Rodentia_A	ANCESTRAL SPECIES	20	ENSGT00940000159983	ENSGT00390000002398	ENSGT00390000005197.a.b	ENSGT01100000263563.c.b	ENSGT00390000015965	ENSGT00390000000214.a.b	ENSGT00940000157221	ENSGT00940000160197	ENSGT00940000153404.b ##16	ENSGT00940000153648.b #17	ENSGT00390000013778	ENSGT00940000159709 #18	ENSGT00940000156247 #19	ENSGT00940000157949 #20	ENSGT00900000143434	ENSGT00940000157456 #22	ENSGT00940000163662	ENSGT00940000162884	ENSGT00940000162201	ENSGT00390000010054.b #24	ENSGT00390000017929	ENSGT00940000155358 #25	ENSGT00590000083165 #26	ENSGT00730000111066 #27	ENSGT00940000157489 #28	ENSGT00390000015224.c.b.a.k.b.a #29	ENSGT00390000006234 #30	ENSGT00390000015355 #31	ENSGT00390000018294	ENSGT00670000098059 #33	ENSGT00940000155155 #34
Hystricomorpha	ANCESTRAL SPECIES	26	ENSGT00950000183177.a.a.b	ENSGT00940000159983	ENSGT00390000002398	ENSGT00390000005197.a.b	ENSGT01100000263563.c.b	ENSGT00390000015965	ENSGT00390000000214.a.b	ENSGT00940000157221	ENSGT00940000160197	ENSGT00940000153404.b ##16	ENSGT00940000153648.b #17	ENSGT00390000013778	ENSGT00940000159709 #18	ENSGT00940000156247 #19	ENSGT00940000157949 #20	ENSGT00940000157456 #22	ENSGT00940000163662	ENSGT00940000162884	ENSGT00940000162201	ENSGT00390000010054.b #24	ENSGT00390000017929	ENSGT00940000155358 #25	ENSGT00590000083165 #26	ENSGT00730000111066 #27	ENSGT00940000157489 #28	ENSGT00390000015224.c.b.a.k.b.a #29	ENSGT00390000006234 #30	ENSGT00390000015355 #31	ENSGT00390000018294	ENSGT00670000098059 #33	ENSGT00940000155155 #34
Hystricomorpha_a	ANCESTRAL SPECIES	23	ENSGT00950000183177.a.a.b	ENSGT00940000159983	ENSGT00390000002398	ENSGT00390000005197.a.b	ENSGT01100000263563.c.b	ENSGT00390000015965	ENSGT00390000000214.a.b	ENSGT00940000157221	ENSGT00940000160197	ENSGT00940000153404.b ##16	ENSGT00940000153648.b #17	ENSGT00390000013778	ENSGT00940000159709 #18	ENSGT00940000156247 #19	ENSGT00940000157949 #20	ENSGT00940000157456 #22	ENSGT00940000163662	ENSGT00940000162884	ENSGT00940000162201	ENSGT00390000010054.b #24	ENSGT00390000017929	ENSGT00940000155358 #25	ENSGT00590000083165 #26	ENSGT00730000111066 #27	ENSGT00940000157489 #28	ENSGT00390000015224.c.b.a.k.b.a #29	ENSGT00390000006234 #30	ENSGT00390000015355 #31	ENSGT00390000018294	ENSGT00940000166010 #32	ENSGT00670000098059 #33
Hystricomorpha_b	ANCESTRAL SPECIES	37	ENSGT00950000183177.a.a.b	ENSGT00940000159983	ENSGT00390000002398	ENSGT00390000005197.a.b	ENSGT01100000263563.c.b	ENSGT00390000015965	ENSGT00390000000214.a.b	ENSGT00940000157221	ENSGT00940000160197	ENSGT00940000153404.b ##16	ENSGT00940000153648.b #17	ENSGT00390000013778	ENSGT00940000159709 #18	ENSGT00940000156247 #19	ENSGT00940000157949 #20	ENSGT00940000157456 #22	ENSGT00940000163662	ENSGT00940000162884	ENSGT00940000162201	ENSGT00390000010054.b #24	ENSGT00390000017929	ENSGT00940000155358 #25	ENSGT00590000083165 #26	ENSGT00730000111066 #27	ENSGT00940000157489 #28	ENSGT00390000015224.c.b.a.k.b.a #29	ENSGT00390000006234 #30	ENSGT00390000015355 #31	ENSGT00390000018294	ENSGT00940000166010 #32	ENSGT00670000098059 #33
