Comparative evaluation of maximum parsimony and Bayesian phylogenetic reconstruction using empirical morphological data.

The use of discrete morphological data in Bayesian phylogenetics has increased significantly over the last years with the proposal of total evidence analysis and the treatment of fossils as terminal taxa in Bayesian molecular dating. Both approaches rely on the assumption that probabilistic Markov models reasonably accommodate all the complexity of morphological evolution of discrete traits. The performance of such morphological models used in Bayesian phylogenetics has been thoroughly investigated, but conclusions so far were based mostly on simulated data. In this study, we have surveyed MorphoBank and obtained a large number of morphological matrices to evaluate Bayesian phylogenetic inference (BI) under Lewis' Mk model in comparison with the maximum parsimony (MP) algorithm. We found that trees estimated by both methods frequently differed and that BI generated a larger amount of polytomic tree topologies. The number of trees contained in the 95% Bayesian credibility interval was significantly greater than the number of equally parsimonious trees. We also investigated which factors mostly influenced the topological difference between maximum parsimony and Bayesian tree topologies and found that the number of terminals in morphological matrices was the variable with the highest association with the topological distance between trees inferred by BI and MP. Surprisingly, we show that differences between both approaches were not influenced by increasing sample size. Our results, which were based on a large set of empirical matrices, corroborate recent findings that BI is less precise than MP.

Conventional simulation of biological sequences leads to a biased assessment of multi-Loci phylogenetic analysis.

Phylogenetic analysis based on multi-loci data sets is performed by means of supermatrix (SM) or supertree (ST) approaches. Recently, methods that rely on species tree (SppT) inference by the multi-species coalescence have also been implemented to tackle this problem. Generally, the relative performance of these three major strategies has been calculated using simulation of biological sequences. However, sequence simulation may not entirely replicate the complexity of the evolutionary process. Thus, issues regarding the usefulness of in silico sequences in studying the performance of phylogenetic methods have been raised. Here, we used both classical simulation and empirical data to investigate the relative performance of ST, SM, and the SppT methods. SM analyses performed better than the ST and SppTs in simulations, but not in empirical analyses where some ST methods significantly outperformed the others. Additionally, SM was the only method that was robust under evolutionary model violations in simulations. These results show that conventional biological sequence simulation cannot adequately resolve which method is most efficient to recover the SppT. In such simulations, the SM approach recovers the established phylogeny in most instances, whereas the performance of the ST and SppT methods is downgraded in simpler cases. When compared, the analyses based on empirical and simulated sequences yielded largely inconsistent results, with the latter showing a bias towards a seemingly superiority of SM approaches.

Testing synchrony in historical biogeography: the case of new world primates and hystricognathi rodents.

The abrupt appearance of primates and hystricognath rodents in early Oligocene deposits of South America has puzzled mastozoologists for decades. Based on the geoclimatic changes that occurred during the Eocene/Oligocene transition period that may have favoured their dispersal, researchers have proposed the hypothesis that these groups arrived in synchrony. Nevertheless, the hypothesis of synchronous origins of platyrrhine and caviomorph in South America has not been explicitly evaluated. Our aim in this work was to apply a formal test for synchronous divergence times to the Platyrrhini and Caviomorpha splits. We have examined a previous work on platyrrhine and hystricognath origins, applied the test to a case where synchrony is known to occur and conducted simulations to show that it is possible to formally test the age of synchronous nodes. We show that the absolute ages of Platyrrhini/Catarrhini and Caviomorpha/Phiomorpha splits depend on data partitioning and that the test applied consistently detected synchronous events when they were known to have happened. The hypothesis that the arrival of primates and hystricognaths to the New World consisted of a unique event cannot be rejected.