Rodentia_A	ANCESTRAL SPECIES	1	ENSGT01030000234592.B	ENSGT00950000183168.A	ENSGT00940000159074	ENSGT00530000063695.a #7	ENSGT00940000153669.a #8	ENSGT01010000223591	ENSGT00950000183201.a #9	ENSGT00390000004986 #10	ENSGT00940000161513 #11	ENSGT00940000158183 #14	ENSGT00940000155492.b #15	ENSGT00940000159713 #16	ENSGT01060000248588.a.d.a #18	ENSGT00940000161966 #20	ENSGT00390000013786 #21	ENSGT00510000047559 #22	ENSGT00510000046760.a #23	ENSGT00940000154175.i.a #24	ENSGT00940000154175.i.b #25	ENSGT00530000063929.b #26	ENSGT00940000160903 #27	ENSGT00940000161277 #28	ENSGT00940000161159 #29	ENSGT00940000161871 #30	ENSGT00940000163375 #31	ENSGT00940000154907.b #32	ENSGT00940000159759 #33	ENSGT00940000162085 #34	ENSGT00940000157450 #35	ENSGT00940000156155 #36	ENSGT00940000154620 #37
Sciuridae	ANCESTRAL SPECIES	2	ENSGT00940000162152.h	ENSGT01030000234592.B	ENSGT00950000183168.A	ENSGT00940000159074	ENSGT00530000063695.a #7	ENSGT00940000153669.a #8	ENSGT00950000183201.a #9	ENSGT00390000004986 #10	ENSGT00940000161513 #11	ENSGT00940000158183 #14	ENSGT00940000155492.b #15	ENSGT00940000159713 #16	ENSGT01060000248588.a.d.a #18	ENSGT00940000161966 #20	ENSGT00390000013786 #21	ENSGT00510000047559 #22	ENSGT00510000046760.a #23	ENSGT00940000154175.i.a #24	ENSGT00940000154175.i.b #25	ENSGT00530000063929.b #26	ENSGT00940000160903 #27	ENSGT00940000161277 #28	ENSGT00940000161159 #29	ENSGT00940000161871 #30	ENSGT00940000163375 #31	ENSGT00940000154907.b #32	ENSGT00940000159759 #33	ENSGT00940000162085 #34	ENSGT00940000157450 #35	ENSGT00940000156155 #36	ENSGT00940000154620 #37
Eurasian red squirrel	MODERN SPECIES	2	CEP57 (ENSSVLG00005010241) #7	MTMR2 (ENSSVLG00005010367) #8	ENSSVLG00005010533 #9	CCDC82 (ENSSVLG00005010580) #10	JRKL (ENSSVLG00005010894) #11	ENSSVLG00005010908 #12	ENSSVLG00005010963 #13	CNTN5 (ENSSVLG00005011074) #14	ARHGAP42 (ENSSVLG00005012065) #15	PGR (ENSSVLG00005012195) #16	ENSSVLG00005012488 #17	TRPC6 (ENSSVLG00005012644) #18	ENSSVLG00005013071 #19	ANGPTL5 (ENSSVLG00005013174) #20	CEP126 (ENSSVLG00005013261) #21	CFAP300 (ENSSVLG00005013383) #22	YAP1 (ENSSVLG00005013738) #23	BIRC3 (ENSSVLG00005013872) #24	BIRC2 (ENSSVLG00005013957) #25	TMEM123 (ENSSVLG00005014049) #26	MMP7 (ENSSVLG00005014206) #27	MMP20 (ENSSVLG00005014300) #28	MMP27 (ENSSVLG00005014388) #29	MMP8 (ENSSVLG00005014523) #30	MMP10 (ENSSVLG00005014643) #31	MMP1 (ENSSVLG00005014774) #32	MMP3 (ENSSVLG00005014901) #33	MMP12 (ENSSVLG00005015038) #34	MMP13 (ENSSVLG00005015162) #35	DCUN1D5 (ENSSVLG00005015275) #36	DYNC2H1 (ENSSVLG00005015721) #37
