Abstract
The monogeneric family Dendrobrachiidae has been a taxonomic curiosity since its original description in 1889. Using one nuclear (18S) and two mitochondrial (mtMutS and cox1) genes, the phylogenetic placement of Dendrobrachiidae within the Octocorallia was investigated based on recently-collected specimens and museum collections. In particular, the relationship between Dendrobrachia and its suspected close allies from the Chrysogorgiidae and Ifalukellidae was examined. Phylogenetic inferences based on nuclear 18S sequences were inconclusive. On the basis of mitochondrial cox1 and mtMutS, the hypothesis that Dendrobrachia is closely related to the Chrysogorgiidae or the Ifalukellidae could be rejected with confidence. Dendrobrachia appeared distantly related to all octocoral groups considered here. However, the phylogenetic placement of Dendrobrachia could not be further clearly resolved.
References
Aurelle, D., Ledoux, J.B., Rocher C., Borsa, P., Chenuil, A. & Féral, J.-P. (2011) Phylogeography of the red coral (Corallium rubrum): inferences on the evolutionary history of a temperate gorgonian. Genetica, 139, 855–869. [Epub 2011 Jul 8]
https://doi.org/10.1007/s10709-011-9589-6
Bayer, F.M. (1955) Contributions to the nomenclature, systematics, and morphology of the Octocorallia. Proceedings of the United States National Museum, 105 (3357), 207–220.
https://doi.org/10.5479/si.00963801.105-3357.207
Bayer, F.M. (1964) The genus Corallium (Gorgonacea: Scleraxonia) in the western North Atlantic Ocean. Bulletin of Marine Science, 14 (3), 465–478.
Bayer, F.M. (1996) Three new species of precious coral (Anthozoa: Gorgonacea, genus Corallium) from Pacific waters. Proceedings of the Biological Society of Washington, 109, 205–22
Bayer, F.M. & Muzik, K.M. (1976) New genera and species of the holaxonian family Chrysogorgiidae (Octocorallia: Gorgonacea). Zoologische Me dedelingen, 50 (5), 65–90.
Benayahu, Y., McFadden, C.S. & Shoham, E. (2017) Search for mesophotic octocorals (Cnidaria, Anthozoa) and their phylogeny: I. A new sclerite-free genus from Eilat, northern Red Sea. ZooKeys, (680), 1.
https://doi.org/10.3897/zookeys.680.12727
Berntson, E., Bayer, F., McArthur, A. & France, S.C. (2001) Phylogenetic relationships within the Octocorallia (Cnidaria: Anthozoa) based on nuclear 18S rRNA sequences. Marine Biology, 138, 235–246.
https://doi.org/10.1007/s002270000457
Berntson, E.A., France, S.C. & Mullineaux, L.S. (1999) Phylogenetic relationships within the class Anthozoa (phylum Cnidaria) based on nuclear 18S rDNA sequences. Molecular Phylogenetics and Evolution, 13, 417–433.
https://doi.org/10.1006/mpev.1999.0649
Bilewitch, J.P. & Degnan, S.M. (2011) A unique horizontal gene transfer event has provided the octocoral mitochondrial genome with an active mismatch repair gene that has potential for an unusual self-contained function. BMC Evolutionary Biology, 11, 228.
https://doi.org/10.1186/1471-2148-11-228
de Blainville, H.M.D. (1830) Zoophytes. In Dictionnaire des Sciences naturelles, dans lequel on traite méthodiquement des différents êtres de la nature, 60, 1–546. [Le Normant]
Brook, G. (1889) Report on the Antipatharia collected by HMS Challenger during the years 1873–1876. Report on the Scientific Results of the voyage of the HMS “Challenger 1873–76. London, Edinburgh, Dublin. Zoology, 32, 1–222.
