Rodentia_A	ANCESTRAL SPECIES	5	ENSGT00940000156699 #9	ENSGT00940000156299 #10	ENSGT00390000015332 #11	ENSGT00940000155789 #12	ENSGT01030000234598.a.b #13	ENSGT00860000135711	ENSGT00940000153421.a.b #14	ENSGT00950000183039.B.b.a #15	ENSGT00730000111202 #16	ENSGT00940000155531.b #17	ENSGT00910000147422	ENSGT00950000183039.B.a #18	ENSGT00940000156335 #19	ENSGT00390000013727.d #20	ENSGT01000000214413.b.a.a #21	ENSGT00940000156305 #22	ENSGT00390000002837 #23	ENSGT00960000190585	ENSGT00390000009980 #24	ENSGT00940000157401 #25	ENSGT00940000155931 #26	ENSGT00390000013701 #27	ENSGT00390000015010 #28	ENSGT00950000183189.a.b.a #29	ENSGT00940000154384.h.b.f #30	ENSGT00940000154384.h.a ##30	ENSGT00940000160614	ENSGT00940000156162.C.k	ENSGT00940000154552.b	ENSGT00940000156941	ENSGT00950000182899.C.a
Hystricomorpha	ANCESTRAL SPECIES	6	ENSGT01100000263484.C.b.a	ENSGT01070000253816.b	ENSGT00940000156699 #9	ENSGT00940000156299 #10	ENSGT00390000015332 #11	ENSGT00940000155789 #12	ENSGT01030000234598.a.b #13	ENSGT00940000153421.a.b #14	ENSGT00950000183039.B.b.a #15	ENSGT00730000111202 #16	ENSGT00940000155531.b #17	ENSGT00950000183039.B.a #18	ENSGT00940000156335 #19	ENSGT00390000013727.d #20	ENSGT01000000214413.b.a.a #21	ENSGT00940000156305 #22	ENSGT00390000002837 #23	ENSGT00390000009980 #24	ENSGT00940000157401 #25	ENSGT00940000155931 #26	ENSGT00390000013701 #27	ENSGT00390000015010 #28	ENSGT00950000183189.a.b.a #29	ENSGT00940000154384.h.a ##30	ENSGT00940000160614	ENSGT00940000156162.C.k	ENSGT00940000154552.a.a.a	ENSGT00940000156941	ENSGT00390000008796	ENSGT00390000016972.b.j.a.a	ENSGT00730000111263
Hystricomorpha_a	ANCESTRAL SPECIES	4	ENSGT01100000263484.C.b.a	ENSGT01070000253816.b	ENSGT00940000156699 #9	ENSGT00940000156299 #10	ENSGT00390000015332 #11	ENSGT00940000155789 #12	ENSGT01030000234598.a.b #13	ENSGT00940000153421.a.b #14	ENSGT00950000183039.B.b.a #15	ENSGT00730000111202 #16	ENSGT00940000155531.b #17	ENSGT00950000183039.B.a #18	ENSGT00940000156335 #19	ENSGT00390000013727.d #20	ENSGT01000000214413.b.a.a #21	ENSGT00940000156305 #22	ENSGT00390000002837 #23	ENSGT00390000009980 #24	ENSGT00940000157401 #25	ENSGT00940000155931 #26	ENSGT00390000013701 #27	ENSGT00390000015010 #28	ENSGT00950000183189.a.b.a #29	ENSGT00940000154384.h.b.f #30	ENSGT00940000154384.h.a ##30	ENSGT00940000160614	ENSGT00940000156162.C.k	ENSGT00940000154552.a.a.a	ENSGT00940000156941	ENSGT00390000008796	ENSGT00390000016972.b.j.a.a
