Rodentia_A	ANCESTRAL SPECIES	1	ENSGT00950000182939.a.b.b #7	ENSGT00940000156431 #8	ENSGT00940000153377.B #9	ENSGT00940000156574.C #10	ENSGT00390000009899.a.d #11	ENSGT00390000009663 #12	ENSGT00940000161379 #13	ENSGT01060000248595.b.a.b.a #14	ENSGT00390000005535 #16	ENSGT00940000170720	ENSGT00930000151035.a #17	ENSGT01030000234639.A.b.a.b.b #18	ENSGT01030000234639.A.b.a.a #19	ENSGT00940000159763 #20	ENSGT01070000254034 #21	ENSGT00940000157816 #22	ENSGT00390000009426 #23	ENSGT00940000160601 #24	ENSGT00940000158825 #25	ENSGT00940000161128 #26	ENSGT00940000157182 #27	ENSGT00390000002105 #28	ENSGT01050000244900.a.a.b #29	ENSGT00940000158565 #30	ENSGT00940000153561.b.a.a.b #32	ENSGT00940000163884 #33	ENSGT00390000000417.a.b #34	ENSGT00390000010152 #35	ENSGT01030000234639.A.b.a.b.a.a.a.b ##36	ENSGT01030000234639.A.b.a.b.a.a.a.a #36	ENSGT00940000159535 #37
Hystricomorpha	ANCESTRAL SPECIES	16	ENSGT00950000182881.a.b.a.b	ENSGT00950000182939.a.b.b #7	ENSGT00940000156431 #8	ENSGT00940000153377.B #9	ENSGT00940000156574.C #10	ENSGT00390000009899.a.d #11	ENSGT00390000009663 #12	ENSGT00940000161379 #13	ENSGT01060000248595.b.a.b.a #14	ENSGT00390000005535 #16	ENSGT00930000151035.a #17	ENSGT01030000234639.A.b.a.b.b #18	ENSGT01030000234639.A.b.a.a #19	ENSGT00940000159763 #20	ENSGT01070000254034 #21	ENSGT00940000157816 #22	ENSGT00390000009426 #23	ENSGT00940000160601 #24	ENSGT00940000158825 #25	ENSGT00940000161128 #26	ENSGT00940000157182 #27	ENSGT00390000002105 #28	ENSGT01050000244900.a.a.b #29	ENSGT00940000158565 #30	ENSGT00940000153561.b.a.a.b #32	ENSGT00940000163884 #33	ENSGT00390000000417.a.b #34	ENSGT00390000010152 #35	ENSGT01030000234639.A.b.a.b.a.a.a.b ##36	ENSGT01030000234639.A.b.a.b.a.a.a.a #36	ENSGT00940000159535 #37
Naked mole-rat female	MODERN SPECIES	14	CHKA (ENSHGLG00000014648) #7	KMT5B (ENSHGLG00000014467) #8	C11orf24 (ENSHGLG00000018642) #9	LRP5 (ENSHGLG00000012372) #10	ENSHGLG00000010435 #11	GAL (ENSHGLG00000013095) #12	TESMIN (ENSHGLG00000006844) #13	CPT1A (ENSHGLG00000009799) #14	ENSHGLG00000041256 #15	MRPL21 (ENSHGLG00000007657) #16	IGHMBP2 (ENSHGLG00000006468) #17	MRGPRD (ENSHGLG00000033970) #18	MRGPRF (ENSHGLG00000042564) #19	TPCN2 (ENSHGLG00000009786) #20	SMIM38 (ENSHGLG00000042963) #21	CCND1 (ENSHGLG00000039478) #22	ORAOV1 (ENSHGLG00000041285) #23	FGF19 (ENSHGLG00000049791) #24	FGF4 (ENSHGLG00000008219) #25	FGF3 (ENSHGLG00000006943) #26	ANO1 (ENSHGLG00000018162) #27	FADD (ENSHGLG00000038686) #28	PPFIA1 (ENSHGLG00000013241) #29	CTTN (ENSHGLG00000011727) #30	SHANK2 (ENSHGLG00000012313) #31	ENSHGLG00000046722 #32	ENSHGLG00000013700 #33	DHCR7 (ENSHGLG00000012353) #34	NADSYN1 (ENSHGLG00000010490) #35	ENSHGLG00000042806 #36	OSBPL5 (ENSHGLG00000009680) #37
