Rodentia_A	ANCESTRAL SPECIES	16	ENSGT00390000003478 #7	ENSGT00730000111231 #8	ENSGT00940000158081 #9	ENSGT00410000025695.b #10	ENSGT00390000002913 #11	ENSGT00940000158163 #12	ENSGT00390000000672.a.a #13	ENSGT00940000160699 #14	ENSGT00390000014856 #15	ENSGT00940000160753 #16	ENSGT00390000017748 #17	ENSGT00940000158649 #18	ENSGT00940000160926 #19	ENSGT00390000012913.a #20	ENSGT00410000025695.a #21	ENSGT00390000012198 #22	ENSGT00390000004097.a #23	ENSGT00940000160464 #24	ENSGT00390000000719 #25	ENSGT00390000007227.b #26	ENSGT00390000008152.B.a #27	ENSGT00940000162643	ENSGT01050000244941.B.c #28	ENSGT00950000183110.a #29	ENSGT00550000075064 #30
Hystricomorpha	ANCESTRAL SPECIES	47	ENSGT00390000003478 #7	ENSGT00730000111231 #8	ENSGT00940000158081 #9	ENSGT00410000025695.b #10	ENSGT00390000002913 #11	ENSGT00940000158163 #12	ENSGT00390000000672.a.a #13	ENSGT00940000160699 #14	ENSGT00390000014856 #15	ENSGT00940000160753 #16	ENSGT00390000017748 #17	ENSGT00940000158649 #18	ENSGT00940000160926 #19	ENSGT00390000012913.a #20	ENSGT00410000025695.a #21	ENSGT00390000012198 #22	ENSGT00390000004097.a #23	ENSGT00940000160464 #24	ENSGT00390000000719 #25	ENSGT00390000007227.b #26	ENSGT00390000008152.B.a #27	ENSGT01050000244941.B.c #28	ENSGT00950000183110.a #29	ENSGT00550000075064 #30
Hystricomorpha_a	ANCESTRAL SPECIES	55	ENSGT00390000003478 #7	ENSGT00730000111231 #8	ENSGT00940000158081 #9	ENSGT00410000025695.b #10	ENSGT00390000002913 #11	ENSGT00940000158163 #12	ENSGT00390000000672.a.a #13	ENSGT00940000160699 #14	ENSGT00390000014856 #15	ENSGT00940000160753 #16	ENSGT00390000017748 #17	ENSGT00940000158649 #18	ENSGT00940000160926 #19	ENSGT00390000012913.a #20	ENSGT00410000025695.a #21	ENSGT00390000012198 #22	ENSGT00390000004097.a #23	ENSGT00940000160464 #24	ENSGT00390000000719 #25	ENSGT00390000007227.b #26	ENSGT00390000008152.B.a #27	ENSGT01050000244941.B.c #28	ENSGT00950000183110.a #29	ENSGT00550000075064 #30	ENSGT01030000234542.b.b.a.a.a.b #36	ENSGT00940000157246 #37	ENSGT00940000161678	ENSGT00940000160466	ENSGT00390000013811	ENSGT00940000157924	ENSGT00940000163163
Hystricomorpha_b	ANCESTRAL SPECIES	66	ENSGT00390000003478 #7	ENSGT00730000111231 #8	ENSGT00940000158081 #9	ENSGT00410000025695.b #10	ENSGT00390000002913 #11	ENSGT00940000158163 #12	ENSGT00390000000672.a.a #13	ENSGT00940000160699 #14	ENSGT00390000014856 #15	ENSGT00940000160753 #16	ENSGT00390000017748 #17	ENSGT00940000158649 #18	ENSGT00940000160926 #19	ENSGT00390000012913.a #20	ENSGT00410000025695.a #21	ENSGT00390000012198 #22	ENSGT00390000004097.a #23	ENSGT00940000160464 #24	ENSGT00390000000719 #25	ENSGT00390000007227.b #26	ENSGT00390000008152.B.a #27	ENSGT01050000244941.B.c #28	ENSGT00950000183110.a #29	ENSGT00550000075064 #30	ENSGT01030000234542.b.b.a.a.a.b #36	ENSGT00940000157246 #37	ENSGT00940000161678	ENSGT00940000160466	ENSGT00390000013811	ENSGT00940000157924	ENSGT00940000155438.b
