#Nexus begin data; dimensions ntax=24 nchar=391; format datatype=standard missing=?; matrix G._gorilla 0000?1??000100101??0000000001?00000?1100(01)0000001120(01)000?30???(01)0100010000002?01010120(01)300010100?010??010000010002100000000020?00001(01)?1011000?10000(01)0?10110001010?001100(01)?00200100(01)0(01)10?001(01)1100(12)0(01)0?0020010(01)010000?1021?00010(01)10?0(01)011??00001010010000??100?12130000?1110000000?0?001010200010?21?11100000200??00010210??1201100100000002100?00????20110??0(01)10?0??1(01)00??01?????00?????????????????????1? P._troglodytes 0000?1??000101101??000001(01)011?00100?010100100001111(01)0(01)0?30???(01)0100010000002?0101011012(01)1210100?010??0100(01)110100210(01)00000(01)02(01)?(01)00010?1011000?1(01)000(01)0?10100001010?00010001101(01)00000001??001(01)110010(01)0?0020010(01)010000?0021110010(01)10?1(01)111??00001020010000?00(01)1?121??00??1120000??0?0?0110101?0010??1?01111001100????????????0??????100000002100?00????20121??1000?0??1001??00?????00?????????????????????1? S._tchadensis 0????????????(01)??1??110??????1?????????10?00???0??11011????????201???????????010????0?0???1?1????1????????0??0?????????????????????0????10????(01)?0???????0????0????1?????????????????????0??????1??????????????(12)?0????????????????????????01?0???????0????0????????????03?1?????????1??????????????0???1?1??1?????????????1?????????????????????????????????0???????000??01?????????????????????????????? Ar._ramidus ?????????????????????????????????????????????????????????????????????????????????????????????????????????????????0????????????????0????????????0???????10????????0???????????????1?0???0?????????????????????????????????????????????????1?????????0???01????????????12?11?????????????1??1?0????0???1?0??2?????????????0?????????000?????????????????????0???0?????1??0??????????????????????????????? Au._anamensis ?????????????????????????????????????????????????????????0??????0????10?0???01?1?????2???????????????????????????0????????????????0????????????0???????00??????????????????????????????0???????????????????????????????????????????????????????????1???01????????????12?11????????1????2??1?0????0???1?1??2?????????????0??????????11??220????????00??????1???0???0?1??01?????????????????????????????? Au._afarensis 0020?1??01000000?00(01)00???000?0??0??0?1110000000?0??00?1??010?012000?(01)101002?01010(01)?011(01)??10?01?00100(12)00001?0100??002????0021?00?100??0?1010??100110????01?11110?001?001??????1?11001??000?0000(12)01?0????00?1(01)?1100?1?0?1????011???11????201?21??1010100?01101211101000130110000000021000201(12)110110(12)1111?0??100010211100000112100001111002200?01????20?????1(01)01?0?11001??00?????11?????????????????????1? Au._africanus 000202???001001010(01)(01)0(01)020(01)0(01)1(01)0010010111(01)110100?1120?0(01)000(01)1?(01)121(01)000101102?(01)1010020(01)102210(01)01011000100001100002101100021021?00011(01)?001(01)(01)10?1111010????01011010?001000(01)11?2110?000011?00101(01)101200(01)00201010102122210211111?0010?10000??101011?10000100?011(01)0111101000130110011000(01)2110021221201102111(01)01??301010420520000201100001111002200?00????20?????1(01)02?