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 | |||||