Guinea pig	MODERN SPECIES	47	ENSCPOG00000024974 #7	ENSCPOG00000024155 #8	NCEH1 (ENSCPOG00000033460) #9	ECT2 (ENSCPOG00000004744) #10	SPATA16 (ENSCPOG00000006395) #11	NLGN1 (ENSCPOG00000005752) #12	NAALADL2 (ENSCPOG00000013413) #13	TBL1XR1 (ENSCPOG00000005472) #14	KCNMB2 (ENSCPOG00000013955) #15	ZMAT3 (ENSCPOG00000003865) #16	PIK3CA (ENSCPOG00000006574) #17	KCNMB3 (ENSCPOG00000025991) #18	ZNF639 (ENSCPOG00000039664) #19	MFN1 (ENSCPOG00000033188) #20	GNB4 (ENSCPOG00000034790) #21	ACTL6A (ENSCPOG00000025370) #22	ENSCPOG00000002312 #23	NDUFB5 (ENSCPOG00000036110) #24	USP13 (ENSCPOG00000002315) #25	PEX5L (ENSCPOG00000002319) #26	TTC14 (ENSCPOG00000015311) #27	CCDC39 (ENSCPOG00000015314) #28	FXR1 (ENSCPOG00000010418) #29	ENSCPOG00000021198 #30	SPTLC1 (ENSCPOG00000015106) #31	ROR2 (ENSCPOG00000021707) #32	AUH (ENSCPOG00000001066) #33	SYK (ENSCPOG00000010410) #34
Hystricomorpha_b	ANCESTRAL SPECIES	9	ENSGT01100000263484.C.b.a	ENSGT01070000253816.b	ENSGT00940000156699 #9	ENSGT00940000156299 #10	ENSGT00390000015332 #11	ENSGT00940000155789 #12	ENSGT01030000234598.a.b #13	ENSGT00940000153421.a.b #14	ENSGT00950000183039.B.b.a #15	ENSGT00730000111202 #16	ENSGT00940000155531.b #17	ENSGT00950000183039.B.a #18	ENSGT00940000156335 #19	ENSGT00390000013727.d #20	ENSGT01000000214413.b.a.a #21	ENSGT00940000156305 #22	ENSGT00390000002837 #23	ENSGT00390000009980 #24	ENSGT00940000157401 #25	ENSGT00940000155931 #26	ENSGT00390000013701 #27	ENSGT00390000015010 #28	ENSGT00950000183189.a.b.a #29	ENSGT00940000154384.h.a ##30	ENSGT00940000160614	ENSGT00940000156162.C.k	ENSGT00940000170892	ENSGT00940000156941	ENSGT00390000008796	ENSGT00390000016972.b.j.a.a	ENSGT00730000111263
Degu	DUPLICATION
Degu	MODERN SPECIES	339														MFN1 (ENSODEG00000002887) #20	GNB4 (ENSODEG00000002845) #21	ENSODEG00000002804 #22	ENSODEG00000002762 #23	NDUFB5 (ENSODEG00000002740) #24	ENSODEG00000002050	ENSODEG00000018753	USP13 (ENSODEG00000001943) #25	PEX5L (ENSODEG00000001608) #26	ENSODEG00000001450 #27	CCDC39 (ENSODEG00000001427) #28	ENSODEG00000001368	ENSODEG00000001069 #29	ENSODEG00000000914 #30
Degu	MODERN SPECIES	71	ENSODEG00000005791	ENSODEG00000005325	KBTBD8 (ENSODEG00000005749)	ENSODEG00000005664	LRIG1 (ENSODEG00000005673)	SLC25A26 (ENSODEG00000006331)	SLC41A3 (ENSODEG00000006800)	ENSODEG00000006480	ENSODEG00000005644	KLF15 (ENSODEG00000005067)	CFAP100 (ENSODEG00000006308)	ZXDC (ENSODEG00000006787)	ENSODEG00000019268	UROC1 (ENSODEG00000006472)	CHST13 (ENSODEG00000006099)	ENSODEG00000005156 #22	ENSODEG00000007573	KCNJ3 (ENSODEG00000005298)	GALNT13 (ENSODEG00000004968)	RPRM (ENSODEG00000019321)
