EAGER: Pioneering gene tree averaging for bacterial phylogenomics

University Of Washington, Seattle WA

Investigators

Abstract

Bacteria are everywhere and essential for life. Bacteria in the ocean regulate global temperatures; bacteria in soil help plants grow; and bacteria in our bodies help us digest and extract nutrition from food. Bacteria change over time through evolution, but because bacteria can gain and lose genes, their evolutionary histories may be hard to determine. This project will use recent advances in mathematics to develop a new method to estimate bacterial evolutionary histories. The method will be benchmarked against existing tools for speed and accuracy. In addition, it will provide advanced training for a postdoctoral researcher from an underrepresented group and create a training workshop for specialists on bacterial evolutionary histories. Accurate estimates of bacterial and archaeal phylogenetic trees are critical for classifying novel strains, interpreting changes in microbial communities, and understanding diversification and adaptation. A major challenge in prokaryotic phylogenetics is that gene transfer and recombination events result in different genes having different evolutionary histories. This project will implement and study a novel method for averaging gene-level phylogenies to obtain an overall phylogeny. The method can average gene trees even when not all genes are shared by all organisms. The project will implement tree-averaging in software and benchmark its performance against the most widely-used bacterial phylogenetics estimators using both simulation and modern bacterial genomics datasets. To support the specific objectives of this project, a postdoctoral researcher whose intersectional identity is underrepresented in the mathematical sciences will be hired, and a bilingual Spanish-English workshop on microbial phylogenetics for the group "Women in Bioinformatics and Data Science Latin America" will be developed. The results of this project will be available at statdivlab.github.io/phylogenetics. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.