JSM 2005 Online Program

Abstract #303457

This is the preliminary program for the 2005 Joint Statistical Meetings in Minneapolis, Minnesota. Currently included in this program is the "technical" program, schedule of invited, topic contributed, regular contributed and poster sessions; Continuing Education courses (August 7-10, 2005); and Committee and Business Meetings. This on-line program will be updated frequently to reflect the most current revisions.

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Activity Number:	474
Type:	Topic Contributed
Date/Time:	Thursday, August 11, 2005 : 8:30 AM to 10:20 AM
Sponsor:	Section on Bayesian Statistical Science
Abstract - #303457
Title:	Resolving Phylogenies for Rapidly Emerging Pathogens with Indel Information
Author(s):	Benjamin Redelings*+ and Marc A. Suchard
Companies:	University of California, Los Angeles and University of California, Los Angeles
Address:	AV-633 Center for the Health Sciences, Los Angeles, CA, 90095-1766,
Keywords:	Bayesian ; alignment ; phylogeny ; indel ; evolution ; MCMC
Abstract:	Phylogenies of rapidly evolving pathogens can be difficult to resolve because of the small number of substitutions that accumulate in the short times since divergence. In order to improve resolution of such phylogenies, we propose using indel information in addition to substitution information by simultaneously estimating the alignment and phylogeny. We accomplish this using a joint reconstruction model in a Bayesian framework and draw inference using Markov chain Monte Carlo (MCMC). We introduce a novel Markov chain transition kernel that improves computational efficiency by proposing nonlocal topology rearrangements and block sampling alignment and topology parameters. We demonstrate the relevance of indel information in examples drawn from HBV, HIV, and SIV and discuss the importance of taking alignment uncertainty into account when using such information.

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