Rodentia_A	ANCESTRAL SPECIES	14	ENSGT00940000162396	ENSGT00940000161652	ENSGT00940000154030.a.b	ENSGT00390000013670	ENSGT00940000157701	ENSGT00940000156464	ENSGT00940000156714	ENSGT01030000234564.a.a.a.a.b	ENSGT00940000155623 #15	ENSGT00390000003990 #16	ENSGT00940000155699 #17	ENSGT00390000008069 #18	ENSGT00940000155443 #19	ENSGT01090000260040.b.b.b.b.a.a ##20	ENSGT00440000033827 #21	ENSGT00940000157612 #22	ENSGT00940000155982 #23	ENSGT00390000016845	ENSGT00390000013305.a.a.v #24	ENSGT00940000154645.A #26	ENSGT00950000182995.e.a.a.a #27	ENSGT00390000007900 #28	ENSGT00390000004263.b #29	ENSGT00940000155646 #30	ENSGT00940000160213 #31	ENSGT00940000154459.B	ENSGT00940000153916.B #33	ENSGT01030000234517.D #34	ENSGT00940000155734.q #35	ENSGT00390000008041.C #36	ENSGT01100000263518.A.a.a.b
Hystricomorpha	ANCESTRAL SPECIES	64								ENSGT00940000155623 #15	ENSGT00390000003990 #16	ENSGT00940000155699 #17	ENSGT00390000008069 #18	ENSGT00940000155443 #19	ENSGT01090000260040.b.b.b.b.a.a ##20	ENSGT01090000260040.b.b.b.b.b #20	ENSGT00440000033827 #21	ENSGT00940000157612 #22	ENSGT00940000155982 #23	ENSGT00390000013305.a.a.u.a ##24	ENSGT00390000016845	ENSGT00390000013305.a.a.v #24	ENSGT00940000154645.A #26	ENSGT00950000182995.e.a.a.a #27	ENSGT00390000007900 #28	ENSGT00390000004263.b #29	ENSGT00940000155646 #30	ENSGT00940000160213 #31	ENSGT00940000154459.B	ENSGT00940000153916.B #33	ENSGT01030000234517.D #34	ENSGT00940000155734.q #35	ENSGT00390000008041.C #36
Hystricomorpha_a	ANCESTRAL SPECIES	70	ENSGT00390000014122.i.b.a.b #7	ENSGT00390000003466 #8	ENSGT00390000008195 #9	ENSGT00390000002448 #10	ENSGT00730000111137 #11	ENSGT00940000155671 #13	ENSGT00940000157666 #14	ENSGT00940000155623 #15	ENSGT00390000003990 #16	ENSGT00940000155699 #17	ENSGT00390000008069 #18	ENSGT00940000155443 #19	ENSGT01090000260040.b.b.b.b.a.a ##20	ENSGT01090000260040.b.b.b.b.b #20	ENSGT00440000033827 #21	ENSGT00940000157612 #22	ENSGT00940000155982 #23	ENSGT00390000013305.a.a.v #24	ENSGT00940000154645.A #26	ENSGT00950000182995.e.a.a.a #27	ENSGT00390000007900 #28	ENSGT00390000004263.b #29	ENSGT00940000155646 #30	ENSGT00940000160213 #31	ENSGT00940000154459.B	ENSGT00940000153916.B #33	ENSGT01030000234517.D #34	ENSGT00940000155734.q #35	ENSGT00390000008041.C #36	ENSGT00940000157219 #37	ENSGT00950000182986.a.b.a
