March 16, 2004: Seminar, Speaker Tanya Berger-Wolf
Speaker: Tanya Berger-Wolf (University of New Mexico)
Title: How to See a Tree for a Forest? Combining Phylogenetic Trees: Reasons, Methods, and Consequences.

Date: Tuesday March 16, 2004
Time: 11:00 AM
Location: Room 1000 SEO

The study of the evolutionary relationships between living organisms, or phylogeny, is central to biology. Relationships among the organisms (or taxa) are modeled as a phylogenetic tree. Phylogeny reconstruction usually produces multiple trees. Having more than one tree is unsatisfactory and the trees are typically combined into one "representative" tree using a consensus method.

In particular, computational methods construct numerous trees with the same objective score. A consensus of the top scoring trees is returned as the answer. Our experiments indicate that the consensus of trees with near optimal scores is sufficiently close topologically to the consensus of trees with the best known scores. Thus, the phylogenetic search heuristics can be stopped significantly earlier than is currently done. This can save weeks of computation for large datasets. We propose an objective criterion that allows a user to decide when the trees are "good enough" and present online consensus algorithms in aid of the implementation of this criterion.

Another source of multiple phylogenetic reconstructions is different types of data, such as morphology, geography, paleontology. The data can be viewed as constraints imposed on the structure of phylogeny. We present a new constraint-based approach for phylogeny reconstruction that is capable of handling heterogeneous data. We view tree consensus methods as techniques for combining various types of constraints and analyze their properties in this context.

This work is joint with Bernard M. E. Moret, Usman Roshan, Tandy J. Warnow, and Tiffani L. Williams.

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