GI-16 lineage (624/I or Q1), there and back again: The history of one of the major threats for poultry farming of our era

Franzo, Giovanni; Cecchinato, Mattia; Tosi, Giovanni; Fiorentini, Laura; Faccin, Francesca; Tucciarone, Claudia Maria; Trogu, Tiziana; Barbieri, Ilaria; Massi, Paola; Moreno, Ana

For each dataset, a 200 million Markov Chain Monte Carlo (MCMC) chain was performed, sampling parameters and trees every 200.000 iterations. Run results, after discharging the first 20% of interactions as burn-in, were evaluated using Tracer 1.5 and accepted only if Estimated Sample Size (ESS) of each parameter was higher than 200 and run mixing and convergence were adequate. Parameter estimation were summarized and reported in term of mean and 95% Highest Posterior Density (HPD). Maximum clade credibility (MCC) trees were constructed and annotated using Treeannotator. Remarkably, the Bayesian approach herein implemented allows to integrate over a huge range of potential trees and parameters, accounting for both phylogenetic and Markov model parameter uncertainty. SpreaD3 [38] was used to summarize and display phylogeographic results and to calculate the BF of different between-countries migration rates. The transmission rate was considered statistically significant (i.e. non-zero) when the BF was higher than 3 [34] .