Rodentia_A	ANCESTRAL SPECIES	22	ENSGT00390000018451 #8	ENSGT00940000158706 #9	ENSGT00390000002316 #10	ENSGT00950000183120.e.b.a.a.a.n ##11	ENSGT00940000156630 #12	ENSGT00390000004952.b #13	ENSGT00940000155349 #14	ENSGT00950000183026.B #15	ENSGT00950000183096.a.a.c.b #16	ENSGT00390000010734.j #17	ENSGT00940000158713 #18	ENSGT00940000164144	ENSGT00390000001504 #19	ENSGT00940000160575 #20	ENSGT00390000002395 #21	ENSGT00940000161261 #22	ENSGT00940000162542	ENSGT00940000154361.A #23	ENSGT00390000003643	ENSGT00550000075160 #24	ENSGT00940000158381 #25	ENSGT00390000014424 #26	ENSGT00940000155647 #27	ENSGT00940000161208 #28	ENSGT00950000182922.a.a.a.b.a.b.b #29	ENSGT00940000153284.a.h ##30	ENSGT01060000248564.b.a.b.a #32	ENSGT00950000182962.a.a	ENSGT00940000157104	ENSGT00940000158530.j	ENSGT00940000165049
Sciuridae	ANCESTRAL SPECIES	34	ENSGT00390000009484 #7	ENSGT00390000018451 #8	ENSGT00940000158706 #9	ENSGT00390000002316 #10	ENSGT00950000183120.e.b.a.a.a.n ##11	ENSGT00940000156630 #12	ENSGT00390000004952.b #13	ENSGT00940000155349 #14	ENSGT00950000183026.B #15	ENSGT00950000183096.a.a.c.b #16	ENSGT00390000010734.j #17	ENSGT00940000158713 #18	ENSGT00390000001504 #19	ENSGT00940000160575 #20	ENSGT00390000002395 #21	ENSGT00940000161261 #22	ENSGT00940000162542	ENSGT00940000154361.A #23	ENSGT00550000075160 #24	ENSGT00940000158381 #25	ENSGT00390000014424 #26	ENSGT00940000155647 #27	ENSGT00940000161208 #28	ENSGT00950000182922.a.a.a.b.a.b.b #29	ENSGT00940000153284.a.g.a #30	ENSGT00950000182922.a.a.a.b.a.a.b.a ##29	ENSGT00940000153284.a.h ##30	ENSGT01060000248564.b.a.b.a #32
Marmotini	ANCESTRAL SPECIES	29	ENSGT00390000018451 #8	ENSGT00940000158706 #9	ENSGT00390000002316 #10	ENSGT00950000183120.e.b.a.a.b.b.b.b #11	ENSGT00950000183120.e.b.a.a.b.b.a.b.b.q ##11	ENSGT00940000156630 #12	ENSGT00390000004952.b #13	ENSGT00940000155349 #14	ENSGT00950000183026.B #15	ENSGT00950000183096.a.a.c.b #16	ENSGT00390000010734.j #17	ENSGT00940000158713 #18	ENSGT00390000001504 #19	ENSGT00940000160575 #20	ENSGT00390000002395 #21	ENSGT00940000161261 #22	ENSGT00940000162542	ENSGT00940000154361.A #23	ENSGT00550000075160 #24	ENSGT00940000158381 #25	ENSGT00390000014424 #26	ENSGT00940000155647 #27	ENSGT00940000161208 #28	ENSGT00950000182922.a.a.a.b.a.b.b #29	ENSGT00940000153284.a.g.a #30	ENSGT00950000182922.a.a.a.b.a.a.b.a ##29	ENSGT00940000153284.a.h ##30	ENSGT01060000248564.b.a.b.a #32	ENSGT00940000158453.a #33	ENSGT01050000244955.a.a #35	ENSGT01050000244897.a.b.b.b #36
