Rodentia_A	ANCESTRAL SPECIES	1	ENSGT00940000157004.a.b	ENSGT00940000154901.C.b.e	ENSGT00940000161239	ENSGT00940000164763	ENSGT00940000162436	ENSGT00940000161499	ENSGT00940000162878	ENSGT00940000154853.c #14	ENSGT00940000154853.d #15	ENSGT00940000158566 #16	ENSGT00940000157482.d #17	ENSGT00600000084617 #18	ENSGT00410000025985 #19	ENSGT00940000155031 #20	ENSGT00940000154196.a #21	ENSGT00390000014903 #22	ENSGT00390000006255.b.b #23	ENSGT00390000006979.a #24	ENSGT00940000159375 #26	ENSGT00940000161450 #25	ENSGT00940000154911 #27	ENSGT00390000013444.a.b.b	ENSGT00390000002731 #28	ENSGT00390000017869 #29	ENSGT00510000048574 #30	ENSGT00940000161844 #31	ENSGT00940000157074 #32	ENSGT00950000182985.b.b #33	ENSGT00940000160539	ENSGT00390000010740 #34	ENSGT00940000153986.b.b #35
Hystricomorpha	ANCESTRAL SPECIES	16	ENSGT00940000160266	ENSGT00940000161328	ENSGT00940000159011	ENSGT00390000016390	ENSGT00940000155211 #8	ENSGT00390000015513.a.a.a #10	ENSGT00390000015513.a.a.b #12	ENSGT00940000154853.c #14	ENSGT00940000154853.d #15	ENSGT00940000158566 #16	ENSGT00940000157482.d #17	ENSGT00600000084617 #18	ENSGT00410000025985 #19	ENSGT00940000155031 #20	ENSGT00940000154196.a #21	ENSGT00390000014903 #22	ENSGT00390000006255.b.b #23	ENSGT00390000006979.a #24	ENSGT00940000161450 #25	ENSGT00940000159375 #26	ENSGT00940000154911 #27	ENSGT00390000013444.a.b.b	ENSGT00390000002731 #28	ENSGT00390000017869 #29	ENSGT00510000048574 #30	ENSGT00940000161844 #31	ENSGT00940000157074 #32	ENSGT00950000182985.b.b #33	ENSGT00940000160539	ENSGT00390000010740 #34	ENSGT00940000153986.b.b #35
Naked mole-rat female	MODERN SPECIES	14	ENSHGLG00000044815 #7	ENSHGLG00000012042 #8	ENSHGLG00000045615 #9	FBP1 (ENSHGLG00000050880) #10	ENSHGLG00000012322 #11	ENSHGLG00000012161 #12	ENSHGLG00000014812 #13	ENSHGLG00000050757 #14	ENSHGLG00000033662 #15	ENSHGLG00000010138 #16	ENSHGLG00000037041 #17	ZFTA (ENSHGLG00000011849) #18	SPINDOC (ENSHGLG00000034024) #19	ENSHGLG00000011808 #20	RCOR2 (ENSHGLG00000014109) #21	NAA40 (ENSHGLG00000013175) #22	COX8A (ENSHGLG00000012316) #23	ENSHGLG00000011812 #24	MACROD1 (ENSHGLG00000018799) #25	FLRT1 (ENSHGLG00000045678) #26	STIP1 (ENSHGLG00000016796) #27	TRPT1 (ENSHGLG00000013748) #28	NUDT22 (ENSHGLG00000012442) #29	DNAJC4 (ENSHGLG00000010363) #30	ENSHGLG00000013921 #31	FKBP2 (ENSHGLG00000037212) #32	PPP1R14B (ENSHGLG00000041422) #33	BAD (ENSHGLG00000013154) #34	GPR137 (ENSHGLG00000010359) #35	KCNK4 (ENSHGLG00000012923) #36	ENSHGLG00000044117 #37
