Rodentia_A	ANCESTRAL SPECIES	13	ENSGT00390000015228 #8	ENSGT00390000003590 #9	ENSGT00940000153189.B #10	ENSGT00940000159722 #11	ENSGT00390000012561.b #12	ENSGT00950000183114.a.b.b.f.a.b #13	ENSGT00950000183114.a.b.b.f.a.a #14	ENSGT00950000183114.a.b.b.f.b #15	ENSGT00940000154107.b #16	ENSGT00530000064234 #17	ENSGT00390000001138.b #18	ENSGT00390000004145 #19	ENSGT00940000158493 #20	ENSGT00390000005550 #21	ENSGT00390000005581.b	ENSGT00390000008096.B #22	ENSGT00940000158407 #23	ENSGT00530000063480.a #24	ENSGT00550000075136 #25	ENSGT00530000063609.a #26	ENSGT01050000244956.b.d #27	ENSGT00390000006350.m.a.c.a ##28	ENSGT00390000005727.a.b.b ##29	ENSGT00390000006350.m.a.c.b.b #28	ENSGT00390000005727.a.b.a.b #29	ENSGT00940000155367 #30	ENSGT00390000018393 #31	ENSGT00950000182908.D #32	ENSGT00390000016484 #33	ENSGT00390000009468	ENSGT00390000016929 #34
Hystricomorpha	ANCESTRAL SPECIES	20	ENSGT00390000011295.a #7	ENSGT00390000015228 #8	ENSGT00390000003590 #9	ENSGT00940000153189.B #10	ENSGT00940000159722 #11	ENSGT00390000012561.b #12	ENSGT00950000183114.a.b.b.f.a.b #13	ENSGT00950000183114.a.b.b.f.a.a #14	ENSGT00950000183114.a.b.b.f.b #15	ENSGT00940000154107.b #16	ENSGT00530000064234 #17	ENSGT00390000001138.b #18	ENSGT00390000004145 #19	ENSGT00940000158493 #20	ENSGT00390000005550 #21	ENSGT00390000008096.B #22	ENSGT00940000158407 #23	ENSGT00530000063480.a #24	ENSGT00550000075136 #25	ENSGT00530000063609.a #26	ENSGT01050000244956.b.d #27	ENSGT00390000006350.m.a.c.b.b #28	ENSGT00390000005727.a.b.a.b #29	ENSGT00940000155367 #30	ENSGT00390000018393 #31	ENSGT00950000182908.D #32	ENSGT00390000016484 #33	ENSGT00390000016929 #34	ENSGT00390000005285 #35	ENSGT00940000167666 #36	ENSGT00940000155466 #37
Hystricomorpha_a	ANCESTRAL SPECIES	17	ENSGT00390000011295.a #7	ENSGT00390000015228 #8	ENSGT00390000003590 #9	ENSGT00940000153189.B #10	ENSGT00940000159722 #11	ENSGT00390000012561.b #12	ENSGT00950000183114.a.b.b.f.a.b #13	ENSGT00950000183114.a.b.b.f.a.a #14	ENSGT00950000183114.a.b.b.f.b #15	ENSGT00940000154107.b #16	ENSGT00530000064234 #17	ENSGT00390000001138.b #18	ENSGT00390000004145 #19	ENSGT00940000158493 #20	ENSGT00390000005550 #21	ENSGT00390000008096.B #22	ENSGT00940000158407 #23	ENSGT00530000063480.a #24	ENSGT00550000075136 #25	ENSGT00530000063609.a #26	ENSGT01050000244956.b.d #27	ENSGT00390000006350.m.a.c.b.b #28	ENSGT00390000005727.a.b.a.b #29	ENSGT00940000155367 #30	ENSGT00390000018393 #31	ENSGT00950000182908.D #32	ENSGT00390000016484 #33	ENSGT00390000016929 #34	ENSGT00390000005285 #35	ENSGT00940000167666 #36	ENSGT00940000155466 #37
