Rodentia_A	ANCESTRAL SPECIES	18	ENSGT01090000260093.a #8	ENSGT00950000182978.A.a.b.a #9	ENSGT00940000160438 #10	ENSGT00940000156118 #11	ENSGT00940000161902.a.a #12	ENSGT00940000155268 #13	ENSGT00390000008325.b.b #14	ENSGT00700000106212 #15	ENSGT00950000182878.b.a.c.a.b #16	ENSGT00940000157063 #17	ENSGT00860000135817 #18	ENSGT00940000154977 #19	ENSGT00900000143784	ENSGT00940000156908 #20	ENSGT00390000011717 #21	ENSGT00390000018710 #22	ENSGT00390000000742 #23	ENSGT00940000156130.b #24	ENSGT00940000159124 #25	ENSGT00940000158635 #26	ENSGT00940000156473 #27	ENSGT00940000158224 #29	ENSGT00940000159542 #31	ENSGT00860000136016 #32	ENSGT00390000001846 #33	ENSGT00530000064276 #34	ENSGT00940000159419 #35	ENSGT00390000004451 #36	ENSGT01030000234597.a.b.b.e.a.a #37	ENSGT00940000157068	ENSGT00390000001057
Sciuridae	ANCESTRAL SPECIES	17	ENSGT01090000260093.a #8	ENSGT00950000182978.A.a.b.a #9	ENSGT00940000160438 #10	ENSGT00940000156118 #11	ENSGT00940000161902.a.a #12	ENSGT00940000155268 #13	ENSGT00390000008325.b.b #14	ENSGT00700000106212 #15	ENSGT00950000182878.b.a.c.a.b.o.a #16	ENSGT00940000157063 #17	ENSGT00860000135817 #18	ENSGT00940000154977 #19	ENSGT00900000143784	ENSGT00940000156908 #20	ENSGT00390000011717 #21	ENSGT00390000018710 #22	ENSGT00390000000742 #23	ENSGT00940000156130.b #24	ENSGT00940000159124 #25	ENSGT00940000158635 #26	ENSGT00940000156473 #27	ENSGT00940000158224 #29	ENSGT00940000159542 #31	ENSGT00860000136016 #32	ENSGT00390000001846 #33	ENSGT00530000064276 #34	ENSGT00940000159419 #35	ENSGT00390000004451 #36	ENSGT01030000234597.a.b.b.e.a.a #37	ENSGT00940000157068	ENSGT00390000001057
Marmotini	ANCESTRAL SPECIES	10	ENSGT00390000001710 #7	ENSGT01090000260093.a #8	ENSGT00950000182978.A.a.b.a #9	ENSGT00940000160438 #10	ENSGT00940000156118 #11	ENSGT00940000161902.a.a #12	ENSGT00940000155268.m #13	ENSGT00390000008325.b.b #14	ENSGT00700000106212 #15	ENSGT00950000182878.b.a.c.a.b.o.a #16	ENSGT00940000157063 #17	ENSGT00860000135817 #18	ENSGT00940000154977 #19	ENSGT00940000156908 #20	ENSGT00390000011717 #21	ENSGT00390000018710 #22	ENSGT00390000000742 #23	ENSGT00940000156130.b #24	ENSGT00940000159124 #25	ENSGT00940000158635 #26	ENSGT00940000156473 #27	ENSGT00390000014682.n #28	ENSGT00940000158224 #29	ENSGT00940000159542 #31	ENSGT00860000136016 #32	ENSGT00390000001846 #33	ENSGT00530000064276 #34	ENSGT00940000159419 #35	ENSGT00390000004451 #36	ENSGT01030000234597.a.b.b.e.a.a #37	ENSGT00940000157068
