PAUP Portable Version 4.0b10 For Unix

D:\Recherche\Articles\2011-2013_Cladistique Miguel\ResultsHSBoot2015.
txt 03 March 2015 16:05
P A U P *
Portable version 4.0b10 for Unix
Thu Feb 19 13:00:10 2015
-----------------------------NOTICE-----------------------------
This is a beta-test version. Please report any crashes,
apparent calculation errors, or other anomalous results.
There are no restrictions on publication of results obtained
with this version, but you should check the WWW site
frequently for bug announcements and/or updated versions.
See the README file on the distribution media for details.
----------------------------------------------------------------
paup> paup> delete Mladec_1 Hofmeyr;
Trees in memory will be invalidated by deletion of taxa. Specify one of the

following options:
(1) Clear trees from memory
(2) Abort taxon deletion
(3) Prune deleted taxa from trees
(1)> 1
All trees cleared from memory.
Taxon-deletion status changed:

2 taxa deleted
Total number of taxa now deleted = 2
Number of nondeleted taxa = 28
paup> paup> Outgroup Dmanisi_2700 KNMER_3733 Sangiran_17;
Outgroup status changed:

3 taxa transferred to outgroup
Total number of taxa now in outgroup = 3
Number of ingroup taxa = 27 (of which 25 are nondeleted)
paup> paup> Set increase=auto;
paup> paup> set autoinc=100;
paup> paup> HSearch;
Heuristic search settings:

Optimality criterion = parsimony
Character-status summary:
Of 93 total characters:
All characters are of type 'unord'
All characters have equal weight
All characters are parsimony-informative
Gaps are treated as "missing"
Starting tree(s) obtained via stepwise addition
Addition sequence: simple (reference taxon = Cro Magnon 1)
Number of trees held at each step during stepwise addition = 1
Branch-swapping algorithm: tree-bisection-reconnection (TBR)
Steepest descent option not in effect
Initial 'MaxTrees' setting = 100 (will be auto-increased by 100)
Branches collapsed (creating polytomies) if maximum branch length is zero
'MulTrees' option in effect
Topological constraints not enforced
-1-
D:\Recherche\Articles\2011-2013_Cladistique Miguel\ResultsHSBoot2015.txt 03 March 2015 16:05
Trees are unrooted
Heuristic search completed

Total number of rearrangements tried = 231282
Score of best tree(s) found = 543
Number of trees retained = 8
Time used = <1 sec (CPU time = 0.06 sec)
paup> paup> Reweight;
Characters reweighted by maximum value of rescaled consistency indices.
paup> paup> hsearch addseq=random nreps=100;
Heuristic search settings:

5 characters have weight 1
88 characters have weights other than 1
Addition sequence: random
Number of replicates = 100
Starting seed = 295077276
Trees are unrooted
Heuristic search completed

Total number of rearrangements tried = 1333456
Score of best tree(s) found = 73.32457
Number of trees retained = 1
Time used = 1 sec (CPU time = 0.72 sec)
Tree-island profile:
First Last First Times
Island Size tree tree Score replicate hit
----------------------------------------------------------------------
1 1 1 1 73.32457 2 66
2 1 - - 73.43604 1 10*
3 1 - - 73.52452 4 24*
Note(s):
* Multiple hits on islands of unsaved trees may in fact represent different
islands
paup> paup> describetrees;
Tree description:
Unrooted tree(s) rooted using outgroup method

-2-

Character-state optimization: Accelerated transformation (ACCTRAN)
Tree number 1 (rooted using user-specified outgroup)
Tree length = 73.32457

