APPENDIX 1. Accuracy of separate, combined, and consensus analysis for two genes (data sets) with different phylogenetic histories, with asymmetric tree topologies and 50 characters in each data set. Each value is the average accuracy from 100 replicated matrices.
|
Branch length |
||||||
|
Case |
0.01 |
0.15 |
0.30 |
0.45 |
0.60 |
|
|
I |
data set 1 |
0.363 |
0.849 |
0.472 |
0.107 |
0.021 |
|
data set 2 |
0.361 |
0.832 |
0.506 |
0.091 |
0.012 |
|
|
consensus |
0.139 |
0.714 |
0.261 |
0.018 |
0.000 |
|
|
combined |
0.601 |
0.955 |
0.744 |
0.185 |
0.021 |
|
|
II |
data set 1 |
0.360 |
0.869 |
0.455 |
0.081 |
0.014 |
|
data set 2 |
0.300 |
0.728 |
0.398 |
0.044 |
0.013 |
|
|
consensus |
0.106 |
0.636 |
0.180 |
0.008 |
000 |
|
|
combined |
0.559 |
0.915 |
0.695 |
0.140 |
0.025 |
|
|
III |
data set 1 |
0.335 |
0.871 |
0.473 |
0.084 |
0.014 |
|
data set 2 |
0.268 |
0.675 |
0.320 |
0.037 |
0.007 |
|
|
consensus |
0.089 |
0.590 |
0.132 |
0.003 |
0.000 |
|
|
combined |
0.497 |
0.856 |
0.641 |
0.149 |
0.019 |
|
|
IV |
data set 1 |
0.333 |
0.744 |
0.402 |
0.066 |
0.013 |
|
data set 2 |
0.304 |
0.784 |
0.412 |
0.083 |
0.008 |
|
|
consensus |
0.097 |
0.567 |
0.159 |
0.003 |
000 |
|
|
combined |
0.517 |
0.858 |
0.649 |
0.149 |
0.014 |
|
|
V |
data set 1 |
0.357 |
0.847 |
0.426 |
0.091 |
0.023 |
|
data set 2 |
0.178 |
0.386 |
0.223 |
0.059 |
0.014 |
|
|
consensus |
0.060 |
0.331 |
0.092 |
0.008 |
000 |
|
|
combined |
0.420 |
0.613 |
0.432 |
0.125 |
0.022 |
|
|
VI |
data set 1 |
0.344 |
0.846 |
0.465 |
0.099 |
0.027 |
|
data set 2 |
0.001 |
0.005 |
0.008 |
0.007 |
0.003 |
|
|
consensus |
0.001 |
0.003 |
0.008 |
0.001 |
0.000 |
|
|
combined |
0.261 |
0.370 |
0.203 |
0.038 |
0.012 |
|
|
VII |
data set 1 |
0.195 |
0.364 |
0.241 |
0.056 |
0.009 |
|
data set 2 |
0.154 |
0.293 |
0.172 |
0.049 |
0.019 |
|
|
consensus |
0.000 |
0.010 |
0.004 |
0.001 |
000 |
|
|
combined |
0.264 |
0.398 |
0.132 |
0 044 |
0.004 |
|
APPENDIX 2. Accuracy of separate, combined, and consensus analysis for two genes (data sets) with different phylogenetic histories, with symmetric tree topologies and 50 characters in each data set. Each value is the average accuracy from 100 replicated matrices.
