CAI and phylodynamics of West Nile virus lineage 2 sequences.

<p>A) Bayesian maximum clade credibility tree representing a time scaled phylogeny of a WNV lineage 2 polyprotein sequences. Bayesian posterior probabilities > 0.9 are marked with an asterisk at major nodes. Averages for the European epidemic lineage (yellow bar) and a 2^nd European lineage (highlighted in red) are shown. B) Malthusian fitness (<i>Wm</i>) was calculated from 2004–2014, and compared to LOESS trend lines generated from CAI values to the codon usages of C) human house-keeping genes, D) human immune/antiviral genes, E) pigeon (Columba livia) genes, and F) mosquito (<i>Culex pipiens</i>) genes. G) The Spearman’s rank correlation test was used to test if there were any correlations between the 2010 to 2012 CAI increase in mosquitoes and the CAI increase in vertebrate species from 2012–2014, as well as Wm. The ΔCAI, Δ<i>Wm</i> and <i>rho</i> are shown for clarity. # = for all correlations, <i>p</i>-values were < 0.05.