Rodentia_A ANCESTRAL SPECIES 16 ENSGT00390000012267 ENSGT00940000156708.a.a ENSGT00390000006806 ENSGT01100000263497.E.a.a ENSGT00390000008063 ENSGT00940000159016 ENSGT00390000002121 ENSGT01030000234638.b.a.a ENSGT00950000182755.b.a.a.a.a.a.b.d.b ##16 ENSGT00950000182755.b.a.a.a.a.a.a.b #16 ENSGT00390000016735 #17 ENSGT00390000000053 #18 ENSGT00940000159680 #19 ENSGT00390000005147 #20 ENSGT00940000160257 #21 ENSGT00940000160389 #22 ENSGT00510000047770.c.a #23 ENSGT00940000153116.C.b #24 ENSGT00940000161935 #25 ENSGT00940000160315 #26 ENSGT00390000007170 #27 ENSGT00940000158145 #28 ENSGT00390000008201 #29 ENSGT00390000016298.a #30 ENSGT00940000157552 #31 ENSGT00510000049338 #32 ENSGT00440000034383 #33 ENSGT00940000159313 #34 ENSGT00940000161012 #35 ENSGT00390000005584 ENSGT00940000161046 #36 Hystricomorpha ANCESTRAL SPECIES 19 ENSGT00940000161972 ENSGT00390000006744 ENSGT01060000248544.a.a.b.a.a ENSGT00940000154063.C.a.b ENSGT00940000160446 ENSGT00950000183047.c.a ENSGT00940000154130.a.a.a ENSGT00940000159125 ENSGT00940000162163 #15 ENSGT00950000182755.b.a.a.a.a.a.a.b #16 ENSGT00390000016735 #17 ENSGT00390000000053 #18 ENSGT00940000159680 #19 ENSGT00390000005147 #20 ENSGT00940000160257 #21 ENSGT00940000160389 #22 ENSGT00510000047770.c.a #23 ENSGT00940000153116.C.b #24 ENSGT00940000161935 #25 ENSGT00940000160315 #26 ENSGT00390000007170 #27 ENSGT00940000158145 #28 ENSGT00390000008201 #29 ENSGT00390000016298.a #30 ENSGT00940000157552 #31 ENSGT00510000049338 #32 ENSGT00440000034383 #33 ENSGT00940000159313 #34 ENSGT00940000161012 #35 ENSGT00390000005584 ENSGT00940000161046 #36 Hystricomorpha_a ANCESTRAL SPECIES 15 ENSGT00940000161972 ENSGT00390000006744 ENSGT01060000248544.a.a.b.a.a ENSGT00940000154063.C.a.b ENSGT00940000160446 ENSGT00950000183047.c.a ENSGT00940000154130.a.a.a ENSGT00940000159125 ENSGT00940000162163 #15 ENSGT00950000182755.b.a.a.a.a.a.a.b #16 ENSGT00390000016735 #17 ENSGT00390000000053 #18 ENSGT00940000159680 #19 ENSGT00390000005147 #20 ENSGT00940000160257 #21 ENSGT00940000160389 #22 ENSGT00510000047770.c.a #23 ENSGT00940000153116.C.b #24 ENSGT00940000161935 #25 ENSGT00940000160315 #26 ENSGT00390000007170 #27 ENSGT00940000158145 #28 ENSGT00390000008201 #29 ENSGT00390000016298.a #30 ENSGT00940000157552 #31 ENSGT00510000049338 #32 ENSGT00440000034383 #33 ENSGT00940000159313 #34 ENSGT00940000161012 #35 ENSGT00390000005584 ENSGT00940000161046 #36 Guinea pig MODERN SPECIES 214 ENSCPOG00000021349 #15 ZNF709 (ENSCPOG00000039326) #16 ACP5 (ENSCPOG00000001006) #17 ELOF1 (ENSCPOG00000040714) #18 CNN1 (ENSCPOG00000009855) #19 ECSIT (ENSCPOG00000020901) #20 ZNF653 (ENSCPOG00000010842) #21 ELAVL3 (ENSCPOG00000001793) #22 PRKCSH (ENSCPOG00000020528) #23 