Rodentia_A	ANCESTRAL SPECIES	7	ENSGT00390000008107.c.a #7	ENSGT00550000074890 #8	ENSGT00390000018706.m.b.a #9	ENSGT00510000048902.a #10	ENSGT00940000159721 #11	ENSGT00940000162618 #12	ENSGT00940000155305 #13	ENSGT00940000155123.b #14	ENSGT00940000156667 #15	ENSGT00940000154170.A #16	ENSGT00390000004454 #17	ENSGT00950000182940.b.b #18	ENSGT01050000244840.A.b.b #20	ENSGT00950000183076.b #19	ENSGT01050000244840.A.a.b #21	ENSGT01050000244840.A.a.a #22	ENSGT00940000161125 #23	ENSGT00390000001362 #24	ENSGT00730000111121	ENSGT00940000164103	ENSGT00940000157817	ENSGT00390000017026.c	ENSGT00940000159952	ENSGT00390000009710	ENSGT00940000157603	ENSGT00940000157310	ENSGT00990000203589.b.b	ENSGT00940000158270	ENSGT00940000158176	ENSGT00390000003122.c.b	ENSGT00390000003122.c.a
Sciuridae	ANCESTRAL SPECIES	18	ENSGT00390000008107.c.a #7	ENSGT00550000074890 #8	ENSGT00390000018706.m.b.a #9	ENSGT00510000048902.a #10	ENSGT00940000159721 #11	ENSGT00940000162618 #12	ENSGT00940000155305 #13	ENSGT00940000155123.b #14	ENSGT00940000156667 #15	ENSGT00940000154170.A #16	ENSGT00390000004454 #17	ENSGT00950000182940.b.b #18	ENSGT01050000244840.A.b.b #20	ENSGT00950000183076.b #19	ENSGT01050000244840.A.a.b #21	ENSGT01050000244840.A.a.a #22	ENSGT00940000161125 #23	ENSGT00390000001362 #24
Marmotini	ANCESTRAL SPECIES	23	ENSGT00390000008107.c.a #7	ENSGT00550000074890 #8	ENSGT00390000018706.m.b.a #9	ENSGT00510000048902.a #10	ENSGT00940000159721 #11	ENSGT00940000162618 #12	ENSGT00940000155305 #13	ENSGT00940000155123.b #14	ENSGT00940000156667 #15	ENSGT00940000154170.A #16	ENSGT00390000004454 #17	ENSGT00950000182940.b.b #18	ENSGT01050000244840.A.b.b #20	ENSGT00950000183076.b #19	ENSGT01050000244840.A.a.b #21	ENSGT01050000244840.A.a.a #22	ENSGT00940000161125 #23	ENSGT00390000001362 #24
Marmotini_b	ANCESTRAL SPECIES	92	ENSGT00390000008107.c.a #7	ENSGT00550000074890 #8	ENSGT00390000018706.m.b.a #9	ENSGT00510000048902.a #10	ENSGT00940000159721 #11	ENSGT00940000162618 #12	ENSGT00940000155305 #13	ENSGT00940000155123.b #14	ENSGT00940000156667 #15	ENSGT00940000154170.A #16	ENSGT00390000004454 #17	ENSGT00950000182940.b.b #18	ENSGT01050000244840.A.b.b #20	ENSGT00950000183076.b #19	ENSGT01050000244840.A.a.b #21	ENSGT01050000244840.A.a.a #22	ENSGT00940000161125 #23	ENSGT00390000001362 #24
Arctic ground squirrel	MODERN SPECIES	299	HEXB (ENSUPAG00010004984) #7	GFM2 (ENSUPAG00010005333) #8	NSA2 (ENSUPAG00010005383) #9	FAM169A (ENSUPAG00010005409) #10	GCNT4 (ENSUPAG00010005440) #11	ENSUPAG00010005442 #12	HMGCR (ENSUPAG00010005462) #13	ENSUPAG00010005498 #14	POLK (ENSUPAG00010005814) #15	ANKDD1B (ENSUPAG00010005945) #16	POC5 (ENSUPAG00010005963) #17	SV2C (ENSUPAG00010006006) #18	IQGAP2 (ENSUPAG00010006026) #19	F2RL2 (ENSUPAG00010006042) #20	F2R (ENSUPAG00010006053) #21	F2RL1 (ENSUPAG00010006060) #22	S100Z (ENSUPAG00010006063) #23	CRHBP (ENSUPAG00010006069) #24
