1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
|
#NEXUS
BEGIN DATA;
DIMENSIONS NTAX=12 NCHAR=898;
[!A portion of primate mitochondrial DNA. Site names correspond to Anderson (1981) numbering scheme.
This portion includes parts of two protein-coding genes, as well as 3 tRNA's:
tRNA His: 459-528
tRNA Ser (AGY): 529-588
tRNA Leu (CUN): 589-659
Data from:
Hayasaka, K., T. Gojobori, and S. Horai. 1988. Molecular phylogeny and evolution of primate mitochondrial DNA. Mol. Biol. Evol., 5:626-644.
See pp. 335-339 of the MacClade book.]
FORMAT DATATYPE=DNA MISSING=? GAP=- MATCHCHAR=. INTERLEAVE ;OPTIONS IGNORE=UNINFORM ;
CHARLABELS
[1] A_11680 [2] A_11681 [3] A_11682 [4] A_11683 [5] A_11684
[6] A_11685 [7] A_11686 [8] A_11687 [9] A_11688 [10] A_11689
[11] A_11690 [12] A_11691 [13] A_11692 [14] A_11693 [15] A_11694
[16] A_11695 [17] A_11696 [18] A_11697 [19] A_11698 [20] A_11699
[21] A_11700 [22] A_11701 [23] A_11702 [24] A_11703 [25] A_11704
[26] A_11705 [27] A_11706 [28] A_11707 [29] A_11708 [30] A_11709
[31] A_11710 [32] A_11711 [33] A_11712 [34] A_11713 [35] A_11714
[36] A_11715 [37] A_11716 [38] A_11717 [39] A_11718 [40] A_11719
[41] A_11720 [42] A_11721 [43] A_11722 [44] A_11723 [45] A_11724
[46] A_11725 [47] A_11726 [48] A_11727 [49] A_11728 [50] A_11729
[51] A_11730 [52] A_11731 [53] A_11732 [54] A_11733 [55] A_11734
[56] A_11735 [57] A_11736 [58] A_11737 [59] A_11738 [60] A_11739
[61] A_11740 [62] A_11741 [63] A_11742 [64] A_11743 [65] A_11744
[66] A_11745 [67] A_11746 [68] A_11747 [69] A_11748 [70] A_11749
[71] A_11750 [72] A_11751 [73] A_11752 [74] A_11753 [75] A_11754
[76] A_11755 [77] A_11756 [78] A_11757 [79] A_11758 [80] A_11759
[81] A_11760 [82] A_11761 [83] A_11762 [84] A_11763 [85] A_11764
[86] A_11765 [87] A_11766 [88] A_11767 [89] A_11768 [90] A_11769
[91] A_11770 [92] A_11771 [93] A_11772 [94] A_11773 [95] A_11774
[96] A_11775 [97] A_11776 [98] A_11777 [99] A_11778 [100] A_11779
[101] A_11780 [102] A_11781 [103] A_11782 [104] A_11783 [105] A_11784
[106] A_11785 [107] A_11786 [108] A_11787 [109] A_11788 [110] A_11789
[111] A_11790 [112] A_11791 [113] A_11792 [114] A_11793 [115] A_11794
[116] A_11795 [117] A_11796 [118] A_11797 [119] A_11798 [120] A_11799
[121] A_11800 [122] A_11801 [123] A_11802 [124] A_11803 [125] A_11804
[126] A_11805 [127] A_11806 [128] A_11807 [129] A_11808 [130] A_11809
[131] A_11810 [132] A_11811 [133] A_11812 [134] A_11813 [135] A_11814
[136] A_11815 [137] A_11816 [138] A_11817 [139] A_11818 [140] A_11819
[141] A_11820 [142] A_11821 [143] A_11822 [144] A_11823 [145] A_11824
[146] A_11825 [147] A_11826 [148] A_11827 [149] A_11828 [150] A_11829
[151] A_11830 [152] A_11831 [153] A_11832 [154] A_11833 [155] A_11834
[156] A_11835 [157] A_11836 [158] A_11837 [159] A_11838 [160] A_11839
[161] A_11840 [162] A_11841 [163] A_11842 [164] A_11843 [165] A_11844
[166] A_11845 [167] A_11846 [168] A_11847 [169] A_11848 [170] A_11849
[171] A_11850 [172] A_11851 [173] A_11852 [174] A_11853 [175] A_11854
[176] A_11855 [177] A_11856 [178] A_11857 [179] A_11858 [180] A_11859
[181] A_11860 [182] A_11861 [183] A_11862 [184] A_11863 [185] A_11864
[186] A_11865 [187] A_11866 [188] A_11867 [189] A_11868 [190] A_11869
[191] A_11870 [192] A_11871 [193] A_11872 [194] A_11873 [195] A_11874
