Rodentia_A	ANCESTRAL SPECIES	5	ENSGT00510000047914.b	ENSGT00940000162172	ENSGT00940000156311 #7	ENSGT00970000194716 #8	ENSGT00940000156022.b #9	ENSGT00390000001652.f.b #10	ENSGT00950000183153.c.b.a.a #12	ENSGT00940000159593 #13	ENSGT00940000155387 #14	ENSGT00730000111162 #15	ENSGT00390000006126 #16	ENSGT01090000260076.a #17	ENSGT00940000153270.b.b #18	ENSGT00390000001750 #19	ENSGT00390000003511 #20	ENSGT00390000011058.b #22	ENSGT00940000155929 #23	ENSGT01050000244976.b.a #24	ENSGT00940000156634 #26	ENSGT00940000160327 #27	ENSGT00940000159448 #28	ENSGT00550000074851 #29	ENSGT00940000159619.a #30	ENSGT00860000135828	ENSGT00940000163072 #31	ENSGT00940000161771 #32	ENSGT00940000162953 #33	ENSGT00940000155941.A #34	ENSGT00390000018718 #35	ENSGT00940000156442 #36	ENSGT00940000161593 #37
Sciuridae	ANCESTRAL SPECIES	12	ENSGT00510000047914.b	ENSGT00940000162172	ENSGT00940000156311 #7	ENSGT00970000194716 #8	ENSGT00940000156022.b #9	ENSGT00390000001652.f.b #10	ENSGT00950000183153.c.b.a.a #12	ENSGT00940000159593 #13	ENSGT00940000155387 #14	ENSGT00730000111162 #15	ENSGT00390000006126 #16	ENSGT01090000260076.a #17	ENSGT00940000153270.b.b #18	ENSGT00390000001750 #19	ENSGT00390000003511 #20	ENSGT00390000011058.b #22	ENSGT00940000155929 #23	ENSGT01050000244976.b.a #24	ENSGT00940000156634 #26	ENSGT00940000160327 #27	ENSGT00940000159448 #28	ENSGT00550000074851 #29	ENSGT00940000159619.a #30	ENSGT00860000135828	ENSGT00940000163072 #31	ENSGT00940000161771 #32	ENSGT00940000162953 #33	ENSGT00940000155941.A #34	ENSGT00390000018718 #35	ENSGT00940000156442 #36	ENSGT00940000161593 #37
Eurasian red squirrel	MODERN SPECIES	1	ENSSVLG00005008392 #7	ENSSVLG00005008361 #8	LPP (ENSSVLG00005008318) #9	TPRG1 (ENSSVLG00005008266) #10	ENSSVLG00005008233 #11	TP63 (ENSSVLG00005007416) #12	P3H2 (ENSSVLG00005006989) #13	CLDN1 (ENSSVLG00005006941) #14	CLDN16 (ENSSVLG00005006918) #15	TMEM207 (ENSSVLG00005006891) #16	IL1RAP (ENSSVLG00005006739) #17	GMNC (ENSSVLG00005006667) #18	OSTN (ENSSVLG00005006607) #19	UTS2B (ENSSVLG00005006554) #20	ENSSVLG00005006532 #21	CCDC50 (ENSSVLG00005006494) #22	FGF12 (ENSSVLG00005006414) #23	MB21D2 (ENSSVLG00005006368) #24	ENSSVLG00005006347 #25	PLAAT1 (ENSSVLG00005006328) #26	ATP13A5 (ENSSVLG00005006143) #27	ATP13A4 (ENSSVLG00005005773) #28	OPA1 (ENSSVLG00005005536) #29	HES1 (ENSSVLG00005005416) #30	CPN2 (ENSSVLG00005005406) #31	LRRC15 (ENSSVLG00005005394) #32	GP5 (ENSSVLG00005005382) #33	ENSSVLG00005005145 #34	TMEM44 (ENSSVLG00005005023) #35	LSG1 (ENSSVLG00005004993) #36	FAM43A (ENSSVLG00005004980) #37