Consistency index (CI) = 0.4100
Homoplasy index (HI) = 0.5900
Retention index (RI) = 0.7027
Rescaled consistency index (RC) = 0.2881
/------------ Cro Magnon 1

|
| /---- Abri Pataud 1
/--56 /--31
| | | \---- Chancelade 1
| \--32
/--55 \-------- Ohalo II
| |
/--54 \---------------- LH18
| |
/--53 \-------------------- Qafzeh 6
| |
| \------------------------ Qafzeh 9
/---52
| | /---- Skhul V
| \----------------------33
/--51 \---- Jebel Irhoud 1
| |
| | /---- Florisbad
| \---------------------------50
| \---- Jinniushan
|
| /---------------- Saccopastore 1
| |
| | /---- Gibraltar 1
/--49 /--38 /------34
| | | | | \---- Amud 1
| | | | |
| | | \--37 /---- La Ferrasie 1
| | | | /--35
| | /--39 | | \---- La Chapelle-aux-
| | | | \--36
/--48 | | | \-------- Guattari
| | \-----------40 |
| | | \-------------------- Steinheim
| | |
/--47 | \------------------------ Atapuerca SH5
| | |
| | \----------------------------------------- Bodo
/--46 |
| | \--------------------------------------------- Kabwe 1
| |
/--45 \------------------------------------------------- Petralona
| |
| | /---- Ceprano
/--43 \-----------------------------------------------44
| | \---- Arago 21
| |
| \--------------------------------------------------------- Dali
|
-3-
42 /---- KNMER 3733

+-------------------------------------------------------41
| \---- Dmanisi 2700
|
\------------------------------------------------------------- Sangiran 17
paup> paup> savetrees brlens file=TREE_HS.tre;
OK to replace file "~/NewHeid2014/11-14/TREE_HS.tre"? (Y/n) y
1 tree saved to file "~/NewHeid2014/11-14/TREE_HS.tre"
paup> paup> bootstrap nreps=10000 method=heuristic;
Bootstrap method with heuristic search:

Number of bootstrap replicates = 10000
Simple weighting used for bootstrap
Addition sequence: random
Number of replicates = 100
Trees are unrooted
Elapsed Random Taxa Rearr. -- No. of trees -- --- Best trees ---
time rep added tried saved left-to-swap this rep overall
----------------------------------------------------------------------------
0:01:00 Bootstrap replicate 70...
0:01:00 24 28 773309 1 1 69.11224 68.84554
0:01:01 100 - 3314383 0 0 69.11224 68.84554
0:02:01 64 28 1418604 3 1 74.65360 74.43404
0:02:01 100 - 2100246 0 0 74.43404 74.43404
0:03:01 85 28 1374073 1 1 72.35477 71.60834
0:03:01 100 - 1605376 0 0 72.49104 71.60834
0:04:01 34 28 576770 3 1 71.44670 71.13699
0:04:02 100 - 1649209 0 0 71.13699 71.13699
0:05:02 54 28 879880 1 1 66.95788 66.56145
0:05:02 100 - 1615390 0 0 66.97029 66.56145
0:06:02 53 28 789930 1 1 74.14385 73.87097
0:06:02 100 - 1438483 0 0 73.88123 73.87097
0:07:02 61 28 729022 1 1 80.18050 76.37174
0:07:03 100 - 1218423 0 0 76.62047 76.37174
-4-

