@article {Figueroa2014,
	title = {{Complete mitochondrial genomes elucidate phylogenetic relationships of the deep-sea octocoral families Coralliidae and Paragorgiidae}},
	journal = {Biology and Geology of Deep-Sea Coral Ecosystems: Proceedings of the Fifth International Symposium on Deep Sea Corals},
	volume = {99},
	year = {2014},
	pages = {83{\textendash}91},
	abstract = {In the past decade, molecular phylogenetic analyses of octocorals have shown that the current morphological taxonomic classification of these organisms needs to be revised. The latest phylogenetic analyses show that most octocorals can be divided into three main clades. One of these clades contains the families Coralliidae and Paragorgiidae. These families share several taxonomically important characters and it has been suggested that they may not be monophyletic; with the possibility of the Coralliidae being a derived branch of the Paragorgiidae. Uncertainty exists not only in the relationship of these two families, but also in the classification of the two genera that make up the Coralliidae, Corallium and Paracorallium. Molecular analyses suggest that the genus Corallium is paraphyletic, and it can be divided into two main clades, with the Paracorallium as members of one of these clades. In this study we sequenced the whole mitochondrial genome of five species of Paragorgia and of five species of Corallium to use in a phylogenetic analysis to achieve two main objectives; the first to elucidate the phylogenetic relationship between the Paragorgiidae and Coralliidae and the second to determine whether the genera Corallium and Paracorallium are monophyletic. Our results show that other members of the Coralliidae share the two novel mitochondrial gene arrangements found in a previous study in Corallium konojoi and Paracorallium japonicum; and that the Corallium konojoi arrangement is also found in the Paragorgiidae. Our phylogenetic reconstruction based on all the protein coding genes and ribosomal RNAs of the mitochondrial genome suggest that the Coralliidae are not a derived branch of the Paragorgiidae, but rather a monophyletic sister branch to the Paragorgiidae. While our manuscript was in review a study was published using morphological data and several fragments from mitochondrial genes to redefine the taxonomy of the Coralliidae. Paracorallium was subsumed into Corallium and the genus Hemicorallium was resurrected. This left two disjunct clades as Corallium, making that genus paraphyletic. One of the clades includes the type specimens of Corallium, indicating that clade should remain Corallium. For the other clade, we support the resurrection of the genus Pleurocorallium to fix the paraphyly of Corallium. Based on congruent phylogenies in both studies, the genus Pleurocorallium includes the species C. secundum, C. kishinouyei, C. konojoi, C. elatius, and C. niveum.},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {0967-0645},
	doi = {10.1016/j.dsr2.2013.06.001},
	url = {http://www.sciencedirect.com/science/article/pii/S0967064513002312},
	author = {Figueroa, D F and Baco, A R}
}
@article {Herrera2010,
	title = {{Molecular systematics of the bubblegum coral genera (Paragorgiidae, Octocorallia) and description of a new deep-sea species}},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {55},
	number = {1},
	year = {2010},
	pages = {123{\textendash}135},
	abstract = {Bubblegum octocorals (Paragorgia and Sibogagorgia) play an important ecological role in many deep-sea ecosystems. However, these organisms are currently threatened by destructive fishing methods such as bottom trawling. Taxonomic knowledge of conservation targets is necessary for the creation and implementation of efficient conservation strategies. However, for most deep-sea coral groups this knowledge remains incomplete. For instance, despite its similarities with Paragorgia, Sibogagorgia is particular in lacking polyp sclerites, which are present in groups like Paragorgia and the Coralliidae. Although two kinds of sclerites are very similar between Paragorgia and Sibogagorgia, other characters challenge the monophyly of these genera. Here we help to clarify the taxonomy and evolutionary relationships of the bubblegum octocorals and related taxa by examining molecular data. We employed nucleotide sequences of mitochondrial (ND6, ND6-ND3 intergenic spacer, ND3, ND2, COI, msh1 and 16S) and nuclear (28S and ITS2) genomic regions from several taxa to infer molecular phylogenetics and to examine the correspondence of morphological features with the underlying genetic information. Our data strongly supported the monophyly of the genus Paragorgia, the family Coralliidae (precious corals), and a group of undescribed specimens resembling Sibogagorgia. Further morphological observations were congruent regarding the uniqueness of the undescribed specimens, here defined as a new species, Sibogagorgia cauliflora sp. nov., which occurs in both sides of the North American landmass at depths below 1700 m. This new species resembles S. dennisgordoni with branching in one plane but has fairly different radiate sclerites and significantly divergent DNA sequences. The existence of several diagnostic characters of Sibogagorgia in S. cauliflora indicates that they indeed belong to this genus. It is however remarkable that a small number of medullar canals are also found in this species; medullar canals have been considered as the main diagnostic character of Paragorgia. Thus, the evidence generated here indicates that the presence or absence of these canals per se is not a conclusively diagnostic character for either genus. The lack of internal-node resolution in the inferred phylogenetic hypotheses of these genera does not allow us to propose a clear scenario regarding the evolution of these traits.},
