Rodentia_A	ANCESTRAL SPECIES	7	ENSGT00390000003426	ENSGT00940000160017	ENSGT00390000000537	ENSGT00940000153451.a.a.b	ENSGT00940000158129	ENSGT00950000182938.a	ENSGT00940000158761	ENSGT01030000234641.b.a.b.a.b	ENSGT00940000155857	ENSGT00940000159824 #15	ENSGT00390000000483.a.a #16	ENSGT00640000091672	ENSGT00940000154998.a.a #17	ENSGT00940000154979 #18	ENSGT00390000005989.a #21	ENSGT00940000158996 #22	ENSGT00390000014412 #23	ENSGT00390000007125.b #24	ENSGT00940000156866 #25	ENSGT00390000014165.c.b	ENSGT00530000063113.C #26	ENSGT00940000159044 #27	ENSGT00940000157079.a #28	ENSGT00940000158396 #30	ENSGT00940000156641 #31	ENSGT00390000007501 #32	ENSGT00940000156818 #33	ENSGT00940000155898 #34	ENSGT00390000017300 #35	ENSGT00940000159553	ENSGT00940000153052.c.b.b.b
Hystricomorpha	ANCESTRAL SPECIES	30	ENSGT00910000144291	ENSGT00390000003426	ENSGT00940000160017	ENSGT00390000000537	ENSGT00940000153451.a.a.b.e	ENSGT00940000158129	ENSGT00950000182938.a	ENSGT00940000158761	ENSGT01030000234641.b.a.b.a.b	ENSGT00940000155857	ENSGT00940000159824 #15	ENSGT00390000000483.a.a #16	ENSGT00940000154998.a.a #17	ENSGT00940000154979 #18	ENSGT00390000005989.a #21	ENSGT00940000158996 #22	ENSGT00390000014412 #23	ENSGT00390000007125.b #24	ENSGT00940000156866 #25	ENSGT00390000014165.c.b	ENSGT00530000063113.C #26	ENSGT00940000159044 #27	ENSGT00940000157079.a #28	ENSGT00940000158396 #30	ENSGT00940000156641 #31	ENSGT00390000007501 #32	ENSGT00940000156818 #33	ENSGT00940000155898 #34	ENSGT00390000017300 #35	ENSGT00940000159553	ENSGT00940000153052.c.b.a.b
Hystricomorpha_a	ANCESTRAL SPECIES	28	ENSGT00910000144291	ENSGT00390000003426	ENSGT00940000160017	ENSGT00390000000537	ENSGT00940000153451.a.a.b.e	ENSGT00940000158129	ENSGT00950000182938.a	ENSGT00940000158761	ENSGT01030000234641.b.a.b.a.b	ENSGT00940000155857	ENSGT00940000159824 #15	ENSGT00390000000483.a.a #16	ENSGT00940000154998.a.a #17	ENSGT00940000154979 #18	ENSGT00390000005989.a #21	ENSGT00940000158996 #22	ENSGT00390000014412 #23	ENSGT00390000007125.b #24	ENSGT00940000156866 #25	ENSGT00390000014165.c.b	ENSGT00530000063113.C #26	ENSGT00940000159044 #27	ENSGT00940000157079.a #28	ENSGT00940000158396 #30	ENSGT00940000156641 #31	ENSGT00390000007501 #32	ENSGT00940000156818 #33	ENSGT00940000155898 #34	ENSGT00390000017300 #35	ENSGT00940000159553	ENSGT00940000153052.c.b.a.b
