Rodentia_A	ANCESTRAL SPECIES	3	ENSGT00940000154971	ENSGT00510000049735 #8	ENSGT00940000158799 #9	ENSGT00940000153173.b.b #10	ENSGT00940000154994.b	ENSGT00940000157202 #11	ENSGT00940000157943.b #13	ENSGT00940000155338 #14	ENSGT00510000048410 #15	ENSGT00390000007911 #16	ENSGT00940000154881 #17	ENSGT00940000159275 #18	ENSGT00940000154664 #19	ENSGT00390000012959.a #20	ENSGT00940000156331 #21	ENSGT00940000153814.b #22	ENSGT00940000156395 #23	ENSGT00940000162183	ENSGT00390000014792 #24	ENSGT00390000015789.c.a.b ##25	ENSGT00940000163247 #26	ENSGT00940000160681.C #27	ENSGT00940000154602.b ##29	ENSGT00940000154602.a #29	ENSGT00940000162894	ENSGT00940000155258.t	ENSGT00940000154403.a.a ##28	ENSGT00940000154403.a.b #30	ENSGT00940000161311	ENSGT00940000161787 #31	ENSGT00940000161991 #32
Hystricomorpha	ANCESTRAL SPECIES	3	ENSGT00940000156363	ENSGT00940000154971	ENSGT00510000049735 #8	ENSGT00940000158799 #9	ENSGT00940000153173.b.b #10	ENSGT00940000157202 #11	ENSGT00940000157943.b #13	ENSGT00940000155338 #14	ENSGT00510000048410 #15	ENSGT00390000007911 #16	ENSGT00940000154881 #17	ENSGT00940000159275 #18	ENSGT00940000154664 #19	ENSGT00390000012959.a #20	ENSGT00940000156331 #21	ENSGT00940000153814.b #22	ENSGT00940000156395 #23	ENSGT00390000014792 #24	ENSGT00390000015789.c.a.b ##25	ENSGT00940000163247 #26	ENSGT00940000160681.C #27	ENSGT00940000154602.b ##29	ENSGT00940000154602.a #29	ENSGT00940000162894	ENSGT00940000155258.t	ENSGT00940000154403.a.a ##28	ENSGT00940000154403.a.b #30	ENSGT00940000161311	ENSGT00940000161787 #31	ENSGT00940000161991 #32	ENSGT00940000163426 #34
Naked mole-rat female	MODERN SPECIES	12	ENSHGLG00000046408 #7	ENSHGLG00000032125 #8	KAT2A (ENSHGLG00000014215) #9	DHX58 (ENSHGLG00000011529) #10	ZNF385C (ENSHGLG00000013481) #11	ENSHGLG00000034407 #12	ENSHGLG00000039749 #13	DNAJC7 (ENSHGLG00000016992) #14	CNP (ENSHGLG00000016638) #15	ODAD4 (ENSHGLG00000016605) #16	ACLY (ENSHGLG00000014233) #17	KLHL11 (ENSHGLG00000037770) #18	KLHL10 (ENSHGLG00000018732) #19	NT5C3B (ENSHGLG00000015568) #20	FKBP10 (ENSHGLG00000016119) #21	P3H4 (ENSHGLG00000016255) #22	JUP (ENSHGLG00000019242) #23	GAST (ENSHGLG00000013252) #24	ENSHGLG00000014274 #25	ENSHGLG00000014114 #26	KRT17 (ENSHGLG00000014256) #27	ENSHGLG00000018762 #28	KRT14 (ENSHGLG00000014710) #29	ENSHGLG00000017248 #30	KRT35 (ENSHGLG00000014815) #31	KRT32 (ENSHGLG00000017222) #32	ENSHGLG00000041581 #33	KRT34 (ENSHGLG00000048614) #34	ENSHGLG00000042231 #35	ENSHGLG00000045464 #36	KRTAP29-1 (ENSHGLG00000047368) #37
