Rodentia_A ANCESTRAL SPECIES 20 ENSGT00940000159983 ENSGT00390000002398 #7 ENSGT00390000005197.a.b #8 ENSGT01100000263563.c.b #9 ENSGT00390000015965 ENSGT00390000000214.a.b #10 ENSGT00940000157221 #12 ENSGT00940000160197 #13 ENSGT00940000153404.b #14 ENSGT00940000153648.b #15 ENSGT00390000013778 #17 ENSGT00940000159709 #18 ENSGT00940000156247 #19 ENSGT00940000157949 #20 ENSGT00900000143434 #21 ENSGT00940000157456 #22 ENSGT00940000163662 #23 ENSGT00940000162884 #24 ENSGT00940000162201 #25 ENSGT00390000010054.b #26 ENSGT00390000017929 #27 ENSGT00940000155358 #28 ENSGT00590000083165 #29 ENSGT00730000111066 #30 ENSGT00940000157489 #31 ENSGT00390000015224.c.b.a.k.b.a ##33 ENSGT00390000006234 #34 ENSGT00390000015355 #35 ENSGT00390000018294 #36 ENSGT00670000098059 #37 ENSGT00940000155155 Sciuridae ANCESTRAL SPECIES 19 ENSGT00940000159983 ENSGT00390000002398 #7 ENSGT00390000005197.a.b #8 ENSGT01100000263563.c.b #9 ENSGT00390000015965 ENSGT00390000000214.a.b #10 ENSGT00940000157221 #12 ENSGT00940000160197 #13 ENSGT00940000153404.b #14 ENSGT00940000153648.b #15 ENSGT00390000013778 #17 ENSGT00940000159709 #18 ENSGT00940000156247 #19 ENSGT00940000157949 #20 ENSGT00900000143434 #21 ENSGT00940000157456 #22 ENSGT00940000163662 #23 ENSGT00940000162884 #24 ENSGT00940000162201 #25 ENSGT00990000210295 ENSGT00390000010054.b #26 ENSGT00390000017929 #27 ENSGT00940000155358 #28 ENSGT00590000083165 #29 ENSGT00730000111066 #30 ENSGT00940000157489 #31 ENSGT00390000015224.c.b.a.k.a.a.b ##33 ENSGT00390000006234 #34 ENSGT00390000015355 #35 ENSGT00390000018294 #36 ENSGT00670000098059 #37 Marmotini ANCESTRAL SPECIES 26 ENSGT00940000159983 ENSGT00390000002398 #7 ENSGT00390000005197.a.b #8 ENSGT01100000263563.c.b #9 ENSGT00390000015965 ENSGT00390000000214.a.b #10 ENSGT00940000157221 #12 ENSGT00940000160197 #13 ENSGT00940000153404.b #14 ENSGT00940000153648.b #15 ENSGT00390000013778 #17 ENSGT00940000159709 #18 ENSGT00940000156247 #19 ENSGT00940000157949 #20 ENSGT00900000143434 #21 ENSGT00940000157456 #22 ENSGT00940000163662 #23 ENSGT00940000162884 #24 ENSGT00940000162201 #25 ENSGT00390000010054.b #26 ENSGT00390000017929 #27 ENSGT00940000155358 #28 ENSGT00590000083165 #29 ENSGT00730000111066 #30 ENSGT00940000157489 #31 ENSGT00390000015224.c.b.a.k.a.a.b ##33 ENSGT00390000015224.c.b.a.l #33 ENSGT00390000006234 #34 ENSGT00390000015355 #35 ENSGT00390000018294.k.a #36 ENSGT00670000098059 #37 Alpin marmot MODERN SPECIES 9 SMIM20 (ENSMMMG00000017386) #7 RBPJ (ENSMMMG00000017407) #8 CCKAR (ENSMMMG00000017438) #9 STIM2 (ENSMMMG00000017470) #10 ENSMMMG00000017503 #11 ENSMMMG00000017519 #12 ARAP2 (ENSMMMG00000017527) #13 DTHD1 (ENSMMMG00000017544) #14 NWD2 (ENSMMMG00000017559) #15 ENSMMMG00000017574 #16 C4orf19 (ENSMMMG00000017577) #17 RELL1 (ENSMMMG00000017587) #18 PGM2 (ENSMMMG00000017606) #19 TBC1D1 (ENSMMMG00000017620) #20 ENSMMMG00000017716 #21 KLF3 (ENSMMMG00000017721) #22 TLR10 (ENSMMMG00000017725) #23 TLR1 (ENSMMMG00000017739) #24 TLR6 (ENSMMMG00000017761) #25 FAM114A1 (ENSMMMG00000017765) #26 TMEM156 (ENSMMMG00000017773) #27 KLHL5 (ENSMMMG00000017784) #28 WDR19 (ENSMMMG00000017829) #29 RFC1 (ENSMMMG00000017905) #30 KLB (ENSMMMG00000017911) #31 ENSMMMG00000017920 #32 ENSMMMG00000017936 #33 LIAS (ENSMMMG00000017957) #34 UGDH (ENSMMMG00000017978) #35 ENSMMMG00000018002 #36 UBE2K (ENSMMMG00000018022) #37 Marmotini_b ANCESTRAL SPECIES 48 ENSGT01030000234945 ENSGT00940000157221 #12 ENSGT00950000182841.b.a.a.b.b.p.a ENSGT00940000160197 #13 ENSGT00940000153404.b #14 ENSGT00940000153648.b #15 ENSGT00390000013778 #17 ENSGT00940000159709 #18 ENSGT00940000156247 #19 ENSGT00940000157949 #20 ENSGT00940000157456 #22 ENSGT00940000163662 #23 ENSGT00940000162884 #24 ENSGT00940000162201 #25 ENSGT00390000010054.b #26 ENSGT00390000017929 #27 ENSGT00940000155358 #28 ENSGT00590000083165 #29 ENSGT00730000111066 #30 ENSGT00940000157489 #31 ENSGT00390000015224.c.b.a.k.a.a.b ##33 ENSGT00390000006234 #34 ENSGT00390000015355 #35 ENSGT00390000018294.k.a #36 ENSGT00670000098059 #37 ENSGT00940000155155 Arctic ground squirrel MODERN SPECIES 2 ENSUPAG00010016796 PCDH7 (ENSUPAG00010016798) #12 ENSUPAG00010016821 ARAP2 (ENSUPAG00010016832) #13 DTHD1 (ENSUPAG00010016950) #14 NWD2 (ENSUPAG00010016964) #15 C4orf19 (ENSUPAG00010016983) #17 RELL1 (ENSUPAG00010016993) #18 PGM2 (ENSUPAG00010017012) #19 TBC1D1 (ENSUPAG00010017027) #20 KLF3 (ENSUPAG00010017209) #22 TLR10 (ENSUPAG00010017218) #23 TLR1 (ENSUPAG00010017233) #24 TLR6 (ENSUPAG00010017235) #25 FAM114A1 (ENSUPAG00010017240) #26 TMEM156 (ENSUPAG00010017254) #27 KLHL5 (ENSUPAG00010017266) #28 WDR19 (ENSUPAG00010017295) #29 RFC1 (ENSUPAG00010017359) #30 KLB (ENSUPAG00010018497) #31 ENSUPAG00010018508 #33 LIAS (ENSUPAG00010018541) #34 UGDH (ENSUPAG00010018571) #35 ENSUPAG00010018587 #36 UBE2K (ENSUPAG00010018605) #37 PDS5A (ENSUPAG00010018683) Squirrel MODERN SPECIES 82 PCDH7 (ENSSTOG00000009192) #12 ENSSTOG00000029131 ENSSTOG00000028351 ARAP2 (ENSSTOG00000019405) #13 DTHD1 (ENSSTOG00000003003) #14 NWD2 (ENSSTOG00000019543) #15 C4orf19 (ENSSTOG00000003425) #17 RELL1 (ENSSTOG00000001374) #18 PGM2 (ENSSTOG00000008176) #19 ENSSTOG00000020687 #20 KLF3 (ENSSTOG00000010881) #22 TLR1 (ENSSTOG00000021581) #24 TLR6 (ENSSTOG00000025480) #25 FAM114A1 (ENSSTOG00000001171) #26 TMEM156 (ENSSTOG00000004246) #27 KLHL5 (ENSSTOG00000007013) #28 WDR19 (ENSSTOG00000007054) #29 RFC1 (ENSSTOG00000007088) #30 KLB (ENSSTOG00000002069) #31 ENSSTOG00000002077 ##33 LIAS (ENSSTOG00000002082) #34 UGDH (ENSSTOG00000002096) #35 SMIM14 (ENSSTOG00000034581) ##36 UBE2K (ENSSTOG00000012447) #37 PDS5A (ENSSTOG00000012451) N4BP2 (ENSSTOG00000020354) Eurasian red squirrel DUPLICATION Eurasian red squirrel MODERN SPECIES 18 ENSSVLG00005011695 ENSSVLG00005011631 ENSSVLG00005011572 PCDH7 (ENSSVLG00005011515) #12 ENSSVLG00005011423 ARAP2 (ENSSVLG00005010880) #13 DTHD1 (ENSSVLG00005010509) #14 ENSSVLG00005010441 #15 ENSSVLG00005010374 #15 C4orf19 (ENSSVLG00005010352) #17 RELL1 (ENSSVLG00005010318) #18 ENSSVLG00005010293 PGM2 (ENSSVLG00005010275) #19 TBC1D1 (ENSSVLG00005010172) #20 ENSSVLG00005010135 #21 ENSSVLG00005010086 #22 ENSSVLG00005010070 TLR10 (ENSSVLG00005010051) #23 TLR1 (ENSSVLG00005010028) #24 TLR6 (ENSSVLG00005009982) #25 ENSSVLG00005009942 TMEM156 (ENSSVLG00005009879) #27 KLHL5 (ENSSVLG00005009665) #28 WDR19 (ENSSVLG00005009349) #29 RFC1 (ENSSVLG00005009235) #30 KLB (ENSSVLG00005009120) #31 ENSSVLG00005009038 ##33 LIAS (ENSSVLG00005008848) #34 UGDH (ENSSVLG00005008677) #35 ENSSVLG00005008623 ENSSVLG00005008568 #36 Eurasian red squirrel MODERN SPECIES 57 ENSSVLG00005020536 #22 ENSSVLG00005020551 ENSSVLG00005020569 ENSSVLG00005020585 ENSSVLG00005020631 ENSSVLG00005020710 Hystricomorpha ANCESTRAL SPECIES 26 ENSGT00950000183177.a.a.b ENSGT00940000159983 ENSGT00390000002398 #7 ENSGT00390000005197.a.b #8 ENSGT01100000263563.c.b #9 ENSGT00390000015965 ENSGT00390000000214.a.b #10 ENSGT00940000157221 #12 ENSGT00940000160197 #13 ENSGT00940000153404.b #14 ENSGT00940000153648.b #15 ENSGT00390000013778 #17 ENSGT00940000159709 #18 ENSGT00940000156247 #19 ENSGT00940000157949 #20 ENSGT00940000157456 #22 ENSGT00940000163662 #23 ENSGT00940000162884 #24 ENSGT00940000162201 #25 ENSGT00390000010054.b #26 ENSGT00390000017929 #27 ENSGT00940000155358 #28 ENSGT00590000083165 #29 ENSGT00730000111066 #30 ENSGT00940000157489 #31 ENSGT00390000015224.c.b.a.k.b.a ##33 ENSGT00390000006234 #34 ENSGT00390000015355 #35 ENSGT00390000018294 #36 ENSGT00670000098059 #37 ENSGT00940000155155 Hystricomorpha_a ANCESTRAL SPECIES 23 ENSGT00950000183177.a.a.b ENSGT00940000159983 ENSGT00390000002398 #7 ENSGT00390000005197.a.b #8 ENSGT01100000263563.c.b #9 ENSGT00390000015965 ENSGT00390000000214.a.b #10 ENSGT00940000157221 #12 ENSGT00940000160197 #13 ENSGT00940000153404.b #14 ENSGT00940000153648.b #15 ENSGT00390000013778 #17 ENSGT00940000159709 #18 ENSGT00940000156247 #19 ENSGT00940000157949 #20 ENSGT00940000157456 #22 ENSGT00940000163662 #23 ENSGT00940000162884 #24 ENSGT00940000162201 #25 ENSGT00390000010054.b #26 ENSGT00390000017929 #27 ENSGT00940000155358 #28 ENSGT00590000083165 #29 ENSGT00730000111066 #30 ENSGT00940000157489 #31 ENSGT00390000015224.c.b.a.k.b.a ##33 ENSGT00390000006234 #34 ENSGT00390000015355 #35 ENSGT00390000018294 #36 ENSGT00940000166010 ENSGT00670000098059 #37 Hystricomorpha_b ANCESTRAL SPECIES 37 ENSGT00950000183177.a.a.b ENSGT00940000159983 ENSGT00390000002398 #7 ENSGT00390000005197.a.b #8 ENSGT01100000263563.c.b #9 ENSGT00390000015965 ENSGT00390000000214.a.b #10 ENSGT00940000157221 #12 ENSGT00940000160197 #13 ENSGT00940000153404.b #14 ENSGT00940000153648.b #15 ENSGT00390000013778 #17 ENSGT00940000159709 #18 ENSGT00940000156247 #19 ENSGT00940000157949 #20 ENSGT00940000157456 #22 ENSGT00940000163662 #23 ENSGT00940000162884 #24 ENSGT00940000162201 #25 ENSGT00390000010054.b #26 ENSGT00390000017929 #27 ENSGT00940000155358 #28 ENSGT00590000083165 #29 ENSGT00730000111066 #30 ENSGT00940000157489 #31 ENSGT00390000015224.c.b.a.k.b.a ##33 ENSGT00390000006234 #34 ENSGT00390000015355 #35 ENSGT00390000018294 #36 ENSGT00940000166010 ENSGT00670000098059 #37 Long-tailed chinchilla MODERN SPECIES 150 SLC34A2 (ENSCLAG00000002636) SEL1L3 (ENSCLAG00000002362) SMIM20 (ENSCLAG00000002089) #7 RBPJ (ENSCLAG00000002065) #8 CCKAR (ENSCLAG00000001729) #9 TBC1D19 (ENSCLAG00000001699) STIM2 (ENSCLAG00000002849) #10 PCDH7 (ENSCLAG00000002605) #12 ARAP2 (ENSCLAG00000012467) #13 DTHD1 (ENSCLAG00000011952) #14 NWD2 (ENSCLAG00000010818) #15 C4orf19 (ENSCLAG00000010706) #17 RELL1 (ENSCLAG00000010401) #18 PGM2 (ENSCLAG00000010266) #19 TBC1D1 (ENSCLAG00000002236) #20 KLF3 (ENSCLAG00000004459) #22 TLR10 (ENSCLAG00000004336) #23 TLR1 (ENSCLAG00000017579) #24 TLR6 (ENSCLAG00000017630) #25 FAM114A1 (ENSCLAG00000003993) #26 TMEM156 (ENSCLAG00000003928) #27 KLHL5 (ENSCLAG00000002937) #28 WDR19 (ENSCLAG00000002775) #29 RFC1 (ENSCLAG00000001564) #30 KLB (ENSCLAG00000001476) #31 ENSCLAG00000001418 ##33 LIAS (ENSCLAG00000001354) #34 UGDH (ENSCLAG00000001307) #35 SMIM14 (ENSCLAG00000002664) #36 ENSCLAG00000006068 ENSCLAG00000006013 Degu MODERN SPECIES 199 ENSODEG00000002273 ##14 NWD2 (ENSODEG00000002293) #15 RELL1 (ENSODEG00000002376) #18 ENSODEG00000002408 #19 TBC1D1 (ENSODEG00000002549) #20 ENSODEG00000018891 KLF3 (ENSODEG00000002620) #22 ENSODEG00000002637 FAM114A1 (ENSODEG00000003086) #26 KLHL5 (ENSODEG00000003160) #28 WDR19 (ENSODEG00000003235) #29 RFC1 (ENSODEG00000003452) #30 KLB (ENSODEG00000003829) #31 ENSODEG00000003855 ##33 LIAS (ENSODEG00000003971) #34 ENSODEG00000003708 #35 ENSODEG00000003741 UBE2K (ENSODEG00000003840) #37 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) #15 C4orf19 (ENSCPOG00000035167) #17 RELL1 (ENSCPOG00000009761) #18 PGM2 (ENSCPOG00000013611) #19 TBC1D1 (ENSCPOG00000013615) #20 KLF3 (ENSCPOG00000030471) #22 TLR10 (ENSCPOG00000015283) #23 TLR1 (ENSCPOG00000012205) #24 TLR6 (ENSCPOG00000005088) #25 FAM114A1 (ENSCPOG00000013554) #26 TMEM156 (ENSCPOG00000013560) #27 KLHL5 (ENSCPOG00000004478) #28 WDR19 (ENSCPOG00000004240) #29 RFC1 (ENSCPOG00000004248) #30 KLB (ENSCPOG00000004539) #31 ENSCPOG00000004543 ##33 LIAS (ENSCPOG00000004547) #34 UGDH (ENSCPOG00000004550) #35 ENSCPOG00000039840 UBE2K (ENSCPOG00000014798) #37 ENSCPOG00000023886 Naked mole-rat female MODERN SPECIES 1 ENSHGLG00000037767 NWD2 (ENSHGLG00000000298) #15 ENSHGLG00000040844 #17 ENSHGLG00000040492 #17 ENSHGLG00000043452 #18 PGM2 (ENSHGLG00000001842) #19 ENSHGLG00000002323 ENSHGLG00000003063 ENSHGLG00000000606 ENSHGLG00000019811 ENSHGLG00000033549 ENSHGLG00000034348 ENSHGLG00000043517 #20 ENSHGLG00000044532 #20 ENSHGLG00000019798 KLF3 (ENSHGLG00000049437) #22 ENSHGLG00000000855 ENSHGLG00000019856 #24 ENSHGLG00000001742 TLR6 (ENSHGLG00000050436) #25 FAM114A1 (ENSHGLG00000002258) #26 TMEM156 (ENSHGLG00000002626) #27 ENSHGLG00000033489 KLHL5 (ENSHGLG00000001944) #28 WDR19 (ENSHGLG00000002756) #29 ENSHGLG00000002546 #30 ENSHGLG00000032109 KLB (ENSHGLG00000002389) #31 ENSHGLG00000002318 ##33 LIAS (ENSHGLG00000002264) #34 UGDH (ENSHGLG00000002204) #35