Computer Science Corporate Affiliates Meeting
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Phylogenetic Networks and Reconstruction of Horizontal Gene Transfer
Luay Nakhleh, Rice University
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| Abstract: Phylogenies, i.e., evolutionary histories, play a major role in modeling the relationships among groups of taxa, such as genes, species, and languages. Due to their pervasiveness, and given that they are at best partially known, biologists, mathematicians, and computer scientists have designed various methodologies for their accurate reconstruction. Almost all of these methodologies assume that evolution is a process of strict divergence, and hence they seek to reconstruct evolutionary trees. However, when events such as hybrid speciation (e.g., in plants) and horizontal gene transfer (e.g., in bacteria) occur, the evolutionary history of the organisms can no longer be modeled by a tree; rather, a phylogenetic network is the appropriate model. |
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In this talk, I will describe the various phylogenetic network models, and discuss various issues with their reconstruction. In particular, I will discuss the separate analysis approach for reconstructing phylogenetic networks. In a nutshell, this approach has two steps: (1) identify gene orthology groups and reconstruct gene trees; (2) reconcile the gene trees into a species network. I will describe the challenges facing it, and outline our proposed solutions, including a set of new heuristics for reconstructing and evaluating phylogenetic networks.
Return to 2006 Meeting Agenda
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