Rodentia_A	ANCESTRAL SPECIES	16	ENSGT01030000234519.e.a.a.b.a.a.a #16	ENSGT01030000234519.e.a.a.b.a.a.b.a.a #15	ENSGT01030000234519.e.a.a.b.a.a.b.a.b.a.a #14	ENSGT00940000161033 #13	ENSGT00940000161736 #12	ENSGT01050000244887.B #11	ENSGT00500000044945.a #10	ENSGT00940000154201.a.a.b.d	ENSGT00950000182916.a.a	ENSGT00940000154660.a	ENSGT00390000003403	ENSGT00500000044957	ENSGT00950000183104.B.a.a #19	ENSGT00390000004282 #21	ENSGT00390000005318.a #20	ENSGT00940000161213 #22	ENSGT00390000003420.b #23	ENSGT01030000234559.a.a.a #24	ENSGT00950000183102.A.a #25	ENSGT00940000159258 #26	ENSGT00940000160036 #27	ENSGT00940000160384 #28	ENSGT00390000001201 #29	ENSGT00940000163572	ENSGT00940000160775 #30	ENSGT00940000162148 #31	ENSGT00940000158364 #32	ENSGT00940000159842 #33	ENSGT00940000161753	ENSGT00940000154662	ENSGT01030000234539.a.a.a
Hystricomorpha	ANCESTRAL SPECIES	19	ENSGT00500000044957	ENSGT00390000003403	ENSGT00940000154660.a	ENSGT00950000182916.a.a	ENSGT00940000154201.a.a.b.d	ENSGT00500000044945.a #10	ENSGT01050000244887.B #11	ENSGT00940000161736 #12	ENSGT00940000161033 #13	ENSGT01030000234519.e.a.a.b.a.a.b.a.b.a.a #14	ENSGT01030000234519.e.a.a.b.a.a.b.a.a #15	ENSGT01030000234519.e.a.a.b.a.a.a #16	ENSGT00950000183104.B.a.a #19	ENSGT00390000004282 #21	ENSGT00390000005318.a #20	ENSGT00940000161213 #22	ENSGT00390000003420.b #23	ENSGT01030000234559.a.a.a #24	ENSGT00950000183102.A.a #25	ENSGT00940000159258 #26	ENSGT00940000160036 #27	ENSGT00940000160384 #28	ENSGT00390000001201 #29	ENSGT00940000160775 #30	ENSGT00940000162148 #31	ENSGT00940000158364 #32	ENSGT00940000159842 #33	ENSGT00390000014000.i #34	ENSGT00940000159993 #35	ENSGT00940000158753 #36	ENSGT00510000047872 #37
Naked mole-rat female	MODERN SPECIES	21	ENSHGLG00000034587 #7	ENSHGLG00000002680 #8	ENSHGLG00000040658 #9	ENSHGLG00000010518 #10	S1PR4 (ENSHGLG00000042045) #11	GNA15 (ENSHGLG00000033945) #12	GNA11 (ENSHGLG00000035049) #13	AES (ENSHGLG00000036417) #14	TLE2 (ENSHGLG00000013600) #15	ENSHGLG00000037855 #16	ENSHGLG00000049208 #17	ENSHGLG00000016167 #18	FZR1 (ENSHGLG00000019224) #19	ENSHGLG00000014588 #20	ENSHGLG00000033274 #21	HMG20B (ENSHGLG00000015242) #22	GIPC3 (ENSHGLG00000016188) #23	TBXA2R (ENSHGLG00000012829) #24	CACTIN (ENSHGLG00000016228) #25	ENSHGLG00000016360 #26	TJP3 (ENSHGLG00000014455) #27	APBA3 (ENSHGLG00000014560) #28	MRPL54 (ENSHGLG00000006157) #29	MATK (ENSHGLG00000006614) #30	ZFR2 (ENSHGLG00000010154) #31	ATCAY (ENSHGLG00000012464) #32	ENSHGLG00000005723 #33	TIMM13 (ENSHGLG00000042587) #34	TMPRSS9 (ENSHGLG00000006952) #35	SPPL2B (ENSHGLG00000008911) #36	LSM7 (ENSHGLG00000010587) #37