ODAD3 (ENSCPOG00000025979) #24 RGL3 (ENSCPOG00000009865) #25 EPOR (ENSCPOG00000004895) #26 SWSAP1 (ENSCPOG00000001918) #27 PLPPR2 (ENSCPOG00000005664) #28 ENSCPOG00000005662 #29 TMEM205 (ENSCPOG00000026260) #30 RAB3D (ENSCPOG00000030555) #31 TSPAN16 (ENSCPOG00000020079) #32 ANGPTL8 (ENSCPOG00000030760) #33 DOCK6 (ENSCPOG00000026620) #34 KANK2 (ENSCPOG00000027433) #35 LDLR (ENSCPOG00000006816) #36 SMARCA4 (ENSCPOG00000015549) #37 Hystricomorpha_b ANCESTRAL SPECIES 17 ENSGT00940000161972 ENSGT00390000006744 ENSGT01060000248544.a.a.b.a.a ENSGT00940000154063.C.a.b ENSGT00940000160446 ENSGT00950000183047.c.a ENSGT00940000154130.a.a.a ENSGT00940000159125 ENSGT00940000162163 #15 ENSGT00950000182755.b.a.a.a.a.a.a.b #16 ENSGT00390000016735 #17 ENSGT00390000000053 #18 ENSGT00940000159680 #19 ENSGT00390000005147 #20 ENSGT00940000160257 #21 ENSGT00940000160389 #22 ENSGT00510000047770.c.a #23 ENSGT00940000153116.C.b #24 ENSGT00940000161935 #25 ENSGT00940000160315 #26 ENSGT00390000007170 #27 ENSGT00940000158145 #28 ENSGT00390000008201 #29 ENSGT00390000016298.a #30 ENSGT00940000157552 #31 ENSGT00510000049338 #32 ENSGT00440000034383 #33 ENSGT00940000159313 #34 ENSGT00940000161012 #35 ENSGT00390000005584 ENSGT00940000161046 #36 Long-tailed chinchilla MODERN SPECIES 202 ENSCLAG00000009403 ENSCLAG00000009197 TNFSF14 (ENSCLAG00000008813) C3 (ENSCLAG00000008464) GPR108 (ENSCLAG00000012060) TRIP10 (ENSCLAG00000009696) SH2D3A (ENSCLAG00000009886) VAV1 (ENSCLAG00000008423) ENSCLAG00000011723 #15 ZNF709 (ENSCLAG00000014910) #16 ACP5 (ENSCLAG00000013793) #17 ELOF1 (ENSCLAG00000013181) #18 CNN1 (ENSCLAG00000013547) #19 ECSIT (ENSCLAG00000013338) #20 ZNF653 (ENSCLAG00000016100) #21 ELAVL3 (ENSCLAG00000016404) #22 PRKCSH (ENSCLAG00000011549) #23 ODAD3 (ENSCLAG00000008412) #24 RGL3 (ENSCLAG00000008655) #25 EPOR (ENSCLAG00000007667) #26 SWSAP1 (ENSCLAG00000011027) #27 PLPPR2 (ENSCLAG00000008970) #28 ENSCLAG00000007718 #29 TMEM205 (ENSCLAG00000007329) #30 RAB3D (ENSCLAG00000007049) #31 TSPAN16 (ENSCLAG00000008629) #32 ANGPTL8 (ENSCLAG00000007166) #33 DOCK6 (ENSCLAG00000015319) #34 LDLR (ENSCLAG00000015453) #36 SMARCA4 (ENSCLAG00000011946) #37 TIMM29 (ENSCLAG00000014951) Degu MODERN SPECIES 91 ENSODEG00000015175 ENSODEG00000020289 TNFSF14 (ENSODEG00000015436) C3 (ENSODEG00000015506) GPR108 (ENSODEG00000016288) TRIP10 (ENSODEG00000015929) VAV1 (ENSODEG00000015478) ENSODEG00000020296 ENSODEG00000015977 #16 ENSODEG00000020329 ACP5 (ENSODEG00000015797) #17 ENSODEG00000015688 #18 CNN1 (ENSODEG00000016009) #19 ECSIT (ENSODEG00000016279) #20 ZNF653 (ENSODEG00000015477) #21 ELAVL3 (ENSODEG00000015790) #22 PRKCSH (ENSODEG00000015657) #23 ODAD3 (ENSODEG00000015468) #24 RGL3 (ENSODEG00000015605) #25 