Rodentia_A	ANCESTRAL SPECIES	4	ENSGT00390000002190	ENSGT01030000234515.a.a.a #7	ENSGT00940000158313 #8	ENSGT00940000163376	ENSGT00940000154409 #11	ENSGT00950000182997.a.b.b.b #12	ENSGT00940000158200 #13	ENSGT00940000161878 #14	ENSGT00940000154786 #15	ENSGT00940000162804 #17	ENSGT00940000155330 #16	ENSGT00950000183167.a.b.b.b #18	ENSGT00950000183072.b.a #19	ENSGT00940000157629 #20	ENSGT00940000160106 #21	ENSGT00390000000685 #22	ENSGT00390000010077 #23	ENSGT00950000182882.A.a #25	ENSGT01030000234528.B.b.a.a.a #26	ENSGT00940000160845 #27	ENSGT00940000157422 #28	ENSGT00940000156263 #29	ENSGT00940000161971 #30	ENSGT00500000044852.b #31	ENSGT00940000161446 #32	ENSGT00940000157032 #33	ENSGT00530000063734.b #34	ENSGT00950000183038.a.b.a #35	ENSGT00390000016511 #36	ENSGT00390000009755	ENSGT00940000161279 #37
Hystricomorpha	ANCESTRAL SPECIES	9	ENSGT00390000002190	ENSGT01030000234515.a.a.a #7	ENSGT00940000158313 #8	ENSGT00940000163376	ENSGT00940000154409 #11	ENSGT00950000182997.a.b.b.b #12	ENSGT00940000158200 #13	ENSGT00940000161878 #14	ENSGT00940000154786 #15	ENSGT00940000155330 #16	ENSGT00940000162804 #17	ENSGT00950000183167.a.b.b.b #18	ENSGT00950000183072.b.a #19	ENSGT00940000157629 #20	ENSGT00940000160106 #21	ENSGT00390000000685 #22	ENSGT00390000010077 #23	ENSGT00950000182882.A.a #25	ENSGT01030000234528.B.b.a.a.a #26	ENSGT00940000160845 #27	ENSGT00940000157422 #28	ENSGT00940000156263 #29	ENSGT00940000161971 #30	ENSGT00500000044852.b #31	ENSGT00940000161446 #32	ENSGT00940000157032 #33	ENSGT00530000063734.b #34	ENSGT00950000183038.a.b.a #35	ENSGT00390000016511 #36	ENSGT00390000009755	ENSGT00940000161279 #37
Hystricomorpha_a	ANCESTRAL SPECIES	7	ENSGT00390000003114.e.a	ENSGT01030000234515.a.a.a #7	ENSGT00940000158313 #8	ENSGT01100000263763 #10	ENSGT00940000154409 #11	ENSGT00950000182997.a.b.b.b #12	ENSGT00940000158200 #13	ENSGT00940000161878 #14	ENSGT00940000154786 #15	ENSGT00940000155330 #16	ENSGT00940000162804 #17	ENSGT00950000183167.a.b.b.b #18	ENSGT00950000183072.b.a #19	ENSGT00940000157629 #20	ENSGT00940000160106 #21	ENSGT00390000000685 #22	ENSGT00390000010077 #23	ENSGT00950000182882.A.a #25	ENSGT01030000234528.B.b.a.a.a #26	ENSGT00940000160845 #27	ENSGT00940000157422 #28	ENSGT00940000156263 #29	ENSGT00940000161971 #30	ENSGT00500000044852.b #31	ENSGT00940000161446 #32	ENSGT00940000157032 #33	ENSGT00530000063734.b #34	ENSGT00950000183038.a.b.a #35	ENSGT00390000016511 #36	ENSGT00940000161279 #37	ENSGT00940000161303