Calderón, I., Garrabou, J. & Aurelle, D. (2006) Evaluation of the utility of COI and ITS markers as tools for population genetic studies of temperate gorgonians. Journal of Experimental Marine Biology and Ecology, 336, 184–197.
https://doi.org/10.1016/j.jembe.2006.05.006
Castresana, J. (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular biology and evolution, 17, 540–552.
https://doi.org/10.1093/oxfordjournals.molbev.a026334
Chernomor, O., von Haeseler, A. & Minh, B.Q. (2016) Terrace aware data structure for phylogenomic inference from supermatrices. Systematic Biology, 65, 997–1008.
https://doi.org/10.1093/sysbio/syw037
Cuvier, G. (1798) Tableau élémentaire de l’histoire naturelle des animaux. Baudoin, Paris, xvi pp.
https://doi.org/10.5962/bhl.title.45918
Daly, M., Brugler, M.R., Cartwright, P., Collins, A.G., Dawson, M.N., Fautin, D.G., France, S.C., McFadden, C.S., Opresko, D., Rodriguez, E., Romano, J.C. & Stake, J.L. (2007) The phylum Cnidaria: a review of phylogenetic patterns and diversity 300 years after Linnaeus. Zootaxa, 1668, 127–182.
Dereeper, A., Guignon, V., Blanc, G., Audic, S., Buffet, S., Chevenet, F., Dufayard, J.F., Guindon, S., Lefort, V., Lescot, M., Claverie, J.M. & Gascuel, O. (2008) Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Research, 1, 36 (Web Server issue), W465-9. [Epub 19 April 2008]
https://doi.org/10.1093/nar/gkn180
Duchassaing, P. & Michelotti, J. (1864) Supplément au mémoire sur les coralliaires des Antilles. Mémoires de l’Académie des Sciences de Turin, Series 2, 23, 97–206.
https://doi.org/10.5962/bhl.title.105196
Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32, 1792–1797.
https://doi.org/10.1093/nar/gkh340
Esper, E.J.C. (1788) Die Pflanzenthiere in Abbildungen nach der Natur mit Farben erleuchtet nebst Beschreibungen. Vol. 2. In der Kaspeschen Buchhandlung, 303 pp.
Fabricius, K.K. & Alderslade, P.P. (2001) Soft corals and sea fans: a comprehensive guide to the tropical shallow water genera of the central-west Pacific, the Indian Ocean and the Red Sea. Australian Institute of Marine Science, Townsville, 264 pp.
Gray, D.J.E. (1857) Synopsis of the families and genera of axiferous zoophytes or barked corals. Proceedings of the Zoological Society of London, 25 (1), 278–294.
https://doi.org/10.1111/j.1096-3642.1857.tb01242.x
Gray, J.E. (1870) Catalogue of Lithophytes Or Stony Corals in the Collection of the British Museum. Printed by order of the Trustees, London, 50 pp.
https://doi.org/10.5962/bhl.title.11307
Herrera, S. & Shank, T.M. (2016) RAD sequencing enables unprecedented phylogenetic resolution and objective species delimitation in recalcitrant divergent taxa. Molecular Phylogenetics and Evolution, 100, 70–79.
https://doi.org/10.1016/j.ympev.2016.03.010
Hickson, S.J. (1904) The Alcyonaria of the Cape of Good Hope. Part II, Marine Investigations in South Africa, 3, 211–239.
Huelsenbeck, J. & Ronquist, F. (2001) MrBayes: Bayesian inference of phylogeny. Bioinformatics, 17, 754–755.
https://doi.org/10.1093/bioinformatics/17.8.754
Kalyaanamoorthy, S., Minh, B.Q., Wong, T.K.F., von Haeseler, A. & Jermiin, L.S. (2017) ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Methods, 14, 587–589.
https://doi.org/10.1038/nmeth.4285
Kölliker, A.V. (1865) Von der erhärteten Bindesubstanz oder den Skelettbildungen der Coelenteraten. Icones histiologicae, oder Atlas der vergleichenden Gewebelehre, 1865, 117–171.
https://doi.org/10.5962/bhl.title.82233
de Lacaze-Duthiers, H. (1897) Faune du golfe du Lion: coralliaires, zoanthaires, sclérodermés Coralliaires. Zoanthaires Sclerodermas. Archives de Zoologie Expérimentale et Générale, 1897, 3.
