Rodentia_A	ANCESTRAL SPECIES	8	ENSGT00390000004692.d.b	ENSGT00940000169249	ENSGT00390000002403	ENSGT00620000087993.a.a	ENSGT00390000015655.b	ENSGT00390000003223	ENSGT00940000162914	ENSGT00940000156535	ENSGT00940000157334	ENSGT00940000160831	ENSGT00530000063353.a.b.a	ENSGT01050000244879.b.a.b.b	ENSGT00940000158416	ENSGT00640000091497.b	ENSGT01050000244950.a.a.b	ENSGT00390000008232 #22	ENSGT00500000044869.a.a #23	ENSGT00940000156772 #24	ENSGT00390000009168	ENSGT01030000234610.b.b	ENSGT00390000003880.b.b	ENSGT01030000234610.a.b	ENSGT01030000234610.a.a	ENSGT00390000006522.b	ENSGT00940000162821	ENSGT00940000162991	ENSGT00940000154317.a.b	ENSGT00940000155676	ENSGT00940000163953	ENSGT00940000156987	ENSGT00940000158991
Sciuridae	ANCESTRAL SPECIES	1	ENSGT00390000004692.d.b	ENSGT00940000169249	ENSGT00390000002403	ENSGT00620000087993.a.a	ENSGT00390000015655.b	ENSGT00390000003223	ENSGT00940000162914	ENSGT00940000156535	ENSGT00940000157334	ENSGT00940000160831	ENSGT00530000063353.a.b.a	ENSGT01050000244879.b.a.b.b	ENSGT00940000158416	ENSGT00640000091497.b	ENSGT01050000244950.a.a.b	ENSGT00390000008232 #22	ENSGT00500000044869.a.a #23	ENSGT00940000156772.x ##24	ENSGT00940000156772.w #24	ENSGT00390000009168	ENSGT01030000234610.b.b	ENSGT00390000003880.b.b	ENSGT01030000234610.a.b	ENSGT01030000234610.a.a	ENSGT00390000006522.b	ENSGT00940000162821	ENSGT00940000162991	ENSGT00940000163953	ENSGT00940000155676	ENSGT00940000154317.a.b	ENSGT00940000156987
Marmotini	ANCESTRAL SPECIES	11	ENSGT01090000260080.b.a	ENSGT00390000002403	ENSGT00620000087993.a.a	ENSGT00390000015655.b	ENSGT00390000003223	ENSGT00940000162914	ENSGT01100000266009	ENSGT00940000156535	ENSGT00940000157334	ENSGT00940000160831	ENSGT00530000063353.a.b.a	ENSGT01050000244879.b.a.b.b	ENSGT00940000158416	ENSGT00640000091497.b	ENSGT01050000244950.a.a.b	ENSGT00390000008232 #22	ENSGT00500000044869.a.a #23	ENSGT00940000156772.x ##24	ENSGT00940000156772.w #24	ENSGT00390000009168	ENSGT01030000234610.b.b	ENSGT01030000234610.a.b	ENSGT00390000003880.b.b	ENSGT01030000234610.a.a	ENSGT00390000006522.b	ENSGT00940000162821	ENSGT00940000162991	ENSGT00940000154317.a.b	ENSGT00940000155676	ENSGT00940000163953	ENSGT00940000156987
Marmotini_b	ANCESTRAL SPECIES	178	ENSGT01090000260080.b.a	ENSGT00390000002403	ENSGT00620000087993.a.a	ENSGT00390000015655.b	ENSGT00390000003223	ENSGT00940000162914	ENSGT01100000266009	ENSGT00940000156535	ENSGT00940000157334	ENSGT00940000160831	ENSGT00530000063353.a.b.a	ENSGT01050000244879.b.a.b.b	ENSGT00940000158416	ENSGT00640000091497.b	ENSGT01050000244950.a.a.b	ENSGT00390000008232 #22	ENSGT00500000044869.a.a #23
Squirrel	MODERN SPECIES	604																ZUP1 (ENSSTOG00000012338) #22	RSPH4A (ENSSTOG00000033876) #23	ENSSTOG00000025159 #24
Arctic ground squirrel	MODERN SPECIES	133	MCM9 (ENSUPAG00010021995)	PLN (ENSUPAG00010021993)	CEP85L (ENSUPAG00010021985)	SLC35F1 (ENSUPAG00010021982)	NUS1 (ENSUPAG00010021980)	ENSUPAG00010021978	ENSUPAG00010021976	GOPC (ENSUPAG00010021972)	DCBLD1 (ENSUPAG00010021968)	ROS1 (ENSUPAG00010021948)	VGLL2 (ENSUPAG00010021945)	RFX6 (ENSUPAG00010021936)	GPRC6A (ENSUPAG00010021931)	FAM162B (ENSUPAG00010021928)	KPNA5 (ENSUPAG00010021924)	ENSUPAG00010021922 #22