Hystricomorpha_b	ANCESTRAL SPECIES	19	ENSGT00910000144291	ENSGT00390000003426	ENSGT00940000160017	ENSGT00390000000537	ENSGT00940000153451.a.a.b.e	ENSGT00940000158129	ENSGT00950000182938.a	ENSGT00940000158761	ENSGT01030000234641.b.a.b.a.b	ENSGT00940000155857	ENSGT00940000159824 #15	ENSGT00390000000483.a.a #16	ENSGT00940000154998.a.a #17	ENSGT00940000154979 #18	ENSGT00390000005989.a #21	ENSGT00940000158996 #22	ENSGT00390000014412 #23	ENSGT00390000007125.b #24	ENSGT00940000156866 #25	ENSGT00390000014165.c.b	ENSGT00530000063113.C #26	ENSGT00940000159044 #27	ENSGT00940000157079.a #28	ENSGT00940000158396 #30	ENSGT00940000156641 #31	ENSGT00390000007501 #32	ENSGT00940000156818 #33	ENSGT00940000155898 #34	ENSGT00390000017300 #35	ENSGT00940000159553	ENSGT00940000153052.c.b.a.b
Degu	MODERN SPECIES	253									MSX2 (ENSODEG00000001847) #15	NSG2 (ENSODEG00000001862) #16	CPEB4 (ENSODEG00000001934) #17	ENSODEG00000001973 #18	ENSODEG00000002042 #19	ENSODEG00000018739 #20	STC2 (ENSODEG00000002102) #21	NKX2-5 (ENSODEG00000002184) #22	BNIP1 (ENSODEG00000002196) #23	CREBRF (ENSODEG00000002364) #24	ATP6V0E1 (ENSODEG00000001083) #25	ERGIC1 (ENSODEG00000001101) #26	DUSP1 (ENSODEG00000001126) #27	NEURL1B (ENSODEG00000001134) #28	ENSODEG00000001166 #29	SH3PXD2B (ENSODEG00000001294) #30	UBTD2 (ENSODEG00000001390) #31	EFCAB9 (ENSODEG00000001416) #32	STK10 (ENSODEG00000001477) #33	FBXW11 (ENSODEG00000001754) #34	SMIM23 (ENSODEG00000001818) #35
Long-tailed chinchilla	MODERN SPECIES	115	ARL10 (ENSCLAG00000015048)	KIAA1191 (ENSCLAG00000013315)	ENSCLAG00000013733	ENSCLAG00000014990	THOC3 (ENSCLAG00000015924)	CPLX2 (ENSCLAG00000013505)	HRH2 (ENSCLAG00000015189)	SFXN1 (ENSCLAG00000016110)	DRD1 (ENSCLAG00000014757)	MSX2 (ENSCLAG00000014001) #15	NSG2 (ENSCLAG00000014316) #16	CPEB4 (ENSCLAG00000013156) #17	ENSCLAG00000016125 #18	ENSCLAG00000014408	STC2 (ENSCLAG00000013045) #21	NKX2-5 (ENSCLAG00000013992) #22	BNIP1 (ENSCLAG00000015919) #23	CREBRF (ENSCLAG00000014588) #24	ATP6V0E1 (ENSCLAG00000014664) #25	RPL26L1 (ENSCLAG00000014524)	ERGIC1 (ENSCLAG00000014304) #26	DUSP1 (ENSCLAG00000013473) #27	NEURL1B (ENSCLAG00000014210) #28	SH3PXD2B (ENSCLAG00000015389) #30	UBTD2 (ENSCLAG00000015134) #31	EFCAB9 (ENSCLAG00000013040) #32	STK10 (ENSCLAG00000015147) #33	FBXW11 (ENSCLAG00000013691) #34	SMIM23 (ENSCLAG00000012177) #35	FGF18 (ENSCLAG00000013051)	ENSCLAG00000014392
