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I. 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Available:<ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/digital.csic.es\/handle\/10261\/3243?mode=full&submit_simple=Showfullitemrecord\" xlink:type=\"simple\">http:\/\/digital.csic.es\/handle\/10261\/3243?mode=full&amp;submit_simple=Showfullitemrecord<\/ext-link>. Accessed 7 August 2012."},{"key":"ref21","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1007\/BF00392669","article-title":"Nitrogen fixation on a coral reef","volume":"98","author":"AWD Larkum","year":"1988","journal-title":"Marine Biology"},{"key":"ref22","first-page":"381","article-title":"Sur quelques cyanophyc\u00e9es vivant dans le tissu des \u00e9ponges de banyules.Second volume jubilaire Tome 75, p. 331 \u00e0 404. 1er D\u00e9cembre 1933","volume":"75","author":"J Feldmann","year":"1935","journal-title":"Archives de zoologie exp\u00e9rimentale et g\u00e9n\u00e9rale"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1007\/s00248-003-1062-3","article-title":"The biogeography and phylogeny of unicellular cyanobacterial symbionts in sponges from Australia and the Mediterranean","volume":"48","author":"KM Usher","year":"2004","journal-title":"Microb Ecol"},{"key":"ref24","unstructured":"Larkum L (1999) The cyanobacteria of coral reefs. Marine Cyanobacteria. In: Charpy, L, Larkum, AWD (Eds.). Bull I\u2019Inst oceanograph Monaco Num special 19 Monaco Musee Oceanograph, 149\u2013167."},{"key":"ref25","doi-asserted-by":"crossref","first-page":"327","DOI":"10.2216\/i0031-8884-21-3-327.1","article-title":"The ultrastructure of Oscillatoria spongeliae, the blue-green algal endosymbiont of the sponge Dysidea herbacea","volume":"21","author":"RJ Berthold","year":"1982","journal-title":"Phycologia"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"7366","DOI":"10.1128\/AEM.71.11.7366-7375.2005","article-title":"Investigation of Oscillatoria spongeliae-Dominated Bacterial Communities in Four Dictyoceratid Sponges","volume":"71","author":"CP Ridley","year":"2005","journal-title":"Appl Environ Microbiol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1007\/s00227-002-0971-x","article-title":"Host specificity of the symbiotic cyanobacterium Oscillatoria spongeliae in marine sponges,Dysidea spp","volume":"142","author":"RW Thacker","year":"2003","journal-title":"Marine Biology"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"2937","DOI":"10.1111\/j.1365-294X.2008.03808.x","article-title":"Cryptic diversity of the symbiotic cyanobacterium Synechococcus spongiarum among sponge hosts","volume":"17","author":"PM Erwin","year":"2008","journal-title":"Molecular Ecology"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"4431","DOI":"10.1128\/AEM.68.9.4431-4440.2002","article-title":"Molecular Evidence for a Uniform Microbial Community in Sponges from Different Oceans","volume":"68","author":"U Hentschel","year":"2002","journal-title":"Appl Environ Microbiol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1146\/annurev.ecolsys.38.091206.095641","article-title":"Exploring Cyanobacterial Mutualisms","volume":"38","author":"KM Usher","year":"2007","journal-title":"Annu Rev Ecol Evol Syst"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"70","DOI":"10.2307\/1543169","article-title":"Late Larval Development and Onset of Symbiosis in the Scleractinian Coral Fungia scutaria","volume":"196","author":"JA Schwarz","year":"1999","journal-title":"Biol Bull"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1146\/annurev.es.18.110187.002421","article-title":"Intraspecific Phylogeography: The Mitochondrial DNA Bridge Between Population Genetics and Systematics","volume":"18","author":"JC Avise","year":"1987","journal-title":"Annual Review of Ecology and Systematics"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1007\/s00338-009-0554-0","article-title":"Genetic assessment of connectivity in the common reef sponge, Callyspongia vaginalis (Demospongiae: Haplosclerida) reveals high population structure along the Florida reef tract","volume":"29","author":"MB DeBiasse","year":"2010","journal-title":"Coral Reefs"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.ympev.2010.03.030","article-title":"Molecular evidence of cryptic speciation in the \u201ccosmopolitan\u201d