RUI: Quartet-Based Approaches to Phylogenomics

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A modernization of the mathematical and statistical tools used to uncover the evolutionary history of life on earth is required to keep pace with the rapid expansion in the availability of genetic data. Moreover, different segments of genetic information can tell conflicting evolutionary histories about a collection of organisms. This project develops mathematical tools for reconstructing the evolutionary history of large collections of organisms, and for constructing a single tree that encapsulates the conflicting stories told by different pieces of the genome. Ten undergraduate students, many recruited from groups underrepresented in STEM fields at this primarily undergraduate institution, will be trained in techniques at the intersection of mathematics, statistics, and biology that are required for the algorithmic developments. Most methods of super-tree or species tree reconstruction rely on accurately reconstructed gene trees. In practice, however, most inferred gene trees used in these reconstructions do contain errors. By identifying and explicitly accounting for gene tree estimation error, this project will improve algorithms for super-tree and species tree reconstruction. Alternative approaches for which species trees are reconstructed without dependence on the prior estimation of gene trees will also be developed.