Alpin marmot	MODERN SPECIES	16	LACTB2 (ENSMMMG00000004742) #7	XKR9 (ENSMMMG00000004758) #8	EYA1 (ENSMMMG00000004783) #9	MSC (ENSMMMG00000004901) #10	TRPA1 (ENSMMMG00000004948) #11	KCNB2 (ENSMMMG00000005040) #12	ENSMMMG00000005060 #13	SBSPON (ENSMMMG00000005085) #14	C8orf89 (ENSMMMG00000005106) #15	RPL7 (ENSMMMG00000005128) #16	RDH10 (ENSMMMG00000005136) #17	ENSMMMG00000005173 #18	STAU2 (ENSMMMG00000005198) #19	ENSMMMG00000005257 #20	ENSMMMG00000005290 #21	TMEM70 (ENSMMMG00000005317) #22	LY96 (ENSMMMG00000005320) #23	JPH1 (ENSMMMG00000005340) #24	GDAP1 (ENSMMMG00000005361) #25	PI15 (ENSMMMG00000005399) #26	CRISPLD1 (ENSMMMG00000005425) #27	ENSMMMG00000005479 #28	HNF4G (ENSMMMG00000005503) #29	ENSMMMG00000005554 #30	ZFHX4 (ENSMMMG00000005581) #31	ENSMMMG00000005619 #32	PEX2 (ENSMMMG00000005624) #33	PKIA (ENSMMMG00000005670) #34	ZC2HC1A (ENSMMMG00000005695) #35	IL7 (ENSMMMG00000005732) #36	STMN2 (ENSMMMG00000005764) #37
Marmotini_b	ANCESTRAL SPECIES	52	ENSGT00510000046470.a.a.a.d.a	ENSGT00390000001710 #7	ENSGT01090000260093.a #8	ENSGT00950000182978.A.a.b.a #9	ENSGT00940000160438 #10	ENSGT00940000156118 #11	ENSGT00940000161902.a.a #12	ENSGT00940000155268.m #13	ENSGT00390000008325.b.b #14	ENSGT00700000106212 #15	ENSGT00950000182878.b.a.c.a.b.o.a #16	ENSGT00940000157063 #17	ENSGT00940000154977 #19	ENSGT00940000156908 #20	ENSGT00390000011717 #21	ENSGT00390000018710 #22	ENSGT00390000000742 #23	ENSGT00940000159124 #25	ENSGT00940000158635 #26	ENSGT00390000014682.n #28	ENSGT00940000158224 #29
Arctic ground squirrel	MODERN SPECIES	183	TRAM1 (ENSUPAG00010010848)	LACTB2 (ENSUPAG00010010856) #7	XKR9 (ENSUPAG00010010873) #8	EYA1 (ENSUPAG00010010877) #9	MSC (ENSUPAG00010010953) #10	TRPA1 (ENSUPAG00010010963) #11	KCNB2 (ENSUPAG00010011054) #12	TERF1 (ENSUPAG00010011060) #13	SBSPON (ENSUPAG00010011134) #14	C8orf89 (ENSUPAG00010011139) #15	ENSUPAG00010011144 #16	RDH10 (ENSUPAG00010011147) #17	STAU2 (ENSUPAG00010011157) #19	UBE2W (ENSUPAG00010011274) #20	ELOC (ENSUPAG00010011281) #21	TMEM70 (ENSUPAG00010011291) #22	LY96 (ENSUPAG00010011295) #23
Eurasian red squirrel	DUPLICATION
