Rodentia_A	ANCESTRAL SPECIES	17	ENSGT00870000136554 #12	ENSGT00390000005826.a.b #13	ENSGT00900000141212 #14	ENSGT00910000144356 #15	ENSGT00940000162636.B ##16	ENSGT00940000162636.A #16	ENSGT00940000162294 #17	ENSGT00940000163249 #18	ENSGT00940000161877.c.a	ENSGT00940000161877.c.b	ENSGT00940000164098	ENSGT00940000161877.d	ENSGT00940000154755.c.a ##20	ENSGT00940000154755.c.b #20	ENSGT00950000183147.B #21	ENSGT00940000160277 #22	ENSGT00440000039984.a #23	ENSGT00940000158550 #24	ENSGT00940000160793 #25	ENSGT01100000263540.A.a #26	ENSGT00950000183148.b.b #27	ENSGT00940000160517 #28	ENSGT00390000013968 #29	ENSGT00660000095541.a.a #30	ENSGT00390000003094 #31	ENSGT00940000164901	ENSGT00940000161179	ENSGT00520000055634.b	ENSGT00940000161638	ENSGT00490000044517	ENSGT00530000063880.a
Hystricomorpha	ANCESTRAL SPECIES	10	ENSGT00940000155999 #8	ENSGT00940000163276 #9	ENSGT00940000156996 #10	ENSGT00940000162041 #11	ENSGT00870000136554 #12	ENSGT00390000005826.a.b #13	ENSGT00900000141212 #14	ENSGT00910000144356 #15	ENSGT00940000162636.A #16	ENSGT00940000162294 #17	ENSGT00940000163249 #18	ENSGT00940000161877.d	ENSGT00940000154755.c.a ##20	ENSGT00940000154755.c.b #20	ENSGT00950000183147.B #21	ENSGT00940000160277 #22	ENSGT00440000039984.a #23	ENSGT00940000158550 #24	ENSGT00940000160793 #25	ENSGT01100000263540.A.a #26	ENSGT00950000183148.b.b #27	ENSGT00940000160517 #28	ENSGT00390000013968 #29	ENSGT00660000095541.a.a #30	ENSGT00390000003094 #31	ENSGT00960000186656.a.b	ENSGT00520000055567.a.a.a	ENSGT00940000153311.a.b.a	ENSGT00940000161179	ENSGT00520000055634.b	ENSGT00940000161638
Hystricomorpha_a	ANCESTRAL SPECIES	8	ENSGT00940000163276 #9	ENSGT00940000156996 #10	ENSGT00940000162041 #11	ENSGT00870000136554 #12	ENSGT00390000005826.a.b #13	ENSGT00900000141212 #14	ENSGT00910000144356 #15	ENSGT00940000162636.A #16	ENSGT00940000162294 #17	ENSGT00940000163249 #18	ENSGT00940000161877.d	ENSGT00940000154755.c.a ##20	ENSGT00940000154755.c.b.d #19	ENSGT00940000154755.c.b.c #20	ENSGT00950000183147.B #21	ENSGT00940000160277 #22	ENSGT00440000039984.a #23	ENSGT00940000158550 #24	ENSGT00940000160793 #25	ENSGT01100000263540.A.a #26	ENSGT00950000183148.b.b #27	ENSGT00940000160517 #28	ENSGT00390000013968 #29	ENSGT00660000095541.a.a #30	ENSGT00390000003094 #31	ENSGT00520000055567.a.a.a	ENSGT00940000153311.a.b.a	ENSGT00940000161179	ENSGT00520000055634.b	ENSGT00940000161638	ENSGT00530000063880.a
Hystricomorpha_b	ANCESTRAL SPECIES	31	ENSGT00940000155999 #8	ENSGT00940000163276 #9	ENSGT00940000156996 #10	ENSGT00940000162041 #11	ENSGT00870000136554 #12	ENSGT00390000005826.a.b #13	ENSGT00900000141212 #14	ENSGT00910000144356 #15	ENSGT00940000162636.A #16	ENSGT00940000162294 #17	ENSGT00940000163249 #18	ENSGT00940000154755.c.a ##20	ENSGT00940000154755.c.b.d #19	ENSGT00940000154755.c.b.c #20	ENSGT00950000183147.B #21	ENSGT00940000160277 #22	ENSGT00440000039984.a #23	ENSGT00940000158550 #24	ENSGT00940000160793 #25	ENSGT01100000263540.A.a #26	ENSGT00950000183148.b.b #27	ENSGT00940000160517 #28	ENSGT00390000013968 #29	ENSGT00660000095541.a.a #30	ENSGT00390000003094 #31	ENSGT01030000234638.b.a.a #33	ENSGT00390000002121 #34	ENSGT00940000159016 #35	ENSGT00390000008063 #36	ENSGT01100000263497.E.a.a	ENSGT00390000006806 #37
