Graduate Computational Algebraic Geometry Seminar
Julia Chifman
Mathematical Biosciences Institute
Use of phylogenetic invariants to estimate species trees under the coalescent model
Abstract: A phylogenetic tree, or phylogeny, is a graph that displays
the evolutionary relationships of ancestry and descent among a
collection of organisms. Estimation of phylogenies is a fundamental
problem in evolutionary biology, since accurate estimation is crucial
to forming and evaluating hypotheses about the historical demography
and movement of populations as well as to mapping and studying trait
evolution.
Due to the increasing ease with which DNA sequence data can be
obtained, much of current phylogenetics involves use of the
information contained in representative DNA sequences for a set of
sampled organisms for estimation. The sequence data available for a
phylogenetic analysis often include samples taken from multiple genes
within each organism. When data are collected in this manner, it
becomes necessary to model 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. We consider the development of
methods based on phylogenetic invariants developed specifically for
species trees, as opposed to gene trees.
(joint work with Laura Kubatko)
Thursday April 15, 2010 at 11:00 AM in SEO 612