excavating sponge Cliona celata (Porifera, Clionaidae)","volume":"56","author":"JR Xavier","year":"2010","journal-title":"Mol Phylogenet Evol"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"e24344","DOI":"10.1371\/journal.pone.0024344","article-title":"Phylogenetic Relationships of the Marine Haplosclerida (Phylum Porifera) Employing Ribosomal (28S rRNA) and Mitochondrial (cox1, nad1) Gene Sequence Data","volume":"6","author":"NE Redmond","year":"2011","journal-title":"PLoS ONE"},{"key":"ref36","unstructured":"Cabioch L (1968) Contribution \u0105 la connaissance de la faune des spongiaires de la Manche occidentale: d\u00e9mosponges de la r\u00e9gion de Roscoff. Cahiers de Biologie marine."},{"key":"ref37","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1007\/s10482-006-9070-1","article-title":"Culturable actinobacteria from the marine sponge Hymeniacidon perleve: isolation and phylogenetic diversity by 16S rRNA gene-RFLP analysis","volume":"90","author":"H Zhang","year":"2006","journal-title":"Antonie Van Leeuwenhoek"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1007\/s10482-008-9270-y","article-title":"Culture-independent nested PCR method reveals high diversity of actinobacteria associated with the marine sponges Hymeniacidon perleve and Sponge sp","volume":"94","author":"Y Xin","year":"2008","journal-title":"Antonie Van Leeuwenhoek"},{"key":"ref39","first-page":"875","article-title":"Phylogenetic diversity of endocellular bacteria marine sponge Hymeniacidon perleve","volume":"46","author":"Y Jin","year":"2006","journal-title":"Wei Sheng Wu Xue Bao"},{"key":"ref40","unstructured":"Ackers RG., Moss D, Picton B. (1992) Sponges of the British Isles (\u2019Sponge V\u2019), a colour guide and working document."},{"key":"ref41","doi-asserted-by":"crossref","first-page":"1896","DOI":"10.1101\/gr.095612.109","article-title":"GenGIS: A geospatial information system for genomic data","volume":"19","author":"DH Parks","year":"2009","journal-title":"Genome Res"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"e2723","DOI":"10.1371\/journal.pone.0002723","article-title":"Seventeen New Complete mtDNA Sequences Reveal Extensive Mitochondrial Genome Evolution within the Demospongiae","volume":"3","author":"X Wang","year":"2008","journal-title":"PLoS ONE"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1080\/10635150590945377","article-title":"Evaluating Intraspecific \u201cNetwork\u201d Construction Methods Using Simulated Sequence Data: Do Existing Algorithms Outperform the Global Maximum Parsimony Approach?","volume":"54","author":"I Cassens","year":"2005","journal-title":"Systematic Biology"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"4127","DOI":"10.1128\/AEM.71.7.4127-4131.2005","article-title":"16S rRNA phylogeny of sponge-associated cyanobacteria","volume":"71","author":"L Steindler","year":"2005","journal-title":"Appl Environ Microbiol"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"67","DOI":"10.2307\/3226942","article-title":"Algal Symbionts in the Tunics of Six New Zealand Ascidians (Chordata, Ascidiacea)","volume":"115","author":"G Lambert","year":"1996","journal-title":"Invertebrate Biology"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1016\/S0003-9365(11)80241-1","article-title":"Fresh-Water Epiphytic Cyanoprokaryotes from Central Mexico.2. Heterogeneity of the Genus Xenococcus","volume":"144","author":"G Montejano","year":"1994","journal-title":"Archiv Fur Protistenkunde"},{"key":"ref47","unstructured":"Wilmotte A (2004) Molecular Evolution and Taxonomy of the Cyanobacteria. In: Bryant DA, editor. The Molecular Biology of Cyanobacteria. Dordrecht: Kluwer Academic Publishers, Vol. 1. 1\u201325. Available:<ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.springerlink.com\/content\/jw7w22r10l477720\/\" xlink:type=\"simple\">http:\/\/www.springerlink.com\/content\/jw7w22r10l477720\/<\/ext-link>. Accessed 24 September 2011."