EPOR (ENSODEG00000015732) #26 SWSAP1 (ENSODEG00000015882) #27 PLPPR2 (ENSODEG00000018491) #28 ENSODEG00000015784 #29 TMEM205 (ENSODEG00000016141) #30 ENSODEG00000015574 #31 DOCK6 (ENSODEG00000016301) #34 ANGPTL8 (ENSODEG00000015983) #33 KANK2 (ENSODEG00000015842) #35 SPC24 (ENSODEG00000016091) LDLR (ENSODEG00000015446) #36 SMARCA4 (ENSODEG00000017127) #37 Naked mole-rat female DUPLICATION Naked mole-rat female MODERN SPECIES 21 ALKBH7 (ENSHGLG00000018436) ENSHGLG00000010702 ENSHGLG00000048812 ENSHGLG00000007120 ENSHGLG00000005716 #15 ENSHGLG00000045280 ##16 ENSHGLG00000045808 #16 ENSHGLG00000041157 ENSHGLG00000049858 ENSHGLG00000033621 ENSHGLG00000016971 #17 ENSHGLG00000015081 #18 CNN1 (ENSHGLG00000015039) #19 ECSIT (ENSHGLG00000015014) #20 ZNF653 (ENSHGLG00000015197) #21 ENSHGLG00000015199 #22 PRKCSH (ENSHGLG00000011876) #23 ODAD3 (ENSHGLG00000010231) #24 ENSHGLG00000032994 #25 EPOR (ENSHGLG00000017626) #26 SWSAP1 (ENSHGLG00000015941) #27 PLPPR2 (ENSHGLG00000015100) #28 ENSHGLG00000040073 #29 TMEM205 (ENSHGLG00000014918) #30 RAB3D (ENSHGLG00000015577) #31 TSPAN16 (ENSHGLG00000017884) #32 DOCK6 (ENSHGLG00000009688) #34 ENSHGLG00000034129 #33 KANK2 (ENSHGLG00000006720) #35 SPC24 (ENSHGLG00000005561) LDLR (ENSHGLG00000014530) #36 Naked mole-rat female MODERN SPECIES 16 PDC (ENSHGLG00000007016) ENSHGLG00000013464 TPR (ENSHGLG00000018823) PRG4 (ENSHGLG00000037640) HMCN1 (ENSHGLG00000019222) ENSHGLG00000038341 IVNS1ABP (ENSHGLG00000003305) SWT1 (ENSHGLG00000006542) ENSHGLG00000003135 ENSHGLG00000004191 ENSHGLG00000021138 ENSHGLG00000013124 ENSHGLG00000040450 ENSHGLG00000036708 ENSHGLG00000007310 ENSHGLG00000019379 #22 ENSHGLG00000041312 ENSHGLG00000014856 ENSHGLG00000018157 ENSHGLG00000044661 ENSHGLG00000021029 ENSHGLG00000043630 ENSHGLG00000018727 COLGALT2 (ENSHGLG00000038139) APOBEC4 (ENSHGLG00000040323) RGL1 (ENSHGLG00000018901) ARPC5 (ENSHGLG00000013926) NCF2 (ENSHGLG00000018696) ENSHGLG00000048289 ENSHGLG00000048693 SMG7 (ENSHGLG00000009353) Sciuridae ANCESTRAL SPECIES 20 ENSGT00390000012267 ENSGT00940000156708.a.a ENSGT00390000006806 ENSGT01100000263497.E.a.a ENSGT00390000008063 ENSGT00940000159016 ENSGT00390000002121 ENSGT01030000234638.b.a.a ENSGT00950000182755.b.a.a.a.a.a.b.d.b ##16 ENSGT00950000182755.b.a.a.a.a.a.a.b #16 ENSGT00390000016735 #17 ENSGT00390000000053 #18 ENSGT00940000159680 #19 ENSGT00390000005147 #20 ENSGT00940000160257 #21 ENSGT00940000160389 #22 ENSGT00510000047770.c.a #23 ENSGT00940000153116.C.b #24 ENSGT00940000161935 #25 ENSGT00940000160315 #26 ENSGT00390000007170 #27 ENSGT00940000158145 #28 ENSGT00390000008201 #29 ENSGT00390000016298.a #30 ENSGT00940000157552 #31 ENSGT00510000049338 #32 ENSGT00440000034383 #33 