Squirrel	MODERN SPECIES	149	ENSSTOG00000027827	HEXB (ENSSTOG00000007903) #7	GFM2 (ENSSTOG00000007931) #8	ENSSTOG00000007959 ##9	FAM169A (ENSSTOG00000007975) #10	ANKRD31 (ENSSTOG00000034383) #12	HMGCR (ENSSTOG00000009610) #13	CERT1 (ENSSTOG00000003170) #14	ENSSTOG00000003205 #15	ANKDD1B (ENSSTOG00000009832) #16	POC5 (ENSSTOG00000009839) #17	SV2C (ENSSTOG00000013490) #18	F2RL2 (ENSSTOG00000034743) #20	IQGAP2 (ENSSTOG00000013504) #19	F2R (ENSSTOG00000008252) #21	F2RL1 (ENSSTOG00000026512) #22	S100Z (ENSSTOG00000009498) #23	CRHBP (ENSSTOG00000009510) #24
Alpin marmot	MODERN SPECIES	48	HEXB (ENSMMMG00000002087) #7	GFM2 (ENSMMMG00000001763) #8	NSA2 (ENSMMMG00000001722) #9	FAM169A (ENSMMMG00000001677) #10	GCNT4 (ENSMMMG00000001657) #11	ENSMMMG00000001628 #12	HMGCR (ENSMMMG00000001547) #13	CERT1 (ENSMMMG00000001422) #14	POLK (ENSMMMG00000001203) #15	ANKDD1B (ENSMMMG00000001142) #16	POC5 (ENSMMMG00000000939) #17	SV2C (ENSMMMG00000000845) #18	F2RL2 (ENSMMMG00000000828) #20	IQGAP2 (ENSMMMG00000000750) #19	F2R (ENSMMMG00000000732) #21	F2RL1 (ENSMMMG00000000723) #22	S100Z (ENSMMMG00000000720) #23
Eurasian red squirrel	DUPLICATION
Eurasian red squirrel	MODERN SPECIES	15	NSA2 (ENSSVLG00005006610) #9	FAM169A (ENSSVLG00005006669) #10	GCNT4 (ENSSVLG00005006815) #11	ANKRD31 (ENSSVLG00005006845) #12	HMGCR (ENSSVLG00005006942) #13	CERT1 (ENSSVLG00005007093) #14	ENSSVLG00005007250	POLK (ENSSVLG00005007352) #15	ANKDD1B (ENSSVLG00005007433) #16	POC5 (ENSSVLG00005007522) #17	ENSSVLG00005007604	SV2C (ENSSVLG00005007661) #18	IQGAP2 (ENSSVLG00005007881) #19	F2RL2 (ENSSVLG00005008481) #20	F2R (ENSSVLG00005008506) #21	ENSSVLG00005008525 #22	ENSSVLG00005008549	S100Z (ENSSVLG00005008555) #23	CRHBP (ENSSVLG00005008579) #24	ENSSVLG00005008651	ENSSVLG00005008740	OCLN (ENSSVLG00005008798)	MARVELD2 (ENSSVLG00005008937)	RAD17 (ENSSVLG00005009140)	ENSSVLG00005009362	CCDC125 (ENSSVLG00005009466)	CDK7 (ENSSVLG00005009632)	ENSSVLG00005009714	CENPH (ENSSVLG00005009762)	CCNB1 (ENSSVLG00005009823)	SLC30A5 (ENSSVLG00005009911)
Eurasian red squirrel	MODERN SPECIES	156	ENSSVLG00005013733	ENSSVLG00005013685	LHFPL1 (ENSSVLG00005013627)	AMOT (ENSSVLG00005013525)	ENSSVLG00005019330	ENSSVLG00005019275	ENSSVLG00005019228	ENSSVLG00005019177	ENSSVLG00005019126	ENSSVLG00005019077	HTR2C (ENSSVLG00005018984)	ENSSVLG00005018928	IL13RA2 (ENSSVLG00005018862)	LRCH2 (ENSSVLG00005018464)	ENSSVLG00005018369	ENSSVLG00005018340 #22	PLS3 (ENSSVLG00005018046)	ENSSVLG00005017980	AGTR2 (ENSSVLG00005017968)	ENSSVLG00005017948	ENSSVLG00005017904	SLC6A14 (ENSSVLG00005017746)	CT83 (ENSSVLG00005017691)	ENSSVLG00005017648	KLHL13 (ENSSVLG00005017370)	WDR44 (ENSSVLG00005017220)	DOCK11 (ENSSVLG00005016279)	IL13RA1 (ENSSVLG00005016116)	ENSSVLG00005016098	ENSSVLG00005016082	LONRF3 (ENSSVLG00005015856)