Hystricomorpha_a	ANCESTRAL SPECIES	12	ENSGT00940000160266	ENSGT00940000161328	ENSGT00940000159011	ENSGT00390000016390	ENSGT00940000155211 #8	ENSGT00390000015513.a.a.a #10	ENSGT00390000015513.a.a.b #12	ENSGT00940000154853.c #14	ENSGT00940000154853.d #15	ENSGT00940000158566 #16	ENSGT00940000157482.d #17	ENSGT00600000084617 #18	ENSGT00410000025985 #19	ENSGT00940000155031 #20	ENSGT00940000154196.a #21	ENSGT00390000014903 #22	ENSGT00390000006255.b.b #23	ENSGT00390000006979.a #24	ENSGT00940000159375 #26	ENSGT00940000161450 #25	ENSGT00940000154911 #27	ENSGT00390000013444.a.b.b	ENSGT00390000002731 #28	ENSGT00390000017869 #29	ENSGT00510000048574 #30	ENSGT00940000161844 #31	ENSGT00940000157074 #32	ENSGT00950000182985.b.b #33	ENSGT00940000160539	ENSGT00390000010740 #34	ENSGT00940000153986.b.b #35
Hystricomorpha_b	ANCESTRAL SPECIES	10	ENSGT00940000161328	ENSGT00940000163752	ENSGT00940000159011	ENSGT00390000016390	ENSGT00940000155211 #8	ENSGT00390000015513.a.a.a #10	ENSGT00390000015513.a.a.b #12	ENSGT00940000154853.c #14	ENSGT00940000154853.d #15	ENSGT00940000158566 #16	ENSGT00940000157482.d #17	ENSGT00600000084617 #18	ENSGT00410000025985 #19	ENSGT00940000155031 #20	ENSGT00940000154196.a #21	ENSGT00390000014903 #22	ENSGT00390000006255.b.b #23	ENSGT00390000006979.a #24	ENSGT00940000159375 #26	ENSGT00940000161450 #25	ENSGT00940000154911 #27	ENSGT00390000013444.a.b.b	ENSGT00390000002731 #28	ENSGT00390000017869 #29	ENSGT00510000048574 #30	ENSGT00940000161844 #31	ENSGT00940000157074 #32	ENSGT00950000182985.b.b #33	ENSGT00940000160539	ENSGT00390000010740 #34	ENSGT00940000153986.b.b #35
Long-tailed chinchilla	MODERN SPECIES	129	ERCC6L2 (ENSCLAG00000016395)	PTCH1 (ENSCLAG00000016919)	FANCC (ENSCLAG00000016996)	ENSCLAG00000017128 #8	ENSCLAG00000016743 #8	FBP1 (ENSCLAG00000017181) #10	FBP2 (ENSCLAG00000016623) #12	PLAAT2 (ENSCLAG00000016552) #14	PLAAT3 (ENSCLAG00000017157) #15	ATL3 (ENSCLAG00000016950) #16	ENSCLAG00000016800 #17	ZFTA (ENSCLAG00000016548) #18	SPINDOC (ENSCLAG00000016329) #19	MARK2 (ENSCLAG00000017063) #20	RCOR2 (ENSCLAG00000017016) #21	NAA40 (ENSCLAG00000016890) #22	COX8A (ENSCLAG00000017185) #23	OTUB1 (ENSCLAG00000017123) #24	FLRT1 (ENSCLAG00000016935) #26	MACROD1 (ENSCLAG00000016401) #25	STIP1 (ENSCLAG00000017164) #27	TRPT1 (ENSCLAG00000016380) #28	FERMT3 (ENSCLAG00000016183)	NUDT22 (ENSCLAG00000016346) #29	DNAJC4 (ENSCLAG00000016759) #30	VEGFB (ENSCLAG00000016750) #31	FKBP2 (ENSCLAG00000017246) #32	PPP1R14B (ENSCLAG00000016868) #33	PLCB3 (ENSCLAG00000016775)	BAD (ENSCLAG00000017103) #34	GPR137 (ENSCLAG00000016909) #35
