Rodentia_A	ANCESTRAL SPECIES	1	ENSGT00390000014065	ENSGT00940000158970 #8	ENSGT00390000016785 #9	ENSGT01020000230346.E #10	ENSGT00940000157349 #11	ENSGT00940000159754 #12	ENSGT00940000157698.b #13	ENSGT00940000156718 #14	ENSGT00940000159068 #15	ENSGT00940000158446 #16	ENSGT00510000047881 #17	ENSGT00950000182973.b.a #18	ENSGT00940000155568 #19	ENSGT00390000012935 #20	ENSGT00940000158287 #21	ENSGT00390000014757 #22	ENSGT00940000154234.b #23	ENSGT00930000151062	ENSGT00940000160630 #24	ENSGT00390000007055 #25	ENSGT00940000154348.c.b.a #26	ENSGT00390000016223 #27	ENSGT00940000160394.a #28	ENSGT00390000007640.b #29	ENSGT00940000156152 #30	ENSGT00860000136066 #31	ENSGT00940000159848 #32	ENSGT00940000156124 #33	ENSGT00940000158758 #34	ENSGT00390000017790 #35	ENSGT00390000018235
Hystricomorpha	ANCESTRAL SPECIES	16	ENSGT00390000014065	ENSGT00940000158970 #8	ENSGT00390000016785 #9	ENSGT01020000230346.E #10	ENSGT00940000157349 #11	ENSGT00940000159754 #12	ENSGT00940000157698.b #13	ENSGT00940000156718 #14	ENSGT00940000159068 #15	ENSGT00940000158446 #16	ENSGT00510000047881 #17	ENSGT00950000182973.b.a #18	ENSGT00940000155568 #19	ENSGT00390000012935 #20	ENSGT00940000158287 #21	ENSGT00390000014757 #22	ENSGT00940000154234.b #23	ENSGT00940000160630 #24	ENSGT00390000007055 #25	ENSGT00940000154348.c.b.a #26	ENSGT00390000016223 #27	ENSGT00940000160394.a #28	ENSGT00390000007640.b #29	ENSGT00940000156152 #30	ENSGT00860000136066 #31	ENSGT00940000159848 #32	ENSGT00940000156124 #33	ENSGT00940000158758 #34	ENSGT00390000017790 #35	ENSGT00390000018235	ENSGT00940000157089.B #36
Hystricomorpha_a	ANCESTRAL SPECIES	12	ENSGT00390000014065	ENSGT00940000158970 #8	ENSGT00390000016785 #9	ENSGT01020000230346.E #10	ENSGT00940000157349 #11	ENSGT00940000159754 #12	ENSGT00940000157698.b #13	ENSGT00940000156718 #14	ENSGT00940000159068 #15	ENSGT00940000158446 #16	ENSGT00510000047881 #17	ENSGT00950000182973.b.a #18	ENSGT00940000155568 #19	ENSGT00390000012935 #20	ENSGT00940000158287 #21	ENSGT00390000014757 #22	ENSGT00940000154234.b #23	ENSGT00940000160630 #24	ENSGT00390000007055 #25	ENSGT00940000154348.c.b.a #26	ENSGT00390000016223 #27	ENSGT00940000160394.a #28	ENSGT00390000007640.b #29	ENSGT00940000156152 #30	ENSGT00860000136066 #31	ENSGT00940000159848 #32	ENSGT00940000156124 #33	ENSGT00940000158758 #34	ENSGT00390000017790 #35	ENSGT00390000018235	ENSGT00940000157089.B #36
