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      Graph hierarchies for phylogeography.

      Philosophical Transactions of the Royal Society B: Biological Sciences

      methods, Phylogeography, Phylogeny, Models, Genetic, Humans, genetics, HIV-1, Dengue Virus, Bayes Theorem, Americas

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          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.

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          Author and article information

          Journal
          10.1098/rstb.2012.0206
          3678330
          23382428

          Chemistry

          methods, Phylogeography, Phylogeny, Models, Genetic, Humans, genetics, HIV-1, Dengue Virus, Bayes Theorem, Americas

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