ABSTRACT: Using genome-wide data for phylogenetic inference and analysis has become commonplace in the post-genomic era, giving rise to the field of phylogenomics. The multispecies coalescent (MSC) model has emerged as the main stochastic process that helps capture the intricate relationship between species trees and gene trees. Combined with models of sequence evolution, the MSC can be viewed as a generative model of genomic sequence data in the context of a (species) phylogenetic tree. A significant outcome of the use of genome-wide data has been the increasing evidence, or hypotheses, of reticulation (e.g., hybridization) during the evolution of various groups of eukaryotic species. Reticulate evolutionary histories are best represented as phylogenetic networks, which extend the tree model to allow for admixtures of genetic material. In this talk, I will describe the multispecies network coalescent (MSNC) model, which extends the MSC model so that it operates within the branches of a phylogenetic network. This extended model naturally allows for modeling vertical and horizontal evolutionary processes acting within and across species boundaries. In particular, it simultaneously accounts for gene tree incongruence across loci due to both hybridization and incomplete lineage sorting. I will then briefly describe a host of methods that we have developed for phylogenetic network inference under the MSNC. The methods differ by the mathematical criterion they employ, the data they take as input, as well as the information they infer. I will also discuss practical issue facing phylogenetic network inference in practice. All methods are implemented and publicly available in the
PhyloNet software package (http://bioinfocs.rice.edu/phylonet).

BIO: Luay Nakhleh is the William and Stephanie Sick Dean of Engineering and Professor of Computer Science at Rice University in Houston, Texas. He received a B.Sc. degree in Computer Science (1996) from the Technion (Israel), a master’s degree in Computer
Science (1998) from Texas A&M University, and a Ph.D. degree in Computer Science (2004) from The University of Texas in Austin. He conducts research in the areas of bioinformatics and computational biology, focusing mainly on questions in evolutionary biology and genomics. Luay is a recipient of multiple awards including the Department of Energy CAREER award, the National Science Foundation CAREER award, the Sloan luay Fellowship, and the Guggenheim Fellowship.
https://www.cs.rice.edu/~nakhleh/