Phylogeny Reconstruction

Abstract

Abstract Phylogenies provide the necessary comparative framework to study biological problems from an evolutionary perspective. Therefore, selecting the appropriate data sources and methods of inference that ensure reconstructing robust phylogenetic hypotheses becomes essential. Molecular phylogenies reconstructed with probabilistic methods (i.e. maximum likelihood and Bayesian inference) are by far the most popular, as they produce powerful statistical estimation of phylogenies from a potentially large number of characters (sequences). Working within a probabilistic framework further allows using available statistical tools for a posteriori analyses on the reconstructed phylogenies. Most recent advances in phylogenetics, including sophisticated evolutionary models, methods that reconcile different gene genealogies, the analysis of genome‐scale data (phylogenomics) or the development of new and more effective computational methods take advantage of probabilistic methods of phylogeny inference. Hence, an understanding of the properties, strengths and limitations of probabilistic methods is fundamental. Key Concepts: Phylogenetic trees represent the evolutionary history of organisms (or sequences) in terms of relationships and the amount of genetic differentiation. Phylogenies are essential to fully understand the evolutionary dimension in any biological discipline. Maximum likelihood and Bayesian inference are probabilistic methods for the statistical estimation of phylogenies based on explicit models of sequence evolution. Probabilistic methods of phylogeny reconstruction provide a statistical framework for estimating historical patterns, inferring intrinsic parameters of evolutionary processes and testing of hypotheses. Methods that attempt to reconcile different gene trees with the underlying species phylogeny have recently been developed as an alternative to data concatenation. The intersection of genome‐scale sequence data and probabilistic methods of phylogeny reconstruction has given rise to phylogenomics, which is emerging as a very promising field in evolutionary studies.