0:08:03 89 28 1528384 3 1 69.00462 69.00462
0:08:03 100 - 1723517 0 0 69.00462 69.00462
0:09:03 52 28 848698 1 1 74.66828 73.99771
0:09:03 100 - 1688011 0 0 74.22081 73.99771
0:10:03 92 28 1172095 1 1 66.41056 64.28582
0:10:03 100 - 1282708 0 0 64.28582 64.28582
0:11:03 64 28 1028491 1 1 65.39645 64.67126
0:11:04 100 - 1584066 0 0 64.80440 64.67126
0:12:04 77 28 2197018 6 1 74.08175 74.07181
0:12:04 100 - 2832598 0 0 74.07181 74.07181
0:13:04 62 28 718056 1 1 69.15553 69.15553
0:13:04 100 - 1176445 0 0 69.15553 69.15553
0:14:04 28 8 390488 - - - 70.01260
0:14:05 100 - 1467576 0 0 70.17634 70.01260
0:15:05 63 28 878524 1 1 76.49620 75.64202
0:15:05 100 - 1441397 0 0 75.64202 75.64202
0:16:05 76 26 1295595 - - - 72.98506
0:16:05 100 - 1715535 0 0 73.05575 72.98506
0:17:05 69 28 1184430 1 1 76.94094 76.46825
0:17:05 100 - 1711452 0 0 76.46825 76.46825
0:18:05 95 28 1343754 1 1 73.87257 72.43719
0:18:05 100 - 1421832 0 0 72.74796 72.43719
0:19:05 11 28 212568 1 1 76.25245 76.19777
0:19:06 100 - 1927529 0 0 76.19777 76.19777
0:20:06 89 28 1282869 1 1 78.25508 77.16900
0:20:06 100 - 1445496 0 0 77.16900 77.16900
0:21:06 52 11 863875 - - - 62.52596
0:21:07 100 - 1606251 0 0 62.54670 62.52596
0:22:07 72 28 1146692 1 1 70.65499 69.97443
0:22:07 100 - 1609675 0 0 69.97443 69.97443
0:23:07 22 28 352725 1 1 65.62469 64.38739
0:23:08 100 - 1677260 0 0 64.44901 64.38739
0:24:08 17 28 310147 1 1 68.83079 68.20398
0:24:08 100 - 1685647 0 0 68.33514 68.20398
0:25:08 54 28 998015 5 1 74.82136 74.76999
0:25:09 100 - 1732776 0 0 74.76999 74.76999
0:26:09 26 28 1062464 1 1 67.72409 67.05136
0:26:10 100 - 3111850 0 0 67.80288 67.05136
0:27:10 34 28 501797 3 1 65.70924 65.70924
0:27:10 100 - 1425365 0 0 65.70924 65.70924
0:28:10 46 28 625359 1 1 68.86541 68.86541
0:28:11 100 - 1383571 0 0 69.13095 68.86541
0:29:11 56 28 738172 1 1 64.78705 64.52630
-5-
0:29:11 100 - 1329375 0 0 64.69077 64.52630

0:30:11 99 28 4207437 11 4 82.52418 82.32774
0:30:11 100 - 4259961 0 0 82.52418 82.32774
0:31:11 95 28 1303928 1 1 74.68602 74.48796
0:31:11 100 - 1372727 0 0 74.68000 74.48796
0:32:11 9 28 221042 1 1 76.24786 76.11497
0:32:12 100 - 2434570 0 0 76.88431 76.11497
0:33:12 22 28 612755 1 1 65.62207 65.40813
0:33:13 100 - 2585377 0 0 65.40813 65.40813
0:34:13 86 28 1210176 1 1 63.98958 63.98958
0:34:13 100 - 1389340 0 0 64.67541 63.98958
0:35:13 30 28 375837 1 1 72.60208 71.65906
0:35:13 100 - 1233714 0 0 71.73049 71.65906
0:36:13 73 28 1529280 6 4 60.94573 60.01440
0:36:14 100 - 2311725 0 0 60.01440 60.01440
0:37:14 9 28 146116 2 1 69.96109 69.87470
0:37:15 100 - 1600508 0 0 70.58252 69.87470
0:38:15 98 28 1589326 3 1 64.89102 64.89102
0:38:15 100 - 1634326 0 0 64.89102 64.89102
0:39:15 34 28 495659 1 1 68.82352 68.82352
0:39:15 100 - 1523508 0 0 69.16792 68.82352
0:40:15 37 28 558138 1 1 77.01559 77.01559
0:40:16 100 - 1477534 0 0 77.01559 77.01559
0:41:16 50 28 734715 1 1 71.46289 70.85659
0:41:16 100 - 1501416 0 0 71.49282 70.85659
0:42:16 81 28 1897804 3 1 65.05501 64.75595
0:42:16 100 - 2382360 0 0 65.28243 64.75595
0:43:16 49 28 612599 1 1 77.53948 76.98328
0:43:17 100 - 1350352 0 0 76.98328 76.98328
0:44:17 94 28 1559911 1 1 77.56624 76.80433
0:44:17 100 - 1716747 0 0 77.00858 76.80433
0:45:17 89 28 1367472 1 1 67.94830 67.94830
0:45:17 100 - 1509481 0 0 67.94830 67.94830
0:46:17 74 28 1685444 1 1 78.68588 74.51910
0:46:17 100 - 2139085 0 0 74.51910 74.51910
0:47:17 18 28 212891 1 1 66.21848 66.19483
0:47:18 100 - 1314142 0 0 66.21848 66.19483
0:48:18 33 28 420174 1 1 73.43802 73.30145
0:48:18 100 - 1254729 0 0 73.30145 73.30145
0:49:18 79 28 1419694 4 2 70.74380 70.02582
0:49:18 100 - 1778918 0 0 70.74380 70.02582
0:50:18 42 28 613030 3 1 68.15970 68.02633
0:50:19 100 - 1621905 0 0 68.27155 68.02633
-6-
0:51:19 66 28 996690 1 1 82.30413 79.92730

