Rodentia_A ANCESTRAL SPECIES 20 ENSGT00940000159983 ENSGT00390000002398 ENSGT00390000005197.a.b ENSGT01100000263563.c.b ENSGT00390000015965 ENSGT00390000000214.a.b ENSGT00940000157221 ENSGT00940000160197 ENSGT00940000153404.b ENSGT00940000153648.b #8 ENSGT00390000013778 #9 ENSGT00940000159709 #11 ENSGT00940000156247 #12 ENSGT00940000157949 #19 ENSGT00900000143434 ENSGT00940000157456 #22 ENSGT00940000163662 ENSGT00940000162884 #24 ENSGT00940000162201 #26 ENSGT00390000010054.b #27 ENSGT00390000017929 #28 ENSGT00940000155358 #30 ENSGT00590000083165 #31 ENSGT00730000111066 #32 ENSGT00940000157489 #34 ENSGT00390000015224.c.b.a.k.b.a #35 ENSGT00390000006234 #36 ENSGT00390000015355 #37 ENSGT00390000018294 ENSGT00670000098059 ENSGT00940000155155 Hystricomorpha ANCESTRAL SPECIES 26 ENSGT00950000183177.a.a.b ENSGT00940000159983 ENSGT00390000002398 ENSGT00390000005197.a.b ENSGT01100000263563.c.b ENSGT00390000015965 ENSGT00390000000214.a.b ENSGT00940000157221 ENSGT00940000160197 ENSGT00940000153404.b ENSGT00940000153648.b #8 ENSGT00390000013778 #9 ENSGT00940000159709 #11 ENSGT00940000156247 #12 ENSGT00940000157949 #19 ENSGT00940000157456 #22 ENSGT00940000163662 ENSGT00940000162884 #24 ENSGT00940000162201 #26 ENSGT00390000010054.b #27 ENSGT00390000017929 #28 ENSGT00940000155358 #30 ENSGT00590000083165 #31 ENSGT00730000111066 #32 ENSGT00940000157489 #34 ENSGT00390000015224.c.b.a.k.b.a #35 ENSGT00390000006234 #36 ENSGT00390000015355 #37 ENSGT00390000018294 ENSGT00670000098059 ENSGT00940000155155 Naked mole-rat female MODERN SPECIES 1 ENSHGLG00000037767 #7 NWD2 (ENSHGLG00000000298) #8 ENSHGLG00000040844 #9 ENSHGLG00000040492 #10 ENSHGLG00000043452 #11 PGM2 (ENSHGLG00000001842) #12 ENSHGLG00000002323 #13 ENSHGLG00000003063 #14 ENSHGLG00000000606 #15 ENSHGLG00000019811 #16 ENSHGLG00000033549 #17 ENSHGLG00000034348 #18 ENSHGLG00000043517 #19 ENSHGLG00000044532 #20 ENSHGLG00000019798 #21 KLF3 (ENSHGLG00000049437) #22 ENSHGLG00000000855 #23 ENSHGLG00000019856 #24 ENSHGLG00000001742 #25 TLR6 (ENSHGLG00000050436) #26 FAM114A1 (ENSHGLG00000002258) #27 TMEM156 (ENSHGLG00000002626) #28 ENSHGLG00000033489 #29 KLHL5 (ENSHGLG00000001944) #30 WDR19 (ENSHGLG00000002756) #31 ENSHGLG00000002546 #32 ENSHGLG00000032109 #33 KLB (ENSHGLG00000002389) #34 ENSHGLG00000002318 #35 LIAS (ENSHGLG00000002264) #36 UGDH (ENSHGLG00000002204) #37 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 ENSGT00940000153648.b #8 ENSGT00390000013778 #9 ENSGT00940000159709 #11 ENSGT00940000156247 #12 ENSGT00940000157949 #19 ENSGT00940000157456 #22 ENSGT00940000163662 ENSGT00940000162884 #24 ENSGT00940000162201 #26 ENSGT00390000010054.b #27 ENSGT00390000017929 #28 ENSGT00940000155358 #30 ENSGT00590000083165 #31 ENSGT00730000111066 #32 ENSGT00940000157489 #34 ENSGT00390000015224.c.b.a.k.b.a #35 