Marmotini	ANCESTRAL SPECIES	20	ENSGT00940000162152.h	ENSGT01030000234592.B	ENSGT00950000183168.A	ENSGT00940000159074	ENSGT00530000063695.a #7	ENSGT00940000153669.a #8	ENSGT00950000183201.a #9	ENSGT00390000004986 #10	ENSGT00940000161513 #11	ENSGT00940000158183 #14	ENSGT00940000155492.b #15	ENSGT00940000159713 #16	ENSGT01060000248588.a.d.a #18	ENSGT00940000161966 #20	ENSGT00390000013786 #21	ENSGT00510000047559 #22	ENSGT00510000046760.a #23	ENSGT00940000154175.i.a #24	ENSGT00940000154175.i.b.e #25	ENSGT00530000063929.b #26	ENSGT00940000160903 #27	ENSGT00940000161277 #28	ENSGT00940000161159 #29	ENSGT00940000161871 #30	ENSGT00940000154907.b #32	ENSGT00940000159759 #33	ENSGT00940000162085 #34	ENSGT00940000157450 #35	ENSGT00940000156155 #36	ENSGT00940000154620 #37	ENSGT00950000182999.a.b
Marmotini_b	ANCESTRAL SPECIES	122										ENSGT00940000158183 #14	ENSGT00940000155492.b #15	ENSGT00940000159713 #16	ENSGT01060000248588.a.d.a #18	ENSGT00940000161966 #20	ENSGT00390000013786 #21	ENSGT00510000047559 #22	ENSGT00510000046760.a #23	ENSGT00940000154175.i.a #24	ENSGT00940000154175.i.b.e #25	ENSGT00530000063929.b #26	ENSGT00940000160903 #27	ENSGT00940000161277 #28	ENSGT00940000161159 #29	ENSGT00940000161871 #30	ENSGT00940000154907.b #32	ENSGT00940000159759 #33	ENSGT00940000162085 #34	ENSGT00940000157450 #35	ENSGT00940000156155 #36	ENSGT00940000154620 #37	ENSGT00950000182999.a.b
Arctic ground squirrel	MODERN SPECIES	103										CNTN5 (ENSUPAG00010019303) #14	ARHGAP42 (ENSUPAG00010019399) #15	PGR (ENSUPAG00010019431) #16	TRPC6 (ENSUPAG00010019447) #18	ANGPTL5 (ENSUPAG00010019480) #20	CEP126 (ENSUPAG00010019487) #21	CFAP300 (ENSUPAG00010019501) #22	YAP1 (ENSUPAG00010019515) #23	BIRC3 (ENSUPAG00010019528) #24	BIRC2 (ENSUPAG00010019549) #25	TMEM123 (ENSUPAG00010019562) #26	MMP7 (ENSUPAG00010019569) #27	MMP20 (ENSUPAG00010019573) #28	MMP27 (ENSUPAG00010019583) #29	MMP8 (ENSUPAG00010019593) #30	MMP3 (ENSUPAG00010019608) #33	MMP1 (ENSUPAG00010019633) #32	MMP12 (ENSUPAG00010019655) #34	MMP13 (ENSUPAG00010019662) #35	DCUN1D5 (ENSUPAG00010019672) #36	DYNC2H1 (ENSUPAG00010019688) #37	PDGFD (ENSUPAG00010019962)
