Rodentia_A ANCESTRAL SPECIES 24 ENSGT00940000162335 ENSGT00940000162895 ENSGT00940000159753 ENSGT00940000154589.b #7 ENSGT00390000002219 #8 ENSGT00940000154340.A #9 ENSGT00940000162789 ENSGT00940000156946 #12 ENSGT01050000244965.b #14 ENSGT00940000158366 #15 ENSGT00940000156627 #17 ENSGT01100000263524.I #18 ENSGT00730000111223 #19 ENSGT00930000151042 #20 ENSGT00390000008798.c #21 ENSGT00940000155140 #22 ENSGT00940000158059 ENSGT00950000182924.B.a.a #23 ENSGT00940000159823 #24 ENSGT00940000157910 #25 ENSGT00390000001376 #26 ENSGT00390000008294.f #27 ENSGT00390000008294.e.b.a.a ##27 ENSGT00940000159660 #28 ENSGT00940000159984 #29 ENSGT00940000157714 #30 ENSGT00940000157370 #32 ENSGT00390000009613.b #33 ENSGT00940000162188 #34 ENSGT00530000069080 #36 ENSGT00940000154950 #37 Sciuridae ANCESTRAL SPECIES 43 ENSGT00940000162642 ENSGT00940000162335 ENSGT00940000162895 ENSGT00940000159753 ENSGT00940000154589.b #7 ENSGT00390000002219 #8 ENSGT00940000154340.A #9 ENSGT00940000156946 #12 ENSGT01050000244965.b #14 ENSGT00940000158366 #15 ENSGT00940000156627 #17 ENSGT01100000263524.I #18 ENSGT00730000111223 #19 ENSGT00930000151042 #20 ENSGT00390000008798.c #21 ENSGT00940000155140 #22 ENSGT00940000158059 ENSGT00950000182924.B.a.a #23 ENSGT00940000159823 #24 ENSGT00940000157910 #25 ENSGT00390000001376 #26 ENSGT00390000008294.e.b.a.b ##27 ENSGT00940000159660 #28 ENSGT00940000159984 #29 ENSGT00940000157714 #30 ENSGT00940000157370 #32 ENSGT00390000009613.b #33 ENSGT00940000162188 #34 ENSGT00530000069080 #36 ENSGT00940000154950 #37 ENSGT00940000158244 Marmotini ANCESTRAL SPECIES 51 ENSGT00940000162642 ENSGT00940000162335 ENSGT00940000162895 ENSGT00940000159753 ENSGT00940000154589.b #7 ENSGT00390000002219 #8 ENSGT00940000154340.A #9 ENSGT00940000156946 #12 ENSGT01050000244965.b #14 ENSGT00940000158366 #15 ENSGT00940000156627 #17 ENSGT01100000263524.I #18 ENSGT00730000111223 #19 ENSGT00930000151042 #20 ENSGT00390000008798.c #21 ENSGT00940000155140 #22 ENSGT00940000158059 ENSGT00950000182924.B.a.a #23 ENSGT00940000159823 #24 ENSGT00940000157910 #25 ENSGT00390000001376 #26 ENSGT00390000008294.f #27 ENSGT00940000159660 #28 ENSGT00940000159984.e #29 ENSGT00940000157714.g #30 ENSGT00940000157714.h #31 ENSGT00940000157370 #32 ENSGT00390000009613.b #33 ENSGT00940000162188 #34 ENSGT00530000069080 #36 ENSGT00940000154950 #37 Alpin marmot MODERN SPECIES 14 TIFA (ENSMMMG00000011166) #7 AP1AR (ENSMMMG00000011129) #8 ENSMMMG00000011118 #9 ENSMMMG00000011114 #10 ENSMMMG00000011061 #11 ENPEP (ENSMMMG00000011011) #12 ENSMMMG00000011001 #13 ELOVL6 (ENSMMMG00000010968) #14 EGF (ENSMMMG00000010685) #15 ENSMMMG00000010673 #16 LRIT3 (ENSMMMG00000010663) #17 RRH (ENSMMMG00000010634) #18 GAR1 (ENSMMMG00000010623) #19 CFI (ENSMMMG00000010613) #20 PLA2G12A (ENSMMMG00000010605) #21 CASP6 (ENSMMMG00000010597) #22 SEC24B (ENSMMMG00000010546) #23 COL25A1 (ENSMMMG00000010402) #24 ETNPPL (ENSMMMG00000010343) #25 OSTC (ENSMMMG00000010326) #26 RPL34 (ENSMMMG00000010314) #27 LEF1 (ENSMMMG00000010193) #28 ENSMMMG00000010164 #29 ENSMMMG00000010161 #30 ENSMMMG00000010155 #31 SGMS2 (ENSMMMG00000010143) #32 PAPSS1 (ENSMMMG00000010079) #33 DKK2 (ENSMMMG00000010025) #34 ENSMMMG00000009991 #35 GIMD1 (ENSMMMG00000009944) #36 AIMP1 (ENSMMMG00000009938) #37 Marmotini_b ANCESTRAL SPECIES 164 ENSGT00940000162642 ENSGT00940000162335 ENSGT00940000162895 ENSGT00940000159753 ENSGT00940000154589.b #7 ENSGT00390000002219 #8 ENSGT00940000154340.A #9 ENSGT00940000156946 #12 ENSGT01050000244965.b #14 ENSGT00940000158366 #15 ENSGT00940000156627 #17 ENSGT01100000263524.I #18 ENSGT00730000111223 #19 ENSGT00930000151042 #20 ENSGT00390000008798.c #21 ENSGT00940000155140 #22 ENSGT00940000158059 ENSGT00950000182924.B.a.a #23 ENSGT00730000111880 ENSGT00940000157910 #25 Squirrel MODERN SPECIES 163 ENSSTOG00000025752 ENSSTOG00000011761 NEUROG2 (ENSSTOG00000011758) ALPK1 (ENSSTOG00000023490) TIFA (ENSSTOG00000024540) #7 AP1AR (ENSSTOG00000011726) #8 FAM241A (ENSSTOG00000026762) #9 ENSSTOG00000025728 #11 ENPEP (ENSSTOG00000019984) #12 ELOVL6 (ENSSTOG00000013096) #14 LRIT3 (ENSSTOG00000019825) #17 RRH (ENSSTOG00000026445) #18 GAR1 (ENSSTOG00000005577) #19 CFI (ENSSTOG00000013356) #20 PLA2G12A (ENSSTOG00000007365) #21 CASP6 (ENSSTOG00000022572) #22 MCUB (ENSSTOG00000012419) SEC24B (ENSSTOG00000025309) #23 ENSSTOG00000030771 ETNPPL (ENSSTOG00000021812) #25 Arctic ground squirrel MODERN SPECIES 681 CASP6 (ENSUPAG00010023134) #22 MCUB (ENSUPAG00010000046) SEC24B (ENSUPAG00010000070) #23 ENSUPAG00010000214 Eurasian red squirrel DUPLICATION Eurasian red squirrel DUPLICATION Eurasian red squirrel MODERN SPECIES 18 ENSSVLG00005025981 #7 ENSSVLG00005025982 #8 FAM241A (ENSSVLG00005025983) #9 ENSSVLG00005025985 ENSSVLG00005025987 #11 ENPEP (ENSSVLG00005025988) #12 ENSSVLG00005025989 ENSSVLG00005025991 ELOVL6 (ENSSVLG00005025992) #14 EGF (ENSSVLG00005025994) #15 LRIT3 (ENSSVLG00005025995) #17 RRH (ENSSVLG00005025996) #18 GAR1 (ENSSVLG00005025997) #19 CFI (ENSSVLG00005025998) #20 PLA2G12A (ENSSVLG00005025999) #21 ENSSVLG00005026000 #22 MCUB (ENSSVLG00005026001) SEC24B (ENSSVLG00005026003) #23 ENSSVLG00005026004 