ENSGT00390000006234 #36 ENSGT00390000015355 #37 ENSGT00390000018294 ENSGT00940000166010 ENSGT00670000098059 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 ENSGT00940000153648.b #8 ENSGT00390000013778 #9 ENSGT00940000159709 #11 ENSGT00940000156247 #12 ENSGT00940000157949 #19 ENSGT00940000157456 #22 ENSGT00940000163662 ENSGT00940000162884 #24 ENSGT00940000162201 #26 ENSGT00390000010054.b #27 ENSGT00390000017929 #28 ENSGT00940000155358 #30 ENSGT00590000083165 #31 ENSGT00730000111066 #32 ENSGT00940000157489 #34 ENSGT00390000015224.c.b.a.k.b.a #35 ENSGT00390000006234 #36 ENSGT00390000015355 #37 ENSGT00390000018294 ENSGT00940000166010 ENSGT00670000098059 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) NWD2 (ENSCLAG00000010818) #8 C4orf19 (ENSCLAG00000010706) #9 RELL1 (ENSCLAG00000010401) #11 PGM2 (ENSCLAG00000010266) #12 TBC1D1 (ENSCLAG00000002236) #19 KLF3 (ENSCLAG00000004459) #22 TLR10 (ENSCLAG00000004336) TLR1 (ENSCLAG00000017579) #24 TLR6 (ENSCLAG00000017630) #26 FAM114A1 (ENSCLAG00000003993) #27 TMEM156 (ENSCLAG00000003928) #28 KLHL5 (ENSCLAG00000002937) #30 WDR19 (ENSCLAG00000002775) #31 RFC1 (ENSCLAG00000001564) #32 KLB (ENSCLAG00000001476) #34 ENSCLAG00000001418 #35 LIAS (ENSCLAG00000001354) #36 UGDH (ENSCLAG00000001307) #37 SMIM14 (ENSCLAG00000002664) ENSCLAG00000006068 ENSCLAG00000006013 Degu MODERN SPECIES 199 ENSODEG00000002273 NWD2 (ENSODEG00000002293) #8 RELL1 (ENSODEG00000002376) #11 ENSODEG00000002408 #12 TBC1D1 (ENSODEG00000002549) #19 ENSODEG00000018891 KLF3 (ENSODEG00000002620) #22 ENSODEG00000002637 FAM114A1 (ENSODEG00000003086) #27 KLHL5 (ENSODEG00000003160) #30 WDR19 (ENSODEG00000003235) #31 RFC1 (ENSODEG00000003452) #32 KLB (ENSODEG00000003829) #34 ENSODEG00000003855 #35 LIAS (ENSODEG00000003971) #36 ENSODEG00000003708 #37 ENSODEG00000003741 UBE2K (ENSODEG00000003840) PDS5A (ENSODEG00000003973) ENSODEG00000019119 N4BP2 (ENSODEG00000004780) ENSODEG00000004818 Guinea pig MODERN SPECIES 24 RANBP2 (ENSCPOG00000000392) CCDC138 (ENSCPOG00000000393) EDAR (ENSCPOG00000011862) SH3RF3 (ENSCPOG00000001631) SEPTIN10 (ENSCPOG00000004533) ENSCPOG00000030940 ENSCPOG00000032789 ENSCPOG00000038259 ENSCPOG00000033829 ENSCPOG00000038611 NWD2 (ENSCPOG00000008345) #8 C4orf19 (ENSCPOG00000035167) #9 RELL1 (ENSCPOG00000009761) #11 PGM2 (ENSCPOG00000013611) #12 TBC1D1 (ENSCPOG00000013615) #19 KLF3 (ENSCPOG00000030471) #22 TLR10 (ENSCPOG00000015283) TLR1 (ENSCPOG00000012205) #24 TLR6 (ENSCPOG00000005088) #26 FAM114A1 (ENSCPOG00000013554) #27 TMEM156 (ENSCPOG00000013560) #28 KLHL5 (ENSCPOG00000004478) #30 WDR19 (ENSCPOG00000004240) #31 RFC1 (ENSCPOG00000004248) #32 KLB (ENSCPOG00000004539) #34 ENSCPOG00000004543 #35 LIAS (ENSCPOG00000004547) #36 UGDH (ENSCPOG00000004550) #37 ENSCPOG00000039840 UBE2K (ENSCPOG00000014798) ENSCPOG00000023886 Sciuridae