Rodentia_A	ANCESTRAL SPECIES	4	ENSGT00940000154457.a.b	ENSGT00950000182825.A.a.b.a.b.a.b.a.b	ENSGT00950000182825.A.a.b.a.b.a.a.a.a.b	ENSGT00950000182825.A.a.b.a.b.a.b.b.b	ENSGT00390000007809.a #10	ENSGT00940000161132 #11	ENSGT00940000161665 #12	ENSGT00940000156707 #13	ENSGT00950000183019.f.b.a #15	ENSGT00390000016495 #16	ENSGT00940000160329 #17	ENSGT00940000160653 #18	ENSGT00950000183080.a.a #19	ENSGT00940000159521 #20	ENSGT00940000153804.B #21	ENSGT00940000158666 #22	ENSGT00940000155606.b #23	ENSGT00950000182837.b.a #24	ENSGT00940000155687 #25	ENSGT00390000010327 #27	ENSGT00940000159544 #28	ENSGT00940000155808 #29	ENSGT00940000165147	ENSGT00940000161726 #30	ENSGT00940000163803	ENSGT00940000162388.B	ENSGT00940000159881.a.a.b	ENSGT00390000014843	ENSGT00940000162202.A #32	ENSGT00940000162202.B ##32	ENSGT00940000162202.C ##32
Hystricomorpha	ANCESTRAL SPECIES	9	ENSGT00940000160203 #8	ENSGT00940000154457.a.b	ENSGT00950000182825.A.a.b.a.b.a.b.a.b	ENSGT00950000182825.A.a.b.a.b.a.a.a.a.b	ENSGT00390000007809.a #10	ENSGT00940000161132 #11	ENSGT00940000161665 #12	ENSGT00940000156707 #13	ENSGT00950000183019.f.b.a #15	ENSGT00390000016495 #16	ENSGT00940000160329 #17	ENSGT00940000160653 #18	ENSGT00950000183080.a.a #19	ENSGT00940000159521 #20	ENSGT00940000153804.B #21	ENSGT00940000158666 #22	ENSGT00940000155606.b #23	ENSGT00950000182837.b.a #24	ENSGT00940000155687 #25	ENSGT00390000010327 #27	ENSGT00940000159544 #28	ENSGT00940000155808 #29	ENSGT00940000165147	ENSGT00940000161726 #30	ENSGT00940000163803	ENSGT00940000162388.B	ENSGT00940000159881.a.a.b	ENSGT00390000014843	ENSGT00940000162202.A #32	ENSGT00940000162202.B ##32	ENSGT00940000162121 #33
Hystricomorpha_a	ANCESTRAL SPECIES	7	ENSGT00390000012132 #7	ENSGT00940000160203 #8	ENSGT00940000154457.a.b	ENSGT00950000182825.A.a.b.a.b.a.a.a.a.b	ENSGT00390000007809.a #10	ENSGT00940000161132 #11	ENSGT00940000161665 #12	ENSGT00940000156707 #13	ENSGT00950000183019.f.b.a #15	ENSGT00390000016495 #16	ENSGT00940000160329 #17	ENSGT00940000160653 #18	ENSGT00950000183080.a.a #19	ENSGT00940000159521 #20	ENSGT00940000153804.B #21	ENSGT00940000158666 #22	ENSGT00940000155606.b #23	ENSGT00950000182837.b.a #24	ENSGT00940000155687 #25	ENSGT00390000010327 #27	ENSGT00940000159544 #28	ENSGT00940000155808 #29	ENSGT00940000165147	ENSGT00940000161726 #30	ENSGT00940000163803	ENSGT00940000162388.B	ENSGT00940000159881.a.a.b	ENSGT00940000164920 #31	ENSGT00390000014843	ENSGT00940000162202.A #32	ENSGT00940000162202.B ##32
