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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Marine Biodiversity in the Atlantic and Pacific Coasts of South
America: Knowledge and Gaps</title><author><name sortKey="Miloslavich, Patricia" sort="Miloslavich, Patricia" uniqKey="Miloslavich P" first="Patricia" last="Miloslavich">Patricia Miloslavich</name><affiliation><nlm:aff id="aff1"><addr-line>Universidad Simón Bolívar, Departamento de Estudios Ambientales and Centro de Biodiversidad Marina, Caracas, Venezuela</addr-line></nlm:aff></affiliation></author><author><name sortKey="Klein, Eduardo" sort="Klein, Eduardo" uniqKey="Klein E" first="Eduardo" last="Klein">Eduardo Klein</name><affiliation><nlm:aff id="aff1"><addr-line>Universidad Simón Bolívar, Departamento de Estudios Ambientales and Centro de Biodiversidad Marina, Caracas, Venezuela</addr-line></nlm:aff></affiliation></author><author><name sortKey="Diaz, Juan M" sort="Diaz, Juan M" uniqKey="Diaz J" first="Juan M." last="Díaz">Juan M. Díaz</name><affiliation><nlm:aff id="aff2"><addr-line>Universidad Nacional de Colombia, Bogotá, Colombia</addr-line></nlm:aff></affiliation></author><author><name sortKey="Hernandez, Cristian E" sort="Hernandez, Cristian E" uniqKey="Hernandez C" first="Cristián E." last="Hernández">Cristián E. Hernández</name><affiliation><nlm:aff id="aff3"><addr-line>Laboratorio de Diversidad Molecular y Filoinformática, Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile</addr-line></nlm:aff></affiliation></author><author><name sortKey="Bigatti, Gregorio" sort="Bigatti, Gregorio" uniqKey="Bigatti G" first="Gregorio" last="Bigatti">Gregorio Bigatti</name><affiliation><nlm:aff id="aff4"><addr-line>Centro Nacional Patagónico, Patagonian National Center – National Research Council, Puerto Madryn, Chubut, Argentina</addr-line></nlm:aff></affiliation></author><author><name sortKey="Campos, Lucia" sort="Campos, Lucia" uniqKey="Campos L" first="Lucia" last="Campos">Lucia Campos</name><affiliation><nlm:aff id="aff5"><addr-line>Universidade Federal do Rio de Janeiro, Departamento de Zoologia - Instituto de Biologia, Rio de Janeiro, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Artigas, Felipe" sort="Artigas, Felipe" uniqKey="Artigas F" first="Felipe" last="Artigas">Felipe Artigas</name><affiliation><nlm:aff id="aff6"><addr-line>ULCO - Laboratoire d'Océanologie et Géosciences, Université Lille Nord de France, CNRS UMR 8187 LOG, MREN, Wimereux, France</addr-line></nlm:aff></affiliation></author><author><name sortKey="Castillo, Julio" sort="Castillo, Julio" uniqKey="Castillo J" first="Julio" last="Castillo">Julio Castillo</name><affiliation><nlm:aff id="aff1"><addr-line>Universidad Simón Bolívar, Departamento de Estudios Ambientales and Centro de Biodiversidad Marina, Caracas, Venezuela</addr-line></nlm:aff></affiliation></author><author><name sortKey="Penchaszadeh, Pablo E" sort="Penchaszadeh, Pablo E" uniqKey="Penchaszadeh P" first="Pablo E." last="Penchaszadeh">Pablo E. Penchaszadeh</name><affiliation><nlm:aff id="aff7"><addr-line>Museo Argentino de Ciencias Naturales, Buenos Aires, Argentina</addr-line></nlm:aff></affiliation></author><author><name sortKey="Neill, Paula E" sort="Neill, Paula E" uniqKey="Neill P" first="Paula E." last="Neill">Paula E. Neill</name><affiliation><nlm:aff id="aff8"><addr-line>Universidad Católica de la Santísima Concepción, Facultad de Ciencias, Departamento de Ecología Costera, Concepción, Chile</addr-line></nlm:aff></affiliation></author><author><name sortKey="Carranza, Alvar" sort="Carranza, Alvar" uniqKey="Carranza A" first="Alvar" last="Carranza">Alvar Carranza</name><affiliation><nlm:aff id="aff9"><addr-line>Museo Nacional de Historia Natural, Montevideo, Uruguay</addr-line></nlm:aff></affiliation></author><author><name sortKey="Retana, Maria V" sort="Retana, Maria V" uniqKey="Retana M" first="María V." last="Retana">María V. Retana</name><affiliation><nlm:aff id="aff4"><addr-line>Centro Nacional Patagónico, Patagonian National Center – National Research Council, Puerto Madryn, Chubut, Argentina</addr-line></nlm:aff></affiliation></author><author><name sortKey="Diaz De Astarloa, Juan M" sort="Diaz De Astarloa, Juan M" uniqKey="Diaz De Astarloa J" first="Juan M." last="Díaz De Astarloa">Juan M. Díaz De Astarloa</name><affiliation><nlm:aff id="aff10"><addr-line>Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras, National Research Council, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina</addr-line></nlm:aff></affiliation></author><author><name sortKey="Lewis, Mirtha" sort="Lewis, Mirtha" uniqKey="Lewis M" first="Mirtha" last="Lewis">Mirtha Lewis</name><affiliation><nlm:aff id="aff4"><addr-line>Centro Nacional Patagónico, Patagonian National Center – National Research Council, Puerto Madryn, Chubut, Argentina</addr-line></nlm:aff></affiliation></author><author><name sortKey="Yorio, Pablo" sort="Yorio, Pablo" uniqKey="Yorio P" first="Pablo" last="Yorio">Pablo Yorio</name><affiliation><nlm:aff id="aff4"><addr-line>Centro Nacional Patagónico, Patagonian National Center – National Research Council, Puerto Madryn, Chubut, Argentina</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff11"><addr-line>Wildlife Conservation Society, Argentina</addr-line></nlm:aff></affiliation></author><author><name sortKey="Piriz, Maria L" sort="Piriz, Maria L" uniqKey="Piriz M" first="María L." last="Piriz">María L. Piriz</name><affiliation><nlm:aff id="aff4"><addr-line>Centro Nacional Patagónico, Patagonian National Center – National Research Council, Puerto Madryn, Chubut, Argentina</addr-line></nlm:aff></affiliation></author><author><name sortKey="Rodriguez, Diego" sort="Rodriguez, Diego" uniqKey="Rodriguez D" first="Diego" last="Rodríguez">Diego Rodríguez</name><affiliation><nlm:aff id="aff10"><addr-line>Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras, National Research Council, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina</addr-line></nlm:aff></affiliation></author><author><name sortKey="Yoneshigue Valentin, Yocie" sort="Yoneshigue Valentin, Yocie" uniqKey="Yoneshigue Valentin Y" first="Yocie" last="Yoneshigue-Valentin">Yocie Yoneshigue-Valentin</name><affiliation><nlm:aff id="aff5"><addr-line>Universidade Federal do Rio de Janeiro, Departamento de Zoologia - Instituto de Biologia, Rio de