Guinea pig	MODERN SPECIES	104	HYCC2 (ENSCPOG00000010108) #7	ORC2 (ENSCPOG00000004552) #8	NIF3L1 (ENSCPOG00000008572) #9	PPIL3 (ENSCPOG00000008570) #10	CLK1 (ENSCPOG00000027067) #11	ENSCPOG00000010449 #12	ENSCPOG00000019962 #13	ENSCPOG00000033032 #14	Aox1 (ENSCPOG00000025955) #15	ENSCPOG00000002722 #16	ENSCPOG00000012077 #17	SPATS2L (ENSCPOG00000003190) #18	MAIP1 (ENSCPOG00000003800) #19	TYW5 (ENSCPOG00000035856) #20	C2orf69 (ENSCPOG00000009934) #21	SATB2 (ENSCPOG00000015198) #22	PLCL1 (ENSCPOG00000011478) #23	BOLL (ENSCPOG00000000390) #24	MARS2 (ENSCPOG00000025973) #25	RFTN2 (ENSCPOG00000010463) #26	MOB4 (ENSCPOG00000012746) #27	ENSCPOG00000027474 #28	HSPD1 (ENSCPOG00000002588) #29	COQ10B (ENSCPOG00000002673) #30	SF3B1 (ENSCPOG00000009353) #31	ANKRD44 (ENSCPOG00000026494) #32	PGAP1 (ENSCPOG00000003177) #33	GTF3C3 (ENSCPOG00000006643) #34	CCDC150 (ENSCPOG00000031267) #35	ENSCPOG00000040067 #36	HECW2 (ENSCPOG00000008908) #37
Hystricomorpha_b	ANCESTRAL SPECIES	24	ENSGT00390000011295.a #7	ENSGT00390000015228 #8	ENSGT00390000003590 #9	ENSGT00940000153189.B #10	ENSGT00940000159722 #11	ENSGT00390000012561.b #12	ENSGT00950000183114.a.b.b.f.a.b #13	ENSGT00950000183114.a.b.b.f.a.a #14	ENSGT00950000183114.a.b.b.f.b #15	ENSGT00940000154107.b #16	ENSGT00530000064234 #17	ENSGT00390000001138.b #18	ENSGT00390000004145 #19	ENSGT00940000158493 #20	ENSGT00390000005550 #21	ENSGT00390000008096.B #22	ENSGT00940000158407 #23	ENSGT00530000063480.a #24	ENSGT00550000075136 #25	ENSGT00530000063609.a #26	ENSGT01050000244956.b.d #27	ENSGT00390000006350.m.a.c.b.b.a.b #28	ENSGT00390000005727.a.b.a.b #29	ENSGT00940000155367 #30	ENSGT00390000018393 #31	ENSGT00950000182908.D #32	ENSGT00390000016484 #33	ENSGT00390000016929 #34	ENSGT00390000005285 #35	ENSGT00940000155466 #37	ENSGT00940000154014.b.b
Degu	MODERN SPECIES	66	ENSODEG00000007860	ORC2 (ENSODEG00000008853) #8	NIF3L1 (ENSODEG00000008894) #9	PPIL3 (ENSODEG00000007592) #10	CLK1 (ENSODEG00000009021) #11	ENSODEG00000019563	ENSODEG00000008411 #12	ENSODEG00000008135 #13	ENSODEG00000011138 #14	AOX1 (ENSODEG00000012914) #15	ENSODEG00000009211 #17	SPATS2L (ENSODEG00000009851) #18	MAIP1 (ENSODEG00000008914) #19	TYW5 (ENSODEG00000009836) #20	C2orf69 (ENSODEG00000008700) #21	SATB2 (ENSODEG00000008383) #22	PLCL1 (ENSODEG00000008918) #23	BOLL (ENSODEG00000008471) #24	RFTN2 (ENSODEG00000008704) #26	MOB4 (ENSODEG00000009609) #27	ENSODEG00000019874	ENSODEG00000011397 #28	ENSODEG00000009026 #29	COQ10B (ENSODEG00000008396) #30	ENSODEG00000011153 #31	ENSODEG00000019820	ENSODEG00000008898 #32	ENSODEG00000008698	ENSODEG00000009525	PGAP1 (ENSODEG00000009932) #33	ENSODEG00000009843 #34
