Accuracy of parsimony analysis using morphological data: A Reappraisal.

In a recent paper, W. F. Lamboy used computer simulations to evaluate the accuracy of parsimony analysis using morphological characters. Based on his simulations, Lamboy concluded that parsimony analysis of morphological data is generally highly inaccurate, that many published trees are likely incorrect, and that current emphasis on phylogeny reconstruction using parsimony Is misplaced. In this paper we argue that these conclusions are the result of: 1) using an unusually small number of characters relative to the number of taxa; 2) generating true trees that contain polytomies; 3) using misleading measures of accuracy; 4) summing across a biased set of simulation results to make general conclusions; and 5) using an inappropriate index to compare simulated data to results in the real world. We provide recommendations for designing more rigorous simulations of phylogenetic questions, and summarize current knowledge of the performance of parsimony analysis based on other simulation studies. In contrast to Lamboy, we see great promise for accurate phylogeny reconstruction using parsimony analysis of morphological data.