Degu	MODERN SPECIES	199										ENSODEG00000002273 #16	NWD2 (ENSODEG00000002293) #17	RELL1 (ENSODEG00000002376) #18	ENSODEG00000002408 #19	TBC1D1 (ENSODEG00000002549) #20	ENSODEG00000018891 #21	KLF3 (ENSODEG00000002620) #22	ENSODEG00000002637 #23	FAM114A1 (ENSODEG00000003086) #24	KLHL5 (ENSODEG00000003160) #25	WDR19 (ENSODEG00000003235) #26	RFC1 (ENSODEG00000003452) #27	KLB (ENSODEG00000003829) #28	ENSODEG00000003855 #29	LIAS (ENSODEG00000003971) #30	ENSODEG00000003708 #31	ENSODEG00000003741 #32	UBE2K (ENSODEG00000003840) #33	PDS5A (ENSODEG00000003973) #34	ENSODEG00000019119 #35	N4BP2 (ENSODEG00000004780) #36	ENSODEG00000004818 #37
Long-tailed chinchilla	MODERN SPECIES	150	SLC34A2 (ENSCLAG00000002636)	SEL1L3 (ENSCLAG00000002362)	SMIM20 (ENSCLAG00000002089)	RBPJ (ENSCLAG00000002065)	CCKAR (ENSCLAG00000001729)	TBC1D19 (ENSCLAG00000001699)	STIM2 (ENSCLAG00000002849)	PCDH7 (ENSCLAG00000002605)	ARAP2 (ENSCLAG00000012467)	DTHD1 (ENSCLAG00000011952) ##16	NWD2 (ENSCLAG00000010818) #17	C4orf19 (ENSCLAG00000010706)	RELL1 (ENSCLAG00000010401) #18	PGM2 (ENSCLAG00000010266) #19	TBC1D1 (ENSCLAG00000002236) #20	KLF3 (ENSCLAG00000004459) #22	TLR10 (ENSCLAG00000004336)	TLR1 (ENSCLAG00000017579)	TLR6 (ENSCLAG00000017630)	FAM114A1 (ENSCLAG00000003993) #24	TMEM156 (ENSCLAG00000003928)	KLHL5 (ENSCLAG00000002937) #25	WDR19 (ENSCLAG00000002775) #26	RFC1 (ENSCLAG00000001564) #27	KLB (ENSCLAG00000001476) #28	ENSCLAG00000001418 #29	LIAS (ENSCLAG00000001354) #30	UGDH (ENSCLAG00000001307) #31	SMIM14 (ENSCLAG00000002664)	ENSCLAG00000006068	ENSCLAG00000006013
Guinea pig	MODERN SPECIES	24	RANBP2 (ENSCPOG00000000392)	CCDC138 (ENSCPOG00000000393)	EDAR (ENSCPOG00000011862)	SH3RF3 (ENSCPOG00000001631)	SEPTIN10 (ENSCPOG00000004533)	ENSCPOG00000030940	ENSCPOG00000032789	ENSCPOG00000038259	ENSCPOG00000033829	ENSCPOG00000038611	NWD2 (ENSCPOG00000008345) #17	C4orf19 (ENSCPOG00000035167)	RELL1 (ENSCPOG00000009761) #18	PGM2 (ENSCPOG00000013611) #19	TBC1D1 (ENSCPOG00000013615) #20	KLF3 (ENSCPOG00000030471) #22	TLR10 (ENSCPOG00000015283)	TLR1 (ENSCPOG00000012205)	TLR6 (ENSCPOG00000005088)	FAM114A1 (ENSCPOG00000013554) #24	TMEM156 (ENSCPOG00000013560)	KLHL5 (ENSCPOG00000004478) #25	WDR19 (ENSCPOG00000004240) #26	RFC1 (ENSCPOG00000004248) #27	KLB (ENSCPOG00000004539) #28	ENSCPOG00000004543 #29	LIAS (ENSCPOG00000004547) #30	UGDH (ENSCPOG00000004550) #31	ENSCPOG00000039840 #32	UBE2K (ENSCPOG00000014798) #33	ENSCPOG00000023886
Naked mole-rat female	MODERN SPECIES	1	ENSHGLG00000037767	NWD2 (ENSHGLG00000000298) #17	ENSHGLG00000040844	ENSHGLG00000040492	ENSHGLG00000043452 #18	PGM2 (ENSHGLG00000001842) #19	ENSHGLG00000002323	ENSHGLG00000003063	ENSHGLG00000000606	ENSHGLG00000019811	ENSHGLG00000033549	ENSHGLG00000034348	ENSHGLG00000043517 #20	ENSHGLG00000044532 #20	ENSHGLG00000019798	KLF3 (ENSHGLG00000049437) #22	ENSHGLG00000000855	ENSHGLG00000019856	ENSHGLG00000001742	TLR6 (ENSHGLG00000050436)	FAM114A1 (ENSHGLG00000002258) #24	TMEM156 (ENSHGLG00000002626)	ENSHGLG00000033489	KLHL5 (ENSHGLG00000001944) #25	WDR19 (ENSHGLG00000002756) #26	ENSHGLG00000002546 #27	ENSHGLG00000032109	KLB (ENSHGLG00000002389) #28	ENSHGLG00000002318 #29	LIAS (ENSHGLG00000002264) #30	UGDH (ENSHGLG00000002204) #31