Long-tailed chinchilla	MODERN SPECIES	110	HYCC2 (ENSCLAG00000011177) #7	ORC2 (ENSCLAG00000013209) #8	NIF3L1 (ENSCLAG00000013524) #9	PPIL3 (ENSCLAG00000014050) #10	CLK1 (ENSCLAG00000011455) #11	BZW1 (ENSCLAG00000012079) #12	ENSCLAG00000011199 #13	ENSCLAG00000014402 #14	AOX1 (ENSCLAG00000011481) #15	ENSCLAG00000012456 #16	ENSCLAG00000014377 #17	SPATS2L (ENSCLAG00000013167) #18	MAIP1 (ENSCLAG00000011913) #19	TYW5 (ENSCLAG00000012009) #20	C2orf69 (ENSCLAG00000012813) #21	SATB2 (ENSCLAG00000016994) #22	PLCL1 (ENSCLAG00000016098) #23	BOLL (ENSCLAG00000017375) #24	MARS2 (ENSCLAG00000010386) #25	RFTN2 (ENSCLAG00000009821) #26	MOB4 (ENSCLAG00000010086) #27	ENSCLAG00000010686 #28	HSPD1 (ENSCLAG00000011541) #29	COQ10B (ENSCLAG00000017377) #30	SF3B1 (ENSCLAG00000014767) #31	ANKRD44 (ENSCLAG00000015396) #32	PGAP1 (ENSCLAG00000011838) #33	GTF3C3 (ENSCLAG00000009827) #34	CCDC150 (ENSCLAG00000012365) #35	HECW2 (ENSCLAG00000011628) #37	STK17B (ENSCLAG00000012520)
Naked mole-rat female	MODERN SPECIES	22	PPIL3 (ENSHGLG00000035729) #10	Clk1 (ENSHGLG00000011322) #11	BZW1 (ENSHGLG00000011961) #12	ENSHGLG00000012205 #13	Aox4 (ENSHGLG00000012471) #14	AOX1 (ENSHGLG00000012876) #15	SGO2 (ENSHGLG00000015359) #16	ENSHGLG00000047532	ENSHGLG00000015370 #17	SPATS2L (ENSHGLG00000015420) #18	ENSHGLG00000017615	MAIP1 (ENSHGLG00000017548) #19	TYW5 (ENSHGLG00000017557) #20	C2orf69 (ENSHGLG00000040936) #21	ENSHGLG00000020697	SATB2 (ENSHGLG00000015892) #22	ENSHGLG00000043283	PLCL1 (ENSHGLG00000015970) #23	BOLL (ENSHGLG00000017562) #24	MARS2 (ENSHGLG00000049320) #25	RFTN2 (ENSHGLG00000017636) #26	MOB4 (ENSHGLG00000050196) #27	ENSHGLG00000042669 #28	HSPD1 (ENSHGLG00000007927) #29	ENSHGLG00000038699 #30	ENSHGLG00000008285 #31	ANKRD44 (ENSHGLG00000008625) #32	ENSHGLG00000049153	ENSHGLG00000040344	ENSHGLG00000008965 #33	ENSHGLG00000042696
Sciuridae	ANCESTRAL SPECIES	10	ENSGT00390000015228 #8	ENSGT00390000003590 #9	ENSGT00940000153189.B #10	ENSGT00940000159722 #11	ENSGT00390000012561.b #12	ENSGT00950000183114.a.b.b.f.a.b #13	ENSGT00950000183114.a.b.b.f.a.a #14	ENSGT00950000183114.a.b.b.f.b #15	ENSGT00940000154107.b #16	ENSGT00530000064234 #17	ENSGT00390000001138.b #18	ENSGT00390000004145 #19	ENSGT00940000158493 #20	