Fig. 2

Phylogenetic tree comparison of Macaque CMV genome and select genes. Trees were generated comparing CyCMV Mauritius, CyCMV Ottawa, RhCMV 68–1 and RhCMV 180.92 using HCMV AD169 as an out-group. Trees were generated using Mr. Bayes, following MAFFT alignment, using a model of evolution selected by JModel test a) from a full genome global alignment; b) from an alignment of putative gB (UL55) ORF, a typical marker of phylogeny; c) from an alignment of US11, an MHC-I down-regulatory gene necessary for superinfection of CMV, Chimpanzee CMV is included; d) from an alignment of US28 genes, for which 5 copies are encoded in each macaque CMV (4 copies of the gene and one copy of a nonfunctional pseudogene for RhCMV 68–1). CyCMV genes CyUS28a-CyUS28e and RhCMV genes rh214-rh220 are relabeled as US28a – US28e, inclusive of the RhCMV 68–1 pseudogene homologous to other macaque CMV US28c, based on order in genome. Numbers at loci indicate posterior probability with color scaled according to probability; genetic distances measured in substitutions per site (sps) are given by scale below