	keywords = {ROV Jason (Remotely Operated Vehicle)},
	issn = {1055-7903},
	doi = {10.1016/j.ympev.2009.12.007},
	url = {http://dx.doi.org/10.1016/j.ympev.2009.12.007},
	author = {Herrera, S and Baco, A R and Sanchez, J A}
}
@article {Fusaro2008,
	title = {{Development and characterization of 12 microsatellite markers from the deep-sea hydrothermal vent siboglinid Riftia pachyptila}},
	journal = {Molecular Ecology Resources},
	volume = {8},
	number = {1},
	year = {2008},
	pages = {132{\textendash}134},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {1755-098X},
	doi = {10.1111/j.1471-8286.2007.01897},
	url = {http://dx.doi.org/10.1111/j.1471-8286.2007.01897},
	author = {Fusaro, A J and Baco, A R and Gerlach, G and Shank, T M}
}
@article {Dahlgren2004,
	title = {{Fauna of whale falls: Systematics and ecology of a new polychaete (Annelida: Chrysopetalidae) from the deep Pacific Ocean.}},
	journal = {Deep-Sea Research. Part I: Oceanographic Research Papers},
	volume = {51},
	number = {12},
	year = {2004},
	pages = {1873{\textendash}1887},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {0967-0637},
	doi = {10.1016/j.dsr.2004.07.017},
	url = {http://dx.doi.org/10.1016/j.dsr.2004.07.017},
	author = {Dahlgren, T and Glover, A G and Baco, A R and Smith, C R}
}
@inbook {Smith2003,
	title = {{The ecology of whale falls at the deep-sea floor}},
	booktitle = {Oceanography and Marine Biology: an Annual Review},
	volume = {41},
	year = {2003},
	pages = {311{\textendash}354},
	publisher = {CRC Press},
	organization = {CRC Press},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	isbn = {0415254639},
	author = {Smith, C R and Baco, A R and Gibson, R N and Atkinson, R J A},
	editor = {Gibson, R N}
}
@article {Baco2003,
	title = {{High species richness in deep-sea chemoautotrophic whale skeleton communities}},
	journal = {Marine Ecology Progress Series},
	volume = {260},
	year = {2003},
	pages = {109{\textendash}114},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {0170-8630},
	doi = {10.3354/meps260109},
	url = {http://dx.doi.org/10.3354/meps260109},
	author = {Baco, A R and Smith, C R}
}
@article {Smith2002,
	title = {{Faunal succession on replicate deep-sea whale falls:time scales and vent-seep affinities}},
	journal = {Cahiers de Biologie Marine},
	volume = {43},
	number = {3-4},
	year = {2002},
	pages = {293{\textendash}297},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {0007-9723},
	url = {http://cbm-online.sb-roscoff.fr/pdf/cb43-3-293-297.pdf},
	author = {Smith, C R and Baco, A R and Glover, A G}
}
@article {Distel2000,
	title = {{Do mussels take wooden steps to deep-sea vents?}},
	journal = {Nature},
	volume = {403},
	number = {6771},
	year = {2000},
	pages = {725{\textendash}726},
	issn = {0028-0836},
	doi = {10.1038/35001667},
	url = {http://dx.doi.org/10.1038/35001667},
	author = {Distel, D L and Baco, A R and Chuang, E and Morrill, W and Cavanaugh, C and Smith, C R}
}
@article {Williams2000a,
	title = {{New species of the genus Paralomis (Decapoda, Anomura, Lithodidae) from a sunken whale carcass in the San Clemente Basin off southern California}},
	journal = {Journal of Crustacean Biology},
	volume = {20},
	number = {Special no. 2},
	year = {2000},
	pages = {281{\textendash}285},
	issn = {0278-0372},
	url = {http://www.jstor.org/stable/1549506},
	author = {Williams, A B and Smith, C R and Baco, A R}
}
@article {Baco1999,
	title = {{The phylogenetic relationships of whale-fall vesicomyid clams based on mitochondrial COI DNA sequences}},
	journal = {Marine Ecology Progress Series},
	volume = {182},
	year = {1999},
	pages = {137{\textendash}147},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {0171-8630},
	doi = {10.3354/meps182137},
	url = {http://dx.doi.org/10.3354/meps182137},
	author = {Baco, A R and Smith, C R and Peek, A S and Roderick, G K and Vrijenhoek, R C}
}
@article {Smith1998a,
	title = {{Sediment community structure around a whale skeleton in the deep Northeast Pacific: Macrofaunal, microbial and bioturbation effects}},
	journal = {Deep-Sea Research. Part II: Topical Studies in Oceanography},
	volume = {45},
	number = {1-3},
	year = {1998},
	pages = {335{\textendash}364},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {0967-0645},
	doi = {10.1016/S0967-0645(97)00043-X},
	url = {http://dx.doi.org/10.1016/S0967-0645(97)00043-X},
	author = {Smith, C R and Maybaum, H L and Baco, A R and Pope, R H and Carpenter, S D and Yager, P L and Macko, S A and Deming, J W}
}