[196] A_11875 [197] A_11876 [198] A_11877 [199] A_11878 [200] A_11879
[201] A_11880 [202] A_11881 [203] A_11882 [204] A_11883 [205] A_11884
[206] A_11885 [207] A_11886 [208] A_11887 [209] A_11888 [210] A_11889
[211] A_11890 [212] A_11891 [213] A_11892 [214] A_11893 [215] A_11894
[216] A_11895 [217] A_11896 [218] A_11897 [219] A_11898 [220] A_11899
[221] A_11900 [222] A_11901 [223] A_11902 [224] A_11903 [225] A_11904
[226] A_11905 [227] A_11906 [228] A_11907 [229] A_11908 [230] A_11909
[231] A_11910 [232] A_11911 [233] A_11912 [234] A_11913 [235] A_11914
[236] A_11915 [237] A_11916 [238] A_11917 [239] A_11918 [240] A_11919
[241] A_11920 [242] A_11921 [243] A_11922 [244] A_11923 [245] A_11924
[246] A_11925 [247] A_11926 [248] A_11927 [249] A_11928 [250] A_11929
[251] A_11930 [252] A_11931 [253] A_11932 [254] A_11933 [255] A_11934
[256] A_11935 [257] A_11936 [258] A_11937 [259] A_11938 [260] A_11939
[261] A_11940 [262] A_11941 [263] A_11942 [264] A_11943 [265] A_11944
[266] A_11945 [267] A_11946 [268] A_11947 [269] A_11948 [270] A_11949
[271] A_11950 [272] A_11951 [273] A_11952 [274] A_11953 [275] A_11954
[276] A_11955 [277] A_11956 [278] A_11957 [279] A_11958 [280] A_11959
[281] A_11960 [282] A_11961 [283] A_11962 [284] A_11963 [285] A_11964
[286] A_11965 [287] A_11966 [288] A_11967 [289] A_11968 [290] A_11969
[291] A_11970 [292] A_11971 [293] A_11972 [294] A_11973 [295] A_11974
[296] A_11975 [297] A_11976 [298] A_11977 [299] A_11978 [300] A_11979
[301] A_11980 [302] A_11981 [303] A_11982 [304] A_11983 [305] A_11984
[306] A_11985 [307] A_11986 [308] A_11987 [309] A_11988 [310] A_11989
[311] A_11990 [312] A_11991 [313] A_11992 [314] A_11993 [315] A_11994
[316] A_11995 [317] A_11996 [318] A_11997 [319] A_11998 [320] A_11999
[321] A_12000 [322] A_12001 [323] A_12002 [324] A_12003 [325] A_12004
[326] A_12005 [327] A_12006 [328] A_12007 [329] A_12008 [330] A_12009
[331] A_12010 [332] A_12011 [333] A_12012 [334] A_12013 [335] A_12014
[336] A_12015 [337] A_12016 [338] A_12017 [339] A_12018 [340] A_12019
[341] A_12020 [342] A_12021 [343] A_12022 [344] A_12023 [345] A_12024
[346] A_12025 [347] A_12026 [348] A_12027 [349] A_12028 [350] A_12029
[351] A_12030 [352] A_12031 [353] A_12032 [354] A_12033 [355] A_12034
[356] A_12035 [357] A_12036 [358] A_12037 [359] A_12038 [360] A_12039
[361] A_12040 [362] A_12041 [363] A_12042 [364] A_12043 [365] A_12044
[366] A_12045 [367] A_12046 [368] A_12047 [369] A_12048 [370] A_12049
[371] A_12050 [372] A_12051 [373] A_12052 [374] A_12053 [375] A_12054
[376] A_12055 [377] A_12056 [378] A_12057 [379] A_12058 [380] A_12059
[381] A_12060 [382] A_12061 [383] A_12062 [384] A_12063 [385] A_12064
[386] A_12065 [387] A_12066 [388] A_12067 [389] A_12068 [390] A_12069
[391] A_12070 [392] A_12071 [393] A_12072 [394] A_12073 [395] A_12074
[396] A_12075 [397] A_12076 [398] A_12077 [399] A_12078 [400] A_12079
[401] A_12080 [402] A_12081 [403] A_12082 [404] A_12083 [405] A_12084
[406] A_12085 [407] A_12086 [408] A_12087 [409] A_12088 [410] A_12089
[411] A_12090 [412] A_12091 [413] A_12092 [414] A_12093 [415] A_12094
[416] A_12095 [417] A_12096 [418] A_12097 [419] A_12098 [420] A_12099
[421] A_12100 [422] A_12101 [423] A_12102 [424] A_12103 [425] A_12104
[426] A_12105 [427] A_12106 [428] A_12107 [429] A_12108 [430] A_12109