Janeiro, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Gamboa, Luiz" sort="Gamboa, Luiz" uniqKey="Gamboa L" first="Luiz" last="Gamboa">Luiz Gamboa</name><affiliation><nlm:aff id="aff12"><addr-line>Universidade Federal Fluminense, Rio de Janeiro, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Martin, Alberto" sort="Martin, Alberto" uniqKey="Martin A" first="Alberto" last="Martín">Alberto Martín</name><affiliation><nlm:aff id="aff1"><addr-line>Universidad Simón Bolívar, Departamento de Estudios Ambientales and Centro de Biodiversidad Marina, Caracas, Venezuela</addr-line></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21304960</idno><idno type="pmc">3031619</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3031619</idno><idno type="RBID">PMC:3031619</idno><idno type="doi">10.1371/journal.pone.0014631</idno><date when="2011">2011</date><idno type="wicri:Area/Pmc/Corpus">000462</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000462</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Marine Biodiversity in the Atlantic and Pacific Coasts of South
America: Knowledge and Gaps</title><author><name sortKey="Miloslavich, Patricia" sort="Miloslavich, Patricia" uniqKey="Miloslavich P" first="Patricia" last="Miloslavich">Patricia Miloslavich</name><affiliation><nlm:aff id="aff1"><addr-line>Universidad Simón Bolívar, Departamento de Estudios Ambientales and Centro de Biodiversidad Marina, Caracas, Venezuela</addr-line></nlm:aff></affiliation></author><author><name sortKey="Klein, Eduardo" sort="Klein, Eduardo" uniqKey="Klein E" first="Eduardo" last="Klein">Eduardo Klein</name><affiliation><nlm:aff id="aff1"><addr-line>Universidad Simón Bolívar, Departamento de Estudios Ambientales and Centro de Biodiversidad Marina, Caracas, Venezuela</addr-line></nlm:aff></affiliation></author><author><name sortKey="Diaz, Juan M" sort="Diaz, Juan M" uniqKey="Diaz J" first="Juan M." last="Díaz">Juan M. Díaz</name><affiliation><nlm:aff id="aff2"><addr-line>Universidad Nacional de Colombia, Bogotá, Colombia</addr-line></nlm:aff></affiliation></author><author><name sortKey="Hernandez, Cristian E" sort="Hernandez, Cristian E" uniqKey="Hernandez C" first="Cristián E." last="Hernández">Cristián E. Hernández</name><affiliation><nlm:aff id="aff3"><addr-line>Laboratorio de Diversidad Molecular y Filoinformática, Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile</addr-line></nlm:aff></affiliation></author><author><name sortKey="Bigatti, Gregorio" sort="Bigatti, Gregorio" uniqKey="Bigatti G" first="Gregorio" last="Bigatti">Gregorio Bigatti</name><affiliation><nlm:aff id="aff4"><addr-line>Centro Nacional Patagónico, Patagonian National Center – National Research Council, Puerto Madryn, Chubut, Argentina</addr-line></nlm:aff></affiliation></author><author><name sortKey="Campos, Lucia" sort="Campos, Lucia" uniqKey="Campos L" first="Lucia" last="Campos">Lucia Campos</name><affiliation><nlm:aff id="aff5"><addr-line>Universidade Federal do Rio de Janeiro, Departamento de Zoologia - Instituto de Biologia, Rio de Janeiro, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Artigas, Felipe" sort="Artigas, Felipe" uniqKey="Artigas F" first="Felipe" last="Artigas">Felipe Artigas</name><affiliation><nlm:aff id="aff6"><addr-line>ULCO - Laboratoire d'Océanologie et Géosciences, Université Lille Nord de France, CNRS UMR 8187 LOG, MREN, Wimereux, France</addr-line></nlm:aff></affiliation></author><author><name sortKey="Castillo, Julio" sort="Castillo, Julio" uniqKey="Castillo J" first="Julio" last="Castillo">Julio Castillo</name><affiliation><nlm:aff id="aff1"><addr-line>Universidad Simón Bolívar, Departamento de Estudios Ambientales and Centro de Biodiversidad Marina, Caracas, Venezuela</addr-line></nlm:aff></affiliation></author><author><name sortKey="Penchaszadeh, Pablo E" sort="Penchaszadeh, Pablo E" uniqKey="Penchaszadeh P" first="Pablo E." last="Penchaszadeh">Pablo E. Penchaszadeh</name><affiliation><nlm:aff id="aff7"><addr-line>Museo Argentino de Ciencias Naturales, Buenos Aires, Argentina</addr-line></nlm:aff></affiliation></author><author><name sortKey="Neill, Paula E" sort="Neill, Paula E" uniqKey="Neill P" first="Paula E." last="Neill">Paula E. Neill</name><affiliation><nlm:aff id="aff8"><addr-line>Universidad Católica de la Santísima Concepción, Facultad de Ciencias, Departamento de Ecología Costera, Concepción, Chile</addr-line></nlm:aff></affiliation></author><author><name sortKey="Carranza, Alvar" sort="Carranza, Alvar" uniqKey="Carranza A" first="Alvar" last="Carranza">Alvar Carranza</name><affiliation><nlm:aff id="aff9"><addr-line>Museo Nacional de Historia Natural, Montevideo, Uruguay</addr-line></nlm:aff></affiliation></author><author><name sortKey="Retana, Maria V" sort="Retana, Maria V" uniqKey="Retana M" first="María V." last="Retana">María V. Retana</name><affiliation><nlm:aff id="aff4"><addr-line>Centro Nacional Patagónico, Patagonian National Center – National Research Council, Puerto Madryn, Chubut, Argentina</addr-line></nlm:aff></affiliation></author><author><name sortKey="Diaz De Astarloa, Juan M" sort="Diaz De Astarloa, Juan M" uniqKey="Diaz De Astarloa J" first="Juan M." last="Díaz De Astarloa">Juan M. Díaz De Astarloa</name><affiliation><nlm:aff id="aff10"><addr-line>Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras, National Research Council, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina</addr-line></nlm:aff></affiliation></author><author><name sortKey="Lewis, Mirtha" sort="Lewis, Mirtha" uniqKey="Lewis M" first="Mirtha" last="Lewis">Mirtha Lewis</name><affiliation><nlm:aff id="aff4"><addr-line>Centro Nacional Patagónico, Patagonian National Center – National Research Council, Puerto Madryn, Chubut, Argentina</addr-line></nlm:aff></affiliation></author><author><name sortKey="Yorio, Pablo" sort="Yorio, Pablo" uniqKey="Yorio P" first="Pablo" last="Yorio">Pablo Yorio</name><affiliation><nlm:aff id="aff4"><addr-line>Centro Nacional Patagónico, Patagonian National Center – National Research Council, Puerto Madryn, Chubut, Argentina</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff11"><addr-line>Wildlife Conservation Society, Argentina</addr-line></nlm:aff></affiliation></author><author><name sortKey="Piriz, Maria L" sort="Piriz, Maria L" uniqKey="Piriz M" first="María L." last="Piriz">María L. Piriz</name><affiliation><nlm:aff