Rodentia_A	ANCESTRAL SPECIES		ENSGT00940000161899	ENSGT00940000154209.a.b #7	ENSGT00940000156661 #8	ENSGT00950000183122.A #9	ENSGT00390000000747 #10	ENSGT01100000263502.A.a.b #11	ENSGT00950000182994.A.n.b	ENSGT00940000160037 #12	ENSGT00510000047676 #14	ENSGT00940000161852 #15	ENSGT00390000008164.d #16	ENSGT00950000183059.b.a.b #18	ENSGT00940000155103.a.b #19	ENSGT00730000111198 #20	ENSGT00940000157060.t #21	ENSGT00940000155092.b #22	ENSGT00390000017364 #24	ENSGT00390000015553.a.a.b #25	ENSGT00940000162691 #26	ENSGT00730000111005 #27	ENSGT00910000147125	ENSGT00390000016158 #28	ENSGT00940000156546 #29	ENSGT00940000160590 #30	ENSGT00940000156992 #31	ENSGT00940000156766 #32	ENSGT00950000183142.a.b.a.b #33	ENSGT00940000171704	ENSGT00390000005861 #34	ENSGT00390000004799 #35	ENSGT00940000163104
Sciuridae	ANCESTRAL SPECIES		ENSGT00530000063808.b	ENSGT00940000161899	ENSGT00940000154209.a.b #7	ENSGT00940000156661 #8	ENSGT00950000183122.A #9	ENSGT00390000000747.h #10	ENSGT01100000263502.A.a.b #11	ENSGT00940000160037 #12	ENSGT00510000047676 #14	ENSGT00390000008164.d #16	ENSGT00940000161852 #15	ENSGT00950000183059.b.a.b #18	ENSGT00940000155103.a.b #19	ENSGT00730000111198 #20	ENSGT00940000157060.t #21	ENSGT00940000155092.b #22	ENSGT00390000017364 #24	ENSGT00390000015553.a.a.b #25	ENSGT00940000162691 #26	ENSGT00730000111005 #27	ENSGT00910000147125	ENSGT00390000016158.i #28	ENSGT00940000156546 #29	ENSGT00940000160590.l #30	ENSGT00940000160590.k ##30	ENSGT00940000156992 #31	ENSGT00940000156766 #32	ENSGT00950000183142.a.b.a.b #33	ENSGT00940000171704	ENSGT00390000005861 #34	ENSGT00390000004799 #35
Marmotini	ANCESTRAL SPECIES	21	ENSGT00530000063808.b	ENSGT00940000161899	ENSGT00940000154209.a.b #7	ENSGT00940000156661 #8	ENSGT00950000183122.A #9	ENSGT00390000000747.h #10	ENSGT01100000263502.A.a.b #11	ENSGT00940000160037 #12	ENSGT00510000047676 #14	ENSGT00390000008164.d #16	ENSGT00940000161852 #15	ENSGT00950000183059.b.a.b #18	ENSGT00940000155103.a.b #19	ENSGT00730000111198 #20	ENSGT00940000157060.t #21	ENSGT00940000155092.b #22	ENSGT01030000235784 #23	ENSGT00390000017364 #24	ENSGT00390000015553.a.a.b #25	ENSGT00940000162691 #26	ENSGT00730000111005 #27	ENSGT00390000016158.i #28	ENSGT00940000156546 #29	ENSGT00940000160590.k ##30	ENSGT00940000156992 #31	ENSGT00940000156766 #32	ENSGT00950000183142.a.b.a.b #33	ENSGT00390000005861 #34	ENSGT00390000004799 #35	ENSGT00940000163104	ENSGT00390000018900