COL25A1 (ENSSVLG00005026005) #24 ENSSVLG00005026006 ETNPPL (ENSSVLG00005026007) #25 OSTC (ENSSVLG00005026008) #26 RPL34 (ENSSVLG00005026009) ##27 ENSSVLG00005026011 ENSSVLG00005026012 #28 HADH (ENSSVLG00005026013) #29 CYP2U1 (ENSSVLG00005026014) #30 SGMS2 (ENSSVLG00005026015) #32 PAPSS1 (ENSSVLG00005026017) #33 DKK2 (ENSSVLG00005026018) #34 Eurasian red squirrel MODERN SPECIES 12 ENSSVLG00005023476 FOXJ1 (ENSSVLG00005023500) EXOC7 (ENSSVLG00005023572) ZACN (ENSSVLG00005023709) GALR2 (ENSSVLG00005023761) ENSSVLG00005023780 SRP68 (ENSSVLG00005023814) EVPL (ENSSVLG00005023880) CDK3 (ENSSVLG00005023973) TEN1 (ENSSVLG00005023999) ACOX1 (ENSSVLG00005024030) FBF1 (ENSSVLG00005024129) MRPL38 (ENSSVLG00005024310) TRIM65 (ENSSVLG00005024357) TRIM47 (ENSSVLG00005024378) ENSSVLG00005024393 #22 ENSSVLG00005024404 WBP2 (ENSSVLG00005024432) UNC13D (ENSSVLG00005024494) UNK (ENSSVLG00005024600) ENSSVLG00005024623 GALK1 (ENSSVLG00005024646) SAP30BP (ENSSVLG00005005528) RECQL5 (ENSSVLG00005005580) ENSSVLG00005005683 SMIM5 (ENSSVLG00005005693) ENSSVLG00005005738 ENSSVLG00005005769 LLGL2 (ENSSVLG00005005886) TSEN54 (ENSSVLG00005005927) ENSSVLG00005005957 Eurasian red squirrel MODERN SPECIES 17 CRYBB3 (ENSSVLG00005010026) CRYBB2 (ENSSVLG00005010113) GRK3 (ENSSVLG00005010169) ENSSVLG00005010401 SEZ6L (ENSSVLG00005010713) ASPHD2 (ENSSVLG00005012225) HPS4 (ENSSVLG00005012268) SRRD (ENSSVLG00005012323) TFIP11 (ENSSVLG00005012439) TPST2 (ENSSVLG00005012485) CRYBB1 (ENSSVLG00005012526) CRYBA4 (ENSSVLG00005012608) MN1 (ENSSVLG00005012679) PITPNB (ENSSVLG00005012735) TTC28 (ENSSVLG00005012954) ENSSVLG00005013048 #22 CHEK2 (ENSSVLG00005013622) HSCB (ENSSVLG00005013889) ENSSVLG00005013977 XBP1 (ENSSVLG00005014110) ENSSVLG00005014358 ZNRF3 (ENSSVLG00005014418) C22orf31 (ENSSVLG00005014531) KREMEN1 (ENSSVLG00005014585) EMID1 (ENSSVLG00005014741) RHBDD3 (ENSSVLG00005015229) ENSSVLG00005015564 GAS2L1 (ENSSVLG00005016901) RASL10A (ENSSVLG00005016957) AP1B1 (ENSSVLG00005017064) ENSSVLG00005017183 Hystricomorpha ANCESTRAL SPECIES 38 ENSGT00940000162895 ENSGT00940000159753 ENSGT00940000154589.b #7 ENSGT00390000002219 #8 ENSGT00940000162789 ENSGT00940000168645 ENSGT00940000154340.A #9 ENSGT00940000156946 #12 ENSGT01050000244965.b #14 ENSGT00940000158366 #15 ENSGT00940000156627 #17 ENSGT01100000263524.I #18 ENSGT00730000111223 #19 ENSGT00930000151042 #20 ENSGT00390000008798.c #21 ENSGT00940000155140 #22 ENSGT00940000158059 ENSGT00950000182924.B.a.a #23 ENSGT00940000159823 #24 ENSGT00940000157910 #25 ENSGT00390000001376 #26 ENSGT00390000008294.f #27 