Guinea pig	MODERN SPECIES	9	CERS5 (ENSCPOG00000000418) #7	LIMA1 (ENSCPOG00000000521) #8	ENSCPOG00000024814 #9	ENSCPOG00000039626 #10	LARP4 (ENSCPOG00000020519) #11	DIP2B (ENSCPOG00000012185) #12	ATF1 (ENSCPOG00000033391) #13	TMPRSS12 (ENSCPOG00000023853) #14	METTL7A (ENSCPOG00000031803) #15	SLC11A2 (ENSCPOG00000039292) #16	HIGD1C (ENSCPOG00000020309) #17	LETMD1 (ENSCPOG00000007913) #18	CSRNP2 (ENSCPOG00000035299) #19	TFCP2 (ENSCPOG00000007923) #20	ENSCPOG00000019712 #21	DAZAP2 (ENSCPOG00000037749) #22	SMAGP (ENSCPOG00000033211) #23	ENSCPOG00000036609 #24	ENSCPOG00000012590 #25	CELA1 (ENSCPOG00000004487) #26	GALNT6 (ENSCPOG00000013531) #27	SLC4A8 (ENSCPOG00000015647) #28	SCN8A (ENSCPOG00000015651) #29	FIGNL2 (ENSCPOG00000019931) #30	ANKRD33 (ENSCPOG00000001133) #31	ACVRL1 (ENSCPOG00000001660) #32	ACVR1B (ENSCPOG00000001136) #33	TAMALIN (ENSCPOG00000003092) #34	NR4A1 (ENSCPOG00000003095) #35	ATG101 (ENSCPOG00000015499) #36	KRT80 (ENSCPOG00000037905) #37
Hystricomorpha_b	ANCESTRAL SPECIES	53	ENSGT00860000135898	ENSGT00390000003114.e.a	ENSGT01030000234515.a.a.a #7	ENSGT00940000158313 #8	ENSGT01100000263763 #10	ENSGT00940000154409 #11	ENSGT00950000182997.a.b.b.b #12	ENSGT00940000158200 #13	ENSGT00940000161878 #14	ENSGT00940000154786 #15	ENSGT00940000155330 #16	ENSGT00950000183167.a.b.b.b #18	ENSGT00950000183072.b.a #19	ENSGT00940000157629 #20	ENSGT00940000160106 #21	ENSGT00390000000685 #22	ENSGT00390000010077 #23	ENSGT00950000182882.A.a #25	ENSGT01030000234528.B.b.a.a.a #26	ENSGT00940000160845 #27	ENSGT00940000157422 #28	ENSGT00940000156263 #29	ENSGT00500000044852.b #31	ENSGT00940000161446 #32	ENSGT00940000157032 #33	ENSGT00530000063734.b #34	ENSGT00950000183038.a.b.a #35	ENSGT00390000016511 #36	ENSGT00940000161279 #37	ENSGT00940000161303	ENSGT00940000154026.b.b.h.f.a.b
Long-tailed chinchilla	MODERN SPECIES	254	ENSCLAG00000001015	GPD1 (ENSCLAG00000001367)	CERS5 (ENSCLAG00000001516) #7	LIMA1 (ENSCLAG00000000738) #8	ENSCLAG00000001798 #10	LARP4 (ENSCLAG00000001829) #11	DIP2B (ENSCLAG00000002317) #12	ATF1 (ENSCLAG00000000957) #13	TMPRSS12 (ENSCLAG00000000986) #14	METTL7A (ENSCLAG00000001191) #15	ENSCLAG00000001253 #16	LETMD1 (ENSCLAG00000000694) #18	CSRNP2 (ENSCLAG00000000767) #19	TFCP2 (ENSCLAG00000000852) #20	POU6F1 (ENSCLAG00000000753) #21	DAZAP2 (ENSCLAG00000000857) #22	SMAGP (ENSCLAG00000000875) #23	ENSCLAG00000000915 #25	CELA1 (ENSCLAG00000001229) #26	GALNT6 (ENSCLAG00000001562) #27	SLC4A8 (ENSCLAG00000001794) #28	SCN8A (ENSCLAG00000001856) #29	ENSCLAG00000000876 #31	ACVRL1 (ENSCLAG00000000983) #32	ACVR1B (ENSCLAG00000003093) #33	TAMALIN (ENSCLAG00000001432) #34	NR4A1 (ENSCLAG00000000908) #35	ATG101 (ENSCLAG00000000951) #36	KRT80 (ENSCLAG00000001104) #37	KRT7 (ENSCLAG00000001185)	ENSCLAG00000001560
Degu	MODERN SPECIES	134	ENSODEG00000019859	ENSODEG00000011824 #13	ENSODEG00000015022 #14	METTL7A (ENSODEG00000012146) #15	ENSODEG00000011220	ENSODEG00000019844	SLC11A2 (ENSODEG00000011252) #16	ENSODEG00000012166	ENSODEG00000012543	ENSODEG00000011859	HIGD1C (ENSODEG00000011715) #17	LETMD1 (ENSODEG00000010964) #18	CSRNP2 (ENSODEG00000013075) #19	ENSODEG00000010792 #20	ENSODEG00000011102 #21	DAZAP2 (ENSODEG00000011237) #22	SMAGP (ENSODEG00000011513) #23	ENSODEG00000012421 #25	CELA1 (ENSODEG00000012871) #26	GALNT6 (ENSODEG00000010915) #27	SLC4A8 (ENSODEG00000011060) #28	SCN8A (ENSODEG00000011035) #29	ENSODEG00000012110	ACVRL1 (ENSODEG00000012774) #32	ACVR1B (ENSODEG00000011919) #33	TAMALIN (ENSODEG00000011304) #34	ENSODEG00000011116	NR4A1 (ENSODEG00000011353) #35	ATG101 (ENSODEG00000011080) #36	KRT80 (ENSODEG00000014114) #37	KRT7 (ENSODEG00000011780)
Naked mole-rat female	MODERN SPECIES	8	ENSHGLG00000041442	ENSHGLG00000005513 #11	DIP2B (ENSHGLG00000006842) #12	ENSHGLG00000035234	ATF1 (ENSHGLG00000044800) #13	ENSHGLG00000003982	ENSHGLG00000033537 #14	METTL7A (ENSHGLG00000007624) #15	ENSHGLG00000015984	SLC11A2 (ENSHGLG00000015898) #16	HIGD1C (ENSHGLG00000010374) #17	LETMD1 (ENSHGLG00000035309) #18	CSRNP2 (ENSHGLG00000038318) #19	TFCP2 (ENSHGLG00000006837) #20	POU6F1 (ENSHGLG00000006104) #21	DAZAP2 (ENSHGLG00000004225) #22	ENSHGLG00000050761 #23	BIN2 (ENSHGLG00000049230) #25	CELA1 (ENSHGLG00000015740) #26	ENSHGLG00000015575	GALNT6 (ENSHGLG00000015114) #27	SLC4A8 (ENSHGLG00000014625) #28	ENSHGLG00000035439	SCN8A (ENSHGLG00000003852) #29	FIGNL2 (ENSHGLG00000048205) #30	ACVRL1 (ENSHGLG00000017593) #32	ACVR1B (ENSHGLG00000015083) #33	TAMALIN (ENSHGLG00000035730) #34	ENSHGLG00000015174	NR4A1 (ENSHGLG00000041656) #35	ATG101 (ENSHGLG00000014036) #36
