MIG Seminar - Matthew Hahn - Phylogenomics and the Procrustean bed of the species tree
Phylogenomics and the Procrustean bed of the species tree
Phylogenomics has revealed unexpected levels of disagreement among gene trees in almost every clade examined. While error in tree inference must play some role in this discordance, biological causes of discordance—primarily incomplete lineage sorting and introgression—provide rich information about the history of organisms. The current “species tree paradigm” for resolving this discordance can reveal the underlying species relationships when incomplete lineage sorting is the only force acting, and sometimes even when there is introgression. Here I question the goal of this approach in resolving species relationships, as it explicitly excludes the gene tree discordance from downstream analyses. I explain how forcing all traits to be analyzed on a single, fixed species tree will often result in incorrect inferences about the direction of evolution and the number of times a trait has evolved. When levels of introgression are high enough, I argue that the species tree should not even be used as a backbone for comparative analyses, as it will lead to incorrect inferences more often than not. Though species networks have been proposed as one alternative to species trees, I suggest that we move beyond resolved species trees and networks by using gene tree variation directly in our analyses. This approach promises to provide a more accurate view of organismal and trait evolution.
Professor Matthew Hahn, Director, Center for Genomics and Bioinformatics
Professor Matthew Hahn
Director, Center for Genomics and Bioinformatics
Matthew Hahn received a BS degree from Cornell University and a PhD from Duke University under the mentorship of Professor Mark Rausher. From 2003 to 2005, he held a US National Science Foundation postdoctoral fellowship to work at the University of California, Davis with Professors Charles Langley and John Gillespie. He is a Professor in the Department of Biology and the Department of Computer Science at Indiana University, where he has held a faculty position since 2005. His research interests include bioinformatics, genomics, population genetics, and phylogenetics. He is an author or coauthor on more than 130 publications in these areas, as well as two books, Introduction to Computational Genomics (Cambridge University Press, 2007) and Molecular Population Genetics (Sinauer/Oxford University Press, 2018). He has received a US National Science Foundation CAREER award (2009), a fellowship from the Alfred P. Sloan Foundation (20102012), and was recently elected a fellow of the American Association for the Advancement of Science (2018).