Dealing with Discordance in the Tree of Life

Professor Matthew Hahn

Picture of Liang Zheng

Written by: Liang Zheng
29 Jun 2023


Professor Matthew Hahn
Professor Matthew Hahn

Time: 9:30am-10:30am, Thursday 29 June 2023

Location: Innovation Space, Level 2, Birch Building 35


Phylogenetics is concerned with uncovering the relationships among organisms (the “Tree of Life”), and computational research has made many important contributions to achieving this goal. In this talk I discuss a major overall challenge facing the field as DNA sequencing efforts have become central to this work: many individual genes have tree topologies that do not match the tree describing relationships among species. Such gene-tree discordance poses many new difficulties for inferring the Tree of Life. Here, I present three approaches for dealing with discordance: 1) a deep-learning method for inferring gene-tree topologies; 2) a quartet summary approach that combines many different gene-tree topologies to construct an accurate species tree, even in the presence of duplication and loss; and 3) a probabilistic approach to reconstructing the history of different traits on a species tree in the presence of discordance. These three problems (and their solutions) represent just a fraction of the challenges now facing the field of phylogenetics.


Matthew Hahn earned his B.S. degree from Cornell University and obtained his Ph.D. from Duke University with Mark Rausher. He was a postdoctoral fellow at the University of California, Davis with Charles Langley and John Gillespie. He is currently a Distinguished Professor of Biology and Computer Science at Indiana University, where he has held a faculty position since 2005. He also directs IU’s Center for Genomics and Bioinformatics.

His research focuses on how evolution has shaped organismal and genomic diversity, and how adaptation is achieved using multiple different types of molecular changes. His lab couples empirical studies of genome sequences with the development of mathematical theory, new statistical models, and the implementation of open-source software. His work introduced the first methods for quantifying and understanding gene gain and loss among species, applying them to primates to understand the differences between humans and our closest relatives. More recent methods developed by his lab have uncovered both the genes and the traits shared between species due to hybridization.

He has published over 175 scientific articles and two books, which have collectively been cited more than 29,000 times. His research program has been supported by the U.S. National Science Foundation and National Institutes of Health. He has been the recipient of an NSF CAREER Award, a fellowship from the Alfred P. Sloan Foundation, the Margaret Dayhoff Award from the Society for Molecular Biology and Evolution, the Stebbins Medal from the International Association for Plant Taxonomy, and the Bicentennial Medal from Indiana University. He is an elected fellow of the American Association for the Advancement of Science.

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