Curole J, Kocher T. Mitogenomics: digging deeper with complete mitochondrial genomes. Trends Ecol Evol. 1999;14:394–8.
Article
PubMed
Google Scholar
Irisarri I, San Mauro D, Green DM, Zardoya R. The complete mitochondrial genome of the relict frog Leiopelma archeyi: insights into the root of the frog tree of life. Mitochondrial DNA. 2010;21:173–82.
Article
CAS
PubMed
Google Scholar
Duchêne S, Archer FI, Vilstrup J, Caballero S, Morin PA. Mitogenome phylogenetics: the impact of using single regions and partitioning schemes on topology, substitution rate and divergence time estimation. PLoS One. 2011;6, e27138.
Article
PubMed
PubMed Central
Google Scholar
Vilstrup J, Ho S, Foote A, Morin P, Kreb D, Krutzen M, et al. Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae. BMC Evol Biol. 2011;11:65.
Article
PubMed
PubMed Central
Google Scholar
Weisrock DW. Concordance analysis in mitogenomic phylogenetics. Mol Phylogenet Evol. 2012;65:194–202.
Article
PubMed
Google Scholar
Osca D, Templado J, Zardoya R. The mitochondrial genome of Ifremeria nautilei and the phylogenetic position of the enigmatic deep-sea Abyssochrysoidea (Mollusca: Gastropoda). Gene. 2014;547:257–66.
Article
CAS
PubMed
Google Scholar
van Oppen MJH, Catmull J, McDonald BJ, Hislop NR, Hagerman PJ, Miller DJ. The mitochondrial genome of Acropora tenuis (Cnidaria; Scleractinia) contains a large group I intron and a candidate control region. J Mol Evol. 2002;55:1–13.
Article
PubMed
Google Scholar
Chen IP, Tang C-Y, Chiou C-Y, Hsu J-H, Wei N, Wallace C, et al. Comparative analyses of coding and noncoding DNA regions indicate that Acropora (Anthozoa: Scleractinia) possesses a similar evolutionary tempo of nuclear vs. mitochondrial genomes as in plants. Mar Biotechnol. 2009;11:141–52.
Article
CAS
PubMed
Google Scholar
Shearer T, van Oppen M, Romano S, Wörheide G. Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). Mol Ecol. 2002;11:2475–87.
Article
CAS
PubMed
Google Scholar
Hellberg M. No variation and low synonymous substitution rates in coral mtDNA despite high nuclear variation. BMC Evol Biol. 2006;6:24.
Article
PubMed
PubMed Central
Google Scholar
Watanabe T, Nishida M, Watanabe K, Wewengkang D, Hidaka M. Polymorphism in nucleotide sequence of mitochondrial intergenic region in scleractinian coral (Galaxea fascicularis). Mar Biotechnol. 2005;7:33–9.
Article
CAS
PubMed
Google Scholar
Chen C, Dai C-F, Plathong S, Chiou C-Y, Chen C. The complete mitochondrial genomes of needle corals, Seriatopora spp. (Scleractinia: Pocilloporidae): an idiosyncratic atp8, duplicated trnW gene, and hypervariable regions used to determine species phylogenies and recently diverged populations. Mol Phylogenet Evol. 2008;46:19–33.
Article
CAS
PubMed
Google Scholar
Fukami H, Knowlton N. Analysis of complete mitochondrial DNA sequences of three members of the Montastraea annularis coral species complex (Cnidaria, Anthozoa, Scleractinia). Coral Reefs. 2005;24:410–7.
Article
Google Scholar
Flot J-F, Tillier S. The mitochondrial genome of Pocillopora (Cnidaria: Scleractinia) contains two variable regions: the putative D-loop and a novel ORF of unknown function. Gene. 2007;401:80–7.
Article
CAS
PubMed
Google Scholar
Emblem A, Karlsen B, Evertsen J, Johansen S. Mitogenome rearrangement in the cold-water scleractinian coral Lophelia pertusa (Cnidaria, Anthozoa) involves a long-term evolving group I intron. Mol Phylogenet Evol. 2011;61:495–503.
Article
PubMed
Google Scholar
Lin M-F, Luzon KS, Licuanan W, Ablan-Lagman MC, Chen C. Seventy-four universal primers for characterizing the complete mitochondrial genomes of scleractinian corals (Cnidaria; Anthozoa). Zool Stud. 2011;50:513–24.
