<i>Coccidioides</i> growth cycle and study overview.

<p><i>Coccidioides</i> growth cycle in culture (<b>A</b>), total RNA was collected at 96 hours from hyphae and spherules, which were grown at 30°C and 39°C, respectively. Lifecycle in culture illustration adapted from Delgado <i>et al</i>, 2003 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041034#pone.0041034-Delgado1" target="_blank">[11]</a>. Samples were collected in biological triplicate and the results from <i>C. immitis</i> isolate RS and <i>C. posadasii</i> isolate C735 were compared (<b>B</b>).</p

Genes of interest from previous studies.

*<p>Expression ratio: parasitic/saprobic expression. Ratios >1.0 indicate higher expression (up-regulation) in the parasitic phase and ratios <1.0 indicate higher expression (up-regulation) in the saprobic phase.</p>**<p>p-value <0.05.</p

Top 15 genes with significantly higher expression (up-regulated) in the parasitic phase.

*<p>Fold difference is the mean parasitic/saprobic-phase expression level in <i>C. immitis</i> and <i>C. posadasii</i>.</p

Top 15 genes with significantly higher expression (up-regulated) in the saprobic phase.

*<p>Fold difference is the mean saprobic/parasitic-phase expression level in <i>C. immitis</i> and <i>C. posadasii</i>.</p

Differentially expressed genes in <i>C. immitis</i> and <i>C. posadasii</i>.

<p>Venn diagrams showing the number of genes commonly differentially regulated in the saprobic vs. parasitic growth phases of <i>C. immitis</i> and <i>C. posadasii</i>.</p

mRNA expression levels of previously identified vaccine candidates [8].

*<p>Parasitic phase expression levels are normalized by library size and gene length.</p>**<p>Differential regulation: Up H: up-regulated in hyphae (saprobic phase), Up S: up-regulated in spherules (parasitic phase).</p

Median-difference boxplots.

<p>Median-difference boxplots showing the interquartile range (box with median line) of individual counts from the median count for all genes. Plot “whiskers” extend 1.5 times the interquartile range; outlier points are not shown. Ci: <i>C. immitis</i>, Cp: <i>C. posadasii</i>, H: hyphae (saprobic phase), S: spherule (parasitic phase).</p

Appendix A. Sampling protocol, site names, and GPS coordinates for vegetation sampling that estimated the depth of occurrence for Lasthenia lineages occupying vernal pools.

Sampling protocol, site names, and GPS coordinates for vegetation sampling that estimated the depth of occurrence for Lasthenia lineages occupying vernal pools

Appendix B. Extended table summarizing the estimates of phylogenetic signal (Blomberg's K statistic) and tests of significance for niche parameters not included in Table 4.

Extended table summarizing the estimates of phylogenetic signal (Blomberg's K statistic) and tests of significance for niche parameters not included in Table 4