Marmotini	ANCESTRAL SPECIES	57	ENSGT00510000047914.b	ENSGT00940000162172	ENSGT00940000156311 #7	ENSGT00900000143836	ENSGT00940000156022.b #9	ENSGT00390000001652.f.b #10	ENSGT00950000183153.c.b.a.a #12	ENSGT00940000159593 #13	ENSGT00940000155387 #14	ENSGT00730000111162 #15	ENSGT00390000006126 #16	ENSGT01090000260076.a #17	ENSGT00940000153270.b.b #18	ENSGT00390000001750 #19	ENSGT00390000003511 #20	ENSGT00390000011058.b #22	ENSGT00940000155929 #23	ENSGT01050000244976.b.a #24	ENSGT00940000156634 #26	ENSGT00940000160327 #27	ENSGT00940000159448 #28	ENSGT00550000074851 #29	ENSGT00940000159619.a #30	ENSGT00860000135828	ENSGT00940000163072 #31	ENSGT00940000161771 #32	ENSGT00940000162953 #33	ENSGT00940000155941.A #34	ENSGT00390000018718 #35	ENSGT00940000156442 #36	ENSGT00940000161593 #37
Alpin marmot	MODERN SPECIES	65	SST (ENSMMMG00000009413)	RTP2 (ENSMMMG00000009435)	BCL6 (ENSMMMG00000009441) #7	ENSMMMG00000009454	LPP (ENSMMMG00000009476) #9	TPRG1 (ENSMMMG00000009493) #10	TP63 (ENSMMMG00000009524) #12	P3H2 (ENSMMMG00000010050) #13	CLDN1 (ENSMMMG00000010077) #14	CLDN16 (ENSMMMG00000010089) #15	TMEM207 (ENSMMMG00000010116) #16	IL1RAP (ENSMMMG00000010137) #17	GMNC (ENSMMMG00000010205) #18	OSTN (ENSMMMG00000010224) #19	UTS2B (ENSMMMG00000010236) #20	CCDC50 (ENSMMMG00000010258) #22	ENSMMMG00000010324 #23	ENSMMMG00000010336 #23	MB21D2 (ENSMMMG00000010348) #24	PLAAT1 (ENSMMMG00000010364) #26	ATP13A5 (ENSMMMG00000010381) #27	ATP13A4 (ENSMMMG00000010493) #28	OPA1 (ENSMMMG00000010558) #29	HES1 (ENSMMMG00000010681) #30	ENSMMMG00000010691	CPN2 (ENSMMMG00000010696) #31	LRRC15 (ENSMMMG00000010700) #32	GP5 (ENSMMMG00000010711) #33	ENSMMMG00000010728 #34	TMEM44 (ENSMMMG00000010743) #35	LSG1 (ENSMMMG00000010772) #36
Marmotini_b	ANCESTRAL SPECIES	324														ENSGT00940000153270.b.b #18	ENSGT00390000001750 #19	ENSGT00390000011058.b #22
Squirrel	MODERN SPECIES	496														ENSSTOG00000004745 #18	OSTN (ENSSTOG00000020025) #19	CCDC50 (ENSSTOG00000000219) #22
Arctic ground squirrel	MODERN SPECIES	1066																CCDC50 (ENSUPAG00010019862) #22
Hystricomorpha	ANCESTRAL SPECIES	6	ENSGT00510000047914.b	ENSGT00940000162172	ENSGT00940000156311 #7	ENSGT00900000143836	ENSGT00940000156022.b #9	ENSGT00390000001652.f.b #10	ENSGT00950000183153.c.b.a.a #12	ENSGT00940000159593 #13	ENSGT00940000155387 #14	ENSGT00730000111162 #15	ENSGT00390000006126 #16	ENSGT01090000260076.a #17	ENSGT00940000153270.b.b #18	ENSGT00390000001750 #19	ENSGT00390000003511 #20	ENSGT00390000011058.b #22	ENSGT00940000155929 #23	ENSGT01050000244976.b.a #24	ENSGT00940000156634 #26	ENSGT00940000160327 #27	ENSGT00940000159448 #28	ENSGT00550000074851 #29	ENSGT00940000159619.a #30	ENSGT00860000135828	ENSGT00940000163072 #31	ENSGT00940000161771 #32	ENSGT00940000162953 #33	ENSGT00940000155941.A #34	ENSGT00390000018718 #35	ENSGT00940000156442 #36	ENSGT00940000161593 #37
