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

(A) Our study includes three sea urchin species: the sister species H. tuberculata (planktotroph) and H. erythrogramma (lecithotroph), which diverged approximately 5 Myr, and an outgroup species L. variegatus (planktotroph), which diverged approximately 35–45 Myr ago [44, 50]. (B) Our developmental time course includes seven stages across each species, from unfertilized eggs to early larvae. (C) 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 L. variegatus from the two Heliocidaris species, corresponding to their phylogenetic relationships.