Long-tailed chinchilla	MODERN SPECIES	122	PAX1 (ENSCLAG00000016362) #7	FOXA2 (ENSCLAG00000014548) #8	THBD (ENSCLAG00000011994) #9	CD93 (ENSCLAG00000012062) #10	NXT1 (ENSCLAG00000012493) #11	GZF1 (ENSCLAG00000014714) #12	NAPB (ENSCLAG00000011540) #13	CSTL1 (ENSCLAG00000012446) #14	ENSCLAG00000011384 #15	ENSCLAG00000015474 #16	ENSCLAG00000015212 #17	ENSCLAG00000017066 #18	ENSCLAG00000015899 #19	ENSCLAG00000012454 #20	SYNDIG1 (ENSCLAG00000012586) #21	CST7 (ENSCLAG00000015428) #22	APMAP (ENSCLAG00000013445) #23	ACSS1 (ENSCLAG00000012190) #24	VSX1 (ENSCLAG00000015160) #25	ENSCLAG00000015639 #26	PYGB (ENSCLAG00000012954) #27	ABHD12 (ENSCLAG00000010950) #28	GINS1 (ENSCLAG00000010830) #29	NINL (ENSCLAG00000011605) #30	NANP (ENSCLAG00000014668) #31	ZNF333 (ENSCLAG00000014959) #32	MAN2B1 (ENSCLAG00000013086) #33	ENSCLAG00000011821 #34	WDR83 (ENSCLAG00000012198) #35	DHPS (ENSCLAG00000012256) #36	FBXW9 (ENSCLAG00000012587) #37
Degu	MODERN SPECIES	114	PAX1 (ENSODEG00000012427) #7	FOXA2 (ENSODEG00000011162) #8	THBD (ENSODEG00000010709) #9	CD93 (ENSODEG00000012518) #10	NXT1 (ENSODEG00000019900) #11	GZF1 (ENSODEG00000013020) #12	NAPB (ENSODEG00000011065) #13	CSTL1 (ENSODEG00000010719) #14	CST11 (ENSODEG00000013274) #15	ENSODEG00000012595 #16	ENSODEG00000010448 #17	ENSODEG00000010611 #18	CST3 (ENSODEG00000012334) ##20	ENSODEG00000019797	SYNDIG1 (ENSODEG00000012369) #21	CST7 (ENSODEG00000011264) #22	APMAP (ENSODEG00000010678) #23	ACSS1 (ENSODEG00000010733) #24	VSX1 (ENSODEG00000010102) #25	ENTPD6 (ENSODEG00000010721) #26	PYGB (ENSODEG00000011290) #27	ABHD12 (ENSODEG00000013149) #28	GINS1 (ENSODEG00000011331) #29	ENSODEG00000014252 #30	ENSODEG00000012295 #31	ENSODEG00000012183	MAN2B1 (ENSODEG00000010434) #33	WDR83OS (ENSODEG00000011674) #34	WDR83 (ENSODEG00000010258) #35	DHPS (ENSODEG00000010756) #36	ENSODEG00000011490
Guinea pig	MODERN SPECIES	8	THBD (ENSCPOG00000030575) #9	CD93 (ENSCPOG00000010252) #10	NXT1 (ENSCPOG00000008817) #11	GZF1 (ENSCPOG00000010790) #12	NAPB (ENSCPOG00000039063) #13	CSTL1 (ENSCPOG00000008734) #14	ENSCPOG00000003822 #15	ENSCPOG00000025993 #16	CST8 (ENSCPOG00000005550) #17	ENSCPOG00000021926 #18	ENSCPOG00000025294	ENSCPOG00000030716 ##20	ENSCPOG00000030984 #19	ENSCPOG00000026799 #20	SYNDIG1 (ENSCPOG00000004943) #21	CST7 (ENSCPOG00000008022) #22	APMAP (ENSCPOG00000008131) #23	ACSS1 (ENSCPOG00000021704) #24	VSX1 (ENSCPOG00000003951) #25	ENTPD6 (ENSCPOG00000009587) #26	PYGB (ENSCPOG00000021215) #27	ABHD12 (ENSCPOG00000004078) #28	GINS1 (ENSCPOG00000000260) #29	NINL (ENSCPOG00000005041) #30	NANP (ENSCPOG00000031912) #31	ENSCPOG00000006435	ENSCPOG00000030176	ENSCPOG00000032111	NSFL1C (ENSCPOG00000004012)	ENSCPOG00000032891	SDCBP2 (ENSCPOG00000021957)