ENSGT00940000159313 #34 ENSGT00940000161012 #35 ENSGT00390000005584 ENSGT00940000161046 #36 Marmotini ANCESTRAL SPECIES 41 ENSGT00390000012267 ENSGT00940000156708.a.a ENSGT00390000006806 ENSGT01100000263497.E.a.a ENSGT00390000008063 ENSGT00940000159016 ENSGT00390000002121 ENSGT01030000234638.b.a.a ENSGT00950000182755.b.a.a.a.b ##16 ENSGT00950000182755.b.a.a.a.a.a.a.b #16 ENSGT00390000016735 #17 ENSGT00390000000053 #18 ENSGT00940000159680 #19 ENSGT00390000005147 #20 ENSGT00940000160257 #21 ENSGT00940000160389 #22 ENSGT00510000047770.c.a #23 ENSGT00940000153116.C.b #24 ENSGT00940000161935 #25 ENSGT00940000160315 #26 ENSGT00390000007170 #27 ENSGT00940000158145 #28 ENSGT00390000008201 #29 ENSGT00390000016298.a #30 ENSGT00940000157552 #31 ENSGT00510000049338 #32 ENSGT00440000034383 #33 ENSGT00940000159313 #34 ENSGT00940000161012 #35 ENSGT00390000005584 ENSGT00940000161046 #36 Alpin marmot MODERN SPECIES 24 TRIR (ENSMMMG00000020777) TNPO2 (ENSMMMG00000020726) FBXW9 (ENSMMMG00000020717) ENSMMMG00000020713 DHPS (ENSMMMG00000020706) WDR83 (ENSMMMG00000020697) WDR83OS (ENSMMMG00000020687) MAN2B1 (ENSMMMG00000020653) ENSMMMG00000020633 ##16 ENSMMMG00000020539 #16 ACP5 (ENSMMMG00000020512) #17 ELOF1 (ENSMMMG00000020499) #18 CNN1 (ENSMMMG00000020489) #19 ECSIT (ENSMMMG00000020481) #20 ZNF653 (ENSMMMG00000020464) #21 ELAVL3 (ENSMMMG00000020248) #22 PRKCSH (ENSMMMG00000020205) #23 ODAD3 (ENSMMMG00000020179) #24 RGL3 (ENSMMMG00000020154) #25 EPOR (ENSMMMG00000020144) #26 SWSAP1 (ENSMMMG00000020143) #27 PLPPR2 (ENSMMMG00000020126) #28 CCDC159 (ENSMMMG00000020119) #29 TMEM205 (ENSMMMG00000020116) #30 RAB3D (ENSMMMG00000020113) #31 TSPAN16 (ENSMMMG00000020105) #32 ANGPTL8 (ENSMMMG00000020098) #33 DOCK6 (ENSMMMG00000019995) #34 KANK2 (ENSMMMG00000019957) #35 SPC24 (ENSMMMG00000019947) LDLR (ENSMMMG00000019891) #36 Marmotini_b ANCESTRAL SPECIES 40 ENSGT00390000012267 ENSGT00940000156708.a.a ENSGT00390000006806 ENSGT01100000263497.E.a.a ENSGT00390000008063 ENSGT00940000159016 ENSGT00390000002121 ENSGT01030000234638.b.a.a ENSGT00950000182755.b.a.a.a.b ##16 ENSGT00950000182755.b.a.a.a.a.a.a.b #16 ENSGT00390000016735 #17 ENSGT00390000000053 #18 ENSGT00940000159680 #19 ENSGT00390000005147 #20 ENSGT00940000160257 #21 ENSGT00940000160389 #22 ENSGT00510000047770.c.a #23 ENSGT00940000153116.C.b #24 ENSGT00940000161935 #25 ENSGT00940000160315 #26 ENSGT00390000007170 #27 ENSGT00940000158145 #28 ENSGT00390000008201 #29 ENSGT00390000016298.a #30 ENSGT00940000157552 #31 ENSGT00510000049338 #32 ENSGT00440000034383 #33 ENSGT00940000159313 #34 ENSGT00940000161012 #35 ENSGT00390000005584 ENSGT00940000161046 #36 Arctic ground squirrel MODERN SPECIES 217 FBXW9 (ENSUPAG00010007705) ENSUPAG00010007702 