ANCESTRAL SPECIES 19 ENSGT00940000159983 ENSGT00390000002398 ENSGT00390000005197.a.b ENSGT01100000263563.c.b ENSGT00390000015965 ENSGT00390000000214.a.b ENSGT00940000157221 ENSGT00940000160197 ENSGT00940000153404.b ENSGT00940000153648.b #8 ENSGT00390000013778 #9 ENSGT00940000159709 #11 ENSGT00940000156247 #12 ENSGT00940000157949 #19 ENSGT00900000143434 ENSGT00940000157456 #22 ENSGT00940000163662 ENSGT00940000162884 #24 ENSGT00940000162201 #26 ENSGT00990000210295 ENSGT00390000010054.b #27 ENSGT00390000017929 #28 ENSGT00940000155358 #30 ENSGT00590000083165 #31 ENSGT00730000111066 #32 ENSGT00940000157489 #34 ENSGT00390000015224.c.b.a.k.a.a.b ##35 ENSGT00390000006234 #36 ENSGT00390000015355 #37 ENSGT00390000018294 ENSGT00670000098059 Marmotini ANCESTRAL SPECIES 26 ENSGT00940000159983 ENSGT00390000002398 ENSGT00390000005197.a.b ENSGT01100000263563.c.b ENSGT00390000015965 ENSGT00390000000214.a.b ENSGT00940000157221 ENSGT00940000160197 ENSGT00940000153404.b ENSGT00940000153648.b #8 ENSGT00390000013778 #9 ENSGT00940000159709 #11 ENSGT00940000156247 #12 ENSGT00940000157949 #19 ENSGT00900000143434 ENSGT00940000157456 #22 ENSGT00940000163662 ENSGT00940000162884 #24 ENSGT00940000162201 #26 ENSGT00390000010054.b #27 ENSGT00390000017929 #28 ENSGT00940000155358 #30 ENSGT00590000083165 #31 ENSGT00730000111066 #32 ENSGT00940000157489 #34 ENSGT00390000015224.c.b.a.k.a.a.b ##35 ENSGT00390000015224.c.b.a.l ##35 ENSGT00390000006234 #36 ENSGT00390000015355 #37 ENSGT00390000018294.k.a ENSGT00670000098059 Marmotini_b ANCESTRAL SPECIES 48 ENSGT01030000234945 ENSGT00940000157221 ENSGT00950000182841.b.a.a.b.b.p.a ENSGT00940000160197 ENSGT00940000153404.b ENSGT00940000153648.b #8 ENSGT00390000013778 #9 ENSGT00940000159709 #11 ENSGT00940000156247 #12 ENSGT00940000157949 #19 ENSGT00940000157456 #22 ENSGT00940000163662 ENSGT00940000162884 #24 ENSGT00940000162201 #26 ENSGT00390000010054.b #27 ENSGT00390000017929 #28 ENSGT00940000155358 #30 ENSGT00590000083165 #31 ENSGT00730000111066 #32 ENSGT00940000157489 #34 ENSGT00390000015224.c.b.a.k.a.a.b ##35 ENSGT00390000006234 #36 ENSGT00390000015355 #37 ENSGT00390000018294.k.a ENSGT00670000098059 ENSGT00940000155155 Arctic ground squirrel MODERN SPECIES 2 ENSUPAG00010016796 PCDH7 (ENSUPAG00010016798) ENSUPAG00010016821 ARAP2 (ENSUPAG00010016832) DTHD1 (ENSUPAG00010016950) NWD2 (ENSUPAG00010016964) #8 C4orf19 (ENSUPAG00010016983) #9 RELL1 (ENSUPAG00010016993) #11 PGM2 (ENSUPAG00010017012) #12 TBC1D1 (ENSUPAG00010017027) #19 KLF3 (ENSUPAG00010017209) #22 TLR10 (ENSUPAG00010017218) TLR1 (ENSUPAG00010017233) #24 TLR6 (ENSUPAG00010017235) #26 FAM114A1 (ENSUPAG00010017240) #27 TMEM156 (ENSUPAG00010017254) #28 KLHL5 (ENSUPAG00010017266) #30 WDR19 (ENSUPAG00010017295) #31 RFC1 (ENSUPAG00010017359) #32 KLB (ENSUPAG00010018497) #34 ENSUPAG00010018508 ##35 LIAS (ENSUPAG00010018541) #36 UGDH (ENSUPAG00010018571) #37 ENSUPAG00010018587 UBE2K (ENSUPAG00010018605) PDS5A (ENSUPAG00010018683) Squirrel MODERN SPECIES 82 PCDH7 (ENSSTOG00000009192) ENSSTOG00000029131 ENSSTOG00000028351 ARAP2 (ENSSTOG00000019405) DTHD1 (ENSSTOG00000003003) NWD2 (ENSSTOG00000019543) #8 C4orf19 (ENSSTOG00000003425) #9 RELL1 (ENSSTOG00000001374) #11 PGM2 (ENSSTOG00000008176) #12 ENSSTOG00000020687 #19 KLF3 (ENSSTOG00000010881) #22 TLR1 (ENSSTOG00000021581) #24 TLR6 (ENSSTOG00000025480) #26 FAM114A1 (ENSSTOG00000001171) #27 TMEM156 (ENSSTOG00000004246) #28 KLHL5 (ENSSTOG00000007013) #30 WDR19 (ENSSTOG00000007054) #31 RFC1 (ENSSTOG00000007088) #32 KLB (ENSSTOG00000002069) #34 ENSSTOG00000002077 ##35 LIAS (ENSSTOG00000002082) #36 UGDH (ENSSTOG00000002096) #37 SMIM14 (ENSSTOG00000034581) UBE2K (ENSSTOG00000012447) PDS5A (ENSSTOG00000012451) N4BP2 (ENSSTOG00000020354) Alpin marmot MODERN SPECIES 9 SMIM20 (ENSMMMG00000017386) RBPJ (ENSMMMG00000017407) CCKAR (ENSMMMG00000017438) STIM2 (ENSMMMG00000017470) ENSMMMG00000017503 ENSMMMG00000017519 ARAP2 (ENSMMMG00000017527) DTHD1 (ENSMMMG00000017544) NWD2 (ENSMMMG00000017559) #8 ENSMMMG00000017574 C4orf19 (ENSMMMG00000017577) #9 RELL1 (ENSMMMG00000017587) #11 PGM2 (ENSMMMG00000017606) #12 TBC1D1 (ENSMMMG00000017620) #19 ENSMMMG00000017716 KLF3 (ENSMMMG00000017721) #22 TLR10 (ENSMMMG00000017725) TLR1 (ENSMMMG00000017739) #24 TLR6 (ENSMMMG00000017761) #26 FAM114A1 (ENSMMMG00000017765) #27 TMEM156 (ENSMMMG00000017773) #28 KLHL5 (ENSMMMG00000017784) #30 WDR19 (ENSMMMG00000017829) #31 RFC1 (ENSMMMG00000017905) #32 KLB (ENSMMMG00000017911) #34 ENSMMMG00000017920 ENSMMMG00000017936 ##35 LIAS (ENSMMMG00000017957) #36 UGDH (ENSMMMG00000017978) #37 ENSMMMG00000018002 UBE2K (ENSMMMG00000018022) Eurasian red squirrel DUPLICATION Eurasian red squirrel MODERN SPECIES 18 ENSSVLG00005011695 ENSSVLG00005011631 ENSSVLG00005011572 PCDH7 (ENSSVLG00005011515) ENSSVLG00005011423 ARAP2 (ENSSVLG00005010880) DTHD1 (ENSSVLG00005010509) ENSSVLG00005010441 #8 ENSSVLG00005010374 #8 C4orf19 (ENSSVLG00005010352) #9 RELL1 (ENSSVLG00005010318) #11 ENSSVLG00005010293 PGM2 (ENSSVLG00005010275) #12 TBC1D1 (ENSSVLG00005010172) #19 ENSSVLG00005010135 ENSSVLG00005010086 #22 ENSSVLG00005010070 TLR10 (ENSSVLG00005010051) TLR1 (ENSSVLG00005010028) #24 TLR6 (ENSSVLG00005009982) #26 ENSSVLG00005009942 TMEM156 (ENSSVLG00005009879) #28 KLHL5 (ENSSVLG00005009665) #30 WDR19 (ENSSVLG00005009349) #31 RFC1 (ENSSVLG00005009235) #32 KLB (ENSSVLG00005009120) #34 ENSSVLG00005009038 ##35 LIAS (ENSSVLG00005008848) #36 UGDH (ENSSVLG00005008677) #37 ENSSVLG00005008623 ENSSVLG00005008568 Eurasian red squirrel MODERN SPECIES 57 ENSSVLG00005020536 #22 ENSSVLG00005020551 ENSSVLG00005020569 ENSSVLG00005020585 ENSSVLG00005020631 ENSSVLG00005020710