Rodentia_A	ANCESTRAL SPECIES	8	ENSGT00940000162484	ENSGT00940000160997 #7	ENSGT00940000154993.k.b #8	ENSGT00940000155371 #9	ENSGT00940000154993.k.a #10	ENSGT00940000161821 #11	ENSGT00940000154723.b #12	ENSGT00940000162353 #15	ENSGT00860000136204	ENSGT00940000160499 #16	ENSGT00940000157293 #17	ENSGT00940000159023 #18	ENSGT00940000159897 #19	ENSGT00940000160381 #20	ENSGT00940000161157 #21	ENSGT00940000153385.b.a.b #22	ENSGT00940000162112 #23	ENSGT00940000162498 #24	ENSGT00940000162390 #25	ENSGT00940000159762 #26	ENSGT00940000159208.B #27	ENSGT00940000160076 #28	ENSGT00940000160668 #29	ENSGT00940000161022 #30	ENSGT00390000008815 #32	ENSGT00390000012691.d ##33	ENSGT00390000012691.c.b.p #33	ENSGT00940000161798 #34	ENSGT00390000007075 #35	ENSGT00390000010512 #36	ENSGT00940000161403 #37
Sciuridae	ANCESTRAL SPECIES	1	ENSGT00940000162484	ENSGT00940000160997 #7	ENSGT00940000154993.k.b #8	ENSGT00940000155371 #9	ENSGT00940000154993.k.a #10	ENSGT00940000161821 #11	ENSGT00940000154723.b #12	ENSGT00940000162353 #15	ENSGT00860000136204	ENSGT00940000160499 #16	ENSGT00940000157293 #17	ENSGT00940000159023 #18	ENSGT00940000159897 #19	ENSGT00940000160381 #20	ENSGT00940000161157 #21	ENSGT00940000153385.b.a.b #22	ENSGT00940000162112 #23	ENSGT00940000162498 #24	ENSGT00940000162390 #25	ENSGT00940000159762 #26	ENSGT00940000159208.B #27	ENSGT00940000160076 #28	ENSGT00940000160668 #29	ENSGT00940000161022 #30	ENSGT00390000008815 #32	ENSGT00390000012691.d ##33	ENSGT00940000161798 #34	ENSGT00390000007075 #35	ENSGT00390000010512 #36	ENSGT00940000161403 #37	ENSGT00940000159200
Eurasian red squirrel	MODERN SPECIES	16	HLA-DRA (ENSSVLG00005007588) #7	ENSSVLG00005007546 #8	ENSSVLG00005007511 #9	ENSSVLG00005007482 #10	ENSSVLG00005007455 #11	HLA-DQB2 (ENSSVLG00005007368) #12	ENSSVLG00005007173 #13	ENSSVLG00005006864 #14	HLA-DOB (ENSSVLG00005006746) #15	TAP2 (ENSSVLG00005006696) #16	PSMB8 (ENSSVLG00005006647) #17	TAP1 (ENSSVLG00005006618) #18	PSMB9 (ENSSVLG00005006563) #19	HLA-DMB (ENSSVLG00005006515) #20	HLA-DMA (ENSSVLG00005006465) #21	BRD2 (ENSSVLG00005006374) #22	HLA-DOA (ENSSVLG00005006335) #23	HLA-DPA1 (ENSSVLG00005006304) #24	HLA-DPB1 (ENSSVLG00005006269) #25	COL11A2 (ENSSVLG00005005202) #26	RXRB (ENSSVLG00005004952) #27	SLC39A7 (ENSSVLG00005004925) #28	HSD17B8 (ENSSVLG00005004902) #29	RING1 (ENSSVLG00005004804) #30	ENSSVLG00005004778 #31	VPS52 (ENSSVLG00005004757) #32	RPS18 (ENSSVLG00005004721) #33	B3GALT4 (ENSSVLG00005004704) #34	WDR46 (ENSSVLG00005004694) #35	ENSSVLG00005004670 #36	RGL2 (ENSSVLG00005004647) #37