Guinea pig	MODERN SPECIES	17	ENSCPOG00000034924	NOP16 (ENSCPOG00000026072)	ARL10 (ENSCPOG00000001642)	KIAA1191 (ENSCPOG00000039242)	ENSCPOG00000023337	THOC3 (ENSCPOG00000025805)	CPLX2 (ENSCPOG00000033149)	HRH2 (ENSCPOG00000003473)	SFXN1 (ENSCPOG00000010321)	DRD1 (ENSCPOG00000039492)	MSX2 (ENSCPOG00000038944) #15	NSG2 (ENSCPOG00000037038) #16	CPEB4 (ENSCPOG00000015530) #17	ENSCPOG00000026033 #18	STC2 (ENSCPOG00000034039) #21	NKX2-5 (ENSCPOG00000026347) #22	BNIP1 (ENSCPOG00000006752) #23	CREBRF (ENSCPOG00000014384) #24	ATP6V0E1 (ENSCPOG00000040227) #25	RPL26L1 (ENSCPOG00000012188)	ERGIC1 (ENSCPOG00000012183) #26	DUSP1 (ENSCPOG00000013344) #27	NEURL1B (ENSCPOG00000040777) #28	SH3PXD2B (ENSCPOG00000039072) #30	UBTD2 (ENSCPOG00000034425) #31	EFCAB9 (ENSCPOG00000026758) #32	STK10 (ENSCPOG00000006502) #33	FBXW11 (ENSCPOG00000009582) #34	SMIM23 (ENSCPOG00000006672) #35	FGF18 (ENSCPOG00000006088)	TLX3 (ENSCPOG00000024190)
Naked mole-rat female	MODERN SPECIES	23	THOC3 (ENSHGLG00000008773)	CPLX2 (ENSHGLG00000033963)	HRH2 (ENSHGLG00000018733)	SFXN1 (ENSHGLG00000045847)	DRD1 (ENSHGLG00000016781)	ENSHGLG00000036934	ENSHGLG00000049074	MSX2 (ENSHGLG00000017569) #15	NSG2 (ENSHGLG00000006062) #16	ENSHGLG00000041184	ENSHGLG00000049916	C5orf47 (ENSHGLG00000040572)	CPEB4 (ENSHGLG00000008897) #17	ENSHGLG00000041881 #18	STC2 (ENSHGLG00000017592) #21	NKX2-5 (ENSHGLG00000017269) #22	BNIP1 (ENSHGLG00000018031) #23	ENSHGLG00000017817 #24	ENSHGLG00000021190	ENSHGLG00000018219 #25	ENSHGLG00000017100	ERGIC1 (ENSHGLG00000050911) #26	DUSP1 (ENSHGLG00000012633) #27	NEURL1B (ENSHGLG00000039883) #28	SH3PXD2B (ENSHGLG00000009542) #30	UBTD2 (ENSHGLG00000044520) #31	EFCAB9 (ENSHGLG00000006358) #32	STK10 (ENSHGLG00000007426) #33	ENSHGLG00000048340	FBXW11 (ENSHGLG00000010874) #34	ENSHGLG00000032517
Sciuridae	ANCESTRAL SPECIES	33	ENSGT01090000260018.C.a	ENSGT00940000162246	ENSGT00570000079564	ENSGT00390000018500.a	ENSGT01100000263521.a.a.b.a.b.b	ENSGT00940000161175	ENSGT00940000158761	ENSGT01030000234641.b.a.b.a.b	ENSGT00940000155857	ENSGT00940000159824 #15	ENSGT00390000000483.a.a #16	ENSGT00640000091672	ENSGT00940000154998.a.a #17	ENSGT00940000154979 #18	ENSGT00390000005989.a #21	ENSGT00940000158996 #22	ENSGT00390000014412 #23	ENSGT00390000007125.b #24	ENSGT00940000156866 #25	ENSGT00390000014165.c.b	ENSGT00530000063113.C #26	ENSGT00940000159044 #27	ENSGT00940000157079.a #28	ENSGT00940000158396 #30	ENSGT00940000156641 #31	ENSGT00390000007501 #32	ENSGT00940000156818 #33	ENSGT00940000155898 #34	ENSGT00390000017300 #35	ENSGT00940000159553	ENSGT00940000153052.c.b.b.b.b.a