CAS
Google Scholar
Lin M-F, Kitahara MV, Tachikawa H, Fukami H, Miller DJ, Chen CA. Novel organization of the mitochondrial genome in the deep-sea coral, Madrepora oculata (Hexacorallia, Scleractinia, Oculinidae) and its taxonomic implications. Mol Phylogenet Evol. 2012;65:323–8.
Article
PubMed
Google Scholar
Lin M-F, Kitahara MV, Luo H, Tracey D, Geller J, Fukami H, et al. Mitochondrial Genome Rearrangements in the Scleractinia/Corallimorpharia Complex: Implications for Coral Phylogeny. Genome Biol Evol. 2014;6:1086–95.
Article
PubMed
PubMed Central
Google Scholar
Kitahara MV, Lin M-F, Forêt S, Huttley G, Miller DJ, Chen CA. The “naked coral” hypothesis revisited—evidence for and against scleractinian monophyly. PLoS One. 2014;9, se94774.
Article
Google Scholar
Zibrowius H. Les scléractiniaires de la Méditerranée et de l'Atlantique nordoriental. Mém Inst Océanogr Monaco. 1980;11:284. 107 pl.
Google Scholar
Cairns SD. Antarctic and subantarctic Scleractinia. Antarct Res Ser. 1982;34:1–74.
Article
Google Scholar
Roberts JM, Wheeler A, Freiwald A, Cairns S. Cold-water corals: the biology and geology of deep-sea coral habitats. Cambridge, UK: Cambridge University Press. 2009, 368 pp.
Le Goff-Vitry MC, Rogers AD, Baglow D. A deep-sea slant on the molecular phylogeny of the Scleractinia. Mol Phylogenet Evol. 2004;30(1):167–77.
Article
PubMed
Google Scholar
Addamo AM, Reimer JD, Taviani M, Freiwald A, Machordom A. Desmophyllum dianthus (Esper, 1794) in the scleractinian phylogeny and its intraspecific diversity. PLoS One. 2012;7, e50215.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stolarski J, Kitahara VM, Miller D, Cairns SD, Mazur M, Meibom A. The ancient evolutionary origins of Scleractinia revealed by azooxanthellate corals. BMC Evol Biol. 2011;11:316.
Article
PubMed
PubMed Central
Google Scholar
Stolarski J. Origin and phylogeny of Guyniidae (Scleractinia) in the light of microstructural data. Lethaia. 2000;33(1):13–38.
Article
Google Scholar
Cairns SD. Scleractinia of the temperate north pacific. Smithson Contrib Zool. 1994;557:150.
Google Scholar
Vertino A. Sclerattiniari plio-pleistocenici e attuali del Mediterraneo (sistematica, biostratinomia e paleoecologia). Unpublished PhD thesis. Italy: University of Messina; 2003. p. 306.
Google Scholar
Beuck L, Vertino A, Stepina E, Karolczak M, Pfannkuche O. Skeletal response of Lophelia pertusa (Scleractinia) to bioeroding sponge infestation visualised with micro-computed tomography. Facies. 2007;53:157–76.
Article
Google Scholar
Addamo AM, Martínez-Baraldés I, Vertino A, López-González PJ, Taviani M, Machordom A. Morphological polymorphism of Desmophyllum dianthus over a wide ecological and biogeographic range: stability in deep habitats? Zool Anz. 2015;259:113–30.
Article
Google Scholar
Mortensen PB, Hovland T, Fosså JH, Furevik DM. Distribution, abundance and size of Lophelia pertusa coral reefs in mid-Norway in relation to seabed characteristics. J Mar Biol Assoc U K. 2001;81(4):581–97.
Article
Google Scholar
Rogers A. The biology of Lophelia pertusa (Linnaeus 1758) and other deep-water reef-forming corals and impacts from human activities. Int Rev Hydrobiol. 1999;84:315–406.
Article
Google Scholar
Freiwald A, Beuck L, Rüggerberg A, Taviani M, Hebbeln D. R/V Meteor cruise M70-1 participants. The white coral community in the central Mediterranean Sea revealed by ROV surveys. Oceanogr. 2009;22(1):58–74.
