Rodentia_A	ANCESTRAL SPECIES	27	ENSGT00940000157922 #10	ENSGT00940000158393 #11	ENSGT00640000091558 #12	ENSGT00390000007159 #13	ENSGT00390000016951 #14	ENSGT00940000155189 #15	ENSGT01020000230394.e.b.a #16	ENSGT00940000160900	ENSGT01030000234549.a.a.a.a.a.b.b #17	ENSGT00390000001016.b #18	ENSGT00530000063687.a #19	ENSGT00390000014874	ENSGT00940000153973.c.a.a #20	ENSGT00390000017740.a.b #21	ENSGT00390000017530	ENSGT00940000156084 #22	ENSGT00950000183077.a.b #23	ENSGT00390000003839 #24	ENSGT00390000013266 #25	ENSGT00940000158273 #26	ENSGT00940000156062 #27	ENSGT00940000159798 #28	ENSGT00390000000616	ENSGT00390000003282.B #30	ENSGT00390000017509 #31	ENSGT00940000160690 #32	ENSGT00940000156027 #33	ENSGT00940000157569 #34	ENSGT00940000161461 #35	ENSGT00940000153393.B #36	ENSGT00390000004064 #37
Sciuridae	ANCESTRAL SPECIES	41	ENSGT00940000157922 #10	ENSGT00940000158393 #11	ENSGT00640000091558 #12	ENSGT00390000007159 #13	ENSGT00390000016951 #14	ENSGT00940000155189 #15	ENSGT01020000230394.e.b.a #16	ENSGT00940000160900	ENSGT01030000234549.a.a.a.a.a.b.b #17	ENSGT00390000001016.b #18	ENSGT00530000063687.a #19	ENSGT00390000014874	ENSGT00940000153973.c.a.a #20	ENSGT00390000017740.a.b #21	ENSGT00390000017530	ENSGT00940000156084 #22	ENSGT00950000183077.a.b #23	ENSGT00390000003839 #24	ENSGT00390000013266 #25	ENSGT00940000158273 #26	ENSGT00940000159798 #28	ENSGT00940000156062 #27	ENSGT00390000000616	ENSGT00390000003282.B #30	ENSGT00390000017509 #31	ENSGT00940000160690 #32	ENSGT00940000156027 #33	ENSGT00940000157569 #34	ENSGT00940000161461 #35	ENSGT00940000153393.B #36	ENSGT00390000004064 #37
Marmotini	ANCESTRAL SPECIES	49	ENSGT00940000157922 #10	ENSGT00940000158393 #11	ENSGT00640000091558 #12	ENSGT00390000007159 #13	ENSGT00390000016951 #14	ENSGT00940000155189 #15	ENSGT01020000230394.e.b.a #16	ENSGT00940000160900	ENSGT01030000234549.a.a.a.a.a.b.b #17	ENSGT00390000001016.b #18	ENSGT00530000063687.a #19	ENSGT00390000014874	ENSGT00940000153973.c.a.a #20	ENSGT00390000017740.a.b #21	ENSGT00390000017530	ENSGT00940000156084 #22	ENSGT00950000183077.a.b #23	ENSGT00390000003839 #24	ENSGT00390000013266 #25	ENSGT00940000158273 #26	ENSGT00940000159798 #28	ENSGT00940000156062 #27	ENSGT00390000000616	ENSGT00390000003282.B #30	ENSGT00390000017509 #31	ENSGT00940000160690 #32	ENSGT00960000190360	ENSGT00940000156027 #33	ENSGT00940000157569 #34	ENSGT00940000161461 #35	ENSGT00940000153393.B #36