|
Branch length |
||||||
|
Case |
0.01 |
0.15 |
0.30 |
0.45 |
0.60 |
|
|
I |
data set 1 |
0.343 |
0.807 |
0.546 |
0.248 |
0.047 |
|
data set 2 |
0.343 |
0.829 |
0.561 |
0.211 |
0.037 |
|
|
consensus |
0.125 |
0.667 |
0.315 |
0.067 |
0.003 |
|
|
combined |
0.577 |
0.956 |
0.749 |
0.342 |
0.052 |
|
|
II |
data set 1 |
0.341 |
0.805 |
0.551 |
0.222 |
0.025 |
|
data set 2 |
0.263 |
0.614 |
0.399 |
0.158 |
0.033 |
|
|
consensus |
0.093 |
0.486 |
0.228 |
0.048 |
0.000 |
|
|
combined |
0.489 |
0.810 |
0.624 |
0.295 |
0.042 |
|
|
III |
data set 1 |
0.353 |
0.827 |
0.548 |
0.183 |
0.053 |
|
data set 2 |
0.208 |
0.441 |
0.253 |
0.098 |
0.023 |
|
|
consensus |
0.066 |
0.350 |
0.136 |
0.020 |
0.000 |
|
|
combined |
0.423 |
0.702 |
0.512 |
0.241 |
0.049 |
|
|
IV |
data set 1 |
0.267 |
0.637 |
0. 394 |
0.161 |
0.037 |
|
data set 2 |
0.266 |
0.632 |
0.395 |
0.124 |
0.036 |
|
|
consensus |
0.069 |
0.353 |
0.120 |
0.015 |
0.003 |
|
|
combined |
0.414 |
0.682 |
0.523 |
0.198 |
0.036 |
|
|
V |
data set 1 |
0.343 |
0.825 |
0.535 |
0.207 |
0.046 |
|
data set 2 |
0.190 |
0.443 |
0.329 |
0.153 |
0.035 |
|
|
consensus |
0.068 |
0.375 |
0.191 |
0.044 |
0.001 |
|
|
combined |
0.420 |
0.708 |
0.555 |
0.267 |
0.044 |
|
|
VI |
data set 1 |
0.363 |
0.824 |
0.514 |
0.219 |
0.047 |
|
data set 2 |
0.087 |
0.195 |
0.148 |
0.057 |
0.019 |
|
|
consensus |
0.040 |
0.163 |
0.090 |
0.018 |
000 |
|
|
combined |
0.300 |
0.532 |
0.386 |
0.155 |
0.040 |
|
|
VII |
data set 1 |
0.202 |
0.444 |
0.312 |
0.153 |
0.025 |
|
data set 2 |
0.200 |
0.450 |
0.348 |
0.134 |
0.026 |
|
|
consensus |
0.031 |
0.156 |
0.093 |
0.029 |
0.002 |
|
|
combined |
0.336 |
0.544 |
0.383 |
0.169 |
0.040 |
|
APPENDIX 3. Accuracy of separate, combined, and consensus analysis for two genes (data sets) with different phylogenetic histories, with asymmetric tree topologies and 250 characters in each data set. Each value is the average accuracy from 100 replicated matrices.
|
Branch length |
||||||
|
Case |
0.01 |
0.15 |
0.30 |
0.45 |
0.60 |
|
|
I |
data set 1 |
0.905 |
1.000 |
0.954 |
0.391 |
0.027 |
|
data set 2 |
0.915 |
1.000 |
0.947 |
0.368 |
0.027 |
|
|
consensus |
0.828 |
1.000 |
0.904 |
0.196 |
0.004 |
|
|
combined |
0.990 |
1.000 |
0.993 |
0.597 |
0.047 |
|
|
II |
data set 1 |
0.933 |
1.000 |
0.959 |
0.370 |
0.110 |
|
data set 2 |
0.797 |
0.888 |
0.860 |
0.309 |
0.082 |
|
|
consensus |
0.749 |
0.888 |
0.823 |
0.120 |
0.010 |
|
|
combined |
0.933 |
0.949 |
0.942 |
0.511 |
0.131 |
|
|
III |
data set 1 |
0.920 |
1.000 |
0.939 |
0.352 |
0.029 |
|
data set 2 |
0.715 |
0.780 |
0.749 |
0.220 |
0.015 |
|
|
consensus |
0.656 |
0.780 |
0.692 |
0.072 |
0.001 |
|
|
combined |
0.865 |
0.888 |
0.881 |
0.541 |
0.034 |
|
|
IV |
data set 1 |
0.818 |
0.889 |
0.867 |
0.319 |
0.030 |
|
data set 2 |
0.812 |
0.889 |
0.853 |
0.283 |
0.025 |
|
|
consensus |
0.654 |
0.778 |
0.721 |
0.077 |
0.003 |
|
|
combined |
0.866 |
0.889 |
0.882 |
0.504 |
0.040 |
|
|
V |
data set 1 |
0.910 |
1.000 |
0.954 |
0.354 |
0.041 |
|
data set 2 |
0.405 |
0.440 |
0.414 |
0.179 |
0.015 |
|
|
consensus |
0.367 |
0.440 |
0.398 |
0.079 |
0.002 |
|
|
combined |
0.733 |
0.639 |
0.491 |
0.308 |
0.033 |
|
|
VI |
data set 1 |
0.894 |
1.000 |
0.968 |
0.382 |
0.036 |
|
data set 2 |
0.000 |
0.000 |
0.000 |
0.001 |
0.000 |
|
|
consensus |
0.000 |
0.000 |
0.000 |
0.001 |
0.000 |
|
|
combined |
0.537 |
0.494 |
0.146 |
0.035 |
0.000 |
|
|
VII |
data set 1 |
0.398 |
0.439 |
0.407 |
0.195 |
0.024 |
|
data set 2 |
0.309 |
0.330 |
0.318 |
0.165 |
0.024 |
|
|
consensus |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
|
|
combined |
0.565 |
0.526 |
0.157 |
0.025 |
0.008 |
|
APPENDIX 4. Accuracy of separate, combined, and consensus analysis for two genes (data sets) with different phylogenetic histories, with symmetric tree topologies and 250 characters in each data set. Each value is the average accuracy from 100 replicated matrices.