Lamarck, J.D. (1816) Histoire naturelle des Animaux sans Vertèbres précédée d’une introduction offrant la détermination des caractères essentiels de l’animal, sa distinction du végétal et des autres corps naturels, enfin, exposition des principes fondamentaux de la zoologie. Verdiére, Libraire, Quai des Augustins, París, 270 pp.
https://doi.org/10.5962/bhl.title.5086
Lamouroux, J.V.F. (1812) Extrait d’un mémoire sur la classification des polypiers coralligènes non entièrement pierreux. Nouveaux Bulletin des Sciences, par la Sociét Philomathique de Paris, 3, 181–188
Lanfear, R., Calcott, B., Ho, S.Y. & Guindon, S. (2012) PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution, 29, 1695–1701.
https://doi.org/10.1093/molbev/mss020
Ledoux, J.-B. & Antunes, A. (2018) Beyond the beaten path: improving natural products bioprospecting using an eco-evolutionary framework—the case of the octocorals. Critical Review in Biotechnology, 38,184–198.
https://doi.org/10.1080/07388551.2017.1331335
López-González, P.J. & Cunha, M.R. (2010) Two new species of Dendrobrachia Brook, 1889 (Cnidaria: Octocorallia: Dendrobrachiidae) from the north-eastern Atlantic and western Mediterranean. Scientia Marina, 74, 423–434.
https://doi.org/10.3989/scimar.2010.74n3423
McFadden, C.S., France, S.C., Sánchez, J.A. & Alderslade, P. (2006) A molecular phylogenetic analysis of the Octocorallia (Cnidaria: Anthozoa) based on mitochondrial protein-coding sequences. Molecular Phylogenetics and Evolution, 41, 513–527.
https://doi.org/10.1016/j.ympev.2006.06.010
McFadden, C.S. & van Ofwegen, L.P. (2012). Stoloniferous octocorals (Anthozoa, Octocorallia) from South Africa, with descriptions of a new family of Alcyonacea, a new genus of Clavulariidae, and a new species of Cornularia (Cornulariidae). Invertebrate Systematics, 26 (4), 331–356.
https://doi.org/10.1071/IS12035
McFadden, C.S. & Van Ofwegen, L.P. (2013) Molecular phylogenetic evidence supports a new family of octocorals and a new genus of Alcyoniidae (Octocorallia, Alcyonacea). ZooKeys, 346, 59–83.
https://doi.org/10.3897/zookeys.346.6270
Milne-Edwards, H. (1857) Histoire naturelle des coralliaires ou polypes proprement dits, vol. 1, 2: Paris. Librairie Encyclopédique de Roret, VIII (1), 326.
https://doi.org/10.5962/bhl.title.11396
Nguyen L.-T., Schmidt, H.A., von Haeseler, A. & Minh, B.Q. (2014) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution, 32, 268–274.
https://doi.org/10.1093/molbev/msu300
Okonechnikov, K., Golosova, O., Fursov, M. & Ugene Team (2012) Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics, 28 (8), 1166–1167.
https://doi.org/10.1093/bioinformatics/bts091
Opresko, D.M. & Bayer, F.M. (1991) Rediscovery of the enigmatic coelenterate Dendrobrachia (Octocorallia: Gorgonacea) with description of two new species. Transaction of the Royal Society of Sciences Australia, 115, 1–19.
Pallas, P.S. (1766) Elenchus zoophytorum sistens generum adumbrations generaliores et specierum cognitarum succintas descriptiones, cumselectis auctorum. Apud Petrum van Cleef Hagae-Comitum, 1766, 1–451.
https://doi.org/10.5962/bhl.title.6595
Pante, E., France, S.C., Couloux, A., Cruaud, C., McFadden, C.S., Samadi, S. & Watling, L. (2012) Deep-Sea Origin and In-Situ Diversification of Chrysogorgiid Octocorals. PLoS ONE, 7 (6), e38357.
https://doi.org/10.1371/journal.pone.0038357
Pante, E., Abdelkrim, J., Viricel, A., Gey, D., France, S.C., Boisselier, M.C. & Samadi, S. (2015) Use of RAD sequencing for delimiting species. Heredity, 114, 450–459.
https://doi.org/10.1038/hdy.2014.105
Pont-Kingdon, G., Okada, N.A., Macfarlane, J.L., Beagley, C.T., Watkins-Sims, L.D., Cavalier-Smith, T., Clark-Walker, G.D. & Wolstenholme, D.R. (1998) Mitochondrial DNA of the coral Sarcophyton glaucum contains a gene for a homologue of bacterial MutS: a possible case of gene transfer from the nucleus to the mitochondrion. Journal of Molecular Evolution, 46, 419–431.