Hystricomorpha_b	ANCESTRAL SPECIES	91	ENSGT00390000014122.i.b.a.b #7	ENSGT00390000003466 #8	ENSGT00390000008195 #9	ENSGT00390000002448 #10	ENSGT00730000111137 #11	ENSGT00940000155671 #13	ENSGT00940000157666 #14	ENSGT00940000155623 #15	ENSGT00390000003990 #16	ENSGT00940000155699 #17	ENSGT00390000008069 #18	ENSGT00940000155443 #19	ENSGT01090000260040.b.b.b.b.a.a ##20	ENSGT01090000260040.b.b.b.b.b #20	ENSGT00440000033827 #21	ENSGT00940000157612 #22	ENSGT00940000155982 #23	ENSGT00390000013305.a.a.v #24	ENSGT00390000013305.a.a.u.a ##24	ENSGT00940000154645.A #26	ENSGT00950000182995.e.a.a.a #27	ENSGT00390000007900 #28	ENSGT00390000004263.b #29	ENSGT00940000155646 #30	ENSGT00940000160213 #31	ENSGT00940000170593 #32	ENSGT00940000153916.B #33	ENSGT01030000234517.D #34	ENSGT00940000155734.q #35	ENSGT00390000008041.C #36	ENSGT00940000157219 #37
Long-tailed chinchilla	MODERN SPECIES	194	RPS7 (ENSCLAG00000002424) #7	RNASEH1 (ENSCLAG00000002440) #8	ADI1 (ENSCLAG00000002464) #9	TRAPPC12 (ENSCLAG00000002486) #10	EIPR1 (ENSCLAG00000002535) #11	ENSCLAG00000001592 #12	MYT1L (ENSCLAG00000001644) #13	PXDN (ENSCLAG00000001727) #14	ASAP2 (ENSCLAG00000001989) #15	ITGB1BP1 (ENSCLAG00000002388) #16	CPSF3 (ENSCLAG00000002727) #17	IAH1 (ENSCLAG00000002879) #18	ADAM17 (ENSCLAG00000003055) #19	YWHAQ (ENSCLAG00000003576) #20	TAF1B (ENSCLAG00000003776) #21	GRHL1 (ENSCLAG00000004000) #22	ENSCLAG00000004146 #23	RRM2 (ENSCLAG00000001926) #24	ENSCLAG00000002025 #25	HPCAL1 (ENSCLAG00000002037) #26	ODC1 (ENSCLAG00000002140) #27	NOL10 (ENSCLAG00000002234) #28	ATP6V1C2 (ENSCLAG00000006612) #29	PDIA6 (ENSCLAG00000006956) #30	KCNF1 (ENSCLAG00000017968) #31	ENSCLAG00000007661 #32	SLC66A3 (ENSCLAG00000008584) #33	ROCK2 (ENSCLAG00000009471) #34	E2F6 (ENSCLAG00000004863) #35	GREB1 (ENSCLAG00000005662) #36	LPIN1 (ENSCLAG00000001810) #37
Degu	MODERN SPECIES	192				MYT1L (ENSODEG00000001544) #13	ENSODEG00000018668	PXDN (ENSODEG00000001228) #14	ASAP2 (ENSODEG00000001497) #15	ENSODEG00000018909	ENSODEG00000003101 #16	CPSF3 (ENSODEG00000003129) #17	IAH1 (ENSODEG00000003362) #18	ADAM17 (ENSODEG00000003472) #19	YWHAQ (ENSODEG00000001504) ##20	ENSODEG00000001535	TAF1B (ENSODEG00000002052) #21	GRHL1 (ENSODEG00000002151) #22	ENSODEG00000002288 #23	RRM2 (ENSODEG00000002317) ##24	ENSODEG00000002415 #26	ODC1 (ENSODEG00000000437) #27	NOL10 (ENSODEG00000000508) #28	ATP6V1C2 (ENSODEG00000000754) #29	ENSODEG00000000842 #30	ENSODEG00000000975 #32	ENSODEG00000000987 #33	ENSODEG00000001162 #34	ENSODEG00000001198 #34	ENSODEG00000001238 #35	GREB1 (ENSODEG00000002144) #36	LPIN1 (ENSODEG00000003117) #37	TRIB2 (ENSODEG00000003153)