|
Branch length |
||||||
|
Case |
0.01 |
0.15 |
0.30 |
0.45 |
0.60 |
|
|
I |
data set 1 |
0.914 |
1.000 |
0.923 |
0.540 |
0.104 |
|
data set 2 |
0.921 |
0.998 |
0.920 |
0.535 |
0.112 |
|
|
consensus |
0.843 |
0.998 |
0.860 |
0.334 |
0.018 |
|
|
combined |
0.992 |
1.000 |
0.974 |
0.684 |
0.162 |
|
|
II |
data set 1 |
0.892 |
0.999 |
0.890 |
0.572 |
0.110 |
|
data set 2 |
0.696 |
0.779 |
0.694 |
0.394 |
0.082 |
|
|
consensus |
0.626 |
0.778 |
0.607 |
0.255 |
0.010 |
|
|
combined |
0.862 |
0.879 |
0.840 |
0.601 |
0.131 |
|
|
III |
data set 1 |
0.905 |
0.996 |
0.917 |
0.545 |
0.090 |
|
data set 2 |
0.497 |
0.559 |
0.479 |
0.236 |
0.063 |
|
|
consensus |
0.445 |
0.554 |
0.424 |
0.119 |
0.009 |
|
|
combined |
0.746 |
0.769 |
0.701 |
0.515 |
0.112 |
|
|
IV |
data set 1 |
0.696 |
0.778 |
0.698 |
0.378 |
0.066 |
|
data set 2 |
0.703 |
0.777 |
0.687 |
0.406 |
0.067 |
|
|
consensus |
0.449 |
0.555 |
0.412 |
0.131 |
0.005 |
|
|
combined |
0.720 |
0.772 |
0.712 |
0.491 |
0.097 |
|
|
V |
data set 1 |
0.902 |
0.997 |
0.905 |
0.572 |
0.110 |
|
data set 2 |
0.508 |
0.560 |
0.516 |
0.335 |
0.078 |
|
|
consensus |
0.458 |
0.559 |
0.488 |
0.217 |
0.011 |
|
|
combined |
0.762 |
0.756 |
0.668 |
0.479 |
0.110 |
|
|
VI |
data set 1 |
0.923 |
0.998 |
0.911 |
0.543 |
0.096 |
|
data set 2 |
0.194 |
0.220 |
0.203 |
0.135 |
0.037 |
|
|
consensus |
0.179 |
0.220 |
0.191 |
0.083 |
0.005 |
|
|
combined |
0.638 |
0.599 |
0.438 |
0.273 |
0.063 |
|
|
VII |
data set 1 |
0.498 |
0.559 |
0.511 |
0.336 |
0.081 |
|
data set 2 |
0.499 |
0.559 |
0.511 |
0.318 |
0.067 |
|
|
consensus |
0.180 |
0.220 |
0.210 |
0.095 |
0.008 |
|
|
combined |
0.598 |
0.662 |
0.465 |
0.276 |
0.064 |
|
APPENDIX 5. Accuracy of separate, combined, and consensus analysis for two genes (data sets) with different phylogenetic histories, with asymmetric tree topologies and 500 characters in each data set. Each value is the average accuracy from 100 replicated matrices.
|
Branch length |
||||||
|
Case |
0.01 |
0.15 |
0.30 |
0.45 |
0.60 |
|
|
I |
data set 1 |
0.996 |
1.000 |
0.994 |
0.579 |
0.067 |
|
data set 2 |
0.989 |
1.000 |
0.994 |
0.625 |
0.067 |
|
|
consensus |
0.985 |
1.000 |
0.989 |
0.405 |
0.008 |
|
|
combined |
1.000 |
1.000 |
1.000 |
0.861 |
0.087 |
|
|
II |
data set 1 |
0.993 |
1.000 |
0.996 |
0.602 |
0.047 |
|
data set 2 |
0.884 |
0.890 |
0.889 |
0.503 |
0.042 |
|
|
consensus |
0.878 |
0.890 |
0.884 |
0.308 |
0.004 |
|
|
combined |
0.938 |
0.939 |
0.948 |
0.767 |
0.076 |
|
|
III |
data set 1 |
0.989 |
1.000 |
0.993 |
0.608 |
0.044 |
|
data set 2 |
0.777 |
0.780 |
0.776 |
0.387 |
0.019 |
|
|
consensus |
0.767 |
0.780 |
0.769 |
0.202 |
0.003 |
|
|
combined |
0.866 |
0.875 |
0.888 |
0.732 |
0.070 |
|
|
IV |
data set 1 |
0.884 |
0.890 |
0.888 |
0.505 |
0.053 |
|
data set 2 |
0.882 |
0.890 |
0.887 |
0466 |
0.035 |
|
|
consensus |
0.769 |
0.780 |
0.774 |
0.190 |
0.000 |
|
|
combined |
0.869 |
0.891 |
0.894 |
0.713 |
0.065 |
|
|
V |
data set 1 |
0.996 |
1.000 |
0.998 |
0.609 |
0.059 |
|
data set 2 |
0.438 |
0.440 |
0.434 |
0.286 |
0.026 |
|
|
consensus |
0.435 |
0.440 |
0.433 |
0.186 |
0.007 |
|
|
combined |
0.731 |
0.655 |
0.466 |
0.388 |
0.040 |
|
|
VI |
data set 1 |
0.993 |
1.000 |
0.999 |
0.569 |
0.045 |
|
data set 2 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
|
|
consensus |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
|
|
combined |
0.649 |
0.500 |
0.128 |
0.021 |
0.000 |
|
|
VII |
data set 1 |
0.437 |
0.440 |
0.434 |
0.298 |
0.027 |
|
data set 2 |
0.329 |
0.330 |
0.329 |
0.243 |
0.041 |
|
|
consensus |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
|
|
combined |
0.700 |
0.516 |
0.114 |
0.026 |
0.003 |
|
APPENDIX 6. Accuracy of separate, combined, and consensus analysis for two genes (data sets) with different phylogenetic histories, with symmetric tree topologies and 500 characters in each data set. Each value is the average accuracy from 100 replicated matrices.