https://doi.org/10.1007/PL00006321
Quattrini, A.M., Faircloth, B.C., Dueñas, L.F., Bridge, T.C.L., Brugler, M.R., Calixto-Botía, I.F., DeLeo, D.M., Forêt, S., Herrera, S., Lee, S.M.Y., Miller, D.J., Prada, C., Rádis-Baptista, G., Ramírez-Portilla, C., Sánchez, J.A., Rodríguez, E. & McFadden, C.S. (2018) Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long-standing problems. Molecular Ecology Resources, 18 (2), 281–295.
https://doi.org/10.1111/1755-0998.12736
Rambaut, A. (2012) FigTree. Version 1.4. Available from: http://tree.bio.ed.ac.uk/software/figtree/ (accessed 20 June 2019)
Ronquist, F. & Huelsenbeck, J.P. (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572–1574.
https://doi.org/10.1093/bioinformatics/btg180
Sánchez, J., McFadden, C., France, S.C. & Lasker, H. (2003) Molecular phylogenetic analyses of shallow-water Caribbean octocorals. Marine Biology, 142, 975–987.
https://doi.org/10.1007/s00227-003-1018-7
Sartoretto, S. (2012) New records of Dendrobrachia bonsai (Octocorallia: Gorgonacea: Dendrobrachiidae) in the western Mediterranean Sea. Marine Biodiversity Records, 5 (e7), 1–4.
https://doi.org/10.1017/S175526721100114X
Strychar, K.B., Hamilton, L.C., Kenchington, E.L. & Scott, D.B. (2005) Genetic circumscription of deep-water coral species in Canada using 18S rRNA. In: Freiwald, A.R. & Roberts, J.M. (Eds.), Cold-water corals and ecosystems. Springer publisher, Berlin Heidelberg, pp. 679–690.
https://doi.org/10.1007/3-540-27673-4_34
Thomson, J.A. (1910) Note On Dendrobrachia fallax Brook, A Rare And Remarkable Antipatharian. Journal of Microscopy, 30, 142–143.
https://doi.org/10.1111/j.1365-2818.1910.tb01708.x
Tu, T.H., Dai, C.F. & Jeng, M.S. (2015) Phylogeny and systematics of deep-sea precious corals (Anthozoa: Octocorallia: Coralliidae). Molecular Phylogenetics and Evolution, 84, 173–184.
https://doi.org/10.1016/j.ympev.2014.09.031
van Beneden, E. (1897) Les Anthozoaires de la «Plankton-Expédition,. Résultats de la “Plankton-Expedition» der Humboldt-Stiftung, 2, 1–222.
https://doi.org/10.1080/00222930903359669
van Ofwegen, L.P. & McFadden, C.S. (2009) A new family of octocorals (Anthozoa: Octocorallia) from Cameroon waters. Journal of Natural History, 44 (1–2), 23–29.
https://doi.org/10.3897/zookeys.462.8533
van Ofwegen, L.P., Aurelle, D. & Sartoretto, S. (2014) A new genus of soft coral (Cnidaria, Octocorallia) from the Republic of Congo (Pointe-Noire Region). ZooKeys, 469, 1–10.
Verrill, A.E. (1883) Report on the Anthozoa, and on some additional species dredged by the «Blake» in 1877- 1879, and by the U. S. Fish Commission Steamer «Fish Hawk» in 1880-82. Bulletin of the Museum of Comparative Zoology Harvard, 11, 1–72.
Verrill, A.E. (1869) Critical remarks on the halcyonoid polyps with descriptions of new species in the museum of Yale College 4. American Journal of Science and Arts, 2 (48), 419–429.
https://doi.org/10.2475/ajs.s2-48.143.244
Vollmer, S.V. & Palumbi, S.R. (2004) Testing the utility of internally transcribed spacer sequences in coral phylogenetics. Molecular Ecology, 13, 2763–2772.
https://doi.org/10.1111/j.1365-294X.2004.02265.x
Watling, L., France, S.C., Pante, E. & Simpson, A. (2011) Biology of Deep-Water Octocorals. Advances in Marine Biology, 60, 41–122.
https://doi.org/10.1016/B978-0-12-385529-9.00002-0