Rodentia_A	ANCESTRAL SPECIES		ENSGT00940000161899	ENSGT00940000154209.a.b	ENSGT00940000156661	ENSGT00950000183122.A	ENSGT00390000000747	ENSGT01100000263502.A.a.b	ENSGT00950000182994.A.n.b	ENSGT00940000160037	ENSGT00510000047676	ENSGT00940000161852	ENSGT00390000008164.d	ENSGT00950000183059.b.a.b #16	ENSGT00940000155103.a.b #19	ENSGT00730000111198 #20	ENSGT00940000157060.t #21	ENSGT00940000155092.b #22	ENSGT00390000017364 #23	ENSGT00390000015553.a.a.b #24	ENSGT00940000162691	ENSGT00730000111005 #25	ENSGT00910000147125	ENSGT00390000016158 #26	ENSGT00940000156546 #27	ENSGT00940000160590 #28	ENSGT00940000156992 #29	ENSGT00940000156766 #30	ENSGT00950000183142.a.b.a.b #31	ENSGT00940000171704	ENSGT00390000005861 #32	ENSGT00390000004799 #33	ENSGT00940000163104 #34
Hystricomorpha	ANCESTRAL SPECIES	49	ENSGT00940000156376	ENSGT00940000162504	ENSGT00390000017528 #8	ENSGT01030000234620.a.b.b.b #9	ENSGT00530000064210 #10	ENSGT00390000011724 #11	ENSGT00950000182836.b.a.b #12	ENSGT00940000156989 #13	ENSGT00960000186787	ENSGT00940000156484.b #14	ENSGT00940000157923 #15	ENSGT00950000183059.b.a.b #16	ENSGT00940000155103.a.b #19	ENSGT00730000111198 #20	ENSGT00940000157060.t #21	ENSGT00940000155092.b #22	ENSGT00390000017364 #23	ENSGT00390000015553.a.a.b #24	ENSGT00940000162691	ENSGT00730000111005 #25	ENSGT00390000016158 #26	ENSGT00940000156546 #27	ENSGT00940000160590 #28	ENSGT00940000156992 #29	ENSGT00940000156766 #30	ENSGT00950000183142.a.b.a.b #31	ENSGT00390000005861 #32	ENSGT00390000004799 #33	ENSGT00940000163104 #34	ENSGT00390000018900 #35	ENSGT01030000234517.H.b #36
Hystricomorpha_a	ANCESTRAL SPECIES	13	ENSGT00940000162770	ENSGT00940000156376	ENSGT00940000162504	ENSGT00390000017528 #8	ENSGT01030000234620.a.b.b.b #9	ENSGT00530000064210 #10	ENSGT00390000011724 #11	ENSGT00950000182836.b.a.b #12	ENSGT00940000156989 #13	ENSGT00940000156484.b #14	ENSGT00940000157923 #15	ENSGT00950000183059.b.a.b #16	ENSGT00940000155103.a.b #19	ENSGT00730000111198 #20	ENSGT00940000157060.t #21	ENSGT00940000155092.b #22	ENSGT00390000017364 #23	ENSGT00390000015553.a.a.b #24	ENSGT00940000162691	ENSGT00730000111005 #25	ENSGT00390000016158 #26	ENSGT00940000156546 #27	ENSGT00940000160590 #28	ENSGT00940000156992 #29	ENSGT00940000156766 #30	ENSGT00950000183142.a.b.a.b #31	ENSGT00390000005861 #32	ENSGT00390000004799 #33	ENSGT00940000163104 #34	ENSGT00390000018900 #35	ENSGT01030000234517.H.b #36