Hystricomorpha_b	ANCESTRAL SPECIES	10	ENSGT00940000158775 #7	ENSGT00940000158970 #8	ENSGT00390000016785 #9	ENSGT01020000230346.E #10	ENSGT00940000157349 #11	ENSGT00940000159754 #12	ENSGT00940000157698.b #13	ENSGT00940000156718 #14	ENSGT00940000159068 #15	ENSGT00940000158446 #16	ENSGT00510000047881 #17	ENSGT00950000182973.b.a #18	ENSGT00940000155568 #19	ENSGT00390000012935 #20	ENSGT00940000158287 #21	ENSGT00390000014757 #22	ENSGT00940000154234.b #23	ENSGT00940000160630 #24	ENSGT00390000007055 #25	ENSGT00940000154348.c.b.a #26	ENSGT00390000016223 #27	ENSGT00940000160394.a #28	ENSGT00390000007640.b #29	ENSGT00940000156152 #30	ENSGT00860000136066 #31	ENSGT00940000159848 #32	ENSGT00940000156124 #33	ENSGT00940000158758 #34	ENSGT00390000017790 #35	ENSGT00390000018235	ENSGT00940000157089.B #36
Long-tailed chinchilla	MODERN SPECIES	129	KBTBD4 (ENSCLAG00000016255) #7	CELF1 (ENSCLAG00000011791) #8	RAPSN (ENSCLAG00000015497) #9	PSMC3 (ENSCLAG00000013916) #10	SLC39A13 (ENSCLAG00000014480) #11	SPI1 (ENSCLAG00000017201) #12	MYBPC3 (ENSCLAG00000015418) #13	MADD (ENSCLAG00000012503) #14	NR1H3 (ENSCLAG00000013563) #15	ACP2 (ENSCLAG00000014608) #16	DDB2 (ENSCLAG00000016473) #17	ENSCLAG00000012709 #18	ARFGAP2 (ENSCLAG00000016467) #19	CSTPP1 (ENSCLAG00000014110) #20	LRP4 (ENSCLAG00000016159) #21	CKAP5 (ENSCLAG00000015801) #22	F2 (ENSCLAG00000015618) #23	ARHGAP1 (ENSCLAG00000013542) #24	ATG13 (ENSCLAG00000015328) #25	HARBI1 (ENSCLAG00000013578) #26	AMBRA1 (ENSCLAG00000015156) #27	CHRM4 (ENSCLAG00000013251) #28	MDK (ENSCLAG00000014462) #29	DGKZ (ENSCLAG00000016057) #30	ENSCLAG00000014194 #31	CREB3L1 (ENSCLAG00000013609) #32	PHF21A (ENSCLAG00000016632) #33	LARGE2 (ENSCLAG00000014846) #34	PEX16 (ENSCLAG00000013695) #35	MAPK8IP1 (ENSCLAG00000014552) #36	ENSCLAG00000014881 #37
Degu	MODERN SPECIES	59	NDUFS3 (ENSODEG00000015948)	KBTBD4 (ENSODEG00000015830) #7	CELF1 (ENSODEG00000015204) #8	RAPSN (ENSODEG00000015194) #9	ENSODEG00000016550 #10	SLC39A13 (ENSODEG00000015895) #11	SPI1 (ENSODEG00000015369) #12	MYBPC3 (ENSODEG00000016030) #13	MADD (ENSODEG00000017645) #14	NR1H3 (ENSODEG00000016180) #15	ACP2 (ENSODEG00000015528) #16	ENSODEG00000015965 #18	ENSODEG00000016456 #19	CSTPP1 (ENSODEG00000016656) #20	LRP4 (ENSODEG00000015720) #21	CKAP5 (ENSODEG00000016409) #22	F2 (ENSODEG00000016157) #23	ARHGAP1 (ENSODEG00000016156) #24	ATG13 (ENSODEG00000017294) #25	ENSODEG00000016339	AMBRA1 (ENSODEG00000016633) #27	CHRM4 (ENSODEG00000020352) #28	MDK (ENSODEG00000015931) #29	DGKZ (ENSODEG00000016309) #30	ENSODEG00000016420 #30	ENSODEG00000016039 #31	CREB3L1 (ENSODEG00000016017) #32	ENSODEG00000016348	ENSODEG00000016543	PHF21A (ENSODEG00000017531) #33	LARGE2 (ENSODEG00000016208) #34