Hystricomorpha_a	ANCESTRAL SPECIES	12	ENSGT00390000003049	ENSGT00950000182881.a.b.a.b	ENSGT00950000182939.a.b.b #7	ENSGT00940000156431 #8	ENSGT00940000153377.B #9	ENSGT00940000156574.C #10	ENSGT00390000009899.a.d #11	ENSGT00390000009663 #12	ENSGT00940000161379 #13	ENSGT01060000248595.b.a.b.a #14	ENSGT00390000005535 #16	ENSGT00930000151035.a #17	ENSGT01030000234639.A.b.a.b.b #18	ENSGT01030000234639.A.b.a.a #19	ENSGT00940000159763 #20	ENSGT00940000157816 #22	ENSGT00390000009426 #23	ENSGT00940000160601 #24	ENSGT00940000158825 #25	ENSGT00940000161128 #26	ENSGT00940000157182 #27	ENSGT00390000002105 #28	ENSGT01050000244900.a.a.b #29	ENSGT00940000158565 #30	ENSGT00940000153561.b.a.a.b #32	ENSGT00940000163884 #33	ENSGT00390000000417.a.b #34	ENSGT00390000010152 #35	ENSGT01030000234639.A.b.a.b.a.a.a.b ##36	ENSGT01030000234639.A.b.a.b.a.a.a.a #36	ENSGT00940000159535 #37
Hystricomorpha_b	ANCESTRAL SPECIES	10	ENSGT00390000003049	ENSGT00950000182881.a.b.a.b	ENSGT00950000182939.a.b.b #7	ENSGT00940000156431 #8	ENSGT00940000153377.B #9	ENSGT00940000156574.C #10	ENSGT00390000009899.a.d #11	ENSGT00390000009663 #12	ENSGT00940000161379 #13	ENSGT01060000248595.b.a.b.a #14	ENSGT00390000005535 #16	ENSGT00930000151035.a #17	ENSGT01030000234639.A.b.a.b.b #18	ENSGT01030000234639.A.b.a.a #19	ENSGT00940000159763 #20	ENSGT00940000157816 #22	ENSGT00390000009426 #23	ENSGT00940000160601 #24	ENSGT00940000158825 #25	ENSGT00940000161128 #26	ENSGT00940000157182 #27	ENSGT00390000002105 #28	ENSGT01050000244900.a.a.b #29	ENSGT00940000158565 #30	ENSGT00940000153561.b.a.a.b #32	ENSGT00940000163884 #33	ENSGT00390000000417.a.b #34	ENSGT00390000010152 #35	ENSGT00940000159535 #37	ENSGT00930000151070.d.a	ENSGT00390000006347.a
Long-tailed chinchilla	MODERN SPECIES	129	NDUFS8 (ENSCLAG00000017156)	TCIRG1 (ENSCLAG00000014792)	CHKA (ENSCLAG00000014223) #7	KMT5B (ENSCLAG00000016628) #8	ENSCLAG00000017122 #9	LRP5 (ENSCLAG00000016254) #10	PPP6R3 (ENSCLAG00000015508) #11	GAL (ENSCLAG00000016374) #12	TESMIN (ENSCLAG00000015628) #13	CPT1A (ENSCLAG00000016594) #14	MRPL21 (ENSCLAG00000016038) #16	IGHMBP2 (ENSCLAG00000015500) #17	MRGPRD (ENSCLAG00000016417) #18	MRGPRF (ENSCLAG00000016323) #19	TPCN2 (ENSCLAG00000016178) #20	CCND1 (ENSCLAG00000014981) #22	LTO1 (ENSCLAG00000014111) #23	FGF19 (ENSCLAG00000015041) #24	ENSCLAG00000014848 #25	FGF3 (ENSCLAG00000015995) #26	ANO1 (ENSCLAG00000015936) #27	FADD (ENSCLAG00000015722) #28	PPFIA1 (ENSCLAG00000015977) #29	CTTN (ENSCLAG00000016832) #30	SHANK2 (ENSCLAG00000017262) #32	ENSCLAG00000016369 #33	DHCR7 (ENSCLAG00000015513) #34	NADSYN1 (ENSCLAG00000016090) #35	OSBPL5 (ENSCLAG00000015702) #37	ENSCLAG00000016141	ENSCLAG00000015017 #25
