Bayesian Phylogeography Finds Its Roots

Abstract

As a key factor in endemic and epidemic dynamics, the geographical distribution of viruses has been frequently interpreted in the light of their genetic histories. Unfortunately, inference of historical dispersal or migration patterns of viruses has mainly been restricted to model-free heuristic approaches that provide little insight into the temporal setting of the spatial dynamics. The introduction of probabilistic models of evolution, however, offers unique opportunities to engage in this statistical endeavor. Here we introduce a Bayesian framework for inference, visualization and hypothesis testing of phylogeographic history. By implementing character mapping in a Bayesian software that samples time-scaled phylogenies, we enable the reconstruction of timed viral dispersal patterns while accommodating phylogenetic uncertainty. Standard Markov model inference is extended with a stochastic search variable selection procedure that identifies the parsimonious descriptions of the diffusion process. In addition, we propose priors that can incorporate geographical sampling distributions or characterize alternative hypotheses about the spatial dynamics. To visualize the spatial and temporal information, we summarize inferences using virtual globe software. We describe how Bayesian phylogeography compares with previous parsimony analysis in the investigation of the influenza A H5N1 origin and H5N1 epidemiological linkage among sampling localities. Analysis of rabies in West African dog populations reveals how virus diffusion may enable endemic maintenance through continuous epidemic cycles. From these analyses, we conclude that our phylogeographic framework will make an important asset in molecular epidemiology that can be easily generalized to infer biogeogeography from genetic data for many organisms.

Spread and Persistence of Influenza A Viruses in Waterfowl Hosts in the North American Mississippi Migratory Flyway

“…As a geographically broader extension to the analysis with the Slatkin and Maddison test, we conducted a discrete phylogeography analysis to determine the rate and directionality of AIV gene migration within the Mississippi flyway and among other flyways (i.e., Atlantic, Central, and Pacific), using time-stamped sequence data with a relaxed Bayesian Markov chain Monte Carlo method as implemented in BEAST v1.8 (40,41). Here we combined our smaller data set of MMF AIV isolates with all available AIV sequences from avian species across all North American flyways between June 2008 and March 2011 from the IRD, as discussed above, to represent the genetic diversity of AIVs in North America.…”

Spatio-Temporal Dynamics of HIV-I Subtype B and Circulating Recombinant Form 01_AE Clades in Iran: A Phylogeographic Approach

“…However, recent advances in molecular biology and biostatistics have made it possible to track the pathways of virus diffusion, over place and time, using the information accumulated in the virus' genome. Such methods are commonly referred to as phylogeography (8). Phylogeography-based methods reconstruct phylogenetic trees (8)(9)(10)(11) to infer evolutionary (i.e.…”

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“…The maximum credibility tree for the calibrated relaxed molecular clock analysis of the genus Cymbidium, using two internal calibration points (15)(16)(17)(18)(19)(20) The phylogeographic tree with divergence rate variation among lineages is depicted in the summarized MCC tree for the homogenous model using a color annotation (Figure 4). All the Asian Cymbidium species formed a monophyletic group with three sub clades displaying the three photosynthetic traits viz.…”

“…We reconstructed the evolution of photosynthetic characters mapping on a robust ancestral states estimation highlighting the migration paths along the branches (Lemey et al, 2009). These studies heavily rely on geographical information in their analysis and phylogeography.…”

“…Molecular dating of the Orchidaceae has been really challenging due the complete absence of reliable orchid fossils and a recent study by Ramirez et al, (2007) hints at a [15][16][17][18][19][20] Ma fossil of an extinct stingless bee (Proplebeia dominicana), covered with pollinia from an orchid species belonging to the subtribe Goodyerinae, that helped temporal calibration of the family. The fossil is used as an internal calibration point, and departing from a phylogenetic tree obtained from the analysis of plastid DNA sequences (matK and rbcL), Ramirez et al Till date there have been no studies on the age estimation of Asian and South East Asian orchids.…”