Rodentia_A	ANCESTRAL SPECIES	4	ENSGT00950000182825.A.a.b.a.b.a.b.b.b ##10	ENSGT00950000182825.A.a.b.a.b.a.a.a.a.b #10	ENSGT00950000182825.A.a.b.a.b.a.b.a.b #9	ENSGT00940000154457.a.b	ENSGT00940000160203 #11	ENSGT00950000185831	ENSGT00390000012132 #12	ENSGT00940000155969 #13	ENSGT00390000012136 #14	ENSGT00390000001138.a #15	ENSGT00940000161742 #16	ENSGT00390000005536 #17	ENSGT00940000162031 #18	ENSGT00930000150980.b #20	ENSGT00940000159962 #21	ENSGT01050000244940.a.a #22	ENSGT00530000063607.a #24	ENSGT00940000153993.B #25	ENSGT01050000244890.a.b.b #27	ENSGT00940000160612.d #28	ENSGT01090000263345	ENSGT00940000161557.b #29	ENSGT01070000257243	ENSGT00940000161949 #30	ENSGT00940000154610.e.b #31	ENSGT00940000158414 #32	ENSGT00940000156629 #33	ENSGT00390000003114.e.a #34	ENSGT00390000002190 #35	ENSGT01030000234515.a.a.a #36	ENSGT00940000158313 #37
Sciuridae	ANCESTRAL SPECIES	15	ENSGT00950000182825.A.a.b.a.b.a.b.b.b ##10	ENSGT00950000182825.A.a.b.a.b.a.a.a.a.b #10	ENSGT00950000182825.A.a.b.a.b.a.b.a.b #9	ENSGT00940000154457.a.b	ENSGT00940000160203 #11	ENSGT00950000185831	ENSGT00390000012132 #12	ENSGT00940000155969 #13	ENSGT00390000012136 #14	ENSGT00390000001138.a #15	ENSGT00940000161742 #16	ENSGT00390000005536 #17	ENSGT00940000162031 #18	ENSGT00930000150980.b #20	ENSGT00940000159962 #21	ENSGT01050000244940.a.a #22	ENSGT00530000063607.a #24	ENSGT00940000153993.B #25	ENSGT01050000244890.a.b.b #27	ENSGT00940000160612.d #28	ENSGT00940000161557.b #29	ENSGT00940000161949 #30	ENSGT00940000154610.e.b #31	ENSGT00940000158414 #32	ENSGT00940000156629 #33	ENSGT00390000003114.e.a #34	ENSGT00390000002190 #35	ENSGT01030000234515.a.a.a #36	ENSGT00940000158313 #37	ENSGT00940000163376	ENSGT00940000154409.i.a
Eurasian red squirrel	MODERN SPECIES	14	LMBR1L (ENSSVLG00005014035) #7	TUBA1B (ENSSVLG00005014122) #8	TUBA1A (ENSSVLG00005014169) #9	TUBA1C (ENSSVLG00005014280) #10	PRPH (ENSSVLG00005014401) #11	TROAP (ENSSVLG00005014514) #12	C1QL4 (ENSSVLG00005014552) #13	DNAJC22 (ENSSVLG00005014577) #14	SPATS2 (ENSSVLG00005014637) #15	KCNH3 (ENSSVLG00005014784) #16	MCRS1 (ENSSVLG00005014844) #17	FAM186B (ENSSVLG00005015063) #18	ENSSVLG00005015194 #19	PRPF40B (ENSSVLG00005015266) #20	FMNL3 (ENSSVLG00005015953) #21	TMBIM6 (ENSSVLG00005016085) #22	ENSSVLG00005016133 #23	NCKAP5L (ENSSVLG00005016159) #24	BCDIN3D (ENSSVLG00005016270) #25	ENSSVLG00005016310 #26	FAIM2 (ENSSVLG00005016322) #27	AQP2 (ENSSVLG00005016529) #28	AQP5 (ENSSVLG00005016577) #29	AQP6 (ENSSVLG00005016621) #30	RACGAP1 (ENSSVLG00005016710) #31	ASIC1 (ENSSVLG00005016755) #32	SMARCD1 (ENSSVLG00005017007) #33	GPD1 (ENSSVLG00005017224) #34	COX14 (ENSSVLG00005017409) #35	CERS5 (ENSSVLG00005017441) #36	LIMA1 (ENSSVLG00005017526) #37