[431] A_12110 [432] A_12111 [433] A_12112 [434] A_12113 [435] A_12114
[436] A_12115 [437] A_12116 [438] A_12117 [439] A_12118 [440] A_12119
[441] A_12120 [442] A_12121 [443] A_12122 [444] A_12123 [445] A_12124
[446] A_12125 [447] A_12126 [448] A_12127 [449] A_12128 [450] A_12129
[451] A_12130 [452] A_12131 [453] A_12132 [454] A_12133 [455] A_12134
[456] A_12135 [457] A_12136 [458] A_12137 [459] A_12138 [460] A_12139
[461] A_12140 [462] A_12141 [463] A_12142 [464] A_12143 [465] A_12144
[466] A_12145 [467] A_12146 [468] A_12147 [469] A_12148 [470] A_12149
[471] A_12150 [472] A_12151 [473] A_12152 [474] A_12153 [475] A_12154
[476] A_12155 [477] A_12156 [478] A_12157 [479] A_12158 [480] A_12159
[481] A_12160 [482] A_12161 [483] A_12162 [484] A_12163 [485] A_12164
[486] A_12165 [487] A_12166 [488] A_12167 [489] A_12168 [490] A_12169
[491] A_12170 [492] A_12171 [493] A_12172 [494] A_12173 [495] A_12174
[496] A_12175 [497] A_12176 [498] A_12177 [499] A_12178 [500] A_12179
[501] A_12180 [502] A_12181 [503] A_12182 [504] A_12183 [505] A_12184
[506] A_12185 [507] A_12186 [508] A_12187 [509] A_12188 [510] A_12189
[511] A_12190 [512] A_12190a [513] A_12191 [514] A_12192 [515] A_12193
[516] A_12194 [517] A_12195 [518] A_12196 [519] A_12197 [520] A_12198
[521] A_12199 [522] A_12200 [523] A_12201 [524] A_12202 [525] A_12203
[526] A_12204 [527] A_12205 [528] A_12206 [529] A_12207 [530] A_12208
[531] A_12209 [532] A_12210 [533] A_12211 [534] A_12212 [535] A_12213
[536] A_12214 [537] A_12215 [538] A_12215a [539] A_12216 [540] A_12217
[541] A_12218 [542] A_12219 [543] A_12220 [544] A_12221 [545] A_12222
[546] A_12223 [547] A_12224 [548] A_12225 [549] A_12226 [550] A_12227
[551] A_12228 [552] A_12229 [553] A_12230 [554] A_12231 [555] A_12232
[556] A_12233 [557] A_12234 [558] A_12235 [559] A_12236 [560] A_12237
[561] A_12238 [562] A_12239 [563] A_12240 [564] A_12241 [565] A_12242
[566] A_12243 [567] A_12244 [568] A_12245 [569] A_12246 [570] A_12247
[571] A_12248 [572] A_12249 [573] A_12250 [574] A_12251 [575] A_12252
[576] A_12253 [577] A_12254 [578] A_12255 [579] A_12256 [580] A_12257
[581] A_12258 [582] A_12259 [583] A_12260 [584] A_12261 [585] A_12262
[586] A_12263 [587] A_12264 [588] A_12265 [589] A_12266 [590] A_12267
[591] A_12268 [592] A_12269 [593] A_12270 [594] A_12271 [595] A_12272
[596] A_12273 [597] A_12274 [598] A_12275 [599] A_12276 [600] A_12277
[601] A_12278 [602] A_12279 [603] A_12280 [604] A_12281 [605] A_12282
[606] A_12283 [607] A_12284 [608] A_12285 [609] A_12286 [610] A_12287
[611] A_12288 [612] A_12289 [613] A_12290 [614] A_12291 [615] A_12292
[616] A_12293 [617] A_12294 [618] A_12295 [619] A_12296 [620] A_12297
[621] A_12298 [622] A_12299 [623] A_12300 [624] A_12301 [625] A_12302
[626] A_12303 [627] A_12304 [628] A_12305 [629] A_12306 [630] A_12307
[631] A_12308 [632] A_12309 [633] A_12310 [634] A_12311 [635] A_12312
[636] A_12313 [637] A_12314 [638] A_12315 [639] A_12316 [640] A_12317
[641] A_12318 [642] A_12319 [643] A_12320 [644] A_12321 [645] A_12322
[646] A_12323 [647] A_12324 [648] A_12325 [649] A_12326 [650] A_12327
[651] A_12328 [652] A_12329 [653] A_12330 [654] A_12331 [655] A_12332
[656] A_12333 [657] A_12334 [658] A_12335 [659] A_12336 [660] A_12337
[661] A_12338 [662] A_12339 [663] A_12340 [664] A_12341 [665] A_12342
[666] A_12343 [667] A_12344 [668] A_12345 [669] A_12346 [670] A_12347