Hystricomorpha_a	ANCESTRAL SPECIES		ENSGT00940000156363	ENSGT00940000154971	ENSGT00510000049735 #8	ENSGT00940000158799 #9	ENSGT00940000153173.b.b #10	ENSGT00940000157202 #11	ENSGT00940000157943.b #13	ENSGT00940000155338 #14	ENSGT00510000048410 #15	ENSGT00390000007911 #16	ENSGT00940000154881 #17	ENSGT00940000159275 #18	ENSGT00940000154664 #19	ENSGT00390000012959.a #20	ENSGT00940000156331 #21	ENSGT00940000153814.b #22	ENSGT00940000156395 #23	ENSGT00390000014792 #24	ENSGT00390000015789.c.a.b ##25	ENSGT00940000163247 #26	ENSGT00940000160681.C #27	ENSGT00940000154602.b ##29	ENSGT00940000154602.a #29	ENSGT00940000162894	ENSGT00940000155258.t	ENSGT00940000154403.a.a ##28	ENSGT00940000154403.a.b #30	ENSGT00940000161311	ENSGT00940000161787 #31	ENSGT00940000161991 #32	ENSGT00940000153980.j.a.a #33
Hystricomorpha_b	ANCESTRAL SPECIES		ENSGT00940000156363	ENSGT00940000154971	ENSGT00510000049735 #8	ENSGT00940000158799 #9	ENSGT00940000153173.b.b #10	ENSGT00940000157202 #11	ENSGT00940000157943.b #13	ENSGT00940000155338 #14	ENSGT00510000048410 #15	ENSGT00390000007911 #16	ENSGT00940000154881 #17	ENSGT00940000159275 #18	ENSGT00940000154664 #19	ENSGT00390000012959.a #20	ENSGT00940000156331 #21	ENSGT00940000153814.b #22	ENSGT00940000156395 #23	ENSGT00390000014792 #24	ENSGT00390000015789.c.a.b ##25	ENSGT00940000163247 #26	ENSGT00940000160681.C #27	ENSGT00940000154602.b ##29	ENSGT00940000154602.a #29	ENSGT00940000162894	ENSGT00940000155258.t	ENSGT00940000154403.a.a ##28	ENSGT00940000154403.a.b #30	ENSGT00940000161311	ENSGT00940000161787 #31	ENSGT00940000161991 #32	ENSGT00940000153980.j.a.a #33
Long-tailed chinchilla	MODERN SPECIES	158	HCRT (ENSCLAG00000016694)	KCNH4 (ENSCLAG00000016815)	RAB5C (ENSCLAG00000016650)	KAT2A (ENSCLAG00000015084) #9	DHX58 (ENSCLAG00000013960) #10	ZNF385C (ENSCLAG00000015100) #11	NKIRAS2 (ENSCLAG00000014896) #13	DNAJC7 (ENSCLAG00000015312) #14	CNP (ENSCLAG00000015883) #15	ODAD4 (ENSCLAG00000014476) #16	ACLY (ENSCLAG00000014600) #17	KLHL11 (ENSCLAG00000017003) #18	KLHL10 (ENSCLAG00000017306) #19	NT5C3B (ENSCLAG00000015634) #20	FKBP10 (ENSCLAG00000016960) #21	P3H4 (ENSCLAG00000015645) #22	JUP (ENSCLAG00000015947) #23	GAST (ENSCLAG00000016052) #24	ENSCLAG00000015732 ##25	ENSCLAG00000015351 #26	KRT16 (ENSCLAG00000016344) ##29	KRT9 (ENSCLAG00000016583)	KRT19 (ENSCLAG00000015425)	KRT15 (ENSCLAG00000013658) ##28	ENSCLAG00000015341 #30	ENSCLAG00000016636 #26	ENSCLAG00000017990	KRTAP16-1 (ENSCLAG00000016554)	ENSCLAG00000015082	ENSCLAG00000017906	ENSCLAG00000015077