Marmotini	ANCESTRAL SPECIES	18	ENSGT00940000162484	ENSGT00940000160997 #7	ENSGT00940000154993.k.b #8	ENSGT00940000154993.k.a #10	ENSGT00940000161821.k #11	ENSGT00940000154723.b #12	ENSGT00940000161821.l.a #11	ENSGT00940000162353.i #15	ENSGT00860000136204	ENSGT00940000160499 #16	ENSGT00940000157293 #17	ENSGT00940000159023 #18	ENSGT00940000159897 #19	ENSGT00940000160381 #20	ENSGT00940000161157 #21	ENSGT00940000153385.b.a.b #22	ENSGT00940000162112 #23	ENSGT00940000162498 #24	ENSGT00940000162390 #25	ENSGT00940000159762 #26	ENSGT00940000159208.B #27	ENSGT00940000160076 #28	ENSGT00940000160668 #29	ENSGT00940000161022 #30	ENSGT00390000008815 #32	ENSGT00390000012691.d ##33	ENSGT00940000161798 #34	ENSGT00390000007075 #35	ENSGT00390000010512 #36	ENSGT00940000161403 #37	ENSGT00940000159200
Marmotini_b	ANCESTRAL SPECIES	8								ENSGT00940000162353.i #15	ENSGT00860000136204	ENSGT00940000160499 #16	ENSGT00940000157293 #17	ENSGT00940000159023 #18	ENSGT00940000159897 #19	ENSGT00940000160381 #20	ENSGT00940000161157 #21	ENSGT00940000153385.b.a.b #22	ENSGT00940000162112 #23	ENSGT00940000162498 #24	ENSGT00940000162390 #25	ENSGT00940000159762 #26	ENSGT00940000159208.B #27	ENSGT00940000160076 #28	ENSGT00940000160668 #29	ENSGT00940000161022 #30	ENSGT00390000008815 #32	ENSGT00390000012691.d ##33	ENSGT00940000161798 #34	ENSGT00390000007075 #35	ENSGT00390000010512 #36	ENSGT00940000161403 #37	ENSGT00940000159200
Arctic ground squirrel	MODERN SPECIES	25														HLA-DMB (ENSUPAG00010005014) #20	HLA-DMA (ENSUPAG00010005022) #21	BRD2 (ENSUPAG00010005033) #22	HLA-DOA (ENSUPAG00010005068) #23	HLA-DPB1 (ENSUPAG00010005123) #25	HLA-DPA1 (ENSUPAG00010012558) #24	COL11A2 (ENSUPAG00010012591) #26	RXRB (ENSUPAG00010013376) #27	SLC39A7 (ENSUPAG00010013405) #28	HSD17B8 (ENSUPAG00010013412) #29	RING1 (ENSUPAG00010013424) #30	VPS52 (ENSUPAG00010013433) #32	ENSUPAG00010013506 ##33	B3GALT4 (ENSUPAG00010013513) #34	WDR46 (ENSUPAG00010013516) #35	PFDN6 (ENSUPAG00010013562) #36	RGL2 (ENSUPAG00010013583) #37	TAPBP (ENSUPAG00010013596)
Squirrel	MODERN SPECIES	76							ENSSTOG00000028098	HLA-DOB (ENSSTOG00000003405) #15	ENSSTOG00000030715	TAP2 (ENSSTOG00000003413) #16	PSMB8 (ENSSTOG00000019724) #17	TAP1 (ENSSTOG00000003451) #18	PSMB9 (ENSSTOG00000003475) #19	HLA-DMB (ENSSTOG00000019821) #20	HLA-DMA (ENSSTOG00000009246) #21	BRD2 (ENSSTOG00000010807) #22	HLA-DOA (ENSSTOG00000010820) #23	HLA-DPA1 (ENSSTOG00000003558) #24	HLA-DPB1 (ENSSTOG00000003567) #25	COL11A2 (ENSSTOG00000003578) #26	RXRB (ENSSTOG00000027099) #27	SLC39A7 (ENSSTOG00000014304) #28	HSD17B8 (ENSSTOG00000020853) #29	RING1 (ENSSTOG00000026166) #30	VPS52 (ENSSTOG00000002397) #32	ENSSTOG00000002417 ##33	B3GALT4 (ENSSTOG00000024877) #34	WDR46 (ENSSTOG00000002433) #35	PFDN6 (ENSSTOG00000027428) #36	RGL2 (ENSSTOG00000024728) #37	TAPBP (ENSSTOG00000025004)
