For bioinformatics researchers working in the relatively new field of phyloinformatics, money was almost literally growing on trees in September, when the National Science Foundation promised nearly $20 million in grants to projects developing computational methods to build large-scale phylogenetic trees.
In February, the NSF put aside $12 million in FY 2003 funding for the phylogeny-based program, called “Assembling the Tree of Life.” Designed to attract researchers from the fields of biology, computer science, geosciences, and social sciences, the multidisciplinary program planned to award between three and six projects for up to five years at around $3 million each for research that would help construct a phylogeny for the 1.7 million described species of life. In particular, the program was seeking projects in data acquisition, analysis, algorithm development, and dissemination in computational phylogenetics and phyloinformatics.
Judging from last month’s awards, the Tree of Life will be rooted in a firm computational foundation. A listing of relevant grants, with total funding for the length of the projects, follows.
Building the Tree of Life — A National Resource for Phyloinformatics and Computational Phylogenetics. Start date: Oct. 1, 2003. Expires: Sept. 30, 2008. Grant awarded to five investigative teams:
- University of New Mexico. Principal investigator: Bernard Moret. Amount: $3,540,907.
- University of California, San Diego. Principal investigator: Francine Berman. Amount: $4,154,000.
- Florida State University. Principal investigator: David Swofford. Amount: $1,817,053
- University of California, Berkeley. Principal investigator: Satish Rao. Amount: $1,229,749.
- University of Texas Austin. Principal investigator: Tandy Warnow. Amount: $839,243.
Project to establish a national computational resource to reconstruct the evolutionary history of all organisms. The resource will include a large computational platform, a collection of interoperable software for phylogenetic analysis, and a large database. The project will support research programs in phyloinformatics —defined as “databases to store multilevel data with detailed annotations and to support complex, tree-oriented queries” — as well as optimization algorithms, Bayesian inference, and symbolic manipulation for phylogeny reconstruction, and in simulation of branching evolution at the genomic level.
A Phylogenomic Toolbox for Assembling the Tree of Life. Start date: Nov. 1, 2003. Expires: Oct. 31, 2008. Grant awarded to three investigative teams:
- University of California Davis. Principal investigator: Michael Sanderson. Amount: $962,782.
- University of Pennsylvania. Principal investigator: Junhyong Kim. Amount: $537,949.
- Iowa State University. Principal investigator: Oliver Eulenstein. Amount: $976,520.
Grants support development of new methods and software tools to construct the genealogical tree of life of all biological species by extracting data “en masse” from sequence databases and then assembling a synthesis. Project members will assess the potential information in sequence databases of various kinds; study methods for the optimal extraction of data from databases to bring the best information to bear on individual tree reconstruction; and integrate these smaller trees into “supertrees.” Each of the three grantee projects will reconstruct particular portions of the tree.
The Tree of Life Project: A Digital Library of Biodiversity Information. Start Date: Jan. 1, 2004. Expires: Dec. 31, 2005. Sponsor: University of Arizona. Principal investigator: David Maddison. Amount: $615,996.
Project aims to make phylogenetic information accessible for non-specialists. Goals include improving the core scientific content of the Tree of Life collection; implementing new technical features focusing on needs of users from the education and research communities; initiating the collection of content aimed at K-16 learners; and developing and implementing policies pertaining to the administrative structure of the Tree of Life, including archiving, editorial policies, peer-review, and intellectual property rights.
Building the Dipteran Tree: Cooperative Research in Phylogenetics and Bioinformatics of True Flies (Insecta: Diptera). Start date: Jan. 1, 2004. Expires: Dec. 31, 2008. Sponsor: North Carolina State University. Principal investigator: Brian Wiegmann. Amount: $2,413,311.
Project will reconstruct the phylogenetic tree for the insect order Diptera (the true flies, which include fruit flies, mosquitoes, house flies, medflies, and others) from “an unprecedentedly large sample” of comparative genetic and anatomical data. The research team will integrate information from the fossil record of Diptera, from genomic and developmental databases, from specimen data, and from previously published phylogenetic trees, and will also develop web-based bioinformatics tools for natural history information about flies, their biology, and its impact on other fields of research.
AmphibiaTree, An Integrated Phylogenetic and Phyloinformatics Approach to the Tree of Amphibians. Start date: Jan. 1, 2004. Expires: Dec. 31, 2008. Grant awarded to four investigative teams:
- University of Texas Austin. Principal investigator: David Cannatella. Amount: $1,325,754.
- University of California Berkeley. Principal investigator: David Wake. Amount: $1,018,000.
- University of Kansas. Principal Investigator: Linda Trueb. Amount: $237,298.
- Sponsor: Harvard University. Principal investigator: James Hanken. Amount: $239,496.
Collaborative project to study the phylogenetic relationships of the living amphibians and their close fossil relatives. Anatomical and morphological data from living and fossil forms will be combined with DNA sequences from a set of defined mitochondrial and nuclear genes for as many species as possible, and will be integrated with existing data sets. Analysis of these data sets will provide insight into such questions as repeated patterns of evolution, geographic patterns, and rates of evolution. AmphibiaWeb, an existing website (http://elib.cs.berkeley.edu/aw/), will be expanded and further developed to provide information on all species of amphibians for professionals and the public at large.