Gene expression during sea urchin development reflects known phylogenetic relationships between species.

<p>(<b>A</b>) Our study includes three sea urchin species: the sister species <i>H</i>. <i>tuberculata</i> (planktotroph) and <i>H</i>. <i>erythrogramma</i> (lecithotroph), which diverged approximately 5 Myr, and an outgroup species <i>L</i>. <i>variegatus</i> (planktotroph), which diverged approximately 35–45 Myr ago [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002391#pbio.1002391.ref044" target="_blank">44</a>, <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002391#pbio.1002391.ref050" target="_blank">50</a>]. (<b>B</b>) Our developmental time course includes seven stages across each species, from unfertilized eggs to early larvae. (<b>C</b>) Principal component (PC) analysis of gene expression (S1 Data). PC1 explains 36% of the overall variation and clearly separated early (egg through 32-cell stage) from later developmental stages (blastula through early larva), whereas PC2 separated <i>L</i>. <i>variegatus</i> from the two <i>Heliocidaris</i> species, corresponding to their phylogenetic relationships.</p>