Guinea pig	MODERN SPECIES	72	PTPMT1 (ENSCPOG00000031147)	CELF1 (ENSCPOG00000036381) #8	RAPSN (ENSCPOG00000015456) #9	PSMC3 (ENSCPOG00000008176) #10	SLC39A13 (ENSCPOG00000008169) #11	SPI1 (ENSCPOG00000022138) #12	MYBPC3 (ENSCPOG00000013368) #13	MADD (ENSCPOG00000013364) #14	NR1H3 (ENSCPOG00000013362) #15	ACP2 (ENSCPOG00000013359) #16	DDB2 (ENSCPOG00000013358) #17	PACSIN3 (ENSCPOG00000013356) #18	ARFGAP2 (ENSCPOG00000013352) #19	CSTPP1 (ENSCPOG00000020334) #20	LRP4 (ENSCPOG00000007072) #21	CKAP5 (ENSCPOG00000007054) #22	F2 (ENSCPOG00000026682) #23	ARHGAP1 (ENSCPOG00000013046) #24	ATG13 (ENSCPOG00000013042) #25	HARBI1 (ENSCPOG00000037304) #26	AMBRA1 (ENSCPOG00000007341) #27	CHRM4 (ENSCPOG00000020788) #28	MDK (ENSCPOG00000007340) #29	DGKZ (ENSCPOG00000009636) #30	CREB3L1 (ENSCPOG00000010073) #32	PHF21A (ENSCPOG00000001299) #33	LARGE2 (ENSCPOG00000033339) #34	PEX16 (ENSCPOG00000027497) #35	FREY1 (ENSCPOG00000032012)	MAPK8IP1 (ENSCPOG00000001298) #36	CRY2 (ENSCPOG00000001296)
Sciuridae	ANCESTRAL SPECIES	2	ENSGT00390000014065	ENSGT00940000158970 #8	ENSGT00390000016785 #9	ENSGT01020000230346.E #10	ENSGT00940000157349 #11	ENSGT00940000159754 #12	ENSGT00940000157698.b #13	ENSGT00940000156718 #14	ENSGT00940000159068 #15	ENSGT00940000158446 #16	ENSGT00510000047881 #17	ENSGT00950000182973.b.a #18	ENSGT00940000155568 #19	ENSGT00390000012935 #20	ENSGT00940000158287 #21	ENSGT00390000014757 #22	ENSGT00940000154234.b #23	ENSGT00930000151062	ENSGT00940000160630 #24	ENSGT00390000007055 #25	ENSGT00940000154348.c.b.a #26	ENSGT00390000016223 #27	ENSGT00940000160394.a #28	ENSGT00390000007640.b #29	ENSGT00940000156152 #30	ENSGT00940000159848 #32	ENSGT00940000156124 #33	ENSGT00940000158758 #34	ENSGT00390000017790 #35	ENSGT00390000018235	ENSGT00940000157089.B #36
Marmotini	ANCESTRAL SPECIES	22	ENSGT00390000014065	ENSGT00940000158970 #8	ENSGT00390000016785 #9	ENSGT01020000230346.E #10	ENSGT00940000157349 #11	ENSGT00940000159754 #12	ENSGT00940000157698.b #13	ENSGT00940000156718 #14	ENSGT00940000159068 #15	ENSGT00940000158446 #16	ENSGT00510000047881 #17	ENSGT00950000182973.b.a #18	ENSGT00940000155568 #19	ENSGT00390000012935 #20	ENSGT00940000158287 #21	ENSGT00390000014757 #22	ENSGT00940000154234.b #23	ENSGT00930000151062	ENSGT00940000160630 #24	ENSGT00390000007055 #25	ENSGT00940000154348.c.b.a #26	ENSGT00390000016223 #27	ENSGT00940000160394.a #28	ENSGT00390000007640.b #29	ENSGT00940000156152 #30	ENSGT00940000159848 #32	ENSGT00940000156124 #33	ENSGT00940000158758 #34	ENSGT00390000017790 #35	ENSGT00390000018235	ENSGT00940000157089.B #36
