1 3 Mar Biol DOI 10.1007/s00227-014-2396-8 ORIGINAL PAPER Molecular phylogeny and DNA barcoding of tropical eastern Pacific shallow-water gorgonian octocorals Sergio Vargas · Hector M. Guzman · Odalisca Breedy · Gert Wörheide Received: 3 December 2012 / Accepted: 16 January 2014 © Springer-Verlag Berlin Heidelberg 2014 Pacific octocorals remain poorly studied. Here, using par- tial mitochondrial MutS and igr1-COI sequences, we pro- vide a phylogenetic assessment of a broad sample of east- ern Pacific shallow-water octocorals and investigate their phylogenetic relationships with Caribbean gorgonians. We corroborate the monophyly of Pacifigorgia, Leptogorgia and Eugorgia and provide evidence of a close relation- ship between Swiftia and Psammogorgia, currently placed in Plexauridae. In addition, the phylogenies obtained here provide insights into the historical biogeography and phy- logenetic diversity of the eastern Pacific octocoral assem- blages and on character evolution among this diverse faunal assemblage. Finally, we evaluate the classification power of DNA barcoding for identifying species of shallow-water eastern Pacific octocorals and assess the use of a nuclear intron (SRP54) to supplement traditional mitochondrial barcodes in this group of organisms. Introduction Gorgonian octocorals (Cnidaria: Octocorallia: Alcyonacea) are conspicuous members of the tropical eastern Pacific marine ecosystems (Guzman et al. 2004; Breedy and Guz- man 2005a). Seven genera in three families occur along the geo-morphologically diverse coastal environments of the region, from Baja California to Peru, where they typically live associated with high-energy habitats (Breedy and Guz- man 2003a, b). In contrast to Caribbean octocorals, the sys- tematics of most eastern Pacific gorgonian genera (Fig. 1) was unclear until recently. A number of taxonomic contri- butions have clarified the status of the species-rich genera Pacifigorgia (Breedy and Guzman 2002) and Leptogorgia (Breedy and Guzman 2007) and the less diverse Eugorgia and Heterogorgia (Breedy et al. 2009; Breedy and Guzman Abstract The octocoral fauna inhabiting the shallow waters (<50 m) of the eastern Pacific has been the subject of renewed interest, and the taxonomy of the most impor- tant genera in the region has been reviewed and clari- fied. Many new species have been described, significantly increasing the known biological diversity of the region. Despite their importance as potential sister-groups of Car- ibbean octocorals, the phylogenetic relationships of eastern Communicated by C. Riginos. Electronic supplementary material The online version of this article (doi:10.1007/s00227-014-2396-8) contains supplementary material, which is available to authorized users. S. Vargas (*) · G. Wörheide Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universtität München, Richard-Wagner Str. 10, 80333 Munich, Germany e-mail: s.vargas@lrz.uni-muenchen.de; sergio.vargas@lmu.de H. M. Guzman · O. Breedy Smithsonian Tropical Research Institute, P.O. Box 0843-03092, Panama, Republic of Panama O. Breedy Centro de Investigación en Ciencias del Mar y Limnología, Universidad de Costa Rica, San José, Costa Rica O. Breedy Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San José, Costa Rica G. Wörheide Bavarian State Collections of Palaeontology and Geology, Richard-Wagner Str. 10, 80333 Munich, Germany G. Wörheide GeoBio-Center, LMU, Richard-Wagner Str. 10, 80333 Munich, Germany