Marmotini_b	ANCESTRAL SPECIES	84		ENSGT00940000161899	ENSGT00940000154209.a.b #7	ENSGT00940000156661 #8	ENSGT00950000183122.A #9	ENSGT00390000000747.h #10	ENSGT01100000263502.A.a.b #11	ENSGT00940000160037 #12	ENSGT00510000047676 #14	ENSGT00390000008164.d #16	ENSGT00940000161852 #15	ENSGT00950000183059.b.a.b #18	ENSGT00940000155103.a.b #19	ENSGT00730000111198 #20	ENSGT00940000157060.t #21	ENSGT00940000155092.b #22	ENSGT01030000235784 #23	ENSGT00390000017364 #24	ENSGT00390000015553.a.a.b #25	ENSGT00940000162691 #26	ENSGT00730000111005 #27	ENSGT00390000016158.i #28	ENSGT00940000156546 #29	ENSGT00940000160590.k ##30	ENSGT00940000156992 #31	ENSGT00940000156766 #32	ENSGT00950000183142.a.b.a.b #33	ENSGT00390000005861 #34	ENSGT00390000004799 #35	ENSGT00940000163104	ENSGT00390000018900
Arctic ground squirrel	MODERN SPECIES	79	GREM2 (ENSUPAG00010018995) #7	RGS7 (ENSUPAG00010018948) #8	FH (ENSUPAG00010018928) #9	KMO (ENSUPAG00010018908) #10	OPN3 (ENSUPAG00010018902) #11	WDR64 (ENSUPAG00010018776) #12	ENSUPAG00010018764 #13	EXO1 (ENSUPAG00010018752) #14	ENSUPAG00010018744 #15	BECN2 (ENSUPAG00010018741) #16	MAP1LC3C (ENSUPAG00010018734) #17	PLD5 (ENSUPAG00010018694) #18	CEP170 (ENSUPAG00010018567) #19	SDCCAG8 (ENSUPAG00010018478) #20	AKT3 (ENSUPAG00010018428) #21	ZBTB18 (ENSUPAG00010018400) #22	ENSUPAG00010018394 #23	C1orf100 (ENSUPAG00010018380) #24	ADSS2 (ENSUPAG00010018358) #25	ENSUPAG00010018323 #26	DESI2 (ENSUPAG00010018313) #27	ENSUPAG00010018307 #28	HNRNPU (ENSUPAG00010018254) #29	EFCAB2 (ENSUPAG00010018238) #30	KIF26B (ENSUPAG00010018207) #31	SMYD3 (ENSUPAG00010018170) #32	ENSUPAG00010018160 #33	CNST (ENSUPAG00010018148) #34	SCCPDH (ENSUPAG00010018131) #35
Squirrel	MODERN SPECIES	126		FMN2 (ENSSTOG00000025339)	GREM2 (ENSSTOG00000007628) #7	RGS7 (ENSSTOG00000006862) #8	FH (ENSSTOG00000012681) #9	KMO (ENSSTOG00000012690) #10	OPN3 (ENSSTOG00000012707) #11	ENSSTOG00000012715 #12	BECN2 (ENSSTOG00000027748) #16	MAP1LC3C (ENSSTOG00000010423) #15	PLD5 (ENSSTOG00000031877) #18	CEP170 (ENSSTOG00000008203) #19	SDCCAG8 (ENSSTOG00000010585) #20	ENSSTOG00000030430	AKT3 (ENSSTOG00000010595) #21	ZBTB18 (ENSSTOG00000004290) #22	C1orf100 (ENSSTOG00000022394) #24	ADSS2 (ENSSTOG00000004376) #25	DESI2 (ENSSTOG00000004752) #27	COX20 (ENSSTOG00000000151) #28	ENSSTOG00000000153 #29	ENSSTOG00000031476 ##30	KIF26B (ENSSTOG00000028101) #31	SMYD3 (ENSSTOG00000028065) #32	TFB2M (ENSSTOG00000034162) #33	CNST (ENSSTOG00000000432) #34	ENSSTOG00000025585	SCCPDH (ENSSTOG00000007502) #35	ENSSTOG00000021998	AHCTF1 (ENSSTOG00000010795)	CDC42BPA (ENSSTOG00000015415)