[671] A_12348 [672] A_12349 [673] A_12350 [674] A_12351 [675] A_12352
[676] A_12353 [677] A_12354 [678] A_12355 [679] A_12356 [680] A_12357
[681] A_12358 [682] A_12359 [683] A_12360 [684] A_12361 [685] A_12362
[686] A_12363 [687] A_12364 [688] A_12365 [689] A_12366 [690] A_12367
[691] A_12368 [692] A_12369 [693] A_12370 [694] A_12371 [695] A_12372
[696] A_12373 [697] A_12374 [698] A_12375 [699] A_12376 [700] A_12377
[701] A_12378 [702] A_12379 [703] A_12380 [704] A_12381 [705] A_12382
[706] A_12383 [707] A_12384 [708] A_12385 [709] A_12386 [710] A_12387
[711] A_12388 [712] A_12389 [713] A_12390 [714] A_12391 [715] A_12392
[716] A_12393 [717] A_12394 [718] A_12395 [719] A_12396 [720] A_12397
[721] A_12398 [722] A_12399 [723] A_12400 [724] A_12401 [725] A_12402
[726] A_12403 [727] A_12404 [728] A_12405 [729] A_12406 [730] A_12407
[731] A_12408 [732] A_12409 [733] A_12410 [734] A_12411 [735] A_12412
[736] A_12413 [737] A_12414 [738] A_12415 [739] A_12416 [740] A_12417
[741] A_12418 [742] A_12419 [743] A_12420 [744] A_12421 [745] A_12422
[746] A_12423 [747] A_12424 [748] A_12425 [749] A_12426 [750] A_12427
[751] A_12428 [752] A_12429 [753] A_12430 [754] A_12431 [755] A_12432
[756] A_12433 [757] A_12434 [758] A_12435 [759] A_12436 [760] A_12437
[761] A_12438 [762] A_12439 [763] A_12440 [764] A_12441 [765] A_12442
[766] A_12443 [767] A_12444 [768] A_12445 [769] A_12446 [770] A_12447
[771] A_12448 [772] A_12449 [773] A_12450 [774] A_12451 [775] A_12452
[776] A_12453 [777] A_12454 [778] A_12455 [779] A_12456 [780] A_12457
[781] A_12458 [782] A_12459 [783] A_12460 [784] A_12461 [785] A_12462
[786] A_12463 [787] A_12464 [788] A_12465 [789] A_12466 [790] A_12467
[791] A_12468 [792] A_12469 [793] A_12470 [794] A_12471 [795] A_12472
[796] A_12473 [797] A_12474 [798] A_12475 [799] A_12476 [800] A_12477
[801] A_12478 [802] A_12479 [803] A_12480 [804] A_12481 [805] A_12482
[806] A_12483 [807] A_12484 [808] A_12485 [809] A_12486 [810] A_12487
[811] A_12488 [812] A_12489 [813] A_12490 [814] A_12491 [815] A_12492
[816] A_12493 [817] A_12494 [818] A_12495 [819] A_12496 [820] A_12497
[821] A_12498 [822] A_12499 [823] A_12500 [824] A_12501 [825] A_12502
[826] A_12503 [827] A_12504 [828] A_12505 [829] A_12506 [830] A_12507
[831] A_12508 [832] A_12509 [833] A_12510 [834] A_12511 [835] A_12512
[836] A_12513 [837] A_12514 [838] A_12515 [839] A_12516 [840] A_12517
[841] A_12518 [842] A_12519 [843] A_12520 [844] A_12521 [845] A_12522
[846] A_12523 [847] A_12524 [848] A_12525 [849] A_12526 [850] A_12527
[851] A_12528 [852] A_12529 [853] A_12530 [854] A_12531 [855] A_12532
[856] A_12533 [857] A_12534 [858] A_12535 [859] A_12536 [860] A_12537
[861] A_12538 [862] A_12539 [863] A_12540 [864] A_12541 [865] A_12542
[866] A_12543 [867] A_12544 [868] A_12545 [869] A_12546 [870] A_12547
[871] A_12548 [872] A_12549 [873] A_12550 [874] A_12551 [875] A_12552
[876] A_12553 [877] A_12554 [878] A_12555 [879] A_12556 [880] A_12557
[881] A_12558 [882] A_12559 [883] A_12560 [884] A_12561 [885] A_12562
[886] A_12563 [887] A_12564 [888] A_12565 [889] A_12566 [890] A_12567
[891] A_12568 [892] A_12569 [893] A_12570 [894] A_12571 [895] A_12572
[896] A_12573 [897] A_12574 [898] A_12575
;
MATRIX
[ 10 20 30 40 50 60 70 80 90 100]
[ . . . . . . . . . .]