Degu	MODERN SPECIES	59	ENSODEG00000017460 #8	C11orf24 (ENSODEG00000017396) #9	LRP5 (ENSODEG00000017493) #10	ENSODEG00000020451	PPP6R3 (ENSODEG00000017311) #11	GAL (ENSODEG00000017519) #12	TESMIN (ENSODEG00000017728) #13	CPT1A (ENSODEG00000017481) #14	MRPL21 (ENSODEG00000017369) #16	IGHMBP2 (ENSODEG00000017354) #17	MRGPRD (ENSODEG00000017313) #18	MRGPRF (ENSODEG00000017539) #19	ENSODEG00000017628	ENSODEG00000017365	TPCN2 (ENSODEG00000017370) #20	CCND1 (ENSODEG00000017314) #22	LTO1 (ENSODEG00000017276) #23	FGF19 (ENSODEG00000017850) #24	FGF4 (ENSODEG00000017332) #25	FGF3 (ENSODEG00000017350) #26	ENSODEG00000017320 #27	ENSODEG00000017541 #27	ENSODEG00000020446	PPFIA1 (ENSODEG00000017203) #29	CTTN (ENSODEG00000017283) #30	SHANK2 (ENSODEG00000018120) #32	ENSODEG00000017405 #33	ENSODEG00000020450	DHCR7 (ENSODEG00000017100) #34	ENSODEG00000017514 #35	OSBPL5 (ENSODEG00000017355) #37
Guinea pig	MODERN SPECIES	42	NDUFS8 (ENSCPOG00000001416)	TCIRG1 (ENSCPOG00000001417)	CHKA (ENSCPOG00000022236) #7	KMT5B (ENSCPOG00000002147) #8	ENSCPOG00000000621 #9	LRP5 (ENSCPOG00000008119) #10	PPP6R3 (ENSCPOG00000007353) #11	GAL (ENSCPOG00000004337) #12	TESMIN (ENSCPOG00000032989) #13	CPT1A (ENSCPOG00000004344) #14	MRPL21 (ENSCPOG00000038509) #16	IGHMBP2 (ENSCPOG00000007063) #17	MRGPRD (ENSCPOG00000025266) #18	MRGPRF (ENSCPOG00000033803) #19	TPCN2 (ENSCPOG00000002580) #20	CCND1 (ENSCPOG00000032886) #22	LTO1 (ENSCPOG00000031028) #23	FGF19 (ENSCPOG00000008147) #24	FGF4 (ENSCPOG00000013920) #25	FGF3 (ENSCPOG00000007355) #26	ANO1 (ENSCPOG00000011005) #27	FADD (ENSCPOG00000011290) #28	PPFIA1 (ENSCPOG00000005552) #29	CTTN (ENSCPOG00000005562) #30	SHANK2 (ENSCPOG00000009737) #32	ENSCPOG00000022995 #33	DHCR7 (ENSCPOG00000011633) #34	NADSYN1 (ENSCPOG00000015147) #35	MRGPRE (ENSCPOG00000004420) ##36	ENSCPOG00000002584 #36	OSBPL5 (ENSCPOG00000015032) #37
Sciuridae	ANCESTRAL SPECIES	22	ENSGT00950000182939.a.b.b #7	ENSGT00940000156431 #8	ENSGT00940000153377.B #9	ENSGT00940000156574.C #10	ENSGT00390000009899.a.d #11	ENSGT00390000009663 #12	ENSGT00940000161379 #13	ENSGT01060000248595.b.a.b.a #14	ENSGT00390000005535 #16	ENSGT00940000170720	ENSGT00930000151035.a #17	ENSGT01030000234639.A.b.a.b.b #18	ENSGT01030000234639.A.b.a.a #19	ENSGT00940000159763 #20	ENSGT01070000254034 #21	ENSGT00940000157816 #22	ENSGT00390000009426 #23	ENSGT00940000160601 #24	ENSGT00940000158825 #25	ENSGT00940000161128 #26	ENSGT00940000157182 #27	ENSGT00390000002105 #28	ENSGT01050000244900.a.a.b #29	ENSGT00940000158565 #30	ENSGT00940000153561.b.a.a.b #32	ENSGT00390000000417.a.b #34	ENSGT00390000010152 #35	ENSGT01030000234639.A.b.a.b.a.a.a.b ##36	ENSGT01030000234639.A.b.a.b.a.a.a.a #36	ENSGT00940000159535 #37	ENSGT00390000006347.a
