Probabilistic modeling and statistical inference for phylogenetic reconstruction and macroevolutionary studies — phylogenetic reconstruction, molecular dating, the comparative method, codon models, molecular evolution, theoretical evolutionary biology.
Probabilities of tree topologies with temporal constraints and diversification shifts Gilles Didier 10.1101/376756
Recommended by Nicolas Lartillot based on reviews by Amaury Lambert, Dominik Schrempf and 1 anonymous reviewer Fitting diversification models on undated or partially dated trees
Phylogenetic trees can be used to extract information about the process of diversification that has generated them. The most common approach to conduct this inference is to rely on a likelihood, defined here as the probability of generating a dated tree T given a diversification model (e.g. a birth-death model), and then use standard maximum likelihood. This idea has been explored extensively in the context of the so-called diversification studies, with many variants for the models and for the q...