|
Branch length |
||||||
|
Case |
0.01 |
0.15 |
0.30 |
0.45 |
0.60 |
|
|
I |
data set 1 |
0.989 |
1.000 |
0.971 |
0.695 |
0.150 |
|
data set 2 |
0.997 |
1.000 |
0.963 |
0.674 |
0.156 |
|
|
consensus |
0.986 |
1.000 |
0.936 |
0.533 |
0.033 |
|
|
combined |
0.999 |
1.000 |
0.996 |
0.790 |
0.231 |
|
|
II |
data set 1 |
0.989 |
1.000 |
0.964 |
0.672 |
0.147 |
|
data set 2 |
0.774 |
0.780 |
0.758 |
0.492 |
0.092 |
|
|
consensus |
0.768 |
0.780 |
0.724 |
0.360 |
0.021 |
|
|
combined |
0.883 |
0.886 |
0.871 |
0.674 |
0.174 |
|
|
III |
data set 1 |
0.992 |
1.000 |
0.976 |
0.687 |
0.135 |
|
data set 2 |
0.558 |
0.560 |
0.518 |
0.314 |
0.068 |
|
|
consensus |
0.554 |
0.560 |
0.499 |
0.219 |
0.017 |
|
|
combined |
0.744 |
0.769 |
0.722 |
0.586 |
0.150 |
|
|
IV |
data set 1 |
0.770 |
0.780 |
0.750 |
0.493 |
0.128 |
|
data set 2 |
0.770 |
0.780 |
0.759 |
0.474 |
0.113 |
|
|
consensus |
0.547 |
0.560 |
0.507 |
0.198 |
0.020 |
|
|
combined |
0.754 |
0.732 |
0.723 |
0.563 |
0.153 |
|
|
V |
data set 1 |
0.996 |
1.000 |
0.961 |
0.708 |
0.161 |
|
data set 2 |
0.220 |
0.560 |
0.548 |
0.395 |
0.117 |
|
|
consensus |
0.218 |
0.560 |
0.537 |
0.320 |
0.025 |
|
|
combined |
0.637 |
0.759 |
0.671 |
0.532 |
0.156 |
|
|
VI |
data set 1 |
0.996 |
1.000 |
0.971 |
0.699 |
0.162 |
|
data set 2 |
0.220 |
0.220 |
0.219 |
0.187 |
0.047 |
|
|
consensus |
0.218 |
0.220 |
0.219 |
0.162 |
0.005 |
|
|
combined |
0.637 |
0.648 |
0.463 |
0.290 |
0.068 |
|
|
VII |
data set 1 |
0.555 |
0.560 |
0.554 |
0.410 |
0.110 |
|
data set 2 |
0.553 |
0.560 |
0.550 |
0.410 |
0.101 |
|
|
consensus |
0.213 |
0.220 |
0.219 |
0.145 |
0.012 |
|
|
combined |
0.713 |
0.664 |
0.459 |
0.294 |
0.076 |
|
APPENDIX 7. Accuracy of separate, combined, and consensus analysis for two genes (data sets) with different phylogenetic histories, with asymmetric tree topologies and 1000 characters in each data set. Each value is the average accuracy from 100 replicated matrices.
