Rodentia_A	ANCESTRAL SPECIES	14	ENSGT00940000154447.z	ENSGT00940000161705	ENSGT01030000234543.A.a	ENSGT00940000156351 #8	ENSGT00940000154761 #9	ENSGT00940000163007 #10	ENSGT00510000047171.n ##11	ENSGT00940000157038 #13	ENSGT00530000064712 #14	ENSGT00390000017613 #15	ENSGT00390000009488 #16	ENSGT00940000159305 #18	ENSGT00940000162822 #19	ENSGT00950000183185.c.a.a #20	ENSGT00390000014909 #21	ENSGT00940000160325.b #22	ENSGT00730000111371 #23	ENSGT00940000160552 #24	ENSGT01030000234578.A.b.a.a.b #25	ENSGT00390000001901 #26	ENSGT00390000007992 #27	ENSGT00940000161711 #28	ENSGT00940000161151 #30	ENSGT00940000157929 #31	ENSGT00920000149138 #33	ENSGT00390000016876 #34	ENSGT00390000002313 #35	ENSGT00390000007547 #37	ENSGT00940000159532	ENSGT00940000160135	ENSGT00950000182832.C
Hystricomorpha	ANCESTRAL SPECIES	8	ENSGT00940000154447.z.f	ENSGT01030000234543.A.a	ENSGT00940000161705	ENSGT00940000156351 #8	ENSGT00940000154761 #9	ENSGT00940000163007 #10	ENSGT00510000047171.n ##11	ENSGT00940000157038 #13	ENSGT00530000064712 #14	ENSGT00390000017613 #15	ENSGT00390000009488 #16	ENSGT00940000159305 #18	ENSGT00940000162822 #19	ENSGT00950000183185.c.a.a #20	ENSGT00390000014909 #21	ENSGT00940000160325.b #22	ENSGT00730000111371 #23	ENSGT00940000160552 #24	ENSGT01030000234578.A.b.a.a.b #25	ENSGT00390000001901 #26	ENSGT00390000007992 #27	ENSGT00940000161711 #28	ENSGT00940000161151 #30	ENSGT00940000157929 #31	ENSGT00920000149138 #33	ENSGT00390000016876 #34	ENSGT00390000002313 #35	ENSGT00390000007547 #37	ENSGT00940000159532	ENSGT00940000160135	ENSGT00950000182832.C
Naked mole-rat female	MODERN SPECIES	23	ENSHGLG00000020983 #7	SUCLG1 (ENSHGLG00000047475) #8	ENSHGLG00000016621 #9	ENSHGLG00000039609 #10	ENSHGLG00000036565 #11	ENSHGLG00000049290 #12	TCF7L1 (ENSHGLG00000044140) #13	ENSHGLG00000007230 #14	RETSAT (ENSHGLG00000009788) #15	ENSHGLG00000005816 #16	ENSHGLG00000043435 #17	CAPG (ENSHGLG00000004995) #18	SH2D6 (ENSHGLG00000016223) #19	MAT2A (ENSHGLG00000018376) #20	GGCX (ENSHGLG00000013929) #21	VAMP8 (ENSHGLG00000012997) #22	ENSHGLG00000012613 #23	RNF181 (ENSHGLG00000045564) #24	TMEM150A (ENSHGLG00000010994) #25	C2orf68 (ENSHGLG00000036696) #26	USP39 (ENSHGLG00000015846) #27	SFTPB (ENSHGLG00000016430) #28	ENSHGLG00000033431 #29	ATOH8 (ENSHGLG00000013394) #30	ST3GAL5 (ENSHGLG00000015817) #31	ENSHGLG00000050264 #32	ENSHGLG00000006334 #33	PTCD3 (ENSHGLG00000007937) #34	IMMT (ENSHGLG00000004647) #35	ENSHGLG00000049882 #36	MRPL35 (ENSHGLG00000042289) #37