Hystricomorpha_b	ANCESTRAL SPECIES	78	ENSGT00940000155969	ENSGT00390000012132 #7	ENSGT00940000160203 #8	ENSGT00950000182825.A.a.b.a.b.a.b.b.a	ENSGT00390000007809.a #10	ENSGT00940000161132 #11	ENSGT00940000161665 #12	ENSGT00940000156707 #13	ENSGT00950000183019.f.b.a #15	ENSGT00390000016495 #16	ENSGT00940000160329 #17	ENSGT00940000160653 #18	ENSGT00950000183080.a.a #19	ENSGT00940000159521 #20	ENSGT00940000153804.B #21	ENSGT00940000158666 #22	ENSGT00940000155606.b #23	ENSGT00950000182837.b.a #24	ENSGT00940000155687 #25	ENSGT00390000010327 #27	ENSGT00940000159544 #28	ENSGT00940000155808.c #29	ENSGT00940000161726 #30	ENSGT00940000164920 #31	ENSGT00390000014843	ENSGT00940000162202.A #32	ENSGT00940000162202.B ##32	ENSGT00940000162121 #33	ENSGT01100000263574.a	ENSGT00390000002978 #36	ENSGT00940000159366 #37
Degu	MODERN SPECIES	141	ENSODEG00000004276 #7	PRPH (ENSODEG00000004229) #8	ENSODEG00000004198 #9	LMBR1L (ENSODEG00000004152) #10	DHH (ENSODEG00000004129) #11	RHEBL1 (ENSODEG00000004107) #12	ENSODEG00000004083 #13	ENSODEG00000004064 #14	ENSODEG00000004046 #15	DDN (ENSODEG00000004034) #16	WNT1 (ENSODEG00000004027) #17	WNT10B (ENSODEG00000004020) #18	ARF3 (ENSODEG00000004009) #19	FKBP11 (ENSODEG00000003672) #20	CCDC65 (ENSODEG00000003640) #21	RND1 (ENSODEG00000003618) #22	DDX23 (ENSODEG00000003592) #23	CACNB3 (ENSODEG00000003562) #24	ADCY6 (ENSODEG00000003474) #25	ENSODEG00000003445 #26	TEX49 (ENSODEG00000003431) #27	ENSODEG00000003425 #28	ENSODEG00000003381 #29	LALBA (ENSODEG00000003342) #30	ENSODEG00000003309 #31	ENSODEG00000003293 #32	ZNF641 (ENSODEG00000003266) #33	ENSODEG00000003244 #34	ENSODEG00000003231 #35	CCDC184 (ENSODEG00000019270) #36	ASB8 (ENSODEG00000004323) #37
Long-tailed chinchilla	MODERN SPECIES	207	ENSCLAG00000004426	TROAP (ENSCLAG00000003387) #7	PRPH (ENSCLAG00000003332) #8	ENSCLAG00000004794	LMBR1L (ENSCLAG00000004048) #10	DHH (ENSCLAG00000003629) #11	RHEBL1 (ENSCLAG00000002358) #12	KMT2D (ENSCLAG00000003665) #13	PRKAG1 (ENSCLAG00000003459) #15	DDN (ENSCLAG00000003076) #16	WNT1 (ENSCLAG00000002943) #17	WNT10B (ENSCLAG00000002817) #18	ARF3 (ENSCLAG00000003101) #19	ENSCLAG00000003008 #20	CCDC65 (ENSCLAG00000002533) #21	RND1 (ENSCLAG00000003094) #22	DDX23 (ENSCLAG00000002986) #23	CACNB3 (ENSCLAG00000002138) #24	ADCY6 (ENSCLAG00000003898) #25	TEX49 (ENSCLAG00000003509) #27	CCNT1 (ENSCLAG00000003430) #28	ENSCLAG00000003022 #29	LALBA (ENSCLAG00000002878) #30	ENSCLAG00000017542	C12orf54 (ENSCLAG00000002462)	ENSCLAG00000017498 #32	ENSCLAG00000002661 ##32	ZNF641 (ENSCLAG00000002291) #33	OR10AD1 (ENSCLAG00000002006)	CCDC184 (ENSCLAG00000017612) #36	ASB8 (ENSCLAG00000003759) #37