Homo_sapiens AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGC [100]
Pan ................A.T..C.................A...............T......................T..T........C......... [100]
Gorilla ..................TG....T.....T........A........A......T...............................A..C.....C... [100]
Pongo ................AC..CC.....G..T.....T..A..C........CC....G.............................A..C.....C... [100]
Hylobates ......T..A..T...AC.G.C.................A..A..C..T..CC.G...........T....................A........C... [100]
Macaca_fuscata ......TT........AC...C..T..G.....T.....A..C..C..T..CA..TAT...........C..T........T.............AC..T [100]
M._mulatta ......TT.T......AC...C.....G..T..T.....A..C..C..T..CA..TAT...........C..T........T.............AC..T [100]
M._fascicularis .......T........AC..CC..T.................C..C..T..CA.GTAT......T.G..C..T........T..G........T.AC..T [100]
M._sylvanus .......T....T...ACT..C..T...G.T.....T..A..C..C..T..CA..TAC......T.G..C....................C.....C... [100]
Saimiri_sciureus ................A.G..C..A........T......T....T..G..TA.G.......................T........A.T......C..A [100]
Tarsius_syrichta ...T....TT..A..CAC..C...T.....T.....T..C..C..C.....CC..T....T...........TA.............AGTC........A [100]
Lemur_catta ........TA..A...AC......A........A..T..C........A..CA..T.......T.....C.....T...........A.TC..T..C..T [100]
[ 110 120 130 140 150 160 170 180 190 200]
[ . . . . . . . . . .]
Homo_sapiens ATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTA [200]
Pan ........T.....C................................C...........C........................C.......T..C.... [200]
Gorilla ........T..............C.....C.................CC.............G...........C....................C.... [200]
Pongo ....................C.................C........CC.C.....................A.......T...C....A.....C..C. [200]
Hylobates ...........A....G...G..C...G.CT..........G.....C..C........CGC......................C............... [200]
Macaca_fuscata .C....C.A..G..C.G...........TC.....T.......C...C.........T.AAC.........TA.......T...C.............C. [200]
M._mulatta .C....C.A..G..C.GG..........TC.....T.......C......C......T.AAC.........TA.......T...C.............C. [200]
M._fascicularis .C....C.A..A..C.G...........T......T...T.G.C...C..C........CAC.........TA.......T...C............... [200]
M._sylvanus ......C.A..A..C.G......C....TC.............C...C..C......T.CAC.........TA....T..T..TC.....T......... [200]
Saimiri_sciureus .CA....CAT.TA...G...G..C.....A...T....G..T....GCC.C........C.......AT...............C.....A.AG...... [200]
Tarsius_syrichta .CA...GCA..AG.C.GT..C........C...T.A..T..TGC...AACA........C..C..C...T.AA.C.....G...C.T.....A..A.... [200]
Lemur_catta .CA...C.A..AG.A.G...GA.C.....CA.T.....T..T.....CACC........A..C..C.....AA.......A...C.....A..T....C. [200]
[ 210 220 230 240 250 260 270 280 290 300]
[ . . . . . . . . . .]
