Phylogenetic discovery bias in Bacillus anthracis using single-nucleotide polymorphisms from whole-genome sequencing

Abstract

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. T he discovery method used to find nonhomoplastic molecular characters can have a great impact on subsequent phylogenetic analyses (1). ''Discovery bias'' will most likely be encountered when polymorphic characters are rare and extraordinary means (i.e., whole-genome sequencing) are necessary to find them. In such cases, only a small subset of the target organisms can be exhaustively examined for genetic differences. When these polymorphisms are assayed across a more extensive and diverse panel of strains, the phylogenetic topology will be impacted greatly by the original choices of strains used for character discovery. Consider a six-taxon dendrogram (Fig. 1) in which nonhomoplastic polymorphic characters are discovered by exhaustive comparisons of two taxa. Mutational events that create character differences on the evolutionary path connecting the two taxa will be discovered, but characters on tangential (i.e., secondary) branches will not. Subsequent character-state determination in all taxa will accurately place them onto a linear phylogeny but will underrepresent the taxonomic complexity by eliminating secondary branching. If the initial character discovery is between two closely related taxa, large diverse clades will be reduced to a single point on a short linear dendrogram (Fig. 1B). This theoretical model assu...

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Application of SNPs for assessing biodiversity and phylogeny among yeast strains

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Operon Prediction for Sequenced Bacterial Genomes without Experimental Information

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