Alpin marmot	MODERN SPECIES	3	ENSMMMG00000015652	CELF1 (ENSMMMG00000015346) #8	RAPSN (ENSMMMG00000015294) #9	PSMC3 (ENSMMMG00000015270) #10	SLC39A13 (ENSMMMG00000015224) #11	SPI1 (ENSMMMG00000015212) #12	MYBPC3 (ENSMMMG00000015189) #13	MADD (ENSMMMG00000014606) #14	NR1H3 (ENSMMMG00000014541) #15	ACP2 (ENSMMMG00000014527) #16	DDB2 (ENSMMMG00000014518) #17	PACSIN3 (ENSMMMG00000014498) #18	ARFGAP2 (ENSMMMG00000014424) #19	CSTPP1 (ENSMMMG00000014382) #20	LRP4 (ENSMMMG00000014335) #21	CKAP5 (ENSMMMG00000013993) #22	F2 (ENSMMMG00000013961) #23	ZNF408 (ENSMMMG00000013944)	ARHGAP1 (ENSMMMG00000013934) #24	ATG13 (ENSMMMG00000013875) #25	HARBI1 (ENSMMMG00000013860) #26	AMBRA1 (ENSMMMG00000013284) #27	CHRM4 (ENSMMMG00000013278) #28	MDK (ENSMMMG00000013259) #29	DGKZ (ENSMMMG00000013155) #30	CREB3L1 (ENSMMMG00000013137) #32	PHF21A (ENSMMMG00000012404) #33	LARGE2 (ENSMMMG00000012317) #34	PEX16 (ENSMMMG00000012310) #35	FREY1 (ENSMMMG00000012302)	MAPK8IP1 (ENSMMMG00000011982) #36
Marmotini_b	ANCESTRAL SPECIES	23	ENSGT00390000014065	ENSGT00940000158970 #8	ENSGT00390000016785 #9	ENSGT01020000230346.E #10	ENSGT00940000157349 #11	ENSGT00940000159754 #12	ENSGT00940000157698.b #13	ENSGT00940000156718 #14	ENSGT00940000159068 #15	ENSGT00940000158446 #16	ENSGT00510000047881 #17	ENSGT00950000182973.b.a #18	ENSGT00940000155568 #19	ENSGT00390000012935 #20	ENSGT00940000158287 #21	ENSGT00390000014757 #22	ENSGT00940000154234.b #23	ENSGT00930000151062	ENSGT00940000160630 #24	ENSGT00390000007055 #25	ENSGT00940000154348.c.b.a #26	ENSGT00390000016223 #27	ENSGT00940000160394.a #28	ENSGT00390000007640.b #29	ENSGT00940000156152 #30	ENSGT00940000159848 #32	ENSGT00940000156124 #33	ENSGT00940000158758 #34	ENSGT00390000017790 #35	ENSGT00390000018235	ENSGT00940000157089.B #36
Arctic ground squirrel	MODERN SPECIES	208	CELF1 (ENSUPAG00010013973) #8	RAPSN (ENSUPAG00010013926) #9	PSMC3 (ENSUPAG00010013908) #10	SLC39A13 (ENSUPAG00010013855) #11	SPI1 (ENSUPAG00010013850) #12	ENSUPAG00010013841	MYBPC3 (ENSUPAG00010013812) #13	MADD (ENSUPAG00010011229) #14	NR1H3 (ENSUPAG00010011188) #15	ACP2 (ENSUPAG00010011162) #16	DDB2 (ENSUPAG00010011149) #17	PACSIN3 (ENSUPAG00010011141) #18	ARFGAP2 (ENSUPAG00010011117) #19	CSTPP1 (ENSUPAG00010011093) #20	