Hystricomorpha_a	ANCESTRAL SPECIES	35	ENSGT00940000154447.z.f	ENSGT01030000234543.A.a	ENSGT00940000161705	ENSGT00940000156351 #8	ENSGT00940000154761 #9	ENSGT00940000163007 #10	ENSGT00510000047171.n ##11	ENSGT00940000157038 #13	ENSGT00530000064712 #14	ENSGT00390000017613 #15	ENSGT00390000009488 #16	ENSGT00940000159305 #18	ENSGT00940000162822 #19	ENSGT00950000183185.c.a.a #20	ENSGT00390000014909 #21	ENSGT00940000160325.b #22	ENSGT00730000111371 #23	ENSGT00940000160552 #24	ENSGT01030000234578.A.b.a.a.b #25	ENSGT00390000001901 #26	ENSGT00390000007992 #27	ENSGT00940000161711 #28	ENSGT00940000161151 #30	ENSGT00940000157929 #31	ENSGT00920000149138 #33	ENSGT00390000016876 #34	ENSGT00390000002313 #35	ENSGT00390000007547 #37	ENSGT00940000159532	ENSGT00940000160135	ENSGT00950000182832.C
Hystricomorpha_b	ANCESTRAL SPECIES	33	ENSGT00940000154447.z.e.a	ENSGT00940000154447.z.f	ENSGT01030000234543.A.a	ENSGT00940000161705	ENSGT00940000156351 #8	ENSGT00940000154761 #9	ENSGT00940000163007 #10	ENSGT00510000047171.n ##11	ENSGT00940000157038 #13	ENSGT00390000017613 #15	ENSGT00390000009488 #16	ENSGT00940000159305 #18	ENSGT00940000162822 #19	ENSGT00950000183185.c.a.a #20	ENSGT00390000014909 #21	ENSGT00940000160325.b #22	ENSGT00730000111371 #23	ENSGT00940000160552 #24	ENSGT01030000234578.A.b.a.a.b #25	ENSGT00390000001901 #26	ENSGT00390000007992 #27	ENSGT00940000161711 #28	ENSGT00940000161151 #30	ENSGT00940000157929 #31	ENSGT00920000149138 #33	ENSGT00390000016876 #34	ENSGT00390000002313 #35	ENSGT00390000007547 #37	ENSGT00940000159532	ENSGT00940000160135	ENSGT00950000182832.C
Long-tailed chinchilla	MODERN SPECIES	131	ENSCLAG00000005858	LRRTM1 (ENSCLAG00000005364)	CTNNA2 (ENSCLAG00000013755)	ENSCLAG00000009325	SUCLG1 (ENSCLAG00000008580) #8	DNAH6 (ENSCLAG00000006035) #9	TMSB10 (ENSCLAG00000010365) #10	KCMF1 (ENSCLAG00000009986) ##11	TCF7L1 (ENSCLAG00000007414) #13	RETSAT (ENSCLAG00000008939) #15	ELMOD3 (ENSCLAG00000009003) #16	CAPG (ENSCLAG00000004481) #18	ENSCLAG00000006141 #19	MAT2A (ENSCLAG00000007205) #20	GGCX (ENSCLAG00000005838) #21	VAMP8 (ENSCLAG00000008880) #22	VAMP5 (ENSCLAG00000009915) #23	RNF181 (ENSCLAG00000006082) #24	TMEM150A (ENSCLAG00000005500) #25	C2orf68 (ENSCLAG00000009438) #26	USP39 (ENSCLAG00000006866) #27	SFTPB (ENSCLAG00000006471) #28	ATOH8 (ENSCLAG00000006142) #30	ST3GAL5 (ENSCLAG00000006950) #31	POLR1A (ENSCLAG00000005187) #33	PTCD3 (ENSCLAG00000007992) #34	IMMT (ENSCLAG00000005278) #35	MRPL35 (ENSCLAG00000004489) #37	REEP1 (ENSCLAG00000012499)	KDM3A (ENSCLAG00000011990)	CHMP3 (ENSCLAG00000009289)
