Comparative clustering strategy reveals cases of expression profile conservation and change within a phylogenetic framework.

<p><b>(A)</b> Cluster centroids identified in the outgroup <i>L</i>. <i>variegatus</i> are shown (S2 Data), along with the number of genes in each species that were assigned to a given cluster. Green = <i>L</i>. <i>variegatus</i>, blue = <i>H</i>. <i>tuberculata</i>, and purple = <i>H</i>. <i>erythrogramma</i>. The <i>x</i>-axis represents developmental time, and the <i>y</i>-axis represents expression change. <b>(B)</b> Comparative clustering strategy identifies genes that exhibit the same expression profile among all three species (conservation), differ among all three species (divergence), differ between <i>L</i>. <i>variegatus</i> and the <i>Heliocidaris</i> species (genus-level change), or change specifically along a particular branch of the phylogeny (cluster jump in <i>H</i>. <i>tuberculata</i> or <i>H</i>. <i>erythrogramma</i>). <b>(C)</b> Using a comparative clustering strategy (see 2B and <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002391#sec017" target="_blank">Methods</a>), we characterized expression profile divergence (white, 29.8%), conservation (dark grey, 19.1%), and genus-level change (light grey, 19.8%) across the transcriptome. We also detected branch-specific change in <i>H</i>. <i>tuberculata</i> (blue, 13.5%) and <i>H</i>. <i>erythrogramma</i> (purple, 17.8%) (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002391#pbio.1002391.s010" target="_blank">S1 Table</a>).