id="aff4"><addr-line>Centro Nacional Patagónico, Patagonian National Center – National Research Council, Puerto Madryn, Chubut, Argentina</addr-line></nlm:aff></affiliation></author><author><name sortKey="Rodriguez, Diego" sort="Rodriguez, Diego" uniqKey="Rodriguez D" first="Diego" last="Rodríguez">Diego Rodríguez</name><affiliation><nlm:aff id="aff10"><addr-line>Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras, National Research Council, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina</addr-line></nlm:aff></affiliation></author><author><name sortKey="Yoneshigue Valentin, Yocie" sort="Yoneshigue Valentin, Yocie" uniqKey="Yoneshigue Valentin Y" first="Yocie" last="Yoneshigue-Valentin">Yocie Yoneshigue-Valentin</name><affiliation><nlm:aff id="aff5"><addr-line>Universidade Federal do Rio de Janeiro, Departamento de Zoologia - Instituto de Biologia, Rio de Janeiro, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Gamboa, Luiz" sort="Gamboa, Luiz" uniqKey="Gamboa L" first="Luiz" last="Gamboa">Luiz Gamboa</name><affiliation><nlm:aff id="aff12"><addr-line>Universidade Federal Fluminense, Rio de Janeiro, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Martin, Alberto" sort="Martin, Alberto" uniqKey="Martin A" first="Alberto" last="Martín">Alberto Martín</name><affiliation><nlm:aff id="aff1"><addr-line>Universidad Simón Bolívar, Departamento de Estudios Ambientales and Centro de Biodiversidad Marina, Caracas, Venezuela</addr-line></nlm:aff></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Cruz, M" 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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">21304960</article-id><article-id pub-id-type="pmc">3031619</article-id><article-id pub-id-type="publisher-id">10-PONE-RW-21231R1</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0014631</article-id><article-categories><subj-group subj-group-type="heading"><subject>Review</subject></subj-group><subj-group subj-group-type="Discipline"><subject>Ecology/Community Ecology and Biodiversity</subject><subject>Marine and Aquatic Sciences/Biological Oceanography</subject><subject>Marine and Aquatic Sciences/Conservation Science</subject></subj-group></article-categories><title-group><article-title>Marine Biodiversity in the Atlantic and Pacific Coasts of South
America: Knowledge and Gaps</article-title><alt-title alt-title-type="running-head">South American Marine Diversity</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Miloslavich</surname><given-names>Patricia</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Klein</surname><given-names>Eduardo</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Díaz</surname><given-names>Juan M.</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Hernández</surname><given-names>Cristián E.</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Bigatti</surname><given-names>Gregorio</given-names></name><xref ref-type="aff" rid="aff4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Campos</surname><given-names>Lucia</given-names></name><xref ref-type="aff" rid="aff5"><sup>5</sup></xref></contrib><contrib contrib-type="author"><name><surname>Artigas</surname><given-names>Felipe</given-names></name><xref ref-type="aff" rid="aff6"><sup>6</sup></xref></contrib><contrib contrib-type="author"><name><surname>Castillo</surname><given-names>Julio</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Penchaszadeh</surname><given-names>Pablo E.</given-names></name><xref ref-type="aff" rid="aff7"><sup>7</sup></xref></contrib><contrib contrib-type="author"><name><surname>Neill</surname><given-names>Paula E.</given-names></name><xref ref-type="aff" rid="aff8"><sup>8</sup></xref></contrib><contrib contrib-type="author"><name><surname>Carranza</surname><given-names>Alvar</given-names></name><xref ref-type="aff" rid="aff9"><sup>9</sup></xref></contrib><contrib contrib-type="author"><name><surname>Retana</surname><given-names>María V.</given-names></name><xref ref-type="aff" rid="aff4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Díaz de Astarloa</surname><given-names>Juan M.</given-names></name><xref ref-type="aff" rid="aff10"><sup>10</sup></xref></contrib><contrib contrib-type="author"><name><surname>Lewis</surname><given-names>Mirtha</given-names></name><xref ref-type="aff" rid="aff4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Yorio</surname><given-names>Pablo</given-names></name><xref ref-type="aff" rid="aff4"><sup>4</sup></xref><xref ref-type="aff" rid="aff11"><sup>11</sup></xref></contrib><contrib contrib-type="author"><name><surname>Piriz</surname><given-names>María L.</given-names></name><xref ref-type="aff" rid="aff4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Rodríguez</surname><given-names>Diego</given-names></name><xref ref-type="aff" rid="aff10"><sup>10</sup></xref></contrib><contrib contrib-type="author"><name><surname>Yoneshigue-Valentin</surname><given-names>Yocie</given-names></name><xref ref-type="aff" rid="aff5"><sup>5</sup></xref></contrib><contrib contrib-type="author"><name><surname>Gamboa</surname><given-names>Luiz</given-names></name><xref ref-type="aff" rid="aff12"><sup>12</sup></xref></contrib><contrib contrib-type="author"><name><surname>Martín</surname><given-names>Alberto</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib></contrib-group><aff id="aff1"><label>1</label><addr-line>Universidad Simón Bolívar, Departamento de Estudios Ambientales and Centro de Biodiversidad Marina, Caracas, Venezuela</addr-line></aff><aff id="aff2"><label>2</label><addr-line>Universidad Nacional de Colombia, Bogotá, Colombia</addr-line></aff><aff id="aff3"><label>3</label><addr-line>Laboratorio de Diversidad Molecular y Filoinformática, Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile</addr-line></aff><aff id="aff4"><label>4</label><addr-line>Centro Nacional Patagónico, Patagonian National Center – National Research Council, Puerto Madryn, Chubut, Argentina</addr-line></aff><aff id="aff5"><label>5</label><addr-line>Universidade Federal do Rio de Janeiro, Departamento de Zoologia - Instituto de Biologia, Rio de Janeiro, Brazil</addr-line></aff><aff id="aff6"><label>6</label><addr-line>ULCO - Laboratoire d'Océanologie et Géosciences, Université Lille Nord de France, CNRS UMR 8187 LOG, MREN, Wimereux, France</addr-line></aff><aff