Degu	MODERN SPECIES	97	KCNH4 (ENSODEG00000018039)	RAB5C (ENSODEG00000017920)	HSPB9 (ENSODEG00000018407) #8	KAT2A (ENSODEG00000018011) #9	DHX58 (ENSODEG00000017902) #10	ZNF385C (ENSODEG00000018049) #11	NKIRAS2 (ENSODEG00000017843) #13	DNAJC7 (ENSODEG00000017953) #14	CNP (ENSODEG00000017962) #15	ODAD4 (ENSODEG00000017939) #16	ACLY (ENSODEG00000018143) #17	KLHL11 (ENSODEG00000017875) #18	KLHL10 (ENSODEG00000018015) #19	NT5C3B (ENSODEG00000018081) #20	FKBP10 (ENSODEG00000017908) #21	P3H4 (ENSODEG00000017979) #22	JUP (ENSODEG00000017964) #23	GAST (ENSODEG00000017853) #24	EIF1 (ENSODEG00000018101) ##25	ENSODEG00000017881 #26	KRT17 (ENSODEG00000017862) #27	KRT16 (ENSODEG00000017857) ##29	KRT14 (ENSODEG00000017873) #29	KRT9 (ENSODEG00000017935)	KRT19 (ENSODEG00000017884)	KRT15 (ENSODEG00000017969) ##28	ENSODEG00000017822 #30	KRT36 (ENSODEG00000017942)	KRT35 (ENSODEG00000017892) #31	KRT32 (ENSODEG00000017895) #32	ENSODEG00000017837 #33
Guinea pig	MODERN SPECIES	53	KCNH4 (ENSCPOG00000027074)	RAB5C (ENSCPOG00000011190)	HSPB9 (ENSCPOG00000026480) #8	KAT2A (ENSCPOG00000040409) #9	DHX58 (ENSCPOG00000023721) #10	ZNF385C (ENSCPOG00000006417) #11	NKIRAS2 (ENSCPOG00000037805) #13	DNAJC7 (ENSCPOG00000023384) #14	CNP (ENSCPOG00000020940) #15	ODAD4 (ENSCPOG00000023846) #16	ACLY (ENSCPOG00000010813) #17	KLHL11 (ENSCPOG00000021621) #18	KLHL10 (ENSCPOG00000002818) #19	NT5C3B (ENSCPOG00000027400) #20	FKBP10 (ENSCPOG00000020998) #21	P3H4 (ENSCPOG00000026262) #22	JUP (ENSCPOG00000003295) #23	GAST (ENSCPOG00000009853) #24	ENSCPOG00000030441 ##25	KRT9 (ENSCPOG00000033124)	KRT19 (ENSCPOG00000035147)	KRT14 (ENSCPOG00000006839) #29	ENSCPOG00000034373 #30	KRT36 (ENSCPOG00000032028)	KRT35 (ENSCPOG00000030708) #31	ENSCPOG00000038800 #33	ENSCPOG00000032896 #33	ENSCPOG00000032218 #33	ENSCPOG00000039793 #33	ENSCPOG00000025665	KRTAP16-1 (ENSCPOG00000020936)
Sciuridae	ANCESTRAL SPECIES	4	ENSGT00940000154971	ENSGT00510000049735 #8	ENSGT00940000158799 #9	ENSGT00940000153173.b.b #10	ENSGT00940000154994.b	ENSGT00940000157202 #11	ENSGT00940000157943.b #13	ENSGT00940000155338 #14	ENSGT00510000048410 #15	ENSGT00390000007911 #16	ENSGT00940000154881 #17	ENSGT00940000159275 #18	ENSGT00940000154664 #19	ENSGT00390000012959.a #20	ENSGT00940000156331 #21	ENSGT00940000153814.b #22	ENSGT00940000156395 #23	ENSGT00940000162183	ENSGT00390000014792 #24	ENSGT00390000015789.c.a.b ##25	ENSGT00940000163247 #26	ENSGT00940000160681.C #27	ENSGT00940000154602.b ##29	ENSGT00940000154602.a #29	ENSGT00940000162894	ENSGT00940000155258.t	ENSGT00940000154403.a.a ##28	ENSGT00950000183311	ENSGT00940000154403.a.b #30	ENSGT00940000161311	ENSGT00940000161787 #31
