Patterns of genetic structure among Hawaiian corals of the genus Pocillopora yield clusters of individuals that are compatible with morphology

Six variable sequence markers are developed and analyzed to find out species boundaries in Hawaiian corals of the genus Pocillopora: the putative mitochondrial control region; a recently discovered, hypervariable mitochondrial open reading frame; the internal transcribed spacer 2 (ITS2), located in the nuclear ribosomal DNA; three nuclear introns of calmodulin, elongation factor- 1 alpha and the ATP synthase beta subunit. Using the first two markers, we identify five distinct mitochondrial lineages and these lineages are compatible with morphology. The situation is more complex with nuclear markers since more than two haplotypes are observed in some individuals. To detect clusters of individuals, haplotype networks are constructed with additional connections drawn between co-occurring haplotypes to delineate potential fields for recombination: few clusters of nuclear haplotypes are found to correspond to clusters of individuals, but those that are detected (mostly in the ITS2 dataset) are also compatible with morphology.