Alpin marmot	MODERN SPECIES	12	FMN2 (ENSMMMG00000023630)	GREM2 (ENSMMMG00000023631) #7	RGS7 (ENSMMMG00000023632) #8	FH (ENSMMMG00000023640) #9	KMO (ENSMMMG00000023641) #10	OPN3 (ENSMMMG00000023648) #11	WDR64 (ENSMMMG00000023654) #12	EXO1 (ENSMMMG00000023668) #14	ENSMMMG00000023670 #15	BECN2 (ENSMMMG00000023671) #16	MAP1LC3C (ENSMMMG00000023673) #15	PLD5 (ENSMMMG00000023675) #18	CEP170 (ENSMMMG00000023685) #19	SDCCAG8 (ENSMMMG00000023689) #20	AKT3 (ENSMMMG00000023693) #21	ENSMMMG00000023698 #22	ENSMMMG00000023703 #23	C1orf100 (ENSMMMG00000023704) #24	ADSS2 (ENSMMMG00000023707) #25	ENSMMMG00000023709 #26	DESI2 (ENSMMMG00000023711) #27	COX20 (ENSMMMG00000023713) #28	HNRNPU (ENSMMMG00000023721) #29	EFCAB2 (ENSMMMG00000024005) ##30	KIF26B (ENSMMMG00000024009) #31	SMYD3 (ENSMMMG00000024012) #32	TFB2M (ENSMMMG00000024017) #33	CNST (ENSMMMG00000024021) #34	SCCPDH (ENSMMMG00000024025) #35	ENSMMMG00000024026	ENSMMMG00000024027
Eurasian red squirrel	DUPLICATION
Eurasian red squirrel	MODERN SPECIES	3	ENSSVLG00005020174	RGS7 (ENSSVLG00005020300) #8	FH (ENSSVLG00005020886) #9	KMO (ENSSVLG00005021004) #10	OPN3 (ENSSVLG00005021384) #11	WDR64 (ENSSVLG00005021468) #12	EXO1 (ENSSVLG00005021837) #14	ENSSVLG00005022002 #15	BECN2 (ENSSVLG00005022043) #16	MAP1LC3C (ENSSVLG00005022067) #15	PLD5 (ENSSVLG00005022151) #18	ENSSVLG00005022301	CEP170 (ENSSVLG00005022337) #19	SDCCAG8 (ENSSVLG00005022441) #20	AKT3 (ENSSVLG00005022494) #21	ZBTB18 (ENSSVLG00005022559) #22	C1orf100 (ENSSVLG00005022598) #24	ENSSVLG00005022682 #25	CATSPERE (ENSSVLG00005022809) #26	DESI2 (ENSSVLG00005023102) #27	ENSSVLG00005023149	ENSSVLG00005023185 #28	HNRNPU (ENSSVLG00005023262) #29	ENSSVLG00005023557 #30	KIF26B (ENSSVLG00005023636) #31	ENSSVLG00005023779	ENSSVLG00005023802	SMYD3 (ENSSVLG00005023822) #32	TFB2M (ENSSVLG00005023868) #33	ENSSVLG00005023906	ENSSVLG00005009011 #34
Eurasian red squirrel	MODERN SPECIES	113															ENSSVLG00005016262	ENSSVLG00005016172 #22
Hystricomorpha	ANCESTRAL SPECIES	49	ENSGT00940000156376	ENSGT00940000162504	ENSGT00390000017528	ENSGT01030000234620.a.b.b.b	ENSGT00530000064210	ENSGT00390000011724	ENSGT00950000182836.b.a.b	ENSGT00940000156989	ENSGT00960000186787	ENSGT00940000156484.b	ENSGT00940000157923	ENSGT00950000183059.b.a.b #18	ENSGT00940000155103.a.b #19	ENSGT00730000111198 #20	ENSGT00940000157060.t #21	ENSGT00940000155092.b #22	ENSGT00390000017364 #24	ENSGT00390000015553.a.a.b #25	ENSGT00940000162691 #26	ENSGT00730000111005 #27	ENSGT00390000016158 #28	ENSGT00940000156546 #29	ENSGT00940000160590 #30	ENSGT00940000156992 #31	ENSGT00940000156766 #32	ENSGT00950000183142.a.b.a.b #33	ENSGT00390000005861 #34	ENSGT00390000004799 #35	ENSGT00940000163104	ENSGT00390000018900	ENSGT01030000234517.H.b