id="aff7"><label>7</label><addr-line>Museo Argentino de Ciencias Naturales, Buenos Aires, Argentina</addr-line></aff><aff id="aff8"><label>8</label><addr-line>Universidad Católica de la Santísima Concepción, Facultad de Ciencias, Departamento de Ecología Costera, Concepción, Chile</addr-line></aff><aff id="aff9"><label>9</label><addr-line>Museo Nacional de Historia Natural, Montevideo, Uruguay</addr-line></aff><aff id="aff10"><label>10</label><addr-line>Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras, National Research Council, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina</addr-line></aff><aff id="aff11"><label>11</label><addr-line>Wildlife Conservation Society, Argentina</addr-line></aff><aff id="aff12"><label>12</label><addr-line>Universidade Federal Fluminense, Rio de Janeiro, Brazil</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Thrush</surname><given-names>Simon</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1">National Institute of Water & Atmospheric Research (NIWA), New Zealand</aff><author-notes><corresp id="cor1">* E-mail: <email>Patricia Miloslavich (pmilos@usb.ve)</email></corresp></author-notes><pub-date pub-type="collection"><year>2011</year></pub-date><pub-date pub-type="epub"><day>31</day><month>1</month><year>2011</year></pub-date><volume>6</volume><issue>1</issue><elocation-id>e14631</elocation-id><history><date date-type="received"><day>16</day><month>7</month><year>2010</year></date><date date-type="accepted"><day>4</day><month>1</month><year>2011</year></date></history><permissions><copyright-statement>Miloslavich et al. This is an open-access article distributed under
the terms of the Creative Commons Attribution License, which permits unrestricted
use, distribution, and reproduction in any medium, provided the original author and
source are credited.</copyright-statement></permissions><counts><page-count count="43"></page-count></counts></article-meta></front><body><p>The marine areas of South America (SA) include almost 30,000 km of coastline and
encompass three different oceanic domains—the Caribbean, the Pacific, and the
Atlantic—ranging in latitude from 12°N to 55°S. The 10 countries that
border these coasts have different research capabilities and taxonomic traditions
that affect taxonomic knowledge. This paper analyzes the status of knowledge of
marine biodiversity in five subregions along the Atlantic and Pacific coasts of
South America (SA): the Tropical East Pacific, the Humboldt Current, the Patagonian
Shelf, the Brazilian Shelves, and the Tropical West Atlantic, and it provides a
review of ecosystem threats and regional marine conservation strategies. South
American marine biodiversity is least well known in the tropical subregions (with
the exception of Costa Rica and Panama). Differences in total biodiversity were
observed between the Atlantic and Pacific oceans at the same latitude. In the north
of the continent, the Tropical East Pacific is richer in species than the Tropical
West Atlantic, however, when standardized by coastal length, there is very little
difference among them. In the south, the Humboldt Current system is much richer than
the Patagonian Shelf. An analysis of endemism shows that 75% of the species
are reported within only one of the SA regions, while about 22% of the
species of SA are not reported elsewhere in the world. National and regional
initiatives focusing on new exploration, especially to unknown areas and ecosystems,
as well as collaboration among countries are fundamental to achieving the goal of
completing inventories of species diversity and distribution. These inventories will
allow accurate interpretation of the biogeography of its two oceanic coasts and
latitudinal trends, and will also provide relevant information for science based
policies.</p><sec id="s2"><title>Introduction</title><sec id="s2a"><title>The South American region</title><p>The marine areas of the South American continent extend for almost 30,000 km of
coastline and encompass three different oceanic domains—the Caribbean, the
Pacific, and the Atlantic. The latitudinal and longitudinal ranges within this
region are similarly wide, from 12°N to 55°S, and from 34° to
81°W. Ten countries border on these coasts, each with different research
capabilities and taxonomic traditions; therefore, taxonomic knowledge differs
among countries. Coastal biodiversity is strongly influenced by the physical and
geological history of these coasts. The eastern tropical Pacific region, which
encompasses the continental coasts of southern Central America (Costa Rica and
Panama) and of northwestern South America (Colombia and Ecuador) is
characterized by cliffs alternating with pocket beaches, alluvial and deltaic
plains with extensive sandy beaches, well-developed mangrove forests, estuaries,
lagoons, and, reefs. It also includes important offshore island systems such as
the Pearl and Galapagos islands <xref ref-type="bibr" rid="pone.0014631-Cruz1">[1]</xref>, <xref ref-type="bibr" rid="pone.0014631-Daz1">[2]</xref>. The Peruvian coast also is diverse with bays, cliffs,
kelp and macroalgal beds, rocky shores and sandy beaches, islands, and
peninsulas, as well as wetlands, which include the southernmost limit to the
tropical Pacific mangrove ecosystem <xref ref-type="bibr" rid="pone.0014631-Tarazona1">[3]</xref>, <xref ref-type="bibr" rid="pone.0014631-FernandezBaca1">[4]</xref>. The Chilean coast is
4,500 km of mainly rocky shores, but does include some sandy-beach bays with
channels and archipelagos toward the south (Patagonian region) <xref ref-type="bibr" rid="pone.0014631-Miethke1">[5]</xref>, <xref ref-type="bibr" rid="pone.0014631-Gallardo1">[6]</xref>. Some of
the most diverse ecosystems in Chile are the beds of kelp
(<italic>Lessonia</italic> and <italic>Macrosystis</italic>) and macroalgae
(<italic>Gracillaria</italic> and <italic>Ulva</italic>). The combination of
the unique oceanographic conditions and coastal heterogeneity in the Chilean
coast has resulted in high levels of endemism (near 40%) in many
invertebrate groups <xref ref-type="bibr" rid="pone.0014631-Miethke1">[5]</xref>, and several marine invertebrate taxa show latitudinal
biodiversity patterns, some of them explained by the presence of Antarctic fauna
