Rodentia_A	ANCESTRAL SPECIES	21	ENSGT01030000234522.C.b.e.a.a.b	ENSGT00390000013415.a.b	ENSGT00950000182864.a.b.a	ENSGT00950000182859.A.a.a.b #8	ENSGT00940000154352.A #10	ENSGT00940000154314 #11	ENSGT00390000008225 #12	ENSGT00940000157734 #13	ENSGT00940000156208 #14	ENSGT00940000161685.A.a	ENSGT00940000161406 #17	ENSGT00900000141143 #18	ENSGT00940000156716 #19	ENSGT00390000005989.b #20	ENSGT00940000162737 #21	ENSGT00940000160930 #22	ENSGT00940000158607 #23	ENSGT00940000172945	ENSGT01100000263540.B.d #24	ENSGT00940000155874 #26	ENSGT00530000063711.a #27	ENSGT00720000108860 #29	ENSGT00940000162957	ENSGT00940000158918 #30	ENSGT00940000162387	ENSGT00940000160355 #32	ENSGT00950000182882.B #33	ENSGT00530000063672.b #34	ENSGT00390000000531 #35	ENSGT00940000160418 #36	ENSGT00940000160558 #37
Hystricomorpha	ANCESTRAL SPECIES	21	ENSGT01030000234527.A.a.b.a.a	ENSGT00390000013415.a.b	ENSGT00950000182864.a.b.a	ENSGT00950000182859.A.a.a.b #8	ENSGT00940000154352.A #10	ENSGT00940000154314 #11	ENSGT00390000008225 #12	ENSGT00940000157734 #13	ENSGT00940000156208 #14	ENSGT00940000161685.A.a	ENSGT00940000161406 #17	ENSGT00900000141143 #18	ENSGT00940000156716 #19	ENSGT00390000005989.b #20	ENSGT00940000162737 #21	ENSGT00940000160930 #22	ENSGT00940000158607 #23	ENSGT00940000172945	ENSGT01100000263540.B.d #24	ENSGT00940000155874 #26	ENSGT00530000063711.a #27	ENSGT00720000108860 #29	ENSGT00940000162957	ENSGT00940000158918 #30	ENSGT00940000162387	ENSGT00940000160355 #32	ENSGT00950000182882.B #33	ENSGT00530000063672.b #34	ENSGT00390000000531 #35	ENSGT00940000160418 #36	ENSGT00940000160558 #37
Hystricomorpha_a	ANCESTRAL SPECIES	20	ENSGT01030000234527.A.a.b.a.a	ENSGT00390000013415.a.b	ENSGT00950000182864.a.b.a	ENSGT00950000182859.A.a.a.b #8	ENSGT00940000154352.A #10	ENSGT00940000154314 #11	ENSGT00390000008225 #12	ENSGT00940000157734 #13	ENSGT00940000156208 #14	ENSGT00940000161685.A.a	ENSGT00940000161406 #17	ENSGT00900000141143 #18	ENSGT00940000156716 #19	ENSGT00390000005989.b #20	ENSGT00940000162737 #21	ENSGT00940000160930 #22	ENSGT00940000158607 #23	ENSGT01100000263540.B.d #24	ENSGT00940000155874 #26	ENSGT00530000063711.a #27	ENSGT00720000108860 #29	ENSGT00940000162957	ENSGT00940000158918 #30	ENSGT00940000162387	ENSGT00940000160355 #32	ENSGT00950000182882.B #33	ENSGT00530000063672.b #34	ENSGT00390000000531 #35	ENSGT00940000160418 #36	ENSGT00940000160558 #37	ENSGT00940000154115.c.a
Hystricomorpha_b	ANCESTRAL SPECIES	30	ENSGT01030000234527.A.a.b.a.a	ENSGT00390000013415.a.b	ENSGT00950000182864.a.b.a	ENSGT00950000182859.A.a.a.b #8	ENSGT00940000154352.A #10	ENSGT00940000154314 #11	ENSGT00390000008225 #12	ENSGT00940000157734 #13	ENSGT00940000156208 #14	ENSGT00940000161685.A.a	ENSGT00940000161406 #17	ENSGT00900000141143 #18	ENSGT00940000156716 #19	ENSGT00390000005989.b #20	ENSGT00940000162737 #21	ENSGT00940000160930 #22	ENSGT00940000158607 #23	ENSGT01100000263540.B.d #24	ENSGT00940000155874 #26	ENSGT00530000063711.a #27	ENSGT00720000108860 #29	ENSGT00940000162957	ENSGT00940000158918 #30	ENSGT00940000162387	ENSGT00940000160355 #32	ENSGT00950000182882.B #33	ENSGT00530000063672.b #34	ENSGT00390000000531 #35	ENSGT00940000160418 #36	ENSGT00940000160558 #37	ENSGT00940000154115.c.a