ENSGT00390000008294.e.b.a.a ##27 ENSGT00940000159660 #28 ENSGT00940000159984 #29 ENSGT00940000157714 #30 ENSGT00940000157370 #32 ENSGT00390000009613.b #33 ENSGT00940000162188 #34 ENSGT00530000069080 #36 ENSGT00940000154950 #37 Naked mole-rat female MODERN SPECIES 19 PAPSS1 (ENSHGLG00000001783) #33 ENSHGLG00000038714 #30 HADH (ENSHGLG00000032988) #29 LEF1 (ENSHGLG00000046551) #28 RPL34 (ENSHGLG00000050296) #27 ENSHGLG00000001959 #26 ENSHGLG00000004469 #25 ENSHGLG00000047113 ENPEP (ENSHGLG00000002965) #12 ELOVL6 (ENSHGLG00000037368) #14 ENSHGLG00000034086 ENSHGLG00000002404 #15 RRH (ENSHGLG00000004643) #18 GAR1 (ENSHGLG00000000493) #19 PLA2G12A (ENSHGLG00000000692) #21 CASP6 (ENSHGLG00000000729) #22 ENSHGLG00000000975 ENSHGLG00000001432 #23 ENSHGLG00000003109 ENSHGLG00000036692 ENSHGLG00000046553 ENSHGLG00000001486 LARP7 (ENSHGLG00000002716) NEUROG2 (ENSHGLG00000044856) ENSHGLG00000020125 ALPK1 (ENSHGLG00000019570) TIFA (ENSHGLG00000033392) #7 ENSHGLG00000002634 #8 ENSHGLG00000035535 ENSHGLG00000048412 #9 ENSHGLG00000037923 Hystricomorpha_a ANCESTRAL SPECIES 34 ENSGT00940000162895 ENSGT00940000159753 ENSGT00940000154589.b #7 ENSGT00390000002219 #8 ENSGT00940000162789 ENSGT00940000168645 ENSGT00940000154340.A #9 ENSGT00940000156946 #12 ENSGT01050000244965.b #14 ENSGT00940000158366 #15 ENSGT00940000156627 #17 ENSGT01100000263524.I #18 ENSGT00730000111223 #19 ENSGT00930000151042 #20 ENSGT00390000008798.c #21 ENSGT00940000155140 #22 ENSGT00940000158059 ENSGT00950000182924.B.a.a #23 ENSGT00940000159823 #24 ENSGT00940000157910 #25 ENSGT00390000001376 #26 ENSGT00390000008294.e.b.a.a ##27 ENSGT00940000159660 #28 ENSGT00940000159984 #29 ENSGT00940000157714 #30 ENSGT00940000157370 #32 ENSGT00390000009613.b #33 ENSGT00940000162188 #34 ENSGT00530000069080 #36 ENSGT00940000154950 #37 ENSGT00940000158244 Guinea pig MODERN SPECIES 43 ENSCPOG00000038161 ALPK1 (ENSCPOG00000008412) TIFA (ENSCPOG00000036501) #7 AP1AR (ENSCPOG00000032660) #8 ENSCPOG00000005214 FAM241A (ENSCPOG00000013964) #9 ENSCPOG00000009459 #11 ENPEP (ENSCPOG00000000701) #12 ELOVL6 (ENSCPOG00000038802) #14 EGF (ENSCPOG00000000779) #15 LRIT3 (ENSCPOG00000000776) #17 RRH (ENSCPOG00000004217) #18 GAR1 (ENSCPOG00000004216) #19 CFI (ENSCPOG00000004214) #20 PLA2G12A (ENSCPOG00000004212) #21 CASP6 (ENSCPOG00000031434) #22 ENSCPOG00000002110 ENSCPOG00000022594 SEC24B (ENSCPOG00000009212) #23 COL25A1 (ENSCPOG00000012595) #24 ETNPPL (ENSCPOG00000015368) #25 OSTC (ENSCPOG00000039456) #26 ENSCPOG00000037181 ##27 LEF1 (ENSCPOG00000013758) #28 HADH (ENSCPOG00000024229) #29 