Markov chain Monte Carlo and its applications to phylogenetic tree construction

This thesis addresses the application of Bayesian methods to problems in phylogenetics. Specifically, we focus on using genetic data to estimate phylogenetic trees representing the evolutionary history of genes and species. Knowledge of this common ancestry has implications for the identification of functions and properties of genes, the effect of mutations and their roles in particular diseases, and other diverse aspects of the biology of cells. Improved algorithms for phylogenetic inference should increase our potential for understanding biological organisms while remaining computationally efficient. To this end, we formulate a novel Bayesian model for phylogenetic tree construction based on recent studies that incorporates known information about the evolutionary history of the species, referred to as the species phylogeny, in a statistically rigorous way. In addition, we develop an inference algorithm for this model based on a Markov chain Monte Carlo method in order to overcome the computational complexity inherent in the problem. Initial results show potential advantages over methods for phylogenetic tree estimation that do not make use of the species phylogeny.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Electrical Engineering and Computer Science.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2007

Author dc:creator

• Luczynska, Marta Magdalena

Advisor dc:contributor.advisor

• Kph-Ping Dunn and Manolis Kellis.

• Electrical Engineering and Computer Science.

Statement 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.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/62989

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/62989