0:51:19 100 - 1492543 0 0 79.92730 79.92730
0:52:19 100 28 1795321 3 1 71.23618 68.99014
0:52:19 100 - 1822732 0 0 68.99014 68.99014
0:53:19 66 28 1255224 3 1 66.09615 65.69552
0:53:19 100 - 1781710 0 0 65.69552 65.69552
0:54:19 20 28 375004 1 1 68.24536 67.91133
0:54:20 100 - 1854420 0 0 67.91133 67.91133
0:55:20 46 28 681403 1 1 68.94624 68.73193
0:55:20 100 - 1480130 0 0 68.73193 68.73193
0:56:20 21 28 386761 1 1 70.90168 70.67332
0:56:21 100 - 1789328 0 0 70.91123 70.67332
0:57:21 98 28 1917000 2 1 74.17745 73.47141
0:57:21 100 - 1949786 0 0 73.50370 73.47141
0:58:21 90 28 2057617 3 1 71.21950 69.70635
0:58:21 100 - 2259913 0 0 69.92308 69.70635
0:59:21 32 28 490440 1 1 66.52310 65.72438
0:59:22 100 - 1501273 0 0 65.72438 65.72438
1:00:22 50 28 550655 1 1 73.25338 73.02333
1:00:22 100 - 1139244 0 0 73.14091 73.02333
1:01:22 49 28 1030400 1 1 64.58966 63.64179
1:01:23 100 - 1861928 0 0 63.76403 63.64179
1:02:23 46 19 717847 - - - 73.93621
1:02:23 100 - 1649933 0 0 75.25770 73.93621
1:03:23 33 28 367272 1 1 78.85105 78.16574
1:03:24 100 - 1190968 0 0 78.20583 78.16574
1:04:24 78 28 1140470 1 1 70.99284 70.99284
1:04:24 100 - 1471342 0 0 70.99284 70.99284
1:05:24 88 28 2144067 6 2 77.60969 77.40598
1:05:24 100 - 2465272 0 0 77.40598 77.40598
1:06:24 19 28 350558 1 1 87.79579 87.47478
1:06:25 100 - 1891156 0 0 87.47478 87.47478
1:07:25 35 28 539003 1 1 77.27454 77.27454
1:07:25 100 - 1608552 0 0 77.27454 77.27454
1:08:25 95 28 1841544 1 1 77.60664 77.11273
1:08:25 100 - 1943734 0 0 77.26090 77.11273
1:09:25 27 28 411706 1 1 70.63769 70.63769
1:09:26 100 - 1531016 0 0 70.63769 70.63769
1:10:26 33 28 360290 1 1 78.04826 77.73772
1:10:26 100 - 1126408 0 0 77.73772 77.73772
1:11:26 56 28 1183880 9 1 68.97731 67.67313
1:11:27 100 - 2569343 0 0 68.63643 67.67313
1:12:27 37 20 440840 - - - 69.98819
1:12:27 100 - 1250147 0 0 70.07464 69.98819
-7-

