P A U P * Version 4.0b3a for 32-bit Microsoft Windows Fri Jan 28 15:54:33 2000 -----------------------------NOTICE----------------------------- This is a beta-test version. It will expire on 15 Jan 2001. 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. ---------------------------------------------------------------- Heuristic search settings: Optimality criterion = maximum parsimony Character-status summary: Of 471 total characters: All characters are of type 'unord' All characters have equal weight 38 characters are constant 87 variable characters are parsimony-uninformative Number of parsimony-informative characters = 346 Starting tree(s) obtained via stepwise addition Addition sequence: random Number of replicates = 100 Starting seed = 1942597998 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 Branches collapsed (creating polytomies) if maximum branch length is zero 'MulTrees' option in effect Topological constraints not enforced Trees are unrooted Heuristic search completed Total number of rearrangements tried = 524560 Score of best tree(s) found = 1041 Number of trees retained = 2 Time used = 1.95 sec Tree-island profile: First Last First Times Island Size tree tree Score replicate hit ---------------------------------------------------------------------- 1 2 1 2 1041 1 52 2 2 - - 1042 2 48* Note(s): * Multiple hits on islands of unsaved trees may in fact represent different islands 2 trees saved to file "C:\WINNT\PROFILES\jimmylin\DESKTOP\char_pars.tre" Bootstrap method with heuristic search: Number of bootstrap replicates = 100 Starting seed = 2014643012 Optimality criterion = maximum parsimony Character-status summary: Of 471 total characters: All characters are of type 'unord' All characters have equal weight 38 characters are constant 87 variable characters are parsimony-uninformative Number of parsimony-informative characters = 346 Starting tree(s) obtained via stepwise addition Addition sequence: random Number of replicates = 100 Starting seed = 1790449400 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 Branches collapsed (creating polytomies) if maximum branch length is zero 'MulTrees' option in effect Topological constraints not enforced Trees are unrooted Bootstrap replicates completed Time used = 00:05:50.2 Trees for each replicate written to treefile: C:\WINNT\PROFILES\jimmylin\DESKTOP\char_pars_boot.tre Bootstrap 50% majority-rule consensus tree /-------------------------------------------------------------------- Cele(1) | +-------------------------------------------------------------------- Scer(2) | | /--------- Mjan(3) | /--57---+ | | \--------- Phor(4) | /---72---+ | | \----------------- Aful(6) | /-----------99-----------+ | | \-------------------------- Mthe(5) | | | +--------------------------------------------------- Aaeo(7) | | | | /--------- Mpne(10) | | /--100--+ | | | \--------- Mgen(11) | | | | /---51---+ /---69---+----------------- Bbur(16) | | | | | | | | | \----------------- Tpal(17) | | | /--98---+ | | | | | /--------- Ctra(19) | | | | \------100-------+ | | | /---98---+ \--------- Cpne(20) | | | | | | | \--74---+ \---------------------------------- Rpro(13) | | | \--100--+ \------------------------------------------- Hpyl(12) | | /-------------------------- Mtub(8) | | +---------------60----------------+ /----------------- Bsub(9) | | | | \---69---+ /--------- Ecol(14) | \--82---+ | \--------- Hinf(15) | \------------------------------------------------------------ Syne(18) Bipartitions found in one or more trees and frequency of occurrence (bootstrap support values): 1 2 12345678901234567890 Freq ------------------------------ ..................** 100.00 .........**......... 100.00 ..****************** 100.00 ..****.............. 99.00 .........**.*..**.** 98.00 .........**....**.** 98.00 .............**..... 81.50 .........****..**.** 73.75 ..**.*.............. 71.75 .........**....**... 69.47 ........*....**..... 69.44 .......**....**..... 60.11 ..**................ 57.35 ..*****..****..**.** 51.25 .........**....*.... 46.25 ......************** 45.75 ...............