Alpin marmot	MODERN SPECIES	13	TEX26 (ENSMMMG00000021931) #7	MEDAG (ENSMMMG00000021928) #8	ALOX5AP (ENSMMMG00000021924) #9	ENSMMMG00000021912 #10	ENSMMMG00000021875 #11	KATNAL1 (ENSMMMG00000021861) #12	UBL3 (ENSMMMG00000021836) #13	SLC7A1 (ENSMMMG00000021811) #14	ENSMMMG00000021777 #15	SLC46A3 (ENSMMMG00000021759) #16	POMP (ENSMMMG00000021745) #17	FLT1 (ENSMMMG00000021722) #18	PAN3 (ENSMMMG00000021592) #19	FLT3 (ENSMMMG00000021498) #20	ENSMMMG00000021485 #21	CDX2 (ENSMMMG00000021482) #22	GSX1 (ENSMMMG00000021480) #23	POLR1D (ENSMMMG00000021469) #24	LNX2 (ENSMMMG00000021459) #25	MTIF3 (ENSMMMG00000021440) #26	GTF3A (ENSMMMG00000021436) #27	RASL11A (ENSMMMG00000021424) #28	RPL21 (ENSMMMG00000021415) #29	ENSMMMG00000021402 #30	ENSMMMG00000021396 #31	GPR12 (ENSMMMG00000021388) #32	SLITRK5 (ENSMMMG00000021362) #33	ENSMMMG00000021355 #34	GPC5 (ENSMMMG00000021337) #35	GPC6 (ENSMMMG00000021294) #36	DCT (ENSMMMG00000021259) #37
Marmotini_b	ANCESTRAL SPECIES	39	ENSGT00390000009484 #7	ENSGT00390000018451 #8	ENSGT00940000158706 #9	ENSGT00390000002316 #10	ENSGT00950000183120.e.b.a.a.b.b.a.b.b.q ##11	ENSGT00940000156630 #12	ENSGT00390000004952.b #13	ENSGT00940000155349 #14	ENSGT00950000183026.B #15	ENSGT00950000183096.a.a.c.b #16	ENSGT00390000010734.j #17	ENSGT00940000158713 #18	ENSGT00390000001504 #19	ENSGT00940000160575 #20	ENSGT00390000002395 #21	ENSGT00940000161261 #22	ENSGT00940000162542	ENSGT00940000154361.A #23	ENSGT00550000075160 #24	ENSGT00940000158381 #25	ENSGT00390000014424 #26	ENSGT00940000155647 #27	ENSGT00940000161208 #28	ENSGT00950000182922.a.a.a.b.a.a.b.a ##29	ENSGT00940000153284.a.h ##30	ENSGT01060000248564.b.a.b.a #32	ENSGT00940000158453.a #33	ENSGT01050000244955.a.a #35	ENSGT01050000244897.a.b.b.b #36	ENSGT00940000156856 #37	ENSGT00940000159196
Arctic ground squirrel	MODERN SPECIES	58	MEDAG (ENSUPAG00010000596) #8	ALOX5AP (ENSUPAG00010000582) #9	USPL1 (ENSUPAG00010000537) #10	ENSUPAG00010000514 ##11	KATNAL1 (ENSUPAG00010000483) #12	UBL3 (ENSUPAG00010000449) #13	SLC7A1 (ENSUPAG00010000429) #14	ENSUPAG00010000338 #15	ENSUPAG00010000323	SLC46A3 (ENSUPAG00010000307) #16	POMP (ENSUPAG00010000279) #17	FLT1 (ENSUPAG00010000212) #18	PAN3 (ENSUPAG00010000039) #19	FLT3 (ENSUPAG00010018139) #20	ENSUPAG00010018133 #21	CDX2 (ENSUPAG00010018125) #22	PDX1 (ENSUPAG00010018122)	GSX1 (ENSUPAG00010018112) #23	POLR1D (ENSUPAG00010018107) #24	LNX2 (ENSUPAG00010018096) #25	MTIF3 (ENSUPAG00010018090) #26	GTF3A (ENSUPAG00010018082) #27	RASL11A (ENSUPAG00010018073) #28	ENSUPAG00010018061 ##29	USP12 (ENSUPAG00010018049) ##30	GPR12 (ENSUPAG00010018043) #32	SLITRK5 (ENSUPAG00010018031) #33