|
Branch length |
||||||
|
Case |
0.01 |
0.15 |
0.30 |
0.45 |
0.60 |
|
|
I |
data set 1 |
1.000 |
1.000 |
1.000 |
0.839 |
0.101 |
|
data set 2 |
1.000 |
1.000 |
1.000 |
0.862 |
0.091 |
|
|
consensus |
1.000 |
1.000 |
1.000 |
0.726 |
0.021 |
|
|
combined |
1.000 |
1.000 |
1.000 |
0.965 |
0.159 |
|
|
II |
data set 1 |
1.000 |
1.000 |
1.000 |
0.823 |
0.090 |
|
data set 2 |
0.890 |
0.890 |
0.890 |
0.719 |
0.070 |
|
|
consensus |
0.890 |
0.890 |
0.890 |
0.585 |
0.014 |
|
|
combined |
0.939 |
0.946 |
0.934 |
0.913 |
0.115 |
|
|
III |
data set 1 |
1.000 |
1.000 |
1.000 |
0.802 |
0.091 |
|
data set 2 |
0.780 |
0.780 |
0.780 |
0.623 |
0.034 |
|
|
consensus |
0.780 |
0.780 |
0.780 |
0.466 |
0.004 |
|
|
combined |
0.891 |
0.883 |
0.873 |
0.873 |
0.088 |
|
|
IV |
data set 1 |
0.890 |
0.890 |
0.890 |
0.748 |
0.080 |
|
data set 2 |
0.890 |
0.890 |
0.890 |
0.705 |
0.081 |
|
|
consensus |
0.780 |
0.780 |
0.780 |
0.486 |
0.008 |
|
|
combined |
0.884 |
0.883 |
0.882 |
0.851 |
0.130 |
|
|
V |
data set 1 |
1.000 |
1.000 |
1.000 |
0.818 |
0.087 |
|
data set 2 |
0.440 |
0.440 |
0.439 |
0.364 |
0.052 |
|
|
consensus |
0.440 |
0.440 |
0.439 |
0.301 |
0.009 |
|
|
combined |
0.768 |
0.602 |
0.480 |
0.417 |
0.070 |
|
|
VI |
data set 1 |
1.000 |
1.000 |
1.000 |
0.836 |
0.103 |
|
data set 2 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
|
|
consensus |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
|
|
combined |
0.715 |
0.479 |
0.080 |
0.008 |
0.001 |
|
|
VII |
data set 1 |
0.440 |
0.440 |
0.440 |
0.363 |
0.044 |
|
data set 2 |
0.330 |
0.330 |
0.330 |
0.295 |
0.037 |
|
|
consensus |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
|
|
combined |
0.733 |
0.551 |
0.093 |
0.003 |
0.000 |
|
APPENDIX 8. Accuracy of separate, combined, and consensus analysis for two genes (data sets) with different phylogenetic histories, with symmetric tree topologies and 1000 characters in each data set. Each value is the average accuracy from 100 replicated matrices.
|
Branch length |
||||||
|
Case |
0.01 |
0.15 |
0.30 |
0.45 |
0.60 |
|
|
I |
data set 1 |
1.000 |
1.000 |
0.996 |
0.792 |
0.230 |
|
data set 2 |
1.000 |
1.000 |
0.993 |
0.782 |
0.210 |
|
|
consensus |
1.000 |
1.000 |
0.989 |
0.681 |
0.055 |
|
|
combined |
1.000 |
1.000 |
0.999 |
0.868 |
0.293 |
|
|
II |
data set 1 |
1.000 |
1.000 |
0.994 |
0.790 |
0.219 |
|
data set 2 |
0.780 |
0.780 |
0.776 |
0.567 |
0.141 |
|
|
consensus |
0.780 |
0.780 |
0.770 |
0.475 |
0.037 |
|
|
combined |
0.875 |
0.892 |
0.880 |
0.750 |
0.252 |
|
|
III |
data set 1 |
1.000 |
1.000 |
0.996 |
0.785 |
0.221 |
|
data set 2 |
0.560 |
0.560 |
0.555 |
0.362 |
0.087 |
|
|
consensus |
0.560 |
0.560 |
0.551 |
0.278 |
0.025 |
|
|
combined |
0.716 |
0.771 |
0.765 |
0.603 |
0.212 |
|
|
IV |
data set 1 |
0.780 |
0.780 |
0.774 |
0.578 |
0.172 |
|
data set 2 |
0.780 |
0.780 |
0.774 |
0.563 |
0.161 |
|
|
consensus |
0.560 |
0.560 |
0.548 |
0.273 |
0.023 |
|
|
combined |
0.701 |
0.760 |
0.746 |
0.604 |
0.204 |
|
|
V |
data set 1 |
1.000 |
1.000 |
0.994 |
0.789 |
0.214 |
|
data set 2 |
0.560 |
0.560 |
0.558 |
0.474 |
0.148 |
|
|
consensus |
0.560 |
0.560 |
0.558 |
0.426 |
0.046 |
|
|
combined |
0.837 |
0.735 |
0.674 |
0.565 |
0.195 |
|
|
VI |
data set 1 |
1.000 |
1.000 |
0.993 |
0.781 |
0.247 |
|
data set 2 |
0.220 |
0.220 |
0.220 |
0.201 |
0.053 |
|
|
consensus |
0.220 |
0.220 |
0.220 |
0.189 |
0.018 |
|
|
combined |
0.670 |
0.651 |
0.463 |
0.286 |
0.088 |
|
|
VII |
data set 1 |
0.560 |
0.560 |
0.556 |
0.489 |
0.146 |
|
data set 2 |
0.560 |
0.560 |
0.556 |
0.475 |
0.153 |
|
|
consensus |
0.220 |
0.220 |
0.220 |
0.200 |
0.025 |
|
|
combined |
0.746 |
0.701 |
0.469 |
0.278 |
0.095 |
|
APPENDIX 9. Accuracy of separate, combined, and consensus analysis for two genes (data sets) with different phylogenetic histories, asymmetric tree topologies, slightly unequal branch lengths (range 0.00--0.15) and different numbers of characters. Each value is the average accuracy from 100 replicated matrices.
