Phylogenetic reconstruction using molecular data is often subject to homoplasy, 
leading to inaccurate conclusions about phylogenetic relationships among 
operational taxonomic units. Compared with other molecular markers, 
single-nucleotide polymorphisms (SNPs) exhibit extremely low mutation rates, 
making them rare in recently emerged pathogens, but they are less prone to 
homoplasy and thus extremely valuable for phylogenetic analyses. Despite their 
phylogenetic potential, ascertainment bias occurs when SNP characters are 
discovered through biased taxonomic sampling; by using whole-genome comparisons 
of five diverse strains of Bacillus anthracis to facilitate SNP discovery, we 
show that only polymorphisms lying along the evolutionary pathway between 
reference strains will be observed. We illustrate this in theoretical and 
simulated data sets in which complex phylogenetic topologies are reduced to 
linear evolutionary models. Using a set of 990 SNP markers, we also show how 
divergent branches in our topologies collapse to single points but provide 
accurate information on internodal distances and points of origin for ancestral 
clades. These data allowed us to determine the ancestral root of B. anthracis, 
showing that it lies closer to a newly described "C" branch than to either of 
two previously described "A" or "B" branches. In addition, subclade rooting of 
the C branch revealed unequal evolutionary rates that seem to be correlated with 
ecological parameters and strain attributes. Our use of nonhomoplastic 
whole-genome SNP characters allows branch points and clade membership to be 
estimated with great precision, providing greater insight into epidemiological, 
ecological, and forensic questions.