Rodentia_A ANCESTRAL SPECIES 3 ENSGT00940000155672 ENSGT00390000010722 ENSGT00390000003769 #7 ENSGT00940000155797 #10 ENSGT00940000155690 ENSGT00390000010822 #11 ENSGT00940000157382 #12 ENSGT00390000013520 ENSGT00390000009552 #13 ENSGT00840000129887 #14 ENSGT00390000018761 #15 ENSGT00940000160834 #18 ENSGT00390000000288 #19 ENSGT00940000156706 #21 ENSGT00390000008122 ENSGT00940000156751 #22 ENSGT00940000160675 #23 ENSGT00390000010789 #24 ENSGT00550000074863 #25 ENSGT00940000153818.a.b.a.b #27 ENSGT00390000016675 #28 ENSGT00520000060616 ENSGT00960000187851 ENSGT00940000165476 ENSGT01100000263482.D #34 ENSGT00390000007247 #35 ENSGT00940000156438 #36 ENSGT00940000159596 #37 ENSGT00390000007830 ENSGT00940000154849.a ENSGT01060000250264 Hystricomorpha ANCESTRAL SPECIES 3 ENSGT00940000155672 ENSGT00390000010722 ENSGT00390000003769 #7 ENSGT00940000155797 #10 ENSGT00940000155690 ENSGT00390000010822 #11 ENSGT00940000157382 #12 ENSGT00390000013520 ENSGT00390000009552 #13 ENSGT00840000129887 #14 ENSGT00390000018761 #15 ENSGT00940000160834 #18 ENSGT00390000000288 #19 ENSGT00940000156706 #21 ENSGT00390000008122 ENSGT00940000156751 #22 ENSGT00940000160675 #23 ENSGT00390000010789 #24 ENSGT00550000074863 #25 ENSGT00940000153818.a.b.a.b #27 ENSGT00390000016675 #28 ENSGT00520000060616 ENSGT00940000166945 #29 ENSGT01100000263482.C.c.a #30 ENSGT01100000263482.C.c.b.b.b #31 ENSGT01100000263482.C.c.b.b.a.b ##30 ENSGT01100000263482.C.c.b.a.a ##30 ENSGT01100000263482.C.c.b.a.b.a ##30 ENSGT01100000263482.C.c.b.a.b.b ##30 ENSGT01100000263482.B ##30 ENSGT01100000263482.D #34 Hystricomorpha_a ANCESTRAL SPECIES ENSGT00940000155672 ENSGT00390000010722 ENSGT00390000003769 #7 ENSGT00940000155797 #10 ENSGT00940000155690 ENSGT00390000010822 #11 ENSGT00940000157382 #12 ENSGT00390000013520 ENSGT00390000009552 #13 ENSGT00840000129887 #14 ENSGT00390000018761 #15 ENSGT00940000160834 #18 ENSGT00390000000288 #19 ENSGT00940000156706 #21 ENSGT00390000008122 ENSGT00940000156751 #22 ENSGT00940000160675 #23 ENSGT00390000010789 #24 ENSGT00550000074863 #25 ENSGT00940000153818.a.b.a.b #27 ENSGT00390000016675 #28 ENSGT00520000060616 ENSGT00940000166945 #29 ENSGT01100000263482.C.c.a #30 ENSGT01100000263482.C.c.b.b.b #31 ENSGT00940000165476 ENSGT01100000263482.D #34 ENSGT00390000007247 #35 ENSGT00940000156438 #36 ENSGT00940000159596 #37 ENSGT00390000007830 Hystricomorpha_b ANCESTRAL SPECIES ENSGT00940000155672 ENSGT00390000010722 