Squirrel	MODERN SPECIES	151										ENSSTOG00000033385	CNTN5 (ENSSTOG00000003745) #14	ARHGAP42 (ENSSTOG00000010760) #15	PGR (ENSSTOG00000020694) #16	TRPC6 (ENSSTOG00000003077) #18	CEP126 (ENSSTOG00000004605) #21	CFAP300 (ENSSTOG00000011163) #22	YAP1 (ENSSTOG00000004960) #23	BIRC3 (ENSSTOG00000005734) #24	ENSSTOG00000005754 #25	ENSSTOG00000026499	TMEM123 (ENSSTOG00000032785) #26	MMP7 (ENSSTOG00000027961) #27	MMP20 (ENSSTOG00000023437) #28	MMP27 (ENSSTOG00000008513) #29	MMP8 (ENSSTOG00000008539) #30	ENSSTOG00000008555 #33	MMP1 (ENSSTOG00000008571) #32	MMP3 (ENSSTOG00000008584) #33	MMP12 (ENSSTOG00000008600) #34	MMP13 (ENSSTOG00000008612) #35	DCUN1D5 (ENSSTOG00000013580) #36
Alpin marmot	MODERN SPECIES	25	ENSMMMG00000003554	FAM76B (ENSMMMG00000003496)	CEP57 (ENSMMMG00000003431) #7	MTMR2 (ENSMMMG00000003375) #8	ENSMMMG00000003357 #9	ENSMMMG00000003341 #9	CCDC82 (ENSMMMG00000003266) #10	JRKL (ENSMMMG00000003254) #11	ENSMMMG00000003243	CNTN5 (ENSMMMG00000003014) #14	ARHGAP42 (ENSMMMG00000002945) #15	PGR (ENSMMMG00000002898) #16	TRPC6 (ENSMMMG00000002831) #18	ANGPTL5 (ENSMMMG00000002794) #20	CEP126 (ENSMMMG00000002769) #21	CFAP300 (ENSMMMG00000002751) #22	YAP1 (ENSMMMG00000002718) #23	BIRC3 (ENSMMMG00000002693) #24	ENSMMMG00000002595 #25	TMEM123 (ENSMMMG00000002579) #26	MMP7 (ENSMMMG00000002551) #27	MMP20 (ENSMMMG00000002519) #28	MMP27 (ENSMMMG00000002490) #29	MMP8 (ENSMMMG00000002471) #30	ENSMMMG00000002452 #33	MMP1 (ENSMMMG00000002402) #32	MMP3 (ENSMMMG00000002377) #33	MMP12 (ENSMMMG00000002359) #34	MMP13 (ENSMMMG00000002337) #35	DCUN1D5 (ENSMMMG00000002318) #36	DYNC2H1 (ENSMMMG00000001718) #37
Hystricomorpha	ANCESTRAL SPECIES	5	ENSGT01030000234592.B	ENSGT00950000183168.A	ENSGT00940000159074	ENSGT00530000063695.a #7	ENSGT00940000153669.a #8	ENSGT01010000223591	ENSGT00950000183201.a #9	ENSGT00390000004986 #10	ENSGT00940000161513 #11	ENSGT00940000158183 #14	ENSGT00940000155492.b #15	ENSGT00940000159713 #16	ENSGT01060000248588.a.d.a #18	ENSGT00940000161966 #20	ENSGT00390000013786 #21	ENSGT00510000047559 #22	ENSGT00510000046760.a #23	ENSGT00940000154175.i.a #24	ENSGT00940000154175.i.b #25	ENSGT00530000063929.b #26	ENSGT00940000160903 #27	ENSGT00940000161277 #28	ENSGT00940000161159 #29	ENSGT00940000161871 #30	ENSGT00940000163375 #31	ENSGT00940000154907.b #32	ENSGT00940000159759 #33	ENSGT00940000162085 #34	ENSGT00940000157450 #35	ENSGT00940000156155 #36	ENSGT00940000154620 #37
