Métodos de reconstrucción filogenética I: máxima verosimilitud

Phylogenetic inference is widely used in evolutionary biology, aiming to find evolutionary relationships between different species and report the result in the form of a phylogenetic tree (phylogeny). There are several statistical methods used for phylogenetic inference. In this review, the method of maximum likelihood for phylogenetic reconstruction is presented. This technique consists of finding the likelihood of multiple candidate phylogenies, and report the one with the highest likelihood as a representative of the evolutionary relationships of a group of species. In this paper, the likelihood calculation of a phylogeny from multiple-species DNA sequences is reviewed. Also, some key DNA mutation models to calculate transition probabilities between nucleotides are presented. Such transition probabilities are used in the likelihood calculation of a given phylogeny. A simple example is shown to illustrate the necessary steps to infer a phylogeny, as well as the most common software for maximum likelihood inference for larger DNA alignments.