Evolutionary Analysis of Inter-Farm Transmission Dynamics in a Highly Pathogenic Avian Influenza Epidemic
Figure 2
Phylogenetic trees of H7N7 viruses.
Time-scaled phylogenies (dates on the horizontal axis) inferred using Bayesian MCMC analysis from (A) HA gene; (B) NA gene; (C) PB2 gene. Nodes supported by ≥0.7 posterior probability are indicated by a grey dot. Posterior probability values from the time-scaled BMCMC method, the MrBayes BMCMC method, and the Maximum Likelihood method (1,000 ML bootstrap replications) are shown for nodes delimitating clusters of transmission (tsBMCMC/MrBMCMC/ML; noted Cluster I–IV). The three samples with discordant phylogenies are indicated by black square (F45), circle (F76), and triangle (F145). Nodes and branches are coloured according the geographical origin of the farm samples. Yellow, Gelderland area; Blue, Central area; Red, Limburg area; Green, Southwest area. Fully annotated trees are available online in supplementary figures S2A–C.