Rodentia_A	ANCESTRAL SPECIES	17	ENSGT00940000161877.c.a	ENSGT00940000163249	ENSGT00940000162294	ENSGT00940000162636.A #7	ENSGT00940000162636.B #8	ENSGT00910000144356 #9	ENSGT00900000141212 #10	ENSGT00390000005826.a.b #11	ENSGT00870000136554 #12	ENSGT00940000162041 #14	ENSGT00940000156996 #15	ENSGT00940000163276 #16	ENSGT00940000156819.a.a #17	ENSGT00940000155999 #19	ENSGT00940000159137 #21	ENSGT00940000159727 #22	ENSGT00940000162247 #23	ENSGT00670000098098 #24	ENSGT00390000010121 #25	ENSGT00950000183139.A #27	ENSGT00940000162552 #28	ENSGT00940000167996	ENSGT00390000004987 #29	ENSGT00550000074931 #31	ENSGT00550000075046 #32	ENSGT00940000154866.B #33	ENSGT01030000234532.A.a.a.b #34	ENSGT00940000154327.b.e.b #35	ENSGT00940000153431.b #36	ENSGT00860000134050	ENSGT00390000006916.c
Sciuridae	ANCESTRAL SPECIES	13	ENSGT00940000161877.c.a	ENSGT00940000163249	ENSGT00940000162294	ENSGT00940000162636.A #7	ENSGT00940000162636.B #8	ENSGT00910000144356 #9	ENSGT00900000141212 #10	ENSGT00390000005826.a.b #11	ENSGT00870000136554 #12	ENSGT00940000162041 #14	ENSGT00940000156996 #15	ENSGT00940000163276 #16	ENSGT00940000156819.a.a #17	ENSGT00940000155999 #19	ENSGT00940000159137 #21	ENSGT00940000159727 #22	ENSGT00940000162247 #23	ENSGT00670000098098 #24	ENSGT00390000010121 #25	ENSGT00950000183139.A #27	ENSGT00940000162552 #28	ENSGT00940000167996	ENSGT00390000004987 #29	ENSGT00550000074931 #31	ENSGT00550000075046 #32	ENSGT00940000154866.B #33	ENSGT01030000234532.A.a.a.b #34	ENSGT00940000154327.b.e.b #35	ENSGT00940000153431.b #36	ENSGT00860000134050	ENSGT00390000006916.c
Eurasian red squirrel	MODERN SPECIES	11	ENSSVLG00005000133 #7	ENSSVLG00005000139 #8	CST11 (ENSSVLG00005000162) #9	CSTL1 (ENSSVLG00005000168) #10	NAPB (ENSSVLG00005000227) #11	GZF1 (ENSSVLG00005000288) #12	ENSSVLG00005000304 #13	ENSSVLG00005000317 #14	CD93 (ENSSVLG00005000330) #15	THBD (ENSSVLG00005000349) #16	SSTR4 (ENSSVLG00005000359) #17	ENSSVLG00005000368 #18	FOXA2 (ENSSVLG00005000389) #19	ENSSVLG00005000403 #20	PAX1 (ENSSVLG00005000421) #21	NKX2-2 (ENSSVLG00005000441) #22	NKX2-4 (ENSSVLG00005000455) #23	XRN2 (ENSSVLG00005000470) #24	KIZ (ENSSVLG00005000513) #25	ENSSVLG00005000546 #26	RALGAPA2 (ENSSVLG00005000611) #27	INSM1 (ENSSVLG00005000689) #28	CFAP61 (ENSSVLG00005000731) #29	ENSSVLG00005000777 #30	CRNKL1 (ENSSVLG00005000792) #31	NAA20 (ENSSVLG00005000837) #32	RIN2 (ENSSVLG00005000879) #33	SLC24A3 (ENSSVLG00005000927) #34	SCP2D1 (ENSSVLG00005000950) #35	DTD1 (ENSSVLG00005000962) #36	ENSSVLG00005000978 #37