Guinea pig	MODERN SPECIES	9	TROAP (ENSCPOG00000014679) #7	PRPH (ENSCPOG00000014881) #8	ENSCPOG00000031519	TUBA1B (ENSCPOG00000039484)	LMBR1L (ENSCPOG00000002999) #10	DHH (ENSCPOG00000002257) #11	RHEBL1 (ENSCPOG00000002998) #12	KMT2D (ENSCPOG00000002973) #13	PRKAG1 (ENSCPOG00000002966) #15	DDN (ENSCPOG00000002960) #16	WNT1 (ENSCPOG00000024490) #17	WNT10B (ENSCPOG00000035034) #18	ARF3 (ENSCPOG00000040787) #19	FKBP11 (ENSCPOG00000031801) #20	CCDC65 (ENSCPOG00000003221) #21	RND1 (ENSCPOG00000003220) #22	DDX23 (ENSCPOG00000003278) #23	CACNB3 (ENSCPOG00000003277) #24	ADCY6 (ENSCPOG00000030377) #25	TEX49 (ENSCPOG00000030293) #27	CCNT1 (ENSCPOG00000038705) #28	KANSL2 (ENSCPOG00000005760) #29	ENSCPOG00000024843	Lalba (ENSCPOG00000027342) #30	ENSCPOG00000033889	ENSCPOG00000000012	ENSCPOG00000013910	ENSCPOG00000039913	ENSCPOG00000040584 #31	ENSCPOG00000012475 #32	ENSCPOG00000036505 ##32
Naked mole-rat female	MODERN SPECIES	8	ENSHGLG00000007474	TUBA1B (ENSHGLG00000036029)	ENSHGLG00000046022	LMBR1L (ENSHGLG00000014791) #10	DHH (ENSHGLG00000034254) #11	RHEBL1 (ENSHGLG00000013261) #12	ENSHGLG00000050567 #13	PRKAG1 (ENSHGLG00000003937) #15	DDN (ENSHGLG00000004151) #16	WNT1 (ENSHGLG00000004305) #17	WNT10B (ENSHGLG00000005760) #18	ARF3 (ENSHGLG00000050677) #19	FKBP11 (ENSHGLG00000008146) #20	CCDC65 (ENSHGLG00000003786) #21	ENSHGLG00000048199	RND1 (ENSHGLG00000004112) #22	DDX23 (ENSHGLG00000004292) #23	CACNB3 (ENSHGLG00000007792) #24	ADCY6 (ENSHGLG00000004662) #25	TEX49 (ENSHGLG00000007195) #27	ENSHGLG00000003361 #28	ENSHGLG00000003714 #29	ENSHGLG00000033115	ENSHGLG00000050339	ENSHGLG00000004311 #30	OR5BS1P (ENSHGLG00000042484)	ENSHGLG00000020586	ENSHGLG00000020517	ENSHGLG00000047106	ENSHGLG00000036300 #32	ENSHGLG00000034108 ##32
Sciuridae	ANCESTRAL SPECIES	15	ENSGT00940000154457.a.b	ENSGT00950000182825.A.a.b.a.b.a.b.a.b	ENSGT00950000182825.A.a.b.a.b.a.a.a.a.b	ENSGT00950000182825.A.a.b.a.b.a.b.b.b	ENSGT00390000007809.a #10	ENSGT00940000161132 #11	ENSGT00940000161665 #12	ENSGT00940000156707 #13	ENSGT00950000183019.f.b.a #15	ENSGT00390000016495 #16	ENSGT00940000160329 #17	ENSGT00940000160653 #18	ENSGT00950000183080.a.a #19	ENSGT00940000159521 #20	ENSGT00940000153804.B #21	ENSGT00940000158666 #22	ENSGT00940000155606.b #23	ENSGT00950000182837.b.a #24	ENSGT00940000155687 #25	ENSGT00390000010327 #27	ENSGT00940000159544 #28	ENSGT00940000155808 #29	ENSGT00940000165147	ENSGT00940000161726 #30	ENSGT00940000163803	ENSGT00940000162388.B	ENSGT00390000014843	ENSGT00940000162202.A #32	ENSGT00940000162202.B ##32	ENSGT00940000162202.C ##32	ENSGT00940000162121 #33
