A total of 54 complete genome sequences of class II aPMV-1 representing different avian hosts, geographic regions, year of isolation, and genotypes (based on previous published phylogenetic grouping) were retrieved from GenBank. The coding genome sequences were aligned using MEGA version 4 [68] . Six separate coding gene sequences datasets (for NP, P, M, F, HN and L genes) were generated (see Table S1 ) and a concatenated genome sequence from these six coding gene sequences was generated using Mesquite version 1.12 (http://mesquiteproject.org). Appropriate model of nucleotide substitution for each dataset was selected by the hierarchical likelihood ratio test implemented in Modeltest version 3.7 [69] . Maximum likelihood (ML) trees were reconstructed for all data sets using the heuristic search option, implementing stepwise addition with 100 random addition replicates and tree bisection-reconnection branch swapping in PAUP* version 4beta10 [70] and PHYML 3.412 [71] with 100 non-parametric bootstrapping replicates analyses. The inferred trees were visualized with FigTree version 1.12 (http://tree.bio.ed. ac.uk/software/figtree/) and the congruency of topology placement of class II aPMV-1 genotypes based on each gene and concatenated genome was tested using the Shimadoira, Hasegawa (SH) test [72] implemented in PAUP. The concatenated tree was constrained and tested versus other gene trees.