Marmotini	ANCESTRAL SPECIES	5	ENSGT00940000161877.c.a	ENSGT00940000163249	ENSGT00940000162294	ENSGT00940000162636.A #7	ENSGT00940000162636.B #8	ENSGT00910000144356 #9	ENSGT00900000141212 #10	ENSGT00390000005826.a.b #11	ENSGT00870000136554 #12	ENSGT00940000162041 #14	ENSGT00940000156996 #15	ENSGT00940000163276 #16	ENSGT00940000156819.a.a #17	ENSGT00940000155999 #19	ENSGT00940000159137 #21	ENSGT00940000159727 #22	ENSGT00940000162247 #23	ENSGT00670000098098 #24	ENSGT00390000010121 #25	ENSGT00390000007696.e.a.a.a	ENSGT00950000183139.A #27	ENSGT00940000162552 #28	ENSGT00940000167996	ENSGT00390000004987 #29	ENSGT00550000074931 #31	ENSGT00550000075046 #32	ENSGT00940000154866.B #33	ENSGT01030000234532.A.a.a.b #34	ENSGT00940000154327.b.e.b #35	ENSGT00940000153431.b #36	ENSGT00860000134050
Marmotini_b	ANCESTRAL SPECIES	140	ENSGT00940000161877.c.a	ENSGT00940000163249	ENSGT00940000162294	ENSGT00940000162636.A #7	ENSGT00940000162636.B #8	ENSGT00910000144356 #9	ENSGT00900000141212 #10	ENSGT00390000005826.a.b #11	ENSGT00870000136554 #12	ENSGT00940000162041 #14	ENSGT00940000156996 #15	ENSGT00940000163276 #16	ENSGT00940000156819.a.a #17	ENSGT00940000155999 #19	ENSGT00940000159137 #21	ENSGT00940000159727 #22	ENSGT00940000162247 #23	ENSGT00670000098098 #24	ENSGT00390000010121 #25	ENSGT00390000007696.e.a.a.a
Squirrel	MODERN SPECIES	220	ENSSTOG00000004129	ENSSTOG00000020102	CST8 (ENSSTOG00000004122)	ENSSTOG00000024532 #7	ENSSTOG00000021841 #8	CST11 (ENSSTOG00000004847) #9	CSTL1 (ENSSTOG00000024563) #10	NAPB (ENSSTOG00000022350) #11	ENSSTOG00000030626	GZF1 (ENSSTOG00000009820) #12	NXT1 (ENSSTOG00000026331) #14	CD93 (ENSSTOG00000024530) #15	SSTR4 (ENSSTOG00000021697) #17	FOXA2 (ENSSTOG00000020150) #19	PAX1 (ENSSTOG00000003000) #21	NKX2-2 (ENSSTOG00000021450) #22	XRN2 (ENSSTOG00000000589) #24	KIZ (ENSSTOG00000007449) #25
Arctic ground squirrel	MODERN SPECIES	114	CST11 (ENSUPAG00010009858) #9	CSTL1 (ENSUPAG00010009856) #10	ENSUPAG00010009855	ENSUPAG00010009850	NAPB (ENSUPAG00010009788) #11	GZF1 (ENSUPAG00010009780) #12	NXT1 (ENSUPAG00010009776) #14	ENSUPAG00010009772	ENSUPAG00010009759	CD93 (ENSUPAG00010009758) #15	THBD (ENSUPAG00010009753) #16	SSTR4 (ENSUPAG00010009751) #17	FOXA2 (ENSUPAG00010009738) #19	ENSUPAG00010009726	PAX1 (ENSUPAG00010009718) #21	NKX2-2 (ENSUPAG00010009710) #22	NKX2-4 (ENSUPAG00010009706) #23	XRN2 (ENSUPAG00010009667) #24	KIZ (ENSUPAG00010009237) #25	ENSUPAG00010009220
Alpin marmot	MODERN SPECIES		CST8 (ENSMMMG00000004504)	ENSMMMG00000004491 #7	ENSMMMG00000004483 #8	CST11 (ENSMMMG00000004467) #9	CSTL1 (ENSMMMG00000004456) #10	ENSMMMG00000004433	NAPB (ENSMMMG00000004419) #11	GZF1 (ENSMMMG00000004407) #12	NXT1 (ENSMMMG00000004405) #14	ENSMMMG00000004398	CD93 (ENSMMMG00000004395) #15	THBD (ENSMMMG00000004391) #16	SSTR4 (ENSMMMG00000004385) #17	FOXA2 (ENSMMMG00000004350) #19	PAX1 (ENSMMMG00000004326) #21	NKX2-2 (ENSMMMG00000004284) #22	XRN2 (ENSMMMG00000004161) #24	KIZ (ENSMMMG00000003881) #25	ENSMMMG00000003871	RALGAPA2 (ENSMMMG00000003453) #27	ENSMMMG00000003417	ENSMMMG00000003408 #29	ENSMMMG00000003290 #29	CRNKL1 (ENSMMMG00000003244) #31	NAA20 (ENSMMMG00000003240) #32	RIN2 (ENSMMMG00000003172) #33	SLC24A3 (ENSMMMG00000003105) #34	SCP2D1 (ENSMMMG00000003079) #35	ENSMMMG00000003073	DTD1 (ENSMMMG00000003060) #36	SMIM26 (ENSMMMG00000003045)