Naked mole-rat female	MODERN SPECIES	16	ENSHGLG00000028910	ENSHGLG00000037874	ENSHGLG00000005464	ENSHGLG00000032112	MAP1LC3C (ENSHGLG00000037027) #15	ENSHGLG00000004656 #18	ENSHGLG00000040176	ENSHGLG00000006833	ENSHGLG00000043505	ENSHGLG00000011191	ENSHGLG00000006465 #19	ENSHGLG00000038674 #19	ENSHGLG00000004271 #20	AKT3 (ENSHGLG00000006424) #21	ENSHGLG00000043051	ZBTB18 (ENSHGLG00000003880) #22	ADSS (ENSHGLG00000007672) #25	ENSHGLG00000009917 #24	ENSHGLG00000041745 #26	ENSHGLG00000035202 #27	ENSHGLG00000015935	ENSHGLG00000043796	COX20 (ENSHGLG00000015836) #28	ENSHGLG00000010594 #29	ENSHGLG00000042794	ENSHGLG00000034325 #30	ENSHGLG00000015928 #31	ENSHGLG00000044814	ENSHGLG00000020542	ENSHGLG00000040776	ENSHGLG00000015190 #32
Hystricomorpha_a	ANCESTRAL SPECIES	13	ENSGT00940000162770	ENSGT00940000156376	ENSGT00940000162504	ENSGT00390000017528	ENSGT01030000234620.a.b.b.b	ENSGT00530000064210	ENSGT00390000011724	ENSGT00950000182836.b.a.b	ENSGT00940000156989	ENSGT00940000156484.b	ENSGT00940000157923	ENSGT00950000183059.b.a.b #18	ENSGT00940000155103.a.b #19	ENSGT00730000111198 #20	ENSGT00940000157060.t #21	ENSGT00940000155092.b #22	ENSGT00390000017364 #24	ENSGT00390000015553.a.a.b #25	ENSGT00940000162691 #26	ENSGT00730000111005 #27	ENSGT00390000016158 #28	ENSGT00940000156546 #29	ENSGT00940000160590 #30	ENSGT00940000156992 #31	ENSGT00940000156766 #32	ENSGT00950000183142.a.b.a.b #33	ENSGT00390000005861 #34	ENSGT00390000004799 #35	ENSGT00940000163104	ENSGT00390000018900	ENSGT01030000234517.H.b
Guinea pig	MODERN SPECIES	13	ENSCPOG00000033847	PACC1 (ENSCPOG00000009329)	PPP2R5A (ENSCPOG00000040049)	DTL (ENSCPOG00000014965)	INTS7 (ENSCPOG00000014960)	LPGAT1 (ENSCPOG00000011269)	NEK2 (ENSCPOG00000011264)	SLC30A1 (ENSCPOG00000013692)	PSEN2 (ENSCPOG00000001827)	PLD5 (ENSCPOG00000033411) #18	ENSCPOG00000002221	ENSCPOG00000002683 #19	ENSCPOG00000034860 #19	SDCCAG8 (ENSCPOG00000015503) #20	AKT3 (ENSCPOG00000015504) #21	ZBTB18 (ENSCPOG00000035384) #22	C1orf100 (ENSCPOG00000002339) #24	ADSS2 (ENSCPOG00000002342) #25	DESI2 (ENSCPOG00000002091) #27	COX20 (ENSCPOG00000032295) #28	HNRNPU (ENSCPOG00000011887) #29	EFCAB2 (ENSCPOG00000024335) #30	KIF26B (ENSCPOG00000001048) #31	SMYD3 (ENSCPOG00000002655) #32	ENSCPOG00000013225 #33	CNST (ENSCPOG00000012012) #34	SCCPDH (ENSCPOG00000029999) #35	ENSCPOG00000036159	AHCTF1 (ENSCPOG00000009216)	CDC42BPA (ENSCPOG00000011457)	COQ8A (ENSCPOG00000011445)