Long-tailed chinchilla	MODERN SPECIES	231	COPE (ENSCLAG00000003621) #7	DDX49 (ENSCLAG00000012844) #8	HOMER3 (ENSCLAG00000011599) #9	SUGP2 (ENSCLAG00000011375) #10	ARMC6 (ENSCLAG00000008215) #11	SLC25A42 (ENSCLAG00000008004) #12	TMEM161A (ENSCLAG00000007578) #13	MEF2B (ENSCLAG00000007377) #14	BORCS8 (ENSCLAG00000004959) #15	RFXANK (ENSCLAG00000004632) #16	NR2C2AP (ENSCLAG00000004378) #17	NCAN (ENSCLAG00000004140) #18	HAPLN4 (ENSCLAG00000003955) #19	TM6SF2 (ENSCLAG00000003633) #20	SUGP1 (ENSCLAG00000003512) #21	MAU2 (ENSCLAG00000006535) #22	GATAD2A (ENSCLAG00000010160) #23	TSSK6 (ENSCLAG00000018107) #24	NDUFA13 (ENSCLAG00000016915) #25	YJEFN3 (ENSCLAG00000016158) #26	CILP2 (ENSCLAG00000015928) #27	LPAR2 (ENSCLAG00000016969) #28	GMIP (ENSCLAG00000008010) #29	ATP13A1 (ENSCLAG00000009549) #30	ENSCLAG00000007428 #31	ENSCLAG00000007229 #32	DDX11 (ENSCLAG00000007090) #33	ENSCLAG00000006498 #34	ENSCLAG00000006263 #35	TPM4 (ENSCLAG00000006213) #36	RAB8A (ENSCLAG00000006073) #37
Degu	MODERN SPECIES	323	COPE (ENSODEG00000011547) #7	DDX49 (ENSODEG00000011203) #8	HOMER3 (ENSODEG00000014870) #9	SUGP2 (ENSODEG00000012058) #10	ARMC6 (ENSODEG00000012613) #11	SLC25A42 (ENSODEG00000012168) #12	TMEM161A (ENSODEG00000012343) #13	MEF2B (ENSODEG00000012357) #14	BORCS8 (ENSODEG00000013003) #15	RFXANK (ENSODEG00000013006) #16	NR2C2AP (ENSODEG00000011486) #17	NCAN (ENSODEG00000011699) #18	HAPLN4 (ENSODEG00000011689) #19	TM6SF2 (ENSODEG00000010936) #20	SUGP1 (ENSODEG00000011538) #21	MAU2 (ENSODEG00000012887) #22	GATAD2A (ENSODEG00000013506) #23	TSSK6 (ENSODEG00000020032) #24	NDUFA13 (ENSODEG00000013435) #25	YJEFN3 (ENSODEG00000011107) #26	CILP2 (ENSODEG00000010764) #27	LPAR2 (ENSODEG00000010920) #28	GMIP (ENSODEG00000010205) #29	ATP13A1 (ENSODEG00000010691) #30	ENSODEG00000019897	ENSODEG00000011452	ENSODEG00000010301	ENSODEG00000011437