LRP4 (ENSUPAG00010011049) #21	CKAP5 (ENSUPAG00010010730) #22	F2 (ENSUPAG00010010714) #23	ZNF408 (ENSUPAG00010010704)	ARHGAP1 (ENSUPAG00010010696) #24	ATG13 (ENSUPAG00010010621) #25	HARBI1 (ENSUPAG00010010611) #26	AMBRA1 (ENSUPAG00010010430) #27	CHRM4 (ENSUPAG00010010417) #28	MDK (ENSUPAG00010010379) #29	DGKZ (ENSUPAG00010010211) #30	CREB3L1 (ENSUPAG00010010194) #32	PHF21A (ENSUPAG00010009105) #33	LARGE2 (ENSUPAG00010008955) #34	PEX16 (ENSUPAG00010008926) #35	FREY1 (ENSUPAG00010008915)	MAPK8IP1 (ENSUPAG00010008856) #36
Squirrel	MODERN SPECIES	162	PTPMT1 (ENSSTOG00000019770)	CELF1 (ENSSTOG00000000613) #8	RAPSN (ENSSTOG00000011047) #9	PSMC3 (ENSSTOG00000011038) #10	SLC39A13 (ENSSTOG00000027722) #11	SPI1 (ENSSTOG00000022735) #12	MYBPC3 (ENSSTOG00000026473) #13	MADD (ENSSTOG00000007626) #14	NR1H3 (ENSSTOG00000007611) #15	ACP2 (ENSSTOG00000007586) #16	DDB2 (ENSSTOG00000007571) #17	PACSIN3 (ENSSTOG00000007547) #18	ARFGAP2 (ENSSTOG00000007524) #19	CSTPP1 (ENSSTOG00000007512) #20	LRP4 (ENSSTOG00000005236) #21	CKAP5 (ENSSTOG00000005158) #22	F2 (ENSSTOG00000005130) #23	ZNF408 (ENSSTOG00000005114)	ARHGAP1 (ENSSTOG00000026557) #24	ATG13 (ENSSTOG00000005077) #25	HARBI1 (ENSSTOG00000005072) #26	AMBRA1 (ENSSTOG00000019411) #27	CHRM4 (ENSSTOG00000022455) #28	MDK (ENSSTOG00000027636) #29	DGKZ (ENSSTOG00000012704) #30	CREB3L1 (ENSSTOG00000012697) #32	PHF21A (ENSSTOG00000011552) #33	LARGE2 (ENSSTOG00000011545) #34	PEX16 (ENSSTOG00000011534) #35	MAPK8IP1 (ENSSTOG00000027362) #36	FREY1 (ENSSTOG00000027622)
Eurasian red squirrel	MODERN SPECIES	2	ENSSVLG00005009993 #10	ENSSVLG00005010167 #11	ENSSVLG00005010225 #10	ENSSVLG00005010302 #11	SPI1 (ENSSVLG00005010597) #12	MYBPC3 (ENSSVLG00005010729) #13	MADD (ENSSVLG00005011762) #14	ENSSVLG00005012055	NR1H3 (ENSSVLG00005012159) #15	ACP2 (ENSSVLG00005012397) #16	DDB2 (ENSSVLG00005012634) #17	PACSIN3 (ENSSVLG00005013010) #18	ARFGAP2 (ENSSVLG00005013354) #19	CSTPP1 (ENSSVLG00005013495) #20	LRP4 (ENSSVLG00005013702) #21	CKAP5 (ENSSVLG00005013939) #22	F2 (ENSSVLG00005014116) #23	ARHGAP1 (ENSSVLG00005014685) #24	ENSSVLG00005014869 #25	HARBI1 (ENSSVLG00005015510) #26	AMBRA1 (ENSSVLG00005015569) #27	CHRM4 (ENSSVLG00005015740) #28	MDK (ENSSVLG00005015782) #29	DGKZ (ENSSVLG00005015887) #30	ENSSVLG00005015926	CREB3L1 (ENSSVLG00005015955) #32	PHF21A (ENSSVLG00005016012) #33	LARGE2 (ENSSVLG00005016132) #34	PEX16 (ENSSVLG00005016392) #35	FREY1 (ENSSVLG00005016461)	MAPK8IP1 (ENSSVLG00005016511) #36