Hystricomorpha_a	ANCESTRAL SPECIES	4	ENSGT00950000183084.b.b	ENSGT00510000047914.b	ENSGT00940000162172	ENSGT00940000156311 #7	ENSGT01100000266402	ENSGT00940000156022.b #9	ENSGT00390000001652.f.b #10	ENSGT00950000183153.c.b.a.a #12	ENSGT00940000159593 #13	ENSGT00940000155387 #14	ENSGT00730000111162 #15	ENSGT00390000006126 #16	ENSGT01090000260076.a #17	ENSGT00940000153270.b.b #18	ENSGT00390000001750 #19	ENSGT00390000011058.b #22	ENSGT00940000155929 #23	ENSGT01050000244976.b.a #24	ENSGT00940000156634 #26	ENSGT00940000160327 #27	ENSGT00940000159448 #28	ENSGT00550000074851 #29	ENSGT00940000159619.a #30	ENSGT00940000163072 #31	ENSGT00940000161771 #32	ENSGT00940000155941.A #34	ENSGT00390000018718 #35	ENSGT00940000156442 #36	ENSGT00940000161593 #37	ENSGT00940000158154	ENSGT00940000156389.a
Hystricomorpha_b	ANCESTRAL SPECIES	9	ENSGT00950000183084.b.b	ENSGT00510000047914.b	ENSGT00940000162172	ENSGT00940000156311 #7	ENSGT01100000266402	ENSGT00940000156022.b #9	ENSGT00390000001652.f.b #10	ENSGT00950000183153.c.b.a.a #12	ENSGT00940000159593 #13	ENSGT00940000155387 #14	ENSGT00730000111162 #15	ENSGT00390000006126 #16	ENSGT01090000260076.a #17	ENSGT00940000153270.b.b #18	ENSGT00390000001750 #19	ENSGT00390000011058.b #22	ENSGT00940000155929 #23	ENSGT01050000244976.b.a #24	ENSGT00940000156634 #26	ENSGT00940000160327 #27	ENSGT00940000159448 #28	ENSGT00550000074851 #29	ENSGT00940000159619.a #30	ENSGT00940000163072 #31	ENSGT00940000161771 #32	ENSGT00940000155941.A #34	ENSGT00940000156442 #36	ENSGT00940000161593 #37	ENSGT00940000158154	ENSGT00940000156389.a	ENSGT00390000004757
Long-tailed chinchilla	MODERN SPECIES	127	RTP1 (ENSCLAG00000013765)	MASP1 (ENSCLAG00000012518)	SST (ENSCLAG00000015832)	RTP2 (ENSCLAG00000014964)	ENSCLAG00000017951	BCL6 (ENSCLAG00000012339) #7	LPP (ENSCLAG00000015949) #9	TPRG1 (ENSCLAG00000013300) #10	TP63 (ENSCLAG00000012538) #12	P3H2 (ENSCLAG00000012801) #13	CLDN1 (ENSCLAG00000013178) #14	CLDN16 (ENSCLAG00000012605) #15	IL1RAP (ENSCLAG00000012363) #17	GMNC (ENSCLAG00000011473) #18	OSTN (ENSCLAG00000013977) #19	CCDC50 (ENSCLAG00000014114) #22	FGF12 (ENSCLAG00000011409) #23	MB21D2 (ENSCLAG00000014657) #24	PLAAT1 (ENSCLAG00000012403) #26	ATP13A5 (ENSCLAG00000012908) #27	ATP13A4 (ENSCLAG00000012524) #28	OPA1 (ENSCLAG00000012734) #29	HES1 (ENSCLAG00000015321) #30	CPN2 (ENSCLAG00000018106) #31	LRRC15 (ENSCLAG00000018110) #32	ATP13A3 (ENSCLAG00000012807) #34	ENSCLAG00000013365 #36	FAM43A (ENSCLAG00000011597) #37	XXYLT1 (ENSCLAG00000011348)	ACAP2 (ENSCLAG00000013413)	ENSCLAG00000012941
Degu	MODERN SPECIES	169	ENSODEG00000000479	SST (ENSODEG00000000486)	RTP2 (ENSODEG00000000495)	BCL6 (ENSODEG00000000516) #7	LPP (ENSODEG00000000601) #9	TPRG1 (ENSODEG00000000645) #10	TP63 (ENSODEG00000000698) #12	P3H2 (ENSODEG00000000751) #13	CLDN1 (ENSODEG00000000775) #14	CLDN16 (ENSODEG00000000787) #15	TMEM207 (ENSODEG00000000814) #16	IL1RAP (ENSODEG00000000880) #17	ENSODEG00000000947	GMNC (ENSODEG00000000968) #18	OSTN (ENSODEG00000000984) #19	CCDC50 (ENSODEG00000001028) #22	ENSODEG00000018632	FGF12 (ENSODEG00000000898) #23	ENSODEG00000000915 #24	PLAAT1 (ENSODEG00000000928) #26	ATP13A5 (ENSODEG00000000942) #27