Squirrel	MODERN SPECIES	72	ENSSTOG00000020892	MEDAG (ENSSTOG00000003534) #8	ALOX5AP (ENSSTOG00000010915) #9	USPL1 (ENSSTOG00000028023) #10	ENSSTOG00000000443 ##11	KATNAL1 (ENSSTOG00000008802) #12	UBL3 (ENSSTOG00000012777) #13	SLC7A1 (ENSSTOG00000012771) #14	ENSSTOG00000022794 #15	SLC46A3 (ENSSTOG00000013694) #16	POMP (ENSSTOG00000013687) #17	FLT1 (ENSSTOG00000021178) #18	PAN3 (ENSSTOG00000009453) #19	FLT3 (ENSSTOG00000002925) #20	ENSSTOG00000028014 #21	ENSSTOG00000002918 #22	PDX1 (ENSSTOG00000028173)	GSX1 (ENSSTOG00000029234) #23	POLR1D (ENSSTOG00000013877) #24	LNX2 (ENSSTOG00000013869) #25	MTIF3 (ENSSTOG00000013866) #26	GTF3A (ENSSTOG00000013853) #27	RASL11A (ENSSTOG00000023879) #28	ENSSTOG00000033637 ##29	USP12 (ENSSTOG00000011364) ##30	ENSSTOG00000023839	GPR12 (ENSSTOG00000011362) #32	SLITRK5 (ENSSTOG00000022257) #33	ENSSTOG00000029870 #35	GPC6 (ENSSTOG00000025649) #36	DCT (ENSSTOG00000010422) #37
Eurasian red squirrel	MODERN SPECIES	13	TEX26 (ENSSVLG00005022083) #7	MEDAG (ENSSVLG00005022152) #8	ALOX5AP (ENSSVLG00005022177) #9	USPL1 (ENSSVLG00005022232) #10	ENSSVLG00005022302 ##11	KATNAL1 (ENSSVLG00005022343) #12	UBL3 (ENSSVLG00005022374) #13	SLC7A1 (ENSSVLG00005022416) #14	MTUS2 (ENSSVLG00005022484) #15	SLC46A3 (ENSSVLG00005022784) #16	POMP (ENSSVLG00005022839) #17	FLT1 (ENSSVLG00005022893) #18	PAN3 (ENSSVLG00005022998) #19	FLT3 (ENSSVLG00005023095) #20	URAD (ENSSVLG00005023233)	CDX2 (ENSSVLG00005023249) #22	PDX1 (ENSSVLG00005023276)	GSX1 (ENSSVLG00005023295) #23	POLR1D (ENSSVLG00005023318) #24	LNX2 (ENSSVLG00005023366) #25	MTIF3 (ENSSVLG00005023396) #26	GTF3A (ENSSVLG00005023413) #27	RASL11A (ENSSVLG00005023466) #28	ENSSVLG00005000213 ##29	ENSSVLG00005000350 ##30	GPR12 (ENSSVLG00005000385) #32	ENSSVLG00005000420	ENSSVLG00005000440	SLITRK5 (ENSSVLG00005000517) #33	ENSSVLG00005000527	ENSSVLG00005000550
Hystricomorpha	ANCESTRAL SPECIES	25	ENSGT00390000018451 #8	ENSGT00940000158706 #9	ENSGT00390000002316 #10	ENSGT00950000183120.e.b.a.a.a.n ##11	ENSGT00940000156630 #12	ENSGT00390000004952.b #13	ENSGT00940000155349 #14	ENSGT00950000183026.B #15	ENSGT00950000183096.a.a.c.b #16	ENSGT00390000010734.j.p #17	ENSGT00940000158713 #18	ENSGT00940000164144	ENSGT00390000001504 #19	ENSGT00940000160575 #20	ENSGT00390000002395 #21	ENSGT00940000161261 #22	ENSGT00940000162542	ENSGT00940000154361.A #23	ENSGT00390000003643	ENSGT00550000075160 #24	ENSGT00940000158381 #25	ENSGT00390000014424 #26	ENSGT00940000155647.c #27	ENSGT00940000161208 #28	ENSGT00950000182922.a.a.a.b.a.b.b #29	ENSGT00940000153284.a.h ##30	ENSGT01060000248564.b.a.b.a #32	ENSGT00950000182962.a.a	ENSGT00940000157104	ENSGT00940000158530.j	ENSGT00940000165049