ENSGT00390000003769 #7 ENSGT00940000155797 #10 ENSGT00940000155690 ENSGT00390000010822 #11 ENSGT00940000157382 #12 ENSGT00390000013520 ENSGT00390000009552 #13 ENSGT00840000129887 #14 ENSGT00390000018761 #15 ENSGT00940000160834 #18 ENSGT00390000000288 #19 ENSGT00940000156706 #21 ENSGT00390000008122 ENSGT00940000156751 #22 ENSGT00940000160675 #23 ENSGT00390000010789 #24 ENSGT00550000074863 #25 ENSGT00940000153818.a.b.a.b #27 ENSGT00390000016675 #28 ENSGT00520000060616 ENSGT00940000166945 #29 ENSGT01100000263482.C.c.a #30 ENSGT01100000263482.C.c.b.b.b #31 ENSGT01100000263482.C.c.b.a.a ##30 ENSGT01100000263482.C.c.b.a.b.a ##30 ENSGT00940000165476 ENSGT01100000263482.D #34 ENSGT00390000007247 #35 ENSGT00940000156438 #36 Degu MODERN SPECIES 205 CHCT1 (ENSODEG00000013458) #7 ENSODEG00000012951 #8 ENSODEG00000013719 #9 ENSODEG00000015311 #10 ENSODEG00000012868 #11 MYO19 (ENSODEG00000013791) #12 GGNBP2 (ENSODEG00000012950) #13 ENSODEG00000012529 #14 ENSODEG00000013042 #15 ENSODEG00000012953 #16 ENSODEG00000013680 #17 LHX1 (ENSODEG00000012895) #18 AATF (ENSODEG00000013074) #19 ENSODEG00000013269 #20 ACACA (ENSODEG00000014030) #21 TADA2A (ENSODEG00000014579) #22 DUSP14 (ENSODEG00000020057) #23 SYNRG (ENSODEG00000013858) #24 ENSODEG00000012814 #25 ENSODEG00000012382 #26 HNF1B (ENSODEG00000012709) #27 HEATR6 (ENSODEG00000013428) #28 ENSODEG00000013109 #29 ENSODEG00000013480 #30 ENSODEG00000013198 #31 ENSODEG00000013395 #32 ENSODEG00000013298 #33 ENSODEG00000012792 #34 HEATR9 (ENSODEG00000012621) #35 ENSODEG00000012915 #36 MMP28 (ENSODEG00000016303) #37 Long-tailed chinchilla MODERN SPECIES 158 PPM1D (ENSCLAG00000010623) APPBP2 (ENSCLAG00000014528) CHCT1 (ENSCLAG00000015267) #7 ENSCLAG00000012909 #10 CA4 (ENSCLAG00000014926) ZNHIT3 (ENSCLAG00000013180) #11 MYO19 (ENSCLAG00000011498) #12 PIGW (ENSCLAG00000010868) GGNBP2 (ENSCLAG00000015068) #13 DHRS11 (ENSCLAG00000012667) #14 MRM1 (ENSCLAG00000010960) #15 LHX1 (ENSCLAG00000014662) #18 AATF (ENSCLAG00000014631) #19 C17orf78 (ENSCLAG00000013611) ACACA (ENSCLAG00000015071) #21 TADA2A (ENSCLAG00000016976) #22 DUSP14 (ENSCLAG00000012666) #23 SYNRG (ENSCLAG00000013031) #24 DDX52 (ENSCLAG00000016292) #25 HNF1B (ENSCLAG00000016506) #27 HEATR6 (ENSCLAG00000010390) #28 ENSCLAG00000012435 ENSCLAG00000011924 ENSCLAG00000016754 #29 ENSCLAG00000012634 #30 ENSCLAG00000014501 #31 Guinea pig MODERN SPECIES 32 BCAS3 (ENSCPOG00000001933) PPM1D (ENSCPOG00000000343) APPBP2 (ENSCPOG00000033874) CHCT1 (ENSCPOG00000005521) #7 ENSCPOG00000005504 #10 CA4 (ENSCPOG00000026479) ZNHIT3 (ENSCPOG00000031447) #11 MYO19 (ENSCPOG00000004270) #12 PIGW (ENSCPOG00000004275) GGNBP2 (ENSCPOG00000004278) #13 DHRS11 (ENSCPOG00000036629) #14 MRM1 (ENSCPOG00000004283) #15 LHX1 (ENSCPOG00000027154) #18 AATF (ENSCPOG00000006037) #19 ACACA (ENSCPOG00000006043) #21 TADA2A (ENSCPOG00000001869) #22 DUSP14 (ENSCPOG00000032995) #23 SYNRG (ENSCPOG00000004643) #24 DDX52 (ENSCPOG00000001232) #25 HNF1B (ENSCPOG00000001234) #27 HEATR6 (ENSCPOG00000015165) #28 ENSCPOG00000036860 ENSCPOG00000035230 #29 ENSCPOG00000032867 #30 ENSCPOG00000033663 #31 ENSCPOG00000037138 #31 ENSCPOG00000026400 ##30 ENSCPOG00000039417 ##30 CCL14 (ENSCPOG00000035450) ##30 ENSCPOG00000008852 #34 HEATR9 (ENSCPOG00000010117) #35 Naked mole-rat female MODERN SPECIES 12 ENSHGLG00000008032 ENSHGLG00000045654 ENSHGLG00000050018 ENSHGLG00000009096 #10 ENSHGLG00000010334 ENSHGLG00000034474 #11 ENSHGLG00000011039 #12 PIGW (ENSHGLG00000012822) GGNBP2 (ENSHGLG00000013148) #13 DHRS11 (ENSHGLG00000035143) #14 MRM1 (ENSHGLG00000008701) #15 LHX1 (ENSHGLG00000042105) #18 AATF (ENSHGLG00000009510) #19 ENSHGLG00000038049 ACACA (ENSHGLG00000011781) #21 TADA2A (ENSHGLG00000003972) #22 DUSP14 (ENSHGLG00000033195) #23 ENSHGLG00000047903 SYNRG (ENSHGLG00000004431) #24 DDX52 (ENSHGLG00000006235) #25 ENSHGLG00000007638 #27 ENSHGLG00000001663 ENSHGLG00000001698 POLG2 (ENSHGLG00000037428) DDX5 (ENSHGLG00000001771) ENSHGLG00000044021 ENSHGLG00000001847 ENSHGLG00000001992 ENSHGLG00000002095 ENSHGLG00000002130 ENSHGLG00000047592 Sciuridae ANCESTRAL SPECIES 4 ENSGT00940000155672 ENSGT00390000010722 ENSGT00390000003769 #7 ENSGT00940000155797 #10 ENSGT00940000155690 ENSGT00390000010822 #11 ENSGT00940000157382 #12 ENSGT00390000013520 ENSGT00390000009552 #13 ENSGT00840000129887 #14 ENSGT00390000018761 #15 ENSGT00940000160834 #18 ENSGT00390000000288 #19 ENSGT00940000156706 #21 ENSGT00390000008122 ENSGT00940000156751 #22 ENSGT00940000160675 #23 ENSGT00390000010789 #24 ENSGT00550000074863 #25 ENSGT00940000153818.a.b.a.b #27 ENSGT00390000016675 #28 ENSGT00520000060616 ENSGT00960000187851 ENSGT00940000166945 #29 ENSGT01100000263482.C.c.a #30 ENSGT01100000263482.C.c.b.b.a.b ##30 ENSGT00940000165476 ENSGT01100000263482.C.c.b.a.b.a ##30 ENSGT01100000263482.C.c.b.a.b.b ##30 ENSGT01100000263482.B ##30 ENSGT01100000263482.D #34 Marmotini ANCESTRAL SPECIES 8 ENSGT00940000153288.a.b.a.a