Alpin marmot	MODERN SPECIES	2	ENSMMMG00000016017	PLN (ENSMMMG00000016004)	CEP85L (ENSMMMG00000015976)	SLC35F1 (ENSMMMG00000015966)	NUS1 (ENSMMMG00000015950)	ENSMMMG00000015941	ENSMMMG00000015939	GOPC (ENSMMMG00000015918)	DCBLD1 (ENSMMMG00000015903)	ROS1 (ENSMMMG00000015799)	VGLL2 (ENSMMMG00000015787)	RFX6 (ENSMMMG00000015641)	GPRC6A (ENSMMMG00000015597)	FAM162B (ENSMMMG00000015589)	KPNA5 (ENSMMMG00000015469)	ZUP1 (ENSMMMG00000015434) #22	RSPH4A (ENSMMMG00000015424) #23	ENSMMMG00000015402 ##24	ENSMMMG00000015383 #24	ENSMMMG00000015375 #24	RWDD1 (ENSMMMG00000015368)	CALHM4 (ENSMMMG00000015364)	CALHM5 (ENSMMMG00000015357)	CALHM6 (ENSMMMG00000015349)	DSE (ENSMMMG00000015341)	TSPYL4 (ENSMMMG00000015326)	ENSMMMG00000015321	ENSMMMG00000015316	FRK (ENSMMMG00000015306)	HS3ST5 (ENSMMMG00000015290)	HDAC2 (ENSMMMG00000015264)
Eurasian red squirrel	MODERN SPECIES	16	ENSSVLG00005007753	CEP85L (ENSSVLG00005007817)	ENSSVLG00005008007	PLN (ENSSVLG00005008023)	ENSSVLG00005008035	SLC35F1 (ENSSVLG00005008070)	ENSSVLG00005008163	ENSSVLG00005008200	GOPC (ENSSVLG00005008267)	ROS1 (ENSSVLG00005008411)	VGLL2 (ENSSVLG00005008910)	RFX6 (ENSSVLG00005008988)	GPRC6A (ENSSVLG00005009132)	FAM162B (ENSSVLG00005009241)	KPNA5 (ENSSVLG00005009288)	ZUP1 (ENSSVLG00005009321) #22	RSPH4A (ENSSVLG00005009389) #23	ENSSVLG00005009507 #24	ENSSVLG00005009556	CALHM4 (ENSSVLG00005009602)	TRAPPC3L (ENSSVLG00005009643)	CALHM5 (ENSSVLG00005009693)	CALHM6 (ENSSVLG00005009719)	DSE (ENSSVLG00005009768)	TSPYL1 (ENSSVLG00005009835)	TSPYL4 (ENSSVLG00005009852)	NT5DC1 (ENSSVLG00005009872)	COL10A1 (ENSSVLG00005009901)	FRK (ENSSVLG00005009937)	ENSSVLG00005010009	ENSSVLG00005010037
Hystricomorpha	ANCESTRAL SPECIES	39	ENSGT00390000004692.d.b	ENSGT01090000260080.b.a	ENSGT00390000002403	ENSGT00620000087993.a.a	ENSGT00390000015655.b	ENSGT00390000003223	ENSGT00940000162914	ENSGT00940000156535	ENSGT00940000157334	ENSGT00940000160831	ENSGT00530000063353.a.b.a	ENSGT01050000244879.b.a.b.b	ENSGT00940000158416	ENSGT00640000091497.b	ENSGT01050000244950.a.a.b	ENSGT00390000008232 #22	ENSGT00500000044869.a.a #23	ENSGT00940000155081.D	ENSGT00390000002581	ENSGT00940000158276	ENSGT00940000157935	ENSGT00940000157565	ENSGT00390000009155	ENSGT00940000155884	ENSGT00940000159583	ENSGT00390000018730.B	ENSGT00940000155134	ENSGT00940000155933.b.a	ENSGT00940000154550.a.f	ENSGT00390000004660.C.a.a.b	ENSGT00950000182984.a
Hystricomorpha_a	ANCESTRAL SPECIES	30																ENSGT00390000008232 #22	ENSGT00500000044869.a.a #23	ENSGT01050000244950.a.a.b	ENSGT00640000091497.b	ENSGT00940000158416	ENSGT01050000244879.b.a.b.b	ENSGT00530000063353.a.b.a	ENSGT00940000160831	ENSGT00940000157334	ENSGT00940000156535	ENSGT00940000162914	ENSGT00390000003223	ENSGT00390000015655.b	ENSGT00620000087993.a.a	ENSGT00390000002403	ENSGT01090000260080.b.a
