Selected article for: "bayesian analysis and random field"
Author: Yang, Qiqi; Zhao, Xiang; Lemey, Philippe; Suchard, Marc A.; Bi, Yuhai; Shi, Weifeng; Liu, Di; Qi, Wenbao; Zhang, Guogang; Stenseth, Nils Chr.; Pybus, Oliver G.; Tian, Huaiyu
Title: Assessing the role of live poultry trade in community-structured transmission of avian influenza in China
  • Document date: 2020_3_17
    • ID: 197zzk9w_23
    Snippet: Phylogeographic Inference. Time-measured phylogenies were inferred using the Bayesian discrete phylogeographic approach (14) implemented in the Bayesian Evolutionary Analysis Sampling Trees (BEAST) program, version 1.8.2 (32) . We used an uncorrelated lognormal (UCLN) relaxed molecular clock model (33) , the SRD06 nucleotide substitution model (34) , and the Gaussian Markov random field (GMRF) Bayesian skyride coalescent tree prior (35) . We used.....
    Document: Phylogeographic Inference. Time-measured phylogenies were inferred using the Bayesian discrete phylogeographic approach (14) implemented in the Bayesian Evolutionary Analysis Sampling Trees (BEAST) program, version 1.8.2 (32) . We used an uncorrelated lognormal (UCLN) relaxed molecular clock model (33) , the SRD06 nucleotide substitution model (34) , and the Gaussian Markov random field (GMRF) Bayesian skyride coalescent tree prior (35) . We used Bayesian stochastic search variable selection (BSSVS) to determine 1) the most probable locations of ancestral nodes in the phylogeny and 2) the history and rates of lineage movement among locations (14) . To ensure that the relationships between distance and lineage movement were not a consequence of the prior used, we repeated the analysis after randomizing the locations assigned to each sequence (SI Appendix, Fig. S13) . The raw transition rates between locations were obtained from the analyses reported in Fig. 1 . Shown are two means: blue = mean transition rate for pairs of locations in LPTCs; red = mean transition rate for pairs of locations in the same LPTC. Dotted vertical lines show the two means calculated using the empirically derived (true) LPTC network (Fig. 3) . The histograms show the same mean values, calculated using 1,000 RGCs (see Methods for details). Results shown for (A) H5N1, (B) H5N6, and (C) H7N9.

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