CYP2U1 (ENSCPOG00000011750) #30 SGMS2 (ENSCPOG00000032233) #32 PAPSS1 (ENSCPOG00000011505) #33 DKK2 (ENSCPOG00000030616) #34 AIMP1 (ENSCPOG00000006734) #37 TBCK (ENSCPOG00000006708) Hystricomorpha_b ANCESTRAL SPECIES 52 ENSGT00940000162895 ENSGT00940000159753 ENSGT00940000154589.b #7 ENSGT00390000002219 #8 ENSGT00940000168645 ENSGT00940000154340.A #9 ENSGT00940000162789 ENSGT00940000156946 #12 ENSGT01050000244965.b #14 ENSGT00940000158366 #15 ENSGT00940000156627 #17 ENSGT01100000263524.I #18 ENSGT00730000111223 #19 ENSGT00930000151042 #20 ENSGT00390000008798.c #21 ENSGT00940000155140 #22 ENSGT00940000158059 ENSGT00950000182924.B.a.a #23 ENSGT00940000159823 #24 ENSGT00940000157910 #25 ENSGT00390000001376 #26 ENSGT00390000008294.f #27 ENSGT00390000008294.e.b.a.a ##27 ENSGT00940000159660 #28 ENSGT00940000159984 #29 ENSGT00940000157714 #30 ENSGT00940000157370 #32 ENSGT00390000009613.b #33 ENSGT00940000162188 #34 ENSGT00530000069080 #36 ENSGT00940000154950 #37 Degu MODERN SPECIES 57 ENSODEG00000009949 ENSODEG00000019796 ENSODEG00000010616 FAM241A (ENSODEG00000011489) #9 ENSODEG00000019979 PITX2 (ENSODEG00000010082) ENSODEG00000010195 #12 ENSODEG00000011196 #14 ENSODEG00000009818 #15 ENSODEG00000010355 LRIT3 (ENSODEG00000014302) #17 RRH (ENSODEG00000010773) #18 GAR1 (ENSODEG00000011083) #19 CFI (ENSODEG00000010069) #20 ENSODEG00000011603 #21 CASP6 (ENSODEG00000010252) #22 MCUB (ENSODEG00000010641) SEC24B (ENSODEG00000011940) #23 ENSODEG00000019962 ENSODEG00000011204 COL25A1 (ENSODEG00000011565) #24 ETNPPL (ENSODEG00000011007) #25 OSTC (ENSODEG00000011874) #26 ENSODEG00000012716 #27 ENSODEG00000019987 LEF1 (ENSODEG00000010436) #28 HADH (ENSODEG00000011168) #29 CYP2U1 (ENSODEG00000010344) #30 SGMS2 (ENSODEG00000010387) #32 PAPSS1 (ENSODEG00000012464) #33 DKK2 (ENSODEG00000013005) #34 Long-tailed chinchilla MODERN SPECIES 203 ENSCLAG00000002990 ELOVL6 (ENSCLAG00000003163) #14 EGF (ENSCLAG00000003331) #15 LRIT3 (ENSCLAG00000004694) #17 RRH (ENSCLAG00000005130) #18 GAR1 (ENSCLAG00000005335) #19 CFI (ENSCLAG00000006216) #20 PLA2G12A (ENSCLAG00000006595) #21 CASP6 (ENSCLAG00000003293) #22 MCUB (ENSCLAG00000003597) SEC24B (ENSCLAG00000004027) #23 ENSCLAG00000002421 COL25A1 (ENSCLAG00000002719) #24 ETNPPL (ENSCLAG00000002982) #25 OSTC (ENSCLAG00000003790) #26 ENSCLAG00000003911 ##27 LEF1 (ENSCLAG00000003044) #28 HADH (ENSCLAG00000003966) #29 CYP2U1 (ENSCLAG00000002674) #30 SGMS2 (ENSCLAG00000002723) #32 PAPSS1 (ENSCLAG00000002840) #33 DKK2 (ENSCLAG00000002881) #34 GIMD1 (ENSCLAG00000003485) #36 AIMP1 (ENSCLAG00000003954) #37