Degu	MODERN SPECIES	77	ENSODEG00000007854 #7	EBF2 (ENSODEG00000007640) #8	ENSODEG00000006905 #9	ENSODEG00000007418 #10	KCTD9 (ENSODEG00000008616) #11	GNRH1 (ENSODEG00000007834) #12	DOCK5 (ENSODEG00000007523) #13	NEFL (ENSODEG00000007183) #14	NEFM (ENSODEG00000008392) #15	ENSODEG00000007521 #16	ADAM7 (ENSODEG00000007547) #17	ADAMDEC1 (ENSODEG00000008034) #18	ADAM28 (ENSODEG00000007875) #19	STC1 (ENSODEG00000007382) #20	NKX2-6 (ENSODEG00000007413) #21	NKX3-1 (ENSODEG00000007004) #22	SLC25A37 (ENSODEG00000007363) #23	ENTPD4 (ENSODEG00000009788) #24	ENSODEG00000009404 #25	LOXL2 (ENSODEG00000006938) #26	R3HCC1 (ENSODEG00000007529) #27	ENSODEG00000019474 #28	ENSODEG00000007294 #29	RHOBTB2 (ENSODEG00000007111) #30	ENSODEG00000008725 #31	EGR3 (ENSODEG00000007442) #32	BIN3 (ENSODEG00000006965) #33	CCAR2 (ENSODEG00000008466) #34	C8orf58 (ENSODEG00000006637) #35	PDLIM2 (ENSODEG00000006028) #36	SORBS3 (ENSODEG00000007179) #37
Long-tailed chinchilla	MODERN SPECIES	110	BNIP3L (ENSCLAG00000016223)	PPP2R2A (ENSCLAG00000013984)	EBF2 (ENSCLAG00000013500) #8	CDCA2 (ENSCLAG00000011981) #10	KCTD9 (ENSCLAG00000013948) #11	GNRH1 (ENSCLAG00000014234) #12	DOCK5 (ENSCLAG00000015174) #13	NEFL (ENSCLAG00000014935) #14	ENSCLAG00000013799	ADAM7 (ENSCLAG00000013174) #17	ENSCLAG00000015375 #18	ADAM28 (ENSCLAG00000016310) #19	ENSCLAG00000015807	STC1 (ENSCLAG00000014786) #20	NKX2-6 (ENSCLAG00000014720) #21	NKX3-1 (ENSCLAG00000013957) #22	SLC25A37 (ENSCLAG00000014235) #23	ENTPD4 (ENSCLAG00000013899) #24	LOXL2 (ENSCLAG00000016283) #26	R3HCC1 (ENSCLAG00000015556) #27	CHMP7 (ENSCLAG00000015529) #29	ENSCLAG00000013896	RHOBTB2 (ENSCLAG00000014037) #30	PEBP4 (ENSCLAG00000015116)	EGR3 (ENSCLAG00000016373) #32	BIN3 (ENSCLAG00000016398) #33	CCAR2 (ENSCLAG00000014299) #34	C8orf58 (ENSCLAG00000014186) #35	ENSCLAG00000014272 #36	SORBS3 (ENSCLAG00000014309) #37	PPP3CC (ENSCLAG00000015203)
Guinea pig	MODERN SPECIES	1	ADRA1A (ENSCPOG00000038399)	DPYSL2 (ENSCPOG00000025679)	BNIP3L (ENSCPOG00000034680)	PPP2R2A (ENSCPOG00000026784)	EBF2 (ENSCPOG00000001463) #8	CDCA2 (ENSCPOG00000036890) #10	KCTD9 (ENSCPOG00000015540) #11	GNRH1 (ENSCPOG00000015538) #12	DOCK5 (ENSCPOG00000015533) #13	NEFL (ENSCPOG00000023838) #14	ENSCPOG00000027410	ADAM7 (ENSCPOG00000001538) #17	ADAMDEC1 (ENSCPOG00000038140) #18	ADAM28 (ENSCPOG00000009707) #19	STC1 (ENSCPOG00000034351) #20	NKX3-1 (ENSCPOG00000040229) #22	SLC25A37 (ENSCPOG00000035237) #23	ENTPD4 (ENSCPOG00000009705) #24	LOXL2 (ENSCPOG00000009701) #26	R3HCC1 (ENSCPOG00000009696) #27	CHMP7 (ENSCPOG00000002456) #29	RHOBTB2 (ENSCPOG00000039763) #30	PEBP4 (ENSCPOG00000015616)	EGR3 (ENSCPOG00000038322) #32	BIN3 (ENSCPOG00000010994) #33	CCAR2 (ENSCPOG00000010985) #34	C8orf58 (ENSCPOG00000039428) #35	ENSCPOG00000020871 #36	SORBS3 (ENSCPOG00000001115) #37	PPP3CC (ENSCPOG00000001113)	SLC39A14 (ENSCPOG00000001112)