Naked mole-rat female	MODERN SPECIES	2	USPL1 (ENSHGLG00000036213) #10	ENSHGLG00000003352 #11	KATNAL1 (ENSHGLG00000003538) #12	UBL3 (ENSHGLG00000040587) #13	ENSHGLG00000033244	ENSHGLG00000019220 #14	ENSHGLG00000013589 #15	ENSHGLG00000012383	ENSHGLG00000039882 ##17	SLC46A3 (ENSHGLG00000007999) #16	ENSHGLG00000008991 #17	FLT1 (ENSHGLG00000003643) #18	PAN3 (ENSHGLG00000018782) #19	FLT3 (ENSHGLG00000005717) #20	URAD (ENSHGLG00000008479)	CDX2 (ENSHGLG00000009166) #22	PDX1 (ENSHGLG00000010243)	GSX1 (ENSHGLG00000039858) #23	ENSHGLG00000003202	POLR1D (ENSHGLG00000039229) #24	LNX2 (ENSHGLG00000003410) #25	MTIF3 (ENSHGLG00000003959) #26	ENSHGLG00000004173 #27	RASL11A (ENSHGLG00000005304) #28	ENSHGLG00000005660 ##29	ENSHGLG00000006711 ##30	GPR12 (ENSHGLG00000042343) #32	WASF3 (ENSHGLG00000006350)	ENSHGLG00000006446	CDK8 (ENSHGLG00000007563)	RNF6 (ENSHGLG00000008194)
Hystricomorpha_a	ANCESTRAL SPECIES	21	ENSGT00390000018451 #8	ENSGT00940000158706 #9	ENSGT00390000002316 #10	ENSGT00950000183120.e.b.a.a.a.n ##11	ENSGT00940000156630 #12	ENSGT00390000004952.b #13	ENSGT00940000155349 #14	ENSGT00950000183026.B #15	ENSGT00950000183096.a.a.c.b #16	ENSGT00390000010734.j.p #17	ENSGT00940000158713 #18	ENSGT00940000164144	ENSGT00390000001504 #19	ENSGT00940000160575 #20	ENSGT00390000002395 #21	ENSGT00940000161261 #22	ENSGT00940000162542	ENSGT00940000154361.A #23	ENSGT00390000003643	ENSGT00550000075160 #24	ENSGT00940000158381 #25	ENSGT00390000014424 #26	ENSGT00940000155647.c #27	ENSGT00940000161208 #28	ENSGT00950000182922.a.a.a.b.a.b.b #29	ENSGT00940000153284.a.h ##30	ENSGT01060000248564.b.a.b.a #32	ENSGT00950000182962.a.a	ENSGT00940000157104	ENSGT00940000158530.j	ENSGT00940000165049
Guinea pig	MODERN SPECIES	6	ENSCPOG00000035490	ENSCPOG00000007441	MEDAG (ENSCPOG00000003921) #8	ALOX5AP (ENSCPOG00000032690) #9	USPL1 (ENSCPOG00000009937) #10	HMGB1 (ENSCPOG00000031835) ##11	KATNAL1 (ENSCPOG00000000804) #12	UBL3 (ENSCPOG00000036242) #13	SLC7A1 (ENSCPOG00000005590) #14	ENSCPOG00000005581 #15	SLC46A3 (ENSCPOG00000015460) #16	POMP (ENSCPOG00000001710) #17	FLT1 (ENSCPOG00000013357) #18	PAN3 (ENSCPOG00000013349) #19	FLT3 (ENSCPOG00000007285) #20	CDX2 (ENSCPOG00000007276) #22	PDX1 (ENSCPOG00000024534)	ENSCPOG00000026854	ENSCPOG00000033461	LNX2 (ENSCPOG00000010152) #25	MTIF3 (ENSCPOG00000010148) #26	GTF3A (ENSCPOG00000010143) #27	RASL11A (ENSCPOG00000031264) #28	ENSCPOG00000008784 #29	USP12 (ENSCPOG00000005241) ##30	ENSCPOG00000020112	WASF3 (ENSCPOG00000010156)	CDK8 (ENSCPOG00000040435)	RNF6 (ENSCPOG00000009120)	SHISA2 (ENSCPOG00000009049)	ATP8A2 (ENSCPOG00000032003)