Marmotini_b	ANCESTRAL SPECIES	62	ENSGT00940000157922 #10	ENSGT00940000158393 #11	ENSGT00640000091558 #12	ENSGT00390000007159 #13	ENSGT00390000016951 #14	ENSGT00940000155189 #15	ENSGT01020000230394.e.b.a #16	ENSGT00940000160900	ENSGT01030000234549.a.a.a.a.a.b.b #17	ENSGT00390000001016.b #18	ENSGT00530000063687.a #19	ENSGT00390000014874	ENSGT00940000153973.c.a.a #20	ENSGT00390000017740.a.b #21	ENSGT00390000017530	ENSGT00940000156084 #22	ENSGT00950000183077.a.b #23	ENSGT00390000003839 #24	ENSGT00390000013266 #25	ENSGT00940000158273 #26	ENSGT00940000159798 #28	ENSGT00940000156062 #27	ENSGT00390000000616	ENSGT00390000003282.B #30	ENSGT00390000017509 #31	ENSGT00940000160690 #32	ENSGT00960000190360	ENSGT00940000156027 #33	ENSGT00940000157569 #34	ENSGT00940000161461 #35	ENSGT00940000153393.B #36
Squirrel	MODERN SPECIES	202	GRIP2 (ENSSTOG00000000954) #7	CCDC174 (ENSSTOG00000027414) #8	C3orf20 (ENSSTOG00000002907) #9	FGD5 (ENSSTOG00000005202) #10	NR2C2 (ENSSTOG00000005250) #11	MRPS25 (ENSSTOG00000030962) #12	RBSN (ENSSTOG00000022986) #13	TRH (ENSSTOG00000026247) #14	TMCC1 (ENSSTOG00000019869) #15	PLXND1 (ENSSTOG00000024621) #16	RHO (ENSSTOG00000028352) #17	IFT122 (ENSSTOG00000004353) #18	MBD4 (ENSSTOG00000020663) #19	ENSSTOG00000026505 #20	CAND2 (ENSSTOG00000023136) #21	RAF1 (ENSSTOG00000025146) #22	MKRN2 (ENSSTOG00000010520) #23	MKRN2OS (ENSSTOG00000031428) #24	TSEN2 (ENSSTOG00000000538) #25	PPARG (ENSSTOG00000012778) #26	SYN2 (ENSSTOG00000011519) #27	TIMP4 (ENSSTOG00000034531) #28	ENSSTOG00000028589 #29	VGLL4 (ENSSTOG00000025247) #30	ATG7 (ENSSTOG00000015288) #31	HRH1 (ENSSTOG00000015286) #32	SLC6A1 (ENSSTOG00000007598) #33	SLC6A11 (ENSSTOG00000028999) #34	ATP2B2 (ENSSTOG00000014026) #35	SEC13 (ENSSTOG00000014017) #36	GHRL (ENSSTOG00000022095) #37
Arctic ground squirrel	MODERN SPECIES	23	NR2C2 (ENSUPAG00010000576) #11	MRPS25 (ENSUPAG00010000567) #12	RBSN (ENSUPAG00010000555) #13	TRH (ENSUPAG00010000545) #14	TMCC1 (ENSUPAG00010000491) #15	PLXND1 (ENSUPAG00010000023) #16	H1-8 (ENSUPAG00010023069)	RHO (ENSUPAG00010023066) #17	IFT122 (ENSUPAG00010023058) #18	ENSUPAG00010023053 #19	ENSUPAG00010023052 #19	EFCAB12 (ENSUPAG00010023049)	ENSUPAG00010023046 #20	CAND2 (ENSUPAG00010023044) #21	TMEM40 (ENSUPAG00010023040)	RAF1 (ENSUPAG00010023038) #22	MKRN2 (ENSUPAG00010023036) #23	MKRN2OS (ENSUPAG00010023035) #24	TSEN2 (ENSUPAG00010023034) #25	PPARG (ENSUPAG00010023031) #26	TIMP4 (ENSUPAG00010023029) #28	SYN2 (ENSUPAG00010023028) #27	ENSUPAG00010023027	VGLL4 (ENSUPAG00010023024) #30	ATG7 (ENSUPAG00010023011) #31	HRH1 (ENSUPAG00010023010) #32	ENSUPAG00010023009	SLC6A1 (ENSUPAG00010023006) #33	SLC6A11 (ENSUPAG00010023004) #34	ATP2B2 (ENSUPAG00010022999) #35	SEC13 (ENSUPAG00010022998) #36