ENSGT00390000010722 ENSGT00390000003769 #7 ENSGT00940000155797 #10 ENSGT00940000155690 ENSGT00390000010822 #11 ENSGT00940000157382 #12 ENSGT00390000013520 ENSGT00390000009552 #13 ENSGT00840000129887 #14 ENSGT00390000018761 #15 ENSGT00940000160834 #18 ENSGT00390000000288 #19 ENSGT00940000156706 #21 ENSGT00390000008122 ENSGT00940000156751 #22 ENSGT00940000160675 #23 ENSGT00390000010789 #24 ENSGT00550000074863 #25 ENSGT00940000153818.a.b.a.b #27 ENSGT00390000016675 #28 ENSGT00520000060616 ENSGT01100000263482.C.c.a #30 ENSGT01100000263482.C.c.b.b.a.b ##30 ENSGT00390000010003.ab ENSGT01100000263482.C.c.b.a.b.a ##30 ENSGT01100000263482.C.c.b.a.b.b ##30 ENSGT01100000263482.B ##30 ENSGT01100000263482.D #34 ENSGT00390000007247 #35 ENSGT00940000156438 #36 Marmotini_b ANCESTRAL SPECIES 5 ENSGT00940000153288.a.b.a.a ENSGT00390000010722 ENSGT00390000003769 #7 ENSGT00940000155797 #10 ENSGT00940000155690 ENSGT00390000010822 #11 ENSGT00940000157382 #12 ENSGT00390000013520 ENSGT00390000009552 #13 ENSGT00840000129887 #14 ENSGT00390000018761 #15 ENSGT00940000160834 #18 ENSGT00390000000288 #19 ENSGT00940000156706 #21 ENSGT00390000008122 ENSGT00940000156751 #22 ENSGT00940000160675 #23 ENSGT00390000010789 #24 ENSGT00550000074863 #25 ENSGT00940000153818.a.b.a.b #27 ENSGT00390000016675 #28 ENSGT00520000060616 ENSGT01100000263482.C.c.a #30 ENSGT01100000263482.C.c.b.b.a.b ##30 ENSGT00390000010003.ab ENSGT01100000263482.C.c.b.a.b.a ##30 ENSGT01100000263482.C.c.b.a.b.b ##30 ENSGT01100000263482.B ##30 ENSGT01100000263482.D #34 ENSGT00390000007247 #35 ENSGT00940000156438 #36 Squirrel MODERN SPECIES 90 PPM1D (ENSSTOG00000021256) APPBP2 (ENSSTOG00000011350) CHCT1 (ENSSTOG00000003182) #7 ENSSTOG00000029070 #10 CA4 (ENSSTOG00000010432) ZNHIT3 (ENSSTOG00000013559) #11 MYO19 (ENSSTOG00000013563) #12 PIGW (ENSSTOG00000034045) GGNBP2 (ENSSTOG00000002398) #13 DHRS11 (ENSSTOG00000002410) #14 MRM1 (ENSSTOG00000002422) #15 LHX1 (ENSSTOG00000022593) #18 AATF (ENSSTOG00000002458) #19 C17orf78 (ENSSTOG00000002508) ACACA (ENSSTOG00000002468) #21 TADA2A (ENSSTOG00000002518) #22 DUSP14 (ENSSTOG00000002528) #23 SYNRG (ENSSTOG00000002530) #24 DDX52 (ENSSTOG00000002550) #25 HNF1B (ENSSTOG00000012440) #27 HEATR6 (ENSSTOG00000026901) #28 ENSSTOG00000032858 ENSSTOG00000013313 #30 ENSSTOG00000027458 ##30 ENSSTOG00000031610 ENSSTOG00000027899 ##30 ENSSTOG00000034887 ##30 CCL14 (ENSSTOG00000033490) ##30 ENSSTOG00000015833 #34 HEATR9 (ENSSTOG00000028751) #35 TAF15 (ENSSTOG00000002081) #36 Arctic ground squirrel MODERN SPECIES 193 PPM1D (ENSUPAG00010011169) ENSUPAG00010011175 APPBP2 (ENSUPAG00010011180) CHCT1 (ENSUPAG00010011193) #7 ENSUPAG00010011211 #10 CA4 (ENSUPAG00010011234) ENSUPAG00010011238 MYO19 (ENSUPAG00010011260) #12 GGNBP2 (ENSUPAG00010011289) #13 DHRS11 (ENSUPAG00010011375) #14 MRM1 (ENSUPAG00010011380) #15 LHX1 (ENSUPAG00010011394) #18 AATF (ENSUPAG00010011404) #19 ACACA (ENSUPAG00010011440) #21 C17orf78 (ENSUPAG00010011568) TADA2A (ENSUPAG00010011582) #22 DUSP14 (ENSUPAG00010011617) #23 SYNRG (ENSUPAG00010011623) #24 DDX52 (ENSUPAG00010012034) #25 HNF1B (ENSUPAG00010012073) #27 HEATR6 (ENSUPAG00010012102) #28 ENSUPAG00010012127 Alpin marmot MODERN SPECIES 42 ENSMMMG00000019748 APPBP2 (ENSMMMG00000019739) CHCT1 (ENSMMMG00000019735) #7 ENSMMMG00000019716 #10 ENSMMMG00000019712 ZNHIT3 (ENSMMMG00000019709) #11 MYO19 (ENSMMMG00000019686) #12 PIGW (ENSMMMG00000019680) GGNBP2 (ENSMMMG00000019594) #13 DHRS11 (ENSMMMG00000019586) #14 MRM1 (ENSMMMG00000019574) #15 LHX1 (ENSMMMG00000019565) #18 ENSMMMG00000019558 ACACA (ENSMMMG00000019480) #21 C17orf78 (ENSMMMG00000019471) TADA2A (ENSMMMG00000019464) #22 DUSP14 (ENSMMMG00000019458) #23 SYNRG (ENSMMMG00000019201) #24 DDX52 (ENSMMMG00000019175) #25 ENSMMMG00000019174 ENSMMMG00000019173 HNF1B (ENSMMMG00000019142) #27 HEATR6 (ENSMMMG00000019131) #28 ENSMMMG00000019129 ENSMMMG00000019125 #29 ENSMMMG00000019119 #30 ENSMMMG00000019116 ENSMMMG00000019105 ##30 ENSMMMG00000019093 ##30 ENSMMMG00000019090 ##30 ENSMMMG00000019088 Eurasian red squirrel MODERN SPECIES 12 APPBP2 (ENSSVLG00005007432) CHCT1 (ENSSVLG00005007474) #7 ENSSVLG00005007515 #10 CA4 (ENSSVLG00005007650) ZNHIT3 (ENSSVLG00005007716) #11 ENSSVLG00005007764 #12 PIGW (ENSSVLG00005007830) GGNBP2 (ENSSVLG00005007850) #13 DHRS11 (ENSSVLG00005007894) #14 MRM1 (ENSSVLG00005007932) #15 LHX1 (ENSSVLG00005007965) #18 AATF (ENSSVLG00005008003) #19 ACACA (ENSSVLG00005008078) #21 ENSSVLG00005008470 ENSSVLG00005008508 TADA2A (ENSSVLG00005008528) #22 ENSSVLG00005008610 SYNRG (ENSSVLG00005008671) #24 DDX52 (ENSSVLG00005008941) #25 HNF1B (ENSSVLG00005008984) #27 HEATR6 (ENSSVLG00005009203) #28 ENSSVLG00005009414 ENSSVLG00005009438 ENSSVLG00005009477 #30 ENSSVLG00005009573 ##30 ENSSVLG00005009611 ##30 ENSSVLG00005009720 ENSSVLG00005009747 ##30 CCL14 (ENSSVLG00005009782) ##30 CCL16 (ENSSVLG00005009830) ##30 ENSSVLG00005009862 #34