Marmotini	ANCESTRAL SPECIES	19	ENSGT00950000182825.A.a.b.a.b.a.b.b.b ##10	ENSGT00950000182825.A.a.b.a.b.a.a.a.a.b #10	ENSGT00950000182825.A.a.b.a.b.a.b.a.b #9	ENSGT00940000154457.a.b	ENSGT00940000160203 #11	ENSGT00950000185831	ENSGT00390000012132 #12	ENSGT00940000155969 #13	ENSGT00390000012136 #14	ENSGT00390000001138.a #15	ENSGT00940000161742 #16	ENSGT00390000005536 #17	ENSGT00940000162031 #18	ENSGT00930000150980.b #20	ENSGT00940000159962 #21	ENSGT01050000244940.a.a #22	ENSGT00530000063607.a #24	ENSGT00940000153993.B #25	ENSGT01050000244890.a.b.b #27	ENSGT00940000160612.d #28	ENSGT00940000161557.b #29	ENSGT00940000161949 #30	ENSGT00940000154610.e.b.j #31	ENSGT00940000158414 #32	ENSGT00940000156629 #33	ENSGT00390000003114.e.a #34	ENSGT00390000002190 #35	ENSGT01030000234515.a.a.a #36	ENSGT00940000158313 #37	ENSGT00940000163376	ENSGT00940000154409.i.a
Marmotini_b	ANCESTRAL SPECIES	11	ENSGT00940000161132	ENSGT00390000007809.a #7	ENSGT00950000182825.A.a.b.a.b.a.b.b.b ##10	ENSGT00950000182825.A.a.b.a.b.a.a.a.a.b #10	ENSGT00940000154457.a.b	ENSGT00940000160203 #11	ENSGT00390000012132 #12	ENSGT00940000155969 #13	ENSGT00390000012136 #14	ENSGT00390000001138.a #15	ENSGT00940000161742 #16	ENSGT00390000005536 #17	ENSGT00940000162031 #18	ENSGT00930000150980.b #20	ENSGT00940000159962 #21	ENSGT01050000244940.a.a #22	ENSGT00530000063607.a #24	ENSGT00940000153993.B #25	ENSGT01050000244890.a.b.b #27	ENSGT00940000160612.d #28	ENSGT00940000161557.b #29	ENSGT00940000161949 #30	ENSGT00940000154610.e.b.j #31	ENSGT00940000158414 #32	ENSGT00940000156629.u #33	ENSGT00390000003114.e.a #34	ENSGT00390000002190 #35	ENSGT01030000234515.a.a.a #36	ENSGT00940000158313 #37	ENSGT00940000163376	ENSGT00940000154409.i.a
Arctic ground squirrel	MODERN SPECIES	348	RHEBL1 (ENSUPAG00010009539)	DHH (ENSUPAG00010009573)	LMBR1L (ENSUPAG00010009579) #7	TUBA1B (ENSUPAG00010009604) #10	TUBA1C (ENSUPAG00010009626) #10	PRPH (ENSUPAG00010009633) #11	ENSUPAG00010009642	C1QL4 (ENSUPAG00010009646) #13	DNAJC22 (ENSUPAG00010009654) #14	SPATS2 (ENSUPAG00010009659) #15	KCNH3 (ENSUPAG00010009677) #16	MCRS1 (ENSUPAG00010009699) #17	FAM186B (ENSUPAG00010009728) #18	