Rodentia_A	ANCESTRAL SPECIES	5	ENSGT00940000153783.b.b.c.a.a.a	ENSGT00940000153783.b.b.c.b	ENSGT00940000153783.b.b.c.a.b	ENSGT00550000074917 #11	ENSGT00940000159828 #12	ENSGT00940000157053 #13	ENSGT00940000161858 #14	ENSGT00950000183084.b.b #15	ENSGT00940000162610	ENSGT00510000047914.b #17	ENSGT00940000162172 #18	ENSGT00940000156311 #19	ENSGT00970000194716	ENSGT00940000156022.b #20	ENSGT00390000001652.f.b #21	ENSGT00950000183153.c.b.a.a #22	ENSGT00940000159593 #23	ENSGT00940000155387 #24	ENSGT00730000111162 #25	ENSGT00390000006126 #26	ENSGT01090000260076.a #27	ENSGT00940000153270.b.b #29	ENSGT00390000001750 #30	ENSGT00390000003511	ENSGT00390000011058.b #31	ENSGT00940000155929 #33	ENSGT01050000244976.b.a #34	ENSGT00940000156634 #35	ENSGT00940000160327 #36	ENSGT00940000159448	ENSGT00550000074851
Hystricomorpha	ANCESTRAL SPECIES	6	ENSGT00950000182930.A.b ##10	ENSGT00950000182930.A.a #9	ENSGT00950000182930.B #10	ENSGT00940000153783.b.b.c.a.b	ENSGT00550000074917 #11	ENSGT00940000159828 #12	ENSGT00940000157053 #13	ENSGT00940000161858 #14	ENSGT00950000183084.b.b #15	ENSGT00510000047914.b #17	ENSGT00940000162172 #18	ENSGT00940000156311 #19	ENSGT00900000143836	ENSGT00940000156022.b #20	ENSGT00390000001652.f.b #21	ENSGT00950000183153.c.b.a.a #22	ENSGT00940000159593 #23	ENSGT00940000155387 #24	ENSGT00730000111162 #25	ENSGT00390000006126 #26	ENSGT01090000260076.a #27	ENSGT00940000153270.b.b #29	ENSGT00390000001750 #30	ENSGT00390000003511	ENSGT00390000011058.b #31	ENSGT00940000155929 #33	ENSGT01050000244976.b.a #34	ENSGT00940000156634 #35	ENSGT00940000160327 #36	ENSGT00940000159448	ENSGT00550000074851
Hystricomorpha_a	ANCESTRAL SPECIES	4	ENSGT00950000182930.A.b ##10	ENSGT00950000182930.A.a #9	ENSGT00950000182930.B #10	ENSGT00940000153783.b.b.c.a.b	ENSGT00550000074917 #11	ENSGT00940000159828 #12	ENSGT00940000157053 #13	ENSGT00940000161858 #14	ENSGT00950000183084.b.b #15	ENSGT00510000047914.b #17	ENSGT00940000162172 #18	ENSGT00940000156311 #19	ENSGT01100000266402	ENSGT00940000156022.b #20	ENSGT00390000001652.f.b #21	ENSGT00950000183153.c.b.a.a #22	ENSGT00940000159593 #23	ENSGT00940000155387 #24	ENSGT00730000111162 #25	ENSGT00390000006126 #26	ENSGT01090000260076.a #27	ENSGT00940000153270.b.b #29	ENSGT00390000001750 #30	ENSGT00390000011058.b #31	ENSGT00940000155929 #33	ENSGT01050000244976.b.a #34	ENSGT00940000156634 #35	ENSGT00940000160327 #36	ENSGT00940000159448	ENSGT00550000074851	ENSGT00940000159619.a