<xref ref-type="bibr" rid="pone.0014631-Gallardo2">[7]</xref>–<xref ref-type="bibr" rid="pone.0014631-Clarke1">[9]</xref>. Ecuador, Peru, and Chile are under the influence of
the Humboldt upwelling system and subject to high environmental variability
caused by the ENSO (El Niño Southern Oscillation) and LNSO (La
Niña Southern Oscillation), which cause important changes in community
composition and abundance, particularly of the plankton <xref ref-type="bibr" rid="pone.0014631-Cruz1">[1]</xref>, <xref ref-type="bibr" rid="pone.0014631-Escribano1">[10]</xref>.</p><p>The Atlantic coast of the South American continent is distinctly different from
the Pacific coast. It includes three major rivers (Orinoco, Amazon, and La
Plata), which discharge enormous amounts of freshwater and sediment to the
ocean, and the coast has an extensive continental platform. Argentina's
coast has mostly sandy beaches <xref ref-type="bibr" rid="pone.0014631-Gallardo1">[6]</xref>, <xref ref-type="bibr" rid="pone.0014631-Lutz1">[11]</xref> and some rocky formations
located mainly at Mar del Plata and at Peninsula Valdes. At Mar del Plata, these
rocky shores are dominated by two mussel species and by a diverse macroalgal
community with a clear tidal zonation <xref ref-type="bibr" rid="pone.0014631-Negri1">[12]</xref>, <xref ref-type="bibr" rid="pone.0014631-Boschi1">[13]</xref>. The Uruguayan coast is
dominated by sandy beaches with a narrow portion of rocky habitats known to
sustain a rich biological diversity <xref ref-type="bibr" rid="pone.0014631-Calliari1">[14]</xref>. Observed variations in
community composition and distribution may be related to the salinity gradient
caused by La Plata River discharge <xref ref-type="bibr" rid="pone.0014631-Mayta1">[15]</xref>.</p><p>The coast of Brazil, extending almost 7,500 km, is under the influence of the
warm Brazil Current, the cold Malvinas/Falklands Current, and many rivers and
upwelling regions <xref ref-type="bibr" rid="pone.0014631-Prates1">[16]</xref>. The warm northern coast, where the Amazon discharges
into the ocean, is characterized by a combination of freshwater, estuarine, and
marine ecosystems, with diverse but poorly known habitats <xref ref-type="bibr" rid="pone.0014631-Couto1">[17]</xref>. The colder southern coast
is characterized by a variety of ecosystems, including mangrove forests,
seagrass beds, coral reefs, sandy beaches, rocky shores, lagoons, and estuaries.
Because of its vastness, extensive areas of Brazil's coast remain
unexplored. North of Brazil are Suriname, French Guiana, Guyana, and the
Venezuelan Atlantic Front. This area, including about 1,900 km of coastline, is
under the strong influence of the Amazon River. Therefore, the typical
ecosystems are estuaries, mudflats, sandy beaches, and mangrove forests, which
extend along most of the coastline <xref ref-type="bibr" rid="pone.0014631-Artigas1">[18]</xref>. The Venezuelan Atlantic
coast is also under the influence of the Orinoco River, with coastal mudflats
and extensive mangrove forests <xref ref-type="bibr" rid="pone.0014631-Martn1">[19]</xref>.</p><p>In this paper, we analyze the status of knowledge of marine biodiversity in five
subregions along the Atlantic and Pacific coasts of South America. As most of
the information is based in national reports, these subregions were based in the
Large Marine Ecosystem boundaries as defined for South America, with a few
practical adaptations, based in country political borders. The paper also
provides an updated review of ecosystem threats, such as invasive species, and
the marine conservation strategies employed by South American countries with
access to the coast, excluding the Caribbean coasts of Venezuela and Colombia,
as these are included in another paper of this collection <xref ref-type="bibr" rid="pone.0014631-Miloslavich1">[20]</xref>.</p></sec><sec id="s2b"><title>History of research and species discovery in the region</title><p>The first studies of the South American coastal biota were carried out during a
series of expeditions by European and North American researchers in the late
1700s and first half of the 1800s with naturalists Alejandro Malaspina, Roberto
A. Philippi, Alcyde d'Orbigny, Alexander Von Humboldt, Aimé
Bonpland, Charles Darwin, and Henry A. Pilsbry, among others <xref ref-type="bibr" rid="pone.0014631-Scarabino1">[21]</xref>, <xref ref-type="bibr" rid="pone.0014631-DOrbigny1">[22]</xref>. In the
late 1800s, several other important oceanographic expeditions, including the HMS
<italic>Challenger</italic>, collected samples along the coasts of Ecuador,
Peru, Chile, Argentina, Uruguay, and Brazil <xref ref-type="bibr" rid="pone.0014631-Bate1">[23]</xref>. In the 1900s, the Deutsche
Sudpolar Expeditions in 1901–03 <xref ref-type="bibr" rid="pone.0014631-Lenz1">[24]</xref>, the Swedish Lund University
expedition to Chile in 1948–49 <xref ref-type="bibr" rid="pone.0014631-Lenz1">[24]</xref>, the Royal Society Expedition
to Southern Chile <xref ref-type="bibr" rid="pone.0014631-Brattstrm1">[25]</xref>, the Soviet Antarctic Expedition in 1955–58
<xref ref-type="bibr" rid="pone.0014631-Zarenkov1">[26]</xref>,
and the Calypso campaigns in 1961–62 <xref ref-type="bibr" rid="pone.0014631-Haig1">[27]</xref>, <xref ref-type="bibr" rid="pone.0014631-Forest1">[28]</xref> were among the most
significant European expeditions to South America. Other important
campaignsduring the second half of the twentieth century which increased the
knowledge of marine biodiversity and strengthened the local research capacities
were carried out by the R/V <italic>Academik Knipovich</italic> (1967), the R/V
<italic>Almirante Saldanha</italic> (1966), the R/V <italic>Atlantis
II</italic>, (1971), the R/V <italic>El Austral</italic> (1966–67),
the R/V <italic>Vema</italic> (1962), and the R/V <italic>Walther
Herwig</italic> (1966–71). At present, the oceanographic vessel
<italic>Polarstern</italic> from the Alfred Wegener Institute (Germany) has
been carrying out exploration voyages for more than 20 years to the southern
regions of the continent as well as Antarctica.</p><p>In the northern latitudes of the continent, the Tropical Eastern Pacific (TEP)
Biogeographic Region has a rich history of oceanographic and biological
explorations dating back to the voyage of Charles Darwin to the Galapagos aboard
the HMS <italic>Beagle</italic> in 1835 and other scientific expeditions.
