Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data.

Published

Journal Article

Molecular sequences obtained at different sampling times from populations of rapidly evolving pathogens and from ancient subfossil and fossil sources are increasingly available with modern sequencing technology. Here, we present a Bayesian statistical inference approach to the joint estimation of mutation rate and population size that incorporates the uncertainty in the genealogy of such temporally spaced sequences by using Markov chain Monte Carlo (MCMC) integration. The Kingman coalescent model is used to describe the time structure of the ancestral tree. We recover information about the unknown true ancestral coalescent tree, population size, and the overall mutation rate from temporally spaced data, that is, from nucleotide sequences gathered at different times, from different individuals, in an evolving haploid population. We briefly discuss the methodological implications and show what can be inferred, in various practically relevant states of prior knowledge. We develop extensions for exponentially growing population size and joint estimation of substitution model parameters. We illustrate some of the important features of this approach on a genealogy of HIV-1 envelope (env) partial sequences.

Full Text

Cited Authors

  • Drummond, AJ; Nicholls, GK; Rodrigo, AG; Solomon, W

Published Date

  • July 2002

Published In

Volume / Issue

  • 161 / 3

Start / End Page

  • 1307 - 1320

PubMed ID

  • 12136032

Pubmed Central ID

  • 12136032

Electronic International Standard Serial Number (EISSN)

  • 1943-2631

International Standard Serial Number (ISSN)

  • 0016-6731

Language

  • eng