Hystricomorpha_b	ANCESTRAL SPECIES	9	ENSGT00950000182930.A.b ##10	ENSGT00950000182930.A.a #9	ENSGT00950000182930.B #10	ENSGT00940000153783.b.b.c.a.b	ENSGT00550000074917 #11	ENSGT00940000159828 #12	ENSGT00940000157053 #13	ENSGT00940000161858 #14	ENSGT00950000183084.b.b #15	ENSGT00510000047914.b #17	ENSGT00940000162172 #18	ENSGT00940000156311 #19	ENSGT01100000266402	ENSGT00940000156022.b #20	ENSGT00390000001652.f.b #21	ENSGT00950000183153.c.b.a.a #22	ENSGT00940000159593 #23	ENSGT00940000155387 #24	ENSGT00730000111162 #25	ENSGT00390000006126 #26	ENSGT01090000260076.a #27	ENSGT00940000153270.b.b #29	ENSGT00390000001750 #30	ENSGT00390000011058.b #31	ENSGT00940000155929 #33	ENSGT01050000244976.b.a #34	ENSGT00940000156634 #35	ENSGT00940000160327 #36	ENSGT00940000159448	ENSGT00550000074851	ENSGT00940000159619.a
Degu	MODERN SPECIES	169	DNAJB11 (ENSODEG00000001870) #7	AHSG (ENSODEG00000001885) #8	HRG (ENSODEG00000001904) #9	KNG1 (ENSODEG00000001927) #10	RFC4 (ENSODEG00000001999) #11	ADIPOQ (ENSODEG00000002012) #12	ST6GAL1 (ENSODEG00000002040) #13	RTP1 (ENSODEG00000000396) #14	MASP1 (ENSODEG00000000434) #15	ENSODEG00000000479 #16	SST (ENSODEG00000000486) #17	RTP2 (ENSODEG00000000495) #18	BCL6 (ENSODEG00000000516) #19	LPP (ENSODEG00000000601) #20	TPRG1 (ENSODEG00000000645) #21	TP63 (ENSODEG00000000698) #22	P3H2 (ENSODEG00000000751) #23	CLDN1 (ENSODEG00000000775) #24	CLDN16 (ENSODEG00000000787) #25	TMEM207 (ENSODEG00000000814) #26	IL1RAP (ENSODEG00000000880) #27	ENSODEG00000000947 #28	GMNC (ENSODEG00000000968) #29	OSTN (ENSODEG00000000984) #30	CCDC50 (ENSODEG00000001028) #31	ENSODEG00000018632 #32	FGF12 (ENSODEG00000000898) #33	ENSODEG00000000915 #34	PLAAT1 (ENSODEG00000000928) #35	ATP13A5 (ENSODEG00000000942) #36
Long-tailed chinchilla	MODERN SPECIES	127	FETUB (ENSCLAG00000015483) ##10	HRG (ENSCLAG00000015542) #9	ENSCLAG00000017074 #10	EIF4A2 (ENSCLAG00000014891)	RFC4 (ENSCLAG00000014582) #11	ADIPOQ (ENSCLAG00000016452) #12	ST6GAL1 (ENSCLAG00000015941) #13	RTP1 (ENSCLAG00000013765) #14	MASP1 (ENSCLAG00000012518) #15	SST (ENSCLAG00000015832) #17	RTP2 (ENSCLAG00000014964) #18	ENSCLAG00000017951	BCL6 (ENSCLAG00000012339) #19	LPP (ENSCLAG00000015949) #20	TPRG1 (ENSCLAG00000013300) #21	TP63 (ENSCLAG00000012538) #22	P3H2 (ENSCLAG00000012801) #23	CLDN1 (ENSCLAG00000013178) #24	CLDN16 (ENSCLAG00000012605) #25	IL1RAP (ENSCLAG00000012363) #27	GMNC (ENSCLAG00000011473) #29	OSTN (ENSCLAG00000013977) #30	CCDC50 (ENSCLAG00000014114) #31	FGF12 (ENSCLAG00000011409) #33	MB21D2 (ENSCLAG00000014657) #34	PLAAT1 (ENSCLAG00000012403) #35	ATP13A5 (ENSCLAG00000012908) #36	ATP13A4 (ENSCLAG00000012524)	OPA1 (ENSCLAG00000012734)	HES1 (ENSCLAG00000015321)	CPN2 (ENSCLAG00000018106)
