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Maximum likelihood estimation of phylogenetic tree with evolutionary parameters

Wang, Qiang
http://rave.ohiolink.edu/etdc/view?acc_num=osu1083177084

Abstract Details

2004, Doctor of Philosophy, Ohio State University, Statistics.
This thesis deals with issues in the maximum likelihood estimation of phylogenetic tree construction. The maximum likelihood estimator (MLE) of evolutionary parameters is shown to be asymptotically efficient with the number of sites approaching infinity, when the tree is assumed to be known. Through simulation, a Monte Carlo Sampling method for approximating the expected Fisher information is demonstrated to be superior to using the observed Fisher information implemented in a phylogenetic analysis package to estimate the variability of MLE. Simulations also revealed the underestimation of the variability when the tree is unknown and needs to be simultaneously estimated. The large-sample property of the joint MLE for tree topology, branch lengths vector and evolutionary parameters is established. As the number of sites approaches infinity, the probability of recovering the true tree topology tends to one and the joint MLE for the branch lengths vector and evolutionary parameters are shown to be efficient. In order to estimate the variability of the MLE for evolutionary parameters, a standard bootstrap algorithm and a bootstrap method motivated by the conditional variance principle (CVB) are proposed for practical implementation. Based on simulation evidence, a parametric version of the bootstrap methods is recommended, and CVB method in particular performs reasonably well and provides substantial computational time savings. Lastly, the method is applied to nucleotide data of 30 papillomavirus strains
Dennis Pearl (Advisor)
167 p.
Biology, Biostatistics
Phylogenetic tree; Maximum likelihood estimation; bootstrap

Recommended Citations

Citations

  • Wang, Q. (2004). Maximum likelihood estimation of phylogenetic tree with evolutionary parameters [Doctoral dissertation, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1083177084

    APA Style (7th edition)

  • Wang, Qiang. Maximum likelihood estimation of phylogenetic tree with evolutionary parameters. 2004. Ohio State University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1083177084.

    MLA Style (8th edition)

  • Wang, Qiang. "Maximum likelihood estimation of phylogenetic tree with evolutionary parameters." Doctoral dissertation, Ohio State University, 2004. http://rave.ohiolink.edu/etdc/view?acc_num=osu1083177084

    Chicago Manual of Style (17th edition)

osu1083177084
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© 2004, all rights reserved.
This open access ETD is published by The Ohio State University and OhioLINK.