.B	ENSGT01100000263532.C.c.b	ENSGT00940000155850	ENSGT00940000159964	ENSGT00950000183140.a.b	ENSGT00940000157618	ENSGT00940000156791	ENSGT00680000100059	ENSGT00940000157883.a.b.e.a	ENSGT00940000162151	ENSGT00390000010116.gb	ENSGT00940000156112 #21	ENSGT00950000182892.a.a.b #22	ENSGT00940000153147.m.a.a.a.b.a.b	ENSGT00950000182919.C #23	ENSGT00940000161892	ENSGT00940000160027 #24	ENSGT00940000157270 #25	ENSGT00940000161653 #26	ENSGT00940000161503 #27	ENSGT00940000158266 #28	ENSGT00940000161308 #29	ENSGT00940000159938 #30	ENSGT00940000161457 #31	ENSGT00940000161025	ENSGT00390000001859 #32	ENSGT00940000154298.a.a.xb.a #33	ENSGT00940000156582 #34
Arctic ground squirrel	MODERN SPECIES	96	ENSUPAG00010005828	ENSUPAG00010005845	ENSUPAG00010005849	ENSUPAG00010005854	ENSUPAG00010005857	PLEKHA3 (ENSUPAG00010005864)	FKBP7 (ENSUPAG00010005868)	PJVK (ENSUPAG00010005878)	PRKRA (ENSUPAG00010005881)	OSBPL6 (ENSUPAG00010005891)	RBM45 (ENSUPAG00010006036)	ENSUPAG00010006054	PDE11A (ENSUPAG00010006062)	ENSUPAG00010006082	AGPS (ENSUPAG00010006084) #21	NFE2L2 (ENSUPAG00010006108) #22	HNRNPA3 (ENSUPAG00010006133)
Squirrel	MODERN SPECIES	109	ENSSTOG00000034976	ENSSTOG00000033165	ENSSTOG00000032305	ENSSTOG00000032899	ENSSTOG00000006208	PLEKHA3 (ENSSTOG00000006191)	FKBP7 (ENSSTOG00000006176)	PJVK (ENSSTOG00000028411)	PRKRA (ENSSTOG00000006156)	OSBPL6 (ENSSTOG00000006092)	RBM45 (ENSSTOG00000002708)	ENSSTOG00000008853	PDE11A (ENSSTOG00000012639)	ENSSTOG00000003267	AGPS (ENSSTOG00000012623) #21	NFE2L2 (ENSSTOG00000000313) #22	HNRNPA3 (ENSSTOG00000025125)	ENSSTOG00000030884	MTX2 (ENSSTOG00000014688) #23	HOXD1 (ENSSTOG00000012230)	HOXD3 (ENSSTOG00000014680) #24	HOXD4 (ENSSTOG00000029055) #25	ENSSTOG00000023453 #26	HOXD9 (ENSSTOG00000026761) #27	HOXD10 (ENSSTOG00000003935) #28	HOXD12 (ENSSTOG00000004918) #30	HOXD13 (ENSSTOG00000004117) #31	EVX2 (ENSSTOG00000014512)	LNPK (ENSSTOG00000014498) #32	ENSSTOG00000013572 #33	ATF2 (ENSSTOG00000014079) #34
Eurasian red squirrel	MODERN SPECIES	12	CCDC141 (ENSSVLG00005020180)	ENSSVLG00005008368	PLEKHA3 (ENSSVLG00005005206)	FKBP7 (ENSSVLG00005005181)	ENSSVLG00005005163	PJVK (ENSSVLG00005005095)	PRKRA (ENSSVLG00005005027)	OSBPL6 (ENSSVLG00005004465)	RBM45 (ENSSVLG00005004137)	ENSSVLG00005004113	PDE11A (ENSSVLG00005004050)	ENSSVLG00005004018	ENSSVLG00005004006	ENSSVLG00005003996	AGPS (ENSSVLG00005003959) #21	ENSSVLG00005003903 #22	ENSSVLG00005003881	MTX2 (ENSSVLG00005003812) #23	HOXD1 (ENSSVLG00005003762)	HOXD4 (ENSSVLG00005003676) #25	HOXD8 (ENSSVLG00005003645) #26	HOXD9 (ENSSVLG00005003618) #27	HOXD10 (ENSSVLG00005003599) #28	HOXD11 (ENSSVLG00005003581) #29	HOXD12 (ENSSVLG00005003565) #30	HOXD13 (ENSSVLG00005003554) #31	EVX2 (ENSSVLG00005003539)	LNPK (ENSSVLG00005003500) #32	ENSSVLG00005003466	ENSSVLG00005003430 #33	ENSSVLG00005003279 #34