Homo_sapiens ACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTC [300]
Pan .T..C..A..G........C............T.A................C............C......T...........A..........G..... [300]
Gorilla .......A.....G.....C..A...........A..............C.C...C..TT...........TCT.........A.T........G..... [300]
Pongo ....T..A...........C..A...A..G...TA.....T.....T..C.....CA.......A..................A.....A.......... [300]
Hylobates ....C..A..T.......TC..A...A.GG..T.C........GG....C.CT...A.TAC...C..C..G......G.....A....G........... [300]
Macaca_fuscata .T.....A..T.......T...AA.C.C....T.A...........CC.......CA.TA.G..A........T......T..A.T..G.....C..... [300]
M._mulatta .......A..T.......T...AA.C.CG...T.A........G..CC.......CA.TA..T.A......T.T.........A.T..G.....C..... [300]
M._fascicularis .T.....A..C.......T...AA.CAC...TT.A..T........CC.......CA.TG.GT.A..G..C..T..T......A..........C..... [300]
M._sylvanus .T........C.......TC..AA.C.C....T.A..T........CC.C.....CA..A....A........G.........A.T........C..... [300]
Saimiri_sciureus .T...G.A......T.ACTCACAA.C...T.TT.C.....T.....C..CT.T...A.TA..T.C........T..T......A.T.....A..C..... [300]
Tarsius_syrichta .TT..A.C..T.....G..C..AA..A..G.AG.A..T..A..G...C.CC.A...A.TA.CT.AGT...C..T....CC..TA....C........T.. [300]
Lemur_catta .TT..A.T..C.....A.TC..CACTA..G.AT.C.....A........C..T..AA.TA.CT.A.T...CT.A..T..G..CA....C..T..C..T.. [300]
[ 310 320 330 340 350 360 370 380 390 400]
[ . . . . . . . . . .]
Homo_sapiens CCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACAC [400]
Pan .........G.................A.......................T........G....................T..T.....A..TT..... [400]
Gorilla ...T..T....................A...C.......A........C.C..................T.............T......A.....G... [400]
Pongo T.....T.....C............C.A..TA...C...A........C..............T..T........C.....T.........C........ [400]
Hylobates ...T..........T..T.......C.A...A....T..A...........A...............C...............TAT.A..AC.T..G... [400]
Macaca_fuscata T...C.......C..T.........C.A..AA.......A..T.....A.T.........G...C.C.................AT.A..A......... [400]
M._mulatta ....C.......C............C.A..AG.......A..T.....A.T.............C.C................TAT.A..A......... [400]
M._fascicularis T...C....G..C.TT...GT....C.A..AA.......A........A.T...T.........C.C................TAT.A..A......... [400]
M._sylvanus T..TC.......C............C.A..AG.G.....A........A.TT...........AC.T................TAT.A..AC........ [400]
Saimiri_sciureus A..TC.T..G.A.G..T.T.....GC.A..TC....T..AT..AG..CC.G...T........AAT...T...........T..G..A..A..T.....T [400]
Tarsius_syrichta ...A..T...C.A.T..T...T...C.A..AAA.TA...AT.T..T..C.....T..C.TG...C.T.....C........T..AT.A..AA........ [400]
Lemur_catta ......T.....A..T..T......C.A..AAA......AT.T..TTCGC.....C....C..A..C..T.................T..A.C....... [400]
[ 410 420 430 440 450 460 470 480 490 500]
[ . . . . . . . . . .]
Homo_sapiens CTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACA [500]
Pan ...........C.....T...........T..T..T.....C..T..A..CA....C........................................... [500]
Gorilla ...........C.......................T..T..C........CA....C.........................................T. [500]
Pongo ...........C......T..............AG......CG.T.....CG...AC.........................T.............A.T. [500]
Hylobates ..C.T....C.C.........A..........TA..........T..C...A.TC.C......C.........T........T.............A... [500]
Macaca_fuscata ..CG.T..A...A....T...............A.......CCTG......A....C....G............T......CT.............A..C [500]
M._mulatta ..CG.T..A..CA..........T.........A.......CCTG......A.T..C....G............T.......T.............A..C [500]
M._fascicularis ..CG.T..A...A....T.....T.........A.......CCTG......A....C.................T.......T.............A..T [500]
M._sylvanus ..CG.T..A...A.T..T.....T..T......A........CTA..A...A.T..C................TT.......T...C.........A..T [500]
Saimiri_sciureus A..A.A..A..C........TA..T.G.G....A.GG.A....TA..ACCC..AC.......T.........G.T.......T.............A.T. [500]
Tarsius_syrichta ....TT...T.AA....A.....TAC.......A.AG.A....TA..AACCATG.AC................A........T.........G...A.T. [500]
Lemur_catta A..CT....C.......AT.TA..T.A......A.A..T...CTA..ACCCA.G.AC................A-......CT............CAGA. [499]
[ 510 520 530 540 550 560 570 580 590 600]
[ . . . . . . . . . .]
