An alternative to ITS, a hypervariable, single-copy nuclear intron in corals, and its use in detecting cryptic species within the octocoral genus Carijoa

Here we report a highly variable nuclear marker that can be used for both soft and stony corals. Primers that amplify a ∼177 bp fragment from the nuclear gene encoding the 54 kDa subunit of the signal recognition particle (SRP54) were developed for the octocoral genus Carijoa. Cloning results from 141 individuals suggest that this hypervariable nuclear locus is a single-copy gene. Sequencing revealed a potential cryptic species previously thought to be Carijoa riisei. Results from an Analysis of Molecular Variance (AMOVA) based on mitochondrial DNA (mtDNA) explained <10% of the variation between Atlantic and Pacific samples of C. riisei (F _st = 0.47), whereas the same comparison with SRP54 explained >33% of the variation (F _st = 0.54). Using previously reported degenerate primers for SRP54, high levels of sequence variation were found at this locus across both scleractinian and octocorals. For example, pairwise sequence divergence within octocorals was ∼8–13 times greater with SRP54 than with mtDNA, and, up to 2.8% pairwise sequence divergence was found in SRP54 among individuals of Pocillopora whereas no variation at all was found in mtDNA markers. This case study with the octocoral C. riisei shows that variation in SRP54 appears sufficient to address questions of phylogeography as well as systematics of closely related species.