Guinea pig	MODERN SPECIES	13	ENSCPOG00000033847 #7	PACC1 (ENSCPOG00000009329) #8	PPP2R5A (ENSCPOG00000040049) #9	DTL (ENSCPOG00000014965) #10	INTS7 (ENSCPOG00000014960) #11	LPGAT1 (ENSCPOG00000011269) #12	NEK2 (ENSCPOG00000011264) #13	SLC30A1 (ENSCPOG00000013692) #14	PSEN2 (ENSCPOG00000001827) #15	PLD5 (ENSCPOG00000033411) #16	ENSCPOG00000002221 #17	ENSCPOG00000002683 #18	ENSCPOG00000034860 #19	SDCCAG8 (ENSCPOG00000015503) #20	AKT3 (ENSCPOG00000015504) #21	ZBTB18 (ENSCPOG00000035384) #22	C1orf100 (ENSCPOG00000002339) #23	ADSS2 (ENSCPOG00000002342) #24	DESI2 (ENSCPOG00000002091) #25	COX20 (ENSCPOG00000032295) #26	HNRNPU (ENSCPOG00000011887) #27	EFCAB2 (ENSCPOG00000024335) #28	KIF26B (ENSCPOG00000001048) #29	SMYD3 (ENSCPOG00000002655) #30	ENSCPOG00000013225 #31	CNST (ENSCPOG00000012012) #32	SCCPDH (ENSCPOG00000029999) #33	ENSCPOG00000036159 #34	AHCTF1 (ENSCPOG00000009216) #35	CDC42BPA (ENSCPOG00000011457) #36	COQ8A (ENSCPOG00000011445) #37
Hystricomorpha_b	ANCESTRAL SPECIES	4	ENSGT00940000156376	ENSGT00940000162504	ENSGT00390000017528 #8	ENSGT01030000234620.a.b.b.b #9	ENSGT00530000064210 #10	ENSGT00390000011724 #11	ENSGT00950000182836.b.a.b #12	ENSGT00940000156989 #13	ENSGT00940000156484.b #14	ENSGT00940000157923 #15	ENSGT00950000183059.b.a.b #16	ENSGT00660000097201 #17	ENSGT00940000155103.a.b #19	ENSGT00730000111198 #20	ENSGT00940000157060.t #21	ENSGT00940000155092.b #22	ENSGT00390000017364 #23	ENSGT00390000015553.a.a.b #24	ENSGT00940000162691	ENSGT00730000111005 #25	ENSGT00390000016158 #26	ENSGT00940000156546 #27	ENSGT00940000160590 #28	ENSGT00940000156992 #29	ENSGT00940000156766 #30	ENSGT00950000183142.a.b.a.b #31	ENSGT00390000005861 #32	ENSGT00390000004799 #33	ENSGT00940000163104 #34	ENSGT00390000018900 #35	ENSGT01030000234517.H.b #36
Long-tailed chinchilla	MODERN SPECIES	113	ATF3 (ENSCLAG00000013767)	ENSCLAG00000007912 #7	PACC1 (ENSCLAG00000009570) #8	PPP2R5A (ENSCLAG00000012816) #9	DTL (ENSCLAG00000014236) #10	INTS7 (ENSCLAG00000011748) #11	LPGAT1 (ENSCLAG00000011509) #12	NEK2 (ENSCLAG00000010880) #13	SLC30A1 (ENSCLAG00000009695) #14	PSEN2 (ENSCLAG00000013788) #15	PLD5 (ENSCLAG00000014400) #16	ENSCLAG00000010377	CEP170 (ENSCLAG00000015564) #19	SDCCAG8 (ENSCLAG00000011676) #20	ENSCLAG00000009649 #21	ZBTB18 (ENSCLAG00000015788) #22	C1orf100 (ENSCLAG00000007599) #23	ADSS2 (ENSCLAG00000008748) #24	CATSPERE (ENSCLAG00000009169)	DESI2 (ENSCLAG00000011829) #25	HNRNPU (ENSCLAG00000007100) #27	ENSCLAG00000007770 #26	EFCAB2 (ENSCLAG00000008343) #28	KIF26B (ENSCLAG00000012108) #29	SMYD3 (ENSCLAG00000010031) #30	TFB2M (ENSCLAG00000008614) #31	CNST (ENSCLAG00000008046) #32	SCCPDH (ENSCLAG00000009869) #33	ENSCLAG00000014434 #34	AHCTF1 (ENSCLAG00000007804) #35	CDC42BPA (ENSCLAG00000012875) #36
