Estimating Species Trees Under the Coalescent Model Using Site Pattern Frequencies

Laura Kubatko
Ohio State University

The sequence data available for phylogenetic inference often include samples taken from multiple genes within each organism. This necessitates modeling of the evolutionary process at two distinct
scales. First, given an overall phylogeny representing the actual evolutionary history of the species, individual genes evolve their own histories, called gene trees. Then, along each gene tree, sequence
data evolve, leading to the observed data that is used for inference. The coalescent model provides the link between the evolution of the gene trees given the species tree, and the evolution of the sequence data given the gene trees. Phylogenetic invariants have been proposed as a tool for inferring phylogenies using data from a single gene, and their mathematical properties have been widely studied. In this talk, we consider the development of methods based on phylogenetic invariants developed specifically for species trees, as opposed to gene trees. We discuss methods for finding invariants and demonstrate their utility on both simulated and empirical genomic data

This is joint work with Dr. Julia Chifman.

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