Guinea pig	MODERN SPECIES	7	FETUB (ENSCPOG00000011207) ##10	HRG (ENSCPOG00000025939) #9	KNG1 (ENSCPOG00000012757) #10	ENSCPOG00000011183	RFC4 (ENSCPOG00000011191) #11	ADIPOQ (ENSCPOG00000036737) #12	ST6GAL1 (ENSCPOG00000001200) #13	RTP1 (ENSCPOG00000001203) #14	MASP1 (ENSCPOG00000015723) #15	SST (ENSCPOG00000009662) #17	RTP2 (ENSCPOG00000009665) #18	BCL6 (ENSCPOG00000004090) #19	ENSCPOG00000033304	LPP (ENSCPOG00000015584) #20	TPRG1 (ENSCPOG00000007437) #21	TP63 (ENSCPOG00000014770) #22	P3H2 (ENSCPOG00000004329) #23	CLDN1 (ENSCPOG00000037018) #24	CLDN16 (ENSCPOG00000008643) #25	IL1RAP (ENSCPOG00000008554) #27	GMNC (ENSCPOG00000019517) #29	OSTN (ENSCPOG00000024963) #30	CCDC50 (ENSCPOG00000013365) #31	FGF12 (ENSCPOG00000038518) #33	MB21D2 (ENSCPOG00000011028) #34	PLAAT1 (ENSCPOG00000008871) #35	ATP13A5 (ENSCPOG00000008873) #36	ATP13A4 (ENSCPOG00000008886)	OPA1 (ENSCPOG00000005925)	HES1 (ENSCPOG00000036195)	CPN2 (ENSCPOG00000037149)
Naked mole-rat female	MODERN SPECIES	27	ST6GAL1 (ENSHGLG00000037893) #13	ENSHGLG00000036874	RTP1 (ENSHGLG00000013919) #14	MASP1 (ENSHGLG00000013470) #15	ENSHGLG00000048542	ENSHGLG00000046703	ENSHGLG00000012948	SST (ENSHGLG00000019161) #17	RTP2 (ENSHGLG00000016449) #18	BCL6 (ENSHGLG00000016440) #19	ENSHGLG00000021340	LPP (ENSHGLG00000016385) #20	ENSHGLG00000036742	ENSHGLG00000042236	ENSHGLG00000039972 #21	TP63 (ENSHGLG00000016277) #22	P3H2 (ENSHGLG00000019175) #23	CLDN1 (ENSHGLG00000038289) #24	CLDN16 (ENSHGLG00000018130) #25	ENSHGLG00000035223	TMEM207 (ENSHGLG00000037564) #26	IL1RAP (ENSHGLG00000018108) #27	ENSHGLG00000036963 #27	ENSHGLG00000019218	GMNC (ENSHGLG00000017131) #29	ENSHGLG00000040250	ENSHGLG00000016933	ENSHGLG00000016923	OSTN (ENSHGLG00000039251) #30	ENSHGLG00000042558	CCDC50 (ENSHGLG00000016906) #31