},{"key":"ref48","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1146\/annurev.ecolsys.110308.120206","article-title":"The Ecology and Evolution of Microbes that Manipulate Host Reproduction","volume":"40","author":"J Engelst\u00e4dter","year":"2009","journal-title":"Annu Rev Ecol Evol Syst"},{"key":"ref49","first-page":"185","article-title":"Reproduction of some demosponges in a temperate Australian shallow water habitat","volume":"44","author":"J Fromont","year":"1999","journal-title":"MEMOIRS-QUEENSLAND MUSEUM"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"7912","DOI":"10.1128\/AEM.01148-06","article-title":"Molecular Detection of Epiphytic Acaryochloris spp. on Marine Macroalgae","volume":"72","author":"S Ohkubo","year":"2006","journal-title":"Appl Environ Microbiol"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1038\/383402a0","article-title":"Chlorophyll d as a major pigment","volume":"383","author":"H Miyashita","year":"1996","journal-title":"Nature"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"820","DOI":"10.1038\/433820a","article-title":"Ecology: A niche for cyanobacteria containing chlorophyll d","volume":"433","author":"M Kuhl","year":"2005","journal-title":"Nature"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"e23938","DOI":"10.1371\/journal.pone.0023938","article-title":"Cyanobacterial Diversity and a New Acaryochloris-Like Symbiont from Bahamian Sea-Squirts","volume":"6","author":"S L\u00f3pez-Legentil","year":"2011","journal-title":"PLoS ONE"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"e26806","DOI":"10.1371\/journal.pone.0026806","article-title":"Phylogenetic diversity, host-specificity and community profiling of sponge-associated bacteria in the northern Gulf of Mexico","volume":"6","author":"PM Erwin","year":"2011","journal-title":"PLoS ONE"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1007\/s00227-003-1178-5","article-title":"Low levels of genetic variation in mtDNA sequences over the western Mediterranean and Atlantic range of the sponge Crambe crambe (Poecilosclerida)","volume":"144","author":"S Duran","year":"2004","journal-title":"Marine Biology"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1007\/s00227-005-0134-y","article-title":"Low variation in partial cytochrome oxidase subunit I (COI) mitochondrial sequences in the coralline demosponge Astrosclera willeyana across the Indo-Pacific","volume":"148","author":"G W\u00f6rheide","year":"2006","journal-title":"Marine Biology"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1111\/j.1469-7998.1970.tb02048.x","article-title":"Growth and reproduction of Hymeniacidon perleve (Montagu) (Porifera) in Langstone Harbour Hampshire","volume":"161","author":"AR Stone","year":"2009","journal-title":"Journal of Zoology"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"47","DOI":"10.2174\/1874450801004010047","article-title":"Reproduction of the Intertidal Sponge Hymeniacidon perlevis (Montagu) Along a Bathymetric Gradient","volume":"4","author":"E Gaino","year":"2010","journal-title":"The Open Marine Biology Journal"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"169","DOI":"10.3354\/meps138169","article-title":"Effects of physical factors on larval behavior, settlement and recruitment of four tropical demosponges","volume":"138","author":"M Manuel","year":"1996","journal-title":"Mar Ecol Prog Ser"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1111\/j.1461-0248.2004.00585.x","article-title":"Climate change, genotypic diversity and gene flow in reef-building corals","volume":"7","author":"DJ Ayre","year":"2004","journal-title":"Ecology Letters"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1007\/s10750-008-9295-2","article-title":"Contrasting genetic structure of two Pacific Hymeniacidon species","volume":"603","author":"S Hoshino","year":"2008","journal-title":"Hydrobiologia"},{"key":"ref62","doi-asserted-by":"crossref","unstructured":"Brooks DR, McLennan DA (1991) Phylogeny, Ecology, and Behavior: A Research Program in Comparative Biology. 1st ed. University Of Chicago Press. 