Eurasian red squirrel	MODERN SPECIES		EYA1 (ENSSVLG00005001545) #9	MSC (ENSSVLG00005001842) #10	TRPA1 (ENSSVLG00005001874) #11	KCNB2 (ENSSVLG00005001924) #12	TERF1 (ENSSVLG00005001939) #13	SBSPON (ENSSVLG00005001957) #14	ENSSVLG00005001968	C8orf89 (ENSSVLG00005001984) #15	ENSSVLG00005001995 #16	RDH10 (ENSSVLG00005002017) #17	ENSSVLG00005002033 #18	STAU2 (ENSSVLG00005002079) #19	ENSSVLG00005002189	UBE2W (ENSSVLG00005002205) #20	ENSSVLG00005002231 #21	ENSSVLG00005002242 #22	LY96 (ENSSVLG00005002267) #23	ENSSVLG00005002291	JPH1 (ENSSVLG00005002301) #24	GDAP1 (ENSSVLG00005002320) #25	PI15 (ENSSVLG00005002347) #26	CRISPLD1 (ENSSVLG00005002386) #27	HNF4G (ENSSVLG00005002470) #29	ZFHX4 (ENSSVLG00005002527) #31	ENSSVLG00005002565 #32	PEX2 (ENSSVLG00005002571) #33	ENSSVLG00005002588	PKIA (ENSSVLG00005002593) #34	ZC2HC1A (ENSSVLG00005002603) #35	IL7 (ENSSVLG00005002623) #36	STMN2 (ENSSVLG00005002665) #37
Eurasian red squirrel	MODERN SPECIES	2	OR52W1 (ENSSVLG00005007793)	C11orf42 (ENSSVLG00005007762)	FHIP1B (ENSSVLG00005007692)	CNGA4 (ENSSVLG00005007640)	CCKBR (ENSSVLG00005007574)	CAVIN3 (ENSSVLG00005007510)	SMPD1 (ENSSVLG00005007479)	APBB1 (ENSSVLG00005007218)	HPX (ENSSVLG00005007102)	ENSSVLG00005007076	ARFIP2 (ENSSVLG00005006992)	TIMM10B (ENSSVLG00005006936)	ENSSVLG00005006905	ENSSVLG00005006876	ENSSVLG00005006819	ENSSVLG00005006785 #22	ENSSVLG00005006757	ENSSVLG00005006676	ILK (ENSSVLG00005006591)	ENSSVLG00005006530	TPP1 (ENSSVLG00005006235)	DCHS1 (ENSSVLG00005006133)	ENSSVLG00005006101	ENSSVLG00005006080	ENSSVLG00005006064	ENSSVLG00005006043	ENSSVLG00005006008	ENSSVLG00005005978	ENSSVLG00005005953	ENSSVLG00005005924	ENSSVLG00005005882
Hystricomorpha	ANCESTRAL SPECIES	12	ENSGT00510000046470.a.a.a.d.a	ENSGT00390000001710 #7	ENSGT01090000260093.a #8	ENSGT00950000182978.A.a.b.a #9	ENSGT00940000160438 #10	ENSGT00940000156118 #11	ENSGT00940000161902.a.a #12	ENSGT00940000155268 #13	ENSGT00390000008325.b.b #14	ENSGT00700000106212 #15	ENSGT00950000182878.b.a.c.a.b #16	ENSGT00940000157063 #17	ENSGT00940000154977 #19	ENSGT00940000156908 #20	ENSGT00390000011717 #21	ENSGT00390000018710 #22	ENSGT00390000000742 #23	ENSGT00940000156130.b #24	ENSGT00940000159124 #25	ENSGT00940000158635 #26	ENSGT00940000156473 #27	ENSGT00940000158224 #29	ENSGT00940000159542 #31	ENSGT00390000001846 #33	ENSGT00530000064276 #34	ENSGT00940000159419 #35	ENSGT00390000004451 #36	ENSGT01030000234597.a.b.b.e.a.a #37	ENSGT00940000157068	ENSGT00390000001057	ENSGT00940000155294