Guinea pig	MODERN SPECIES	125																GRHL1 (ENSCPOG00000010783) #22	KLF11 (ENSCPOG00000025767) #23	RRM2 (ENSCPOG00000008652) #24	HPCAL1 (ENSCPOG00000034185) #26	ODC1 (ENSCPOG00000008476) #27	NOL10 (ENSCPOG00000007706) #28	ATP6V1C2 (ENSCPOG00000008738) #29	PDIA6 (ENSCPOG00000010804) #30	KCNF1 (ENSCPOG00000015432) #31	C2orf50 (ENSCPOG00000034329)	SLC66A3 (ENSCPOG00000031555) #33	ROCK2 (ENSCPOG00000012664) #34	E2F6 (ENSCPOG00000019385) #35	GREB1 (ENSCPOG00000006588) #36	LPIN1 (ENSCPOG00000013546) #37	TRIB2 (ENSCPOG00000040411)
Naked mole-rat female	MODERN SPECIES	19															ENSHGLG00000001858 #21	GRHL1 (ENSHGLG00000004863) #22	KLF11 (ENSHGLG00000033218) #23	ENSHGLG00000002385	RRM2 (ENSHGLG00000000884) #24	HPCAL1 (ENSHGLG00000000540) #26	ENSHGLG00000000300 #27	NOL10 (ENSHGLG00000001564) #28	ATP6V1C2 (ENSHGLG00000001064) #29	PDIA6 (ENSHGLG00000000403) #30	ENSHGLG00000047929	ENSHGLG00000050301	KCNF1 (ENSHGLG00000003808) #31	ENSHGLG00000000514 #34	ENSHGLG00000001946	SLC66A3 (ENSHGLG00000001582) #33	ENSHGLG00000046079
Sciuridae	ANCESTRAL SPECIES	16	ENSGT00940000162396	ENSGT00940000161652	ENSGT00940000154030.a.b	ENSGT00390000013670	ENSGT00940000157701	ENSGT00940000156464	ENSGT00940000156714	ENSGT01030000234564.a.a.a.a.b	ENSGT00940000155623 #15	ENSGT00390000003990 #16	ENSGT00940000155699 #17	ENSGT00390000008069 #18	ENSGT00940000155443 #19	ENSGT01090000260040.b.b.b.b.a.a ##20	ENSGT00440000033827 #21	ENSGT00940000157612 #22	ENSGT00940000155982.b #23	ENSGT00390000016845	ENSGT00390000013305.a.a.v.b #24	ENSGT00940000154645.A #26	ENSGT00950000182995.e.a.a.a #27	ENSGT00390000007900 #28	ENSGT00390000004263.b #29	ENSGT00940000155646 #30	ENSGT00940000160213 #31	ENSGT00940000154459.B	ENSGT00940000153916.B #33	ENSGT01030000234517.D #34	ENSGT00940000155734.q #35	ENSGT00390000008041.C #36	ENSGT01100000263518.A.a.a.b
Eurasian red squirrel	DUPLICATION
Eurasian red squirrel	MODERN SPECIES	5	SOX11 (ENSSVLG00005021089)	CMPK2 (ENSSVLG00005020981)	RSAD2 (ENSSVLG00005020911)	RNF144A (ENSSVLG00005020868)	ID2 (ENSSVLG00005020830)	KIDINS220 (ENSSVLG00005020790)	MBOAT2 (ENSSVLG00005020748)	ASAP2 (ENSSVLG00005020310) #15	ITGB1BP1 (ENSSVLG00005020179) #16	CPSF3 (ENSSVLG00005020098) #17	IAH1 (ENSSVLG00005019997) #18	ADAM17 (ENSSVLG00005019936) #19	YWHAQ (ENSSVLG00005019899) ##20	ENSSVLG00005019881	ENSSVLG00005019695 #21	ENSSVLG00005019438 #22	KLF11 (ENSSVLG00005019337) #23	CYS1 (ENSSVLG00005019295)	ENSSVLG00005019233 #24	HPCAL1 (ENSSVLG00005019176) #26	ENSSVLG00005019056 #27	NOL10 (ENSSVLG00005018977) #28	ENSSVLG00005018931	ATP6V1C2 (ENSSVLG00005018543) #29	PDIA6 (ENSSVLG00005018305) #30	KCNF1 (ENSSVLG00005018274) #31	C2orf50 (ENSSVLG00005018240)	SLC66A3 (ENSSVLG00005018165) #33	ROCK2 (ENSSVLG00005018051) #34	ENSSVLG00005017989	ENSSVLG00005017788 #35