Sciuridae	ANCESTRAL SPECIES	15	ENSGT00390000002190	ENSGT01030000234515.a.a.a #7	ENSGT00940000158313 #8	ENSGT00940000163376	ENSGT00940000154409.i.a #11	ENSGT00950000182997.a.b.b.b #12	ENSGT00940000158200 #13	ENSGT00940000161878 #14	ENSGT00940000154786 #15	ENSGT00940000162804 #17	ENSGT00940000155330 #16	ENSGT00950000183167.a.b.b.b #18	ENSGT00950000183072.b.a #19	ENSGT00940000157629 #20	ENSGT00940000160106 #21	ENSGT00390000000685 #22	ENSGT00390000010077 #23	ENSGT00950000182882.A.a #25	ENSGT01030000234528.B.b.a.a.a #26	ENSGT00940000160845 #27	ENSGT00940000157422 #28	ENSGT00940000156263 #29	ENSGT00940000161971 #30	ENSGT00500000044852.b #31	ENSGT00940000161446 #32	ENSGT00940000157032 #33	ENSGT00530000063734.b #34	ENSGT00950000183038.a.b.a #35	ENSGT00390000016511 #36	ENSGT00390000009755	ENSGT00940000161279 #37
Marmotini	ANCESTRAL SPECIES	19	ENSGT00390000002190	ENSGT01030000234515.a.a.a #7	ENSGT00940000158313 #8	ENSGT00940000163376	ENSGT00940000154409.i.a #11	ENSGT00950000182997.a.b.b.b #12	ENSGT00940000158200 #13	ENSGT00940000161878 #14	ENSGT00940000154786.x #15	ENSGT00940000162804 #17	ENSGT00940000155330 #16	ENSGT00950000183167.a.b.b.b #18	ENSGT00950000183072.b.a #19	ENSGT00940000157629 #20	ENSGT00940000160106 #21	ENSGT00390000000685 #22	ENSGT00390000010077 #23	ENSGT00950000182882.A.a #25	ENSGT01030000234528.B.b.a.a.a #26	ENSGT00940000160845 #27	ENSGT00940000157422 #28	ENSGT00940000156263 #29	ENSGT00940000161971 #30	ENSGT00500000044852.b #31	ENSGT00940000161446 #32	ENSGT00940000157032 #33	ENSGT00530000063734.b #34	ENSGT00950000183038.a.b.a #35	ENSGT00390000016511 #36	ENSGT00390000009755	ENSGT00940000161279 #37
Alpin marmot	MODERN SPECIES	34	ENSMMMG00000023269	DIP2B (ENSMMMG00000023271) #12	ATF1 (ENSMMMG00000023289) #13	TMPRSS12 (ENSMMMG00000023294) #14	ENSMMMG00000023296 #15	ENSMMMG00000023301	ENSMMMG00000023303 #15	ENSMMMG00000023306 #15	HIGD1C (ENSMMMG00000023308) #17	SLC11A2 (ENSMMMG00000023309) #16	ENSMMMG00000023319	LETMD1 (ENSMMMG00000023321) #18	CSRNP2 (ENSMMMG00000023325) #19	ENSMMMG00000023332 #20	POU6F1 (ENSMMMG00000023342) #21	DAZAP2 (ENSMMMG00000023349) #22	SMAGP (ENSMMMG00000023352) #23	BIN2 (ENSMMMG00000023357) #25	CELA1 (ENSMMMG00000023359) #26	GALNT6 (ENSMMMG00000023362) #27	SLC4A8 (ENSMMMG00000000045) #28	SCN8A (ENSMMMG00000000177) #29	ANKRD33 (ENSMMMG00000000684) #31	ACVRL1 (ENSMMMG00000000708) #32	ACVR1B (ENSMMMG00000000817) #33	NR4A1 (ENSMMMG00000000858) #35	ATG101 (ENSMMMG00000000874) #36	SMIM41 (ENSMMMG00000000888)	KRT80 (ENSMMMG00000000902) #37	KRT7 (ENSMMMG00000000950)	ENSMMMG00000000969
