NOTE: We submitted a formal correction to PLoS in July 2013. Until the formal correction is linked to the article, we are posting the text of the correction here in the comments. We are unable to post the corrected figure using the comments tool, but I am happy to send a copy to anyone who would like to see it. The changes are very minor and do not affect the conclusions drawn in the article, but I thought it was important to make sure people are aware of them. Please contact me at knharpe@gmail.com with any questions or comments.

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A mistake in Table 2 has come to our attention. The sequence information for the Nichols and Mexico A strains at nucleotide position 2,388 of the tp92 gene was inadvertently switched. The correct sequence at this position is as follows: a deletion in Mexico A and an A in Nichols.

The incorrect information in Table 2 was used to create the phylogenetic tree in Figure 2, so we present a corrected tree here. After analyzing the correct sequence information, the topology changed slightly in a subclade of the tree that was not discussed in our article. The resolution among T. pallidum subsp. pallidum strains improved a bit, with two new groupings identified: (1) the Grady, Philadelphia 1, Mexico A, and South Africa strains; and (2) the Dallas 1, Madras, and Nichols strains. In addition, bootstrap support for the subclades including the baboon strains from Serengeti National Park and Guinea increased, while the T. pallidum subsp. endemicum node, which was identified with very weak bootstrap support in the original tree, collapsed. These changes, which occurred in parts of the tree that should not have been affected by the corrected sequence, are probably due to minor differences in the methods used to create the two trees, described below.

Note on methods: Analyses were performed in MEGA5 [1], as a GUI version of PAUP* is no longer available. Although the methods were as similar to the original ones as possible, the two programs offer slightly different options. The methods for this tree were as follows:

The evolutionary history was inferred using the Maximum Parsimony (MP) and Maximum Likelihood (ML) methods. Bootstrap consensus trees inferred from 1000 replicates were taken to represent the evolutionary history of the taxa analyzed, and bootstrap values for both methods are shown at each node [2]. The MP tree was obtained using the Tree-Bisection-Regrafting (TBR) algorithm [3] with search level 1 in which the initial trees were obtained by the random addition of sequences (10 replicates). The ML tree was obtained using the Kimura 2-parameter model of nucleotide substitution [4], and initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with superior log likelihood value.The ML tree with the highest log likelihood (-134.1929) was chosen for display. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates using either method were collapsed.

References:

1. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, and Kumar S. (2011). MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution 28: 2731-2739.
2. Felsenstein J. (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
3. Nei M and Kumar S. (2000). Molecular Evolution and Phylogenetics. Oxford University Press, New York.
4. Kimura M. (1980). A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16:111-120.