Event Date
Speaker: Sebastien Roch, Vilas Distinguished Achievement Professor, Mathematics, University of Wisconsin
Title: "Large-scale inference of phylogenetic tree mixtures via nucleotide site pattern scoring"
Abstract: The reconstruction of species phylogenies from genomic data is a key step in modern evolutionary studies. This task is complicated by the fact that genes evolve under biological phenomena that produce discordant histories. These include hybrid speciation, horizontal gene transfer, gene duplication and loss, and incomplete lineage sorting, all of which can be modeled using gene tree mixture models building on well-studied discrete stochastic processes (branching processes, the coalescent, random rearrangements, etc.). Gene trees are in turn estimated from molecular sequences using graphical models on trees. The rigorous analysis of the resulting complex models can help guide the design of new reconstruction methods with computational and statistical guarantees. I will discuss a recent state-of-the-art method that avoids the error-prone gene tree estimation step, instead working directly with nucleotide site patterns. Specifically, I will introduce an algebraic framework to characterize the possible site pattern scoring schemes for a general class of mixture models and establish their statistical properties. No biology background will be assumed.
Faculty web-page (links to Univ. Wisconsin): https://people.math.wisc.edu/~roch/