**... 42.53 ..****...****..**.** 41.55 ......*..****..**.** 29.89 ..*****..****..***** 24.13 ..***............... 22.00 .......**....**..*.. 21.45 ...*.*.............. 19.75 ..*.*............... 19.50 ..***************.** 18.62 ........*....*...... 17.50 ...............**.** 16.53 ......*..****..***** 13.95 ..*****.*********.** 13.28 .......**....*...... 12.50 .......**........... 11.17 .........****.***.** 10.00 .........**.......** 9.80 ......*..**.*..**.** 8.35 ......*..****.***.** 8.00 ..*****.************ 7.93 ..*****..**.*..**.** 6.95 .........**.....*... 6.58 ..*****............. 6.50 ..*****..****.***.** 6.00 .......**....*...*.. 6.00 ..****.....*........ 5.50 ..*..*.............. 5.40 .........**....*..** 5.13 ......*..****.****** 5.00 (groups with relative frequency < 5% not shown) 1 tree saved to file "C:\WINNT\PROFILES\jimmylin\DESKTOP\char_pars_boot_final.tre" Optimality criterion set to distance. Heuristic search settings: Optimality criterion = distance (minimum evolution) Negative branch lengths allowed, but set to zero for tree-score calculation Distance measure = mean character difference Starting tree(s) obtained via neighbor-joining Branch-swapping algorithm: tree-bisection-reconnection (TBR) Steepest descent option not in effect Initial 'MaxTrees' setting = 100 Zero-length branches not collapsed 'MulTrees' option in effect Topological constraints not enforced Trees are unrooted NOTE: Random-addition-sequence option is ignored when starting trees are obtained using neighbor-joining. Heuristic search completed Total number of rearrangements tried = 2623 Score of best tree(s) found = 1.93678 Number of trees retained = 1 Time used = 0.21 sec 1 tree saved to file "C:\WINNT\PROFILES\jimmylin\DESKTOP\char_dist.tre" Bootstrap method with heuristic search: Number of bootstrap replicates = 100 Starting seed = 105995762 Optimality criterion = distance (minimum evolution) Negative branch lengths allowed, but set to zero for tree-score calculation Distance measure = mean character difference Starting tree(s) obtained via neighbor-joining Branch-swapping algorithm: tree-bisection-reconnection (TBR) Steepest descent option not in effect Initial 'MaxTrees' setting = 100 Zero-length branches not collapsed 'MulTrees' option in effect Topological constraints not enforced Trees are unrooted NOTE: Random-addition-sequence option is ignored when starting trees are obtained using neighbor-joining. Bootstrap replicates completed Time used = 26.20 sec Trees for each replicate written to treefile: C:\WINNT\PROFILES\jimmylin\DESKTOP\char_dist_boot.tre Bootstrap 50% majority-rule consensus tree /-------------------------------------------------------------------- Cele(1) | +-------------------------------------------------------------------- Scer(2) | | /--------- Mjan(3) | | | /--58---+--------- Phor(4) | | | | /-------------------100--------------------+ \--------- Aful(6) | | | | | \----------------- Mthe(5) | | | | /----------------- Aaeo(7) | | | | | | /--------- Mtub(8) | | +--61---+ | | | \--------- Bsub(9) | | /---------------56----------------+ \--100--+ | | /--------- Ecol(14) | | +--61---+ | | | \--------- Hinf(15) | | | | | \----------------- Syne(18) | | | | /--------- Mpne(10) | | /--100--+ | | | \--------- Mgen(11) \---65---+ /---98---+ | | | /--------- Bbur(16) | | \--68---+ | /--93---+ \--------- Tpal(17) | | | | | | /--------- Ctra(19) | /---76---+ \------100-------+ | | | \--------- Cpne(20) | | | \--76---+ \---------------------------------- Rpro(13) | \------------------------------------------- Hpyl(12) Bipartitions found in one or more trees and frequency of occurrence (bootstrap support values): 1 2 12345678901234567890 Freq ------------------------------ ..................** 100.00 .........**......... 100.00 ..****************** 100.00 ..****.............. 100.00 .........**....**... 98.00 .........**....**.** 93.00 .........**.*..**.** 76.00 .........****..**.** 76.00 ...............**... 68.00 ......************** 65.00 .............**..... 61.00 .......**........... 61.00 ..**.