1:13:27 42 28 1138451 1 1 70.95783 68.11153
1:13:28 100 - 2943542 0 0 68.11153 68.11153
1:14:28 26 28 823147 3 1 74.21874 73.82259
1:14:29 100 - 3121181 0 0 74.04844 73.82259
1:15:29 57 28 1001034 1 1 64.82971 64.36781
1:15:29 100 - 1770194 0 0 64.36781 64.36781
1:16:29 76 28 1885014 5 1 66.73977 65.55038
1:16:30 100 - 2587176 0 0 66.00907 65.55038
1:17:30 4 28 49853 1 1 74.54751 74.54751
1:17:31 100 - 1522835 0 0 74.80743 74.39473
1:18:31 89 28 1388073 1 1 68.97685 68.45037
1:18:31 100 - 1583244 0 0 68.45037 68.45037
1:19:31 49 28 760903 5 1 72.47732 71.67065
1:19:31 100 - 1622032 0 0 72.55418 71.67065
1:20:31 98 28 3484580 6 1 79.70213 79.13436
1:20:31 100 - 3613810 0 0 79.70213 79.13436
1:21:31 55 28 977340 6 2 66.79354 64.31229
1:21:32 100 - 1905685 0 0 65.17786 64.31229
1:22:32 73 28 1052290 1 1 66.16020 65.76093
1:22:32 100 - 1431003 0 0 65.93927 65.76093
1:23:32 38 28 520101 3 1 75.43879 75.30619
1:23:32 100 - 1488438 0 0 75.30619 75.30619
1:24:32 70 28 917860 1 1 73.55441 73.53363
1:24:33 100 - 1342077 0 0 73.53363 73.53363
1:25:33 35 28 466754 1 1 71.33773 71.23864
1:25:33 100 - 1349077 0 0 71.23864 71.23864
1:26:33 100 28 2583113 6 1 73.15848 73.06390
1:26:33 100 - 2597058 0 0 73.15848 73.06390
1:27:33 15 23 357160 - - - 74.07003
1:27:34 100 - 2365537 0 0 74.39178 74.07003
1:28:34 11 28 364168 3 1 70.41956 70.03276
1:28:35 100 - 3350094 0 0 70.40882 70.03276
1:29:35 93 28 1458572 1 1 67.44320 67.44320
1:29:35 100 - 1542904 0 0 68.05222 67.44320
1:30:35 20 28 346420 1 1 74.08238 73.04474
1:30:36 100 - 1916379 0 0 74.55906 73.04474
1:31:36 76 28 1787982 1 1 67.20512 67.18615
1:31:36 100 - 2389984 0 0 67.18615 67.18615
1:32:36 83 28 1404481 1 1 67.45357 67.20671
1:32:37 100 - 1679159 0 0 67.25349 67.20671
1:33:37 83 28 1254292 1 1 66.67845 65.82999
1:33:37 100 - 1518646 0 0 65.97106 65.82999
1:34:37 77 28 1174069 1 1 73.41019 73.14638
-8-
1:34:37 100 - 1515166 0 0 73.14638 73.14638

1:35:37 44 28 664799 1 1 72.82623 70.03049
1:35:38 100 - 1750959 0 0 70.32629 70.03049
1:36:38 96 28 1322078 1 1 84.78790 84.44422
1:36:38 100 - 1382248 0 0 84.78790 84.44422
1:37:38 77 28 1635037 1 1 83.39666 83.26619
1:37:38 100 - 2118047 0 0 83.26619 83.26619
1:38:38 1 28 5222 1 1 72.14886 72.14886
1:38:39 100 - 1481891 0 0 72.36573 72.14886
1:39:39 3 28 37626 1 1 75.39887 72.42346
1:39:39 100 - 1597886 0 0 72.42346 72.42346
1:40:39 84 28 1589699 1 1 66.77581 66.77581
1:40:40 100 - 1892255 0 0 66.77581 66.77581
1:41:40 28 28 417627 1 1 71.89856 70.92513
1:41:40 100 - 1542769 0 0 71.03923 70.92513
1:42:40 20 28 254565 1 1 66.65995 66.65995
1:42:41 100 - 1342449 0 0 66.65995 66.65995
1:43:41 3 28 60210 1 1 77.42095 77.39973
1:43:41 100 - 2050479 0 0 77.93589 77.39973
1:44:41 31 28 382510 1 1 74.54826 74.54826
1:44:42 100 - 1316912 0 0 75.29533 74.54826
1:45:42 66 28 866017 1 1 81.62661 80.64034
1:45:42 100 - 1317623 0 0 80.64034 80.64034
1:46:42 69 28 1145076 3 1 74.84954 74.70429
1:46:42 100 - 1719157 0 0 75.61836 74.70429
1:47:42 6 28 82377 3 1 71.31481 71.31481
1:47:43 100 - 1331121 0 0 71.44073 71.31481
1:48:43 22 22 268727 - - - 69.74537
1:48:44 100 - 1239512 0 0 70.12520 69.51828
1:49:44 27 28 391189 1 1 76.79332 75.13799
1:49:44 100 - 1459043 0 0 75.13799 75.13799
1:50:44 89 28 1288905 1 1 81.45172 80.86081
1:50:44 100 - 1442930 0 0 80.86081 80.86081
1:51:44 50 28 598439 1 1 81.58599 80.36389
1:51:45 100 - 1240078 0 0 80.46932 80.36389
1:52:45 55 17 969147 - - - 76.92911
1:52:45 100 - 1841071 0 0 77.12560 76.92911
1:53:45 23 28 364937 1 1 65.87967 65.87967
1:53:46 100 - 1519885 0 0 66.43068 65.87967
1:54:46 13 28 238772 1 1 67.18842 66.99815
1:54:46 100 - 1846589 0 0 66.99815 66.99815
1:55:46 87 28 1281276 1 1 72.73372 72.72807
1:55:47 100 - 1495770 0 0 72.72807 72.72807
-9-
1:56:47 80 28 1142352 1 1 78.38429 78.16672