Hystricomorpha_b	ANCESTRAL SPECIES	4	ENSGT00940000156376	ENSGT00940000162504	ENSGT00390000017528	ENSGT01030000234620.a.b.b.b	ENSGT00530000064210	ENSGT00390000011724	ENSGT00950000182836.b.a.b	ENSGT00940000156989	ENSGT00940000156484.b	ENSGT00940000157923	ENSGT00950000183059.b.a.b #18	ENSGT00660000097201	ENSGT00940000155103.a.b #19	ENSGT00730000111198 #20	ENSGT00940000157060.t #21	ENSGT00940000155092.b #22	ENSGT00390000017364 #24	ENSGT00390000015553.a.a.b #25	ENSGT00940000162691 #26	ENSGT00730000111005 #27	ENSGT00390000016158 #28	ENSGT00940000156546 #29	ENSGT00940000160590 #30	ENSGT00940000156992 #31	ENSGT00940000156766 #32	ENSGT00950000183142.a.b.a.b #33	ENSGT00390000005861 #34	ENSGT00390000004799 #35	ENSGT00940000163104	ENSGT00390000018900	ENSGT01030000234517.H.b
Long-tailed chinchilla	MODERN SPECIES	113	ATF3 (ENSCLAG00000013767)	ENSCLAG00000007912	PACC1 (ENSCLAG00000009570)	PPP2R5A (ENSCLAG00000012816)	DTL (ENSCLAG00000014236)	INTS7 (ENSCLAG00000011748)	LPGAT1 (ENSCLAG00000011509)	NEK2 (ENSCLAG00000010880)	SLC30A1 (ENSCLAG00000009695)	PSEN2 (ENSCLAG00000013788)	PLD5 (ENSCLAG00000014400) #18	ENSCLAG00000010377	CEP170 (ENSCLAG00000015564) #19	SDCCAG8 (ENSCLAG00000011676) #20	ENSCLAG00000009649 #21	ZBTB18 (ENSCLAG00000015788) #22	C1orf100 (ENSCLAG00000007599) #24	ADSS2 (ENSCLAG00000008748) #25	CATSPERE (ENSCLAG00000009169) #26	DESI2 (ENSCLAG00000011829) #27	HNRNPU (ENSCLAG00000007100) #29	ENSCLAG00000007770 #28	EFCAB2 (ENSCLAG00000008343) #30	KIF26B (ENSCLAG00000012108) #31	SMYD3 (ENSCLAG00000010031) #32	TFB2M (ENSCLAG00000008614) #33	CNST (ENSCLAG00000008046) #34	SCCPDH (ENSCLAG00000009869) #35	ENSCLAG00000014434	AHCTF1 (ENSCLAG00000007804)	CDC42BPA (ENSCLAG00000012875)
Degu	MODERN SPECIES	58	INTS7 (ENSODEG00000013809)	LPGAT1 (ENSODEG00000013429)	ENSODEG00000014021	ENSODEG00000013939	SLC30A1 (ENSODEG00000014581)	PSEN2 (ENSODEG00000013898)	PLD5 (ENSODEG00000013817) #18	ENSODEG00000014152	ENSODEG00000014979	ENSODEG00000013620 #19	ENSODEG00000016144 #19	ENSODEG00000014847 #19	SDCCAG8 (ENSODEG00000013437) #20	ENSODEG00000013767	AKT3 (ENSODEG00000013255) #21	ZBTB18 (ENSODEG00000014080) #22	C1orf100 (ENSODEG00000012902) #24	ADSS2 (ENSODEG00000015411) #25	ENSODEG00000013295 #27	ENSODEG00000013410	ENSODEG00000013336 #28	ENSODEG00000014458 #29	ENSODEG00000014016	ENSODEG00000014131	EFCAB2 (ENSODEG00000013516) #30	KIF26B (ENSODEG00000013218) #31	SMYD3 (ENSODEG00000012912) #32	ENSODEG00000013735 #33	ENSODEG00000020123	CNST (ENSODEG00000013290) #34	SCCPDH (ENSODEG00000013300) #35