Marmotini_b	ANCESTRAL SPECIES	11	ENSGT00390000002190	ENSGT01030000234515.a.a.a #7	ENSGT00940000158313 #8	ENSGT00940000163376	ENSGT00940000154409.i.a #11	ENSGT00950000182997.a.b.b.b #12	ENSGT00940000158200 #13	ENSGT00940000161878 #14	ENSGT00940000154786.x #15	ENSGT00940000162804 #17	ENSGT00940000155330 #16	ENSGT00950000183167.a.b.b.b #18	ENSGT00950000183072.b.a #19	ENSGT00940000157629 #20	ENSGT00940000160106 #21	ENSGT00390000000685 #22	ENSGT00390000010077 #23	ENSGT00950000182882.A.a #25	ENSGT01030000234528.B.b.a.a.a #26	ENSGT00940000160845 #27	ENSGT00940000157422 #28	ENSGT00940000156263 #29	ENSGT00940000161971 #30	ENSGT00500000044852.b #31	ENSGT00940000161446 #32	ENSGT00940000157032 #33	ENSGT00530000063734.b #34	ENSGT00950000183038.a.b.a #35	ENSGT00390000016511 #36	ENSGT00390000009755	ENSGT00940000161279 #37
Squirrel	MODERN SPECIES	112	COX14 (ENSSTOG00000004975)	CERS5 (ENSSTOG00000004980) #7	LIMA1 (ENSSTOG00000004992) #8	ENSSTOG00000032900 #10	LARP4 (ENSSTOG00000003553) #11	DIP2B (ENSSTOG00000003833) #12	ATF1 (ENSSTOG00000010742) #13	TMPRSS12 (ENSSTOG00000000180) #14	METTL7A (ENSSTOG00000021095) #15	HIGD1C (ENSSTOG00000022352) #17	SLC11A2 (ENSSTOG00000013293) #16	LETMD1 (ENSSTOG00000009107) #18	CSRNP2 (ENSSTOG00000009118) #19	TFCP2 (ENSSTOG00000009123) #20	POU6F1 (ENSSTOG00000009140) #21	DAZAP2 (ENSSTOG00000027739) #22	SMAGP (ENSSTOG00000026431) #23	ENSSTOG00000009185 #25	CELA1 (ENSSTOG00000009200) #26	GALNT6 (ENSSTOG00000009225) #27	SLC4A8 (ENSSTOG00000000454) #28	SCN8A (ENSSTOG00000000463) #29	FIGNL2 (ENSSTOG00000029947) #30	ENSSTOG00000000474 #31	ACVRL1 (ENSSTOG00000000477) #32	ACVR1B (ENSSTOG00000000480) #33	TAMALIN (ENSSTOG00000000486) #34	NR4A1 (ENSSTOG00000019650) #35	ATG101 (ENSSTOG00000000488) #36	KRT80 (ENSSTOG00000024405) #37	KRT7 (ENSSTOG00000022599)
Arctic ground squirrel	DUPLICATION
Arctic ground squirrel	MODERN SPECIES	202										HIGD1C (ENSUPAG00010003220) #17	SLC11A2 (ENSUPAG00010003188) #16	LETMD1 (ENSUPAG00010003179) #18	CSRNP2 (ENSUPAG00010003165) #19	TFCP2 (ENSUPAG00010003132) #20	POU6F1 (ENSUPAG00010003099) #21	DAZAP2 (ENSUPAG00010003086) #22	SMAGP (ENSUPAG00010003076) #23	BIN2 (ENSUPAG00010003062) #25	CELA1 (ENSUPAG00010003046) #26	GALNT6 (ENSUPAG00010003019) #27	SLC4A8 (ENSUPAG00010002963) #28	SCN8A (ENSUPAG00010002238) #29	ANKRD33 (ENSUPAG00010002209) #31	ACVRL1 (ENSUPAG00010002166) #32	ACVR1B (ENSUPAG00010002146) #33	TAMALIN (ENSUPAG00010002130) #34	NR4A1 (ENSUPAG00010002102) #35	ATG101 (ENSUPAG00010002091) #36	SMIM41 (ENSUPAG00010002088)	KRT80 (ENSUPAG00010002062) #37	KRT7 (ENSUPAG00010002035)