Long-tailed chinchilla	MODERN SPECIES	127	NCEH1 (ENSCLAG00000011865) #9	ENSCLAG00000013454	ECT2 (ENSCLAG00000015030) #10	SPATA16 (ENSCLAG00000016484) #11	NLGN1 (ENSCLAG00000010604) #12	NAALADL2 (ENSCLAG00000012428) #13	ENSCLAG00000018045	TBL1XR1 (ENSCLAG00000013893) #14	KCNMB2 (ENSCLAG00000014319) #15	ZMAT3 (ENSCLAG00000013464) #16	PIK3CA (ENSCLAG00000015135) #17	KCNMB3 (ENSCLAG00000014741) #18	ZNF639 (ENSCLAG00000011168) #19	MFN1 (ENSCLAG00000015912) #20	GNB4 (ENSCLAG00000015522) #21	ACTL6A (ENSCLAG00000012251) #22	ENSCLAG00000015039 #23	ENSCLAG00000014903 #24	USP13 (ENSCLAG00000015308) #25	PEX5L (ENSCLAG00000014042) #26	TTC14 (ENSCLAG00000013302) #27	CCDC39 (ENSCLAG00000012683) #28	FXR1 (ENSCLAG00000014182) #29	DNAJC19 (ENSCLAG00000011246) ##30	SOX2 (ENSCLAG00000017978)	ATP11B (ENSCLAG00000012551)	ENSCLAG00000014207	MCCC1 (ENSCLAG00000014174)	LMLN (ENSCLAG00000011520)	ENSCLAG00000012348	IQCG (ENSCLAG00000013851)
Naked mole-rat female	MODERN SPECIES	27	ENSHGLG00000033259	TBL1XR1 (ENSHGLG00000044077) #14	ENSHGLG00000050422	ENSHGLG00000019115	ENSHGLG00000038549	ENSHGLG00000016930	KCNMB2 (ENSHGLG00000041894) #15	ENSHGLG00000011277	ZMAT3 (ENSHGLG00000011523) #16	ENSHGLG00000011894 #17	KCNMB3 (ENSHGLG00000012132) #18	ZNF639 (ENSHGLG00000050776) #19	MFN1 (ENSHGLG00000012515) #20	ENSHGLG00000044219	GNB4 (ENSHGLG00000012880) #21	ACTL6A (ENSHGLG00000013350) #22	MRPL47 (ENSHGLG00000033799) #23	NDUFB5 (ENSHGLG00000014377) #24	USP13 (ENSHGLG00000014472) #25	PEX5L (ENSHGLG00000016946) #26	ENSHGLG00000016952	TTC14 (ENSHGLG00000016959) #27	CCDC39 (ENSHGLG00000016969) #28	ENSHGLG00000039606	FXR1 (ENSHGLG00000018814) #29	ENSHGLG00000014387 ##30	ENSHGLG00000050891	ENSHGLG00000032116	SOX2 (ENSHGLG00000046210)	ATP11B (ENSHGLG00000014553)	ENSHGLG00000014589
Sciuridae	ANCESTRAL SPECIES	12	ENSGT00940000156699 #9	ENSGT00940000156299 #10	ENSGT00390000015332 #11	ENSGT00940000155789 #12	ENSGT01030000234598.a.b #13	ENSGT00860000135711	ENSGT00940000153421.a.b #14	ENSGT00950000183039.B.b.a #15	ENSGT00730000111202 #16	ENSGT00940000155531.b #17	ENSGT00910000147422	ENSGT00950000183039.B.a #18	ENSGT00940000156335 #19	ENSGT00390000013727.d #20	ENSGT01000000214413.b.a.a #21	ENSGT00940000156305 #22	ENSGT00390000002837 #23	ENSGT00960000190585	ENSGT00390000009980.k #24	ENSGT00940000157401 #25	ENSGT00940000155931 #26	ENSGT00390000013701 #27	ENSGT00390000015010 #28	ENSGT00950000183189.a.b.a #29	ENSGT00940000154384.g ##30	ENSGT00940000154384.h.b.f #30	ENSGT00940000160614	ENSGT00940000156162.C.k	ENSGT00940000154552.b	ENSGT00940000156941	ENSGT00950000182899.C.a
Eurasian red squirrel	DUPLICATION
