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 will 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 will also give a brief introduction to tree-based statistical hypothesis testing.

Almir Pepato:

Almir Pepato is a professor at Universidade Federal de Minas Gerais (UFMG, Brazil), where he has worked since 2011. His graduate and postdoctoral research focused on mite higher-level phylogeny and morphology. Drawing on his research experience, he has taught intensive courses on phylogenetic inference, employing molecular data and species delimitation theory, at the Zoology Postgraduate Program at UFMG. Currently, he is working on a comprehensive coastal biogeographic study, in a long-term partnership with Dr. Pavel Klimov (University of Michigan).

Pavel Klimov:

Pavel Klimov has been working at the University of Michigan since 2000. He has authored 59 papers, as well as a monograph on phylogenetic systematics, coevolution, and biogeography. Dr. Klimov also teaches the Acarological Summer Course at the Ohio State University. He is particularly interested in the relationship between mites and human health, and has been a key contributor in recent genomic sequencing of the American House Dust Mite. In 2014-2017, Drs. Almir Pepato and Klimov obtained funding from the Brazilian government to investigate the biogeography of the Brazilian coast. Klimov’s notable co-authors include Edward O. Wilson, one of the founders of island biogeography.