Degu	MODERN SPECIES	225	ENSODEG00000016127	PTCH1 (ENSODEG00000016019)	ENSODEG00000015865	FANCC (ENSODEG00000016098)	ENSODEG00000015655 #8	FBP1 (ENSODEG00000015932) #10	FBP2 (ENSODEG00000016600) #12	ENSODEG00000020437	PLAAT3 (ENSODEG00000015571) #15	ATL3 (ENSODEG00000017260) #16	ENSODEG00000016120 #17	ZFTA (ENSODEG00000015496) #18	SPINDOC (ENSODEG00000015595) #19	MARK2 (ENSODEG00000017191) #20	RCOR2 (ENSODEG00000015765) #21	NAA40 (ENSODEG00000015735) #22	ENSODEG00000015780 #23	ENSODEG00000015747 #24	FLRT1 (ENSODEG00000020298) #26	MACROD1 (ENSODEG00000015291) #25	STIP1 (ENSODEG00000015289) #27	FERMT3 (ENSODEG00000015869)	TRPT1 (ENSODEG00000015724) #28	NUDT22 (ENSODEG00000015641) #29	DNAJC4 (ENSODEG00000016243) #30	VEGFB (ENSODEG00000016602) #31	FKBP2 (ENSODEG00000015505) #32	PPP1R14B (ENSODEG00000015767) #33	PLCB3 (ENSODEG00000015366)	BAD (ENSODEG00000016677) #34	GPR137 (ENSODEG00000016470) #35
Guinea pig	MODERN SPECIES	42	ENSCPOG00000005956	HSD17B3 (ENSCPOG00000000609)	ENSCPOG00000004544	PTCH1 (ENSCPOG00000002376)	FANCC (ENSCPOG00000032150)	AOPEP (ENSCPOG00000038711) #8	FBP2 (ENSCPOG00000001636) #12	PLAAT2 (ENSCPOG00000002122) #14	PLAAT3 (ENSCPOG00000034238) #15	ATL3 (ENSCPOG00000003766) #16	ENSCPOG00000004811 #17	ZFTA (ENSCPOG00000033792) #18	SPINDOC (ENSCPOG00000004724) #19	MARK2 (ENSCPOG00000004728) #20	RCOR2 (ENSCPOG00000004737) #21	NAA40 (ENSCPOG00000001891) #22	COX8A (ENSCPOG00000031964) #23	OTUB1 (ENSCPOG00000022165) #24	MACROD1 (ENSCPOG00000011720) #25	FLRT1 (ENSCPOG00000020108) #26	STIP1 (ENSCPOG00000002914) #27	FERMT3 (ENSCPOG00000002919)	TRPT1 (ENSCPOG00000002923) #28	NUDT22 (ENSCPOG00000032982) #29	DNAJC4 (ENSCPOG00000040213) #30	VEGFB (ENSCPOG00000032042) #31	FKBP2 (ENSCPOG00000002928) #32	PPP1R14B (ENSCPOG00000002930) #33	PLCB3 (ENSCPOG00000021694)	ENSCPOG00000005670	GPR137 (ENSCPOG00000015677) #35
Sciuridae	ANCESTRAL SPECIES	22						ENSGT00940000154853.c.c #14	ENSGT00940000162878	ENSGT00940000154853.c.d.b #14	ENSGT00940000154853.d #15	ENSGT00940000158566 #16	ENSGT00940000157482.d #17	ENSGT00600000084617 #18	ENSGT00410000025985 #19	ENSGT00940000155031 #20	ENSGT00940000154196.a #21	ENSGT00390000014903 #22	ENSGT00390000006255.b.b #23	ENSGT00390000006979.a #24	ENSGT00940000159375 #26	ENSGT00940000161450 #25	ENSGT00940000154911 #27	ENSGT00390000013444.a.b.b	ENSGT00390000002731 #28	ENSGT00390000017869 #29	ENSGT00510000048574 #30	ENSGT00940000161844 #31	ENSGT00940000157074 #32	ENSGT00950000182985.b.b #33	ENSGT00940000160539	ENSGT00390000010740 #34	ENSGT00940000153986.b.b #35