|
Number of characters |
|||||
|
Case |
50 |
250 |
500 |
1000 |
|
|
I |
data set 1 |
0.747 |
0.926 |
0.957 |
0.978 |
|
data set 2 |
0.753 |
0.919 |
0.959 |
0.975 |
|
|
consensus |
0.606 |
0.880 |
0.931 |
0.965 |
|
|
combined |
0.878 |
0.955 |
0.965 |
0.985 |
|
|
II |
data set 1 |
0.734 |
0.949 |
0.959 |
0.970 |
|
data set 2 |
0.646 |
0.850 |
0.847 |
0.865 |
|
|
consensus |
0.523 |
0.822 |
0.829 |
0.849 |
|
|
combined |
0.790 |
0.913 |
0.915 |
0.928 |
|
|
III |
data set 1 |
0.727 |
0.938 |
0.959 |
0.979 |
|
data set 2 |
0.582 |
0.728 |
0.752 |
0.761 |
|
|
consensus |
0.463 |
0.694 |
0.737 |
0.754 |
|
|
combined |
0.742 |
0.850 |
0.866 |
0.879 |
|
|
IV |
data set 1 |
0.670 |
0.832 |
0.847 |
0.867 |
|
data set 2 |
0.673 |
0.818 |
0.864 |
0.871 |
|
|
consensus |
0.470 |
0.694 |
0.728 |
0.751 |
|
|
combined |
0.772 |
0.849 |
0.869 |
0.867 |
|
|
V |
data set 1 |
0.760 |
0.935 |
0.961 |
0.977 |
|
data set 2 |
0.348 |
0.420 |
0.429 |
0.431 |
|
|
consensus |
0.295 |
0.401 |
0.418 |
0.423 |
|
|
combined |
0.639 |
0.708 |
0.747 |
0.705 |
|
|
VI |
data set 1 |
0.741 |
0.944 |
0.966 |
0.969 |
|
data set 2 |
0.004 |
0.001 |
0.001 |
0.001 |
|
|
consensus |
0.003 |
0.001 |
0.001 |
0.001 |
|
|
combined |
0.431 |
0.514 |
0.547 |
0.538 |
|
|
VII |
data set 1 |
0.346 |
0.424 |
0.429 |
0.433 |
|
data set 2 |
0.263 |
0.316 |
0.321 |
0.321 |
|
|
consensus |
0.007 |
0.005 |
0.000 |
0.001 |
|
|
combined |
0.465 |
0.540 |
0.575 |
0.646 |
|
APPENDIX 10. Accuracy of separate, combined, and consensus analysis for two genes (data sets) with different phylogenetic histories, symmetric tree topologies, slightly unequal branch lengths (range 0.00--0.15) and different numbers of characters. Each value is the average accuracy from 100 replicated matrices.
