Expression levels of <i>spvA</i> (black bars), <i>mgtA</i> (light grey bars) and <i>rpoS</i> (dark grey bars) in the StpA(E42Del) and the PhoQ(L13Q) mutant relative to wild type levels.

<p>All expression levels are relative to the <i>dnaE</i> mRNA levels in each RNA sample. Error-bars are SEM.</p

Competitive indexes of reconstructed and parental mutants.

<p>Competitive indexes of reconstructed and parental mutants.</p

Strains of <i>S. typhimurium</i> used in this study.

<p>Strains of <i>S. typhimurium</i> used in this study.</p

Motility testing on motility agar.

<p>A) Illustrating how motility is scored on motility agar. Motility is scored on a 5 step scale where (−) is non-motile and+++is fully motile. B) Motility and phase variation of wild type and evolved Salmonella typhimurium strains. FljBA^ON cells expressing <i>fljB</i> type of flagellum and FljBA^OFF cells expressing <i>fliC</i> type of flagellum. Percentage indicates the fraction of cells (based on whole-genome sequencing) in mouse-adapted population that were in FljBA^ON state.</p

SNP Discovery in New North American <i>Y. pestis</i> Genome Sequences.

<p>The number of strain-specific newly identified SNPs relative to CO92 is plotted for each isolate. Previously sequenced strains are indicated by shaded bars with the location of origin and the number of strains showing identical genotypes in parentheses. ^* Number of newly identified SNPs described in references <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031604#pone.0031604-Touchman1" target="_blank">[10]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031604#pone.0031604-Auerbach1" target="_blank">[11]</a>.</p

Genetic Diversity of the 2009 Plague Isolates.

<p>Distribution of mutations through the 2009 isolates. Mutations relative to the parent strain (CO92) are indicated by black squares. Grey squares indicate that the mutation was not called automatically but was evident by manual inspection of the assembly. Mutation 31 from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031604#pone-0031604-t002" target="_blank">Table 2</a> is not shown nor incorporated into the phylogeny as it is an expansion of a 10 bp repeating sequence.</p

Identification of New IS Element Insertion Points in 2009 Strains.

<p><b>A</b>) Locations of new IS element insertions. IS element insertions were identified in templated assembly experiments using CO92 as a reference. New insertion points were identified using Newbler's 454HCStructVars.txt file and the identity of the newly inserted element was determined by BLAST analysis of sequence reads containing novel junctions. Shaded square indicates the presence of an IS element beginning at the indicated nucleotide position. <b>B</b>) Phylogenetic analysis of 2009 strains using Maximum Likelihood method. Each insertion was treated as a single character. <b>C</b>) Phylogenetic analysis using Maximum Parsimony method.</p

IS Element Variation Between Strains.

<p>*<i>pldA/IS100</i> chimeric reads are present in a subset of 25% of reads that map to this position (See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031604#pone.0031604.s002" target="_blank">Figure S2</a>). The remainder of the reads corresponded to an intact <i>pldA</i> gene.</p

Phylogenetic Analysis of 2009 Plague Isolates.

<p>The phylogenies of the 2009 isolates were inferred from MLVA data (Panels A and B) or the SNP/Indel data (panels C and D). In all cases, the Pestoides F strain was utilized as an outgroup. <b>Panels A and B</b>: Reconstruction of relationships from MLVA data. (<b>A</b>) Neighbor Joining Analysis of MLVA data. Numbers above branches represent NJ analysis bootstrap proportions, greater than 50%, based on 1000 replications; numbers below branches represent MP analysis bootstrap support. (<b>B</b>) Maximum Parsimony analysis. Numbers above branches represent bootstrap proportions, greater than 50%, based on 1000 replications; numbers below branches represent Majority Rule consensus values. <b>Panels C and D</b>: Phylogenetic analysis using newly identified SNPs/Indels using the (<b>C</b>) Maximum Likelihood method. The tree with the highest log likelihood (−411.0996) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. (<b>D</b>) Phylogenetic analysis using the Maximum Parsimony method. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. Additional details for the methods employed in phylogenetic reconstructions can be found in Materials and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031604#s2" target="_blank">Methods</a>.</p

New Mexico is a Portion of the Enduring North American Plague Focus.

<p>Highly virulent <i>Yersinia pestis</i> can be found among numerous rodent and animal hosts, occasionally infecting humans and their pets when they come into contact with infected animals or fleas. Samples were chosen for sequencing to represent examples coming from each broad geographic region. Common hosts include squirrels, cats, prairie dogs (<i>Cynomys gunnissoni</i>) and rabbits (<i>Sylvilagus audubonii</i>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031604#pone.0031604-Perry1" target="_blank">[3]</a>. Sequenced isolates are shown with red markers; other cases with green markers (Location map on right). Locations of isolation of strains were mapped using Google Earth®. Source: New Mexico State Dept. of Public Health <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031604#pone.0031604-New1" target="_blank">[32]</a>.</p