DHPS (ENSUPAG00010007686) WDR83 (ENSUPAG00010007673) WDR83OS (ENSUPAG00010007669) MAN2B1 (ENSUPAG00010007651) ENSUPAG00010007643 ##16 ENSUPAG00010007642 ##16 ENSUPAG00010007638 #16 ENSUPAG00010007632 ACP5 (ENSUPAG00010007588) #17 ELOF1 (ENSUPAG00010007576) #18 CNN1 (ENSUPAG00010007563) #19 ECSIT (ENSUPAG00010007553) #20 ZNF653 (ENSUPAG00010007541) #21 ELAVL3 (ENSUPAG00010007525) #22 PRKCSH (ENSUPAG00010007493) #23 ODAD3 (ENSUPAG00010007463) #24 RGL3 (ENSUPAG00010007340) #25 EPOR (ENSUPAG00010007323) #26 SWSAP1 (ENSUPAG00010007321) #27 PLPPR2 (ENSUPAG00010007227) #28 CCDC159 (ENSUPAG00010007207) #29 TMEM205 (ENSUPAG00010007186) #30 RAB3D (ENSUPAG00010007164) #31 TSPAN16 (ENSUPAG00010007148) #32 ANGPTL8 (ENSUPAG00010007137) #33 DOCK6 (ENSUPAG00010003421) #34 KANK2 (ENSUPAG00010003372) #35 SPC24 (ENSUPAG00010003350) LDLR (ENSUPAG00010003299) #36 Squirrel MODERN SPECIES 259 TRIR (ENSSTOG00000006978) TNPO2 (ENSSTOG00000006952) FBXW9 (ENSSTOG00000006921) ENSSTOG00000030269 DHPS (ENSSTOG00000006900) WDR83 (ENSSTOG00000006883) WDR83OS (ENSSTOG00000006874) MAN2B1 (ENSSTOG00000029598) ENSSTOG00000034910 ##16 ZNF709 (ENSSTOG00000029196) #16 ACP5 (ENSSTOG00000003699) #17 ELOF1 (ENSSTOG00000003687) #18 CNN1 (ENSSTOG00000003674) #19 ECSIT (ENSSTOG00000003653) #20 ZNF653 (ENSSTOG00000003640) #21 ELAVL3 (ENSSTOG00000021111) #22 PRKCSH (ENSSTOG00000003132) #23 ODAD3 (ENSSTOG00000019506) #24 RGL3 (ENSSTOG00000003004) #25 EPOR (ENSSTOG00000002992) #26 SWSAP1 (ENSSTOG00000002990) #27 PLPPR2 (ENSSTOG00000010119) #28 CCDC159 (ENSSTOG00000005786) #29 TMEM205 (ENSSTOG00000005779) #30 RAB3D (ENSSTOG00000027509) #31 TSPAN16 (ENSSTOG00000002961) #32 ANGPTL8 (ENSSTOG00000026191) #33 DOCK6 (ENSSTOG00000023652) #34 KANK2 (ENSSTOG00000008035) #35 SPC24 (ENSSTOG00000008026) LDLR (ENSSTOG00000007999) #36 Eurasian red squirrel MODERN SPECIES 7 FBXW9 (ENSSVLG00005025161) ENSSVLG00005025134 DHPS (ENSSVLG00005025110) ENSSVLG00005025092 ENSSVLG00005025070 ENSSVLG00005025050 ENSSVLG00005025025 ##16 ENSSVLG00005025001 ##16 ENSSVLG00005024969 #16 ACP5 (ENSSVLG00005024901) #17 ENSSVLG00005024870 #18 CNN1 (ENSSVLG00005024841) #19 ENSSVLG00005024824 #20 ENSSVLG00005024804 #20 ENSSVLG00005024790 #21 ELAVL3 (ENSSVLG00005024773) #22 PRKCSH (ENSSVLG00005024745) #23 ODAD3 (ENSSVLG00005024648) #24 RGL3 (ENSSVLG00005024512) #25 EPOR (ENSSVLG00005024468) #26 SWSAP1 (ENSSVLG00005024453) #27 PLPPR2 (ENSSVLG00005024405) #28 CCDC159 (ENSSVLG00005024349) #29 TMEM205 (ENSSVLG00005024312) #30 RAB3D (ENSSVLG00005024280) #31 TSPAN16 (ENSSVLG00005024177) #32 ANGPTL8 (ENSSVLG00005024122) #33 DOCK6 (ENSSVLG00005024084) #34 KANK2 (ENSSVLG00005024021) #35 SPC24 (ENSSVLG00005024002) LDLR (ENSSVLG00005023861) #36