Sciuridae	ANCESTRAL SPECIES	12	ENSGT00950000182930.B #10	ENSGT00860000135739	ENSGT00940000153783.b.b.c.a.a.a	ENSGT00550000074917 #11	ENSGT00940000159828 #12	ENSGT00940000157053 #13	ENSGT00940000161858 #14	ENSGT00950000183084.b.b #15	ENSGT00940000162610	ENSGT00510000047914.b #17	ENSGT00940000162172 #18	ENSGT00940000156311 #19	ENSGT00970000194716	ENSGT00940000156022.b #20	ENSGT00390000001652.f.b #21	ENSGT00950000183153.c.b.a.a #22	ENSGT00940000159593 #23	ENSGT00940000155387 #24	ENSGT00730000111162 #25	ENSGT00390000006126 #26	ENSGT01090000260076.a #27	ENSGT00940000153270.b.b #29	ENSGT00390000001750 #30	ENSGT00390000003511	ENSGT00390000011058.b #31	ENSGT00940000155929 #33	ENSGT01050000244976.b.a #34	ENSGT00940000156634 #35	ENSGT00940000160327 #36	ENSGT00940000159448	ENSGT00550000074851
Marmotini	ANCESTRAL SPECIES	57	ENSGT00950000182930.B #10	ENSGT00860000135739	ENSGT00940000153783.b.b.c.a.a.a.a	ENSGT00550000074917 #11	ENSGT00940000159828 #12	ENSGT00940000157053 #13	ENSGT00940000161858 #14	ENSGT00950000183084.b.b #15	ENSGT00940000162610	ENSGT00510000047914.b #17	ENSGT00940000162172 #18	ENSGT00940000156311 #19	ENSGT00900000143836	ENSGT00940000156022.b #20	ENSGT00390000001652.f.b #21	ENSGT00950000183153.c.b.a.a #22	ENSGT00940000159593 #23	ENSGT00940000155387 #24	ENSGT00730000111162 #25	ENSGT00390000006126 #26	ENSGT01090000260076.a #27	ENSGT00940000153270.b.b #29	ENSGT00390000001750 #30	ENSGT00390000003511	ENSGT00390000011058.b #31	ENSGT00940000155929 #33	ENSGT01050000244976.b.a #34	ENSGT00940000156634 #35	ENSGT00940000160327 #36	ENSGT00940000159448	ENSGT00550000074851
Marmotini_b	ANCESTRAL SPECIES	79	ENSGT00950000182930.B #10	ENSGT00860000135739	ENSGT00940000153783.b.b.c.a.a.a.a	ENSGT00550000074917 #11	ENSGT00940000159828 #12	ENSGT00940000157053 #13	ENSGT00940000161858 #14	ENSGT00950000183084.b.b #15	ENSGT00940000162610	ENSGT00510000047914.b #17	ENSGT00940000162172 #18	ENSGT00940000156311 #19	ENSGT00900000143836	ENSGT00940000156022.b #20	ENSGT00390000001652.f.b #21	ENSGT00950000183153.c.b.a.a #22	ENSGT00940000159593 #23	ENSGT00940000155387 #24	ENSGT00730000111162 #25	ENSGT00390000006126 #26	ENSGT01090000260076.a #27
Squirrel	MODERN SPECIES	178	FETUB (ENSSTOG00000012584) ##10	HRG (ENSSTOG00000012587) #9	KNG1 (ENSSTOG00000027812) #10	ENSSTOG00000012601	ENSSTOG00000012616 #11	ADIPOQ (ENSSTOG00000016020) #12	ST6GAL1 (ENSSTOG00000015751) #13	RTP1 (ENSSTOG00000010261) #14	MASP1 (ENSSTOG00000010265) #15	ENSSTOG00000010275	SST (ENSSTOG00000015070) #17	RTP2 (ENSSTOG00000025837) #18	BCL6 (ENSSTOG00000000843) #19	LPP (ENSSTOG00000004791) #20	TPRG1 (ENSSTOG00000013052) #21	TP63 (ENSSTOG00000013771) #22	P3H2 (ENSSTOG00000006501) #23	CLDN1 (ENSSTOG00000009637) #24	CLDN16 (ENSSTOG00000008723) #25