PRPF40B (ENSUPAG00010009744) #20	FMNL3 (ENSUPAG00010009805) #21	TMBIM6 (ENSUPAG00010009879) #22	NCKAP5L (ENSUPAG00010009897) #24	BCDIN3D (ENSUPAG00010009912) #25	FAIM2 (ENSUPAG00010009920) #27	AQP2 (ENSUPAG00010009953) #28	AQP5 (ENSUPAG00010009963) #29	AQP6 (ENSUPAG00010009981) #30	RACGAP1 (ENSUPAG00010009990) #31	ENSUPAG00010010033	ASIC1 (ENSUPAG00010010041) #32	ENSUPAG00010010097 #33	GPD1 (ENSUPAG00010010135) #34	CERS5 (ENSUPAG00010010155) #36	LIMA1 (ENSUPAG00010010198) #37	FAM186A (ENSUPAG00010010227)	LARP4 (ENSUPAG00010010256)
Squirrel	MODERN SPECIES	112	DHH (ENSSTOG00000000186)	LMBR1L (ENSSTOG00000008752) #7	TUBA1A (ENSSTOG00000033698) ##10	TUBA1B (ENSSTOG00000021170) #10	ENSSTOG00000020227	PRPH (ENSSTOG00000000282) #11	ENSSTOG00000004941 #12	C1QL4 (ENSSTOG00000024334) #13	DNAJC22 (ENSSTOG00000029066) #14	SPATS2 (ENSSTOG00000009081) #15	KCNH3 (ENSSTOG00000001084) #16	MCRS1 (ENSSTOG00000001093) #17	FAM186B (ENSSTOG00000026279) #18	PRPF40B (ENSSTOG00000001132) #20	FMNL3 (ENSSTOG00000001149) #21	TMBIM6 (ENSSTOG00000001165) #22	NCKAP5L (ENSSTOG00000022659) #24	BCDIN3D (ENSSTOG00000021275) #25	FAIM2 (ENSSTOG00000027904) #27	AQP2 (ENSSTOG00000011259) #28	AQP5 (ENSSTOG00000011261) #29	AQP6 (ENSSTOG00000025554) #30	ENSSTOG00000011264 #31	ASIC1 (ENSSTOG00000004908) #32	SMARCD1 (ENSSTOG00000032441) #33	GPD1 (ENSSTOG00000004948) #34	COX14 (ENSSTOG00000004975) #35	CERS5 (ENSSTOG00000004980) #36	LIMA1 (ENSSTOG00000004992) #37	ENSSTOG00000032900	LARP4 (ENSSTOG00000003553)
Alpin marmot	MODERN SPECIES	34	LMBR1L (ENSMMMG00000023056) #7	TUBA1A (ENSMMMG00000023062) #9	TUBA1C (ENSMMMG00000023064) #10	PRPH (ENSMMMG00000023068) #11	ENSMMMG00000023070	ENSMMMG00000023075 #12	C1QL4 (ENSMMMG00000023079) #13	DNAJC22 (ENSMMMG00000023081) #14	ENSMMMG00000023084	SPATS2 (ENSMMMG00000023085) #15	KCNH3 (ENSMMMG00000023088) #16	MCRS1 (ENSMMMG00000023094) #17	FAM186B (ENSMMMG00000023098) #18	PRPF40B (ENSMMMG00000023101) #20	FMNL3 (ENSMMMG00000023122) #21	TMBIM6 (ENSMMMG00000023160) #22	NCKAP5L (ENSMMMG00000023183) #24	BCDIN3D (ENSMMMG00000023186) #25	FAIM2 (ENSMMMG00000023188) #27	AQP2 (ENSMMMG00000023195) #28	AQP5 (ENSMMMG00000023197) #29	AQP6 (ENSMMMG00000023204) #30	ENSMMMG00000023206 #31	ASIC1 (ENSMMMG00000023219) #32	SMARCD1 (ENSMMMG00000023232) #33	GPD1 (ENSMMMG00000023246) #34	COX14 (ENSMMMG00000023249) #35	CERS5 (ENSMMMG00000023250) #36	LIMA1 (ENSMMMG00000023257) #37	ENSMMMG00000023263	ENSMMMG00000023269
