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Summary of Whiting et al. NSF award #0120718 "BIOCOMPLEXITY: Hexapod Phylogenomics - Bringing Phylogenetic Supercomputing to the Masses"

Investigators:

PI: Michael Whiting; Co-PI's: Keith Crandall, Quinn Snell, Mark Clement (Computer Science), and David Whiting (Statistics).

Funding:

$1,340,000 over 5 years, beginning January 1, 2002

Summary:

Research on the phylogeny and evolution of the hexapod arthropods (insects and their allies) will be accomplished by developing novel genetic markers for phylogenetic inference, sequencing these markers across 2500 spp. representing hexapod diversity, sequencing the entire statistical resources to effectively analyze this vast amount of data. This project has an international component with collaborators at the University of Queensland (mitochondrial genome evolution) and at the British Museum of Natural History, Imperial College (development of novel genetic loci for phylogenetic inference). This funding is to support 5 postdoctoral positions (4 postdocs over 2 years, 1 post doc over 3 years), 6 years of graduate support, and 5 years of undergraduate support. It also includes travel, supplies, and partial support (180K, ~50%) for a high-throughput DNA sequencer required to meet the sequencing needs of this proposal (~700,000 sequences over 5 years).

Competitiveness:

The grant proposal was submitted to a new NSF initiative: Genetics in the Environment: Biocomplexity. This competition funded in two discrete arenas: Tree of Life and Environment Biocomplexity. These proposals consisted of large scale collaborations among PI's from many universities, both nationally and internationally. Of the 52 proposals, 8 awards were made (~15% funding rate), 4 were given Tree of Life and 4 to Environment Biocomplexity for a total of $10.5 million. We received one of the four made to Tree of Life.

Sample of Reviewer Comments

"Overall, this is an exceptional proposal and deserves to be funded at the suggested level. Additionally, it is well thought out, contains a major component of undergraduate to postgraduate education, and admirably represents an international collaboration mixed with a multidisciplinary approach towards resolving a group of high research interest."
"I found the reasons for the two sequencing components to be compelling. The PI is experienced in high throughput sequencing and the goals seem feasible. The resulting sequence resource will be valuable for understanding the evolution of a very large and diverse group of hexapod animals."
"A significant intellectual gain is realized by the interdisciplinary nature of the research agenda i.e., the incorporation of computer scientists and a statistician with the research team. The research and education program map well on to each other. The team approach makes it more likely that postdocs, graduate, and undergraduate students will learn about all the facets of the research activity (especially the analytical/computational aspects) rather than being relegated to producing sequencing data."
"Each of the aims is directed at genome scale analysis, and is therefore in line with the goals of the GEN-EN initiative. The team is interdisciplinary, consisting of two systematists, two computer scientists, a statistician, and collaborators are experts in mt genome evolution and the development of new molecular markers. The methodologies are quantitative, and the studies of the influence of different variables on computational performance are an important component of the proposal. Education would consist of involving 5 postdocs, 6 grad students, and 6 under graduates in the project, and post-docs and students would be reciprocally exchanged 'across the Atlantic' during collaboration."
"This is a very ambitious proposal with two primary parts, one to generate a very large amount of sequence data, the other to develop and implement phylogenetic analytical methods involving parallel computing. The project is phylogenetically significant in the hexapods are a key group of the earth's biota, and it is clear that additional work on the group is needed. The team assembled for this, all at BYU, is clearly interdisciplinary, including empirical systematists/evolutionists with good theoretical skills as well as computer scientists."