Hystricomorpha	ANCESTRAL SPECIES	10	ENSGT00940000154755.c.b	ENSGT00940000154755.c.a	ENSGT00940000161877.d	ENSGT00940000163249	ENSGT00940000162294	ENSGT00940000162636.A #7	ENSGT00910000144356 #9	ENSGT00900000141212 #10	ENSGT00390000005826.a.b #11	ENSGT00870000136554 #12	ENSGT00940000162041 #14	ENSGT00940000156996 #15	ENSGT00940000163276 #16	ENSGT00940000155999 #19	ENSGT00940000159137 #21	ENSGT00940000159727 #22	ENSGT00940000162247 #23	ENSGT00670000098098 #24	ENSGT00390000010121 #25	ENSGT00950000183139.A #27	ENSGT00940000162552 #28	ENSGT00940000167996	ENSGT00390000004987.n.a #29	ENSGT00550000074931 #31	ENSGT00550000075046 #32	ENSGT00940000154866.B #33	ENSGT01030000234532.A.a.a.b #34	ENSGT00940000153431.b #36	ENSGT00390000006916.c	ENSGT00390000014861	ENSGT00390000009679
Hystricomorpha_a	ANCESTRAL SPECIES	8	ENSGT00940000154755.c.b.d	ENSGT00940000154755.c.a	ENSGT00940000161877.d	ENSGT00940000163249	ENSGT00940000162294	ENSGT00940000162636.A #7	ENSGT00910000144356 #9	ENSGT00900000141212 #10	ENSGT00390000005826.a.b #11	ENSGT00870000136554 #12	ENSGT00940000162041 #14	ENSGT00940000156996 #15	ENSGT00940000163276 #16	ENSGT00940000155999 #19	ENSGT00940000159137 #21	ENSGT00940000159727 #22	ENSGT00940000162247 #23	ENSGT00670000098098 #24	ENSGT00390000010121 #25	ENSGT00950000183139.A #27	ENSGT00940000162552 #28	ENSGT00940000167996	ENSGT00390000004987.n.a #29	ENSGT00550000074931 #31	ENSGT00550000075046 #32	ENSGT00940000154866.B #33	ENSGT01030000234532.A.a.a.b #34	ENSGT00940000153431.b #36	ENSGT00390000006916.c	ENSGT00390000014861	ENSGT00390000009679
Hystricomorpha_b	ANCESTRAL SPECIES	31	ENSGT00940000154755.c.b.c	ENSGT00940000154755.c.b.d	ENSGT00940000154755.c.a	ENSGT00940000163249	ENSGT00940000162294	ENSGT00940000162636.A #7	ENSGT00910000144356 #9	ENSGT00900000141212 #10	ENSGT00390000005826.a.b #11	ENSGT00870000136554 #12	ENSGT00940000162041 #14	ENSGT00940000156996 #15	ENSGT00940000163276 #16	ENSGT00940000155999 #19	ENSGT00940000159137 #21	ENSGT00940000159727 #22	ENSGT00940000162247 #23	ENSGT00670000098098 #24	ENSGT00390000010121 #25	ENSGT00950000183139.A #27	ENSGT00940000162552 #28	ENSGT00940000167996	ENSGT00390000004987.n.a #29	ENSGT00550000074931 #31	ENSGT00550000075046 #32	ENSGT00940000154866.B #33	ENSGT01030000234532.A.a.a.b #34	ENSGT00940000153431.b #36	ENSGT00390000006916.c	ENSGT00390000014861	ENSGT00390000009679
Long-tailed chinchilla	MODERN SPECIES	122	SYNDIG1 (ENSCLAG00000012586)	ENSCLAG00000012454	ENSCLAG00000015899	ENSCLAG00000017066	ENSCLAG00000015212	ENSCLAG00000015474 #7	ENSCLAG00000011384 #9	CSTL1 (ENSCLAG00000012446) #10	NAPB (ENSCLAG00000011540) #11	GZF1 (ENSCLAG00000014714) #12	NXT1 (ENSCLAG00000012493) #14	CD93 (ENSCLAG00000012062) #15	THBD (ENSCLAG00000011994) #16	FOXA2 (ENSCLAG00000014548) #19	PAX1 (ENSCLAG00000016362) #21	NKX2-2 (ENSCLAG00000016430) #22	XRN2 (ENSCLAG00000013419) #24	KIZ (ENSCLAG00000012565) #25	RALGAPA2 (ENSCLAG00000012502) #27	CFAP61 (ENSCLAG00000014155) #29	CRNKL1 (ENSCLAG00000013859) #31	NAA20 (ENSCLAG00000014313) #32	RIN2 (ENSCLAG00000015234) #33	SLC24A3 (ENSCLAG00000015547) #34	DTD1 (ENSCLAG00000015302) #36	SEC23B (ENSCLAG00000014924)	RBBP9 (ENSCLAG00000014851)	POLR3F (ENSCLAG00000016296)	DZANK1 (ENSCLAG00000013160)	ZNF133 (ENSCLAG00000015115)	KAT14 (ENSCLAG00000012590)