Eurasian red squirrel	MODERN SPECIES	42					ENSSVLG00005018207	ENSSVLG00005018167	ENSSVLG00005018123	ENSSVLG00005018056	ENSSVLG00005018030	ENSSVLG00005017990	ENSSVLG00005017973	ENSSVLG00005017934	ENSSVLG00005017901	ENSSVLG00005017853	ENSSVLG00005017798	ENSSVLG00005017762 #22
Marmotini	ANCESTRAL SPECIES	14	ENSGT00940000162396	ENSGT00940000161652	ENSGT00940000154030.a.b	ENSGT00390000013670	ENSGT00940000157701	ENSGT00940000156464	ENSGT00940000156714	ENSGT01030000234564.a.a.a.a.b	ENSGT00940000155623 #15	ENSGT00390000003990 #16	ENSGT00940000155699 #17	ENSGT00390000008069.k.a #18	ENSGT00940000155443 #19	ENSGT01090000260040.b.b.b.b.a.a ##20	ENSGT00440000033827 #21	ENSGT00940000157612 #22	ENSGT00940000155982.b #23	ENSGT00390000016845	ENSGT00390000013305.a.a.v.b #24	ENSGT00940000154645.A #26	ENSGT00950000182995.e.a.a.a #27	ENSGT00390000007900 #28	ENSGT00390000004263.b #29	ENSGT00940000155646 #30	ENSGT00940000160213 #31	ENSGT00940000154459.B	ENSGT00940000153916.B #33	ENSGT01030000234517.D #34	ENSGT00940000155734.q #35	ENSGT00390000008041.C #36	ENSGT01100000263518.A.a.a.b
Marmotini_b	ANCESTRAL SPECIES	17	ENSGT00940000162396	ENSGT00940000161652	ENSGT00940000154030.a.b	ENSGT00390000013670	ENSGT00940000157701	ENSGT00940000156464	ENSGT00940000156714	ENSGT01030000234564.a.a.a.a.b	ENSGT00940000155623 #15	ENSGT00390000003990 #16	ENSGT00940000155699 #17	ENSGT00390000008069.k.a #18	ENSGT00940000155443 #19	ENSGT01090000260040.b.b.b.b.a.b ##20	ENSGT00440000033827 #21	ENSGT00940000157612 #22	ENSGT00940000155982.b #23	ENSGT00390000013305.a.a.v.b #24	ENSGT00940000154645.A #26	ENSGT00950000182995.e.a.a.a #27	ENSGT00390000007900 #28	ENSGT00390000004263.b #29	ENSGT00940000155646 #30	ENSGT00940000160213 #31	ENSGT00940000154459.B	ENSGT00940000153916.B #33	ENSGT01030000234517.D #34	ENSGT00940000155734.q #35	ENSGT00390000008041.C #36	ENSGT01100000263518.A.a.a.b	ENSGT00940000157219 #37