Naked mole-rat female	MODERN SPECIES	25	ENSHGLG00000036572	ENSHGLG00000018824 #11	GNRH1 (ENSHGLG00000017902) #12	DOCK5 (ENSHGLG00000017514) #13	ENSHGLG00000050046	NEFL (ENSHGLG00000017653) #14	ENSHGLG00000019352	ENSHGLG00000036278	ADAM7 (ENSHGLG00000017673) #17	ADAMDEC1 (ENSHGLG00000011872) #18	ADAM28 (ENSHGLG00000018858) #19	ENSHGLG00000040240	STC1 (ENSHGLG00000040196) #20	NKX2-6 (ENSHGLG00000014624) #21	ENSHGLG00000044875	NKX3-1 (ENSHGLG00000049073) #22	SLC25A37 (ENSHGLG00000036264) #23	ENSHGLG00000032907	ENSHGLG00000010644 #24	LOXL2 (ENSHGLG00000012019) #26	R3HCC1 (ENSHGLG00000010517) #27	ENSHGLG00000009513 #29	ENSHGLG00000032756	RHOBTB2 (ENSHGLG00000016441) #30	ENSHGLG00000049596	PEBP4 (ENSHGLG00000042512)	EGR3 (ENSHGLG00000040205) #32	BIN3 (ENSHGLG00000014664) #33	CCAR2 (ENSHGLG00000015483) #34	ENSHGLG00000010238 #35	PDLIM2 (ENSHGLG00000007806) #36
Sciuridae	ANCESTRAL SPECIES	29	ENSGT00390000013415.a.b	ENSGT00950000182864.a.b.a	ENSGT00950000182859.A.a.a.b #8	ENSGT00940000154352.A #10	ENSGT00940000154314.j #11	ENSGT00390000008225 #12	ENSGT00940000157734 #13	ENSGT00940000156208 #14	ENSGT00940000161685.A.a	ENSGT00940000154418.a.b #15	ENSGT00940000161406 #17	ENSGT00900000141143 #18	ENSGT00940000156716 #19	ENSGT00390000005989.b #20	ENSGT00940000162737 #21	ENSGT00940000160930 #22	ENSGT00940000158607 #23	ENSGT01100000263540.B.d #24	ENSGT00940000155874 #26	ENSGT00530000063711.a #27	ENSGT00720000108860 #29	ENSGT00940000162957	ENSGT00940000158918 #30	ENSGT00940000162387	ENSGT00940000160355 #32	ENSGT00950000182882.B #33	ENSGT00530000063672.b #34	ENSGT00390000000531 #35	ENSGT00940000160418 #36	ENSGT00940000160558 #37	ENSGT00940000154115.c.a
Marmotini	ANCESTRAL SPECIES	30	ENSGT00390000013415.a.b	ENSGT00950000182864.a.b.a	ENSGT00950000182859.A.a.a.b #8	ENSGT00940000154352.A #10	ENSGT00940000154314.j #11	ENSGT00390000008225 #12	ENSGT00940000157734 #13	ENSGT00940000156208 #14	ENSGT00940000161685.A.a	ENSGT00940000161406 #17	ENSGT00900000141143 #18	ENSGT00940000156716 #19	ENSGT00940000159453.e.b	ENSGT00390000005989.b #20	ENSGT00940000162737 #21	ENSGT00940000160930 #22	ENSGT00940000158607 #23	ENSGT01100000263540.B.d #24	ENSGT00940000155874 #26	ENSGT00530000063711.a #27	ENSGT00720000108860 #29	ENSGT00940000162957	ENSGT00940000158918 #30	ENSGT00940000162387	ENSGT00940000160355 #32	ENSGT00950000182882.B #33	ENSGT00530000063672.b #34	ENSGT00390000000531 #35	ENSGT00940000160418 #36	ENSGT00940000160558 #37	ENSGT00940000154115.c.a