Hystricomorpha_a	ANCESTRAL SPECIES	15	ENSGT00940000159037	ENSGT00950000183171.A.b.a.b	ENSGT00500000044957	ENSGT00940000154660.a	ENSGT00950000182916.a.a	ENSGT00940000154201.a.a.b.d	ENSGT00500000044945.a #10	ENSGT01050000244887.B #11	ENSGT00940000161736 #12	ENSGT00940000161033 #13	ENSGT01030000234519.e.a.a.b.a.a.b.a.b.a.a #14	ENSGT01030000234519.e.a.a.b.a.a.b.a.a #15	ENSGT00950000183104.B.a.a #19	ENSGT00390000004282 #21	ENSGT00390000005318.a #20	ENSGT00940000161213 #22	ENSGT00390000003420.b #23	ENSGT01030000234559.a.a.a #24	ENSGT00950000183102.A.a #25	ENSGT00940000159258 #26	ENSGT00940000160036 #27	ENSGT00940000160384 #28	ENSGT00390000001201 #29	ENSGT00940000160775 #30	ENSGT00940000162148 #31	ENSGT00940000158364 #32	ENSGT00940000159842 #33	ENSGT00390000014000.i #34	ENSGT00940000159993 #35	ENSGT00940000158753 #36	ENSGT00510000047872 #37
Guinea pig	MODERN SPECIES	288									ENSCPOG00000004974 #12	GNA11 (ENSCPOG00000036119) #13	TLE5 (ENSCPOG00000036640) #14	TLE2 (ENSCPOG00000004144) #15	FZR1 (ENSCPOG00000019570) #19	TEKTIP1 (ENSCPOG00000024460) #21	MFSD12 (ENSCPOG00000009074) #20	HMG20B (ENSCPOG00000010777) #22	GIPC3 (ENSCPOG00000023224) #23	TBXA2R (ENSCPOG00000031050) #24	CACTIN (ENSCPOG00000003880) #25	PIP5K1C (ENSCPOG00000001951) #26
Hystricomorpha_b	ANCESTRAL SPECIES	17	ENSGT00950000183171.A.b.a.b	ENSGT00500000044957	ENSGT00940000154660.a	ENSGT00950000182916.a.a	ENSGT00940000154201.a.a.b.d	ENSGT00500000044945.a #10	ENSGT01050000244887.B #11	ENSGT00940000161736 #12	ENSGT00940000161033 #13	ENSGT01030000234519.e.a.a.b.a.a.b.a.b.a.a #14	ENSGT01030000234519.e.a.a.b.a.a.b.a.a #15	ENSGT00950000182965.b.fb #17	ENSGT00950000183104.B.a.a #19	ENSGT00390000004282 #21	ENSGT00390000005318.a #20	ENSGT00940000161213 #22	ENSGT00390000003420.b #23	ENSGT01030000234559.a.a.a #24	ENSGT00950000183102.A.a #25	ENSGT00940000159258 #26	ENSGT00940000160036 #27	ENSGT00940000160384 #28	ENSGT00390000001201 #29	ENSGT00940000160775 #30	ENSGT00940000162148 #31	ENSGT00940000158364 #32	ENSGT00940000159842 #33	ENSGT00390000014000.i #34	ENSGT00940000159993 #35	ENSGT00940000158753 #36	ENSGT00510000047872 #37
Long-tailed chinchilla	MODERN SPECIES	202	THOP1 (ENSCLAG00000015063)	DOHH (ENSCLAG00000007817)	SMIM24 (ENSCLAG00000007177)	NFIC (ENSCLAG00000007526)	CELF5 (ENSCLAG00000009940)	NCLN (ENSCLAG00000008645) #10	S1PR4 (ENSCLAG00000017878) #11	GNA15 (ENSCLAG00000009774) #12	GNA11 (ENSCLAG00000010957) #13	TLE5 (ENSCLAG00000015307) #14	TLE2 (ENSCLAG00000007966) #15	ENSCLAG00000014106 #17	FZR1 (ENSCLAG00000014081) #19	TEKTIP1 (ENSCLAG00000009360) #21	MFSD12 (ENSCLAG00000008160) #20	HMG20B (ENSCLAG00000012030) #22	GIPC3 (ENSCLAG00000009638) #23	TBXA2R (ENSCLAG00000010610) #24	CACTIN (ENSCLAG00000010714) #25	PIP5K1C (ENSCLAG00000011318) #26	TJP3 (ENSCLAG00000008035) #27	APBA3 (ENSCLAG00000010718) #28	MRPL54 (ENSCLAG00000007908) #29	MATK (ENSCLAG00000008473) #30	ZFR2 (ENSCLAG00000010137) #31	ATCAY (ENSCLAG00000013570) #32	NMRK2 (ENSCLAG00000008930) #33	ENSCLAG00000009705 #34	TMPRSS9 (ENSCLAG00000007396) #35	SPPL2B (ENSCLAG00000010153) #36	LSM7 (ENSCLAG00000011635) #37
Degu	MODERN SPECIES	91	DOHH (ENSODEG00000014181)	ENSODEG00000015846	NFIC (ENSODEG00000015267)	CELF5 (ENSODEG00000014460)	NCLN (ENSODEG00000013853) #10	S1PR4 (ENSODEG00000020319) #11	GNA15 (ENSODEG00000014085) #12	GNA11 (ENSODEG00000015009) #13	ENSODEG00000020164	ENSODEG00000014482 #14	TLE2 (ENSODEG00000014073) #15	ENSODEG00000013786 #17	FZR1 (ENSODEG00000014514) #19	TEKTIP1 (ENSODEG00000013282) #21	MFSD12 (ENSODEG00000014260) #20	HMG20B (ENSODEG00000014653) #22	GIPC3 (ENSODEG00000013296) #23	TBXA2R (ENSODEG00000013384) #24	ENSODEG00000014734 #25	PIP5K1C (ENSODEG00000013830) #26	TJP3 (ENSODEG00000013512) #27	APBA3 (ENSODEG00000013581) #28	MRPL54 (ENSODEG00000013969) #29	MATK (ENSODEG00000014649) #30	ATCAY (ENSODEG00000013730) #32	NMRK2 (ENSODEG00000013977) #33	TIMM13 (ENSODEG00000014422) #34	TMPRSS9 (ENSODEG00000014906) #35	ENSODEG00000014560 #36	ENSODEG00000013590 #37	LINGO3 (ENSODEG00000020375)
Sciuridae	ANCESTRAL SPECIES	23	ENSGT01030000234519.e.a.a.b.a.a.a #16	ENSGT01030000234519.e.a.a.b.a.a.b.a.a #15	ENSGT01030000234519.e.a.a.b.a.a.b.a.b.a.a #14	ENSGT00940000161033 #13	ENSGT00940000161736 #12	ENSGT01050000244887.B #11	ENSGT00500000044945.a #10	ENSGT00940000154201.a.a.b.d	ENSGT00950000182916.a.a	ENSGT00940000154660.a	ENSGT00390000003403	ENSGT00500000044957	ENSGT00950000183104.B.a.a #19	ENSGT00390000004282 #21	ENSGT00390000005318.a #20	ENSGT00940000161213 #22	ENSGT00390000003420.b #23	ENSGT01030000234559.a.a.a #24	ENSGT00950000183102.A.a #25	ENSGT00940000159258 #26	ENSGT00940000160036 #27	ENSGT00940000160384 #28	ENSGT00390000001201 #29	ENSGT00940000163572	ENSGT00940000160775 #30	ENSGT00940000162148 #31	ENSGT00940000158364 #32	ENSGT00940000159842 #33	ENSGT00940000161753	ENSGT00940000154662	ENSGT01030000234539.a.a.a
