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.

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.

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.