Marmotini	ANCESTRAL SPECIES	38	ENSGT01090000260045.C.e.a.b	ENSGT00940000162246	ENSGT01090000259995.b.b.b	ENSGT00390000018500.a	ENSGT01100000263521.a.a.b.a.b.b	ENSGT00940000161175	ENSGT00940000158761	ENSGT01030000234641.b.a.b.a.b	ENSGT00940000155857	ENSGT00940000159824 #15	ENSGT00390000000483.a.a #16	ENSGT00640000091672	ENSGT00940000154998.a.a #17	ENSGT00940000154979 #18	ENSGT00390000005989.a #21	ENSGT00940000158996 #22	ENSGT00390000014412 #23	ENSGT00390000007125.b #24	ENSGT00940000156866 #25	ENSGT00390000014165.c.b	ENSGT00530000063113.C #26	ENSGT00940000159044 #27	ENSGT00940000157079.a #28	ENSGT00940000158396 #30	ENSGT00940000156641 #31	ENSGT00390000007501 #32	ENSGT00940000156818 #33	ENSGT00940000155898 #34	ENSGT00390000017300 #35	ENSGT00940000159553	ENSGT00940000153052.c.b.b.b.b.a
Marmotini_b	ANCESTRAL SPECIES	127		ENSGT01090000259995.a.a.a	ENSGT00390000010671	ENSGT00390000018500.a	ENSGT01100000263521.a.a.b.a.b.b	ENSGT00940000161175	ENSGT00940000158761	ENSGT01030000234641.b.a.b.a.b	ENSGT00940000155857	ENSGT00940000159824 #15	ENSGT00390000000483.a.a #16	ENSGT00640000091672	ENSGT00940000154998.a.a #17	ENSGT00940000154979 #18	ENSGT00390000005989.a #21	ENSGT00940000158996 #22	ENSGT00390000014412 #23	ENSGT00390000007125.b #24	ENSGT00940000156866 #25	ENSGT00390000014165.c.b	ENSGT00530000063113.C #26	ENSGT00940000159044 #27	ENSGT00940000157079.a #28	ENSGT00940000158396 #30	ENSGT00940000156641 #31	ENSGT00390000007501 #32	ENSGT00940000156818 #33	ENSGT00940000155898 #34	ENSGT00390000017300 #35	ENSGT00940000159553	ENSGT00940000153052.c.b.b.b.b.a
Squirrel	MODERN SPECIES	209	ENSSTOG00000025133	ENSSTOG00000027395	ENSSTOG00000034328	ENSSTOG00000026307	SH3BP5L (ENSSTOG00000022558)	ENSSTOG00000027630	ZNF692 (ENSSTOG00000023210)	HRH2 (ENSSTOG00000007422)	SFXN1 (ENSSTOG00000028251)	DRD1 (ENSSTOG00000029229)	MSX2 (ENSSTOG00000000399) #15	NSG2 (ENSSTOG00000011148) #16	CPEB4 (ENSSTOG00000020645) #17	ENSSTOG00000030887 #18	STC2 (ENSSTOG00000004413) #21	NKX2-5 (ENSSTOG00000004407) #22	BNIP1 (ENSSTOG00000004393) #23	CREBRF (ENSSTOG00000004368) #24	ATP6V0E1 (ENSSTOG00000025255) #25	RPL26L1 (ENSSTOG00000026876)	ERGIC1 (ENSSTOG00000025246) #26	DUSP1 (ENSSTOG00000023698) #27	NEURL1B (ENSSTOG00000025420) #28	SH3PXD2B (ENSSTOG00000028124) #30	UBTD2 (ENSSTOG00000014298) #31	EFCAB9 (ENSSTOG00000020218) #32	STK10 (ENSSTOG00000026208) #33	FBXW11 (ENSSTOG00000023506) #34	SMIM23 (ENSSTOG00000024706) #35	FGF18 (ENSSTOG00000023666)	ENSSTOG00000014732