Article
Google Scholar
Vertino A, Spezzaferri S, Rueggeberg A, Stalder C, Wheeler A, and the Eurofleets CWC-Moira cruise scientific party. An overview on cold-water coral ecosystems and facies. In: Spezzaferri S, Rueggeberg A, Stalder C, editors. Atlas of benthic foraminifera from cold-water coral reefs. J Foraminiferal Res, Special Issue. 2015;44:12–19.
Rosso A, Vertino A, Di Geronimo I, Sanfilippo R, Sciuto F, Di Geronimo R, et al. Hard-and soft-bottom thanatofacies from the Santa Maria di Leuca deep-water coral province, Mediterranean. Deep-Sea Res PT II. 2010;57(5):360–79.
Article
Google Scholar
Vertino A, Savini A, Rosso A, Di Geronimo I, Mastrototaro F, Sanfilippo R. Benthic habitat characterization and distribution from two representative sites of the deep-water SML coral province (Mediterranean). Deep-Sea Res PT II. 2010;57(5–6):380–96.
Article
Google Scholar
Taviani M, Colantoni P. Paléobiocoenoses profondes à scléractiniaires sur l’escarpement de Malte-Syracuse (Mer Méditerranée): leur structure, leur âge et leur signification. Oil Gas Sci Technol. 1984;39:547–59.
Google Scholar
Freiwald A, Beuck L, Rüggerberg A, Taviani M, Hellben D, ND R/V Meteor Cruise M70-1 Participants. White coral community. Oceanography. 2009;22(1):58–74.
Article
Google Scholar
Taviani M, Vertino A, López Correa M, Savini A, De Mol B, Remia A, et al. Pleistocene to recent deep-water corals and coral facies in the eastern Mediterranean. Facies. 2011;57(4):579–603.
Article
Google Scholar
Försterra G, Häussermann V. First report on large scleractinian (Cnidaria: Anthozoa) accumulations in cold-temperate shallow water of south Chilean fjords. Zool Verhandel. 2003;345:117–28.
Google Scholar
Cairns SD, Häussermann V, Försterra G. A review of the Scleractinia (Cnidaria: Anthozoa) of Chile, with the description of two new species. Zootaxa. 2005;1018:15–46.
Google Scholar
Rapp H, Sneli J. Lophelia pertusa—myths and reality. In: Abstracts of the 2nd Nordic Marine Science Meeting, Hirtshals, Denmark 2nd–4th March 1999.
Fosså JH, Mortensen PB, Furevik DM. The deep-water coral Lophelia pertusa in Norwegian waters: distribution and fishery impacts. Hydrobiologia. 2002;471:1–12.
Article
Google Scholar
Morrison C, Johnson R, King T, Ross S, Nizinski M. Molecular assessment of deep-sea scleractinian coral biodiversity and population structure of Lophelia pertusa in the Gulf of Mexico. In: Sulak JK, Randall MT, Luke KE, Norem AD, Miller JM, editors. Characterization of northern Gulf of Mexico deepwater hard bottom communities with emphasis on Lophelia coral—Lophelia reef megafaunal community structure, biotopes, genetics, microbial ecology, and geology. New Orleans, LA, USA: USGS Open-File Report; 2008. p. 4.1-4.70.
Morrison C, Eackles M, Johnson R, King T. Characterization of 13 microsatellite loci for the deep-sea coral, Lophelia pertusa (Linnaeus 1758), from the western north Atlantic ocean and gulf of Mexico. Mol Ecol Resour. 2008;8:1037–9.
Article
CAS
PubMed
Google Scholar
Arrigoni R, Vacherie B, Benzoni F, Barbe V. The complete mitochondrial genome of Acanthastrea maxima (Cnidaria, Scleractinia, Lobophylliidae). Mitochondr. DNA. 2014;27(2):927-8.
Addamo AM, García Jiménez R, Taviani M, Machordom A. Development of microsatellite markers in the deep-sea cup coral Desmophyllum dianthus and cross-species amplifications in the Scleractinia order. J Hered. 2015;106(3):322–30.
Article
PubMed
Google Scholar
Cairns SD. The deep-water Scleractinia of the Caribbean Sea and adjacent waters. Stud Fauna Curaçao Caribbean Is. 1979;57(180):341.
Google Scholar
Stolarski J. Ontogenetic development of the thecal structures in Caryophylliine scleractinian corals. Acta Palaeontol Pol. 1995;40:19–44.