Naked mole-rat female	MODERN SPECIES	24	ENSHGLG00000016013	ENSHGLG00000042652	MMP12 (ENSHGLG00000001493) #34	MMP3 (ENSHGLG00000001578) #33	MMP1 (ENSHGLG00000002821) #32	MMP10 (ENSHGLG00000003158) #31	MMP8 (ENSHGLG00000003235) #30	ENSHGLG00000003321 #29	ENSHGLG00000002861 #14	ENSHGLG00000000253 #15	PGR (ENSHGLG00000001843) #16	TRPC6 (ENSHGLG00000000680) #18	ENSHGLG00000000414	ANGPTL5 (ENSHGLG00000047251) #20	CEP126 (ENSHGLG00000000639) #21	CFAP300 (ENSHGLG00000048492) #22	YAP1 (ENSHGLG00000000291) #23	ENSHGLG00000019794	ENSHGLG00000005333	BIRC3 (ENSHGLG00000004954) #24	BIRC2 (ENSHGLG00000004179) #25	ENSHGLG00000044313	ENSHGLG00000047684 #26	MMP7 (ENSHGLG00000003863) #27	ENSHGLG00000003570 #28	ENSHGLG00000042812	ENSHGLG00000041631	ENSHGLG00000041058	CCDC82 (ENSHGLG00000013992) #10	JRKL (ENSHGLG00000049214) #11	ENSHGLG00000049135
Hystricomorpha_a	ANCESTRAL SPECIES	10	ENSGT00940000162152	ENSGT01030000234592.B	ENSGT00950000183168.A	ENSGT00940000159074	ENSGT00530000063695.a #7	ENSGT00940000153669.a #8	ENSGT00950000183201.a #9	ENSGT00390000004986 #10	ENSGT00940000161513 #11	ENSGT00940000158183 #14	ENSGT00940000155492.b #15	ENSGT00940000159713 #16	ENSGT01060000248588.a.d.a #18	ENSGT00940000161966 #20	ENSGT00390000013786 #21	ENSGT00510000047559 #22	ENSGT00510000046760.a #23	ENSGT00940000154175.i.a #24	ENSGT00940000154175.i.b #25	ENSGT00940000160903 #27	ENSGT00940000161277 #28	ENSGT00940000161159 #29	ENSGT00940000161871 #30	ENSGT00940000163375 #31	ENSGT00940000154907.b #32	ENSGT00940000159759 #33	ENSGT00940000162085 #34	ENSGT00940000157450 #35	ENSGT00940000156155 #36	ENSGT00940000154620 #37	ENSGT00940000159575
Guinea pig	MODERN SPECIES	19			ENDOD1 (ENSCPOG00000002204)	SESN3 (ENSCPOG00000019467)	FAM76B (ENSCPOG00000040456)	CEP57 (ENSCPOG00000008497) #7	MTMR2 (ENSCPOG00000008505) #8	MAML2 (ENSCPOG00000008516) #9	CCDC82 (ENSCPOG00000033086) #10	CNTN5 (ENSCPOG00000011322) #14	ARHGAP42 (ENSCPOG00000007842) #15	ENSCPOG00000030258 #16	TRPC6 (ENSCPOG00000005560) #18	ANGPTL5 (ENSCPOG00000001842) #20	CEP126 (ENSCPOG00000001844) #21	CFAP300 (ENSCPOG00000011737) #22	YAP1 (ENSCPOG00000033105) #23	BIRC3 (ENSCPOG00000034907) #24	BIRC2 (ENSCPOG00000010349) #25	ENSCPOG00000038069 #27	MMP20 (ENSCPOG00000036970) #28	MMP27 (ENSCPOG00000035593) #29	MMP8 (ENSCPOG00000013813) #30	MMP10 (ENSCPOG00000035812) #31	MMP1 (ENSCPOG00000006548) #32	MMP3 (ENSCPOG00000033163) #33	MMP12 (ENSCPOG00000036913) #34	MMP13 (ENSCPOG00000000221) #35	DCUN1D5 (ENSCPOG00000036831) #36	DYNC2H1 (ENSCPOG00000014189) #37	PDGFD (ENSCPOG00000038919)