Sciuridae	ANCESTRAL SPECIES	19	ENSGT00940000159983	ENSGT00390000002398	ENSGT00390000005197.a.b	ENSGT01100000263563.c.b	ENSGT00390000015965	ENSGT00390000000214.a.b	ENSGT00940000157221	ENSGT00940000160197	ENSGT00940000153404.b ##16	ENSGT00940000153648.b #17	ENSGT00390000013778	ENSGT00940000159709 #18	ENSGT00940000156247 #19	ENSGT00940000157949 #20	ENSGT00900000143434	ENSGT00940000157456 #22	ENSGT00940000163662	ENSGT00940000162884	ENSGT00940000162201	ENSGT00990000210295	ENSGT00390000010054.b #24	ENSGT00390000017929	ENSGT00940000155358 #25	ENSGT00590000083165 #26	ENSGT00730000111066 #27	ENSGT00940000157489 #28	ENSGT00390000015224.c.b.a.k.a.a.b ##29	ENSGT00390000006234 #30	ENSGT00390000015355 #31	ENSGT00390000018294	ENSGT00670000098059 #33
Marmotini	ANCESTRAL SPECIES	26	ENSGT00940000159983	ENSGT00390000002398	ENSGT00390000005197.a.b	ENSGT01100000263563.c.b	ENSGT00390000015965	ENSGT00390000000214.a.b	ENSGT00940000157221	ENSGT00940000160197	ENSGT00940000153404.b ##16	ENSGT00940000153648.b #17	ENSGT00390000013778	ENSGT00940000159709 #18	ENSGT00940000156247 #19	ENSGT00940000157949 #20	ENSGT00900000143434	ENSGT00940000157456 #22	ENSGT00940000163662	ENSGT00940000162884	ENSGT00940000162201	ENSGT00390000010054.b #24	ENSGT00390000017929	ENSGT00940000155358 #25	ENSGT00590000083165 #26	ENSGT00730000111066 #27	ENSGT00940000157489 #28	ENSGT00390000015224.c.b.a.k.a.a.b ##29	ENSGT00390000015224.c.b.a.l ##29	ENSGT00390000006234 #30	ENSGT00390000015355 #31	ENSGT00390000018294.k.a	ENSGT00670000098059 #33
Marmotini_b	ANCESTRAL SPECIES	48						ENSGT01030000234945	ENSGT00940000157221	ENSGT00950000182841.b.a.a.b.b.p.a	ENSGT00940000160197	ENSGT00940000153404.b ##16	ENSGT00940000153648.b #17	ENSGT00390000013778	ENSGT00940000159709 #18	ENSGT00940000156247 #19	ENSGT00940000157949 #20	ENSGT00940000157456 #22	ENSGT00940000163662	ENSGT00940000162884	ENSGT00940000162201	ENSGT00390000010054.b #24	ENSGT00390000017929	ENSGT00940000155358 #25	ENSGT00590000083165 #26	ENSGT00730000111066 #27	ENSGT00940000157489 #28	ENSGT00390000015224.c.b.a.k.a.a.b ##29	ENSGT00390000006234 #30	ENSGT00390000015355 #31	ENSGT00390000018294.k.a	ENSGT00670000098059 #33	ENSGT00940000155155 #34
Arctic ground squirrel	MODERN SPECIES	2						ENSUPAG00010016796	PCDH7 (ENSUPAG00010016798)	ENSUPAG00010016821	ARAP2 (ENSUPAG00010016832)	DTHD1 (ENSUPAG00010016950) ##16	NWD2 (ENSUPAG00010016964) #17	C4orf19 (ENSUPAG00010016983)	RELL1 (ENSUPAG00010016993) #18	PGM2 (ENSUPAG00010017012) #19	TBC1D1 (ENSUPAG00010017027) #20	KLF3 (ENSUPAG00010017209) #22	TLR10 (ENSUPAG00010017218)	TLR1 (ENSUPAG00010017233)	TLR6 (ENSUPAG00010017235)	FAM114A1 (ENSUPAG00010017240) #24	TMEM156 (ENSUPAG00010017254)	KLHL5 (ENSUPAG00010017266) #25	WDR19 (ENSUPAG00010017295) #26	RFC1 (ENSUPAG00010017359) #27	KLB (ENSUPAG00010018497) #28	ENSUPAG00010018508 ##29	LIAS (ENSUPAG00010018541) #30	UGDH (ENSUPAG00010018571) #31	ENSUPAG00010018587	UBE2K (ENSUPAG00010018605) #33	PDS5A (ENSUPAG00010018683) #34