Marmotini	ANCESTRAL SPECIES	6	ENSGT00940000161239	ENSGT00940000164763.f	ENSGT00940000164763.e	ENSGT00940000162436	ENSGT00940000154853.c.d.b.a.a #14	ENSGT00940000162878	ENSGT00940000154853.c.c.a #14	ENSGT00940000154853.c.d.b.b #14	ENSGT00940000154853.d #15	ENSGT00940000158566 #16	ENSGT00940000157482.d #17	ENSGT00600000084617 #18	ENSGT00410000025985 #19	ENSGT00940000155031 #20	ENSGT00940000154196.a #21	ENSGT00390000014903 #22	ENSGT00390000006255.b.b #23	ENSGT00390000006979.a #24	ENSGT00940000159375 #26	ENSGT00940000161450 #25	ENSGT00940000154911 #27	ENSGT00390000013444.a.b.b	ENSGT00390000002731 #28	ENSGT00390000017869 #29	ENSGT00510000048574 #30	ENSGT00940000161844 #31	ENSGT00940000157074 #32	ENSGT00950000182985.b.b #33	ENSGT00940000160539	ENSGT00390000010740 #34	ENSGT00940000153986.b.b #35
Marmotini_b	ANCESTRAL SPECIES	19								ENSGT00940000154853.c.d.b.a.b #14	ENSGT00940000154853.d #15	ENSGT00940000158566 #16	ENSGT00940000157482.d #17	ENSGT00600000084617 #18	ENSGT00410000025985 #19	ENSGT00940000155031 #20	ENSGT00940000154196.a #21	ENSGT00390000014903 #22	ENSGT00390000006255.b.b #23	ENSGT00390000006979.a #24	ENSGT00940000159375 #26	ENSGT00940000161450 #25	ENSGT00940000154911 #27	ENSGT00390000013444.a.b.b	ENSGT00390000002731 #28	ENSGT00390000017869 #29	ENSGT00510000048574 #30	ENSGT00940000161844 #31	ENSGT00940000157074 #32	ENSGT00950000182985.b.b #33	ENSGT00940000160539	ENSGT00390000010740 #34	ENSGT00940000153986.b.b #35
Squirrel	MODERN SPECIES	199									PLAAT3 (ENSSTOG00000022553) #15	ATL3 (ENSSTOG00000000194) #16	ENSSTOG00000000199 #17	ZFTA (ENSSTOG00000027225) #18	SPINDOC (ENSSTOG00000008900) #19	MARK2 (ENSSTOG00000020436) #20	RCOR2 (ENSSTOG00000011347) #21	NAA40 (ENSSTOG00000011363) #22	COX8A (ENSSTOG00000011372) #23	OTUB1 (ENSSTOG00000026099) #24	FLRT1 (ENSSTOG00000019831) #26	MACROD1 (ENSSTOG00000034108) #25	STIP1 (ENSSTOG00000014262) #27	TRPT1 (ENSSTOG00000014285) #28	FERMT3 (ENSSTOG00000014271)	NUDT22 (ENSSTOG00000021715) #29	DNAJC4 (ENSSTOG00000026335) #30	VEGFB (ENSSTOG00000014290) #31	FKBP2 (ENSSTOG00000028785) #32	PPP1R14B (ENSSTOG00000021959) #33	PLCB3 (ENSSTOG00000008397)	BAD (ENSSTOG00000008441) #34	GPR137 (ENSSTOG00000024794) #35
Arctic ground squirrel	MODERN SPECIES	620								ENSUPAG00010010469 #14	PLAAT3 (ENSUPAG00010010461) #15	ATL3 (ENSUPAG00010008777) #16	RTN3 (ENSUPAG00010008723) #17	ZFTA (ENSUPAG00010008715) #18	SPINDOC (ENSUPAG00010008697) #19	MARK2 (ENSUPAG00010008066) #20	RCOR2 (ENSUPAG00010008026) #21	NAA40 (ENSUPAG00010008016) #22	COX8A (ENSUPAG00010008008) #23	OTUB1 (ENSUPAG00010007945) #24	FLRT1 (ENSUPAG00010007939) #26	MACROD1 (ENSUPAG00010007872) #25	STIP1 (ENSUPAG00010007782) #27	FERMT3 (ENSUPAG00010007770)	TRPT1 (ENSUPAG00010007757) #28	NUDT22 (ENSUPAG00010007753) #29	DNAJC4 (ENSUPAG00010007738) #30	VEGFB (ENSUPAG00010007726) #31	FKBP2 (ENSUPAG00010007718) #32	PPP1R14B (ENSUPAG00010007704) #33	PLCB3 (ENSUPAG00010007660)	BAD (ENSUPAG00010007644) #34	GPR137 (ENSUPAG00010007604) #35