Hystricomorpha_b	ANCESTRAL SPECIES	23	ENSGT00940000160158	ENSGT00390000012084.u	ENSGT00940000162152	ENSGT00950000183168.A	ENSGT00940000159074	ENSGT00530000063695.a #7	ENSGT00940000153669.a #8	ENSGT00950000183201.a #9	ENSGT00390000004986 #10	ENSGT00940000161513 #11	ENSGT00940000158183 #14	ENSGT00940000155492.b #15	ENSGT00940000159713 #16	ENSGT01060000248588.a.d.a #18	ENSGT00390000013786 #21	ENSGT00510000047559 #22	ENSGT00510000046760.a #23	ENSGT00940000154175.i.a #24	ENSGT00940000154175.i.b #25	ENSGT00940000160903 #27	ENSGT00940000161277 #28	ENSGT00940000161159 #29	ENSGT00940000161871 #30	ENSGT00940000163375 #31	ENSGT00940000154907.b #32	ENSGT00940000159759 #33	ENSGT00940000162085 #34	ENSGT00940000157450 #35	ENSGT00940000156155 #36	ENSGT00940000154620 #37	ENSGT00940000159575
Degu	MODERN SPECIES	53	CEP57 (ENSODEG00000013214) #7	MTMR2 (ENSODEG00000013402) #8	ENSODEG00000020097	MAML2 (ENSODEG00000015630) #9	CCDC82 (ENSODEG00000012847) #10	JRKL (ENSODEG00000020217) #11	ENSODEG00000014051	ENSODEG00000012986	CNTN5 (ENSODEG00000014105) #14	ENSODEG00000013901	ARHGAP42 (ENSODEG00000013928) #15	ENSODEG00000013619 #16	TRPC6 (ENSODEG00000014288) #18	ENSODEG00000013426	CEP126 (ENSODEG00000014031) #21	CFAP300 (ENSODEG00000014307) #22	ENSODEG00000013051	YAP1 (ENSODEG00000012897) #23	ENSODEG00000012579	ENSODEG00000013275 #24	ENSODEG00000012602 #25	MMP7 (ENSODEG00000012568) #27	MMP20 (ENSODEG00000012590) #28	MMP27 (ENSODEG00000012636) #29	MMP8 (ENSODEG00000013316) #30	MMP10 (ENSODEG00000014848) #31	MMP3 (ENSODEG00000012755) #33	MMP12 (ENSODEG00000012714) #34	MMP13 (ENSODEG00000012128) #35	DCUN1D5 (ENSODEG00000012893) #36	DYNC2H1 (ENSODEG00000012699) #37
Long-tailed chinchilla	MODERN SPECIES	119			SESN3 (ENSCLAG00000016066)	FAM76B (ENSCLAG00000010250)	ENSCLAG00000011257 #7	MTMR2 (ENSCLAG00000011747) #8	MAML2 (ENSCLAG00000014659) #9	CCDC82 (ENSCLAG00000014287) #10	JRKL (ENSCLAG00000017853) #11	ENSCLAG00000018078	CNTN5 (ENSCLAG00000010625) #14	ARHGAP42 (ENSCLAG00000014100) #15	ENSCLAG00000013886 #16	TRPC6 (ENSCLAG00000011949) #18	CEP126 (ENSCLAG00000012819) #21	CFAP300 (ENSCLAG00000013914) #22	YAP1 (ENSCLAG00000011113) #23	BIRC3 (ENSCLAG00000010783) #24	BIRC2 (ENSCLAG00000013394) #25	MMP7 (ENSCLAG00000015356) #27	MMP20 (ENSCLAG00000013214) #28	MMP27 (ENSCLAG00000010798) #29	MMP8 (ENSCLAG00000014040) #30	MMP10 (ENSCLAG00000013443) #31	MMP1 (ENSCLAG00000011491) #32	MMP3 (ENSCLAG00000012886) #33	MMP12 (ENSCLAG00000014288) #34	MMP13 (ENSCLAG00000011293) #35	DCUN1D5 (ENSCLAG00000010606) #36	DYNC2H1 (ENSCLAG00000014268) #37	PDGFD (ENSCLAG00000013637)