Alpin marmot	DUPLICATION
Alpin marmot	MODERN SPECIES	24	ENSMMMG00000023121	RAB8A (ENSMMMG00000023118)	TPM4 (ENSMMMG00000022621)	ENSMMMG00000022612	ENSMMMG00000022610	ENSMMMG00000022564	ENSMMMG00000022557	CYP4F2 (ENSMMMG00000022533)	CYP4F8 (ENSMMMG00000022511)	CYP4F22 (ENSMMMG00000022504)	PGLYRP2 (ENSMMMG00000022496)	RASAL3 (ENSMMMG00000022474)	ENSMMMG00000022459	AKAP8L (ENSMMMG00000022438)	AKAP8 (ENSMMMG00000022416)	ENSMMMG00000022411 #22	ENSMMMG00000022407	EPHX3 (ENSMMMG00000022401)	NOTCH3 (ENSMMMG00000022356)	ENSMMMG00000022351	ILVBL (ENSMMMG00000022300)	SYDE1 (ENSMMMG00000022294)	OR1I1 (ENSMMMG00000022293)	CASP14 (ENSMMMG00000022289)	CCDC105 (ENSMMMG00000022286)	SLC1A6 (ENSMMMG00000022279)	ENSMMMG00000022278	ENSMMMG00000022277	ENSMMMG00000022259	ENSMMMG00000022258	ENSMMMG00000022253
Alpin marmot	MODERN SPECIES	20	ENSMMMG00000018777 #8	ENSMMMG00000018780 #10	ENSMMMG00000018785 #11	ENSMMMG00000018797	ENSMMMG00000018808 #12	ENSMMMG00000020395	ENSMMMG00000024056 #12	ENSMMMG00000024215	HLA-DOB (ENSMMMG00000024217) #15	TAP2 (ENSMMMG00000024218) #16	PSMB8 (ENSMMMG00000024220) #17	TAP1 (ENSMMMG00000024221) #18	PSMB9 (ENSMMMG00000024222) #19	HLA-DMB (ENSMMMG00000024223) #20	HLA-DMA (ENSMMMG00000024224) #21	BRD2 (ENSMMMG00000024225) #22	HLA-DOA (ENSMMMG00000024226) #23	HLA-DPA1 (ENSMMMG00000024227) #24	HLA-DPB1 (ENSMMMG00000024228) #25	COL11A2 (ENSMMMG00000024229) #26	RXRB (ENSMMMG00000024230) #27	SLC39A7 (ENSMMMG00000024231) #28	HSD17B8 (ENSMMMG00000024232) #29	RING1 (ENSMMMG00000024233) #30	VPS52 (ENSMMMG00000024234) #32	ENSMMMG00000024235 ##33	B3GALT4 (ENSMMMG00000024236) #34	WDR46 (ENSMMMG00000024237) #35	PFDN6 (ENSMMMG00000024238) #36	RGL2 (ENSMMMG00000024239) #37	TAPBP (ENSMMMG00000024240)
Hystricomorpha	ANCESTRAL SPECIES	1	ENSGT00940000162079	ENSGT00940000162484	ENSGT00940000160997 #7	ENSGT00940000155371 #9	ENSGT00940000154993.k.a #10	ENSGT00940000162892	ENSGT00940000161821 #11	ENSGT00940000154723.b #12	ENSGT00940000162353 #15	ENSGT00940000160499 #16	ENSGT00940000157293 #17	ENSGT00940000159023 #18	ENSGT00940000159897 #19	ENSGT00940000160381 #20	ENSGT00940000161157 #21	ENSGT00940000153385.b.a.b #22	ENSGT00940000162112 #23	ENSGT00940000162498 #24	ENSGT00940000162390 #25	ENSGT00940000159762 #26	ENSGT00940000159208.B #27	ENSGT00940000160076 #28	ENSGT00940000160668 #29	ENSGT00940000161022 #30	ENSGT00390000008815 #32	ENSGT00390000012691.d ##33	ENSGT00390000012691.c.b.p #33	ENSGT00940000161798 #34	ENSGT00390000007075 #35	ENSGT00390000010512 #36	ENSGT00940000161403 #37
