ITR: Evaluating Phylogeny Reconstruction Algorithms with Digital Organisms

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EIA-0219229Torng, Eric KMichigan State UniversityITR: Evaluating Phylogeny Reconstruction Algorithms with Digital OrganismsThe investigators study methods of determining the historic relationshipbetween species using only knowledge of currently existing organisms, a technique called "phylogenetic tree reconstruction". Many tree reconstruction algorithms are known, but it is difficult to properly test them for the veryreason that the algorithms are useful -- the original trees are lost tohistory.The studies proposed make use of a new evaluation methodology based on anartificial evolving system called Avida. In Avida, populations of digitalorganisms (self-replicating computer programs) experience natural selectionas they compete for limited resources, and will evolve into new speciesoften with entirely new genes. The history of such a system can bemonitored, and hence a reconstruction from the final state can have itsaccuracy measured.The proposed activity has several broader impacts on society. It is a coreactivity in the Center for Biological Modeling, a new interdisciplinaryresearch and education center at Michigan State University. Undergraduatestudents including underrepresented minorities will be involved by studyingsmall, self-contained questions. Finally, enhanced understanding ofphylogeny reconstruction algorithms will improve our ability to interpretthesequences of genes, aiding in drug design and helping efforts to reconstructan evolutionary "tree of life".