Phylogenetic networks

dc.contributor.advisorWarnow, Tandyen
dc.creatorNakhleh, Luayen
dc.description.abstractPhylogenies, i.e., evolutionary histories, play a major role in representing the relationships among groups of entities, such as species, genes, and languages. Their pervasiveness has led scientists, mainly biologists, mathematicians, and computer scientists, to develop methods and tools for their accurate reconstruction. Most of these tools, however, assume that the underlying model of speciation is a tree. While a good first approximation, trees fail to model the evolutionary histories in the presence of complex evolutionary events, such as lateral gene transfer and hybrid speciation among biological entities, and borrowing of linguistic features among natural languages. These events lead to “networks”, rather than trees, of relationships. In this dissertation, we present two methodologies for reconstructing phylogenetic networks. In the biological context, our method is based on the observation that contained within the branches of a (species) phylogenetic networks are phylogenetic trees that model the evolution of individual genes. To study the accuracy of our new method, as well as existing methods, we have developed a suite of simulation tools and error measures. Our simulation studies show a clear outperformance of existing methods. In historical linguistics, we extend the Ringe-Warnow model of language evolution, to incorporate non-treelike evolutionary events; our new methodology is called “perfect phylogenetic networks”. We have implemented a reconstruction method, based on the new methodology, and analyzed a dataset of Indo-European languages.
dc.description.departmentComputer Sciencesen
dc.rightsCopyright is held by the author. Presentation of this material on the Libraries' web site by University Libraries, The University of Texas at Austin was made possible under a limited license grant from the author who has retained all copyrights in the works.en
dc.subject.lcshPhylogeny--Mathematical modelsen
dc.subject.lcshEvolution (Biology)--Mathematical modelsen
dc.subject.lcshLanguage and languages--Classification--Mathematical modelsen
dc.subject.lcshHistorical linguistics--Mathematical modelsen
dc.titlePhylogenetic networksen
dc.type.genreThesisen Sciencesen Sciencesen University of Texas at Austinen of Philosophyen

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