Title: Estimating and evaluating evolutionary relationships using large-scale genomic data sets
Speaker: Ruchi Chaudhary, Postdoctoral Research Associate, University of Florida. Visiting Researcher
Abstract: Phylogenetic trees, graphical representations of the evolutionary relationships of species, are important for many problems in evolutionary biology, ecology, and conservation. The advent of next-generation sequencing technologies makes it possible to estimate the evolutionary relationships using datasets with thousands of gene sequences. Yet the complex processes of genome evolution create enormous computational challenges for phylogenetic inference. In this talk, I will review the fundamental challenges in phylogenetic inference from genes with a possible history of duplication, loss, and horizontal transfer. These evolutionary processes can create conflict among gene trees, which can obscure or mislead phylogenetic analyses. I will then describe our new method for estimating evolutionary trees from enormous genomic data sets. This approach can estimate credible plant and mammalian trees from tens of thousands of gene trees in a matter of hours, and it outperforms existing approaches in simulations. I will also discuss experiments to assess various probabilistic and non-probabilistic phylogenetic methods through gene family simulations. Finally, I will demonstrate approaches to assess the quality of phylogenetic trees of all life using a phylogeny of all ~2.2 million named species.
Speaker Bio: Ruchi Chaudhary received the BS in Computer Science and Mathematics, and the Master of Computer Application (MCA) degrees in 2002 and 2005, respectively, from Banasthali University, India. After her MCA, she worked for Indian software giant Tata Consultancy Services as a software engineer for two years. She received her PhD from the Department of Computer Science at Iowa State University in Spring 2013. Since then, she is a Postdoctoral Research Associate in the Department of Biology at the University of Florida, Gainesville, and a visiting researcher in the Department of Computer Science at Iowa State University. Her research is in bioinformatics and computational biology, with an emphasis on estimating and evaluating evolutionary relationships using large-scale genomic data sets. She is a contributor in the Open Tree of Life Project (opentreeoflife.org). She received Research Excellence Award from Iowa State University’s Graduate College, and Gold Medal for first rank in BS from Banasthali University.