Guinea pig	MODERN SPECIES	7	RTP1 (ENSCPOG00000001203)	MASP1 (ENSCPOG00000015723)	SST (ENSCPOG00000009662)	RTP2 (ENSCPOG00000009665)	BCL6 (ENSCPOG00000004090) #7	ENSCPOG00000033304	LPP (ENSCPOG00000015584) #9	TPRG1 (ENSCPOG00000007437) #10	TP63 (ENSCPOG00000014770) #12	P3H2 (ENSCPOG00000004329) #13	CLDN1 (ENSCPOG00000037018) #14	CLDN16 (ENSCPOG00000008643) #15	IL1RAP (ENSCPOG00000008554) #17	GMNC (ENSCPOG00000019517) #18	OSTN (ENSCPOG00000024963) #19	CCDC50 (ENSCPOG00000013365) #22	FGF12 (ENSCPOG00000038518) #23	MB21D2 (ENSCPOG00000011028) #24	PLAAT1 (ENSCPOG00000008871) #26	ATP13A5 (ENSCPOG00000008873) #27	ATP13A4 (ENSCPOG00000008886) #28	OPA1 (ENSCPOG00000005925) #29	HES1 (ENSCPOG00000036195) #30	CPN2 (ENSCPOG00000037149) #31	LRRC15 (ENSCPOG00000005131) #32	ATP13A3 (ENSCPOG00000005136) #34	TMEM44 (ENSCPOG00000021309) #35	ENSCPOG00000002586 #36	FAM43A (ENSCPOG00000021729) #37	XXYLT1 (ENSCPOG00000009208)	ACAP2 (ENSCPOG00000009213)
Naked mole-rat female	DUPLICATION
Naked mole-rat female	MODERN SPECIES	27	TP63 (ENSHGLG00000016277) #12	P3H2 (ENSHGLG00000019175) #13	CLDN1 (ENSHGLG00000038289) #14	CLDN16 (ENSHGLG00000018130) #15	ENSHGLG00000035223	TMEM207 (ENSHGLG00000037564) #16	IL1RAP (ENSHGLG00000018108) #17	ENSHGLG00000036963 #17	ENSHGLG00000019218	GMNC (ENSHGLG00000017131) #18	ENSHGLG00000040250	ENSHGLG00000016933	ENSHGLG00000016923	OSTN (ENSHGLG00000039251) #19	ENSHGLG00000042558 #20	CCDC50 (ENSHGLG00000016906) #22	FGF12 (ENSHGLG00000043378) #23	MB21D2 (ENSHGLG00000017083) #24	ENSHGLG00000017096	ENSHGLG00000035086	PLAAT1 (ENSHGLG00000017074) #26	ATP13A5 (ENSHGLG00000017059) #27	ATP13A4 (ENSHGLG00000017044) #28	OPA1 (ENSHGLG00000017084) #29	HES1 (ENSHGLG00000032453) #30	ENSHGLG00000040383	CPN2 (ENSHGLG00000045241) #31	LRRC15 (ENSHGLG00000017428) #32	GP5 (ENSHGLG00000038390) #33	ATP13A3 (ENSHGLG00000017411) #34	LSG1 (ENSHGLG00000017390) #36
Naked mole-rat female	MODERN SPECIES	7	CCSER2 (ENSHGLG00000008612)	GRID1 (ENSHGLG00000009129)	ENSHGLG00000007130	ENSHGLG00000006795	ENSHGLG00000045643	ENSHGLG00000001304	ENSHGLG00000000772	UTP15 (ENSHGLG00000000745)	ARHGEF28 (ENSHGLG00000000602)	ENSHGLG00000040928	ENC1 (ENSHGLG00000000552)	Hexb (ENSHGLG00000000527)	GFM2 (ENSHGLG00000000419)	NSA2 (ENSHGLG00000000324)	ENSHGLG00000035328	ENSHGLG00000032803 #22	ENSHGLG00000000294	ENSHGLG00000000270	ANKRD31 (ENSHGLG00000000230)	ENSHGLG00000043427	ENSHGLG00000040348	ENSHGLG00000000135	ENSHGLG00000034320	ENSHGLG00000002129	ENSHGLG00000036754	ENSHGLG00000002239	ENSHGLG00000040666	ENSHGLG00000035363	ENSHGLG00000001390	ENSHGLG00000001449	ENSHGLG00000041239