Relationship between phylogeny and gene loss.

<p>Strains with their corresponding allele type (AT) and sequence type (ST) are shown in the left columns. Strains were clustered according to their position in the phylogenetic tree as shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046407#pone-0046407-g001" target="_blank">Fig. 1</a>. Colouring of ATs is as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046407#pone-0046407-g001" target="_blank">Fig. 1</a>. DNA loci with corresponding gene designations <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046407#pone.0046407-Parkhill1" target="_blank">[46]</a> are shown in the top row. The two strains used for the Dutch whole cell vaccine, B0005 and B0006, are indicated in the two bottom rows. Absence and presence of DNA loci are indicated by + and −, respectively and deletions showing homoplasy are indicated with asterisks in the top row. Abbreviations: AT, allele type; ST, sequence type; VS, vaccine strain used for the Dutch WCV.