Hystricomorpha	ANCESTRAL SPECIES	9	ENSGT00940000161132	ENSGT00390000007809.a #7	ENSGT00950000182825.A.a.b.a.b.a.a.a.a.b #10	ENSGT00950000182825.A.a.b.a.b.a.b.a.b #9	ENSGT00940000154457.a.b	ENSGT00940000160203 #11	ENSGT00390000012132 #12	ENSGT00940000155969 #13	ENSGT00390000012136 #14	ENSGT00390000001138.a #15	ENSGT00940000161742 #16	ENSGT00390000005536 #17	ENSGT00940000162031 #18	ENSGT00930000150980.b #20	ENSGT00940000159962 #21	ENSGT01050000244940.a.a #22	ENSGT00530000063607.a #24	ENSGT00940000153993.B #25	ENSGT01050000244890.a.b.b #27	ENSGT00940000160612.d #28	ENSGT01090000263345	ENSGT00940000161557.b #29	ENSGT01070000257243	ENSGT00940000161949 #30	ENSGT00940000154610.e.b #31	ENSGT00940000158414 #32	ENSGT00940000156629 #33	ENSGT00860000135898	ENSGT00390000003114.e.a #34	ENSGT00390000002190 #35	ENSGT01030000234515.a.a.a #36
Hystricomorpha_a	ANCESTRAL SPECIES	7	ENSGT00940000161665	ENSGT00940000161132	ENSGT00390000007809.a #7	ENSGT00950000182825.A.a.b.a.b.a.a.a.a.b #10	ENSGT00940000154457.a.b	ENSGT00940000160203 #11	ENSGT00390000012132 #12	ENSGT00940000155969 #13	ENSGT00390000012136 #14	ENSGT00390000001138.a #15	ENSGT00940000161742 #16	ENSGT00390000005536 #17	ENSGT00940000162031 #18	ENSGT00930000150980.b #20	ENSGT00940000159962 #21	ENSGT01050000244940.a.a #22	ENSGT00530000063607.a #24	ENSGT00940000153993.B #25	ENSGT01050000244890.a.b.b #27	ENSGT00940000160612.d #28	ENSGT00940000161557.b #29	ENSGT00940000161949 #30	ENSGT00940000154610.e.b #31	ENSGT00940000158414 #32	ENSGT00940000156629 #33	ENSGT00860000135898	ENSGT00390000003114.e.a #34	ENSGT01030000234515.a.a.a #36	ENSGT00940000158313 #37	ENSGT01100000263763	ENSGT00940000154409
Hystricomorpha_b	ANCESTRAL SPECIES	53											ENSGT00940000161742 #16	ENSGT00390000005536 #17	ENSGT00940000162031 #18	ENSGT00930000150980.b #20	ENSGT00940000159962 #21	ENSGT01050000244940.a.a #22	ENSGT00530000063607.a #24	ENSGT00940000153993.B #25	ENSGT01050000244890.a.b.b #27	ENSGT00940000160612.d #28	ENSGT00940000161557.b #29	ENSGT00940000161949 #30	ENSGT00940000154610.e.b #31	ENSGT00940000158414 #32	ENSGT00940000156629 #33	ENSGT00860000135898	ENSGT00390000003114.e.a #34	ENSGT01030000234515.a.a.a #36	ENSGT00940000158313 #37	ENSGT01100000263763	ENSGT00940000154409