Guinea pig	MODERN SPECIES	72	CERS1 (ENSCPOG00000033783)	COPE (ENSCPOG00000013624) #7	DDX49 (ENSCPOG00000013626) #8	HOMER3 (ENSCPOG00000004565) #9	SUGP2 (ENSCPOG00000006372) #10	ARMC6 (ENSCPOG00000006374) #11	SLC25A42 (ENSCPOG00000013086) #12	TMEM161A (ENSCPOG00000013640) #13	MEF2B (ENSCPOG00000032781) #14	BORCS8 (ENSCPOG00000036178) #15	RFXANK (ENSCPOG00000003121) #16	NR2C2AP (ENSCPOG00000032927) #17	HAPLN4 (ENSCPOG00000023683) #19	TM6SF2 (ENSCPOG00000022916) #20	SUGP1 (ENSCPOG00000007797) #21	MAU2 (ENSCPOG00000003755) #22	GATAD2A (ENSCPOG00000015396) #23	TSSK6 (ENSCPOG00000024320) #24	NDUFA13 (ENSCPOG00000019995) #25	YJEFN3 (ENSCPOG00000023842) #26	CILP2 (ENSCPOG00000007219) #27	LPAR2 (ENSCPOG00000012652) #28	GMIP (ENSCPOG00000011161) #29	ATP13A1 (ENSCPOG00000011167) #30	ENSCPOG00000022796
Naked mole-rat female	MODERN SPECIES	21	ENSHGLG00000006789 #8	HOMER3 (ENSHGLG00000006851) #9	ARMC6 (ENSHGLG00000008147) #11	SLC25A42 (ENSHGLG00000008826) #12	TMEM161A (ENSHGLG00000009517) #13	ENSHGLG00000003123 #14	MEF2BNB (ENSHGLG00000047513) #15	RFXANK (ENSHGLG00000003396) #16	NR2C2AP (ENSHGLG00000033726) #17	NCAN (ENSHGLG00000034381) #18	HAPLN4 (ENSHGLG00000003896) #19	TM6SF2 (ENSHGLG00000004113) #20	ENSHGLG00000042474 #21	ENSHGLG00000039617 #10	ENSHGLG00000048186 #21	ENSHGLG00000049094 #22	GATAD2A (ENSHGLG00000003176) #23	TSSK6 (ENSHGLG00000020778) #24	NDUFA13 (ENSHGLG00000018628) #25	YJEFN3 (ENSHGLG00000019524) #26	CILP2 (ENSHGLG00000018931) #27	LPAR2 (ENSHGLG00000035704) #28	ENSHGLG00000013806 #29	ENSHGLG00000003184 ##31	ENSHGLG00000042271	ENSHGLG00000044603	ENSHGLG00000046812	ENSHGLG00000039559	ENSHGLG00000049921	ENSHGLG00000020580	ENSHGLG00000021231
Sciuridae	ANCESTRAL SPECIES	20	ENSGT00390000003478 #7	ENSGT00730000111231 #8	ENSGT00940000158081 #9	ENSGT00410000025695.b #10	ENSGT00390000002913 #11	ENSGT00940000158163 #12	ENSGT00390000000672.a.a #13	ENSGT00940000160699 #14	ENSGT00390000014856 #15	ENSGT00940000160753 #16	ENSGT00390000017748 #17	ENSGT00940000158649 #18	ENSGT00940000160926 #19	ENSGT00390000012913.a #20	ENSGT00410000025695.a #21	ENSGT00390000012198 #22	ENSGT00390000004097.a #23	ENSGT00940000160464 #24	ENSGT00390000000719 #25	ENSGT00390000007227.b #26	ENSGT00390000008152.B.a #27	ENSGT00940000162643	ENSGT01050000244941.B.c #28	ENSGT00950000183110.a #29	ENSGT00550000075064 #30	ENSGT00960000186612.B.a.b.a.b.a.b.i.a.a.b	ENSGT00390000000410	ENSGT00940000160737	ENSGT00940000159742	ENSGT00940000158279	ENSGT00940000156347
Marmotini	ANCESTRAL SPECIES	12	ENSGT00390000003478 #7	ENSGT00730000111231 #8	ENSGT00940000158081 #9	ENSGT00410000025695.b #10	ENSGT00390000002913 #11	ENSGT00940000158163 #12	ENSGT00390000000672.a.a #13	ENSGT00940000160699 #14	ENSGT00390000014856 #15	ENSGT00940000160753 #16	ENSGT00390000017748 #17	ENSGT00940000158649 #18	ENSGT00940000160926 #19	ENSGT00390000012913.a #20	