Grand Challenges in Phylogenomics

Estimating the Tree of Life will likely involve a two-step procedure, where in the first step trees are estimated on many genes, and then the gene trees are combined into a tree on all the taxa. However, the true gene trees may not agree with with the species tree due to biological processes such as deep coalescence, gene duplication and loss, and horizontal gene transfer. Statistically consistent methods based on the multi-species coalescent model have been developed to estimate species trees in the presence of incomplete lineage sorting; however, the relative accuracy of these methods compared to the usual "concatenation" approach is a matter of substantial debate within the research community.  In this talk I will present new state of the art methods (Statistical Binning, Science 2014, ASTRAL ECCB 2014 and ISMB 2015) we have developed for estimating species trees in the presence of incomplete lineage sorting (ILS), and show how they can be used to estimate species trees from genome-scale datasets.

Tandy Warnow is the Founder Professor of Engineering at the University of Illinois at Urbana-Champaign. She has a dual appointment between Computer Science and Bioengineering, and is a member of the Carl R. Woese Institute for Genomic Biology, a member of the National Center for Supercomputing Applications, and an affiliate in six other departments at UIUC (Statistics, Mathematics, Electrical and Computer Engineering, Plant Biology, Animal Biology, and Entomology). Tandy received her PhD in Mathematics at UC Berkeley under the direction of Gene Lawler, and did postdoctoral training with Simon Tavaré and Michael Waterman at the University of Southern California. She received the National Science Foundation Young Investigator Award in 1994, the David and Lucile Packard Foundation Award in Science and Engineering in 1996, an Emeline Bigelow Conland Fellowship at the Radcliffe Institute for Advanced Study in 2006, a Guggenheim Foundation Fellowship for 2011, and was elected an ACM Fellow in 2016. Her research combines mathematics, computer science, and statistics to develop improved models and algorithms for reconstructing complex and large-scale evolutionary histories in both biology and historical linguistics. Her current research focuses on phylogeny and alignment estimation for very large datasets (10,000 to 1,000,000 sequences), estimating species trees from collections of gene trees, and metagenomics.  Overall, Tandy has published more than 130 papers in the area of computational molecular biology.