|
Number of characters |
|||||
|
Case |
50 |
250 |
500 |
1000 |
|
|
I |
data set 1 |
0.732 |
0.923 |
0.957 |
0.980 |
|
data set 2 |
0.740 |
0.922 |
0.957 |
0.987 |
|
|
consensus |
0.601 |
0.888 |
0.936 |
0.974 |
|
|
combined |
0.843 |
0.949 |
0.977 |
0.988 |
|
|
II |
data set 1 |
0.757 |
0.941 |
0.967 |
0.976 |
|
data set 2 |
0.575 |
0.720 |
0.754 |
0.752 |
|
|
consensus |
0.482 |
0.696 |
0.741 |
0.743 |
|
|
combined |
0.748 |
0.848 |
0.858 |
0.838 |
|
|
III |
data set 1 |
0.702 |
0.931 |
0.963 |
0.975 |
|
data set 2 |
0.408 |
0.519 |
0.541 |
0.548 |
|
|
consensus |
0.314 |
0.506 |
0.530 |
0.539 |
|
|
combined |
0.632 |
0.684 |
0.757 |
0.708 |
|
|
IV |
data set 1 |
0.554 |
0.722 |
0.732 |
0.758 |
|
data set 2 |
0.544 |
0.718 |
0.747 |
0.758 |
|
|
consensus |
0.289 |
0.488 |
0.503 |
0.535 |
|
|
combined |
0.642 |
0.724 |
0.720 |
0.739 |
|
|
V |
data set 1 |
0.727 |
0.912 |
0.954 |
0.974 |
|
data set 2 |
0.413 |
0.522 |
0.523 |
0.547 |
|
|
consensus |
0.332 |
0.487 |
0.510 |
0.537 |
|
|
combined |
0.643 |
0.753 |
0.798 |
0.800 |
|
|
VI |
data set 1 |
0.715 |
0.939 |
0.959 |
0.969 |
|
data set 2 |
0.169 |
0.207 |
0.212 |
0.217 |
|
|
consensus |
0.134 |
0.197 |
0.205 |
0.212 |
|
|
combined |
0.504 |
0.607 |
0.608 |
0.632 |
|
|
VII |
data set 1 |
0.398 |
0.507 |
0.541 |
0.546 |
|
data set 2 |
0.408 |
0.509 |
0.526 |
0.549 |
|
|
consensus |
0.145 |
0.194 |
0.211 |
0.213 |
|
|
combined |
0.496 |
0.623 |
0.661 |
0684 |
|
APPENDIX 11. Accuracy of separate, combined, and consensus analysis for two genes (data sets) with different phylogenetic histories, asymmetric tree topologies, highly unequal branch lengths (range 0.00-0.75) and different numbers of characters. Each value is the average accuracy from 100 replicated matrices.
|
Number of characters |
|||||
|
Case |
50 |
250 |
500 |
1000 |
|
|
I |
data set 1 |
0.132 |
0.307 |
0.327 |
0.423 |
|
data set 2 |
0.159 |
0.298 |
0.323 |
0.416 |
|
|
consensus |
0.072 |
0.192 |
0.224 |
0.314 |
|
|
combined |
0.215 |
0.373 |
0.370 |
0.445 |
|
|
II |
data set 1 |
0.142 |
0.278 |
0.357 |
0.401 |
|
data set 2 |
0.114 |
0.249 |
0.316 |
0.340 |
|
|
consensus |
0.049 |
0.143 |
0.214 |
0.252 |
|
|
combined |
0.200 |
0.319 |
0.412 |
0.419 |
|
|
III |
data set 1 |
0.154 |
0.296 |
0.348 |
0.417 |
|
data set 2 |
0.107 |
0.215 |
0.250 |
0.271 |
|
|
consensus |
0.048 |
0.118 |
0.150 |
0.202 |
|
|
combined |
0.152 |
0.340 |
0.350 |
0.403 |
|
|
IV |
data set 1 |
0.128 |
0.233 |
0.318 |
0.287 |
|
data set 2 |
0.126 |
0.247 |
0.328 |
0.329 |
|
|
consensus |
0.033 |
0.112 |
0.173 |
0.168 |
|
|
combined |
0.175 |
0.294 |
0.412 |
0.373 |
|
|
V |
data set 1 |
0.122 |
0.294 |
0.351 |
0.408 |
|
data set 2 |
0.089 |
0.153 |
0.186 |
0.216 |
|
|
consensus |
0.042 |
0.000 |
0.112 |
0.138 |
|
|
combined |
0.154 |
0.241 |
0.277 |
0.305 |
|
|
VI |
data set 1 |
0.159 |
0.337 |
0.335 |
0.397 |
|
data set 2 |
0.024 |
0.020 |
0.009 |
0.018 |
|
|
consensus |
0.012 |
0.018 |
0.009 |
0.018 |
|
|
combined |
0.102 |
0.120 |
0.107 |
0.145 |
|
|
VII |
data set 1 |
0.108 |
0.169 |
0.186 |
0.197 |
|
data set 2 |
0.102 |
0.134 |
0.156 |
0.191 |
|
|
consensus |
0.013 |
0.018 |
0.014 |
0.017 |
|
|
combined |
0.104 |
0.117 |
0.111 |
0.120 |
|
APPENDIX 12. Accuracy of separate, combined, and consensus analysis for two genes (data sets) with different phylogenetic histories, symmetric tree topologies, highly unequal branch lengths (range 0.00--0.75) and different numbers of characters. Each value is the average accuracy from 100 replicated matrices.