Naked mole-rat female	MODERN SPECIES	6	ENSHGLG00000043445	FOXA2 (ENSHGLG00000048805) #8	PAX1 (ENSHGLG00000015866) #7	NKX2-2 (ENSHGLG00000048629)	NKX2-4 (ENSHGLG00000008824)	XRN2 (ENSHGLG00000014831)	KIZ (ENSHGLG00000014057)	ENSHGLG00000037468	ENSHGLG00000016477	ENSHGLG00000047697	ENSHGLG00000013572	ENSHGLG00000035992 ##20	ENSHGLG00000001178 #20	ENSHGLG00000049828	ENSHGLG00000001156 #21	CST7 (ENSHGLG00000001075) #22	APMAP (ENSHGLG00000045360) #23	ENSHGLG00000042834 #24	ENSHGLG00000034236 #24	ENSHGLG00000039362	ENTPD6 (ENSHGLG00000000193) #26	PYGB (ENSHGLG00000000176) #27	ABHD12 (ENSHGLG00000035916) #28	ENSHGLG00000035611 #29	ENSHGLG00000040387	ENSHGLG00000000136	RASGRF1 (ENSHGLG00000000128)	ENSHGLG00000000119	ENSHGLG00000000106	ENSHGLG00000041324	ENSHGLG00000000301
Sciuridae	ANCESTRAL SPECIES	13	ENSGT00870000136554 #12	ENSGT00390000005826.a.b #13	ENSGT00900000141212 #14	ENSGT00910000144356 #15	ENSGT00940000162636.B ##16	ENSGT00940000162636.A #16	ENSGT00940000162294 #17	ENSGT00940000163249 #18	ENSGT00940000161877.c.a	ENSGT00940000161877.d	ENSGT00940000161877.c.b	ENSGT00940000164098	ENSGT00940000154755.c.a ##20	ENSGT00940000154755.c.b.e #20	ENSGT00950000183147.B #21	ENSGT00940000160277 #22	ENSGT00440000039984.a #23	ENSGT00940000158550 #24	ENSGT00940000160793 #25	ENSGT01100000263540.A.a #26	ENSGT00950000183148.b.b #27	ENSGT00940000160517 #28	ENSGT00390000013968 #29	ENSGT00660000095541.a.a #30	ENSGT00390000003094 #31
Marmotini	ANCESTRAL SPECIES	5	ENSGT00870000136554 #12	ENSGT00390000005826.a.b #13	ENSGT00900000141212 #14	ENSGT00910000144356 #15	ENSGT00940000162636.B ##16	ENSGT00940000162636.A #16	ENSGT00940000162294 #17	ENSGT00940000163249 #18	ENSGT00940000161877.c.a	ENSGT00940000161877.d	ENSGT00940000161877.c.b	ENSGT00940000154755.c.a ##20	ENSGT00940000154755.c.b.e #20	ENSGT00940000154755.c.b.f #20	ENSGT00950000183147.B #21	ENSGT00940000160277 #22	ENSGT00440000039984.a #23	ENSGT00940000158550 #24	ENSGT00940000160793 #25	ENSGT01100000263540.A.a #26	ENSGT00950000183148.b.b #27	ENSGT00940000160517 #28	ENSGT00390000013968 #29	ENSGT00660000095541.a.a #30	ENSGT00390000003094 #31	ENSGT00940000154617.B
Marmotini_b	ANCESTRAL SPECIES	140	ENSGT00870000136554 #12	ENSGT00390000005826.a.b #13	ENSGT00900000141212 #14	ENSGT00910000144356 #15	ENSGT00940000162636.B ##16	ENSGT00940000162636.A #16	ENSGT00940000162294 #17	ENSGT00940000163249 #18	ENSGT00940000161877.c.a	ENSGT00940000161877.d	ENSGT00940000161877.c.b	ENSGT00940000154755.c.a ##20	ENSGT00940000154755.c.b.e #20	ENSGT00940000154755.c.b.f #20	ENSGT00950000183147.B #21	ENSGT00940000160277 #22	ENSGT00440000039984.a #23	ENSGT00940000158550 #24	ENSGT00940000160793 #25	ENSGT01100000263540.A.a #26	ENSGT00950000183148.b.b #27	ENSGT00940000160517 #28	ENSGT00390000013968 #29	ENSGT00660000095541.a.a #30	ENSGT00390000003094 #31	ENSGT00940000154617.B