Degu	MODERN SPECIES	114	CST3 (ENSODEG00000012334)	ENSODEG00000010611	ENSODEG00000010448	ENSODEG00000012595 #7	CST11 (ENSODEG00000013274) #9	CSTL1 (ENSODEG00000010719) #10	NAPB (ENSODEG00000011065) #11	GZF1 (ENSODEG00000013020) #12	NXT1 (ENSODEG00000019900) #14	CD93 (ENSODEG00000012518) #15	THBD (ENSODEG00000010709) #16	FOXA2 (ENSODEG00000011162) #19	PAX1 (ENSODEG00000012427) #21	ENSODEG00000019878	ENSODEG00000019885	NKX2-2 (ENSODEG00000012371) #22	ENSODEG00000012687	NKX2-4 (ENSODEG00000010842) #23	ENSODEG00000010745 #24	ENSODEG00000011188	KIZ (ENSODEG00000011491) #25	RALGAPA2 (ENSODEG00000011023) #27	INSM1 (ENSODEG00000020028) #28	ENSODEG00000011346	ENSODEG00000012124 #29	ENSODEG00000012675 #29	CRNKL1 (ENSODEG00000012175) #31	NAA20 (ENSODEG00000011704) #32	RIN2 (ENSODEG00000012000) #33	SLC24A3 (ENSODEG00000012016) #34	DTD1 (ENSODEG00000012785) #36
Guinea pig	MODERN SPECIES	8	ENSCPOG00000030984	ENSCPOG00000030716	ENSCPOG00000025294	ENSCPOG00000021926	CST8 (ENSCPOG00000005550)	ENSCPOG00000025993 #7	ENSCPOG00000003822 #9	CSTL1 (ENSCPOG00000008734) #10	NAPB (ENSCPOG00000039063) #11	GZF1 (ENSCPOG00000010790) #12	NXT1 (ENSCPOG00000008817) #14	CD93 (ENSCPOG00000010252) #15	THBD (ENSCPOG00000030575) #16	FOXA2 (ENSCPOG00000033370) #19	PAX1 (ENSCPOG00000002886) #21	NKX2-2 (ENSCPOG00000000408) #22	XRN2 (ENSCPOG00000009407) #24	KIZ (ENSCPOG00000005683) #25	RALGAPA2 (ENSCPOG00000001602) #27	ENSCPOG00000038064	ENSCPOG00000039658 #29	ENSCPOG00000001594 #29	CRNKL1 (ENSCPOG00000004418) #31	NAA20 (ENSCPOG00000001593) #32	RIN2 (ENSCPOG00000013179) #33	SLC24A3 (ENSCPOG00000011970) #34	DTD1 (ENSCPOG00000002416) #36	SEC23B (ENSCPOG00000002406)	RBBP9 (ENSCPOG00000036556)	POLR3F (ENSCPOG00000002400)	DZANK1 (ENSCPOG00000002397)
Naked mole-rat female	MODERN SPECIES	6	ENSHGLG00000044421	ENSHGLG00000048121	ENSHGLG00000014789	ENSHGLG00000016940	ENSHGLG00000017168	ENSHGLG00000011435	CST8 (ENSHGLG00000011126)	ENSHGLG00000009572 #7	CST11 (ENSHGLG00000009307) #9	CSTL1 (ENSHGLG00000016858) #10	NAPB (ENSHGLG00000016842) #11	ENSHGLG00000037985 #12	ENSHGLG00000043445	FOXA2 (ENSHGLG00000048805) #19	PAX1 (ENSHGLG00000015866) #21	NKX2-2 (ENSHGLG00000048629) #22	NKX2-4 (ENSHGLG00000008824) #23	XRN2 (ENSHGLG00000014831) #24	KIZ (ENSHGLG00000014057) #25	ENSHGLG00000037468	ENSHGLG00000016477 #27	ENSHGLG00000047697	ENSHGLG00000013572 #29	ENSHGLG00000035992	ENSHGLG00000001178	ENSHGLG00000049828	ENSHGLG00000001156	CST7 (ENSHGLG00000001075)	APMAP (ENSHGLG00000045360)	ENSHGLG00000042834	ENSHGLG00000034236