Degu	MODERN SPECIES	58	INTS7 (ENSODEG00000013809) #11	LPGAT1 (ENSODEG00000013429) #12	ENSODEG00000014021 #13	ENSODEG00000013939	SLC30A1 (ENSODEG00000014581) #14	PSEN2 (ENSODEG00000013898) #15	PLD5 (ENSODEG00000013817) #16	ENSODEG00000014152 #17	ENSODEG00000014979	ENSODEG00000013620 #19	ENSODEG00000016144 #19	ENSODEG00000014847 #19	SDCCAG8 (ENSODEG00000013437) #20	ENSODEG00000013767	AKT3 (ENSODEG00000013255) #21	ZBTB18 (ENSODEG00000014080) #22	C1orf100 (ENSODEG00000012902) #23	ADSS2 (ENSODEG00000015411) #24	ENSODEG00000013295 #25	ENSODEG00000013410	ENSODEG00000013336 #26	ENSODEG00000014458 #27	ENSODEG00000014016	ENSODEG00000014131	EFCAB2 (ENSODEG00000013516) #28	KIF26B (ENSODEG00000013218) #29	SMYD3 (ENSODEG00000012912) #30	ENSODEG00000013735 #31	ENSODEG00000020123	CNST (ENSODEG00000013290) #32	SCCPDH (ENSODEG00000013300) #33
Naked mole-rat female	MODERN SPECIES	16	ENSHGLG00000028910	ENSHGLG00000037874 #14	ENSHGLG00000005464 #15	ENSHGLG00000032112	MAP1LC3C (ENSHGLG00000037027)	ENSHGLG00000004656 #16	ENSHGLG00000040176	ENSHGLG00000006833	ENSHGLG00000043505	ENSHGLG00000011191	ENSHGLG00000006465 #19	ENSHGLG00000038674 #19	ENSHGLG00000004271 #20	AKT3 (ENSHGLG00000006424) #21	ENSHGLG00000043051	ZBTB18 (ENSHGLG00000003880) #22	ADSS (ENSHGLG00000007672) #24	ENSHGLG00000009917 #23	ENSHGLG00000041745	ENSHGLG00000035202 #25	ENSHGLG00000015935	ENSHGLG00000043796	COX20 (ENSHGLG00000015836) #26	ENSHGLG00000010594 #27	ENSHGLG00000042794	ENSHGLG00000034325 #28	ENSHGLG00000015928 #29	ENSHGLG00000044814	ENSHGLG00000020542	ENSHGLG00000040776	ENSHGLG00000015190 #30
Sciuridae	ANCESTRAL SPECIES		ENSGT00530000063808.b	ENSGT00940000161899	ENSGT00940000154209.a.b	ENSGT00940000156661	ENSGT00950000183122.A	ENSGT00390000000747.h	ENSGT01100000263502.A.a.b	ENSGT00940000160037	ENSGT00510000047676	ENSGT00390000008164.d	ENSGT00940000161852	ENSGT00950000183059.b.a.b #16	ENSGT00940000155103.a.b #19	ENSGT00730000111198 #20	ENSGT00940000157060.t #21	ENSGT00940000155092.b #22	ENSGT00390000017364 #23	ENSGT00390000015553.a.a.b #24	ENSGT00940000162691	ENSGT00730000111005 #25	ENSGT00910000147125	ENSGT00390000016158.i #26	ENSGT00940000156546 #27	ENSGT00940000160590.l #28	ENSGT00940000160590.k #28	ENSGT00940000156992 #29	ENSGT00940000156766 #30	ENSGT00950000183142.a.b.a.b #31	ENSGT00940000171704	ENSGT00390000005861 #32	ENSGT00390000004799 #33
