Efficient Bayesian inference under the structured coalescent

Motivation: Population structure significantly affects evolutionary dynamics. Such structure may be due to spatial segregation, but may also reflect any other gene-flow-limiting aspect of a model. In combination with the structured coalescent, this fact can be used to inform phylogenetic tree recons...

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Vydáno v:Bioinformatics (Oxford, England) Ročník 30; číslo 16; s. 2272 - 2279
Hlavní autoři: Vaughan, Timothy G., Kühnert, Denise, Popinga, Alex, Welch, David, Drummond, Alexei J.
Médium: Journal Article
Jazyk:angličtina
Vydáno: England Oxford University Press 15.08.2014
Témata:
Algorithms
Bayes Theorem
Influenza A Virus, H3N2 Subtype - genetics
Markov Chains
Monte Carlo Method
Mutation Rate
Original Papers
Phylogeny
ISSN:1367-4803, 1367-4811, 1367-4811
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Shrnutí:Motivation: Population structure significantly affects evolutionary dynamics. Such structure may be due to spatial segregation, but may also reflect any other gene-flow-limiting aspect of a model. In combination with the structured coalescent, this fact can be used to inform phylogenetic tree reconstruction, as well as to infer parameters such as migration rates and subpopulation sizes from annotated sequence data. However, conducting Bayesian inference under the structured coalescent is impeded by the difficulty of constructing Markov Chain Monte Carlo (MCMC) sampling algorithms (samplers) capable of efficiently exploring the state space. Results: In this article, we present a new MCMC sampler capable of sampling from posterior distributions over structured trees: timed phylogenetic trees in which lineages are associated with the distinct subpopulation in which they lie. The sampler includes a set of MCMC proposal functions that offer significant mixing improvements over a previously published method. Furthermore, its implementation as a BEAST 2 package ensures maximum flexibility with respect to model and prior specification. We demonstrate the usefulness of this new sampler by using it to infer migration rates and effective population sizes of H3N2 influenza between New Zealand, New York and Hong Kong from publicly available hemagglutinin (HA) gene sequences under the structured coalescent. Availability and implementation: The sampler has been implemented as a publicly available BEAST 2 package that is distributed under version 3 of the GNU General Public License at http://compevol.github.io/MultiTypeTree. Contact:  tgvaughan@gmail.com Supplementary information:  Supplementary Data are available at Bioinformatics online.
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Associate Editor: David Posada
ISSN:1367-4803
1367-4811
1367-4811
DOI:10.1093/bioinformatics/btu201