Hystricomorpha_b	ANCESTRAL SPECIES	48	ENSGT00390000018451 #8	ENSGT00940000158706 #9	ENSGT00390000002316 #10	ENSGT00950000183120.e.b.a.a.a.n ##11	ENSGT00940000156630 #12	ENSGT00390000004952.b #13	ENSGT00940000155349 #14	ENSGT00950000183026.B #15	ENSGT00950000183096.a.a.c.b #16	ENSGT00390000010734.j.p #17	ENSGT00940000158713 #18	ENSGT00940000164144	ENSGT00390000001504 #19	ENSGT00940000160575 #20	ENSGT00390000002395 #21	ENSGT00940000161261 #22	ENSGT00940000162542	ENSGT00940000154361.A #23	ENSGT00390000003643	ENSGT00550000075160 #24	ENSGT00940000158381 #25	ENSGT00390000014424 #26	ENSGT00940000155647.c #27	ENSGT00940000161208 #28	ENSGT00950000182922.a.a.a.b.a.a.b.b ##29	ENSGT00940000153284.a.h ##30	ENSGT01060000248564.b.a.b.a #32	ENSGT00950000182962.a.a	ENSGT00940000157104	ENSGT00940000158530.j	ENSGT00940000165049
Degu	MODERN SPECIES	79	ENSODEG00000006120 ##11	KATNAL1 (ENSODEG00000005926) #12	UBL3 (ENSODEG00000005571) #13	ENSODEG00000005438	SLC7A1 (ENSODEG00000005306) #14	ENSODEG00000005871 #15	ENSODEG00000006635	SLC46A3 (ENSODEG00000006238) #16	ENSODEG00000005569	ENSODEG00000005111 #17	ENSODEG00000006274 #18	ENSODEG00000006016	PAN3 (ENSODEG00000005038) #19	FLT3 (ENSODEG00000007884) #20	ENSODEG00000007620 #21	CDX2 (ENSODEG00000007340) #22	PDX1 (ENSODEG00000005235)	ENSODEG00000019134	GSX1 (ENSODEG00000005135) #23	ENSODEG00000006454	ENSODEG00000005294 #24	LNX2 (ENSODEG00000006222) #25	MTIF3 (ENSODEG00000006818) #26	GTF3A (ENSODEG00000006725) #27	RASL11A (ENSODEG00000005775) #28	ENSODEG00000005022 ##29	USP12 (ENSODEG00000006744) ##30	GPR12 (ENSODEG00000006388) #32	WASF3 (ENSODEG00000005353)	ENSODEG00000005140	ENSODEG00000006456
Long-tailed chinchilla	MODERN SPECIES	204											SLC46A3 (ENSCLAG00000009379) #16	POMP (ENSCLAG00000008609) #17	FLT1 (ENSCLAG00000008187) #18	PAN3 (ENSCLAG00000007575) #19	FLT3 (ENSCLAG00000007093) #20	CDX2 (ENSCLAG00000006810) #22	PDX1 (ENSCLAG00000006652)	GSX1 (ENSCLAG00000004357) #23	ENSCLAG00000004320	POLR1D (ENSCLAG00000017623) #24	LNX2 (ENSCLAG00000004148) #25	MTIF3 (ENSCLAG00000004080) #26	GTF3A (ENSCLAG00000003912) #27	RASL11A (ENSCLAG00000003867) #28	Rpl21 (ENSCLAG00000003656) ##29	USP12 (ENSCLAG00000003543) ##30	GPR12 (ENSCLAG00000003409) #32	WASF3 (ENSCLAG00000003372)	CDK8 (ENSCLAG00000003311)	RNF6 (ENSCLAG00000003242)	ENSCLAG00000003030