Marmotini	ANCESTRAL SPECIES	21	ENSGT00530000063808.b	ENSGT00940000161899	ENSGT00940000154209.a.b	ENSGT00940000156661	ENSGT00950000183122.A	ENSGT00390000000747.h	ENSGT01100000263502.A.a.b	ENSGT00940000160037	ENSGT00510000047676	ENSGT00390000008164.d	ENSGT00940000161852	ENSGT00950000183059.b.a.b #16	ENSGT00940000155103.a.b #19	ENSGT00730000111198 #20	ENSGT00940000157060.t #21	ENSGT00940000155092.b #22	ENSGT01030000235784	ENSGT00390000017364 #23	ENSGT00390000015553.a.a.b #24	ENSGT00940000162691	ENSGT00730000111005 #25	ENSGT00390000016158.i #26	ENSGT00940000156546 #27	ENSGT00940000160590.k #28	ENSGT00940000156992 #29	ENSGT00940000156766 #30	ENSGT00950000183142.a.b.a.b #31	ENSGT00390000005861 #32	ENSGT00390000004799 #33	ENSGT00940000163104 #34	ENSGT00390000018900 #35
Alpin marmot	MODERN SPECIES	12	FMN2 (ENSMMMG00000023630)	GREM2 (ENSMMMG00000023631)	RGS7 (ENSMMMG00000023632)	FH (ENSMMMG00000023640)	KMO (ENSMMMG00000023641)	OPN3 (ENSMMMG00000023648)	WDR64 (ENSMMMG00000023654)	EXO1 (ENSMMMG00000023668)	ENSMMMG00000023670	BECN2 (ENSMMMG00000023671)	MAP1LC3C (ENSMMMG00000023673)	PLD5 (ENSMMMG00000023675) #16	CEP170 (ENSMMMG00000023685) #19	SDCCAG8 (ENSMMMG00000023689) #20	AKT3 (ENSMMMG00000023693) #21	ENSMMMG00000023698 #22	ENSMMMG00000023703	C1orf100 (ENSMMMG00000023704) #23	ADSS2 (ENSMMMG00000023707) #24	ENSMMMG00000023709	DESI2 (ENSMMMG00000023711) #25	COX20 (ENSMMMG00000023713) #26	HNRNPU (ENSMMMG00000023721) #27	EFCAB2 (ENSMMMG00000024005) #28	KIF26B (ENSMMMG00000024009) #29	SMYD3 (ENSMMMG00000024012) #30	TFB2M (ENSMMMG00000024017) #31	CNST (ENSMMMG00000024021) #32	SCCPDH (ENSMMMG00000024025) #33	ENSMMMG00000024026	ENSMMMG00000024027
Marmotini_b	ANCESTRAL SPECIES	84		ENSGT00940000161899	ENSGT00940000154209.a.b	ENSGT00940000156661	ENSGT00950000183122.A	ENSGT00390000000747.h	ENSGT01100000263502.A.a.b	ENSGT00940000160037	ENSGT00510000047676	ENSGT00390000008164.d	ENSGT00940000161852	ENSGT00950000183059.b.a.b #16	ENSGT00940000155103.a.b #19	ENSGT00730000111198 #20	ENSGT00940000157060.t #21	ENSGT00940000155092.b #22	ENSGT01030000235784	ENSGT00390000017364 #23	ENSGT00390000015553.a.a.b #24	ENSGT00940000162691	ENSGT00730000111005 #25	ENSGT00390000016158.i #26	ENSGT00940000156546 #27	ENSGT00940000160590.k #28	ENSGT00940000156992 #29	ENSGT00940000156766 #30	ENSGT00950000183142.a.b.a.b #31	ENSGT00390000005861 #32	ENSGT00390000004799 #33	ENSGT00940000163104 #34	ENSGT00390000018900 #35