Hystricomorpha	ANCESTRAL SPECIES	20	ENSGT00940000155611.s	ENSGT00730000111148	ENSGT00440000038972	ENSGT01100000263523.A	ENSGT01100000263523.B	ENSGT01100000263532.C.c.b	ENSGT00940000155850	ENSGT00940000159964	ENSGT00950000183140.a.b	ENSGT00940000157618	ENSGT00940000156791	ENSGT00680000100059	ENSGT00940000162151	ENSGT00390000010116	ENSGT00940000156112 #21	ENSGT00950000182892.a.a.b #22	ENSGT00940000154808.a.a	ENSGT00950000182919.C #23	ENSGT00940000161892	ENSGT00940000160027 #24	ENSGT00940000157270 #25	ENSGT00940000161653 #26	ENSGT00940000161503 #27	ENSGT00940000158266 #28	ENSGT00940000161308 #29	ENSGT00940000159938 #30	ENSGT00940000161457 #31	ENSGT00940000161025	ENSGT00390000001859 #32	ENSGT00940000154298.a.a #33	ENSGT00940000156582 #34
Hystricomorpha_a	ANCESTRAL SPECIES	17	ENSGT00940000155611.s	ENSGT00730000111148	ENSGT00440000038972	ENSGT01100000263523.A	ENSGT01100000263523.B	ENSGT01100000263532.C.c.b	ENSGT00940000155850	ENSGT00940000159964	ENSGT00950000183140.a.b	ENSGT00940000157618	ENSGT00940000156791	ENSGT00680000100059	ENSGT00940000162151	ENSGT00390000010116	ENSGT00940000156112 #21	ENSGT00950000182892.a.a.b #22	ENSGT00940000154808.a.a	ENSGT00950000182919.C #23	ENSGT00940000161892	ENSGT00940000160027 #24	ENSGT00940000157270 #25	ENSGT00940000161653 #26	ENSGT00940000161503 #27	ENSGT00940000158266 #28	ENSGT00940000161308 #29	ENSGT00940000159938 #30	ENSGT00940000161457 #31	ENSGT00940000161025	ENSGT00390000001859 #32	ENSGT00940000154298.a.a #33	ENSGT00940000156582 #34
Hystricomorpha_b	ANCESTRAL SPECIES	24	ENSGT01100000263523.A	ENSGT01100000263523.B	ENSGT00900000143159	ENSGT00900000143154	ENSGT00920000150542	ENSGT01100000263532.C.c.b	ENSGT00940000155850	ENSGT00940000159964	ENSGT00950000183140.a.b	ENSGT00940000157618	ENSGT00940000156791	ENSGT00680000100059	ENSGT00940000162151	ENSGT00390000010116	ENSGT00940000156112 #21	ENSGT00950000182892.a.a.b #22	ENSGT00940000154808.a.a	ENSGT00950000182919.C #23	ENSGT00940000161892	ENSGT00940000160027 #24	ENSGT00940000157270 #25	ENSGT00940000161653 #26	ENSGT00940000161503 #27	ENSGT00940000158266 #28	ENSGT00940000161308 #29	ENSGT00940000159938 #30	ENSGT00940000161457 #31	ENSGT00940000161025	ENSGT00390000001859 #32	ENSGT00940000154298.a.a #33	ENSGT00940000156582 #34
Long-tailed chinchilla	MODERN SPECIES	110	ENSCLAG00000014023	ENSCLAG00000015797	ENSCLAG00000015650	ENSCLAG00000016023	PLEKHA3 (ENSCLAG00000014135)	PRKRA (ENSCLAG00000010338)	PJVK (ENSCLAG00000010713)	OSBPL6 (ENSCLAG00000011433)	RBM45 (ENSCLAG00000015215)	PDE11A (ENSCLAG00000013013)	ENSCLAG00000013714	ENSCLAG00000017938	AGPS (ENSCLAG00000013279) #21	ENSCLAG00000013627	ENSCLAG00000012626	NFE2L2 (ENSCLAG00000013122) #22	HNRNPA3 (ENSCLAG00000012855)	ENSCLAG00000011088	MTX2 (ENSCLAG00000011598) #23	HOXD1 (ENSCLAG00000012505)	ENSCLAG00000013605 #24	HOXD4 (ENSCLAG00000014461) #25	ENSCLAG00000011108 #26	HOXD9 (ENSCLAG00000012447) #27	HOXD10 (ENSCLAG00000012482) #28	ENSCLAG00000012563 #29	HOXD12 (ENSCLAG00000013058) #30	HOXD13 (ENSCLAG00000013095) #31	EVX2 (ENSCLAG00000014389)	LNPK (ENSCLAG00000015033) #32	TRIML1 (ENSCLAG00000014494)