Eurasian red squirrel	MODERN SPECIES	7	ZNF77 (ENSSVLG00005022489)	ENSSVLG00005022518 #16	TLE2 (ENSSVLG00005022632) #15	TLE5 (ENSSVLG00005022954) #14	GNA11 (ENSSVLG00005023021) #13	GNA15 (ENSSVLG00005023052) #12	S1PR4 (ENSSVLG00005023097) #11	NCLN (ENSSVLG00005023124) #10	CELF5 (ENSSVLG00005023165)	NFIC (ENSSVLG00005023336)	ENSSVLG00005023514	DOHH (ENSSVLG00005023586)	FZR1 (ENSSVLG00005023633) #19	TEKTIP1 (ENSSVLG00005023668) #21	MFSD12 (ENSSVLG00005023702) #20	HMG20B (ENSSVLG00005023762) #22	GIPC3 (ENSSVLG00005023804) #23	TBXA2R (ENSSVLG00005023817) #24	CACTIN (ENSSVLG00005023836) #25	PIP5K1C (ENSSVLG00005023887) #26	TJP3 (ENSSVLG00005023962) #27	MRPL54 (ENSSVLG00005024184) #29	RAX2 (ENSSVLG00005024207)	MATK (ENSSVLG00005024229) #30	ZFR2 (ENSSVLG00005024341) #31	ATCAY (ENSSVLG00005024510) #32	ENSSVLG00005024541 #33	DAPK3 (ENSSVLG00005024571)	ENSSVLG00005024605	PIAS4 (ENSSVLG00005024634)	ZBTB7A (ENSSVLG00005024657)
Marmotini	ANCESTRAL SPECIES	24	ENSGT01030000234519.e.a.a.b.a.a.a #16	ENSGT01030000234519.e.a.a.b.a.a.b.a.a #15	ENSGT01030000234519.e.a.a.b.a.a.b.a.b.a.a #14	ENSGT00940000161033 #13	ENSGT00940000161736 #12	ENSGT01050000244887.B #11	ENSGT00500000044945.a #10	ENSGT00940000154201.a.a.b.d	ENSGT00950000182916.a.a	ENSGT00940000154660.a	ENSGT00390000003403	ENSGT00500000044957	ENSGT00950000183104.B.a.a #19	ENSGT00390000004282 #21	ENSGT00390000005318.a #20	ENSGT00940000161213 #22	ENSGT00390000003420.b #23	ENSGT01030000234559.a.a.a #24	ENSGT00950000183102.A.a #25	ENSGT00940000159258 #26	ENSGT00940000160036 #27	ENSGT00940000160384 #28	ENSGT00390000001201 #29	ENSGT00940000163572	ENSGT00940000160775 #30	ENSGT00940000162148 #31	ENSGT00940000158364 #32	ENSGT00940000159842 #33	ENSGT00940000161753	ENSGT00940000154662	ENSGT01030000234539.a.a.a
Alpin marmot	MODERN SPECIES	88	SLC39A3 (ENSMMMG00000016507)	SGTA (ENSMMMG00000016510)	THOP1 (ENSMMMG00000016515)	ENSMMMG00000016520	ZNF77 (ENSMMMG00000016522)	ENSMMMG00000016524 #15	ENSMMMG00000016526 #15	GNA11 (ENSMMMG00000016538) #13	ENSMMMG00000016752 #12	ENSMMMG00000016760	ENSMMMG00000016765	ENSMMMG00000016774 #21	DOHH (ENSMMMG00000016778)	ENSMMMG00000016780 #19	ENSMMMG00000016792 #20	HMG20B (ENSMMMG00000016794) #22	GIPC3 (ENSMMMG00000016813) #23	ENSMMMG00000016827	CACTIN (ENSMMMG00000016832) #25	TJP3 (ENSMMMG00000016855) #27	APBA3 (ENSMMMG00000016885) #28	ZFR2 (ENSMMMG00000016959) #31	NMRK2 (ENSMMMG00000017009) #33	DAPK3 (ENSMMMG00000017015)	EEF2 (ENSMMMG00000017019)	PIAS4 (ENSMMMG00000017032)	MAP2K2 (ENSMMMG00000017211)	ANKRD24 (ENSMMMG00000018078)	ENSMMMG00000018130	YJU2 (ENSMMMG00000018139)	SHD (ENSMMMG00000018157)