441 p.","DOI":"10.2307\/1446122"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1111\/j.1574-6968.2008.01471.x","article-title":"Immunolocalization of the uptake hydrogenase in the marine cyanobacterium Lyngbya majuscula CCAP 1446\/4 and two Nostoc strains","volume":"292","author":"R Seabra","year":"2009","journal-title":"FEMS Microbiol Lett"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"3327","DOI":"10.1128\/AEM.63.8.3327-3332.1997","article-title":"PCR primers to amplify 16S rRNA genes from cyanobacteria","volume":"63","author":"U N\u00fcbel","year":"1997","journal-title":"Appl Environ Microbiol"},{"key":"ref65","first-page":"1399","article-title":"Molecular detection and characterization of specific bacterial groups associated with tropical sponges. Proceedings of the 8th International Coral Reef Symposium, Panama. Vol","volume":"24","author":"MC Diaz","year":"1997"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1111\/j.0014-3820.2005.tb00899.x","article-title":"Fine scale endemism on coral reefs: archipelagic differentiation in turbinid gastropods","volume":"59","author":"CP Meyer","year":"2005","journal-title":"Evolution"},{"key":"ref67","doi-asserted-by":"crossref","unstructured":"Rua CPJ, Zilberberg C, Sole-Cava AM (2011) New Polymorphic Mitochondrial Markers for Sponge Phylogeography. Journal of the Marine Biological Association of the United Kingdom FirstView: 1\u20138. doi:10.1017\/S0025315410002122.","DOI":"10.1017\/S0025315410002122"},{"key":"ref68","first-page":"95","article-title":"BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95\/98\/NT","volume":"41","author":"T Hall","year":"1999","journal-title":"Nucleic Acids Symposium Series"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1093\/oxfordjournals.molbev.a026334","article-title":"Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis","volume":"17","author":"J Castresana","year":"2000","journal-title":"Mol Biol Evol"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1080\/10635150701472164","article-title":"Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments","volume":"56","author":"G Talavera","year":"2007","journal-title":"Syst Biol"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1093\/nar\/27.2.573","article-title":"Tandem repeats finder: a program to analyze DNA sequences","volume":"27","author":"G Benson","year":"1999","journal-title":"Nucleic Acids Res"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1093\/genetics\/105.2.437","article-title":"Evolutionary relationship of DNA sequences in finite populations","volume":"105","author":"F Tajima","year":"1983","journal-title":"Genetics"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"1451","DOI":"10.1093\/bioinformatics\/btp187","article-title":"DnaSP v5: a software for comprehensive analysis of DNA polymorphism data","volume":"25","author":"P Librado","year":"2009","journal-title":"Bioinformatics"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1093\/oxfordjournals.molbev.a026036","article-title":"Median-joining networks for inferring intraspecific phylogenies","volume":"16","author":"HJ Bandelt","year":"1999","journal-title":"Molecular Biology and Evolution"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1007\/BF01732868","article-title":"A graph theoretic approach to the development of minimal phylogenetic trees","volume":"13","author":"LR Foulds","year":"1979","journal-title":"J Mol Evol"},{"key":"ref76","first-page":"406","article-title":"The neighbor-joining method: a new method for reconstructing phylogenetic trees","volume":"4","author":"N Saitou","year":"1987","journal-title":"Mol Biol Evol"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"2731","DOI":"10.1093\/molbev\/msr121","article-title":"MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods","volume":"28","author":"K Tamura","year":"2011","journal-title":"Mol Biol Evol"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1038\/ismej.2009.97","article-title":"Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data","volume":"4","author":"M Hamady","year":"2010","journal-title":"ISME J"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/1748-7188-5-16","article-title":"Jane: a new tool for the cophylogeny reconstruction problem","volume":"5","author":"C Conow","year":"2010","journal-title":"Algorithms Mol Biol"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0051834","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,2,3]],"date-time":"2022-02-03T12:40:07Z","timestamp":1643892007000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0051834"}},"subtitle":[],"editor":[{"given":"Paul J.","family":"Planet","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2012,12,14]]},"references-count":79,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2012,12,14]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0051834","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,12,14]]}}}