Hystricomorpha_a	ANCESTRAL SPECIES	42	ENSGT00940000162450	ENSGT00940000162079	ENSGT00940000162484	ENSGT00940000160997 #7	ENSGT00940000155371 #9	ENSGT00940000154993.k.a #10	ENSGT00940000161821 #11	ENSGT00940000154723.b #12	ENSGT00940000162353 #15	ENSGT00940000160499 #16	ENSGT00940000157293 #17	ENSGT00940000159023 #18	ENSGT00940000159897 #19	ENSGT00940000160381 #20	ENSGT00940000161157 #21	ENSGT00940000153385.b.a.b #22	ENSGT00940000162112 #23	ENSGT00940000162498 #24	ENSGT00940000162390 #25	ENSGT00940000159762 #26	ENSGT00940000159208.B #27	ENSGT00940000160076 #28	ENSGT00940000160668 #29	ENSGT00940000161022 #30	ENSGT00390000008815 #32	ENSGT00390000012691.d ##33	ENSGT00390000012691.c.b.p #33	ENSGT00940000161798 #34	ENSGT00390000007075 #35	ENSGT00390000010512 #36	ENSGT00940000161403 #37
Hystricomorpha_b	ANCESTRAL SPECIES	3	ENSGT00980000198621	ENSGT00940000162450	ENSGT00940000162079	ENSGT00940000162484	ENSGT00940000160997 #7	ENSGT00940000155371 #9	ENSGT00940000161821 #11	ENSGT00940000154723.b #12	ENSGT00940000162353 #15	ENSGT00940000160499 #16	ENSGT00940000157293 #17	ENSGT00940000159023 #18	ENSGT00940000159897 #19	ENSGT00940000160381 #20	ENSGT00940000161157 #21	ENSGT00940000153385.b.a.b #22	ENSGT00940000162112 #23	ENSGT00940000162498 #24	ENSGT00940000162390 #25	ENSGT00940000159762 #26	ENSGT00940000159208.B #27	ENSGT00940000160076 #28	ENSGT00940000160668 #29	ENSGT00940000161022 #30	ENSGT00390000008815 #32	ENSGT00390000012691.d.o ##33	ENSGT00940000161798 #34	ENSGT00390000007075 #35	ENSGT00390000010512 #36	ENSGT00940000161403 #37	ENSGT00940000159200
Long-tailed chinchilla	MODERN SPECIES	144	ENSCLAG00000011744	ENSCLAG00000015677	BTNL2 (ENSCLAG00000007142)	HLA-DRA (ENSCLAG00000009768) #7	ENSCLAG00000013098 #9	ENSCLAG00000016042 #9	ENSCLAG00000009507 #11	HLA-DQB2 (ENSCLAG00000011869) #12	HLA-DOB (ENSCLAG00000011735) #15	TAP2 (ENSCLAG00000012654) #16	PSMB8 (ENSCLAG00000006990) #17	TAP1 (ENSCLAG00000008052) #18	PSMB9 (ENSCLAG00000007918) #19	HLA-DMB (ENSCLAG00000008468) #20	HLA-DMA (ENSCLAG00000014679) #21	BRD2 (ENSCLAG00000009750) #22	HLA-DOA (ENSCLAG00000011531) #23	HLA-DPB1 (ENSCLAG00000013126) #25	HLA-DPA1 (ENSCLAG00000010668) #24	COL11A2 (ENSCLAG00000007783) #26	RXRB (ENSCLAG00000013699) #27	SLC39A7 (ENSCLAG00000014475) #28	HSD17B8 (ENSCLAG00000007885) #29	RING1 (ENSCLAG00000009149) #30	VPS52 (ENSCLAG00000008115) #32	RPS18 (ENSCLAG00000008982) ##33	WDR46 (ENSCLAG00000007512) #35	PFDN6 (ENSCLAG00000010475) #36	RGL2 (ENSCLAG00000009780) #37	TAPBP (ENSCLAG00000010992)	DAXX (ENSCLAG00000010016)