Marmotini	ANCESTRAL SPECIES	19	ENSGT00940000154457.a.b	ENSGT00950000182825.A.a.b.a.b.a.b.a.b	ENSGT00950000182825.A.a.b.a.b.a.a.a.a.b	ENSGT00950000182825.A.a.b.a.b.a.b.b.b	ENSGT00390000007809.a #10	ENSGT00940000161132 #11	ENSGT00940000161665 #12	ENSGT00940000156707 #13	ENSGT00950000183019.f.b.a #15	ENSGT00390000016495 #16	ENSGT00940000160329 #17	ENSGT00940000160653 #18	ENSGT00950000183080.a.a #19	ENSGT00940000159521 #20	ENSGT00940000153804.B #21	ENSGT00940000158666 #22	ENSGT00940000155606.b #23	ENSGT00950000182837.b.a #24	ENSGT00940000155687 #25	ENSGT00390000010327 #27	ENSGT00940000159544 #28	ENSGT00940000155808 #29	ENSGT00940000165147	ENSGT00940000161726 #30	ENSGT00940000163803	ENSGT00940000162388.B	ENSGT00940000159881.a.b.a	ENSGT00940000162202.A #32	ENSGT00940000162202.B ##32	ENSGT00940000162202.C ##32	ENSGT00940000162121 #33
Alpin marmot	MODERN SPECIES	34	ENSMMMG00000023075 #7	ENSMMMG00000023070	PRPH (ENSMMMG00000023068) #8	TUBA1C (ENSMMMG00000023064)	TUBA1A (ENSMMMG00000023062)	LMBR1L (ENSMMMG00000023056) #10	DHH (ENSMMMG00000023054) #11	RHEBL1 (ENSMMMG00000023043) #12	ENSMMMG00000023038 #13	ENSMMMG00000023022 #13	ENSMMMG00000023013 #15	DDN (ENSMMMG00000023006) #16	WNT10B (ENSMMMG00000022992) #18	FKBP11 (ENSMMMG00000022980) #20	CCDC65 (ENSMMMG00000022974) #21	RND1 (ENSMMMG00000022971) #22	DDX23 (ENSMMMG00000022958) #23	CACNB3 (ENSMMMG00000022935) #24	ADCY6 (ENSMMMG00000022920) #25	TEX49 (ENSMMMG00000022917) #27	CCNT1 (ENSMMMG00000022910) #28	KANSL2 (ENSMMMG00000022904) #29	LALBA (ENSMMMG00000022893) #30	OR5BS1P (ENSMMMG00000022891)	ENSMMMG00000022889	ENSMMMG00000022886	ENSMMMG00000022885 #32	ENSMMMG00000022881 ##32	ENSMMMG00000022878 ##32	ZNF641 (ENSMMMG00000022873) #33	H1-7 (ENSMMMG00000022871)
Marmotini_b	ANCESTRAL SPECIES	11	ENSGT00940000160203 #8	ENSGT00940000154457.a.b	ENSGT00950000182825.A.a.b.a.b.a.a.a.a.b	ENSGT00950000182825.A.a.b.a.b.a.b.b.b	ENSGT00390000007809.a #10	ENSGT00940000161132 #11	ENSGT00940000161665 #12	ENSGT00940000156707 #13	ENSGT00950000183019.f.b.a #15	ENSGT00390000016495 #16	ENSGT00940000160329 #17	ENSGT00940000160653 #18	ENSGT00950000183080.a.a #19	ENSGT00940000159521 #20	ENSGT00940000153804.B #21	ENSGT00940000158666 #22	ENSGT00940000155606.b #23	ENSGT00950000182837.b.a #24	ENSGT00940000155687 #25	ENSGT00390000010327 #27	ENSGT00940000159544 #28	ENSGT00940000155808 #29	ENSGT00940000165147	ENSGT00940000161726 #30	ENSGT00940000163803	ENSGT00940000162388.B	ENSGT00940000159881.a.b.a	ENSGT00940000162202.A #32	ENSGT00940000162202.B ##32	ENSGT00940000162202.C ##32	ENSGT00940000162121 #33