Alpin marmot	MODERN SPECIES	3	ENSMMMG00000005768	ENSMMMG00000005778	PLAAT5 (ENSMMMG00000006630)	ENSMMMG00000006639 #14	ENSMMMG00000006645	ENSMMMG00000006652 #14	ENSMMMG00000006663	ENSMMMG00000006666 #14	ENSMMMG00000006716 #14	PLAAT3 (ENSMMMG00000006751) #15	ATL3 (ENSMMMG00000006763) #16	ENSMMMG00000006783 #17	SPINDOC (ENSMMMG00000006798) #19	MARK2 (ENSMMMG00000006813) #20	RCOR2 (ENSMMMG00000007445) #21	NAA40 (ENSMMMG00000007472) #22	COX8A (ENSMMMG00000007506) #23	OTUB1 (ENSMMMG00000007484) #24	MACROD1 (ENSMMMG00000007514) #25	FLRT1 (ENSMMMG00000007522) #26	STIP1 (ENSMMMG00000007560) #27	FERMT3 (ENSMMMG00000007580)	TRPT1 (ENSMMMG00000007609) #28	NUDT22 (ENSMMMG00000007628) #29	DNAJC4 (ENSMMMG00000007635) #30	VEGFB (ENSMMMG00000007651) #31	FKBP2 (ENSMMMG00000007672) #32	PPP1R14B (ENSMMMG00000007711) #33	PLCB3 (ENSMMMG00000007736)	BAD (ENSMMMG00000007784) #34	GPR137 (ENSMMMG00000007790) #35
Eurasian red squirrel	DUPLICATION
Eurasian red squirrel	MODERN SPECIES	2	ENSSVLG00005022993	PLAAT5 (ENSSVLG00005022788)	ENSSVLG00005022666	ENSSVLG00005022469 #14	ENSSVLG00005022391	ENSSVLG00005022359 #14	ENSSVLG00005022253	PLAAT3 (ENSSVLG00005022200) #15	ATL3 (ENSSVLG00005022126) #16	RTN3 (ENSSVLG00005021816) #17	ZFTA (ENSSVLG00005021728) #18	ENSSVLG00005021665 #19	MARK2 (ENSSVLG00005020452) #20	RCOR2 (ENSSVLG00005020151) #21	ENSSVLG00005020084	ENSSVLG00005019870 #22	COX8A (ENSSVLG00005019802) #23	OTUB1 (ENSSVLG00005019708) #24	FLRT1 (ENSSVLG00005019639) #26	MACROD1 (ENSSVLG00005019517) #25	STIP1 (ENSSVLG00005019327) #27	FERMT3 (ENSSVLG00005019185)	TRPT1 (ENSSVLG00005018880) #28	NUDT22 (ENSSVLG00005018795) #29	DNAJC4 (ENSSVLG00005018674) #30	FKBP2 (ENSSVLG00005018547) #32	PPP1R14B (ENSSVLG00005018431) #33	PLCB3 (ENSSVLG00005018092)	BAD (ENSSVLG00005018004) #34	GPR137 (ENSSVLG00005017667) #35	KCNK4 (ENSSVLG00005017540) #36
Eurasian red squirrel	MODERN SPECIES	10	ENSSVLG00005019961	ENSSVLG00005019920	ENSSVLG00005019882	ENSSVLG00005019823	ENSSVLG00005019757	ENSSVLG00005019723	ENSSVLG00005019649	ENSSVLG00005019581	ENSSVLG00005019512	ENSSVLG00005019453	ENSSVLG00005019418	ENSSVLG00005019357	ENSSVLG00005019319	ENSSVLG00005019247	ENSSVLG00005019218	ENSSVLG00005019156 #22	ENSSVLG00005019062	ENSSVLG00005018957	ENSSVLG00005018911	ENSSVLG00005018882	ENSSVLG00005018846	C3orf22 (ENSSVLG00005018804)	ENSSVLG00005018790	CHST13 (ENSSVLG00005018700)	UROC1 (ENSSVLG00005018326)	ZXDC (ENSSVLG00005018229)	CFAP100 (ENSSVLG00005018018)	KLF15 (ENSSVLG00005017974)	ALDH1L1 (ENSSVLG00005017107)	SLC41A3 (ENSSVLG00005016742)	IQSEC1 (ENSSVLG00005015858)