*.............. 58.00 ......***....**..*.. 56.00 .......**....**..... 49.00 ......*..........*.. 39.00 .......**....**..*.. 38.00 ........*....*...... 37.00 ..*..*.............. 36.50 ..**................ 30.50 .........**....*.... 29.00 .......**........*.. 26.00 ..*.*............... 26.00 ........*....**..... 25.00 ..*.**.............. 25.00 ...........**....... 23.00 ..****...****..**.** 22.00 ..*****..****..**.** 22.00 .......*.........*.. 19.00 ......*..****..**.** 16.00 .......**....*...... 16.00 ...*.*.............. 15.00 ......*....*........ 11.00 ......***..*.**..*.. 10.00 ..*****..****..***** 9.00 .......**....*...*.. 6.00 ....**.............. 6.00 ............*.....** 5.00 ..***************.** 5.00 (groups with relative frequency < 5% not shown) 1 tree saved to file "C:\WINNT\PROFILES\jimmylin\DESKTOP\char_dist_boot_final.tre" Pairwise distances between taxa Below diagonal: Total character differences Above diagonal: Mean character differences (adjusted for missing data) 1 2 3 4 5 6 7 8 1 Cele - 0.23142 0.46284 0.44374 0.42675 0.40340 0.43949 0.39703 2 Scer 109 - 0.35456 0.38217 0.31847 0.32484 0.32272 0.31423 3 Mjan 218 167 - 0.15074 0.12527 0.13588 0.23992 0.31210 4 Phor 209 180 71 - 0.17834 0.15924 0.28025 0.33970 5 Mthe 201 150 59 84 - 0.14225 0.20382 0.29724 6 Aful 190 153 64 75 67 - 0.23992 0.27389 7 Aaeo 207 152 113 132 96 113 - 0.18259 8 Mtub 187 148 147 160 140 129 86 - 9 Bsub 204 157 156 169 143 142 93 73 10 Mpne 236 201 150 139 153 166 131 165 11 Mgen 245 206 147 142 152 171 134 170 12 Hpyl 205 162 119 130 100 117 66 100 13 Rpro 220 189 138 139 123 140 85 125 14 Ecol 215 180 171 188 158 149 128 114 15 Hinf 217 164 147 162 142 157 100 106 16 Bbur 227 204 153 150 148 159 114 154 17 Tpal 222 189 146 135 139 142 105 137 18 Syne 191 144 139 158 124 137 74 82 19 Ctra 209 176 135 132 132 151 98 124 20 Cpne 207 176 143 136 136 153 96 126 Pairwise distances between taxa (continued) Below diagonal: Total character differences Above diagonal: Mean character differences (adjusted for missing data) 9 10 11 12 13 14 15 16 1 Cele 0.43312 0.50106 0.52017 0.43524 0.46709 0.45648 0.46072 0.48195 2 Scer 0.33333 0.42675 0.43737 0.34395 0.40127 0.38217 0.34820 0.43312 3 Mjan 0.33121 0.31847 0.31210 0.25265 0.29299 0.36306 0.31210 0.32484 4 Phor 0.35881 0.29512 0.30149 0.27601 0.29512 0.39915 0.34395 0.31847 5 Mthe 0.30361 0.32484 0.32272 0.21231 0.26115 0.33546 0.30149 0.31423 6 Aful 0.30149 0.35244 0.36306 0.24841 0.29724 0.31635 0.33333 0.33758 7 Aaeo 0.19745 0.27813 0.28450 0.14013 0.18047 0.27176 0.21231 0.24204 8 Mtub 0.15499 0.35032 0.36093 0.21231 0.26539 0.24204 0.22505 0.32696 9 Bsub - 0.36093 0.37580 0.21444 0.29299 0.20170 0.20594 0.31210 10 Mpne 170 - 0.03609 0.23992 0.22505 0.41826 0.30361 0.16773 11 Mgen 177 17 - 0.25478 0.23567 0.43312 0.30998 0.17834 12 Hpyl 101 113 120 - 0.15499 0.28450 0.19108 0.22081 13 Rpro 138 106 111 73 - 0.33758 0.24841 0.21444 14 Ecol 95 197 204 134 159 - 0.19958 0.36943 15 Hinf 97 143 146 90 117 94 - 0.27176 16 Bbur 147 79 84 104 101 174 128 - 17 Tpal 142 84 87 87 96 171 121 59 18 Syne 95 167 174 88 113 130 114 148 19 Ctra 131 95 96 94 81 160 102 80 20 Cpne 129 91 94 90 83 162 104 78 Pairwise distances between taxa (continued) Below diagonal: Total character differences Above diagonal: Mean character differences (adjusted for missing data) 17 18 19 20 1 Cele 0.47134 0.40552 0.44374 0.43949 2 Scer 0.40127 0.30573 0.37367 0.37367 3 Mjan 0.30998 0.29512 0.28662 0.30361 4 Phor 0.28662 0.33546 0.28025 0.28875 5 Mthe 0.29512 0.26327 0.28025 0.28875 6 Aful 0.30149 0.29087 0.32059 0.32484 7 Aaeo 0.22293 0.15711 0.20807 0.20382 8 Mtub 0.29087 0.17410 0.26327 0.26752 9 Bsub 0.30149 0.20170 0.27813 0.27389 10 Mpne 0.17834 0.35456 0.20170 0.19321 11 Mgen 0.18471 0.36943 0.20382 0.19958 12 Hpyl 0.18471 0.18684 0.19958 0.19108 13 Rpro 0.20382 0.23992 0.17197 0.17622 14 Ecol 0.36306 0.27601 0.33970 0.34395 15 Hinf 0.25690 0.24204 0.21656 0.22081 16 Bbur 0.12527 0.31423 0.16985 0.16561 17 Tpal - 0.27389 0.15924 0.15499 18 Syne 129 - 0.25902 0.24628 19 Ctra 75 122 - 0.05096 20 Cpne 73 116 24 -