Arctic ground squirrel	MODERN SPECIES	348	C1QL4 (ENSUPAG00010009646)	ENSUPAG00010009642	PRPH (ENSUPAG00010009633) #8	TUBA1C (ENSUPAG00010009626)	TUBA1B (ENSUPAG00010009604)	LMBR1L (ENSUPAG00010009579) #10	DHH (ENSUPAG00010009573) #11	RHEBL1 (ENSUPAG00010009539) #12	PRKAG1 (ENSUPAG00010009337) #15	DDN (ENSUPAG00010009325) #16	WNT1 (ENSUPAG00010009320) #17	WNT10B (ENSUPAG00010009270) #18	ARF3 (ENSUPAG00010009256) #19	FKBP11 (ENSUPAG00010009234) #20	CCDC65 (ENSUPAG00010009212) #21	RND1 (ENSUPAG00010009175) #22	DDX23 (ENSUPAG00010009132) #23	CACNB3 (ENSUPAG00010008993) #24	ADCY6 (ENSUPAG00010008904) #25	TEX49 (ENSUPAG00010008891) #27	CCNT1 (ENSUPAG00010008871) #28	KANSL2 (ENSUPAG00010008805) #29	ENSUPAG00010008799	LALBA (ENSUPAG00010008774) #30	OR5BS1P (ENSUPAG00010008767)
Squirrel	MODERN SPECIES	112	PRPH (ENSSTOG00000000282) #8	ENSSTOG00000020227	TUBA1B (ENSSTOG00000021170)	TUBA1A (ENSSTOG00000033698)	LMBR1L (ENSSTOG00000008752) #10	DHH (ENSSTOG00000000186) #11	RHEBL1 (ENSSTOG00000003967) #12	KMT2D (ENSSTOG00000003904) #13	PRKAG1 (ENSSTOG00000014648) #15	DDN (ENSSTOG00000028408) #16	WNT1 (ENSSTOG00000003902) #17	WNT10B (ENSSTOG00000004303) #18	ARF3 (ENSSTOG00000004295) #19	FKBP11 (ENSSTOG00000023089) #20	CCDC65 (ENSSTOG00000004267) #21	RND1 (ENSSTOG00000004257) #22	DDX23 (ENSSTOG00000004219) #23	CACNB3 (ENSSTOG00000004199) #24	ADCY6 (ENSSTOG00000004149) #25	TEX49 (ENSSTOG00000004134) #27	CCNT1 (ENSSTOG00000021508) #28	KANSL2 (ENSSTOG00000004118) #29	ENSSTOG00000019743	LALBA (ENSSTOG00000033863) #30	ENSSTOG00000032648	ENSSTOG00000033401	ENSSTOG00000005852 #31	ENSSTOG00000033341 ##32	ZNF641 (ENSSTOG00000001970) #33	OR10AD1 (ENSSTOG00000001963)	CCDC184 (ENSSTOG00000001957) #36
Eurasian red squirrel	MODERN SPECIES	14	TUBA1C (ENSSVLG00005014280)	TUBA1A (ENSSVLG00005014169)	TUBA1B (ENSSVLG00005014122)	LMBR1L (ENSSVLG00005014035) #10	DHH (ENSSVLG00005013965) #11	RHEBL1 (ENSSVLG00005013912) #12	ENSSVLG00005013789 #13	ENSSVLG00005013748 #13	PRKAG1 (ENSSVLG00005013661) #15	DDN (ENSSVLG00005013335) #16	WNT1 (ENSSVLG00005013249) #17	WNT10B (ENSSVLG00005013159) #18	ARF3 (ENSSVLG00005012987) #19	FKBP11 (ENSSVLG00005012794) #20	CCDC65 (ENSSVLG00005012567) #21	RND1 (ENSSVLG00005012510) #22	DDX23 (ENSSVLG00005012479) #23	CACNB3 (ENSSVLG00005012131) #24	ADCY6 (ENSSVLG00005011914) #25	TEX49 (ENSSVLG00005011832) #27	CCNT1 (ENSSVLG00005011525) #28	KANSL2 (ENSSVLG00005011410) #29	ENSSVLG00005011395	ENSSVLG00005011295	LALBA (ENSSVLG00005011187) #30	OR5BS1P (ENSSVLG00005011139)	C12orf54 (ENSSVLG00005011007)	ENSSVLG00005010951 #32	ZNF641 (ENSSVLG00005010861) #33	H1-7 (ENSSVLG00005010817)	OR10AD1 (ENSSVLG00005010756)