ENSGT00390000005550 #21	ENSGT00390000005581.b	ENSGT00390000008096.B #22	ENSGT00940000158407 #23	ENSGT00530000063480.a #24	ENSGT00550000075136 #25	ENSGT00530000063609.a #26	ENSGT01050000244956.b.d #27	ENSGT00390000006350.m.a.c.a ##28	ENSGT00390000005727.a.b.b ##29	ENSGT00390000005727.a.b.a.b #29	ENSGT00940000155367 #30	ENSGT00390000018393 #31	ENSGT00950000182908.D #32	ENSGT00390000016484 #33	ENSGT00390000016929 #34	ENSGT00390000005285 #35	ENSGT00940000167666 #36
Marmotini	ANCESTRAL SPECIES	2	ENSGT00390000003590 #9	ENSGT00940000153189.B #10	ENSGT00940000159722 #11	ENSGT00390000012561.b.v #12	ENSGT00950000183114.a.b.b.f.a.b #13	ENSGT00950000183114.a.b.b.f.a.a #14	ENSGT00950000183114.a.b.b.f.b #15	ENSGT00940000154107.b #16	ENSGT00530000064234 #17	ENSGT00390000001138.b #18	ENSGT00390000004145 #19	ENSGT00940000158493 #20	ENSGT00390000005550 #21	ENSGT00390000005581.b	ENSGT00390000012178.g.a.a	ENSGT00390000008096.B #22	ENSGT00940000158407 #23	ENSGT00530000063480.a #24	ENSGT00550000075136 #25	ENSGT00530000063609.a #26	ENSGT01050000244956.b.d #27	ENSGT00390000006350.m.a.c.a.v ##28	ENSGT00390000005727.a.b.b ##29	ENSGT00940000155367 #30	ENSGT00390000018393 #31	ENSGT00950000182908.D #32	ENSGT00390000016484 #33	ENSGT00390000016929 #34	ENSGT00390000005285 #35	ENSGT00940000167666 #36	ENSGT00940000155466 #37
Marmotini_b	ANCESTRAL SPECIES	91						ENSGT00950000183114.a.b.b.f.a.a #14	ENSGT00950000183114.a.b.b.f.b #15	ENSGT00940000154107.b #16	ENSGT00530000064234 #17	ENSGT00390000001138.b #18	ENSGT00390000004145 #19	ENSGT00940000158493 #20	ENSGT00390000005550 #21	ENSGT00390000005581.b	ENSGT00390000012178.g.a.a	ENSGT00390000008096.B #22	ENSGT00940000158407 #23	ENSGT00530000063480.a #24	ENSGT00550000075136 #25	ENSGT00530000063609.a #26	ENSGT01050000244956.b.d #27	ENSGT00390000006350.m.a.c.a.v ##28	ENSGT00390000005727.a.b.b ##29	ENSGT00940000155367 #30	ENSGT00390000018393 #31	ENSGT00950000182908.D #32	ENSGT00390000016484 #33	ENSGT00390000016929 #34	ENSGT00390000005285 #35	ENSGT00940000167666 #36	ENSGT00940000155466 #37
Squirrel	MODERN SPECIES	106																SATB2 (ENSSTOG00000024964) #22	PLCL1 (ENSSTOG00000026164) #23	BOLL (ENSSTOG00000003536) #24	MARS2 (ENSSTOG00000015451) #25	RFTN2 (ENSSTOG00000015446) #26	MOB4 (ENSSTOG00000021024) #27	ENSSTOG00000031333 ##28	ENSSTOG00000028470 ##29	COQ10B (ENSSTOG00000011048) #30	SF3B1 (ENSSTOG00000011034) #31	ANKRD44 (ENSSTOG00000012130) #32	PGAP1 (ENSSTOG00000010633) #33	GTF3C3 (ENSSTOG00000011894) #34	ENSSTOG00000014552 #35	HECW2 (ENSSTOG00000015188) #37	STK17B (ENSSTOG00000020599)