Squirrel	MODERN SPECIES	82						PCDH7 (ENSSTOG00000009192)	ENSSTOG00000029131	ENSSTOG00000028351	ARAP2 (ENSSTOG00000019405)	DTHD1 (ENSSTOG00000003003) ##16	NWD2 (ENSSTOG00000019543) #17	C4orf19 (ENSSTOG00000003425)	RELL1 (ENSSTOG00000001374) #18	PGM2 (ENSSTOG00000008176) #19	ENSSTOG00000020687 #20	KLF3 (ENSSTOG00000010881) #22	TLR1 (ENSSTOG00000021581)	TLR6 (ENSSTOG00000025480)	FAM114A1 (ENSSTOG00000001171) #24	TMEM156 (ENSSTOG00000004246)	KLHL5 (ENSSTOG00000007013) #25	WDR19 (ENSSTOG00000007054) #26	RFC1 (ENSSTOG00000007088) #27	KLB (ENSSTOG00000002069) #28	ENSSTOG00000002077 ##29	LIAS (ENSSTOG00000002082) #30	UGDH (ENSSTOG00000002096) #31	SMIM14 (ENSSTOG00000034581)	UBE2K (ENSSTOG00000012447) #33	PDS5A (ENSSTOG00000012451) #34	N4BP2 (ENSSTOG00000020354) #36
Alpin marmot	MODERN SPECIES	9	SMIM20 (ENSMMMG00000017386)	RBPJ (ENSMMMG00000017407)	CCKAR (ENSMMMG00000017438)	STIM2 (ENSMMMG00000017470)	ENSMMMG00000017503	ENSMMMG00000017519	ARAP2 (ENSMMMG00000017527)	DTHD1 (ENSMMMG00000017544) ##16	NWD2 (ENSMMMG00000017559) #17	ENSMMMG00000017574	C4orf19 (ENSMMMG00000017577)	RELL1 (ENSMMMG00000017587) #18	PGM2 (ENSMMMG00000017606) #19	TBC1D1 (ENSMMMG00000017620) #20	ENSMMMG00000017716	KLF3 (ENSMMMG00000017721) #22	TLR10 (ENSMMMG00000017725)	TLR1 (ENSMMMG00000017739)	TLR6 (ENSMMMG00000017761)	FAM114A1 (ENSMMMG00000017765) #24	TMEM156 (ENSMMMG00000017773)	KLHL5 (ENSMMMG00000017784) #25	WDR19 (ENSMMMG00000017829) #26	RFC1 (ENSMMMG00000017905) #27	KLB (ENSMMMG00000017911) #28	ENSMMMG00000017920	ENSMMMG00000017936 ##29	LIAS (ENSMMMG00000017957) #30	UGDH (ENSMMMG00000017978) #31	ENSMMMG00000018002	UBE2K (ENSMMMG00000018022) #33
Eurasian red squirrel	DUPLICATION
Eurasian red squirrel	MODERN SPECIES	18	ENSSVLG00005011695	ENSSVLG00005011631	ENSSVLG00005011572	PCDH7 (ENSSVLG00005011515)	ENSSVLG00005011423	ARAP2 (ENSSVLG00005010880)	DTHD1 (ENSSVLG00005010509) ##16	ENSSVLG00005010441 #17	ENSSVLG00005010374 #17	C4orf19 (ENSSVLG00005010352)	RELL1 (ENSSVLG00005010318) #18	ENSSVLG00005010293	PGM2 (ENSSVLG00005010275) #19	TBC1D1 (ENSSVLG00005010172) #20	ENSSVLG00005010135	ENSSVLG00005010086 #22	ENSSVLG00005010070	TLR10 (ENSSVLG00005010051)	TLR1 (ENSSVLG00005010028)	TLR6 (ENSSVLG00005009982)	ENSSVLG00005009942	TMEM156 (ENSSVLG00005009879)	KLHL5 (ENSSVLG00005009665) #25	WDR19 (ENSSVLG00005009349) #26	RFC1 (ENSSVLG00005009235) #27	KLB (ENSSVLG00005009120) #28	ENSSVLG00005009038 ##29	LIAS (ENSSVLG00005008848) #30	UGDH (ENSSVLG00005008677) #31	ENSSVLG00005008623	ENSSVLG00005008568
Eurasian red squirrel	MODERN SPECIES	57																ENSSVLG00005020536 #22	ENSSVLG00005020551	ENSSVLG00005020569	ENSSVLG00005020585	ENSSVLG00005020631	ENSSVLG00005020710