sj-pdf-1-ivi-10.1177_14738716241239018 – Supplemental material for Principal trade-off analysis

Supplemental material, sj-pdf-1-ivi-10.1177_14738716241239018 for Principal trade-off analysis by Alexander Strang, David Sewell, Alexander Kim, Kevin Alcedo and David Rosenbluth in Information Visualization</p

Maximum likelihood phylogenetic tree of 121 <i>L</i>. <i>monocytogenes</i> isolates collected from US dairies.

<p>The displayed phylogeentic tree is based on 166,603 core-genome SNPs identified among the study isolates. The phylogenetic tree was inferred using the General Time Reversible model of nucleotide substitution in RAxML with 100 bootstrap replicates. Bar length represents number of substitutions per site.</p

Frequency of detection for all lineage I clonal complexes.

<p>Frequency of detection for all lineage I clonal complexes.</p

Numbers of isolates, states from which these isolates were recovered, sequence types, clonal complexes (including singletons), virulence types, and epidemic clones (VT epidemic clones) for each lineage represented in this study.

<p>Numbers of isolates, states from which these isolates were recovered, sequence types, clonal complexes (including singletons), virulence types, and epidemic clones (VT epidemic clones) for each lineage represented in this study.</p

Presence/absence of genes associated with virulence among the study isolates.

<p>Blue = detected. Light blue = shorter than the reference gene used in the analysis. Red = not detected. Columns 1 to 62 (at the bottom of the figure) were based on the analysis described by Kuenne et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0197053#pone.0197053.ref047" target="_blank">47</a>] and columns 63 to 76 were based on the analysis described by Maury et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0197053#pone.0197053.ref009" target="_blank">9</a>].</p

Presence/absence of genomic island and pathogenicity islands identified among the study CCs.

<p>Blue = detected. Red = not detected.</p

Frequency of detection for all lineage II clonal complexes.

<p>Frequency of detection for all lineage II clonal complexes.</p

Virulence factors that were more frequently detected in one lineage than the other (lineages I and II).

<p>Virulence factors that were more frequently detected in one lineage than the other (lineages I and II).</p