Professors David Fernandez-Baca and Oliver Eulenstein have received a 3-year $800,000 grant from the National Science Foundation's "Assembling the Tree of Life" (AToL) Program to investigate the construction of phylogenetic trees for comparative biology.
Phylogenetic trees, which depict the genealogical relationships of organisms to each other, are a key tool for organizing and analyzing information about biological diversity. The proposed research will take advantage of the phenomenal breadth of data in the GenBank molecular sequence database (currently including sequences from 185,000 species, or some 10% of all species known to science) to build an electronic repository of over a billion small but well-supported phylogenetic trees. A system will be constructed that will provide user-friendly search and retrieval tools that match trees in the repository to any query list of species in which a user may be interested. As no single tree in the database is likely to contain the query species, many trees may have to be pieced together to produce an answer, and there may be multiple ways in which an answer can be constructed. Among the algorithmic challenges this work will address are the development of efficient methods to reconcile conflicting phylogenetic information, and of mechanisms for scoring and ranking query results.
The primary impact of this research will be outside of the phylogenetics research community. Users of phylogenetic trees span most areas of modern biology: epidemiologists, genomicists, functional morphologists, conservation biologists, and community ecologists, to name a few.
This research is a collaborative effort with Professors Michael Sanderson and Michelle McMahon of the University of Arizona. The total size of the award is $1.25M. This is the second AToL grant awarded to Professors Eulenstein, Sanderson, and David Fernandez-Baca.