Degu	MODERN SPECIES	203		ENSODEG00000002222	ENSODEG00000002212	SUCLG1 (ENSODEG00000002195) #8	DNAH6 (ENSODEG00000003756) #9	ENSODEG00000003596 #10	ENSODEG00000003586 ##11	TCF7L1 (ENSODEG00000003559) #13	RETSAT (ENSODEG00000003469) #15	ELMOD3 (ENSODEG00000003393) #16	CAPG (ENSODEG00000003321) #18	ENSODEG00000018929	SH2D6 (ENSODEG00000003239) #19	ENSODEG00000003186 #20	GGCX (ENSODEG00000003141) #21	VAMP8 (ENSODEG00000003107) #22	VAMP5 (ENSODEG00000003093) #23	RNF181 (ENSODEG00000003046) #24	TMEM150A (ENSODEG00000003753) #25	C2orf68 (ENSODEG00000003734) #26	USP39 (ENSODEG00000003717) #27	SFTPB (ENSODEG00000003695) #28	ATOH8 (ENSODEG00000003670) #30	ST3GAL5 (ENSODEG00000003647) #31	ENSODEG00000018941	POLR1A (ENSODEG00000003542) #33	PTCD3 (ENSODEG00000003461) #34	IMMT (ENSODEG00000003274) #35	MRPL35 (ENSODEG00000003180) #37	REEP1 (ENSODEG00000003133)	KDM3A (ENSODEG00000003061)
Guinea pig	MODERN SPECIES	37	ENSCPOG00000004885	ENSCPOG00000032214	LRRTM1 (ENSCPOG00000001371)	CTNNA2 (ENSCPOG00000023564)	SUCLG1 (ENSCPOG00000003017) #8	DNAH6 (ENSCPOG00000015041) #9	KCMF1 (ENSCPOG00000023050) ##11	TCF7L1 (ENSCPOG00000014492) #13	ENSCPOG00000037555 #14	RETSAT (ENSCPOG00000022640) #15	ELMOD3 (ENSCPOG00000007973) #16	CAPG (ENSCPOG00000007978) #18	ENSCPOG00000012229 #19	MAT2A (ENSCPOG00000001533) #20	GGCX (ENSCPOG00000001534) #21	VAMP8 (ENSCPOG00000001409) #22	VAMP5 (ENSCPOG00000021802) #23	RNF181 (ENSCPOG00000001938) #24	TMEM150A (ENSCPOG00000025516) #25	C2orf68 (ENSCPOG00000009311) #26	USP39 (ENSCPOG00000009315) #27	SFTPB (ENSCPOG00000035291) #28	ATOH8 (ENSCPOG00000006364) #30	ST3GAL5 (ENSCPOG00000000993) #31	POLR1A (ENSCPOG00000012350) #33	PTCD3 (ENSCPOG00000012371) #34	IMMT (ENSCPOG00000012379) #35	MRPL35 (ENSCPOG00000012387) #37	REEP1 (ENSCPOG00000012389)	KDM3A (ENSCPOG00000023055)	CHMP3 (ENSCPOG00000001723)
Sciuridae	ANCESTRAL SPECIES	53						ENSGT00940000163478	ENSGT00390000004352	ENSGT00940000157038 #13	ENSGT00530000064712 #14	ENSGT00390000017613 #15	ENSGT00390000009488 #16	ENSGT00940000159305 #18	ENSGT00940000162822 #19	ENSGT00950000183185.c.a.a #20	ENSGT00390000014909 #21	ENSGT00940000160325.b #22	ENSGT00730000111371 #23	ENSGT00940000160552 #24	ENSGT01030000234578.A.b.a.a.b #25	ENSGT00390000001901 #26	ENSGT00390000007992 #27	ENSGT00940000161711 #28	ENSGT00940000161151 #30	ENSGT00940000157929 #31	ENSGT00920000149138 #33	ENSGT00390000016876 #34	ENSGT00390000002313 #35	ENSGT00390000007547 #37	ENSGT00940000159532	ENSGT00940000160135	ENSGT00950000182832.C