Marmotini_b	ANCESTRAL SPECIES	87										ENSGT00940000161406 #17	ENSGT00900000141143 #18	ENSGT00940000156716 #19	ENSGT00940000159453.e.b	ENSGT00390000005989.b #20	ENSGT00940000162737 #21	ENSGT00940000160930 #22	ENSGT00940000158607 #23	ENSGT01100000263540.B.d #24	ENSGT00940000155874 #26	ENSGT00530000063711.a #27	ENSGT00720000108860 #29	ENSGT00940000162957	ENSGT00940000158918 #30	ENSGT00940000162387	ENSGT00940000160355 #32	ENSGT00950000182882.B #33	ENSGT00530000063672.b #34	ENSGT00390000000531 #35	ENSGT00940000160418 #36	ENSGT00940000160558 #37	ENSGT00940000154115.c.a
Arctic ground squirrel	MODERN SPECIES	186										ADAM7 (ENSUPAG00010017328) #17	ADAMDEC1 (ENSUPAG00010017356) #18	ADAM28 (ENSUPAG00010017386) #19	ENSUPAG00010017423	STC1 (ENSUPAG00010017427) #20	NKX2-6 (ENSUPAG00010017433) #21	NKX3-1 (ENSUPAG00010017442) #22	SLC25A37 (ENSUPAG00010017448) #23	ENTPD4 (ENSUPAG00010017458) #24	LOXL2 (ENSUPAG00010017498) #26	R3HCC1 (ENSUPAG00010017502) #27	CHMP7 (ENSUPAG00010017507) #29	ENSUPAG00010017525	RHOBTB2 (ENSUPAG00010017538) #30	PEBP4 (ENSUPAG00010017546)	EGR3 (ENSUPAG00010017554) #32	BIN3 (ENSUPAG00010017563) #33	CCAR2 (ENSUPAG00010017585) #34	C8orf58 (ENSUPAG00010017613) #35	PDLIM2 (ENSUPAG00010017621) #36	SORBS3 (ENSUPAG00010017635) #37	PPP3CC (ENSUPAG00010017686)
Squirrel	MODERN SPECIES	155											ADAM7 (ENSSTOG00000012955) #17	ADAMDEC1 (ENSSTOG00000032677) #18	ADAM28 (ENSSTOG00000006248) #19	STC1 (ENSSTOG00000007507) #20	NKX2-6 (ENSSTOG00000025482) #21	NKX3-1 (ENSSTOG00000029597) #22	SLC25A37 (ENSSTOG00000025533) #23	ENTPD4 (ENSSTOG00000015892) #24	LOXL2 (ENSSTOG00000015878) #26	R3HCC1 (ENSSTOG00000027130) #27	CHMP7 (ENSSTOG00000015867) #29	ENSSTOG00000001440	RHOBTB2 (ENSSTOG00000029109) #30	PEBP4 (ENSSTOG00000032426)	EGR3 (ENSSTOG00000021065) #32	BIN3 (ENSSTOG00000011677) #33	CCAR2 (ENSSTOG00000011666) #34	C8orf58 (ENSSTOG00000021866) #35	PDLIM2 (ENSSTOG00000024161) #36	SORBS3 (ENSSTOG00000011660) #37	PPP3CC (ENSSTOG00000028936)
Eurasian red squirrel	MODERN SPECIES	14	ENSSVLG00005003080	EBF2 (ENSSVLG00005003172) #8	CDCA2 (ENSSVLG00005003275) #10	KCTD9 (ENSSVLG00005003331) #11	GNRH1 (ENSSVLG00005003367) #12	DOCK5 (ENSSVLG00005003397) #13	ENSSVLG00005003428	ENSSVLG00005003443	NEFL (ENSSVLG00005003461) #14	NEFM (ENSSVLG00005003494) #15	ADAM7 (ENSSVLG00005003562) #17	ADAMDEC1 (ENSSVLG00005003660) #18	ADAM28 (ENSSVLG00005003701) #19	STC1 (ENSSVLG00005003730) #20	NKX2-6 (ENSSVLG00005003752) #21	NKX3-1 (ENSSVLG00005003772) #22	SLC25A37 (ENSSVLG00005003790) #23	ENTPD4 (ENSSVLG00005003809) #24	LOXL2 (ENSSVLG00005003840) #26	R3HCC1 (ENSSVLG00005003877) #27	CHMP7 (ENSSVLG00005003902) #29	RHOBTB2 (ENSSVLG00005003947) #30	PEBP4 (ENSSVLG00005003991)	ENSSVLG00005004016	BIN3 (ENSSVLG00005004049) #33	CCAR2 (ENSSVLG00005004079) #34	C8orf58 (ENSSVLG00005004115) #35	PDLIM2 (ENSSVLG00005004159) #36	SORBS3 (ENSSVLG00005004211) #37	ENSSVLG00005004276	SLC39A14 (ENSSVLG00005004424)