Marmotini	ANCESTRAL SPECIES	8	ENSGT00940000154971	ENSGT00510000049735 #8	ENSGT00940000158799 #9	ENSGT00940000153173.b.b #10	ENSGT00940000154994.b	ENSGT00940000157202 #11	ENSGT00940000157943.b #13	ENSGT00940000155338 #14	ENSGT00510000048410 #15	ENSGT00390000007911 #16	ENSGT00940000154881 #17	ENSGT00940000159275 #18	ENSGT00940000154664 #19	ENSGT00390000012959.a #20	ENSGT00940000156331 #21	ENSGT00940000153814.b #22	ENSGT00940000156395 #23	ENSGT00940000162183	ENSGT00390000014792 #24	ENSGT00390000015789.c.a.b ##25	ENSGT00940000163247 #26	ENSGT00940000160681.C #27	ENSGT00940000154602.b ##29	ENSGT00940000154602.a #29	ENSGT00940000162894	ENSGT00940000155258.t	ENSGT00940000154403.a.a ##28	ENSGT00940000154403.a.b #30	ENSGT00940000161311	ENSGT00940000161787 #31	ENSGT00940000161991 #32
Marmotini_b	ANCESTRAL SPECIES	5	ENSGT00940000154971	ENSGT00510000049735 #8	ENSGT00940000158799 #9	ENSGT00940000153173.b.b #10	ENSGT00940000154994.b	ENSGT00940000157202 #11	ENSGT00940000157943.b.i #13	ENSGT00940000155338 #14	ENSGT00510000048410 #15	ENSGT00390000007911 #16	ENSGT00940000154881 #17	ENSGT00940000159275 #18	ENSGT00940000154664 #19	ENSGT00390000012959.a #20	ENSGT00940000156331 #21	ENSGT00940000153814.b #22	ENSGT00940000156395 #23	ENSGT00940000162183	ENSGT00390000014792 #24	ENSGT00390000015789.c.a.b ##25	ENSGT00940000163247 #26	ENSGT00940000160681.C #27	ENSGT00940000154602.b ##29	ENSGT00940000154602.a #29	ENSGT00940000162894	ENSGT00940000155258.t	ENSGT00940000154403.a.a ##28	ENSGT00940000154403.a.b #30	ENSGT00940000161311	ENSGT00940000161787 #31	ENSGT00940000161991 #32
Arctic ground squirrel	MODERN SPECIES	46	RAB5C (ENSUPAG00010009535)	HSPB9 (ENSUPAG00010009527) #8	KAT2A (ENSUPAG00010009504) #9	DHX58 (ENSUPAG00010009486) #10	C17orf113 (ENSUPAG00010009476)	ZNF385C (ENSUPAG00010009440) #11	NKIRAS2 (ENSUPAG00010009426) #13	DNAJC7 (ENSUPAG00010009401) #14	CNP (ENSUPAG00010009395) #15	ODAD4 (ENSUPAG00010009389) #16	ACLY (ENSUPAG00010009305) #17	KLHL11 (ENSUPAG00010009300) #18	KLHL10 (ENSUPAG00010009288) #19	NT5C3B (ENSUPAG00010009269) #20	FKBP10 (ENSUPAG00010009227) #21	P3H4 (ENSUPAG00010009210) #22	JUP (ENSUPAG00010009167) #23	HAP1 (ENSUPAG00010009150)	GAST (ENSUPAG00010009145) #24	ENSUPAG00010009142 ##25	ENSUPAG00010009125 #26	KRT17 (ENSUPAG00010009109) #27	KRT16 (ENSUPAG00010009069) ##29	KRT14 (ENSUPAG00010009018) #29	KRT9 (ENSUPAG00010009000)	KRT19 (ENSUPAG00010008984)	KRT15 (ENSUPAG00010008970) ##28	ENSUPAG00010008946 #30	KRT36 (ENSUPAG00010008919)	KRT35 (ENSUPAG00010008898) #31	KRT32 (ENSUPAG00010008877) #32
