Rodentia_A	ANCESTRAL SPECIES	14	ENSGT00940000153311.a.b.b #10	ENSGT00390000001660 #11	ENSGT00390000005318.b.b.a.g ##12	ENSGT00520000055567.a.b #13	ENSGT00550000074694.b #14	ENSGT00940000158824 #15	ENSGT00940000162581	ENSGT00590000083139 #16	ENSGT00390000009688 #17	ENSGT00940000160140.b	ENSGT00390000013092 #18	ENSGT00950000182945.b.a.a.b.b.b	ENSGT00940000162520.d #19	ENSGT00940000157575 #20	ENSGT00900000143081 #21	ENSGT00940000161171 #22	ENSGT00940000153446.b #23	ENSGT00940000157581 #24	ENSGT00940000155745 #25	ENSGT00390000011905 #26	ENSGT00940000158993 #27	ENSGT00390000017767.b.a #28	ENSGT00940000160181 #29	ENSGT00940000155979 #30	ENSGT00530000063712.a.b #31	ENSGT00940000159266 #32	ENSGT00550000074816.A.a #33	ENSGT00940000156513 #34	ENSGT00470000042500	ENSGT00390000015159.a.b	ENSGT00940000158432.cb
Hystricomorpha	ANCESTRAL SPECIES	8	ENSGT00390000005908 #9	ENSGT00940000153311.a.b.b #10	ENSGT00390000001660 #11	ENSGT00390000005318.b.b.a.h.a #12	ENSGT00520000055567.a.b #13	ENSGT00550000074694.b #14	ENSGT00940000158824 #15	ENSGT00590000083139 #16	ENSGT00390000009688 #17	ENSGT00940000160140.b	ENSGT00390000013092 #18	ENSGT00950000182945.b.a.a.b.b.b	ENSGT00940000162520.d #19	ENSGT00940000157575 #20	ENSGT00900000143081 #21	ENSGT00940000161171 #22	ENSGT00940000153446.b #23	ENSGT00940000157581 #24	ENSGT00940000155745 #25	ENSGT00390000011905 #26	ENSGT00940000158993 #27	ENSGT00390000017767.b.a #28	ENSGT00940000160181 #29	ENSGT00940000155979 #30	ENSGT00530000063712.a.b #31	ENSGT00940000159266 #32	ENSGT00550000074816.A.a #33	ENSGT00940000156513 #34
Hystricomorpha_a	ANCESTRAL SPECIES	31	ENSGT00390000005908 #9	ENSGT00940000153311.a.b.b #10	ENSGT00390000001660 #11	ENSGT00390000005318.b.b.a.g ##12	ENSGT00520000055567.a.b #13	ENSGT00550000074694.b #14	ENSGT00940000158824 #15	ENSGT00590000083139 #16	ENSGT00390000009688 #17	ENSGT00940000160140.b	ENSGT00390000013092 #18	ENSGT00950000182945.b.a.a.b.b.b	ENSGT00940000162520.d #19	ENSGT00940000157575 #20	ENSGT00900000143081 #21	ENSGT00940000161171 #22	ENSGT00940000153446.b #23	ENSGT00940000157581 #24	ENSGT00940000155745 #25	ENSGT00390000011905 #26	ENSGT00940000158993 #27	ENSGT00390000017767.b.a #28	ENSGT00940000160181 #29	ENSGT00940000155979 #30	ENSGT00530000063712.a.b #31	ENSGT00940000159266 #32	ENSGT00550000074816.A.a #33	ENSGT00940000156513 #34
Guinea pig	MODERN SPECIES	18	FAM228B (ENSCPOG00000030306) #7	PFN4 (ENSCPOG00000009683) #8	SF3B6 (ENSCPOG00000008016) #9	FKBP1B (ENSCPOG00000039379) #10	WDCP (ENSCPOG00000019263) #11	MFSD2B (ENSCPOG00000022662) #12	UBXN2A (ENSCPOG00000038294) #13	ATAD2B (ENSCPOG00000014176) #14	KLHL29 (ENSCPOG00000014174) #15	APOB (ENSCPOG00000004931) #16	LDAH (ENSCPOG00000012586) #17	HS1BP3 (ENSCPOG00000000278) #18	ENSCPOG00000037907 #19	PUM2 (ENSCPOG00000031996) #20	ENSCPOG00000007075 #21	SDC1 (ENSCPOG00000008875) #22	LAPTM4A (ENSCPOG00000009690) #23	MATN3 (ENSCPOG00000004739) #24	WDR35 (ENSCPOG00000007053) #25	TTC32 (ENSCPOG00000033658) #26	OSR1 (ENSCPOG00000002025) #27	NT5C1B (ENSCPOG00000012761) #28	RDH14 (ENSCPOG00000022651) #29	KCNS3 (ENSCPOG00000009232) #30	MSGN1 (ENSCPOG00000003061) #31	GEN1 (ENSCPOG00000033894) #32	SMC6 (ENSCPOG00000014752) #33	VSNL1 (ENSCPOG00000030283) #34
