bayesian phylogeography finds its roots贝叶斯phylogeography找到其根源.pdfVIP

Bayesian Phylogeography Finds Its Roots 1 2 3 4,5 Philippe Lemey *, Andrew Rambaut , Alexei J. Drummond , Marc A. Suchard 1 Department of Microbiology and Immunology, Katholieke Universiteit Leuven, Leuven, Belgium, 2 Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom, 3 Department of Computer Science, University of Auckland, Auckland, New Zealand, 4 Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America, 5 Department of Biostatistics, School of Public Health, University of California, Los Angeles, California, United States of America 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