Eurasian red squirrel	MODERN SPECIES	1	SPATA16 (ENSSVLG00005008419) #11	NLGN1 (ENSSVLG00005008366) #12	ENSSVLG00005008340	NAALADL2 (ENSSVLG00005008257) #13	TBL1XR1 (ENSSVLG00005008184) #14	ENSSVLG00005008160	KCNMB2 (ENSSVLG00005008096) #15	ENSSVLG00005008059	ZMAT3 (ENSSVLG00005008037) #16	PIK3CA (ENSSVLG00005007992) #17	KCNMB3 (ENSSVLG00005007870) #18	ENSSVLG00005007822	ENSSVLG00005007788 #19	MFN1 (ENSSVLG00005007726) #20	GNB4 (ENSSVLG00005007689) #21	ENSSVLG00005007595 #22	MRPL47 (ENSSVLG00005007505) #23	ENSSVLG00005007458 #24	USP13 (ENSSVLG00005007303) #25	ENSSVLG00005007236	PEX5L (ENSSVLG00005006552) #26	ENSSVLG00005006293	TTC14 (ENSSVLG00005006262) #27	CCDC39 (ENSSVLG00005006018) #28	ENSSVLG00005005952	FXR1 (ENSSVLG00005005627) #29	ENSSVLG00005005504 ##30	SOX2 (ENSSVLG00005005486)	ENSSVLG00005005467	ATP11B (ENSSVLG00005005419)	DCUN1D1 (ENSSVLG00005005371)
Eurasian red squirrel	MODERN SPECIES	2	ENSSVLG00005014167	ENSSVLG00005014346	ENSSVLG00005014416	ENSSVLG00005014453	ENSSVLG00005014497	ENSSVLG00005014517	ENSSVLG00005014539	ENSSVLG00005014578	ENSSVLG00005014632	ENSSVLG00005014679	ENSSVLG00005014732	ENSSVLG00005014776	ENSSVLG00005014856	OR8B8 (ENSSVLG00005014922)	ENSSVLG00005014945	ENSSVLG00005014960 #22	OR8B12 (ENSSVLG00005015073)	OR8A1 (ENSSVLG00005015091)	PANX3 (ENSSVLG00005015110)	TBRG1 (ENSSVLG00005015166)	SIAE (ENSSVLG00005015262)	SPA17 (ENSSVLG00005015480)	NRGN (ENSSVLG00005015507)	VSIG2 (ENSSVLG00005015545)	ESAM (ENSSVLG00005015674)	MSANTD2 (ENSSVLG00005015771)	ENSSVLG00005015859	ENSSVLG00005015882	ENSSVLG00005015942	ROBO4 (ENSSVLG00005016212)	HEPACAM (ENSSVLG00005016550)
Marmotini	ANCESTRAL SPECIES	59	ENSGT00940000156699 #9	ENSGT00940000156299 #10	ENSGT00390000015332 #11	ENSGT00940000155789 #12	ENSGT01030000234598.a.b #13	ENSGT00860000135711	ENSGT00940000153421.a.b #14	ENSGT00950000183039.B.b.a #15	ENSGT00730000111202 #16	ENSGT00940000155531.b #17	ENSGT00910000147422	ENSGT00950000183039.B.a #18	ENSGT00940000156335 #19	ENSGT00390000013727.d #20	ENSGT01000000214413.b.a.a #21	ENSGT00940000156305 #22	ENSGT00390000002837 #23	ENSGT00960000190585	ENSGT00390000009980.k #24	ENSGT00940000157401 #25	ENSGT00940000155931 #26	ENSGT00390000013701 #27	ENSGT00390000015010 #28	ENSGT00950000183189.a.b.a #29	ENSGT00940000154384.g ##30	ENSGT00940000154384.h.b.f #30	ENSGT00940000160614	ENSGT00940000156162.C.k	ENSGT00940000154552.b	ENSGT00940000156941	ENSGT00950000182899.C.a
Alpin marmot	MODERN SPECIES	37	SPATA16 (ENSMMMG00000004708) #11	NLGN1 (ENSMMMG00000004664) #12	ENSMMMG00000004633	ENSMMMG00000004628	NAALADL2 (ENSMMMG00000004611) #13	ENSMMMG00000004587	ENSMMMG00000004514 #14	KCNMB2 (ENSMMMG00000004486) #15	ZMAT3 (ENSMMMG00000004454) #16	PIK3CA (ENSMMMG00000004387) #17	ENSMMMG00000004373	KCNMB3 (ENSMMMG00000004362) #18	ENSMMMG00000004333 #19	MFN1 (ENSMMMG00000004267) #20	GNB4 (ENSMMMG00000004203) #21	ACTL6A (ENSMMMG00000004175) #22	MRPL47 (ENSMMMG00000004133) #23	ENSMMMG00000004120	NDUFB5 (ENSMMMG00000004098) #24	USP13 (ENSMMMG00000004025) #25	PEX5L (ENSMMMG00000003637) #26	ENSMMMG00000003599	ENSMMMG00000003524 #27	ENSMMMG00000003512 #27	CCDC39 (ENSMMMG00000003487) #28	ENSMMMG00000003471	FXR1 (ENSMMMG00000003158) #29	ENSMMMG00000003137 ##30	ENSMMMG00000003124	SOX2 (ENSMMMG00000003111)	ENSMMMG00000003075
