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Agricultural and geographic factors shaped the North American 2015 highly pathogenic avian influenza H5N2 outbreak

Fig 1

Evolutionary history of HPAI H5N2 isolated from commercial poultry premises, 2015.

(A) Bayes factor (BF) tests between molecular clock and coalescent evolutionary models. For each coalescent model (exponential growth [Expo] and extended Bayesian skyline plot [EBSP]), BF was calculated using the constant coalescent model as reference (Const, indicated with asterisk) under the same molecular clock model. Two horizontal gray reference lines denote log(BF) = 1 and log(BF) = 5, which represent support and very strong support, respectively, for improved fit over the reference. (B) Molecular clock rate (substitutions per site per year) comparison between molecular clock and coalescent evolutionary models. (C) The estimated time of the most recent common ancestor (TMRCA; decimal year) compared between molecular clock and coalescent evolutionary models. (D) Maximum clade credibility tree representing the ancestral reconstruction of poultry industry (layer chicken vs. turkey) across the evolutionary history of the outbreak. The ancestral reconstruction assumed an EBSP coalescent and strict molecular clock evolutionary model. Tree branches are colored based on the most probable poultry industry of the descendant node. Thin gray node bars represent the 95% highest posterior density (HPD) of the node height (i.e., the time at which that ancestor is estimated to have existed).

Fig 1