Octocorals are among the largest and most diverse invertebrates on seamounts and in deep water but most of their systematics remains misunderstood. Molecular studies have produced new insights at higher levels. Unfortunately, most DNA sequences from both mitochondrial and nuclear genes
have exhibited much conservation, preventing their use for closely related species. The internal transcribed spacers (ITSs) from the nuclear ribosomal-DNA have shown considerable variation among octocorals, and the ITS2 sequence has turned out to be a promising region. Here we provide new
sequences and predicted RNA secondary structures for the ITS2 of fourteen octocorals. The sequences exhibited the highly conserved six-helicoidal ring-model structure found in yeast, insects, and vertebrates. A molecular morpho-metrics approach of 14 octocoral species produced 49 characters
and 15 equally parsimonious trees. Consensus trees retained most of the relationships found with conserved mtDNA sequences. For instance, the node grouping Alaskagorgia aleutiana Sanchez and Cairns, 2004 with Muricea muricata (Pallas, 1766) was highly supported, which comprises
independent support for the placement of this recently described deep-water species with the Plexauridae, in spite of having poor affinities according to morphology. Molecular morphometrics skips the issue of dealing with multiple insertions and deletions, and saturation in the primary information
from sequence alignments. Nonetheless, the reliability and phylogenetic signal of ITS2 is better for intrageneric studies.
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