Squirrel	MODERN SPECIES	132	ALLC (ENSSTOG00000002136)	DCDC2C (ENSSTOG00000020234)	CMPK2 (ENSSTOG00000019402)	RSAD2 (ENSSTOG00000006147)	RNF144A (ENSSTOG00000027570)	ID2 (ENSSTOG00000019401)	KIDINS220 (ENSSTOG00000013232)	MBOAT2 (ENSSTOG00000020147)	ASAP2 (ENSSTOG00000004398) #15	ITGB1BP1 (ENSSTOG00000004464) #16	CPSF3 (ENSSTOG00000004476) #17	ENSSTOG00000004500 #18	ADAM17 (ENSSTOG00000004510) #19	ENSSTOG00000024378 ##20	TAF1B (ENSSTOG00000002419) #21	GRHL1 (ENSSTOG00000019842) #22	ENSSTOG00000030936 #23	ENSSTOG00000033669 #24	HPCAL1 (ENSSTOG00000001514) #26	ENSSTOG00000000386 #27	NOL10 (ENSSTOG00000005485) #28	ATP6V1C2 (ENSSTOG00000005527) #29	PDIA6 (ENSSTOG00000005550) #30	C2orf50 (ENSSTOG00000002600)	SLC66A3 (ENSSTOG00000027023) #33	ROCK2 (ENSSTOG00000002624) #34	E2F6 (ENSSTOG00000003316) #35	GREB1 (ENSSTOG00000026032) #36	NTSR2 (ENSSTOG00000010000)	LPIN1 (ENSSTOG00000010854) #37	ENSSTOG00000002702
Arctic ground squirrel	MODERN SPECIES			SOX11 (ENSUPAG00010012315)	CMPK2 (ENSUPAG00010012310)	RSAD2 (ENSUPAG00010012305)	RNF144A (ENSUPAG00010012263)	ID2 (ENSUPAG00010012253)	KIDINS220 (ENSUPAG00010012028)	MBOAT2 (ENSUPAG00010011957)	ASAP2 (ENSUPAG00010011650) #15	ITGB1BP1 (ENSUPAG00010011629) #16	CPSF3 (ENSUPAG00010011610) #17	ENSUPAG00010011577 #18	ADAM17 (ENSUPAG00010011539) #19	YWHAQ (ENSUPAG00010011534) #20	TAF1B (ENSUPAG00010011508) #21	GRHL1 (ENSUPAG00010011483) #22	KLF11 (ENSUPAG00010011457) #23	CYS1 (ENSUPAG00010011444)	HPCAL1 (ENSUPAG00010011428) #26	ODC1 (ENSUPAG00010011416) #27	NOL10 (ENSUPAG00010011386) #28	ATP6V1C2 (ENSUPAG00010011265) #29	PDIA6 (ENSUPAG00010011237) #30	KCNF1 (ENSUPAG00010011227) #31	C2orf50 (ENSUPAG00010011218)	SLC66A3 (ENSUPAG00010011204) #33	ROCK2 (ENSUPAG00010011170) #34	ENSUPAG00010011160	E2F6 (ENSUPAG00010011151) #35	GREB1 (ENSUPAG00010011107) #36	NTSR2 (ENSUPAG00010011106)
Alpin marmot	MODERN SPECIES	6	ENSMMMG00000022822	SOX11 (ENSMMMG00000022819)	CMPK2 (ENSMMMG00000022812)	RSAD2 (ENSMMMG00000022810)	RNF144A (ENSMMMG00000022809)	ID2 (ENSMMMG00000022803)	KIDINS220 (ENSMMMG00000022748)	MBOAT2 (ENSMMMG00000022735)	ASAP2 (ENSMMMG00000022671) #15	ITGB1BP1 (ENSMMMG00000022669) #16	CPSF3 (ENSMMMG00000022663) #17	IAH1 (ENSMMMG00000022658) #18	ADAM17 (ENSMMMG00000022654) #19	YWHAQ (ENSMMMG00000022652) ##20	TAF1B (ENSMMMG00000022638) #21	GRHL1 (ENSMMMG00000022631) #22	KLF11 (ENSMMMG00000022629) #23	ENSMMMG00000022625	ENSMMMG00000022624 #24	HPCAL1 (ENSMMMG00000022618) #26	ODC1 (ENSMMMG00000022615) #27	NOL10 (ENSMMMG00000022607) #28	ATP6V1C2 (ENSMMMG00000022583) #29	PDIA6 (ENSMMMG00000022575) #30	KCNF1 (ENSMMMG00000022573) #31	C2orf50 (ENSMMMG00000022565)	SLC66A3 (ENSMMMG00000022562) #33	ROCK2 (ENSMMMG00000022550) #34	E2F6 (ENSMMMG00000022544) #35	GREB1 (ENSMMMG00000022514) #36	LPIN1 (ENSMMMG00000022468) #37