(01)?0100(01)??10?????11?????????????????????1? Au._garhi 0???????????00????0000??????10?????0?11??00??????????????0???0120?0???0?0?2?010??????1?????????0?????????1????????????????????????????????????????????????????????????????????????????????????1???0????1???????????????????????????????????????????1????1?011????????1??110?????????10?2??2??????2????????1????????????????????????????????????????????????????????????0??????????????????????????????? K._platyops 0????????????0?????101????????????????1??10???0??1?0?????0????2?1?1???0?1???0????????0???0?????00????????1????????????????????????(01)????????????0???????00????????????????????????1?0??????????(01)????????????????1???????????????????????00??????????1?????1???????????(01)??1?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? P._robustus 010??0??0?0100(01)0201112????0?11??0??0?1111011100?11111110?123?11220101211010?111110?01001210110110001(12)0010011000??1???????02?????1?(01)??0?02?1??211??1????11?100???11(01)?010??????1?01110??011??01023??0????10?00?2121?112??????111???10????202122?2?11122??0(12)0100122010?0131211002?1?120210203212?11?1111113??401?20421110??0202101002112112310?01????00?????1102?1?1(12)100??10?????11?????????????????????1? P._boisei 0100?0??0101001(01)201112000100110000000110(01)0(01)1100?1110(01)11(01)?123?(01)1220100211(01)10?00(01)110?01000210(01)11110000201100010111110211020120?010111?001(01)(12)?1?1211?11????11000100?11101201011001110011??0(01)101(01)1123010002011000121(01)1?1121?100?0010?00011??212122?2111122??120100?11000?0131210??2?1?1202102?3212?11?2111113??400?21131300??0103?010?2112102310?(01)1????00?????1113?1?11100??10?????22?????????????????????1? P._aethiopicus 0000?0??010?0011101012????0?10??0??0??1110(01)1100?11111111?123?11220100211000?011??0??100020??11?1000020000001000??0???????0??????0?0??0?(01)1?0?1211??0????01?111???111?001??????1?0??????001??00121??0????00?10?2101?112??????001????1????011?21?01?0?2????1?100????????(01)??1??????????02?02??212??1?211111???40???????????????????0????2???(23)10?01?????0?????11(01)2?1??1100??10?????????????????????????????? Au._sediba 0?0??2????111?0??11100????1??1??0??1??01001?01?????00?21?011?10?120?0??11?2?010??1??210?????0011101011??12?0?????0???????0????????(01)??1????????????????????????????????0???????????????011??1??0???1?1?0????????2???????????????????????????????????1????1?101?11000?013?211001?0?12001010?212?31?21111?1??311?00410420???1011001????????110?11????01?????1102?0?0?01(01)??1??????????????????????????????? H._habilis 11020(12)0?0001100011(01)100000(01)01(01)000(01)0011101(01)010100?112000211(01)(01)1?(01)(01)112001001(01)011(01)10111101(12)12110100101010110011101000000(01)1001(012)020?11011(01)01110(12)?(01)?121(01)(01)00????(01)1001110?0(01)(01)10?11(01)11(01)1001(01)1001?011(01)0(01)10(01)200(01)0010100(01)102112211(01)1011000(01)10?0(01)0100?00(12)112?220(01)01?0?01(01)(01)(01)1?111000113?11101101012011(01)21?2021200(12)0(01)1101??110000320220000101100101111002310?11????30?????1102?1?0101(01)??10?????11?????????????????????1? H._rudolfensis 21(01)??2??10001100211101?0010(01)(01)(01)000001011(012)(01)11?100?1120?121100??0(12)2111?1?01100100011(01)??111010?1?01000?0110011?0?000000020??10?1??(01)???(01)0?11(01)1????21(01)??0????0???1????00??0?110??10??????????1100(01)10020?1?(01)0010?0102122???(01)?0??000110???0????0???2?????(01)010??01?101111100?012?110011?1?12010121?2(01)2?21?(12)(01)111?1??110?00320220??0101100101???0??310?11????31?????1102?(01)?11(01)01??10?????11??????????????????????? African_H._erectus (123)1(012)20(12)0000(01)111(01)0211200000(01)01(01)000(01)111010(012)(01)011110?112001211(01)12(25)0(12)21200120(01)(01)0(02)10(01)0111?01(012)1111010010101011001(012)101002000(01)00(01)020?0011111(01)011102(12)1(01)?