Google Scholar
Flot J-F, Dahl M, André C. Lophelia pertusa corals from the Ionian and Barents seas share identical nuclear ITS2 and near-identical mitochondrial genome sequences. BMC Res Notes. 2013;6:144.
Article
PubMed
PubMed Central
Google Scholar
Nei M, Kumar S. Molecular Evolution and Phylogenetics. New York, USA: Oxford University Press. 2000, 333pp.
van Oppen MJH, McDonald BJ, Willis B, Miller DJ. The evolutionary history of the coral genus Acropora (Scleractinia, Cnidaria) based on a mitochondrial and a nuclear marker: reticulation, incomplete lineage sorting, or morphological convergence? Mol Biol Evol. 2001;18:1315–29.
Article
PubMed
Google Scholar
Huang D. Threatened reef corals of the world. PLoS One. 2012;7(3), e34459.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chatrou LW, Escribano MP, Vireul MA, Maas JW, Richardson JE, Hormaza JI. Flanking regions of monomorphic microsatellite loci provide a new source of data for plant species-level phylogenetics. Mol Phylogenet Evol. 2009;53(3):726–33.
Article
CAS
PubMed
Google Scholar
Primmer CR, Møller AP, Ellegren H. A wide-range survey of cross-species microsatellites amplification in birds. Mol Ecol. 2009;5(3):365–78.
Article
Google Scholar
Zardoya R, Vollmer DM, Craddock C, Streelman JT, Karl S, Meyer A. Evolutionary conservation of microsatellite flanking regions and their use in resolving the phylogeny of cichlid fishes (Pisces: Perciformes). P Roy Soc Lond B Biol Sci . 1996;263(1376):1589–98.
Article
CAS
Google Scholar
Estoup A, Tailliez C, Cornuet JM, Solignac M. Size homoplasy and mutational processes of interrupted microsatellites in two bee species, Apis mellifera and Bombus terrestris (Apidae). Mol Biol Evol. 1995;12:1074–84.
CAS
PubMed
Google Scholar
Le Goff MC, Rogers AD. Characterization of 10 microsatellite loci for the deep-sea coral Lophelia pertusa (Linnaeus 1758). Mol Ecol Notes. 2002;2:164–6.
Article
Google Scholar
Kornobis E, Cabellos L, Aguilar F, Frías-López C, Rozas J, Marco J, et al. TRUFA: a USer-friendly Web server for de novo RNA-seq analysis using cluster computing. Evol Bioinform Online. 2015;11:97–104.
Article
PubMed
PubMed Central
Google Scholar
Zuffardi-Comerci R. Corallari-zoantari fossili del Miocene della "collina di Torino". Palaeontogr Ital. 1932;33:85–132.
Google Scholar
Vertino A, Stolarski J, Bosellini FR, Taviani M. Mediterranean corals through time: from Miocene to Present. In: Goffredo S, Dubinsky Z, editors. The Mediterranean Sea: Its history and present challenges, chapter: 14. New York, London: Springer Dordrecht Heidelberg; 2014. p. 257–74.
Budd AF, Romano SL, Smith ND, Barbeitos MS. Rethinking the phylogeny of scleractinian corals: a review of morphological and molecular data. Integr Comp Biol. 2010;50(3):411–27.
Article
PubMed
Google Scholar
Cairns SD. A revision of the shallow-water azooxanthellate Scleractinia of the western Atlantic. Stud Fauna Curacao Caribbean Isl. 2000;75:1–240.
Google Scholar
Käsbauer T, Towb P, Alexandrova O, David CN, Dall’Armi E, Staudigl A, et al. The notch signaling pathway in the cnidarian. Hydra Dev Biol. 2007;303:376–90.
Article
PubMed
Google Scholar
Marlow H, Roettinger E, Boekhout M, Martindale MQ. Functional roles of notch signaling in the cnidarian Nematostella vectensis. Dev Biol. 2012;362:295–308.
Article
CAS
PubMed
Google Scholar
Hemond EM, Kaluziak ST, Vollmer SV. The genetics of colony form and function in Caribbean Acropora corals. BMC Genomics. 2014;15:1133.
Article
PubMed
PubMed Central
Google Scholar
Barbeitos MS, Romano SL, Lasker HR. Repeated loss of coloniality and symbiosis in scleractinian corals. Proc Natl Acad Sci USA. 2010;107(26):11877–82.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ocaña O, Brito A. Balanopsammia wirtzi, a new genus and species of coral (Anthozoa: Scleractinia: Dendrophylliidae) from the cape Verde islands a comparative study with the Mediterranean Cladopsammia rolandi. Rev Acad Canar Cienc. 2013;25(1):87–104.