Marmotini	ANCESTRAL SPECIES	6	ENSGT00950000182881.a.b.a.b	ENSGT00950000182939.a.b.b #7	ENSGT00940000156431 #8	ENSGT00940000153377.B #9	ENSGT00940000156574.C #10	ENSGT00390000009899.a.d #11	ENSGT00390000009663 #12	ENSGT00940000161379 #13	ENSGT01060000248595.b.a.b.a #14	ENSGT00390000005535 #16	ENSGT00930000151035.a #17	ENSGT01030000234639.A.b.a.b.b #18	ENSGT01030000234639.A.b.a.a #19	ENSGT00940000159763 #20	ENSGT01070000254034 #21	ENSGT00940000157816 #22	ENSGT00390000009426 #23	ENSGT00940000160601 #24	ENSGT00940000158825 #25	ENSGT00940000161128 #26	ENSGT00940000157182 #27	ENSGT00390000002105 #28	ENSGT01050000244900.a.a.b #29	ENSGT00940000158565 #30	ENSGT00940000153561.b.a.a.b #32	ENSGT00390000000417.a.b #34	ENSGT00390000010152 #35	ENSGT01030000234639.A.b.a.b.a.a.a.b ##36	ENSGT01030000234639.A.b.a.b.a.a.a.a #36	ENSGT00940000159535 #37	ENSGT00390000006347.a
Alpin marmot	DUPLICATION
Alpin marmot	MODERN SPECIES	86	NDUFS8 (ENSMMMG00000000351)	ENSMMMG00000000378	CHKA (ENSMMMG00000000678) #7	KMT5B (ENSMMMG00000000789) #8	LRP5 (ENSMMMG00000001048) #10	PPP6R3 (ENSMMMG00000001095) #11	GAL (ENSMMMG00000001246) #12	TESMIN (ENSMMMG00000001259) #13	CPT1A (ENSMMMG00000001336) #14	MRPL21 (ENSMMMG00000001368) #16	IGHMBP2 (ENSMMMG00000001381) #17	MRGPRD (ENSMMMG00000001512) #18	MRGPRF (ENSMMMG00000001519) #19	TPCN2 (ENSMMMG00000001627) #20	ENSMMMG00000003260 #22	ENSMMMG00000003262 #22	LTO1 (ENSMMMG00000003272) #23	FGF19 (ENSMMMG00000003282) #24	FGF4 (ENSMMMG00000003298) #25	FGF3 (ENSMMMG00000003325) #26	ANO1 (ENSMMMG00000003366) #27	FADD (ENSMMMG00000003409) #28	PPFIA1 (ENSMMMG00000003424) #29	CTTN (ENSMMMG00000003602) #30	SHANK2 (ENSMMMG00000003690) #32	DHCR7 (ENSMMMG00000004168) #34	NADSYN1 (ENSMMMG00000004190) #35	MRGPRG (ENSMMMG00000004231) #36	OSBPL5 (ENSMMMG00000004241) #37	CARS1 (ENSMMMG00000004312)	NAP1L4 (ENSMMMG00000004457)
Alpin marmot	MODERN SPECIES	86	ALDH3B1 (ENSMMMG00000000301)	NDUFS8 (ENSMMMG00000000351)	ENSMMMG00000000378	CHKA (ENSMMMG00000000678) #7	KMT5B (ENSMMMG00000000789) #8	LRP5 (ENSMMMG00000001048) #10	PPP6R3 (ENSMMMG00000001095) #11	GAL (ENSMMMG00000001246) #12	TESMIN (ENSMMMG00000001259) #13	CPT1A (ENSMMMG00000001336) #14	MRPL21 (ENSMMMG00000001368) #16	IGHMBP2 (ENSMMMG00000001381) #17	MRGPRD (ENSMMMG00000001512) #18	MRGPRF (ENSMMMG00000001519) #19	TPCN2 (ENSMMMG00000001627) #20	ENSMMMG00000003260 #22	ENSMMMG00000003262 #22	LTO1 (ENSMMMG00000003272) #23	FGF19 (ENSMMMG00000003282) #24	FGF4 (ENSMMMG00000003298) #25	FGF3 (ENSMMMG00000003325) #26	ANO1 (ENSMMMG00000003366) #27	FADD (ENSMMMG00000003409) #28	PPFIA1 (ENSMMMG00000003424) #29	CTTN (ENSMMMG00000003602) #30	SHANK2 (ENSMMMG00000003690) #32	DHCR7 (ENSMMMG00000004168) #34	NADSYN1 (ENSMMMG00000004190) #35	MRGPRG (ENSMMMG00000004231) #36	OSBPL5 (ENSMMMG00000004241) #37	CARS1 (ENSMMMG00000004312)