Hystricomorpha_a	ANCESTRAL SPECIES	9	ENSGT00510000046470.a.a.a.d.a	ENSGT00390000001710 #7	ENSGT01090000260093.a #8	ENSGT00950000182978.A.a.b.a #9	ENSGT00940000160438 #10	ENSGT00940000156118 #11	ENSGT00940000161902.a.a #12	ENSGT00940000155268 #13	ENSGT00390000008325.b.b #14	ENSGT00700000106212 #15	ENSGT00950000182878.b.a.c.a.b.n #16	ENSGT00940000157063 #17	ENSGT00940000154977 #19	ENSGT00940000156908 #20	ENSGT00390000011717 #21	ENSGT00390000018710 #22	ENSGT00390000000742 #23	ENSGT00940000156130.b #24	ENSGT00940000159124 #25	ENSGT00940000158635 #26	ENSGT00940000156473 #27	ENSGT00940000158224 #29	ENSGT00940000159542 #31	ENSGT00390000001846 #33	ENSGT00530000064276 #34	ENSGT00940000159419 #35	ENSGT00390000004451 #36	ENSGT01030000234597.a.b.b.e.a.a #37	ENSGT00940000157068	ENSGT00390000001057	ENSGT00940000155294
Guinea pig	MODERN SPECIES		NCOA2 (ENSCPOG00000000493)	TRAM1 (ENSCPOG00000008533)	LACTB2 (ENSCPOG00000007604) #7	EYA1 (ENSCPOG00000000714) #9	MSC (ENSCPOG00000038612) #10	Trpa1 (ENSCPOG00000011519) #11	KCNB2 (ENSCPOG00000000689) #12	TERF1 (ENSCPOG00000009638) #13	SBSPON (ENSCPOG00000010933) #14	C8orf89 (ENSCPOG00000033934) #15	RPL7 (ENSCPOG00000004140) #16	ENSCPOG00000000770 #17	STAU2 (ENSCPOG00000015001) #19	UBE2W (ENSCPOG00000008803) #20	ELOC (ENSCPOG00000032030) #21	TMEM70 (ENSCPOG00000031120) #22	LY96 (ENSCPOG00000033283) #23	JPH1 (ENSCPOG00000002273) #24	GDAP1 (ENSCPOG00000002277) #25	PI15 (ENSCPOG00000036651) #26	CRISPLD1 (ENSCPOG00000002867) #27	HNF4G (ENSCPOG00000011625) #29	ZFHX4 (ENSCPOG00000012693) #31	PEX2 (ENSCPOG00000034224) #33	PKIA (ENSCPOG00000036157) #34	ZC2HC1A (ENSCPOG00000021093) #35	IL7 (ENSCPOG00000031262) #36	ENSCPOG00000010466 #37	HEY1 (ENSCPOG00000008527)	ENSCPOG00000031885	TPD52 (ENSCPOG00000040600)
Hystricomorpha_b	ANCESTRAL SPECIES	25	ENSGT00390000001710 #7	ENSGT01090000260093.a #8	ENSGT00950000182978.A.a.b.a #9	ENSGT00940000160438 #10	ENSGT00940000156118 #11	ENSGT00940000164329	ENSGT00940000161902.a.a #12	ENSGT00940000155268 #13	ENSGT00390000008325.b.b #14	ENSGT00700000106212 #15	ENSGT00950000182878.b.a.c.a.b.n #16	ENSGT00940000157063 #17	ENSGT00940000154977 #19	ENSGT00940000156908 #20	ENSGT00390000011717 #21	ENSGT00390000018710 #22	ENSGT00390000000742 #23	ENSGT00940000156130.b #24	ENSGT00940000159124 #25	ENSGT00940000158635 #26	ENSGT00940000156473 #27	ENSGT00940000158224 #29	ENSGT00940000159542 #31	ENSGT00390000001846 #33	ENSGT00530000064276 #34	ENSGT00940000159419 #35	ENSGT00390000004451 #36	ENSGT01030000234597.a.b.b.e.a.a #37	ENSGT00940000157068	ENSGT00390000001057	ENSGT00940000155294