ENSGT00410000025695.a #21	ENSGT00390000012198 #22	ENSGT00390000004097.a #23	ENSGT00940000160464 #24	ENSGT00390000000719 #25	ENSGT00390000007227.b #26	ENSGT00390000008152.B.a #27	ENSGT00940000162643	ENSGT01050000244941.B.c #28	ENSGT00950000183110.a #29	ENSGT00550000075064 #30	ENSGT00950000182755.b.a.a.b.a.a.l ##34	ENSGT00960000186612.B.a.b.a.b.a.b.i.a.b	ENSGT00960000186612.B.a.b.a.b.a.b.i.a.a.b	ENSGT00390000000410	ENSGT00940000160737	ENSGT00940000159742
Marmotini_b	ANCESTRAL SPECIES	12	ENSGT00390000003478 #7	ENSGT00730000111231 #8	ENSGT00940000158081 #9	ENSGT00410000025695.b #10	ENSGT00390000002913 #11	ENSGT00940000158163 #12	ENSGT00390000000672.a.a #13	ENSGT00940000160699 #14	ENSGT00390000014856 #15	ENSGT00940000160753 #16	ENSGT00390000017748 #17	ENSGT00940000158649 #18	ENSGT00940000160926 #19	ENSGT00390000012913.a #20	ENSGT00410000025695.a #21	ENSGT00390000012198 #22	ENSGT00390000004097.a #23	ENSGT00940000160464 #24	ENSGT00390000000719 #25	ENSGT00390000007227.b #26	ENSGT00390000008152.B.a #27	ENSGT00940000162643	ENSGT01050000244941.B.c #28	ENSGT00950000183110.a #29	ENSGT00550000075064 #30	ENSGT00950000182755.b.a.a.b.a.a.l ##34	ENSGT00960000186612.B.a.b.a.b.a.b.i.a.b	ENSGT00960000186612.B.a.b.a.b.a.b.i.a.a.b	ENSGT00390000000410	ENSGT00940000160737	ENSGT00390000018390.yb
Arctic ground squirrel	MODERN SPECIES	73	COPE (ENSUPAG00010018276) #7	DDX49 (ENSUPAG00010018246) #8	HOMER3 (ENSUPAG00010018230) #9	SUGP2 (ENSUPAG00010018216) #10	ARMC6 (ENSUPAG00010018208) #11	SLC25A42 (ENSUPAG00010018191) #12	TMEM161A (ENSUPAG00010018179) #13	MEF2B (ENSUPAG00010018172) #14	BORCS8 (ENSUPAG00010018165) #15	RFXANK (ENSUPAG00010018152) #16	NR2C2AP (ENSUPAG00010018146) #17	NCAN (ENSUPAG00010018127) #18	HAPLN4 (ENSUPAG00010018121) #19	TM6SF2 (ENSUPAG00010018116) #20	SUGP1 (ENSUPAG00010018104) #21	MAU2 (ENSUPAG00010018075) #22	GATAD2A (ENSUPAG00010018036) #23	TSSK6 (ENSUPAG00010018027) #24	YJEFN3 (ENSUPAG00010018017) #26	CILP2 (ENSUPAG00010018008) #27	PBX4 (ENSUPAG00010017995)	LPAR2 (ENSUPAG00010017989) #28	GMIP (ENSUPAG00010017934) #29	ATP13A1 (ENSUPAG00010017873) #30	ENSUPAG00010017861 ##34	ENSUPAG00010017854	ENSUPAG00010017852	CAMP (ENSUPAG00010017843)	ENSUPAG00010017839	CDC25A (ENSUPAG00010017812)	ENSUPAG00010017794
