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Novel phylogenetic approaches to problems in microbial genomics

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dc.contributor.advisor Eric J. Alm. en_US David, Lawrence A. (Lawrence Anthony) en_US
dc.contributor.other Massachusetts Institute of Technology. Computational and Systems Biology Program. en_US 2011-03-24T18:52:34Z 2011-03-24T18:52:34Z 2010 en_US 2010 en_US
dc.description Thesis (Ph. D.)--Massachusetts Institute of Technology, Computational and Systems Biology Program, 2010. en_US
dc.description This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. en_US
dc.description Cataloged from student-submitted PDF version of thesis. en_US
dc.description Includes bibliographical references (p. 117-126). en_US
dc.description.abstract Present day microbial genomes are the handiwork of over 3 billion years of evolution. Comparisons between these genomes enable stepping backwards through past evolutionary events, and can be formalized using binary tree models known as phylogenies. In this thesis, I present three new phylogenetic methods for gaining insight into how microbes evolve. In Chapter 1, I introduce the algorithm AdaptML, which uses strain ecology information to identify genetically- and ecologically-distinct bacterial populations. Analysis of 1000 marine Vibrionaceae strains by AdaptML finds evidence that niche adaptation may influence patterns of genetic differentiation in bacteria. In Chapter 2, I introduce the algorithm AnGST, which can infer the evolutionary history of a gene family in a chronological context. Analysis of 3968 gene families drawn from 100 modern day organisms with AnGST reveals genomic evidence for a massive expansion in microbial genetic diversity during the Archean eon and the gradual oxygenation of the biosphere over the past 3 billion years. Lastly, I introduce in Chapter 3 the algorithm GAnG, which can construct prokaryotic species trees from thousands of distinct gene trees. GAnG analysis of archaeal gene trees supports hypotheses that the Nanoarchaeota diverged from the last ancestor of the Archaea prior to the Crenarchaeota/Euryarchaeota split. en_US
dc.description.statementofresponsibility by Lawrence A. David. en_US
dc.format.extent 126 p. en_US
dc.language.iso eng en_US
dc.publisher Massachusetts Institute of Technology en_US
dc.rights M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission. en_US
dc.rights.uri en_US
dc.subject Computational and Systems Biology Program. en_US
dc.title Novel phylogenetic approaches to problems in microbial genomics en_US
dc.type Thesis en_US Ph.D. en_US
dc.contributor.department Massachusetts Institute of Technology. Computational and Systems Biology Program. en_US
dc.identifier.oclc 706716481 en_US

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