Hystricomorpha_b	ANCESTRAL SPECIES	26	ENSGT00390000017067 #8	ENSGT00390000005908 #9	ENSGT00940000153311.a.b.b #10	ENSGT00390000001660 #11	ENSGT00390000005318.b.b.a.g ##12	ENSGT00520000055567.a.b #13	ENSGT00550000074694.b #14	ENSGT00940000158824 #15	ENSGT00590000083139 #16	ENSGT00390000009688 #17	ENSGT00940000160140.b	ENSGT00390000013092 #18	ENSGT00950000182945.b.a.a.b.b.b	ENSGT00940000162520.d #19	ENSGT00940000157575 #20	ENSGT00940000161171 #22	ENSGT00940000153446.b #23	ENSGT00940000157581 #24	ENSGT00940000155745 #25	ENSGT00390000011905 #26	ENSGT00940000158993 #27	ENSGT00390000017767.b.a #28	ENSGT00940000160181 #29	ENSGT00940000155979 #30	ENSGT00530000063712.a.b #31	ENSGT00940000159266 #32	ENSGT00550000074816.A.a #33	ENSGT00940000156513 #34
Long-tailed chinchilla	MODERN SPECIES	176	FAM228B (ENSCLAG00000004984) #7	PFN4 (ENSCLAG00000004618) #8	SF3B6 (ENSCLAG00000014512) #9	FKBP1B (ENSCLAG00000011181) #10	WDCP (ENSCLAG00000008275) #11	MFSD2B (ENSCLAG00000014189) ##12	UBXN2A (ENSCLAG00000014610) #13	ATAD2B (ENSCLAG00000005215) #14	KLHL29 (ENSCLAG00000005598) #15	APOB (ENSCLAG00000008056) #16	LDAH (ENSCLAG00000011308) #17	HS1BP3 (ENSCLAG00000008832) #18	RHOB (ENSCLAG00000017801)	ENSCLAG00000005814 #19	PUM2 (ENSCLAG00000006048) #20	SDC1 (ENSCLAG00000007345) #22	LAPTM4A (ENSCLAG00000006983) #23	MATN3 (ENSCLAG00000006019) #24	WDR35 (ENSCLAG00000007929) #25	TTC32 (ENSCLAG00000009839) #26	OSR1 (ENSCLAG00000009423) #27	NT5C1B (ENSCLAG00000008659) #28	RDH14 (ENSCLAG00000009341) #29	KCNS3 (ENSCLAG00000013937) #30	MSGN1 (ENSCLAG00000015119) #31	GEN1 (ENSCLAG00000008865) #32	SMC6 (ENSCLAG00000012919) #33	VSNL1 (ENSCLAG00000011222) #34	ENSCLAG00000013272
Degu	MODERN SPECIES	60	ENSODEG00000009834 #14	ENSODEG00000008786	KLHL29 (ENSODEG00000009928) #15	ENSODEG00000007428	ENSODEG00000019450	ENSODEG00000007994	ENSODEG00000019494	APOB (ENSODEG00000008337) #16	ENSODEG00000008523 #17	GDF7 (ENSODEG00000008847)	HS1BP3 (ENSODEG00000010003) #18	RHOB (ENSODEG00000019841)	ENSODEG00000010362 #19	PUM2 (ENSODEG00000007823) #20	ENSODEG00000008774	SDC1 (ENSODEG00000010758) #22	LAPTM4A (ENSODEG00000008579) #23	MATN3 (ENSODEG00000008451) #24	WDR35 (ENSODEG00000012693) #25	TTC32 (ENSODEG00000009280) #26	OSR1 (ENSODEG00000008728) #27	NT5C1B (ENSODEG00000008929) #28	RDH14 (ENSODEG00000008458) #29	KCNS3 (ENSODEG00000009066) #30	ENSODEG00000019755	MSGN1 (ENSODEG00000009615) #31	GEN1 (ENSODEG00000010156) #32	SMC6 (ENSODEG00000008987) #33	VSNL1 (ENSODEG00000008555) #34	ENSODEG00000008159	SLC10A4 (ENSODEG00000010331)