1:56:47 100 - 1447975 0 0 78.16672 78.16672
1:57:47 32 28 1017336 1 1 70.27753 68.71126
1:57:48 100 - 3225312 0 0 68.79680 68.71126
1:58:48 15 28 253428 1 1 72.60526 72.31484
1:58:49 100 - 1683125 0 0 73.22974 72.31484
1:59:49 75 28 1130669 1 1 72.34213 72.32557
1:59:49 100 - 1532334 0 0 72.34213 72.32557
2:00:49 76 28 1593096 5 1 63.02959 62.84858
2:00:49 100 - 2044002 0 0 62.93019 62.84858
2:01:49 93 28 1379993 1 1 67.19178 63.07835
2:01:49 100 - 1482109 0 0 63.15378 63.07835
2:02:49 54 28 776819 1 1 62.78412 61.55073
2:02:49 100 - 1474761 0 0 61.55073 61.55073
2:03:49 59 28 846802 1 1 73.54866 72.79909
2:03:50 100 - 1421094 0 0 72.79909 72.79909
2:04:50 17 28 371113 4 2 60.09978 59.61714
2:04:51 100 - 2768441 0 0 59.82429 59.61714
2:05:51 77 28 1191277 1 1 65.44147 65.24267
2:05:51 100 - 1528685 0 0 65.41988 65.24267
2:06:51 24 28 278999 1 1 74.59377 72.34465
2:06:51 100 - 1291120 0 0 72.34465 72.34465
2:07:51 22 28 282278 1 1 80.39393 80.39393
2:07:52 100 - 1347874 0 0 80.39393 80.39393
2:08:52 28 28 413621 1 1 63.90370 61.03633
2:08:53 100 - 1502502 0 0 61.15993 61.03633
2:09:53 14 28 968590 24 2 68.18113 68.09367
2:09:56 100 - 9772733 0 0 68.27470 68.09367
2:10:56 78 25 1220097 - - - 69.21242
2:10:56 100 - 1582237 0 0 69.21242 69.21242
2:11:56 10 28 163443 1 1 77.79876 77.79876
2:11:58 100 - 2154419 0 0 77.83817 77.78632
2:12:58 44 28 587916 1 1 69.53230 69.24564
2:12:58 100 - 1426924 0 0 69.47172 69.24564
2:13:58 80 28 1701331 1 1 64.94163 64.81811
2:13:58 100 - 2118712 0 0 65.08104 64.81811
2:14:58 68 28 1183803 1 1 74.82247 70.88315
2:14:59 100 - 1719033 0 0 71.58598 70.88315
2:15:00 100 28 1655604 0 0 68.20155 67.72788
10000 bootstrap replicates completed