However, none of them visited the Pacific mainland shores and shelves of
Colombia and Ecuador. It was the Eastern Pacific Expedition of the U.S National
Museum of Natural History in 1904 aboard the U.S. Fish Commission steamer
<italic>Albatross</italic> that marked the beginning of systematic
oceanographic and biological studies in this region. The
<italic>Albatross</italic> sampled zooplankton and other biological material
in four shallow-water stations along the Colombian shore and nine deep-water
settings off the Panamanian, Colombian, and Ecuadorian coasts. Fish, mollusks,
and jellyfishes, among others, were collected and later described from these
localities <xref ref-type="bibr" rid="pone.0014631-Dall1">[29]</xref>,
<xref ref-type="bibr" rid="pone.0014631-Bigelow1">[30]</xref>,
<xref ref-type="bibr" rid="pone.0014631-Bigelow2">[31]</xref>. A
series of research cruises and expeditions organized by North American
institutions in the first half of the twentieth century contributed greatly to
the knowledge of the marine fauna and flora existing in the rich area between
the low tide mark and 200 m of depth in the Panama Bight, including Panama,
Colombia, and Ecuador. The “Saint George” expedition visited Gorgona
Island in 1927 and collected relevant material of marine organisms, particularly
crustaceans <xref ref-type="bibr" rid="pone.0014631-Garth1">[32]</xref>; the Allan Hancock cruises aboard the
<italic>Velero</italic> III and IV vessels, dating from 1931 to 1941 (see
<xref ref-type="bibr" rid="pone.0014631-Aleem1">[33]</xref>), and
the Askoy Expedition of the American Museum of Natural History in 1941 also
visited and collected material in Panamenian, Colombian, and Ecuadorian waters.
Many new species of fishes, mollusks, polychaetes, crustaceans, and other taxa
were described from material obtained from these cruises <xref ref-type="bibr" rid="pone.0014631-Hertlein1">[34]</xref>, <xref ref-type="bibr" rid="pone.0014631-Haig2">[35]</xref>. A considerable number of
taxonomic and ecological studies have been carried out in the last three decades
in Costa Rica, Panama, Colombia, and Ecuador. However, most of this work has
been geographically concentrated in a few localities such as the Gulf of Nicoya,
the Bay of Panama, the Pearl Islands, the Bay of Buenaventura, Gorgona Island,
and the Gulf of Guayaquil. Important collections or libraries of regional marine
fauna are maintained by the Los Angeles County Museum, the Scripps Institution
of Oceanography at La Jolla, California, the California Academy of Sciences in
San Francisco, and the Smithsonian Tropical Research Institute (STRI) in Panama
City. In the Tropical Western Atlantic (TWA), the natural history of Guyana
(formerly British Guiana) was described by early explorers Sir Walter Raleigh
(circa 1600) and Charles Waterton (early 1800s), who reported his discoveries in
the book <italic>Waterton's Wanderings in South America</italic>, which
served as inspiration to British schoolboys like Charles Darwin and Alfred
Russell Wallace. In French Guiana, the first studies were carried out after
World War II, with fish inventories and later on, in the 1950s, with the benthic
(mostly shrimps) and demersal continental shelf fauna, from 15 to 100 m depth
<xref ref-type="bibr" rid="pone.0014631-Artigas1">[18]</xref>. The
Venezuelan Atlantic Front was until recently almost completely unexplored, and
the little information available concerned commercially valuable species of fish
and shrimp <xref ref-type="bibr" rid="pone.0014631-Martn1">[19]</xref>.</p><p>The local and regional academic community also had significant historic
representatives. Two pioneering figures were the Uruguayan-born (1788)
Dámaso Larrañaga in Uruguay and Argentina, who introduced the
Linnean binomial nomenclature in the continent, and the Argentinean-born (1896)
Irene Bernasconi, who studied the echinoderms. In the 1900s, research in coastal
biodiversity received a strong stimulus due to the immigration of many European
scientists before, during, and after World War II who contributed to knowledge
and capacity building mainly through their involvement in local universities and
natural science museums. Although a few research institutions were established
in the region early in the twentieth century, such as STRI in Panama (1923), the
most important stimulus to regional, autochthonous marine science was given by
the establishment of several marine research institutions, mostly in the 1950s
and 1960s. These institutions include the Instituto Oceanográfico de la
Universidad de Sao Paulo in Brazil (1946), the Montemar Institute of Marine
Biology (1941) founded by the Universidad de Chile and today part of the
Universidad de Valparaíso Faculty of Ocean Sciences, the Instituto de
Biología Marina de Mar del Plata in Argentina (1960, transformed to the
INIDEP in 1977), the Instituto Oceanográfico from the Universidad de
Oriente in Venezuela (∼1960), the Instituto del Mar del Perú
(∼1958), the Colombian Oceanographic Commission (1968), the Colombian
Science Foundation, Colciencias (1968), the departments of marine biology at
universities in Bogotá (1969) and Cali (1973), the Instituto de
Tecnología y Ciencias Marinas in Venezuela (1970), and the Oceanographic
Institute of the Ecuadorian Navy, Inocar (1972), and the Center for Marine
Science and Limnology of the University of Costa Rica (1979). These institutions
changed the way that marine science was done by incorporating into the
traditional taxonomic studies, time series of the environmental variables and
their effect on biodiversity. In the 1960s, the Food and Agriculture
Organization of the United Nations began to develop projects giving an impulse
to fisheries, especially in the southwest Pacific, an upwelling zone of
extraordinary productivity responsible for 20% of the world's
fisheries by the end of that decade. In the 1980s and 1990s, centers for marine
biodiversity research were created along the coasts of several countries,
especially Brazil, Argentina, and Chile. Argentina, developed several
institutions that depend on the national science council CONICET in the
Patagonian region (Puerto Madryn, Ushuaia, and Bahía Blanca), while in
Chile and Brazil, similar institutions are mostly dependent on universities
(e.g., Valdivia and Coquimbo in Chile and FURG, the Federal University of Rio
Grande, in Brazil).</p><p>Access to oceanographic vessels, isolation between researchers, and the lack of
coordination between scientific programs have been an important limitation for
marine research in South America <xref ref-type="bibr" rid="pone.0014631-Ogden1">[36]</xref>. The countries with the best shipping capacities are
Brazil and Chile. The ships are mostly from a national navy or for fisheries