Homo_sapiens ACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGA [598]
Pan .........C.-.........................-T.T............T....AT.......C..G............................. [598]
Gorilla .........C.-.A.......................-.GT....G............A.....G..CT.G............................. [598]
Pongo .T..G.C.CC.-.A.......................-..................TCA.T-......G.G.................G........... [597]
Hylobates .T.......CG-AA...T...GC.............C-...................CTAT.......A.G............................. [598]
Macaca_fuscata .T....A..C.-.C...T................A..-.G....G.........C....TA...G.AC....A.TT.C..T................... [598]
M._mulatta .T....A....-.C...T................A..-.G.G..G.........C....TAT..G.AC....A.TT.C..T................... [598]
M._fascicularis .T......C..-.C..TT................A..-.G....G........TC......T..G.ACT...A.CT.C..T..C................ [598]
M._sylvanus .T...A.....-.C..TT................A..-TG....G..C.....TC..CA..T..G.ACT...A.CT.C..T................... [598]
Saimiri_sciureus .T...A.AA..-TA..TT....A............TG-.G.............T......T....A.A........T......C................ [598]
Tarsius_syrichta .T...A..CC.AA..TTT..........A......TA-TG.....................T....A.A......TG.........T-............ [598]
Lemur_catta .T...A...C.AAC-.TT.................TAATGT.T.............TGCA.T..G.A.A...A..T.C....A................. [598]
[ 610 620 630 640 650 660 670 680 690 700]
[ . . . . . . . . . .]
Homo_sapiens TAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTC [698]
Pan .......C....G.......................................................T.T.....C.........T.......A...C. [698]
Gorilla ........................A.......................................T...T..G....C.........T..G....A..... [698]
Pongo ............C...........AT..................................C.G.....TTT..C..C.....TG....C...T.A..... [697]
Hylobates ........................A.....................................G.A...T....C..C...G...TT.....G..A..C.. [698]
Macaca_fuscata ................AC......AGT......CA............................T.........CC.C..C.TT.TAAC......T.TC.. [698]
M._mulatta ................AC......AGT.......A............................T.........CC....C.TA.TAAC......T.TC.. [698]
M._fascicularis ................AC......AGT......CA............................T.........CC.C..C.TA.TAAC......C.TC.. [698]
M._sylvanus .................C......AGT.......A............................T....T.T..CC.C..C.TA.TAAC...T..C.TC.. [698]
Saimiri_sciureus ..GT..T.................AG.......CA...........................---..A...TTCT.C..C..TCTAA....A..A.T.AG [695]
Tarsius_syrichta ..GA..TA......C.........AA..G....-A............................ATT.ATTTT.AT.CTCC.TTTTA...T.A..T..ACT [697]
Lemur_catta ..GA..TA.........C......AG.......-A............................ATC.ATTAT.CT..T.C...CTTG.C..A....T.AT [697]
[ 710 720 730 740 750 760 770 780 790 800]
[ . . . . . . . . . .]
Homo_sapiens CCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGT [798]
Pan .T......T.........C.........A.........................T...........G.........A....G...........C..T..C [798]
Gorilla .T..........T............T..A.C..T.............G...............C........T..C.................C.....C [798]
Pongo ......C........TACCG.T......A.......C............C..........C.........A.GGCCA........G......C......C [797]
Hylobates ...............TACAG.......TA.......C..T.....G....T......G..C..C......ATG.CCA.T..C..T........A.....C [798]
Macaca_fuscata .....C..T...A..TT..G........A.C......T........CGTC.......AG....C......A.A.CC..AAT..ATG.T..C..C.....C [798]
M._mulatta .....C..T...A..TT..G........A.C......T........CGTC.......AG....C......A.A.CC..AAT..ATG.T..C..C.....C [798]
M._fascicularis ...G.CC.TT..A..TT..G........ACC.....CT.T......CGT........AG.C..C......A.A.CC..AAT..ATG.T.......C.... [798]