Squirrel	MODERN SPECIES	196	COPE (ENSSTOG00000006736) #7	DDX49 (ENSSTOG00000006749) #8	HOMER3 (ENSSTOG00000029095) #9	SUGP2 (ENSSTOG00000026887) #10	ARMC6 (ENSSTOG00000012997) #11	SLC25A42 (ENSSTOG00000022047) #12	TMEM161A (ENSSTOG00000005867) #13	MEF2B (ENSSTOG00000005895) #14	BORCS8 (ENSSTOG00000025422) #15	RFXANK (ENSSTOG00000024080) #16	NR2C2AP (ENSSTOG00000001006) #17	NCAN (ENSSTOG00000001012) #18	HAPLN4 (ENSSTOG00000007240) #19	TM6SF2 (ENSSTOG00000025054) #20	SUGP1 (ENSSTOG00000001020) #21	MAU2 (ENSSTOG00000001026) #22	GATAD2A (ENSSTOG00000022640) #23	TSSK6 (ENSSTOG00000021351) #24	NDUFA13 (ENSSTOG00000022888) #25	YJEFN3 (ENSSTOG00000023979) #26	CILP2 (ENSSTOG00000026823) #27	ENSSTOG00000019762	PBX4 (ENSSTOG00000007166)	LPAR2 (ENSSTOG00000021678) #28	GMIP (ENSSTOG00000007176) #29	ATP13A1 (ENSSTOG00000007205) #30	CAMP (ENSSTOG00000015157)	ENSSTOG00000034924	CDC25A (ENSSTOG00000015144)	ENSSTOG00000024015	ENSSTOG00000026772
Alpin marmot	MODERN SPECIES	24	COPE (ENSMMMG00000002634) #7	DDX49 (ENSMMMG00000002658) #8	HOMER3 (ENSMMMG00000002691) #9	SUGP2 (ENSMMMG00000002743) #10	ARMC6 (ENSMMMG00000002877) #11	SLC25A42 (ENSMMMG00000002914) #12	TMEM161A (ENSMMMG00000002937) #13	MEF2B (ENSMMMG00000002982) #14	BORCS8 (ENSMMMG00000003015) #15	RFXANK (ENSMMMG00000003029) #16	NR2C2AP (ENSMMMG00000003044) #17	NCAN (ENSMMMG00000003066) #18	HAPLN4 (ENSMMMG00000003386) #19	TM6SF2 (ENSMMMG00000003397) #20	SUGP1 (ENSMMMG00000003416) #21	MAU2 (ENSMMMG00000003432) #22	GATAD2A (ENSMMMG00000003539) #23	TSSK6 (ENSMMMG00000003603) #24	NDUFA13 (ENSMMMG00000003609) #25	YJEFN3 (ENSMMMG00000003614) #26	CILP2 (ENSMMMG00000003635) #27	PBX4 (ENSMMMG00000003652)	ENSMMMG00000003669	LPAR2 (ENSMMMG00000003676) #28	GMIP (ENSMMMG00000003685) #29	ATP13A1 (ENSMMMG00000003751) #30	ENSMMMG00000003843 ##34	ENSMMMG00000003852	ENSMMMG00000003860	ENSMMMG00000003867	ENSMMMG00000003887
Eurasian red squirrel	MODERN SPECIES	7	DDX49 (ENSSVLG00005016654) #8	HOMER3 (ENSSVLG00005016701) #9	SUGP2 (ENSSVLG00005016823) #10	ARMC6 (ENSSVLG00005016951) #11	SLC25A42 (ENSSVLG00005017005) #12	TMEM161A (ENSSVLG00005017057) #13	MEF2B (ENSSVLG00005017215) #14	BORCS8 (ENSSVLG00005017305) #15	RFXANK (ENSSVLG00005017362) #16	NR2C2AP (ENSSVLG00005017403) #17	NCAN (ENSSVLG00005017503) #18	ENSSVLG00005017692	HAPLN4 (ENSSVLG00005017756) #19	TM6SF2 (ENSSVLG00005017792) #20	SUGP1 (ENSSVLG00005017843) #21	MAU2 (ENSSVLG00005017993) #22	GATAD2A (ENSSVLG00005018054) #23	TSSK6 (ENSSVLG00005018119) #24	NDUFA13 (ENSSVLG00005018132) #25	YJEFN3 (ENSSVLG00005018175) #26	CILP2 (ENSSVLG00005018243) #27	PBX4 (ENSSVLG00005018272)	LPAR2 (ENSSVLG00005018364) #28	GMIP (ENSSVLG00005018416) #29	ATP13A1 (ENSSVLG00005018497) #30	ENSSVLG00005018537 ##34	ENSSVLG00005018572	ENSSVLG00005018591	ZNF670 (ENSSVLG00005018638)	ENSSVLG00005018685	ENSSVLG00005018729