Long-tailed chinchilla	MODERN SPECIES	254										KCNH3 (ENSCLAG00000001325) #16	MCRS1 (ENSCLAG00000001468) #17	FAM186B (ENSCLAG00000001623) #18	PRPF40B (ENSCLAG00000001663) #20	FMNL3 (ENSCLAG00000000779) #21	ENSCLAG00000001174	TMBIM6 (ENSCLAG00000001272) #22	NCKAP5L (ENSCLAG00000000530) #24	BCDIN3D (ENSCLAG00000000912) #25	FAIM2 (ENSCLAG00000000961) #27	ENSCLAG00000017426	AQP2 (ENSCLAG00000000834) #28	AQP5 (ENSCLAG00000000883) #29	AQP6 (ENSCLAG00000001011) #30	RACGAP1 (ENSCLAG00000001084) #31	ASIC1 (ENSCLAG00000000832) #32	SMARCD1 (ENSCLAG00000000946) #33	ENSCLAG00000001015	GPD1 (ENSCLAG00000001367) #34	CERS5 (ENSCLAG00000001516) #36	LIMA1 (ENSCLAG00000000738) #37	ENSCLAG00000001798
Degu	MODERN SPECIES	134	HPS3 (ENSODEG00000009955)	ENSODEG00000010130	ENSODEG00000010432	ENSODEG00000009993	MYLK3 (ENSODEG00000010367)	ENSODEG00000010804	ENSODEG00000010211	ENSODEG00000012398	ENSODEG00000011171	KCNH3 (ENSODEG00000010379) #16	MCRS1 (ENSODEG00000010219) #17	ENSODEG00000010921 #20	ENSODEG00000010201	FMNL3 (ENSODEG00000011056) #21	ENSODEG00000010356	TMBIM6 (ENSODEG00000009820) #22	ENSODEG00000019759	NCKAP5L (ENSODEG00000009975) #24	BCDIN3D (ENSODEG00000009705) #25	ENSODEG00000019768	ENSODEG00000010974	ENSODEG00000011097	FAIM2 (ENSODEG00000009571) #27	ENSODEG00000012970	AQP2 (ENSODEG00000010450) #28	AQP5 (ENSODEG00000011095) #29	AQP6 (ENSODEG00000009870) #30	RACGAP1 (ENSODEG00000010159) #31	ASIC1 (ENSODEG00000009913) #32	SMARCD1 (ENSODEG00000010234) #33	ENSODEG00000010634
Guinea pig	MODERN SPECIES	9	KMT2D (ENSCPOG00000002973)	RHEBL1 (ENSCPOG00000002998)	DHH (ENSCPOG00000002257)	LMBR1L (ENSCPOG00000002999) #7	TUBA1B (ENSCPOG00000039484) #10	ENSCPOG00000031519	PRPH (ENSCPOG00000014881) #11	TROAP (ENSCPOG00000014679) #12	C1QL4 (ENSCPOG00000020682) #13	SPATS2 (ENSCPOG00000009858) #15	KCNH3 (ENSCPOG00000011165) #16	MCRS1 (ENSCPOG00000011172) #17	FAM186B (ENSCPOG00000033003) #18	PRPF40B (ENSCPOG00000001883) #20	FMNL3 (ENSCPOG00000001888) #21	TMBIM6 (ENSCPOG00000002195) #22	NCKAP5L (ENSCPOG00000013063) #24	BCDIN3D (ENSCPOG00000039774) #25	FAIM2 (ENSCPOG00000037651) #27	AQP2 (ENSCPOG00000022039) #28	AQP5 (ENSCPOG00000027598) #29	AQP6 (ENSCPOG00000004378) #30	RACGAP1 (ENSCPOG00000004383) #31	ASIC1 (ENSCPOG00000000413) #32	SMARCD1 (ENSCPOG00000038875) #33	GPD1 (ENSCPOG00000000417) #34	CERS5 (ENSCPOG00000000418) #36	LIMA1 (ENSCPOG00000000521) #37	ENSCPOG00000024814	ENSCPOG00000039626	LARP4 (ENSCPOG00000020519)
Naked mole-rat female	DUPLICATION