M._sylvanus .....C..TT..A..TT.CG.T.....TA.C.....C.........C..CT...T..AA.C..C......A.AGCC..AAT..ATG.T..C....C...C [798]
Saimiri_sciureus ....C.AG.G..A.....AG.T......A...............GC.CACT......GT.C..C......CTAGCCA..ATC.A.G..C.C....C.... [795]
Tarsius_syrichta .T.....A....AT.TA...TT..AACAAC...AAAAT.TG...C.C.TG.......TT.C..C......AA.TC.A....C.G.G.A.....A.CA..C [797]
Lemur_catta .....C.TTA..T...A...TA.A.G.TACA...ATAT.......CT..C.C..TG.A.CA..C........TTC.A.T....GTG....C..C.CT..C [797]
[ 810 820 830 840 850 860 870 880 890 ]
[ . . . . . . . . . ]
Homo_sapiens CTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT [896]
Pan ..T....................A................C.........A.....G........A................................ [896]
Gorilla ....................TC.A................C.........A.G............A.............TT..A.............. [896]
Pongo ..TA....A...........T..C.......GA......ACC..CG..A.A......TG....A.A..C.....G...CTA..A.....A........ [895]
Hylobates ..A..T.......T.............AC..........ACC.....T..A............A.TG..........GCTAG.A.............. [896]
Macaca_fuscata ...CC.T.A.....TT.......C.T.TC.A........ACA.CC..T.G..G......T...ATA.TG.........CTAG.C..AA.G........ [896]
M._mulatta ...CC.T.A.....TT.......C.T.TC.A........ACA.CC..T.GA.G......T...ATA.T..........CTAG.C..AA.A........ [896]
M._fascicularis ...CC.T.A.....CC.......CCT.TC.A........ACA.CC..T.G..GT.....T...ATA............TTAG.C..AA.A........ [896]
M._sylvanus ....CTT.A.....TT...AT..A.T.T..A........ACA..C....GA.G...G......ATA.T..........CTAAGC..AA.AT....... [896]
Saimiri_sciureus AC...AT.T.T..T.T.C..T..CCTTAC..G.......TCA..A..T..A............ATA..T.T......C.T.A.A..A........... [893]
Tarsius_syrichta ..AG....A.TGCTC.....TC.A.A.AC.A.T......A.A..C..T..C........T...ATA..G.TT..T..T.T.A.AT.A.G......... [895]
Lemur_catta ...A....A..T.T.T....T..C.C.TC..GA......ACA..C..T..C........T...ATA....T......CCTAA.A..A..TA.T..... [895]
;
END;
BEGIN GENETICCode;
StandardNUCLEAR;
END;
BEGIN CODONS;
CODONPOSSET * UNTITLED =
N: 1 458-659 897 898,
1: 2-455\3 660-894\3,
2: 3-456\3 661-895\3,
3: 4-457\3 662-896\3;
CODESET * UNTITLED = mtDNA.mam: all ;
END;
BEGIN ASSUMPTIONS;
USERTYPE ttbias STEPMATRIX= 4
A C G T
[A] . 6 1 6
[C] 6 . 6 1
[G] 1 6 . 6
[T] 6 1 6 .
;
OPTIONS DEFTYPE=unord PolyTcount=MINSTEPS ;
CHARSET tRNA_His = 459-528;
CHARSET 'tRNA_Ser_(AGY)' = 529-588;
CHARSET 'tRNA_Leu_(CUN)' = 589-659;
CHARSET noncoding = 1 458-659 897 898;
CHARSET position1 = 2-455\3 660-894\3;
CHARSET position2 = 3-456\3 661-895\3;
CHARSET position3 = 4-457\3 662-896\3;
EXSET protein_only = noncoding;
EXSET non_protein = position1 position2 position3;
EXSET only_3rds = position1 position2 noncoding;
EXSET only_2nds = position1 position3 noncoding;
EXSET only_1sts = position2 position3 noncoding;
END;
BEGIN TREES;
[!
Heuristic search settings:
Addition sequence: random
Number of replications = 10
Starting seed = 1
Global branch-swapping performed
MULPARS option in effect
Steepest descent option not in effect
Initial MAXTREES setting = 100
Branches having maximum length zero collapsed to yield polytomies
Trees are unrooted
Length of shortest tree found = 998
Number of trees retained = 2
Time used = 50.0 sec
]
TRANSLATE
1 Homo_sapiens,
2 Pan,
3 Gorilla,
4 Pongo,
5 Hylobates,
6 Macaca_fuscata,
7 M._mulatta,
8 M._fascicularis,
9 M._sylvanus,
10 Saimiri_sciureus,
11 Tarsius_syrichta,
12 Lemur_catta
;
TREE * 'Homo-Pan' = [&R] (12,(((((((1,2),3),4),5),(((6,7),8),9)),10),11));
TREE 'Pan-Gorilla' = [&R] (12,((((((1,(2,3)),4),5),(((6,7),8),9)),10),11));
TREE 'Homo-Gorilla' = [&R] (12,(((((((1,3),2),4),5),(((6,7),8),9)),10),11));
END;
BEGIN MACCLADE;
Version 3.05;
LastModified -1425155069;
Singles 0000&/0;
END;
|