Long-tailed chinchilla	MODERN SPECIES	151	TRAM1 (ENSCLAG00000001706)	LACTB2 (ENSCLAG00000001647) #7	XKR9 (ENSCLAG00000004198) #8	EYA1 (ENSCLAG00000003062) #9	MSC (ENSCLAG00000002927) #10	TRPA1 (ENSCLAG00000002418) #11	ENSCLAG00000002142	TERF1 (ENSCLAG00000002076) #13	SBSPON (ENSCLAG00000002049) #14	C8orf89 (ENSCLAG00000002274) #15	ENSCLAG00000002143 #16	RDH10 (ENSCLAG00000002112) #17	STAU2 (ENSCLAG00000001824) #19	UBE2W (ENSCLAG00000002672) #20	ENSCLAG00000002529 #21	ENSCLAG00000002465 #22	LY96 (ENSCLAG00000002393) #23	JPH1 (ENSCLAG00000002323) #24	GDAP1 (ENSCLAG00000002271) #25	PI15 (ENSCLAG00000002216) #26	CRISPLD1 (ENSCLAG00000002069) #27	HNF4G (ENSCLAG00000013756) #29	ZFHX4 (ENSCLAG00000011659) #31	PEX2 (ENSCLAG00000010766) #33	PKIA (ENSCLAG00000010536) #34	ZC2HC1A (ENSCLAG00000009816) #35	ENSCLAG00000003448 #36	ENSCLAG00000003309 #37	HEY1 (ENSCLAG00000003265)	ENSCLAG00000003227	TPD52 (ENSCLAG00000003004)
Degu	MODERN SPECIES	132	ENSODEG00000003933	EYA1 (ENSODEG00000003994) #9	MSC (ENSODEG00000004396) #10	TRPA1 (ENSODEG00000004465) #11	KCNB2 (ENSODEG00000004106) #12	ENSODEG00000004130	ENSODEG00000004166 #13	ENSODEG00000004364	SBSPON (ENSODEG00000004392) #14	C8orf89 (ENSODEG00000004421) #15	ENSODEG00000004457 #16	RDH10 (ENSODEG00000003490) #17	STAU2 (ENSODEG00000003610) #19	UBE2W (ENSODEG00000003806) #20	ENSODEG00000003911 #21	TMEM70 (ENSODEG00000003940) #22	LY96 (ENSODEG00000004007) #23	JPH1 (ENSODEG00000002990) #24	GDAP1 (ENSODEG00000003006) #25	ENSODEG00000003062	PI15 (ENSODEG00000003073) #26	CRISPLD1 (ENSODEG00000003148) #27
Naked mole-rat female	MODERN SPECIES	13	XKR9 (ENSHGLG00000033679) #8	ENSHGLG00000018393	EYA1 (ENSHGLG00000019347) #9	ENSHGLG00000038455	MSC (ENSHGLG00000040745) #10	TRPA1 (ENSHGLG00000017879) #11	KCNB2 (ENSHGLG00000017013) #12	ENSHGLG00000021368	Terf1 (ENSHGLG00000013062) #13	SBSPON (ENSHGLG00000044318) #14	RPL7 (ENSHGLG00000017000) #16	RDH10 (ENSHGLG00000013673) #17	STAU2 (ENSHGLG00000014888) #19	UBE2W (ENSHGLG00000016745) #20	TCEB1 (ENSHGLG00000042986) #21	TMEM70 (ENSHGLG00000042950) #22	LY96 (ENSHGLG00000017254) #23	JPH1 (ENSHGLG00000016053) #24	GDAP1 (ENSHGLG00000040080) #25	PI15 (ENSHGLG00000015916) #26	ENSHGLG00000015637 #27	ENSHGLG00000018758	ENSHGLG00000033328	ENSHGLG00000034560	ENSHGLG00000007710 #29	ENSHGLG00000005959	ENSHGLG00000007968 #31	ENSHGLG00000005277	PEX2 (ENSHGLG00000037973) #33	ENSHGLG00000032661	ENSHGLG00000009819