research, and in some instances, access to researchers from other institutions
is restricted. On the other hand, South America has benefited from regional
cooperation. One example is the establishment of a common fishing zone between
Uruguay and Argentina under the academic leadership of the Universidad de la
República in Montevideo and the DINARA (National Direction for Aquatic
Resources) in Uruguay, as well as the network of marine reserves (Red
Iberoamericana de Reservas Marinas). The natural history museums in South
America have been fundamental to preserving the regional marine biodiversity
patrimony both in collections and in literature and are considered to be
taxonomically indispensable. Some of the most relevant museums are the Museo de
La Plata and the Museo Argentino de Ciencias Naturales (Argentina), the Museo de
Historia Natural (Quinta Normal) in Chile, the Museo Dámaso
Larrañaga and the Museo de Historia Natural in Uruguay, and the Museo de
Boa Vista (Brazil). Other collections are held either at research institutions
such as the STRI in Panama, the IMARPE in Peru, the INVEMAR in Colombia, or at
universities, such as the Universidad de San Marcos in Peru and the Universidad
Simón Bolívar in Venezuela.</p></sec><sec id="s2c"><title>Role of the Census of Marine Life in South America</title><p>The activities of the Census of Marine Life (Census) program on the South
American continent began in October 2002 with the First South American Workshop
on Marine Biodiversity held at the University of Concepción in Chile. In
this workshop, most of the South American countries with access to the sea
reviewed the status of knowledge of their marine biodiversity (Venezuela, French
Guyana, Brazil, Uruguay, Argentina, Chile, Peru, Ecuador, and Colombia). These
reviews were compiled as a special issue of the journal <italic>Gayana</italic>in 2003. During this workshop, a regional South American Steering Committee
(SASC) was established with representatives from each of the above-mentioned
countries as well as representatives from OBIS, the Ocean Biogeographic
Information System established by the Census. The main goal of this committee
was to promote in a coordinated and well-organized way the implementation of
marine biodiversity research in the South American region under the umbrella of
the Census program, with particular emphasis on unexplored areas, and to
integrate the regional biodiversity databases into OBIS through the creation of
regional OBIS nodes located in Argentina, Brazil and Chile (<ext-link ext-link-type="uri" xlink:href="http://www.iobis.org/obis/regional-nodes">http://www.iobis.org/obis/regional-nodes</ext-link>). Since 2002, the SASC
has held several workshops, and researchers in the South American region have
engaged in some of the Census projects: the Natural Geography in Shore Areas
(NaGISA), the Census of Antarctic Life (CAML), the Continental Margins
(COMARGE), the International Census of Marine Microbes (ICoMM), and the
Mid-Atlantic Ridge Ecosystem (MAR-ECO) projects.</p><p>All of these projects have contributed significantly to increase the knowledge of
marine biodiversity in the region. In the nearshore, for example, the NaGISA
project has focused on the benthic diversity associated with rocky shores and on
seagrass communities by using a common protocol worldwide. In the Atlantic and
Pacific coasts of South America, four NaGISA sites were established at different
latitudes in Argentina (Puerto Madryn and Mar del Plata), Brazil (Paranagua
Bay), and Ecuador (Santa Elena). From these sites, preliminary data show that
macroalgae and bivalves are the most abundant groups in the intertidal rocky
shores of Argentina, while macroalgae, gastropods, and echinoderms are the most
abundant groups in the intertidal rocky shores of Ecuador. In the seagrasses of
Paranagua Bay in Brazil, polychaetes are the most abundant and diverse group
<xref ref-type="bibr" rid="pone.0014631-Konar1">[37]</xref>, <xref ref-type="bibr" rid="pone.0014631-Miloslavich2">[38]</xref>. In
the deep sea, on the other hand, the COMARGE project has studied the
biodiversity patterns along and across the Chilean margin through a complexity
of ecosystems such as methane seeps and oxygen minimum zones reporting that such
habitat heterogeneity may influence the biodiversity patterns of the local fauna
<xref ref-type="bibr" rid="pone.0014631-Sellanes1">[39]</xref>–<xref ref-type="bibr" rid="pone.0014631-Sellanes3">[41]</xref>. Furthermore, in these
soft reduced sediments below the oxygen minimum zone off the Chilean margin, a
diverse microbial community composed by a variety of large prokaryotes (mainly
large multi-cellular filamentous “mega bacteria” of the genera
<italic>Thioploca</italic> and <italic>Beggiatoa</italic>, and of
“macrobacteria” including a diversity of phenotypes), protists
(ciliates, flagellates, and foraminifers), as well as small metazoans (mostly
nematodes and polychaetes) has been found <xref ref-type="bibr" rid="pone.0014631-Gallardo3">[42]</xref>. These authors argue that
the likely chemolithotrophic metabolism of most of these mega- and macrobacteria
offer an alternative explanation to fossil findings, in particular to those from
obvious non-littoral origins, suggesting that traditional hypotheses on the
cyanobacterial origin of some fossils may have to be revised.</p><p>One of the major questions studied by the Census South American working groups on
continental margins and the Antarctic was how Antarctic isolation from other
continents by the Southern Ocean is relevant for understanding circulation
patterns in the world oceans and atmosphere, and how biological communities have
responded to past and present environmental changes. To answer this question,
about 50 researchers from South America and several countries in Europe as well
as the USA centralized their data in SCAR-MarBIN (Scientific Committee on
Antarctic Research Marine Biodiversity Information Network) within the framework
of the Antarctic-South America Interactions (ASAI) Workshop held in November
2009. This workshop provided an opportunity to exchange data and to compile an
integrated document on the potential Antarctic South American biodiversity
connections, taking into account all the marine realms. Results are to be
published in a special issue of the journal <italic>Oecologia
Australis</italic>.</p><p>Another regional joint effort in the region is the Latin American and Caribbean
International Census of Marine Microbes (LACar-ICoMM) network launched in 2006
to evaluate the research capabilities and to identify complementary strengths
and possibilities for enhanced collaboration. Artigas et al. <xref ref-type="bibr" rid="pone.0014631-Artigas2">[43]</xref> summarized
some current studies on microbial diversity in both the Caribbean and South