Alpin marmot	MODERN SPECIES	40	C3orf20 (ENSMMMG00000011543) #9	FGD5 (ENSMMMG00000011473) #10	NR2C2 (ENSMMMG00000011464) #11	MRPS25 (ENSMMMG00000011452) #12	RBSN (ENSMMMG00000011435) #13	TRH (ENSMMMG00000011424) #14	TMCC1 (ENSMMMG00000011365) #15	ENSMMMG00000011319 #16	ENSMMMG00000011299	RHO (ENSMMMG00000011272) #17	IFT122 (ENSMMMG00000011068) #18	MBD4 (ENSMMMG00000011043) #19	EFCAB12 (ENSMMMG00000011023)	ENSMMMG00000010997 #20	ENSMMMG00000010993 #21	RAF1 (ENSMMMG00000010957) #22	ENSMMMG00000010950	MKRN2 (ENSMMMG00000010927) #23	MKRN2OS (ENSMMMG00000010915) #24	ENSMMMG00000010907 #25	ENSMMMG00000010899 #25	PPARG (ENSMMMG00000010840) #26	ENSMMMG00000010687 #28	SYN2 (ENSMMMG00000010440) #27	TAMM41 (ENSMMMG00000010322)	VGLL4 (ENSMMMG00000010304) #30	ATG7 (ENSMMMG00000009966) #31	ENSMMMG00000009925	HRH1 (ENSMMMG00000009921) #32	ENSMMMG00000009895	SLC6A1 (ENSMMMG00000009856) #33
Eurasian red squirrel	DUPLICATION
Eurasian red squirrel	MODERN SPECIES	10	NR2C2 (ENSSVLG00005017625) #11	MRPS25 (ENSSVLG00005017966) #12	RBSN (ENSSVLG00005018031) #13	TRH (ENSSVLG00005018181) #14	ENSSVLG00005018231	TMCC1 (ENSSVLG00005018250) #15	PLXND1 (ENSSVLG00005018384) #16	ENSSVLG00005018771	RHO (ENSSVLG00005018827) #17	IFT122 (ENSSVLG00005018941) #18	MBD4 (ENSSVLG00005019308) #19	EFCAB12 (ENSSVLG00005019404)	ENSSVLG00005019450 ##20	CAND2 (ENSSVLG00005019570) #21	TMEM40 (ENSSVLG00005019760)	ENSSVLG00005019978 #22	MKRN2 (ENSSVLG00005020340) #23	MKRN2OS (ENSSVLG00005020454) #24	TSEN2 (ENSSVLG00005020543) #25	PPARG (ENSSVLG00005020780) #26	SYN2 (ENSSVLG00005021130) #27	TIMP4 (ENSSVLG00005021374) #28	TAMM41 (ENSSVLG00005021448)	ENSSVLG00005021494	VGLL4 (ENSSVLG00005021566) #30	ATG7 (ENSSVLG00005021683) #31	HRH1 (ENSSVLG00005021749) #32	SLC6A1 (ENSSVLG00005021844) #33	SLC6A11 (ENSSVLG00005022396) #34	ATP2B2 (ENSSVLG00005022802) #35	SEC13 (ENSSVLG00005023877) #36
Eurasian red squirrel	MODERN SPECIES	8	BCO1 (ENSSVLG00005025719)	ENSSVLG00005025763	C16orf46 (ENSSVLG00005014992)	ENSSVLG00005015037	CENPN (ENSSVLG00005015134)	CMC2 (ENSSVLG00005015210)	CDYL2 (ENSSVLG00005015278)	DYNLRB2 (ENSSVLG00005015349)	ENSSVLG00005015446	WWOX (ENSSVLG00005015526)	ENSSVLG00005015573	CLEC3A (ENSSVLG00005015615)	VAT1L (ENSSVLG00005015671)	NUDT7 (ENSSVLG00005015783)	ADAMTS18 (ENSSVLG00005015898)	ENSSVLG00005016092 #22	SYCE1L (ENSSVLG00005016146)	MON1B (ENSSVLG00005016284)	CNTNAP4 (ENSSVLG00005016453)	ENSSVLG00005017621	DUXB (ENSSVLG00005017671)	TERF2IP (ENSSVLG00005017752)	KARS1 (ENSSVLG00005017790)	ADAT1 (ENSSVLG00005017872)	GABARAPL2 (ENSSVLG00005017970)	TMEM231 (ENSSVLG00005018059)	ENSSVLG00005018139	TMEM170A (ENSSVLG00005018166)	CFDP1 (ENSSVLG00005018315)	BCAR1 (ENSSVLG00005018450)	ENSSVLG00005018505
