Simulation-based and experimental studies are crucial to produce factual arguments to solve theoretical and methodological debates in phylogenetics. However, despite the large number of works that tested the relative efficiency of phylogenetic methods with various evolutionary models, the capacity of methods to manage various sources of error and homoplasy has almost never been studied. By applying ordered and unordered methods to datasets with iterative addition of errors in the ordering scheme, we show that unordered coding in parsimony is not a more cautious option. A second debate concerns how to handle reversals, especially when they are regarded as possible synapomorphies. By comparing analyses of reversible and irreversible characters, we show empirically that three-taxon analysis (3ta) manages reversals better than parsimony. For Brownian motion data, we highlight that 3ta is also more efficient than parsimony in managing random errors, which might result from taphonomic problems or any homoplasy generating events that do not follow the dichotomy reversal/ convergence, such as lateral gene transfer. We show parsimony to be more efficient with numerous character states (more than four), and 3ta to be more efficient with binary characters, both methods being equally efficient with four states per character. We finally compare methods using two empirical cases of known evolution.

Menispermaceae (Moonseed family) are an important family within the basal eudicots. This study is a first attempt to infer phylogenetic relationships within Menispermaceae, focusing on morphological data and using cladistic methodology. Sampling included genera from all the eight tribes usually recognized within the family, and was representative of the morphological diversity and worldwide distribution of the group. Preliminary trees were poorly resolved and were optimized using Reduced Cladistic Consensus (RCC) and NoiseSnapper. The latter program was used for the first time in phylogeny. In addition, fossils of the Eocene of the Paris Basin were included in the analysis. All three approaches were useful as they allowed for improvement of resolution. None of the tribes were found to be monophyletic except Menispermeae. We also show that fruit characters are unreliable and should not be used for classification.