Sciuridae	ANCESTRAL SPECIES	16	ENSGT00940000153311.a.b.b #10	ENSGT00390000001660 #11	ENSGT00390000005318.b.b.a.g ##12	ENSGT00520000055567.a.b #13	ENSGT00550000074694.b #14	ENSGT00940000158824 #15	ENSGT00940000162581	ENSGT00590000083139 #16	ENSGT00390000009688 #17	ENSGT00940000160140.b	ENSGT00390000013092 #18	ENSGT00950000182945.b.a.a.b.b.b	ENSGT00940000162520.d #19	ENSGT00940000157575 #20	ENSGT00900000143081 #21	ENSGT00940000161171 #22	ENSGT00940000153446.b #23	ENSGT00940000157581 #24	ENSGT00940000155745 #25	ENSGT00390000011905 #26	ENSGT00940000158993 #27	ENSGT00390000017767.b.a #28	ENSGT00940000160181 #29	ENSGT00940000155979 #30	ENSGT00530000063712.a.b #31	ENSGT00940000159266 #32	ENSGT00550000074816.A.a #33	ENSGT00940000156513 #34	ENSGT00470000042500	ENSGT00390000015159.a.b	ENSGT00940000158432.cb
Marmotini	ANCESTRAL SPECIES	14	ENSGT00940000153311.a.b.b #10	ENSGT00390000001660 #11	ENSGT00390000005318.b.b.a.g ##12	ENSGT00520000055567.a.b #13	ENSGT00550000074694.b #14	ENSGT00940000158824 #15	ENSGT00940000162581	ENSGT00590000083139 #16	ENSGT00390000009688 #17	ENSGT00940000160140.b	ENSGT00390000013092 #18	ENSGT00950000182945.b.a.a.b.b.b	ENSGT00940000162520.d #19	ENSGT00940000157575 #20	ENSGT00900000143081 #21	ENSGT00940000161171 #22	ENSGT00940000153446.b #23	ENSGT00940000157581 #24	ENSGT00940000155745 #25	ENSGT00390000011905 #26	ENSGT00940000158993 #27	ENSGT00390000017767.b.a.u.a #28	ENSGT00940000160181 #29	ENSGT00940000155979 #30	ENSGT00530000063712.a.b #31	ENSGT00940000159266 #32	ENSGT00550000074816.A.a #33	ENSGT00940000156513 #34	ENSGT00470000042500	ENSGT00390000015159.a.b	ENSGT00940000158432.cb
Marmotini_b	ANCESTRAL SPECIES	17	ENSGT00940000153311.a.b.b #10	ENSGT00390000001660 #11	ENSGT00390000005318.b.b.a.g ##12	ENSGT00520000055567.a.b #13	ENSGT00550000074694.b #14	ENSGT00940000158824 #15	ENSGT00940000162581	ENSGT00590000083139 #16	ENSGT00390000009688 #17	ENSGT00940000160140.b	ENSGT00390000013092 #18	ENSGT00950000182945.b.a.a.b.b.b	ENSGT00940000162520.d #19	ENSGT00940000157575 #20	ENSGT00900000143081 #21	ENSGT00940000161171 #22	ENSGT00940000153446.b #23	ENSGT00940000157581 #24	ENSGT00940000155745 #25	ENSGT00390000011905 #26	ENSGT00940000158993 #27	ENSGT00390000017767.b.a.u.a #28	ENSGT00940000160181 #29	ENSGT00940000155979 #30	ENSGT00530000063712.a.b #31	ENSGT00940000159266 #32	ENSGT00550000074816.A.a #33	ENSGT00940000156513 #34	ENSGT00470000042500	ENSGT00390000015159.a.b	ENSGT00940000158432.cb
Squirrel	MODERN SPECIES	93	WDCP (ENSSTOG00000032257) #11	MFSD2B (ENSSTOG00000003123) ##12	UBXN2A (ENSSTOG00000030412) #13	ATAD2B (ENSSTOG00000021066) #14	KLHL29 (ENSSTOG00000008403) #15	ENSSTOG00000033132 #23	TDRD15 (ENSSTOG00000027567)	APOB (ENSSTOG00000027598) #16	LDAH (ENSSTOG00000026882) #17	GDF7 (ENSSTOG00000027110)	HS1BP3 (ENSSTOG00000004973) #18	ENSSTOG00000014644	ENSSTOG00000023326 #19	PUM2 (ENSSTOG00000006262) #20	ENSSTOG00000033291	SDC1 (ENSSTOG00000028519) #22	ENSSTOG00000007214 #23	MATN3 (ENSSTOG00000019530) #24	WDR35 (ENSSTOG00000007151) #25	TTC32 (ENSSTOG00000007140) #26	OSR1 (ENSSTOG00000015454) #27	NT5C1B (ENSSTOG00000014834) #28	RDH14 (ENSSTOG00000021114) #29	KCNS3 (ENSSTOG00000012420) #30	MSGN1 (ENSSTOG00000013981) #31	GEN1 (ENSSTOG00000013963) #32	SMC6 (ENSSTOG00000013946) #33	VSNL1 (ENSSTOG00000010438) #34	ENSSTOG00000025212	CYRIA (ENSSTOG00000022187)	MYCN (ENSSTOG00000012252)