Hystricomorpha	ANCESTRAL SPECIES	31	ENSGT00390000008107.c.a #7	ENSGT00550000074890 #8	ENSGT00390000018706.m.b.a #9	ENSGT00510000048902.a #10	ENSGT00940000159721 #11	ENSGT00940000162618 #12	ENSGT00940000155305 #13	ENSGT00940000155123.b #14	ENSGT00940000156667 #15	ENSGT00940000154170.A #16	ENSGT00390000004454 #17	ENSGT00950000182940.b.b #18	ENSGT01050000244840.A.b.b #20	ENSGT00950000183076.b #19	ENSGT01050000244840.A.a.b #21	ENSGT01050000244840.A.a.a #22	ENSGT00940000161125 #23	ENSGT00390000001362 #24	ENSGT00730000111121	ENSGT00940000157817	ENSGT00390000017026.c	ENSGT00940000159952	ENSGT00390000009710	ENSGT00940000157603	ENSGT00940000157310	ENSGT00990000203589.b.b	ENSGT00940000158270	ENSGT00940000158176	ENSGT00390000003122.c.b	ENSGT00390000003122.c.a	ENSGT00510000046704.b.a
Hystricomorpha_a	ANCESTRAL SPECIES	72	ENSGT00390000008107.c.a #7	ENSGT00550000074890 #8	ENSGT00390000018706.m.b.a #9	ENSGT00510000048902.a #10	ENSGT00940000159721 #11	ENSGT00940000162618 #12	ENSGT00940000155305 #13	ENSGT00940000155123.b #14	ENSGT00940000156667 #15	ENSGT00940000154170.A #16	ENSGT00390000004454 #17	ENSGT00950000182940.b.b #18	ENSGT00950000183076.b #19	ENSGT01050000244840.A.b.b #20	ENSGT01050000244840.A.a.b #21	ENSGT01050000244840.A.a.a #22	ENSGT00940000161125 #23	ENSGT00390000001362 #24	ENSGT00730000111121	ENSGT00940000157817	ENSGT00390000017026.c	ENSGT00940000159952	ENSGT00390000009710	ENSGT00940000157603	ENSGT00940000157310	ENSGT00990000203589.b.b	ENSGT00940000158270	ENSGT00940000158176	ENSGT00390000003122.c.b	ENSGT00390000003122.c.a	ENSGT00510000046704.b.a
Hystricomorpha_b	ANCESTRAL SPECIES	95	ENSGT00950000182983.B.a.b	ENSGT00390000008107.c.a #7	ENSGT00550000074890 #8	ENSGT00390000018706.m.b.a #9	ENSGT00510000048902.a #10	ENSGT00940000159721 #11	ENSGT00940000162618 #12	ENSGT00940000155305 #13	ENSGT00940000155123.b #14	ENSGT00940000156667 #15	ENSGT00940000154170.A #16	ENSGT00390000004454 #17	ENSGT00950000182940.b.b #18	ENSGT01050000244840.A.b.b #20	ENSGT00950000183076.b #19	ENSGT01050000244840.A.a.a #22	ENSGT00940000161125 #23	ENSGT00390000001362 #24	ENSGT00730000111121	ENSGT00940000157817	ENSGT00390000017026.c	ENSGT00940000159952	ENSGT00390000009710	ENSGT00940000157603	ENSGT00940000157310	ENSGT00990000203589.b.b	ENSGT00940000158270	ENSGT00940000158176	ENSGT00390000003122.c.b	ENSGT00390000003122.c.a	ENSGT00510000046704.b.a