|
Number of characters |
|||||
|
Case |
50 |
250 |
500 |
1000 |
|
|
I |
data set 1 |
0.311 |
0.445 |
0.537 |
0.576 |
|
data set 2 |
0.293 |
0.442 |
0.522 |
0.558 |
|
|
consensus |
0.180 |
0.341 |
0.416 |
0.489 |
|
|
combined |
0.393 |
0.503 |
0.582 |
0.598 |
|
|
II |
data set 1 |
0.253 |
0.454 |
0.525 |
0.517 |
|
data set 2 |
0.191 |
0.349 |
0.372 |
0.378 |
|
|
consensus |
0.108 |
0.258 |
0.289 |
0.301 |
|
|
combined |
0.283 |
0.440 |
0.493 |
0.485 |
|
|
III |
data set 1 |
0.292 |
0.464 |
0.492 |
0.553 |
|
data set 2 |
0.123 |
0.213 |
0.237 |
0.250 |
|
|
consensus |
0.073 |
0.148 |
0.173 |
0.203 |
|
|
combined |
0.261 |
0.373 |
0.422 |
0.427 |
|
|
IV |
data set 1 |
0.196 |
0.318 |
0.355 |
0.415 |
|
data set 2 |
0.182 |
0.322 |
0.368 |
0.411 |
|
|
consensus |
0.065 |
0.136 |
0.162 |
0.221 |
|
|
combined |
0.234 |
0.379 |
0.391 |
0.444 |
|
|
V |
data set 1 |
0.303 |
0.413 |
0.486 |
0.567 |
|
data set 2 |
0.199 |
0.270 |
0.316 |
0.347 |
|
|
consensus |
0.126 |
0.211 |
0.262 |
0.302 |
|
|
combined |
0.309 |
0.373 |
0.406 |
0.449 |
|
|
VI |
data set 1 |
0.300 |
0.452 |
0.492 |
0.539 |
|
data set 2 |
0.092 |
0.123 |
0.142 |
0.151 |
|
|
consensus |
0.065 |
0.107 |
0.122 |
0.138 |
|
|
combined |
0.245 |
0.270 |
0.272 |
0.301 |
|
|
VII |
data set 1 |
0.189 |
0.306 |
0.311 |
0.367 |
|
data set 2 |
0.194 |
0.310 |
0.320 |
0.345 |
|
|
consensus |
0.072 |
0.121 |
0.122 |
0.152 |
|
|
combined |
0.231 |
0.296 |
0.273 |
0.320 |
|
APPENDIX 13. Accuracy of separate, consensus, and combined analysis in different parts of a phylogeny where there is a localized mismatch between gene and species trees in one of two data sets (data set 2). For each tree shape, one column represents the part of the phylogeny directly affected by the mismatch, the other represents those parts that share the same phylogenetic history. There are 250 characters in each data set. Each value is the average accuracy from 100 replicated matrices.
|
Tree shape |
|||||
|
Asymmetric |
Symmetric |
||||
|
Branch length |
Method |
Area of mismatch |
Rest of tree |
Area of mismatch |
Rest of tree |
|
0.01 |
data set 1 |
0.890 |
0.933 |
0.885 |
0.910 |
|
data set 2 |
0.000 |
0.896 |
0.000 |
0.904 |
|
|
consensus |
0.000 |
0.836 |
0.000 |
0.828 |
|
|
combined |
0.460 |
0.992 |
0.435 |
0.984 |
|
|
0.15 |
data set 1 |
1.000 |
1.000 |
1.000 |
1.000 |
|
data set 2 |
0.000 |
1.000 |
0.000 |
0.998 |
|
|
consensus |
0.000 |
1.000 |
0.000 |
0.998 |
|
|
combined |
0.460 |
1.000 |
0.450 |
1.000 |
|
|
0.30 |
data set 1 |
0.990 |
0.960 |
0.970 |
0.942 |
|
data set 2 |
0.000 |
0.963 |
0.000 |
0.956 |
|
|
consensus |
0.000 |
0.924 |
0.000 |
0.904 |
|
|
combined |
0.500 |
0.998 |
0.360 |
0.990 |
|
|
0.45 |
data set 1 |
0.790 |
0.347 |
0.830 |
0.700 |
|
data set 2 |
0.080 |
0.388 |
0.010 |
0.684 |
|
|
consensus |
0.060 |
0.169 |
0.010 |
0.502 |
|
|
combined |
0.450 |
0.600 |
0.345 |
0.832 |
|
|
0.60 |
data set 1 |
0.380 |
0.052 |
0.305 |
0.222 |
|
data set 2 |
0.250 |
0.049 |
0.105 |
0.174 |
|
|
consensus |
0.080 |
0.002 |
0.020 |
0.050 |
|
|
combined |
0.300 |
0.091 |
0.180 |
0.264 |
|