Arctic ground squirrel	MODERN SPECIES	242															STC2 (ENSUPAG00010022254) #21	NKX2-5 (ENSUPAG00010022252) #22	BNIP1 (ENSUPAG00010022250) #23	CREBRF (ENSUPAG00010022247) #24	ATP6V0E1 (ENSUPAG00010022244) #25	RPL26L1 (ENSUPAG00010022239)	ERGIC1 (ENSUPAG00010022238) #26	NEURL1B (ENSUPAG00010022219) #28	SH3PXD2B (ENSUPAG00010022216) #30	UBTD2 (ENSUPAG00010022213) #31	EFCAB9 (ENSUPAG00010022210) #32	STK10 (ENSUPAG00010022207) #33	ENSUPAG00010022184 #34	SMIM23 (ENSUPAG00010022182) #35	FGF18 (ENSUPAG00010022179)	NPM1 (ENSUPAG00010022177)	TLX3 (ENSUPAG00010022175)
Alpin marmot	MODERN SPECIES	31	ENSMMMG00000009757	ENSMMMG00000009765	ENSMMMG00000009785	OR2AJ1 (ENSMMMG00000009826)	SH3BP5L (ENSMMMG00000009857)	ENSMMMG00000009866	ZNF692 (ENSMMMG00000009869)	HRH2 (ENSMMMG00000009886)	SFXN1 (ENSMMMG00000009889)	DRD1 (ENSMMMG00000009915)	MSX2 (ENSMMMG00000009968) #15	NSG2 (ENSMMMG00000009989) #16	CPEB4 (ENSMMMG00000010044) #17	ENSMMMG00000010091 #18	STC2 (ENSMMMG00000010105) #21	NKX2-5 (ENSMMMG00000010122) #22	BNIP1 (ENSMMMG00000010131) #23	CREBRF (ENSMMMG00000010165) #24	RPL26L1 (ENSMMMG00000010196)	ERGIC1 (ENSMMMG00000010202) #26	ENSMMMG00000010217 #27	NEURL1B (ENSMMMG00000010222) #28	SH3PXD2B (ENSMMMG00000010235) #30	UBTD2 (ENSMMMG00000010264) #31	ENSMMMG00000010272 #32	STK10 (ENSMMMG00000010286) #33	FBXW11 (ENSMMMG00000010309) #34	SMIM23 (ENSMMMG00000010399) #35	ENSMMMG00000010418	ENSMMMG00000010435	TLX3 (ENSMMMG00000010459)
Eurasian red squirrel	MODERN SPECIES	15	ENSSVLG00005011447	ENSSVLG00005011500	LYPD8 (ENSSVLG00005011575)	SH3BP5L (ENSSVLG00005011666)	ZNF672 (ENSSVLG00005011715)	ZNF692 (ENSSVLG00005011774)	HRH2 (ENSSVLG00005011848)	ENSSVLG00005011926	DRD1 (ENSSVLG00005012085)	MSX2 (ENSSVLG00005012101) #15	NSG2 (ENSSVLG00005012146) #16	C5orf47 (ENSSVLG00005012218)	CPEB4 (ENSSVLG00005012332) #17	ENSSVLG00005012611 #18	STC2 (ENSSVLG00005012797) #21	NKX2-5 (ENSSVLG00005012867) #22	BNIP1 (ENSSVLG00005012932) #23	CREBRF (ENSSVLG00005013005) #24	ATP6V0E1 (ENSSVLG00005013162) #25	RPL26L1 (ENSSVLG00005013228)	ERGIC1 (ENSSVLG00005013430) #26	DUSP1 (ENSSVLG00005013587) #27	NEURL1B (ENSSVLG00005013785) #28	SH3PXD2B (ENSSVLG00005013894) #30	UBTD2 (ENSSVLG00005013934) #31	EFCAB9 (ENSSVLG00005013993) #32	STK10 (ENSSVLG00005014068) #33	FBXW11 (ENSSVLG00005014207) #34	FGF18 (ENSSVLG00005014519)	ENSSVLG00005014590	TLX3 (ENSSVLG00005014955)