Marmotini	ANCESTRAL SPECIES	86					ENSGT00940000163478	ENSGT00390000004352	ENSGT00940000153165.a.a.c.a.i.b.b.b.a.a	ENSGT00940000157038 #13	ENSGT00530000064712 #14	ENSGT00390000017613 #15	ENSGT00390000009488 #16	ENSGT00940000159305 #18	ENSGT00940000162822 #19	ENSGT00950000183185.c.a.a #20	ENSGT00390000014909 #21	ENSGT00940000160325.b #22	ENSGT00730000111371 #23	ENSGT00940000160552 #24	ENSGT01030000234578.A.b.a.a.b #25	ENSGT00390000001901 #26	ENSGT00390000007992 #27	ENSGT00940000161711 #28	ENSGT00940000161151 #30	ENSGT00940000157929 #31	ENSGT00920000149138 #33	ENSGT00390000016876 #34	ENSGT00390000002313 #35	ENSGT00390000007547 #37	ENSGT00940000159532	ENSGT00940000160135	ENSGT00950000182832.C
Alpin marmot	MODERN SPECIES	118	ENSMMMG00000007007	ENSMMMG00000007012	ENSMMMG00000007026	RPIA (ENSMMMG00000007477)	ENSMMMG00000007572	ENSMMMG00000007617	ENSMMMG00000007627	TCF7L1 (ENSMMMG00000007633) #13	ENSMMMG00000007682 #14	RETSAT (ENSMMMG00000007689) #15	ENSMMMG00000007785 #16	CAPG (ENSMMMG00000007822) #18	ENSMMMG00000007857 #19	MAT2A (ENSMMMG00000007871) #20	GGCX (ENSMMMG00000008142) #21	VAMP8 (ENSMMMG00000008162) #22	VAMP5 (ENSMMMG00000008168) #23	RNF181 (ENSMMMG00000008179) #24	TMEM150A (ENSMMMG00000008189) #25	USP39 (ENSMMMG00000008203) #27	ENSMMMG00000008853 #26	SFTPB (ENSMMMG00000008881) #28	ST3GAL5 (ENSMMMG00000008911) #31	POLR1A (ENSMMMG00000008920) #33	PTCD3 (ENSMMMG00000008977) #34	IMMT (ENSMMMG00000009011) #35	MRPL35 (ENSMMMG00000009181) #37	REEP1 (ENSMMMG00000009193)	KDM3A (ENSMMMG00000009242)	CHMP3 (ENSMMMG00000009359)	RNF103 (ENSMMMG00000009373)
Marmotini_b	ANCESTRAL SPECIES	128					ENSGT00940000163478	ENSGT00390000004352	ENSGT00940000153165.a.a.c.a.i.b.b.b.a.a	ENSGT00940000157038 #13	ENSGT00530000064712 #14	ENSGT00390000017613 #15	ENSGT00390000009488 #16	ENSGT00940000159305 #18	ENSGT00940000162822 #19	ENSGT00950000183185.c.a.a #20	ENSGT00390000014909 #21	ENSGT00940000160325.b #22	ENSGT00730000111371 #23	ENSGT00940000160552 #24	ENSGT01030000234578.A.b.a.a.b #25	ENSGT00390000001901 #26	ENSGT00390000007992 #27	ENSGT00940000161711 #28	ENSGT00940000154129.m.r.b	ENSGT00940000161151 #30	ENSGT00940000157929 #31	ENSGT00920000149138 #33	ENSGT00390000016876 #34	ENSGT00390000002313 #35	ENSGT00390000007547 #37	ENSGT00940000159532	ENSGT00940000160135