Degu	MODERN SPECIES	46	ENSODEG00000017653	ENSODEG00000017401	ENSODEG00000017414	ENSODEG00000017398	ENSODEG00000017435 #8	ENSODEG00000017402 #10	ENSODEG00000017510 #11	ENSODEG00000017249 #12	HLA-DOB (ENSODEG00000017495) #15	TAP1 (ENSODEG00000017484) #18	PSMB9 (ENSODEG00000017656) #19	TAP2 (ENSODEG00000017797) #16	PSMB8 (ENSODEG00000017662) #17	HLA-DMB (ENSODEG00000017802) #20	ENSODEG00000017381 #21	BRD2 (ENSODEG00000017239) #22	HLA-DOA (ENSODEG00000017569) #23	HLA-DPA1 (ENSODEG00000017716) #24	COL11A2 (ENSODEG00000017513) #26	RXRB (ENSODEG00000017146) #27	SLC39A7 (ENSODEG00000017361) #28	HSD17B8 (ENSODEG00000017486) #29	RING1 (ENSODEG00000017691) #30	VPS52 (ENSODEG00000017744) #32	ENSODEG00000017344 ##33	B3GALT4 (ENSODEG00000017281) #34	WDR46 (ENSODEG00000017342) #35	ENSODEG00000017649 #36	RGL2 (ENSODEG00000017326) #37	TAPBP (ENSODEG00000017301)	DAXX (ENSODEG00000017044)
Guinea pig	MODERN SPECIES	15	ENSCPOG00000023019	BTNL2 (ENSCPOG00000004277)	HLA-DRA (ENSCPOG00000012309) #7	ENSCPOG00000036465 #9	ENSCPOG00000003574 #10	ENSCPOG00000040083 #10	ENSCPOG00000014463	HLA-DQB2 (ENSCPOG00000038606) #12	HLA-DOB (ENSCPOG00000033895) #15	TAP2 (ENSCPOG00000038951) #16	PSMB8 (ENSCPOG00000000729) #17	TAP1 (ENSCPOG00000026988) #18	PSMB9 (ENSCPOG00000002121) #19	HLA-DMB (ENSCPOG00000002810) #20	HLA-DMA (ENSCPOG00000015044) #21	BRD2 (ENSCPOG00000002811) #22	HLA-DOA (ENSCPOG00000012562) #23	ENSCPOG00000002427 #24	ENSCPOG00000032859 #25	ENSCPOG00000024142 #25	ENSCPOG00000035477 #24	COL11A2 (ENSCPOG00000020466) #26	RXRB (ENSCPOG00000013936) #27	SLC39A7 (ENSCPOG00000023790) #28	HSD17B8 (ENSCPOG00000013940) #29	RING1 (ENSCPOG00000013943) #30	VPS52 (ENSCPOG00000013947) #32	RPS18 (ENSCPOG00000019675) #33	B3GALT4 (ENSCPOG00000012731) #34	WDR46 (ENSCPOG00000012733) #35	PFDN6 (ENSCPOG00000019520) #36
Naked mole-rat female	MODERN SPECIES	4	GPSM3 (ENSHGLG00000012807)	HLA-DRA (ENSHGLG00000012243) #7	ENSHGLG00000012074 #8	ENSHGLG00000011873 #10	ENSHGLG00000011613 #10	ENSHGLG00000011398	ENSHGLG00000043086	HLA-DQB2 (ENSHGLG00000038840) #12	HLA-DOB (ENSHGLG00000016652) #15	TAP2 (ENSHGLG00000019356) #16	PSMB8 (ENSHGLG00000017087) #17	TAP1 (ENSHGLG00000017081) #18	PSMB9 (ENSHGLG00000036914) #19	HLA-DMB (ENSHGLG00000017060) #20	HLA-DMA (ENSHGLG00000017048) #21	BRD2 (ENSHGLG00000019334) #22	HLA-DOA (ENSHGLG00000019255) #23	HLA-DPA1 (ENSHGLG00000019266) #24	HLA-DPB1 (ENSHGLG00000019389) #25	COL11A2 (ENSHGLG00000018531) #26	RXRB (ENSHGLG00000018456) #27	SLC39A7 (ENSHGLG00000018434) #28	HSD17B8 (ENSHGLG00000019497) #29	RING1 (ENSHGLG00000019474) #30	VPS52 (ENSHGLG00000017226) #32	B3GALT4 (ENSHGLG00000046221) #34	WDR46 (ENSHGLG00000017190) #35	PFDN6 (ENSHGLG00000017170) #36	RGL2 (ENSHGLG00000017158) #37	TAPBP (ENSHGLG00000017138)	ZBTB22 (ENSHGLG00000017146)