Degu	MODERN SPECIES	218	HEXB (ENSODEG00000002081) #7	GFM2 (ENSODEG00000002193) #8	ENSODEG00000002883 ##9	FAM169A (ENSODEG00000002906) #10	ENSODEG00000002941	GCNT4 (ENSODEG00000018869) #11	ANKRD31 (ENSODEG00000003017) #12	HMGCR (ENSODEG00000003319) #13	CERT1 (ENSODEG00000002483) #14	POLK (ENSODEG00000002687) #15	ANKDD1B (ENSODEG00000003019) #16	POC5 (ENSODEG00000003014) #17	SV2C (ENSODEG00000003155) #18	IQGAP2 (ENSODEG00000003459) #19	ENSODEG00000003730	F2RL1 (ENSODEG00000002463) #22	S100Z (ENSODEG00000002505) #23	CRHBP (ENSODEG00000002524) #24	ENSODEG00000002814
Long-tailed chinchilla	MODERN SPECIES	132	GFM2 (ENSCLAG00000013440) #8	NSA2 (ENSCLAG00000010179) #9	FAM169A (ENSCLAG00000009619) #10	ENSCLAG00000011385	GCNT4 (ENSCLAG00000010436) #11	ENSCLAG00000009641	ANKRD31 (ENSCLAG00000011065) #12	HMGCR (ENSCLAG00000010132) #13	CERT1 (ENSCLAG00000011527) #14	POLK (ENSCLAG00000011236) #15	ANKDD1B (ENSCLAG00000010494) #16	POC5 (ENSCLAG00000009830) #17	SV2C (ENSCLAG00000013949) #18	F2RL2 (ENSCLAG00000012739) #20	IQGAP2 (ENSCLAG00000011435) #19	F2RL1 (ENSCLAG00000010304) #22	S100Z (ENSCLAG00000010354) #23	CRHBP (ENSCLAG00000009942) #24	AGGF1 (ENSCLAG00000012928)	PDE8B (ENSCLAG00000011619)	WDR41 (ENSCLAG00000010095)	OTP (ENSCLAG00000011647)	TBCA (ENSCLAG00000011463)	AP3B1 (ENSCLAG00000017374)	ENSCLAG00000017966	SCAMP1 (ENSCLAG00000010430)	LHFPL2 (ENSCLAG00000010028)	ENSCLAG00000009820	ARSB (ENSCLAG00000013316)	DMGDH (ENSCLAG00000014854)	BHMT2 (ENSCLAG00000013633)
Guinea pig	MODERN SPECIES	29												SV2C (ENSCPOG00000008567) #18	IQGAP2 (ENSCPOG00000025031) #19	F2RL2 (ENSCPOG00000002801) #20	F2R (ENSCPOG00000032667) #21	F2RL1 (ENSCPOG00000033414) #22	S100Z (ENSCPOG00000030952) #23	CRHBP (ENSCPOG00000002422) #24	ENSCPOG00000009626	ENSCPOG00000035041	ELOVL7 (ENSCPOG00000037993)	DEPDC1B (ENSCPOG00000011483)	PDE4D (ENSCPOG00000004873)	ENSCPOG00000039531	RAB3C (ENSCPOG00000001394)	PLK2 (ENSCPOG00000021250)	ACTBL2 (ENSCPOG00000011023)	GPBP1 (ENSCPOG00000012341)	ENSCPOG00000015027	SETD9 (ENSCPOG00000015025)	MAP3K1 (ENSCPOG00000015017)
Naked mole-rat female	MODERN SPECIES		USP42 (ENSHGLG00000018062)	ENSHGLG00000035813	EIF2AK1 (ENSHGLG00000015194)	ANKRD61 (ENSHGLG00000005518)	AIMP2 (ENSHGLG00000041958)	PMS2 (ENSHGLG00000007741)	ENSHGLG00000038861	ENSHGLG00000010064	ENSHGLG00000007267	ENSHGLG00000009254	ENSHGLG00000020676	ENSHGLG00000013637	LMTK2 (ENSHGLG00000013780)	BHLHA15 (ENSHGLG00000033900)	TECPR1 (ENSHGLG00000018344)	ENSHGLG00000015104 #22	ENSHGLG00000013687	ENSHGLG00000032492	BAIAP2L1 (ENSHGLG00000017707)	ENSHGLG00000044552	ENSHGLG00000007737	ENSHGLG00000042548	TMEM130 (ENSHGLG00000008380)	TRRAP (ENSHGLG00000013805)	SMURF1 (ENSHGLG00000006003)	ENSHGLG00000009628	ENSHGLG00000043221	ENSHGLG00000017246	ARPC1B (ENSHGLG00000017816)	PDAP1 (ENSHGLG00000013857)	ENSHGLG00000018123