Introduction to phylogenetic inference based on molecular data

Evolution is the unifying theory in biology, a science trying to answer fundamental questions related to the origins and diversity of life in time and space.

One of its basic goals is to understand relationships among biological lineages, which then could allow us to address more complex questions, such as the impact of evolutionary novelties on lineage diversification, or the detection of mass extinctions that have occurred in the past. Inferring accurate phylogenies is also crucial for discovering the origin of pathogen outbreaks, or the evolution of bacterial resistance. In recent years, there has been an explosive growth in usage of DNA sequence data for phylogenetic inference. In addition, an array of analytical and computational techniques questions have been developed for answering phylogenetically-explicit evolutionary questions.

In this course, we outline the principal methods used in molecular phylogenetic inference: DNA sequencing (including Next Generation Sequencing techniques which allow sequencing entire genomes); DNA or amino acid sequence alignment; methods of phylogenetic inference (parsimony, maximum likelihood and Bayesian inference); models of sequence evolution; and estimating the timing of lineage divergence using fossil calibration priors and the molecular clock. We also give a brief introduction to tree-based statistical hypothesis testing.