Time used = 02:15:00 (CPU time = 02:15:00.8)
Bootstrap 50% majority-rule consensus tree
/-------- KNMER 3733(26)
-10-
/-----------------------86-----------------------+
| \-------- Dmanisi 2700(27)
|
| /------------------------ Cro Magnon 1(3)
| |
| | /-------- Abri Pataud 1(4)
| | /--70---+
| | | \-------- Chancelade 1(5)
| /---55---+--53---+
| | | \---------------- Ohalo II(9)
| | |
| | +------------------------ Qafzeh 6(6)
| /--58---+ |
| | | \------------------------ LH18(21)
| | |
| /--67---+ \--------------------------------- Qafzeh 9(7)
| | |
| | | /-------- Skhul V(8)
| | \---------------63---------------+
| | \-------- Jebel Irhoud 1(19)
| |
| | /------------------------ Saccopastore 1(10)
| | |
| | +------------------------ Gibraltar 1(11)
| | |
| | | /-------- La Ferrasie 1(12)
| | /---96---+ /--60---+
| | | | | \-------- La Chapelle-aux-(14)
| | | +--97---+
| | | | \---------------- Guattari(13)
| | /--87---+ |
| | | | \------------------------ Amud 1(15)
| | | |
+--90---+--67---+ \--------------------------------- Steinheim(17)
| | |
| | \----------------------------------------- Atapuerca SH5(16)
| |
| +------------------------------------------------- Petralona(18)
| |
| +------------------------------------------------- Bodo(20)
| |
| +------------------------------------------------- Florisbad(22)
| |
| +------------------------------------------------- Kabwe 1(23)
| |
| +------------------------------------------------- Dali(24)
| |
| +------------------------------------------------- Jinniushan(25)
| |
| | /-------- Ceprano(29)
| \-------------------59-------------------+
| \-------- Arago 21(30)
|
\--------------------------------------------------------- Sangiran 17(28)
Bipartitions found in one or more trees and frequency of occurrence (bootstrap

support values):
111111111122222222223
3456789012345678901234567890 Freq %
---------------------------------------------
.........***................ 9715.00 97.2%
.......******............... 9587.67 95.9%
.......................***.. 9018.33 90.2%
.......******.*............. 8655.92 86.6%
-11-
.......................**... 8646.00 86.5%

.**......................... 7037.33 70.4%
.......********............. 6730.27 67.3%
.......*********.*.********* 6661.33 66.6%
.....*..........*........... 6316.83 63.2%
.........*.*................ 5951.13 59.5%
..........................** 5912.24 59.1%
.....*.***********.********* 5776.48 57.8%
....**.***********.********* 5456.71 54.6%
.**...*..................... 5304.89 53.0%
........*...*............... 4953.67 49.5%
...***.***********.********* 4794.50 47.9%
.......*********.*..******** 4155.40 41.6%
...***.********************* 4143.90 41.4%
.......*....*............... 4027.83 40.3%
.......*********.*..**.***** 3778.05 37.8%
........*****............... 3563.00 35.6%
...............*.....*.***** 3389.33 33.9%
...*..............*......... 3110.70 31.1%
.....................*.***** 2947.52 29.5%
........****................ 2806.00 28.1%
...............*.*..**.***** 2756.50 27.6%
.....................*.***.. 2722.06 27.2%
..........**................ 2570.08 25.7%
...............*....**.***** 2559.77 25.6%
.....*.***********..******** 2558.17 25.6%
.......*********.*.***.***** 2483.57 24.8%
.......*********.*..*..***** 2305.53 23.1%
.....*.*********.*.********* 2173.33 21.7%
...************************* 2005.13 20.1%
...................*.*...... 2004.53 20.0%
...............*.*.***.***** 1879.33 18.8%
...............*...*.*.***** 1841.00 18.4%
...............*...........* 1676.97 16.8%
..*...*..................... 1675.60 16.8%
.......**...*............... 1633.67 16.3%
...............*....*....... 1621.43 16.2%
.......*.****............... 1465.67 14.7%
.**.*.*..................... 1450.03 14.5%
.**...*...........*......... 1401.87 14.0%
.........**................. 1282.53 12.8%
...................*......*. 1256.64 12.6%
.......................*.*.. 1218.00 12.2%
...............*..........** 1191.67 11.9%
...............*...***.***** 1188.40 11.9%
...................*.*.****. 1178.28 11.8%
.......********..*.......... 1170.25 11.7%
...............*.*..*..***** 1165.05 11.7%
.................*.....***.. 1046.33 10.5%
.......********..*..*....... 1044.10 10.4%
.****.*...........*......... 1041.33 10.4%
.................*..*....... 1008.10 10.1%
.......*********.*..*.****** 990.17 9.9%
...................*.*....*. 978.13 9.8%
.......*********.*..*....... 969.67 9.7%
.......*********.*..*......* 963.20 9.6%
.......*********.*..*.....** 943.58 9.4%
...................*.*.***** 877.00 8.8%
...*.*.********************* 859.17 8.6%
.............*.*.*.********* 852.00 8.5%
...................*.*.***.. 829.48 8.3%
.......................****. 799.82 8.0%
.......................***** 793.92 7.9%
...............*.......***** 767.33 7.7%
....*..*********.*.********* 760.22 7.6%
-12-
...*.*.***********.********* 739.50 7.4%