(12)1(01)0100???010001(01)11000102(01)0012(01)(01)(01)0(01)(01)(01)(01)(01)00(01)1(01)01(01)100210100(012)01000102122101(01)1(01)00(01)0(01)1102000(01)01?0(01)1222?22010110?0111021121000113021001111112001(01)21?202100000111?1??110010320120100101100101111?0?3100011100(13)1???200102011(01)1011011021200112????(01)302?2????00002010 Asian_H._erectus (23)?(012)201000001(01)11??1????1(012)(012)(01)(01)1(01)?0(01)(01)10?(01)?(01)(01)(01)0(01)111??11?1?0??30???0(12)?(01)20?1??1(01)0(01)10(01)0?11???11?1????0??10??11001(012)???00(012)001(012)2(01)1101?101(012)110(01)01110(12)01(01)?111010(01)???010(01)11(01)1(01)00(01)102(01)1(01)(01)(012)1(01)10(01)(01)(01)11101?(01)0(01)(01)10020(01)?0(01)(012)0?00(01)10212200?(12)1(01)(01)(01)(01)(01)0(01)1(01)(012)(01)(01)0(01)(01)100?1?2??22??0??0??1??01???10?11?30210??11111200102??2?20?0010111?1??10?0????????10???????1?1111????11001110000???1011021(01)(01)(01)?0?(01)011?2(012)1(01)0110(01)00(01)(01)?(01)1(01)2(01)(012)(01)(01)1100(012)0?0 H._heidelbergensis (34)?(012)?(01)1(01)(012)??1011(01)???????(01)(012)01(01)(01)1?01(01)0(01)?(01)?(01)(01)011?11??11???1??11??(125)???020?1??11?0?00???(12)0??(12)1??????0???0???1??1(12)?????200(01)0(012)1(01)(012)01?0(01)11010(01)?(01)1(01)0(01)111?2110(01)?0???010(01)11(01)11?0(01)1??01(01)1(12)1(01)11(01)(01)(01)1110(01)?0000??0?(01)(01)?0(01)(012)0?00(01)1(01)?12?1(01)?(01)1(01)(01)0(01)0(01)1(01)(01)01(01)000(01)00?????????????1??1??01???10?11?3?211??11111200102??2022?0100111?1??1(01)?1????????11???????1????????110001110(01)(01)1???(12)112(12)(12)11(01)1?0?(01)(01)01?21(012)21??01(01)01(01)1211112(01)100102(01)?0 H._neanderthalensis 4?(012)?1121??1(01)(01)1(01)???????0(012)01001?00(01)1(01)?0?11001?11???1???????(01)??4???020?1???1?0?00???2???(23)???????0???0???1??12?????20010(012)11(02)1(01)?0(01)(01)00(01)10?01100?1(01)?211?0?0???01(01)(01)11(01)1(01)?01(01)??1(01)(01)1(12)1(01)(01)0(01)(01)(01)011(01)0?(01)00(01)??0?(01)1?0(01)01?(01)0(01)10?12??0?110(01)(01)(01)00001(01)0(01)000010?????????????1??1??01???10?11?3?211??11111200102??2022?0101(01)(01)1?1??1(01)?1????????11???????1????????11(01)0(01)1(01)1(012)(01)01???11(01)2(12)1(01)111?0?(01)101?2(012)(012)20??000011(123)1(012)0(23)(012)(012)(01)(01)2(012)0(01)0(01)?1 H._floresiensis ????????????0?0?????????????????1????????1?????????1?????0??????1??????2??????????2???1???????????????????????????11???11??1?11??1??????20??????10???????????10???????0?1??0?1?000???????0??????0???????1???????????1?0?????1????0?????????????????????????????????????????????????????????????1??????????????????????????????????????????0???????1???????????????0???????????????????????????????????? H._sapiens (34)10?12?2??1(01)(01)1(01)01??200(01)0(01)1(01)(01)(01)?01(01)01?011(12)02(01)110001(12)2(01)012?(0123)1??(023)?20(01)20012001?0?0101?1001212110?00?010???1??12201??(012)00122(01)10(02)(01)2(01)11(012)00(01)1?(01)110211102110(01)?011101(01)(01)11(01)1(01)?011??01(01)12(01)(01)(01)(01)(01)111(01)10010000?00?(01)(01)?0(01)001(01)(01)(01)10212??01(01)(01)000(01)0(01)(01)10?