Figure 1. Phylogenetic tree of IBDV based on HVR-VP2.

The model used for phylogenetic inference is shown at the top left. The Cuban IBDV sequences are denoted with black letters and the names of the strains were used as identification (ID) in the tree. For the remaining sequences, an ID for the tree was used (see Table S1). For geographic-trait association, different colours related to the origin of the strain were used and denoted (strains from Asia in orange, Africa in red, Europe in blue, South America in green, North America in pink, Australia in brown and the Caribbean Region with a turquoise star). The pattern of the HVR-VP2 loop structures P_BC, P_DE, P_FG, and P_HI linked to changes in IBDV virulence and escape from vaccination by Coulibaly et al. (2005) are shown as rectangles. Those strains that showed changes in this pattern are highlighted using a grey rectangle; the amino acid substitution is also indicated.