Marmotini_b	ANCESTRAL SPECIES	19	ENSGT00950000182881.a.b.a.b	ENSGT00950000182939.a.b.b #7	ENSGT00940000156431 #8	ENSGT00940000153377.B #9	ENSGT00940000156574.C #10	ENSGT00390000009899.a.d #11	ENSGT00390000009663 #12	ENSGT00940000161379 #13	ENSGT01060000248595.b.a.b.a #14	ENSGT00390000005535 #16	ENSGT00930000151035.a #17	ENSGT01030000234639.A.b.a.b.b #18	ENSGT01030000234639.A.b.a.a #19	ENSGT00940000159763 #20	ENSGT01070000254034 #21	ENSGT00940000157816 #22	ENSGT00390000009426 #23	ENSGT00940000160601 #24	ENSGT00940000158825 #25	ENSGT00940000161128 #26	ENSGT00940000157182 #27	ENSGT00390000002105 #28	ENSGT01050000244900.a.a.b #29	ENSGT00940000158565 #30	ENSGT00940000153561.b.a.a.b #32
Squirrel	MODERN SPECIES	199	NDUFS8 (ENSSTOG00000011500)	TCIRG1 (ENSSTOG00000024529)	CHKA (ENSSTOG00000011503) #7	ENSSTOG00000019647	KMT5B (ENSSTOG00000024331) #8	ENSSTOG00000012277 #9	LRP5 (ENSSTOG00000012285) #10	PPP6R3 (ENSSTOG00000005109) #11	GAL (ENSSTOG00000019759) #12	TESMIN (ENSSTOG00000012841) #13	CPT1A (ENSSTOG00000012856) #14	MRPL21 (ENSSTOG00000032759) #16	IGHMBP2 (ENSSTOG00000003792) #17	MRGPRF (ENSSTOG00000010947) #19	TPCN2 (ENSSTOG00000012097) #20	CCND1 (ENSSTOG00000000408) #22	LTO1 (ENSSTOG00000028728) #23	FGF19 (ENSSTOG00000021758) #24	ENSSTOG00000019792 #25	FGF3 (ENSSTOG00000023034) #26	ANO1 (ENSSTOG00000026271) #27	FADD (ENSSTOG00000033252) #28	PPFIA1 (ENSSTOG00000002704) #29	CTTN (ENSSTOG00000019535) #30	SHANK2 (ENSSTOG00000020969) #32
Arctic ground squirrel	MODERN SPECIES	172	NDUFS8 (ENSUPAG00010007713)	TCIRG1 (ENSUPAG00010007691)	CHKA (ENSUPAG00010007654) #7	KMT5B (ENSUPAG00010007478) #8	ENSUPAG00010007475 #9	LRP5 (ENSUPAG00010007453) #10	PPP6R3 (ENSUPAG00010007337) #11	ENSUPAG00010007325 #12	CPT1A (ENSUPAG00010007209) #14	MRPL21 (ENSUPAG00010007189) #16	IGHMBP2 (ENSUPAG00010007174) #17	MRGPRD (ENSUPAG00010007168) #18	MRGPRF (ENSUPAG00010007158) #19	TPCN2 (ENSUPAG00010007118) #20	SMIM38 (ENSUPAG00010007115) #21	CCND1 (ENSUPAG00010007111) #22	LTO1 (ENSUPAG00010007106) #23
Eurasian red squirrel	MODERN SPECIES	2	ENSSVLG00005024959	ENSSVLG00005024928 #8	ENSSVLG00005024875 #9	LRP5 (ENSSVLG00005024864) #10	ENSSVLG00005024045 #11	GAL (ENSSVLG00005023853) #12	TESMIN (ENSSVLG00005023772) #13	CPT1A (ENSSVLG00005023707) #14	MRPL21 (ENSSVLG00005023646) #16	ENSSVLG00005023637	ENSSVLG00005023620 #17	MRGPRD (ENSSVLG00005023594) #18	MRGPRF (ENSSVLG00005023569) #19	TPCN2 (ENSSVLG00005023184) #20	ENSSVLG00005023121	CCND1 (ENSSVLG00005023090) #22	LTO1 (ENSSVLG00005023000) #23	FGF19 (ENSSVLG00005022961) #24	FGF4 (ENSSVLG00005022938) #25	FGF3 (ENSSVLG00005022895) #26	ANO1 (ENSSVLG00005021586) #27	ENSSVLG00005021335 #28	ENSSVLG00005021293	PPFIA1 (ENSSVLG00005020857) #29	CTTN (ENSSVLG00005020806) #30	ENSSVLG00005020779	SHANK2 (ENSSVLG00005020334) #32	ENSSVLG00005020240 ##32	DHCR7 (ENSSVLG00005020210) #34	NADSYN1 (ENSSVLG00005020150) #35	MRGPRE (ENSSVLG00005020125) ##36