Arctic ground squirrel	MODERN SPECIES		UBXN2A (ENSUPAG00010008734) #13	ATAD2B (ENSUPAG00010008759) #14	KLHL29 (ENSUPAG00010008812) #15	ENSUPAG00010008883	TDRD15 (ENSUPAG00010008953)	APOB (ENSUPAG00010008961) #16	LDAH (ENSUPAG00010009007) #17	ENSUPAG00010009042	ENSUPAG00010009055	HS1BP3 (ENSUPAG00010009063) #18	RHOB (ENSUPAG00010009084)	ENSUPAG00010009092 #19	PUM2 (ENSUPAG00010009123) #20	ENSUPAG00010009301 #21	ENSUPAG00010009303	SDC1 (ENSUPAG00010009310) #22	LAPTM4A (ENSUPAG00010009333) #23	MATN3 (ENSUPAG00010009339) #24	WDR35 (ENSUPAG00010009354) #25	TTC32 (ENSUPAG00010009436) #26	OSR1 (ENSUPAG00010009451) #27	ENSUPAG00010009474 #28	RDH14 (ENSUPAG00010009546) #29	MSGN1 (ENSUPAG00010009556) #31	GEN1 (ENSUPAG00010009557) #32	SMC6 (ENSUPAG00010009564) #33	VSNL1 (ENSUPAG00010009655) #34	RAD51AP2 (ENSUPAG00010009663)	CYRIA (ENSUPAG00010009668)	MYCN (ENSUPAG00010009702)	ENSUPAG00010009708
Alpin marmot	MODERN SPECIES	6	FKBP1B (ENSMMMG00000021830) #10	WDCP (ENSMMMG00000021855) #11	MFSD2B (ENSMMMG00000021873) ##12	ENSMMMG00000021893	ATAD2B (ENSMMMG00000021898) #14	KLHL29 (ENSMMMG00000022005) #15	TDRD15 (ENSMMMG00000022048)	ENSMMMG00000022049 #16	ENSMMMG00000022059 #16	LDAH (ENSMMMG00000022060) #17	HS1BP3 (ENSMMMG00000022083) #18	RHOB (ENSMMMG00000022086)	ENSMMMG00000022089 #19	PUM2 (ENSMMMG00000022116) #20	ENSMMMG00000022129 #21	SDC1 (ENSMMMG00000022131) #22	LAPTM4A (ENSMMMG00000022160) #23	MATN3 (ENSMMMG00000022186) #24	WDR35 (ENSMMMG00000022195) #25	TTC32 (ENSMMMG00000022212) #26	OSR1 (ENSMMMG00000022239) #27	ENSMMMG00000022251 #28	RDH14 (ENSMMMG00000022280) #29	KCNS3 (ENSMMMG00000022292) #30	MSGN1 (ENSMMMG00000022303) #31	GEN1 (ENSMMMG00000022304) #32	SMC6 (ENSMMMG00000022309) #33	VSNL1 (ENSMMMG00000022330) #34	RAD51AP2 (ENSMMMG00000022347)	CYRIA (ENSMMMG00000022371)	ENSMMMG00000022385
Eurasian red squirrel	MODERN SPECIES	5	ENSSVLG00005023387 #9	FKBP1B (ENSSVLG00005023436) #10	WDCP (ENSSVLG00005023512) #11	MFSD2B (ENSSVLG00005023554) ##12	ENSSVLG00005023695 #13	ATAD2B (ENSSVLG00005023756) #14	KLHL29 (ENSSVLG00005023916) #15	TDRD15 (ENSSVLG00005023954)	APOB (ENSSVLG00005023994) #16	LDAH (ENSSVLG00005024216) #17	GDF7 (ENSSVLG00005024288)	HS1BP3 (ENSSVLG00005024304) #18	RHOB (ENSSVLG00005024328)	ENSSVLG00005024370 #19	ENSSVLG00005024506 #20	SDC1 (ENSSVLG00005024647) #22	LAPTM4A (ENSSVLG00005024670) #23	MATN3 (ENSSVLG00005024711) #24	WDR35 (ENSSVLG00005024826) #25	TTC32 (ENSSVLG00005024889) #26	OSR1 (ENSSVLG00005024914) #27	NT5C1B (ENSSVLG00005025002) #28	RDH14 (ENSSVLG00005025062) #29	ENSSVLG00005025079	KCNS3 (ENSSVLG00005025089) #30	MSGN1 (ENSSVLG00005025107) #31	GEN1 (ENSSVLG00005025123) #32	SMC6 (ENSSVLG00005025164) #33	VSNL1 (ENSSVLG00005025182) #34	RAD51AP2 (ENSSVLG00005025196)	ENSSVLG00005025209