Naked mole-rat female	MODERN SPECIES	3	DCAF10 (ENSHGLG00000005287)	SLC25A51 (ENSHGLG00000046859)	SHB (ENSHGLG00000003821)	ENSHGLG00000042112	ENSHGLG00000003240	ENSHGLG00000003016	ENSHGLG00000002600	TDRD7 (ENSHGLG00000001669)	ENSHGLG00000042975	TMOD1 (ENSHGLG00000001466)	TSTD2 (ENSHGLG00000002088)	ENSHGLG00000001882	XPA (ENSHGLG00000001605)	FOXE1 (ENSHGLG00000033854)	TRMO (ENSHGLG00000035772)	ENSHGLG00000049545 #22	HEMGN (ENSHGLG00000002822)	ENSHGLG00000049665	ANP32B (ENSHGLG00000046539)	NANS (ENSHGLG00000002503)	TRIM14 (ENSHGLG00000003771)	CORO2A (ENSHGLG00000043978)	TBC1D2 (ENSHGLG00000002200)	GABBR2 (ENSHGLG00000003518)	ANKS6 (ENSHGLG00000003003)	GALNT12 (ENSHGLG00000002782)	COL15A1 (ENSHGLG00000002025)	TGFBR1 (ENSHGLG00000002925)	ALG2 (ENSHGLG00000002815)	SEC61B (ENSHGLG00000045366)	ENSHGLG00000037562
Naked mole-rat female	DUPLICATION
Naked mole-rat female	MODERN SPECIES	8	ENSHGLG00000046022	TUBA1B (ENSHGLG00000036029) #10	ENSHGLG00000007474	TUBA1A (ENSHGLG00000005735) #9	TUBA1C (ENSHGLG00000016979) #10	PRPH (ENSHGLG00000004209) #11	TROAP (ENSHGLG00000003554) #12	C1QL4 (ENSHGLG00000010938) #13	DNAJC22 (ENSHGLG00000010595) #14	ENSHGLG00000008867 #15	KCNH3 (ENSHGLG00000007224) #16	MCRS1 (ENSHGLG00000006709) #17	PRPF40B (ENSHGLG00000004120) #20	ENSHGLG00000040234	FMNL3 (ENSHGLG00000007126) #21	ENSHGLG00000004558 #22	ENSHGLG00000034506	NCKAP5L (ENSHGLG00000007784) #24	BCDIN3D (ENSHGLG00000048029) #25	FAIM2 (ENSHGLG00000033168) #27	AQP2 (ENSHGLG00000004210) #28	ENSHGLG00000048362	AQP5 (ENSHGLG00000004009) #29	ENSHGLG00000044398	AQP6 (ENSHGLG00000003440) #30	RACGAP1 (ENSHGLG00000005812) #31	Asic1 (ENSHGLG00000004300) #32	SMARCD1 (ENSHGLG00000003601) #33	ENSHGLG00000003935	GPD1 (ENSHGLG00000006106) #34	ENSHGLG00000005048 #35
Naked mole-rat female	MODERN SPECIES	10	PPM1J (ENSHGLG00000009548)	TAFA3 (ENSHGLG00000018506)	ENSHGLG00000034195	ENSHGLG00000016346	LRIG2 (ENSHGLG00000016354)	ENSHGLG00000035626	MAGI3 (ENSHGLG00000005209)	PHTF1 (ENSHGLG00000015252)	RSBN1 (ENSHGLG00000009455)	ENSHGLG00000033150	PTPN22 (ENSHGLG00000010840)	AP4B1 (ENSHGLG00000005105)	DCLRE1B (ENSHGLG00000042662)	HIPK1 (ENSHGLG00000008264)	OLFML3 (ENSHGLG00000009717)	ENSHGLG00000020883 #22	ENSHGLG00000033308	SYT6 (ENSHGLG00000013174)	ENSHGLG00000050970	TRIM33 (ENSHGLG00000015394)	BCAS2 (ENSHGLG00000013708)	ENSHGLG00000015587	AMPD1 (ENSHGLG00000016007)	ENSHGLG00000009388	CSDE1 (ENSHGLG00000009620)	SIKE1 (ENSHGLG00000015408)	ENSHGLG00000032648	ENSHGLG00000004974	ENSHGLG00000047308	ENSHGLG00000006103	TSHB (ENSHGLG00000014600)