Squirrel	MODERN SPECIES	90	KCNH4 (ENSSTOG00000006633)	HSPB9 (ENSSTOG00000006602) #8	RAB5C (ENSSTOG00000006620)	KAT2A (ENSSTOG00000006556) #9	DHX58 (ENSSTOG00000006524) #10	ZNF385C (ENSSTOG00000020287) #11	ENSSTOG00000006159 #13	DNAJC7 (ENSSTOG00000006122) #14	CNP (ENSSTOG00000006116) #15	ODAD4 (ENSSTOG00000006075) #16	ACLY (ENSSTOG00000006029) #17	KLHL11 (ENSSTOG00000026300) #18	KLHL10 (ENSSTOG00000005983) #19	NT5C3B (ENSSTOG00000005969) #20	FKBP10 (ENSSTOG00000005956) #21	P3H4 (ENSSTOG00000028974) #22	JUP (ENSSTOG00000005910) #23	HAP1 (ENSSTOG00000020475)	GAST (ENSSTOG00000005906) #24	EIF1 (ENSSTOG00000002719) ##25	ENSSTOG00000024700 #26	KRT16 (ENSSTOG00000014410) ##29	KRT19 (ENSSTOG00000014403)	KRT15 (ENSSTOG00000014415) ##28	ENSSTOG00000014393 #30	KRT36 (ENSSTOG00000014383)	KRT35 (ENSSTOG00000034016) #31	KRT32 (ENSSTOG00000014374) #32	ENSSTOG00000034013 ##33	ENSSTOG00000013178 #33	ENSSTOG00000033523 ##33
Eurasian red squirrel	DUPLICATION
Eurasian red squirrel	MODERN SPECIES	12	ENSSVLG00005000284	HSPB9 (ENSSVLG00005000293) #8	KAT2A (ENSSVLG00005000319) #9	DHX58 (ENSSVLG00005000354) #10	ZNF385C (ENSSVLG00005000419) #11	C17orf113 (ENSSVLG00005000459)	ENSSVLG00005000476 #13	ENSSVLG00005000498 #14	CNP (ENSSVLG00005000524) #15	ODAD4 (ENSSVLG00005000556) #16	ACLY (ENSSVLG00005000630) #17	KLHL11 (ENSSVLG00005000699) #18	KLHL10 (ENSSVLG00005000723) #19	NT5C3B (ENSSVLG00005000754) #20	FKBP10 (ENSSVLG00005000785) #21	P3H4 (ENSSVLG00005000841) #22	JUP (ENSSVLG00005000914) #23	ENSSVLG00005001006 #22	ENSSVLG00005001022	HAP1 (ENSSVLG00005001065)	ENSSVLG00005001138	GAST (ENSSVLG00005001171) #24	EIF1 (ENSSVLG00005001188) ##25	ENSSVLG00005001226 #26	KRT17 (ENSSVLG00005001282) #27	KRT16 (ENSSVLG00005001321) ##29	KRT14 (ENSSVLG00005001357) #29	ENSSVLG00005001389	KRT19 (ENSSVLG00005001412)	KRT15 (ENSSVLG00005001448) ##28	KRT13 (ENSSVLG00005001499)
Eurasian red squirrel	MODERN SPECIES	12	KAT2A (ENSSVLG00005000319) #9	DHX58 (ENSSVLG00005000354) #10	ZNF385C (ENSSVLG00005000419) #11	C17orf113 (ENSSVLG00005000459)	ENSSVLG00005000476 #13	ENSSVLG00005000498 #14	CNP (ENSSVLG00005000524) #15	ODAD4 (ENSSVLG00005000556) #16	ACLY (ENSSVLG00005000630) #17	KLHL11 (ENSSVLG00005000699) #18	KLHL10 (ENSSVLG00005000723) #19	NT5C3B (ENSSVLG00005000754) #20	FKBP10 (ENSSVLG00005000785) #21	P3H4 (ENSSVLG00005000841) #22	JUP (ENSSVLG00005000914) #23	ENSSVLG00005001006 #22	ENSSVLG00005001022	HAP1 (ENSSVLG00005001065)	ENSSVLG00005001138	GAST (ENSSVLG00005001171) #24	EIF1 (ENSSVLG00005001188) ##25	ENSSVLG00005001226 #26	KRT17 (ENSSVLG00005001282) #27	KRT16 (ENSSVLG00005001321) ##29	KRT14 (ENSSVLG00005001357) #29	ENSSVLG00005001389	KRT19 (ENSSVLG00005001412)	KRT15 (ENSSVLG00005001448) ##28	KRT13 (ENSSVLG00005001499)	KRT36 (ENSSVLG00005001573)	KRT35 (ENSSVLG00005001626) #31