Molecular Ecology and Natural History of Simian Foamy Virus Infection in Wild-Living Chimpanzees
Figure 6
Evolutionary relationships of newly derived SFVcpz strains in the pol-IN region.
Pol-IN (425 bp) sequences were analyzed using the Bayesian Markov chain Monte Carlo (BMCMC) method implemented in BEAST. Sequence LM183 (from a wild bonobo) was included as an outgroup. The maximum clade credibility (MCC) tree topology inferred using TreeAnnotator v1.4.7 is shown, with branch lengths depicting the mean value for that branch in the upper half of the MCMC sample. Posterior probabilities (expressed as percentages) are indicated on well-supported nodes, either as asterisks (100%) or filled circles (90%–99%). Newly identified SFVcpz strains are color coded according to their subspecies of origin (as shown in Figure 1). Representative strains from the database are shown in black. Plus signs (+) denote sequences that represent placeholders of multiple viruses with identical sequences (a complete list is provided in Table S2). Sample WE464 (boxed) was collected in the P. t. vellerosus range, but has a P. t. troglodytes mtDNA haplotype (Figure S1). Arrows identify distinct SFVcpz strains (termed A or B) that were found in the same sample. The scale bar represents 0.02 substitutions per site.