Arctic ground squirrel	MODERN SPECIES	328	PMM1 (ENSUPAG00010005870)	DESI1 (ENSUPAG00010005863)	XRCC6 (ENSUPAG00010005843)	SNU13 (ENSUPAG00010005841)	ENSUPAG00010005838	MEI1 (ENSUPAG00010005795)	CCDC134 (ENSUPAG00010005788)	SREBF2 (ENSUPAG00010005777)	SHISA8 (ENSUPAG00010005772)	TNFRSF13C (ENSUPAG00010005768)	CENPM (ENSUPAG00010005746)	SMIM45 (ENSUPAG00010005741)	ENSUPAG00010005721	ENSUPAG00010005713	ENSUPAG00010005707	ENSUPAG00010005703 #22
Eurasian red squirrel	DUPLICATION
Eurasian red squirrel	MODERN SPECIES	14	ENSSVLG00005017589	ENSSVLG00005017764	ENSSVLG00005010983 #11	ENSSVLG00005012155	DIP2B (ENSSVLG00005012220) #12	ATF1 (ENSSVLG00005012633) #13	TMPRSS12 (ENSSVLG00005012718) #14	ENSSVLG00005012785 #15	ENSSVLG00005012847 #15	HIGD1C (ENSSVLG00005012890) #17	SLC11A2 (ENSSVLG00005012984) #16	LETMD1 (ENSSVLG00005013359) #18	CSRNP2 (ENSSVLG00005013396) #19	TFCP2 (ENSSVLG00005013960) #20	POU6F1 (ENSSVLG00005014412) #21	DAZAP2 (ENSSVLG00005014506) #22	ENSSVLG00005014670 #23	ENSSVLG00005014766 #25	CELA1 (ENSSVLG00005015060) #26	GALNT6 (ENSSVLG00005015159) #27	SLC4A8 (ENSSVLG00005015276) #28	SCN8A (ENSSVLG00005015854) #29	ENSSVLG00005016978	ANKRD33 (ENSSVLG00005017101) #31	ACVRL1 (ENSSVLG00005017128) #32	ACVR1B (ENSSVLG00005017260) #33	TAMALIN (ENSSVLG00005017358) #34	NR4A1 (ENSSVLG00005017404) #35	ATG101 (ENSSVLG00005017654) #36	SMIM41 (ENSSVLG00005017698)	KRT80 (ENSSVLG00005017723) #37
Eurasian red squirrel	MODERN SPECIES	14	CSDC2 (ENSSVLG00005021115)	PMM1 (ENSSVLG00005021168)	DESI1 (ENSSVLG00005021220)	XRCC6 (ENSSVLG00005021287)	ENSSVLG00005021427	MEI1 (ENSSVLG00005021530)	CCDC134 (ENSSVLG00005021846)	SREBF2 (ENSSVLG00005021885)	ENSSVLG00005021918	SHISA8 (ENSSVLG00005021957)	TNFRSF13C (ENSSVLG00005021994)	CENPM (ENSSVLG00005022024)	SMIM45 (ENSSVLG00005022101)	SEPTIN3 (ENSSVLG00005003473)	WBP2NL (ENSSVLG00005003578)	ENSSVLG00005003601 #22	NAGA (ENSSVLG00005003614)	PHETA2 (ENSSVLG00005003635)	SMDT1 (ENSSVLG00005003647)	NDUFA6 (ENSSVLG00005003661)	ENSSVLG00005003686	ENSSVLG00005003721	ENSSVLG00005003890	TCF20 (ENSSVLG00005004152)	NFAM1 (ENSSVLG00005004168)	SERHL2 (ENSSVLG00005004215)	RRP7A (ENSSVLG00005004268)	POLDIP3 (ENSSVLG00005004309)	ENSSVLG00005004382	A4GALT (ENSSVLG00005004406)	ARFGAP3 (ENSSVLG00005004430)