Degu	MODERN SPECIES	106	ENSODEG00000007812	ENSODEG00000008370	ENSODEG00000008948	PLEKHA3 (ENSODEG00000007880)	ENSODEG00000008149	PJVK (ENSODEG00000008177)	ENSODEG00000008743	OSBPL6 (ENSODEG00000009667)	ENSODEG00000019659	RBM45 (ENSODEG00000007959)	ENSODEG00000019574	PDE11A (ENSODEG00000010682)	ENSODEG00000019592	ENSODEG00000020058	AGPS (ENSODEG00000008272) #21	NFE2L2 (ENSODEG00000010043) #22	ENSODEG00000009265	ENSODEG00000009697	MTX2 (ENSODEG00000008062) #23	ENSODEG00000008879	HOXD1 (ENSODEG00000008961)	HOXD3 (ENSODEG00000009722) #24	HOXD4 (ENSODEG00000010297) #25	ENSODEG00000010496 #26	HOXD9 (ENSODEG00000008626) #27	HOXD10 (ENSODEG00000010382) #28	ENSODEG00000010934 #29	HOXD12 (ENSODEG00000008376) #30	HOXD13 (ENSODEG00000008793) #31	EVX2 (ENSODEG00000010771)	ENSODEG00000008992
Guinea pig	MODERN SPECIES	3	CCDC141 (ENSCPOG00000003955)	ENSCPOG00000032370	ENSCPOG00000030784	ENSCPOG00000038729	ENSCPOG00000034673	ENSCPOG00000036479	PLEKHA3 (ENSCPOG00000003906)	FKBP7 (ENSCPOG00000037159)	PJVK (ENSCPOG00000037882)	ENSCPOG00000003900	OSBPL6 (ENSCPOG00000002816)	RBM45 (ENSCPOG00000000684)	PDE11A (ENSCPOG00000000682)	ENSCPOG00000000681	AGPS (ENSCPOG00000000679) #21	NFE2L2 (ENSCPOG00000031261) #22	ENSCPOG00000004251	ENSCPOG00000027250	MTX2 (ENSCPOG00000011099) #23	HOXD1 (ENSCPOG00000005509)	HOXD3 (ENSCPOG00000034932) #24	HOXD4 (ENSCPOG00000036552) #25	HOXD8 (ENSCPOG00000015005) #26	HOXD9 (ENSCPOG00000015006) #27	HOXD10 (ENSCPOG00000011368) #28	ENSCPOG00000019766 #29	HOXD12 (ENSCPOG00000005496) #30	HOXD13 (ENSCPOG00000006722) #31	EVX2 (ENSCPOG00000006711)	LNPK (ENSCPOG00000010971) #32	ATP5MC3 (ENSCPOG00000040161) #33
Naked mole-rat female	MODERN SPECIES	22	CCDC141 (ENSHGLG00000002888)	TTN (ENSHGLG00000036835)	ENSHGLG00000018641	FKBP7 (ENSHGLG00000019268)	PJVK (ENSHGLG00000011003)	ENSHGLG00000010663	ENSHGLG00000003065	ENSHGLG00000040220	ENSHGLG00000045276	ENSHGLG00000007342	ENSHGLG00000006609	ENSHGLG00000005226	TTC30B (ENSHGLG00000042840)	ENSHGLG00000036841	AGPS (ENSHGLG00000007541) #21	NFE2L2 (ENSHGLG00000006475) #22	HNRNPA3 (ENSHGLG00000005451)	ENSHGLG00000036655	ENSHGLG00000046644	ENSHGLG00000012734	MTX2 (ENSHGLG00000004177) #23	HOXD1 (ENSHGLG00000004072)	HOXD3 (ENSHGLG00000003761) #24	HOXD4 (ENSHGLG00000037842) #25	ENSHGLG00000003577 #26	HOXD10 (ENSHGLG00000033462) #28	HOXD9 (ENSHGLG00000007185) #27	HOXD11 (ENSHGLG00000034527) #29	HOXD12 (ENSHGLG00000005403) #30	HOXD13 (ENSHGLG00000050884) #31	EVX2 (ENSHGLG00000004218)