Arctic ground squirrel	MODERN SPECIES	210						ENSUPAG00010015923 #14	AOX1 (ENSUPAG00010015861) #15	SGO2 (ENSUPAG00010015843) #16	KCTD18 (ENSUPAG00010015819) #17	SPATS2L (ENSUPAG00010015777) #18	MAIP1 (ENSUPAG00010015760) #19	TYW5 (ENSUPAG00010015739) #20	C2orf69 (ENSUPAG00010015730) #21	FTCDNL1 (ENSUPAG00010015721)	ENSUPAG00010015718	SATB2 (ENSUPAG00010015643) #22	PLCL1 (ENSUPAG00010015612) #23	BOLL (ENSUPAG00010015589) #24	MARS2 (ENSUPAG00010015585) #25	RFTN2 (ENSUPAG00010015580) #26	ENSUPAG00010015569 ##28	ENSUPAG00010015563 ##29	COQ10B (ENSUPAG00010015540) #30	SF3B1 (ENSUPAG00010015518) #31
Alpin marmot	MODERN SPECIES	8	PPIL3 (ENSMMMG00000012069) #10	CLK1 (ENSMMMG00000012051) #11	ENSMMMG00000012026 #12	ENSMMMG00000011976 #13	ENSMMMG00000011959	ENSMMMG00000011912 #14	AOX1 (ENSMMMG00000011886) #15	ENSMMMG00000011877 #16	KCTD18 (ENSMMMG00000011839) #17	SPATS2L (ENSMMMG00000011689) #18	MAIP1 (ENSMMMG00000011679) #19	TYW5 (ENSMMMG00000011668) #20	C2orf69 (ENSMMMG00000011660) #21	FTCDNL1 (ENSMMMG00000011655)	ENSMMMG00000011650	SATB2 (ENSMMMG00000011551) #22	ENSMMMG00000011481	PLCL1 (ENSMMMG00000011429) #23	BOLL (ENSMMMG00000011354) #24	MARS2 (ENSMMMG00000011347) #25	RFTN2 (ENSMMMG00000011220) #26	ENSMMMG00000011174 #27	ENSMMMG00000011161 ##28	ENSMMMG00000011138 #29	ENSMMMG00000011101 #30	SF3B1 (ENSMMMG00000011081) #31	ANKRD44 (ENSMMMG00000010980) #32	PGAP1 (ENSMMMG00000010912) #33	GTF3C3 (ENSMMMG00000010874) #34	ENSMMMG00000010858 #35	ENSMMMG00000010842 #36
Eurasian red squirrel	MODERN SPECIES	12	NIF3L1 (ENSSVLG00005004091) #9	PPIL3 (ENSSVLG00005004070) #10	CLK1 (ENSSVLG00005004020) #11	BZW1 (ENSSVLG00005003945) #12	ENSSVLG00005003845 #13	ENSSVLG00005003767 #14	AOX1 (ENSSVLG00005003683) #15	SGO2 (ENSSVLG00005003633) #16	ENSSVLG00005003604 #17	SPATS2L (ENSSVLG00005003512) #18	MAIP1 (ENSSVLG00005003433) #19	TYW5 (ENSSVLG00005003405) #20	C2orf69 (ENSSVLG00005003387) #21	FTCDNL1 (ENSSVLG00005003343)	ENSSVLG00005003317	SATB2 (ENSSVLG00005003278) #22	PLCL1 (ENSSVLG00005003227) #23	ENSSVLG00005003207	BOLL (ENSSVLG00005003123) #24	MARS2 (ENSSVLG00005003085) #25	RFTN2 (ENSSVLG00005003057) #26	MOB4 (ENSSVLG00005002989) #27	HSPE1 (ENSSVLG00005002940) ##28	ENSSVLG00005002895 #29	ENSSVLG00005002862 #30	SF3B1 (ENSSVLG00005002801) #31	ANKRD44 (ENSSVLG00005002705) #32	PGAP1 (ENSSVLG00005002564) #33	C2orf66 (ENSSVLG00005002524)	ENSSVLG00005002519	GTF3C3 (ENSSVLG00005002487) #34