Google Scholar
Wells JW. Scleractinia. In: Moore RC, editor. Treatise on invertebrate paleontology. Kansas: Geological Society of America and University of Kansas Press; 1956. p. 328–444.
Google Scholar
Veron JEN. Corals of the world. 1–3rd ed. Townsville: Australian Institute of Marine Science; 2000. p. 1382.
Google Scholar
Cairns SD, Kitahara MV. An illustrated key to the genera and subgenera of the recent azooxanthellate Scleractinia (Cnidaria, Anthozoa), with an attached glossary. ZooKeys. 2012;227:1–47.
Article
PubMed
Google Scholar
Benzoni F, Stefani F, Stolarski J, Pichon M, Mitta G, Galli P. Debating phylogenetic relationships of the scleractinian Psammocora, molecular and morphological evidences. Contrib Zool. 2007;76(1):35–54.
Google Scholar
Budd AF, Stolarski J. Corallite wall and septal microstructure in scleractinian reef corals: comparison of molecular clades within the family Faviidae. J Morphol. 2011;272:66–88.
Article
PubMed
Google Scholar
Schmidt-Roach S, Miller KJ, Lundgren P, Andreakis N. With eyes wide open: a revision of species within and closely related to the Pocillopora damicornis species complex (Scleractinia; Pocilloporidae) using morphology and genetics. Zool J Linn Soc Lond. 2014;170:1–33.
Article
Google Scholar
Spezzaferri S, Vertino A, the E-CWC Moira cruise scientific party. Cold-water coral ecosystems from the Moira Mounds (NE Atlantic): affinities and differences with modern and Pleistocene Mediterranean counterparts. RV Belgica, Cruise No. 2012/16, EUROFLEETS—CWC Moira Cruise Unpublished Report. 2012, 30 pp.
De Mol L, Hilário A, Larmagnat S, Henriet JP. Cruise report Belgica 09/14b, Belgica GENESIS, Leg 2 "Pen duick". Gulf of Cadiz, Ghent: Renard Centre of Marine Geology, Ghent University; 2009. 53 pp.
Google Scholar
van Rooij D, Hebbeln D, Comas M, Vandorpe T, Delivet S. MD194 shipboard scientists. EuroFLEETS cruise summary report “MD194 GATEWAY”, Cádiz (ES)-Lisbon (PT). Belgium: Ghent University; 2013. p. 214. 10–21 June 2013.
Google Scholar
D'Onghia G, Savini A, the MAGIC/CoralFISH shipboard party. Cruise unpublished report, Northern Ionian Sea (Santa Maria di Leuca CWC Province). 2010, 32 pp.
Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol. 2000;132:365–86.
CAS
PubMed
Google Scholar
Lowe T, Eddy S. TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25:955–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wyman SK, Jansen RK, Boore JL. Automatic annotation of organellar genomes with DOGMA. Bioinformatics. 2004;20:3252–5.
Article
CAS
PubMed
Google Scholar
Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, et al. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 2013;69:313–9.
Article
PubMed
Google Scholar
Zhang Z, Li J, Zhao X-Q, Wang J, Wong G-S, Yu J. KaKs_calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics. 2006;4:259–63.
Article
CAS
PubMed
Google Scholar
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, et al. Clustal W and Clustal X version 2.0. Bioinformatics. 2007;23:2947–8.
Article
CAS
PubMed
Google Scholar
Rambaut A. Se-Al. Alignment editor. Version 2.0a11. Oxford: University of Oxford; 2002.
Google Scholar
Swofford DL. PAUP*: phylogeny analysis using parsimony (*and other methods). Sunderland, Massachusetts: Sinauer Associated Inc; 2002.
Google Scholar
Miller K, Gunasekera R. Are seamounts isolated islands or stepping stones for oceanic dispersal? A comparison of genetic connectivity and population structure in two deep sea corals. (submitted)
Stolarski J. 3-dimensional micro- and nanostructural characteristics of the scleractinian corals skeleton: a biocalcification proxy. Acta Palaeontol Pol. 2003;48:497–530.
Google Scholar