Squirrel	MODERN SPECIES	312					RPIA (ENSSTOG00000023312)	ENSSTOG00000034297	ENSSTOG00000031036	TCF7L1 (ENSSTOG00000021988) #13	ENSSTOG00000020177 #14	RETSAT (ENSSTOG00000026131) #15	ELMOD3 (ENSSTOG00000009420) #16	CAPG (ENSSTOG00000009431) #18	ENSSTOG00000010788 #19	MAT2A (ENSSTOG00000010796) #20	GGCX (ENSSTOG00000010797) #21	VAMP8 (ENSSTOG00000005962) #22	VAMP5 (ENSSTOG00000005966) #23	RNF181 (ENSSTOG00000005973) #24	TMEM150A (ENSSTOG00000023355) #25	C2orf68 (ENSSTOG00000032886) #26	USP39 (ENSSTOG00000015986) #27	SFTPB (ENSSTOG00000026197) #28	ENSSTOG00000033478	ATOH8 (ENSSTOG00000006538) #30	ST3GAL5 (ENSSTOG00000024816) #31	ENSSTOG00000012609	POLR1A (ENSSTOG00000012580) #33	PTCD3 (ENSSTOG00000012611) #34	IMMT (ENSSTOG00000012624) #35	MRPL35 (ENSSTOG00000030233) #37	REEP1 (ENSSTOG00000025141)
Arctic ground squirrel	MODERN SPECIES	609					IGKC (ENSUPAG00010018047)	RPIA (ENSUPAG00010018051)	ENSUPAG00010018060	TCF7L1 (ENSUPAG00010018088) #13	ENSUPAG00010018102 #14	RETSAT (ENSUPAG00010018105) #15	ELMOD3 (ENSUPAG00010018158) #16	CAPG (ENSUPAG00010018187) #18	SH2D6 (ENSUPAG00010018214) #19	MAT2A (ENSUPAG00010000075) #20	GGCX (ENSUPAG00010000144) #21	VAMP8 (ENSUPAG00010000178) #22	ENSUPAG00010000192 #23	TMEM150A (ENSUPAG00010000226) #25	RNF181 (ENSUPAG00010000242) #24	ENSUPAG00010000260 #26	USP39 (ENSUPAG00010000286) #27	SFTPB (ENSUPAG00010000319) #28	ENSUPAG00010000360
Eurasian red squirrel	MODERN SPECIES	5	ENSSVLG00005019338	ENSSVLG00005019271	ENSSVLG00005018002	ENSSVLG00005017863	ENSSVLG00005017786	TCF7L1 (ENSSVLG00005017741) #13	ENSSVLG00005017693 #14	RETSAT (ENSSVLG00005017559) #15	ELMOD3 (ENSSVLG00005017414) #16	CAPG (ENSSVLG00005017210) #18	ENSSVLG00005017177	SH2D6 (ENSSVLG00005016979) #19	MAT2A (ENSSVLG00005016926) #20	ENSSVLG00005016868	GGCX (ENSSVLG00005016698) #21	VAMP8 (ENSSVLG00005016627) #22	VAMP5 (ENSSVLG00005016585) #23	RNF181 (ENSSVLG00005016555) #24	TMEM150A (ENSSVLG00005016477) #25	ENSSVLG00005016431 #26	USP39 (ENSSVLG00005016257) #27	SFTPB (ENSSVLG00005015980) #28	ATOH8 (ENSSVLG00005015922) #30	ST3GAL5 (ENSSVLG00005015795) #31	POLR1A (ENSSVLG00005015696) #33	PTCD3 (ENSSVLG00005016912) #34	IMMT (ENSSVLG00005016785) #35	MRPL35 (ENSSVLG00005016713) #37	REEP1 (ENSSVLG00005016418)	KDM3A (ENSSVLG00005016348)	CHMP3 (ENSSVLG00005016280)