Marmotini_b	ANCESTRAL SPECIES	149	ENSGT00940000156299.t #10	ENSGT00390000015332 #11	ENSGT00940000155789 #12	ENSGT01030000234598.a.b #13	ENSGT00860000135711	ENSGT00940000153421.a.b #14	ENSGT00950000183039.B.b.a #15	ENSGT00730000111202 #16	ENSGT00940000155531.b #17	ENSGT00910000147422	ENSGT00950000183039.B.a #18	ENSGT00940000156335 #19	ENSGT00390000013727.d #20	ENSGT01000000214413.b.a.a #21	ENSGT00390000015224.c.b.b.a.a	ENSGT00940000156305 #22	ENSGT00390000002837 #23	ENSGT00390000009980.k #24	ENSGT00940000157401 #25	ENSGT00940000155931 #26	ENSGT00390000013701 #27	ENSGT00390000015010 #28	ENSGT00950000183189.a.b.a #29	ENSGT00940000154384.g ##30	ENSGT00940000154384.h.b.f #30	ENSGT00940000160614	ENSGT00940000156162.C.k	ENSGT00940000154552.b	ENSGT00940000156941	ENSGT00950000182899.C.a	ENSGT00940000159676
Squirrel	MODERN SPECIES	166							TBL1XR1 (ENSSTOG00000014252) #14	KCNMB2 (ENSSTOG00000002726) #15	ZMAT3 (ENSSTOG00000028436) #16	PIK3CA (ENSSTOG00000012906) #17	KCNMB3 (ENSSTOG00000013715) #18	ZNF639 (ENSSTOG00000001442) #19	MFN1 (ENSSTOG00000005167) #20	GNB4 (ENSSTOG00000005210) #21	ENSSTOG00000033903	ACTL6A (ENSSTOG00000010540) #22	MRPL47 (ENSSTOG00000032487) #23	NDUFB5 (ENSSTOG00000010557) #24	USP13 (ENSSTOG00000002367) #25	PEX5L (ENSSTOG00000002383) #26	TTC14 (ENSSTOG00000003827) #27	ENSSTOG00000003847 #28	ENSSTOG00000011392	FXR1 (ENSSTOG00000010612) #29	ENSSTOG00000011508 #30	SOX2 (ENSSTOG00000011011)	ATP11B (ENSSTOG00000016462)	DCUN1D1 (ENSSTOG00000016465)	MCCC1 (ENSSTOG00000010361)	ENSSTOG00000010372	B3GNT5 (ENSSTOG00000010399)
Arctic ground squirrel	MODERN SPECIES	22	SPATA16 (ENSUPAG00010022746) #11	NLGN1 (ENSUPAG00010022744) #12	NAALADL2 (ENSUPAG00010022740) #13	ENSUPAG00010022737	TBL1XR1 (ENSUPAG00010022733) #14	KCNMB2 (ENSUPAG00010022732) #15	ZMAT3 (ENSUPAG00010022730) #16	PIK3CA (ENSUPAG00010022723) #17	ENSUPAG00010022722	KCNMB3 (ENSUPAG00010022719) #18	ENSUPAG00010022718	ZNF639 (ENSUPAG00010022715) #19	MFN1 (ENSUPAG00010022711) #20	GNB4 (ENSUPAG00010022702) #21	ENSUPAG00010022699	ACTL6A (ENSUPAG00010022696) #22	MRPL47 (ENSUPAG00010022693) #23	NDUFB5 (ENSUPAG00010022690) #24	USP13 (ENSUPAG00010022684) #25	PEX5L (ENSUPAG00010022611) #26	TTC14 (ENSUPAG00010022594) #27	CCDC39 (ENSUPAG00010022590) #28	ENSUPAG00010022589	FXR1 (ENSUPAG00010022534) #29	ENSUPAG00010022530 ##30	ATP11B (ENSUPAG00010022507)	DCUN1D1 (ENSUPAG00010022504)	MCCC1 (ENSUPAG00010022499)	ENSUPAG00010022496	ENSUPAG00010022491	ENSUPAG00010022487