Hystricomorpha	ANCESTRAL SPECIES	48	ENSGT00940000157922 #10	ENSGT00940000158393 #11	ENSGT00640000091558 #12	ENSGT00390000007159 #13	ENSGT00940000155189 #15	ENSGT00940000160900	ENSGT00390000016951 #14	ENSGT01020000230394.e.b.a #16	ENSGT01030000234549.a.a.a.a.a.b.b #17	ENSGT00390000001016.b #18	ENSGT00530000063687.a #19	ENSGT00390000014874	ENSGT00940000153973.c.a.a #20	ENSGT00390000017740.a.b #21	ENSGT00390000017530	ENSGT00940000156084 #22	ENSGT00950000183077.a.b #23	ENSGT00390000003839 #24
Hystricomorpha_a	ANCESTRAL SPECIES	6	ENSGT00940000155615 #7	ENSGT00440000033958 #8	ENSGT00940000153655.B #9	ENSGT00940000157922 #10	ENSGT00940000158393 #11	ENSGT00640000091558 #12	ENSGT00390000007159 #13	ENSGT00940000155189 #15	ENSGT01020000230394.e.b.a #16	ENSGT01030000234549.a.a.a.a.a.b.b #17	ENSGT00390000001016.b #18	ENSGT00530000063687.a #19	ENSGT00940000153973.c.a.a #20	ENSGT00390000017740.a.b #21	ENSGT00390000017530	ENSGT00940000156084 #22	ENSGT00950000183077.a.b #23	ENSGT00390000003839 #24	ENSGT00940000157312.h	ENSGT00940000157200	ENSGT00390000005378	ENSGT00390000006066	ENSGT00940000158804	ENSGT00390000003219	ENSGT00940000158155	ENSGT00950000182956.b.b.a.b	ENSGT00940000158225	ENSGT00940000161249	ENSGT00940000155867	ENSGT00440000033504.B	ENSGT00940000156857
Guinea pig	MODERN SPECIES	109	GRIP2 (ENSCPOG00000021047) #7	CCDC174 (ENSCPOG00000039402) #8	C3orf20 (ENSCPOG00000006783) #9	FGD5 (ENSCPOG00000013157) #10	NR2C2 (ENSCPOG00000001512) #11	MRPS25 (ENSCPOG00000020398) #12	RBSN (ENSCPOG00000003200) #13	TMCC1 (ENSCPOG00000009299) #15	PLXND1 (ENSCPOG00000004989) #16	RHO (ENSCPOG00000004984) #17	IFT122 (ENSCPOG00000004975) #18	ENSCPOG00000004970 #19	RPL32 (ENSCPOG00000019967) ##20	CAND2 (ENSCPOG00000023286) #21	TMEM40 (ENSCPOG00000025632)	RAF1 (ENSCPOG00000001210) #22	MKRN2 (ENSCPOG00000001208) #23	MKRN2OS (ENSCPOG00000032819) #24	ENSCPOG00000009944	FKBP4 (ENSCPOG00000002453)	ITFG2 (ENSCPOG00000021230)	ENSCPOG00000005850	ENSCPOG00000031884	ARHGAP21 (ENSCPOG00000004505)	ENKUR (ENSCPOG00000009590)	ENSCPOG00000000291	GPR158 (ENSCPOG00000001565)	ENSCPOG00000034310	ENSCPOG00000013721	ENSCPOG00000039199	GAD2 (ENSCPOG00000013724)
Hystricomorpha_b	ANCESTRAL SPECIES	2	ENSGT00940000155615 #7	ENSGT00440000033958 #8	ENSGT00940000153655.B #9	ENSGT00940000157922 #10	ENSGT00940000158393 #11	ENSGT00640000091558 #12	ENSGT00390000007159 #13	ENSGT00940000155189 #15	ENSGT01020000230394.e.b.a #16	ENSGT01030000234549.a.a.a.a.a.b.b #17	ENSGT00390000001016.b #18	ENSGT00530000063687.a #19	ENSGT00940000153973.c.a.a #20	ENSGT00390000017740.a.b #21	ENSGT00390000017530	ENSGT00940000156084 #22	ENSGT00950000183077.a.b #23	ENSGT00390000003839 #24	ENSGT00940000157312.h	ENSGT00940000157200	ENSGT00390000005378	ENSGT00390000006066	ENSGT00940000158804	ENSGT00390000003219	ENSGT00940000158155	ENSGT00950000182956.b.b.a.b	ENSGT00940000158225	ENSGT00940000161249	ENSGT00940000155867	ENSGT00440000033504.B	ENSGT00940000156857