...............*.*..*....... 729.37 7.3%
....**.***********..******** 721.33 7.2%
...................*..*..... 713.16 7.1%
...**....................... 702.00 7.0%
...*.*.************.******** 648.33 6.5%
.......*.***................ 635.67 6.4%
.......********.....*....... 618.67 6.2%
.......*****................ 616.50 6.2%
.......*********.*.**.****** 598.00 6.0%
......*...........*......... 585.00 5.8%
.......***********.********* 551.67 5.5%
.*.************************* 545.00 5.4%
....**..........*........... 525.47 5.3%
1477 groups at (relative) frequency less than 5% not shown
paup> paup> MajRule=Yes;
Error(#112): Command "MajRule=Yes" is unrecognized.
paup> paup> SaveTrees file=MajRule_Boot.tre;
0 trees saved to file "~/NewHeid2014/11-14/MajRule_Boot.tre"
paup>
-13-

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D:\Recherche\Articles\2011-2013_Cladistique Miguel\ResultsHSBoot2015.

txt 03 March 2015 16:05

paup> paup> delete Mladec_1 Hofmeyr;

Trees in memory will be invalidated by deletion of taxa. Specify one of the

All trees cleared from memory.

Taxon-deletion status changed:

paup> paup> Outgroup Dmanisi_2700 KNMER_3733 Sangiran_17;

Outgroup status changed:

paup> paup> Set increase=auto;

paup> paup> set autoinc=100;

paup> paup> HSearch;

Heuristic search settings:

Trees are unrooted

Heuristic search completed

paup> paup> Reweight;

Characters reweighted by maximum value of rescaled consistency indices.

paup> paup> hsearch addseq=random nreps=100;

Heuristic search settings:

Heuristic search completed

paup> paup> describetrees;

Unrooted tree(s) rooted using outgroup method

All characters are of type 'unord'

Tree number 1 (rooted using user-specified outgroup)

Tree length = 73.32457

/------------ Cro Magnon 1

42 /---- KNMER 3733

paup> paup> savetrees brlens file=TREE_HS.tre;

OK to replace file "~/NewHeid2014/11-14/TREE_HS.tre"? (Y/n) y

1 tree saved to file "~/NewHeid2014/11-14/TREE_HS.tre"

paup> paup> bootstrap nreps=10000 method=heuristic;

Bootstrap method with heuristic search:

0:08:03 Bootstrap replicate 585...

0:29:11 100 - 1329375 0 0 64.69077 64.52630

0:51:19 66 28 996690 1 1 82.30413 79.92730

1:13:27 Bootstrap replicate 5439...

1:34:37 100 - 1515166 0 0 73.14638 73.14638

1:56:47 80 28 1142352 1 1 78.38429 78.16672

10000 bootstrap replicates completed

Bootstrap 50% majority-rule consensus tree

/-------- KNMER 3733(26)

Bipartitions found in one or more trees and frequency of occurrence (bootstrap

.......................**... 8646.00 86.5%

...*.*.***********.********* 739.50 7.4%

1477 groups at (relative) frequency less than 5% not shown

paup> paup> MajRule=Yes;

Error(#112): Command "MajRule=Yes" is unrecognized.

paup> paup> SaveTrees file=MajRule_Boot.tre;

0 trees saved to file "~/NewHeid2014/11-14/MajRule_Boot.tre"

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.....***.* 739.50 7.4%