Format

Send to

Choose Destination
See comment in PubMed Commons below
Philos Trans R Soc Lond B Biol Sci. 2013 Feb 4;368(1614):20120206. doi: 10.1098/rstb.2012.0206. Print 2013 Mar 19.

Graph hierarchies for phylogeography.

Author information

1
Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.

Abstract

Bayesian phylogeographic methods simultaneously integrate geographical and evolutionary modelling, and have demonstrated value in assessing spatial spread patterns of measurably evolving organisms. We improve on existing phylogeographic methods by combining information from multiple phylogeographic datasets in a hierarchical setting. Consider N exchangeable datasets or strata consisting of viral sequences and locations, each evolving along its own phylogenetic tree and according to a conditionally independent geographical process. At the hierarchical level, a random graph summarizes the overall dispersion process by informing which migration rates between sampling locations are likely to be relevant in the strata. This approach provides an efficient and improved framework for analysing inherently hierarchical datasets. We first examine the evolutionary history of multiple serotypes of dengue virus in the Americas to showcase our method. Additionally, we explore an application to intrahost HIV evolution across multiple patients.

PMID:
23382428
PMCID:
PMC3678330
DOI:
10.1098/rstb.2012.0206
[Indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for HighWire Icon for PubMed Central
    Loading ...
    Support Center