Degu	MODERN SPECIES	274	ENSODEG00000002030	RBSN (ENSODEG00000001991) #13	MRPS25 (ENSODEG00000001966) #12	NR2C2 (ENSODEG00000001892) #11	ENSODEG00000001861	ENSODEG00000001849	ENSODEG00000001772	TMCC1 (ENSODEG00000001710) #15	PLXND1 (ENSODEG00000003347) #16	RHO (ENSODEG00000003304) #17	IFT122 (ENSODEG00000003013) #18	ENSODEG00000002902 #19	ENSODEG00000002891 ##20	CAND2 (ENSODEG00000002821) #21	TMEM40 (ENSODEG00000002755)	RAF1 (ENSODEG00000002734) #22	MKRN2 (ENSODEG00000002702) #23	MKRN2OS (ENSODEG00000002688) #24	ENSODEG00000002676	SLC6A11 (ENSODEG00000002665) #34	SLC6A1 (ENSODEG00000002644) #33	ATG7 (ENSODEG00000002299) #31	ENSODEG00000002124 #30	ENSODEG00000018794	TAMM41 (ENSODEG00000002076)	TIMP4 (ENSODEG00000002023) #28	ENSODEG00000001988 #27	PPARG (ENSODEG00000002659) #26	TSEN2 (ENSODEG00000002629) #25	ENSODEG00000002503	HMCES (ENSODEG00000002476)
Long-tailed chinchilla	MODERN SPECIES	136	GRIP2 (ENSCLAG00000013538) #7	CCDC174 (ENSCLAG00000011014) #8	C3orf20 (ENSCLAG00000013841) #9	FGD5 (ENSCLAG00000011953) #10	NR2C2 (ENSCLAG00000011082) #11	MRPS25 (ENSCLAG00000008381) #12	RBSN (ENSCLAG00000011613) #13	TMCC1 (ENSCLAG00000014727) #15	PLXND1 (ENSCLAG00000012627) #16	RHO (ENSCLAG00000006233) #17	IFT122 (ENSCLAG00000006170) #18	MBD4 (ENSCLAG00000008974) #19	ENSCLAG00000007426 #20	CAND2 (ENSCLAG00000007541) #21	TMEM40 (ENSCLAG00000009668)	RAF1 (ENSCLAG00000010316) #22	MKRN2 (ENSCLAG00000008755) #23	MKRN2OS (ENSCLAG00000009109) #24	ENSCLAG00000011764	FKBP4 (ENSCLAG00000013510)	ITFG2 (ENSCLAG00000016639)	TEX52 (ENSCLAG00000013429)	FOXM1 (ENSCLAG00000014183)	RHNO1 (ENSCLAG00000017326)	TULP3 (ENSCLAG00000017345)	TEAD4 (ENSCLAG00000012070)	ENSCLAG00000008194	ENSCLAG00000009091	FAM171A1 (ENSCLAG00000009809)	NMT2 (ENSCLAG00000008204)	RPP38 (ENSCLAG00000010194)
Naked mole-rat female	MODERN SPECIES	27	ENSHGLG00000000266	ENSHGLG00000000240	ENSHGLG00000040044 #15	ENSHGLG00000040416	RHO (ENSHGLG00000006668) #17	IFT122 (ENSHGLG00000009113) #18	MBD4 (ENSHGLG00000009034) #19	ENSHGLG00000015777	ENSHGLG00000040769 #20	ENSHGLG00000015580 #21	ENSHGLG00000015498	ENSHGLG00000033042	ENSHGLG00000039038	ENSHGLG00000032617	ENSHGLG00000037560	ENSHGLG00000018214 #22	ENSHGLG00000018194 #23	ENSHGLG00000017856 #24	ENSHGLG00000045316	ENSHGLG00000032284	ENSHGLG00000019586	ENSHGLG00000039046	ENSHGLG00000000920	GATA2 (ENSHGLG00000000985)	DNAJB8 (ENSHGLG00000046802)	ENSHGLG00000037886	ENSHGLG00000000094	ENSHGLG00000000122	ENSHGLG00000002369 #30	HRH1 (ENSHGLG00000044045) #32	ENSHGLG00000045274 #33