Arctic ground squirrel	MODERN SPECIES	79	GREM2 (ENSUPAG00010018995)	RGS7 (ENSUPAG00010018948)	FH (ENSUPAG00010018928)	KMO (ENSUPAG00010018908)	OPN3 (ENSUPAG00010018902)	WDR64 (ENSUPAG00010018776)	ENSUPAG00010018764	EXO1 (ENSUPAG00010018752)	ENSUPAG00010018744	BECN2 (ENSUPAG00010018741)	MAP1LC3C (ENSUPAG00010018734)	PLD5 (ENSUPAG00010018694) #16	CEP170 (ENSUPAG00010018567) #19	SDCCAG8 (ENSUPAG00010018478) #20	AKT3 (ENSUPAG00010018428) #21	ZBTB18 (ENSUPAG00010018400) #22	ENSUPAG00010018394	C1orf100 (ENSUPAG00010018380) #23	ADSS2 (ENSUPAG00010018358) #24	ENSUPAG00010018323	DESI2 (ENSUPAG00010018313) #25	ENSUPAG00010018307 #26	HNRNPU (ENSUPAG00010018254) #27	EFCAB2 (ENSUPAG00010018238) #28	KIF26B (ENSUPAG00010018207) #29	SMYD3 (ENSUPAG00010018170) #30	ENSUPAG00010018160 #31	CNST (ENSUPAG00010018148) #32	SCCPDH (ENSUPAG00010018131) #33
Squirrel	MODERN SPECIES	126		FMN2 (ENSSTOG00000025339)	GREM2 (ENSSTOG00000007628)	RGS7 (ENSSTOG00000006862)	FH (ENSSTOG00000012681)	KMO (ENSSTOG00000012690)	OPN3 (ENSSTOG00000012707)	ENSSTOG00000012715	BECN2 (ENSSTOG00000027748)	MAP1LC3C (ENSSTOG00000010423)	PLD5 (ENSSTOG00000031877) #16	CEP170 (ENSSTOG00000008203) #19	SDCCAG8 (ENSSTOG00000010585) #20	ENSSTOG00000030430	AKT3 (ENSSTOG00000010595) #21	ZBTB18 (ENSSTOG00000004290) #22	C1orf100 (ENSSTOG00000022394) #23	ADSS2 (ENSSTOG00000004376) #24	DESI2 (ENSSTOG00000004752) #25	COX20 (ENSSTOG00000000151) #26	ENSSTOG00000000153 #27	ENSSTOG00000031476 #28	KIF26B (ENSSTOG00000028101) #29	SMYD3 (ENSSTOG00000028065) #30	TFB2M (ENSSTOG00000034162) #31	CNST (ENSSTOG00000000432) #32	ENSSTOG00000025585	SCCPDH (ENSSTOG00000007502) #33	ENSSTOG00000021998 #34	AHCTF1 (ENSSTOG00000010795) #35	CDC42BPA (ENSSTOG00000015415) #36
Eurasian red squirrel	DUPLICATION
Eurasian red squirrel	MODERN SPECIES	3	ENSSVLG00005020174	RGS7 (ENSSVLG00005020300)	FH (ENSSVLG00005020886)	KMO (ENSSVLG00005021004)	OPN3 (ENSSVLG00005021384)	WDR64 (ENSSVLG00005021468)	EXO1 (ENSSVLG00005021837)	ENSSVLG00005022002	BECN2 (ENSSVLG00005022043)	MAP1LC3C (ENSSVLG00005022067)	PLD5 (ENSSVLG00005022151) #16	ENSSVLG00005022301	CEP170 (ENSSVLG00005022337) #19	SDCCAG8 (ENSSVLG00005022441) #20	AKT3 (ENSSVLG00005022494) #21	ZBTB18 (ENSSVLG00005022559) #22	C1orf100 (ENSSVLG00005022598) #23	ENSSVLG00005022682 #24	CATSPERE (ENSSVLG00005022809)	DESI2 (ENSSVLG00005023102) #25	ENSSVLG00005023149	ENSSVLG00005023185 #26	HNRNPU (ENSSVLG00005023262) #27	ENSSVLG00005023557 #28	KIF26B (ENSSVLG00005023636) #29	ENSSVLG00005023779	ENSSVLG00005023802	SMYD3 (ENSSVLG00005023822) #30	TFB2M (ENSSVLG00005023868) #31	ENSSVLG00005023906	ENSSVLG00005009011 #32
Eurasian red squirrel	MODERN SPECIES	113															ENSSVLG00005016262	ENSSVLG00005016172 #22