Hystricomorpha_b	ANCESTRAL SPECIES	29																ENSGT00390000008232 #22	ENSGT00500000044869.a.a #23	ENSGT01050000244950.a.a.b	ENSGT00940000158416	ENSGT01050000244879.b.a.b.b	ENSGT00530000063353.a.b.a	ENSGT00940000160831	ENSGT00940000157334	ENSGT00940000156535	ENSGT00390000003223	ENSGT00390000015655.b	ENSGT00620000087993.a.a	ENSGT00390000002403	ENSGT01090000260080.b.a	ENSGT00390000004692.d.b	ENSGT00530000063669.b
Long-tailed chinchilla	MODERN SPECIES	143																ZUP1 (ENSCLAG00000007886) #22	RSPH4A (ENSCLAG00000009580) #23	KPNA5 (ENSCLAG00000010089)	GPRC6A (ENSCLAG00000007059)	RFX6 (ENSCLAG00000008090)	ROS1 (ENSCLAG00000007326)	ENSCLAG00000007845	GOPC (ENSCLAG00000008237)	NUS1 (ENSCLAG00000010652)	SLC35F1 (ENSCLAG00000008410)	CEP85L (ENSCLAG00000010088)	PLN (ENSCLAG00000007403)	MCM9 (ENSCLAG00000009689)	ASF1A (ENSCLAG00000013483)	FAM184A (ENSCLAG00000006832)	MAN1A1 (ENSCLAG00000007613)
Degu	MODERN SPECIES	75																ZUP1 (ENSODEG00000004926) #22	RSPH4A (ENSODEG00000005270) #23	ENSODEG00000019159	RFX6 (ENSODEG00000006706)	VGLL2 (ENSODEG00000005506)	ROS1 (ENSODEG00000006047)	ENSODEG00000004793	GOPC (ENSODEG00000005332)	NUS1 (ENSODEG00000005194)	ENSODEG00000019196	SLC35F1 (ENSODEG00000005040)	CEP85L (ENSODEG00000005733)	PLN (ENSODEG00000019260)	MCM9 (ENSODEG00000005446)	ENSODEG00000005478	FAM184A (ENSODEG00000004943)
Guinea pig	MODERN SPECIES	1	FZD3 (ENSCPOG00000009989)	FBXO16 (ENSCPOG00000019834)	ENSCPOG00000034090	AGPAT5 (ENSCPOG00000006565)	MCPH1 (ENSCPOG00000015508)	ANGPT2 (ENSCPOG00000030082)	CSMD1 (ENSCPOG00000015501)	MYOM2 (ENSCPOG00000002402)	KBTBD11 (ENSCPOG00000026453)	ARHGEF10 (ENSCPOG00000022520)	CLN8 (ENSCPOG00000035105)	DLGAP2 (ENSCPOG00000011579)	ENSCPOG00000013031	TDRP (ENSCPOG00000035181)	FBXO25 (ENSCPOG00000008110)	ZUP1 (ENSCPOG00000000534) #22	RSPH4A (ENSCPOG00000000533) #23	KPNA5 (ENSCPOG00000035973)	FAM162B (ENSCPOG00000006389)	RFX6 (ENSCPOG00000015023)	VGLL2 (ENSCPOG00000021559)	ENSCPOG00000012998	DCBLD1 (ENSCPOG00000002737)	GOPC (ENSCPOG00000010125)	ENSCPOG00000027426	ENSCPOG00000031032	NUS1 (ENSCPOG00000039822)	SLC35F1 (ENSCPOG00000029995)	ENSCPOG00000024368	TPD52L1 (ENSCPOG00000013150)	HDDC2 (ENSCPOG00000013151)
Naked mole-rat female	MODERN SPECIES	30	ENSHGLG00000000614	ENSHGLG00000042162	ENSHGLG00000000399	ENSHGLG00000009321	ENSHGLG00000009379	ENSHGLG00000048422	ENSHGLG00000004775	ENSHGLG00000036302	ENSHGLG00000036746	ENSHGLG00000013205	VGLL2 (ENSHGLG00000048393)	RFX6 (ENSHGLG00000019573)	GPRC6A (ENSHGLG00000036750)	ENSHGLG00000008946	KPNA5 (ENSHGLG00000007645)	ENSHGLG00000009896 #22	ENSHGLG00000002525 #23	ENSHGLG00000049438	ENSHGLG00000035661	ENSHGLG00000050402	ENSHGLG00000005874	ENSHGLG00000016052	ENSHGLG00000035693	ENSHGLG00000032597	ABHD16A (ENSHGLG00000011099)	CSNK2B (ENSHGLG00000011657)	GPANK1 (ENSHGLG00000046532)	APOM (ENSHGLG00000012211)	C6orf47 (ENSHGLG00000048233)	BAG6 (ENSHGLG00000012423)	ENSHGLG00000032997