Marmotini_b	ANCESTRAL SPECIES	9	ENSGT01030000234519.e.a.a.b.a.a.a #16	ENSGT01030000234519.e.a.a.b.a.a.b.a.a #15	ENSGT01030000234519.e.a.a.b.a.a.b.a.b.a.a #14	ENSGT00940000161033 #13	ENSGT00940000161736 #12	ENSGT01050000244887.B #11	ENSGT00500000044945.a #10	ENSGT00940000154201.a.a.b.d	ENSGT00950000182916.a.a	ENSGT00940000154660.a	ENSGT00390000003403	ENSGT00500000044957	ENSGT00950000183104.B.a.a #19	ENSGT00390000004282 #21	ENSGT00390000005318.a #20	ENSGT00940000161213 #22	ENSGT00390000003420.b #23	ENSGT01030000234559.a.a.a #24	ENSGT00950000183102.A.a #25	ENSGT00940000159258 #26	ENSGT00940000160036 #27	ENSGT00940000160384 #28	ENSGT00390000001201 #29	ENSGT00940000163572	ENSGT00940000160775 #30	ENSGT00940000162148 #31	ENSGT00940000158364 #32	ENSGT00940000159842 #33	ENSGT00940000161753	ENSGT00940000154662	ENSGT01030000234539.a.a.a
Arctic ground squirrel	MODERN SPECIES	301	ENSUPAG00010008199 #16	TLE2 (ENSUPAG00010008216) #15	TLE5 (ENSUPAG00010008263) #14	GNA11 (ENSUPAG00010008291) #13	GNA15 (ENSUPAG00010008318) #12	S1PR4 (ENSUPAG00010008324) #11	NCLN (ENSUPAG00010008331) #10	ENSUPAG00010008374 #9	NFIC (ENSUPAG00010008410)	ENSUPAG00010008444	SMIM44 (ENSUPAG00010008452)	DOHH (ENSUPAG00010008461)	FZR1 (ENSUPAG00010008472) #19	TEKTIP1 (ENSUPAG00010008492) #21	MFSD12 (ENSUPAG00010008498) #20	HMG20B (ENSUPAG00010008513) #22	GIPC3 (ENSUPAG00010008525) #23	TBXA2R (ENSUPAG00010008535) #24	CACTIN (ENSUPAG00010008542) #25	PIP5K1C (ENSUPAG00010008552) #26	TJP3 (ENSUPAG00010008756) #27	APBA3 (ENSUPAG00010008831) #28	MRPL54 (ENSUPAG00010008838) #29	RAX2 (ENSUPAG00010008848)	MATK (ENSUPAG00010008858) #30	ZFR2 (ENSUPAG00010009277) #31	ATCAY (ENSUPAG00010009286) #32	NMRK2 (ENSUPAG00010009304) #33	DAPK3 (ENSUPAG00010009346)	EEF2 (ENSUPAG00010009366)	PIAS4 (ENSUPAG00010009393)
Squirrel	MODERN SPECIES	188	THOP1 (ENSSTOG00000006054)	ZNF77 (ENSSTOG00000034105)	TLE2 (ENSSTOG00000011134) #15	TLE5 (ENSSTOG00000028243) #14	GNA11 (ENSSTOG00000019951) #13	GNA15 (ENSSTOG00000021930) #12	S1PR4 (ENSSTOG00000024766) #11	NCLN (ENSSTOG00000022427) #10	CELF5 (ENSSTOG00000002384)	NFIC (ENSSTOG00000024218)	SMIM24 (ENSSTOG00000030174)	DOHH (ENSSTOG00000023074)	FZR1 (ENSSTOG00000002807) #19	TEKTIP1 (ENSSTOG00000026760) #21	MFSD12 (ENSSTOG00000002823) #20	HMG20B (ENSSTOG00000022314) #22	GIPC3 (ENSSTOG00000007215) #23	TBXA2R (ENSSTOG00000028290) #24	CACTIN (ENSSTOG00000001235) #25	PIP5K1C (ENSSTOG00000023021) #26	TJP3 (ENSSTOG00000024962) #27	APBA3 (ENSSTOG00000000352) #28	MRPL54 (ENSSTOG00000022378) #29	RAX2 (ENSSTOG00000024315)	MATK (ENSSTOG00000011892) #30	ZFR2 (ENSSTOG00000025821) #31	ATCAY (ENSSTOG00000026376) #32	NMRK2 (ENSSTOG00000021661) #33	DAPK3 (ENSSTOG00000005038)	EEF2 (ENSSTOG00000005050)	PIAS4 (ENSSTOG00000012472)