Arctic ground squirrel	MODERN SPECIES	67	ENSUPAG00010001535	EIF4A2 (ENSUPAG00010001415)	RFC4 (ENSUPAG00010001386) #11	ADIPOQ (ENSUPAG00010001377) #12	ST6GAL1 (ENSUPAG00010001354) #13	RTP1 (ENSUPAG00010001348) #14	ENSUPAG00010001334	MASP1 (ENSUPAG00010001243) #15	ENSUPAG00010001238	SST (ENSUPAG00010001221) #17	RTP2 (ENSUPAG00010001211) #18	BCL6 (ENSUPAG00010001190) #19	ENSUPAG00010001184	LPP (ENSUPAG00010001116) #20	TPRG1 (ENSUPAG00010001096) #21	TP63 (ENSUPAG00010000340) #22	P3H2 (ENSUPAG00010000290) #23	CLDN1 (ENSUPAG00010000275) #24	CLDN16 (ENSUPAG00010000249) #25	TMEM207 (ENSUPAG00010000237) #26	IL1RAP (ENSUPAG00010000152) #27
Alpin marmot	MODERN SPECIES	65	EIF4A2 (ENSMMMG00000009054)	RFC4 (ENSMMMG00000009263) #11	ADIPOQ (ENSMMMG00000009299) #12	ENSMMMG00000009302	ST6GAL1 (ENSMMMG00000009312) #13	RTP1 (ENSMMMG00000009324) #14	MASP1 (ENSMMMG00000009332) #15	ENSMMMG00000009397	ENSMMMG00000009405	SST (ENSMMMG00000009413) #17	RTP2 (ENSMMMG00000009435) #18	BCL6 (ENSMMMG00000009441) #19	ENSMMMG00000009454	LPP (ENSMMMG00000009476) #20	TPRG1 (ENSMMMG00000009493) #21	TP63 (ENSMMMG00000009524) #22	P3H2 (ENSMMMG00000010050) #23	CLDN1 (ENSMMMG00000010077) #24	CLDN16 (ENSMMMG00000010089) #25	TMEM207 (ENSMMMG00000010116) #26	IL1RAP (ENSMMMG00000010137) #27	GMNC (ENSMMMG00000010205) #29	OSTN (ENSMMMG00000010224) #30	UTS2B (ENSMMMG00000010236)	CCDC50 (ENSMMMG00000010258) #31	ENSMMMG00000010324 #33	ENSMMMG00000010336 #33	MB21D2 (ENSMMMG00000010348) #34	PLAAT1 (ENSMMMG00000010364) #35	ATP13A5 (ENSMMMG00000010381) #36	ATP13A4 (ENSMMMG00000010493)
Eurasian red squirrel	MODERN SPECIES	1	ENSSVLG00005008819	RFC4 (ENSSVLG00005008782) #11	ENSSVLG00005008759	ADIPOQ (ENSSVLG00005008730) #12	ST6GAL1 (ENSSVLG00005008652) #13	RTP1 (ENSSVLG00005008628) #14	MASP1 (ENSSVLG00005008564) #15	ENSSVLG00005008533	SST (ENSSVLG00005008514) #17	RTP2 (ENSSVLG00005008485) #18	ENSSVLG00005008392 #19	ENSSVLG00005008361	LPP (ENSSVLG00005008318) #20	TPRG1 (ENSSVLG00005008266) #21	ENSSVLG00005008233	TP63 (ENSSVLG00005007416) #22	P3H2 (ENSSVLG00005006989) #23	CLDN1 (ENSSVLG00005006941) #24	CLDN16 (ENSSVLG00005006918) #25	TMEM207 (ENSSVLG00005006891) #26	IL1RAP (ENSSVLG00005006739) #27	GMNC (ENSSVLG00005006667) #29	OSTN (ENSSVLG00005006607) #30	UTS2B (ENSSVLG00005006554)	ENSSVLG00005006532	CCDC50 (ENSSVLG00005006494) #31	FGF12 (ENSSVLG00005006414) #33	MB21D2 (ENSSVLG00005006368) #34	ENSSVLG00005006347	PLAAT1 (ENSSVLG00005006328) #35	ATP13A5 (ENSSVLG00005006143) #36