Efficacy of the 28S rDNA barcode in differentiating Caribbean octocorals

The ecological landscape of Caribbean reefs is rapidly changing as octocorals fill the void left by declining scleractinian populations. Effective molecular barcodes are necessary to accurately identify these octocorals and monitor this shifting ecosystem. We tested the efficacy of the <i>28S rDNA</i> as a barcode compared to the most commonly used <i>mtMutS</i> barcode on a collection of octocorals from across the Caribbean. Based on pairwise genetic distance values, <i>28S</i> appeared to be more effective at differentiating species within the families Plexauridae and Gorgoniidae, while <i>mtMutS</i> was slightly more effective at distinguishing species of Pterogorgiidae. However, the standard <i>28S</i> rDNA primers did not amplify all species as effectively as <i>mtMutS</i>, especially those belonging to the genus <i>Eunicea</i>. A shorter <i>28S</i> barcode developed for eDNA applications distinguished species as effectively as the complete <i>28S</i> barcode.