(01)(01)0000010112232?11?1110021?011(01)110(01)211302111(12)111112(01)01020?2023(01)0200111010110?0(01)(01)(34)(01)0(01)(02)0010(01)(02)(01)(01)(01)1100111002112(01)1101(012)1(03)1021(012)(01)12(02)(12)010(01)101(01)(01)(12)10(012)(012)(012)(012)0??000000(02)(012)(012)(012)1(012)(012)(01)11(012)(01)0(012)(01)10 H._antecessor ??????????????0?????????????1?????????0??01??????????????1??2????????????????0???1???????????????????????2??????????????????1??????????????1??????????????????????0?????????????1????1?????0?????????????????????????????????????????????????????????0?????????????1??????????1?1????????????0??1????????????1????????10??????????????????0?0?1?00?1????0(01)?021?00???101??21101??001100?110?11?1101110?0 Georgian_H._erectus (12)?(012)?0100??011?(01)??1???????10(01)(01)???0?????(01)100(01)??1??11?1????20????1?(12)20?1??11?0100???12??(13)1?1????0???0???1??1(01)???????(01)(01)(01)???(12)10?110(01)?1(01)0(01)?1?0011??1?1(01)(01)?????01?(01)0101??0(01)???(01)?0??000?0(01)0?(01)??(01)?10?1??0?1???????(01)?0(01)??12?(12)(01)?(012)?(01)0?0?0110??00??1?0??????2??????0?????????????0??????????0?0?????0??????0?0011(01)(01)????????0????????10?????????????????11011(01)(01)00(02)1???1011011(01)(01)1?0?10(12)1?(02)(12)1(01)???1010???220?1211(01)(01)?????0 H._naledi (01)?0??2????111?1???????????1?????0?????01000?11??????????????????020?1??10?0?01???????0???????0???0??11??12???????0???????0??????0?(01)??1?02?0??201???????(01)0?010????10???1??????1?(01)11?0??1?1??0??0?????????1?01??12??1?1??????111???10????0????????????????2??01???10??1?3?211??1?1?1211102??212??(01)?01111?1??10???????????????????1?0111???11??11????01?????1203?0???0?0??1??????????????????????????????? ; end; begin mrbayes; set autoclose=yes nowarn=yes; set usebeagle=yes; ctype ordered: 1 3 4 6 7 17 20 22 40 42 51 57 63-65 68 70 72 75 83 86 88 89 92 101 106 107 112 120 121 123 135 137 142 166 171 191 192 198 206 208 210 213 224 232 234-240 244 245 249 253-255 265 269 270 275 277 280 282 283 285 287 289 290 298 303 306 309 314-316 328 329 331 337 342 344 347-349 354 359 362-365 367 368 375-381 385 388; lset coding=informative rates=gamma; outgroup Gorilla_gorilla; constraint root = 1-. ; constraint PanHomo = 2-. ; constraint Hominin = 3-. ; [ingroup] Calibrate Gorilla_gorilla =fixed(0); Calibrate Pan_troglodytes =fixed(0); Calibrate S_tchadensis =fixed(7.24); Calibrate Ar_ramidus =fixed(4.419); Calibrate Au_anamensis =fixed(4.17); Calibrate Au_afarensis =fixed(3.77); Calibrate Au_africanus =fixed(3.03); Calibrate Au_garhi =fixed(2.5); Calibrate K_platyops =fixed(3.53); Calibrate P_robustus =fixed(1.9); Calibrate P_boisei =fixed(2.3); Calibrate P_aethiopicus =fixed(2.7); Calibrate Au_sediba =fixed(1.977); Calibrate H_habilis =fixed(2.33); Calibrate H_rudolfensis =fixed(2.05); Calibrate H_ergaster =fixed(1.65); Calibrate H_erectus =fixed(1.5); Calibrate H_heidelbergensis =fixed(0.6); Calibrate H_neanderthalensis =fixed(0.130); Calibrate H_floresiensis =fixed(0.019); Calibrate H_sapiens =fixed(0.195); Calibrate H_antecessor =fixed(0.938); Calibrate Dmanisi =fixed(1.81); Calibrate H_naledi=uniform(0, 7.24); Calibrate Au_deyiremeda = fixed(3.5); Calibrate root= uniform(6,8); PRSET brlenspr=clock:birthdeath; PRSET nodeagepr = calibrated; PRSET clockvarpr=igr; PRSET igrvarpr=exponential(10); PRSET clockratepr= normal(0.2, 0.02); PRSET topologypr=constraints(root, PanHomo, Hominin); mcmc ngen=20000000 samplefreq=100 printfr=100 diagnfreq=100 nruns=4 nchain=4 temp=0.2 relburnin=yes burninfrac=0.25 savebrlens=yes filename=MrBayes_naledi; sumt filename=MrBayes_naledi relburnin=yes burninfrac=0.25 contype=allcompat; sump filename=MrBayes_naledi relburnin=yes burninfrac=0.25; end;