Progress on Estimating Phylogenetic Networks

Speaker: Tandy Warnow, Grainger Distinguished Chair in Engineering from The University of Illinois Chicago-Champaign 

 Title: Progress on Estimating Phylogenetic Networks

Date: Wednesday, September 23, 2026

Time: 3:30 p.m–4:30 p.m.

Location: 1132 Harold Frank Hall

Host: Ambuj Singh

Abstract: Phylogenetic networks are models of evolution that go beyond trees, and so represent reticulate events such as horizontal gene transfer or hybridization, which are frequently found in many taxa. Yet, the estimation of phylogenetic networks is extremely computationally challenging, and nearly all methods are limited to very small datasets with perhaps 10–15 species (some limited to even smaller numbers). In this talk, I will present a new method, CAMUS (ISMB 2026 and Bioinformatics 2026), for estimating phylogenetic networks from a set of gene trees. The key step in CAMUS is that it can find an optimal completion of a rooted tree to a level-1 phylogenetic network, which it achieves in polynomial time. Our simulation study shows that a natural pipeline using CAMUS provides high accuracy and scalability, so that it is able to complete in minutes on datasets with thousands of gene trees and up to 201 species. In contrast, prior leading methods (e.g., PhyloNet and SNaQ, both of which try to optimize maximum pseudo-likelihood) are much slower and limited to small datasets. Thus, CAMUS represents a useful scalable approach to the estimation of complex evolutionary histories, going beyond what prior methods could achieve.

Speaker Bio: Tandy Warnow is the Grainger Distinguished Chair in Engineering in the Siebel School of Computing and Data Science at the University of Illinois Urbana-Champaign. Tandy received her PhD in Mathematics at UC Berkeley under the direction of Gene Lawler, and her research focuses on reconstructing complex and large-scale evolutionary histories. She was awarded the David and Lucile Packard Foundation Award (1996), a Radcliffe Institute Fellowship (2003), and the John Simon Guggenheim Foundation Fellowship (2011). She was elected a Fellow of the Association for Computing Machinery (ACM) in 2015 and of the American Association for the Advancement of Science (AAAS) in 2021. In 2024, she received the ISCB Accomplishments by a Senior Scientist Award, and in 2026, she was elected a Member of the American Academy of Arts and Sciences.