Evolutionary Inferences from Phylogenies: A Review of Methods

There are many methods for making evolutionary inferences from phylogenetic trees. Many of these can be divided into three main classes of models: continuous-time Markov chain models with finite state space (CTMC-FSS), multivariate normal models, and birth-death models. Numerous approaches are just restrictions of more general models to focus on particular questions or kinds of data. Methods can be further modified with the addition of tree-stretching algorithms. The recent realization of the effect of correlated trait evolution with diversification rates represents an important advance that is slowly revolutionizing the field. Increased attention to model adequacy may lead to future methodological improvements.