Squirrel	MODERN SPECIES	220	NAPB (ENSSTOG00000022350) #13	CSTL1 (ENSSTOG00000024563) #14	CST11 (ENSSTOG00000004847) #15	ENSSTOG00000021841 ##16	ENSSTOG00000024532 #16	CST8 (ENSSTOG00000004122) #17	ENSSTOG00000020102	ENSSTOG00000004129 #18	ENSSTOG00000028869	ENSSTOG00000015564	ENSSTOG00000026963 ##20	ENSSTOG00000023496	ENSSTOG00000001311 #20	ENSSTOG00000001243 #20	SYNDIG1 (ENSSTOG00000021952) #21	CST7 (ENSSTOG00000005896) #22	APMAP (ENSSTOG00000005903) #23	ACSS1 (ENSSTOG00000005944) #24	VSX1 (ENSSTOG00000026010) #25	ENTPD6 (ENSSTOG00000006956) #26	PYGB (ENSSTOG00000014388) #27	ABHD12 (ENSSTOG00000014396) #28	GINS1 (ENSSTOG00000014406) #29	NINL (ENSSTOG00000014411) #30	NANP (ENSSTOG00000002050) #31
Arctic ground squirrel	MODERN SPECIES	114	ENSUPAG00010009850	ENSUPAG00010009855	CSTL1 (ENSUPAG00010009856) #14	CST11 (ENSUPAG00010009858) #15	ENSUPAG00010009872 ##16	ENSUPAG00010009878 #16	CST8 (ENSUPAG00010009884) #17	ENSUPAG00010009895 #18	ENSUPAG00010009902	ENSUPAG00010009918	ENSUPAG00010009934 ##20	ENSUPAG00010009938 #20	ENSUPAG00010009978 #20	SYNDIG1 (ENSUPAG00010009998) #21	ENSUPAG00010010012	CST7 (ENSUPAG00010010018) #22	APMAP (ENSUPAG00010010025) #23	ACSS1 (ENSUPAG00010010043) #24	ENSUPAG00010010076	VSX1 (ENSUPAG00010010081) #25	ENTPD6 (ENSUPAG00010010093) #26	PYGB (ENSUPAG00010010109) #27	ABHD12 (ENSUPAG00010010127) #28	GINS1 (ENSUPAG00010010140) #29	NINL (ENSUPAG00010010146) #30	NANP (ENSUPAG00010010172) #31	CHRNA7 (ENSUPAG00010010177)
Alpin marmot	MODERN SPECIES	33																CST7 (ENSMMMG00000021618) #22	APMAP (ENSMMMG00000021607) #23	ACSS1 (ENSMMMG00000021594) #24	VSX1 (ENSMMMG00000021586) #25	ENTPD6 (ENSMMMG00000021571) #26	PYGB (ENSMMMG00000021556) #27	ABHD12 (ENSMMMG00000021545) #28	GINS1 (ENSMMMG00000021538) #29	NINL (ENSMMMG00000021519) #30	ENSMMMG00000021516	NANP (ENSMMMG00000021513) #31	CHRNA7 (ENSMMMG00000021504)	ENSMMMG00000021501	OTUD7A (ENSMMMG00000021494)	ENSMMMG00000021489	ENSMMMG00000021473
Eurasian red squirrel	MODERN SPECIES	11	NAPB (ENSSVLG00005000227) #13	CSTL1 (ENSSVLG00005000168) #14	CST11 (ENSSVLG00005000162) #15	ENSSVLG00005000139 ##16	ENSSVLG00005000133 #16	CST8 (ENSSVLG00005000126) #17	ENSSVLG00005012871 #18	ENSSVLG00005012823	ENSSVLG00005012749	ENSSVLG00005012678	ENSSVLG00005012635 ##20	ENSSVLG00005012618	ENSSVLG00005012569 #20	ENSSVLG00005012499 #20	SYNDIG1 (ENSSVLG00005012463) #21	CST7 (ENSSVLG00005012392) #22	APMAP (ENSSVLG00005012325) #23	ACSS1 (ENSSVLG00005012262) #24	ENSSVLG00005012189	VSX1 (ENSSVLG00005012048) #25	PYGB (ENSSVLG00005011885) #27	ABHD12 (ENSSVLG00005011759) #28	GINS1 (ENSSVLG00005011707) #29	NINL (ENSSVLG00005011654) #30	NANP (ENSSVLG00005011598) #31	ARL2BP (ENSSVLG00005011550)	ENSSVLG00005011535	CTXND1 (ENSSVLG00005011512)	ARNT2 (ENSSVLG00005011111)	ENSSVLG00005011041	ABHD17C (ENSSVLG00005010975)