American regions. LACar has also submitted a set of samples to the ICoMM
“454-tag sequencing” program in 2007, a metagenomics project
especially targeting Eubacteria and Archaea in a latitudinal gradient from the
southwest Atlantic (Patagonian littoral and shelf sediments and waters) to the
Caribbean (Puerto Rico sediment and bays), including large estuarine systems
(Río de la Plata and Amazon), and coastal brackish waters of Laguna de
Rocha and Guanabara Bay. Three other projects are under way dealing with the
giant bacteria of the oxygen minimum zone (OMZ) of the upwelling system in the
southeastern Pacific (Chile), the bacterial diversity at different depths of the
Cariaco Basin (Venezuela), and in French Guiana the bacterial diversity in the
fluid muds originating in the Amazon River. Although microbial metabolism and
productivity are at present being described in a variety of ecosystems in South
America and the Caribbean, only scarce information on microbial dynamics and
community composition is available for the planktonic and benthic realms of many
coastal and oceanic regions of the area. Such information is important to fully
understand topics such as biogeochemical processes and gradients in these
systems that are submitted to increasing pressure from human activities and
climate-change issues. The use of a wide range of available methods, techniques,
and protocols in molecular biology, electron microscopy, and in situ and remote
sensing facilities allow us to study all groups in a better and more systematic
way. All the data collected from the Census field projects in the South American
region as well as from museums, academic institutions, scientific literature,
and species databases, are being integrated in the South American regional nodes
of OBIS, which have contributed with nearly 300,000 records to OBIS from almost
7,000 species.</p></sec><sec id="s2d"><title>Marine biodiversity of the South American Atlantic and Pacific
regions</title><p>This paper reviews and analyzes the marine biodiversity in five subregions of the
South American Pacific and Atlantic coasts. The areas considered here are based
in the Large Marine Ecosystem classification or LMEs (<ext-link ext-link-type="uri" xlink:href="http://www.lme.noaa.gov/">http://www.lme.noaa.gov/</ext-link>) which are defined as “areas of
the ocean characterized by distinct bathymetry, hydrology, productivity and
trophic interactions”, however with certain practical (political) border
considerations. The subregions as reviewed in this paper are: (1) the Tropical
East Pacific which includes the Pacific coasts of Colombia, Ecuador, Panama and
Costa Rica, and excluding the Galapagos Islands, (2) the Humboldt Current system
which includes Chile and Peru, (3) the Patagonian Shelf which includes Argentina
and Uruguay, (4) the Brazilian shelves which includes the north, south, and east
shelves of Brazil, and (5) the Tropical West Atlantic which includes the
Venezuelan Atlantic Front, Guyana, Suriname, and French Guiana (<xref ref-type="fig" rid="pone-0014631-g001">Figure 1</xref>). The paper also
assesses the research capacity in each of these five subregions as well as the
threats to biodiversity and the conservation initiatives to protect it.</p><fig id="pone-0014631-g001" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0014631.g001</object-id><label>Figure 1</label><caption><title>Map of South America defining the five subregions as analyzed in this
paper: Tropical East Pacific (blue), Humboldt Current system (light
purple), Tropical West Atlantic (orange), Brazilian shelves (light
blue), and Patagonian Shelf (pink).</title><p>[The Caribbean subregion (yellow) is subject of another article
within this collection <xref ref-type="bibr" rid="pone.0014631-Miloslavich1">[20]</xref>. Bathymetry
scale in meters.</p></caption><graphic xlink:href="pone.0014631.g001"></graphic></fig></sec></sec><sec sec-type="methods" id="s3"><title>Methods</title><p>The total number of species was compiled from different sources depending on the
subregion, and using the OBIS database as a point of departure. Species diversity in
the area corresponding to the Tropical East Pacific region (see Sherman &
Hempel, 2009) was reviewed and compiled from the literature and open-access
databases and sources including local, country/territory, and regional checklists
and inventories, (see <xref ref-type="supplementary-material" rid="pone.0014631.s001">Table S1</xref> for information sources). Species
diversity in the area corresponding to the Humboldt Current system (Chile and Peru)
was reviewed and compiled from sources including OBIS and other electronic databases
such as SeaLifeBase <xref ref-type="bibr" rid="pone.0014631-Palomares1">[44]</xref> and Algaebase <xref ref-type="bibr" rid="pone.0014631-Guiry1">[45]</xref>. For Cnidaria, the database
linked to SeaLifeBase provided only species names, so the taxonomy was completed
using the Global Biodiversity Information Facility (GBIF) (<ext-link ext-link-type="uri" xlink:href="http://data.gbif.org/welcome.htm">http://data.gbif.org/welcome.htm</ext-link>). Other sources used were the
database by Lee et al. <xref ref-type="bibr" rid="pone.0014631-Lee1">[46]</xref>, which provides information about free-living benthic
marine fauna of Chile, and the species list in Castilla & Neill <xref ref-type="bibr" rid="pone.0014631-Castilla1">[47]</xref>. Species
diversity in the area corresponding to the Patagonian Shelf (Argentina and Uruguay)
was reviewed and compiled from OBIS through the Argentinean OBIS node AROBIS and
from other electronic databases and sources. Data on vertebrate species were
reviewed from publications as well as information available in OBIS (AROBIS node).
These OBIS records combine published information from scientific papers and reports
of pinnipeds, whales, and dolphins in the southwestern Atlantic and Magellanic
region. Offshore records include reported sightings from scientific vessels and
satellite tracking for seabirds, seals, and sea lions. These censuses include the
distribution at or near shore waters of open coast, sheltered fjords, bays, and
river mouths. Different records encompassing counting, sighting, and stranding
programs, personal communications with trained individuals, photographs, unpublished
abstracts from meetings, books newspaper articles, and specimen collections from
academic institutions and museums (INIDEP-UNMdP) were also considered. The oldest
records were accepted by the authors when the documentation and synonymy were
reviewed. In addition, surveys made onboard fishing vessels provided additional
biological information on targeted species and bycatch. Data on invertebrate taxa
were obtained from the available literature, technical reports, databases, museum
data collections, and the NaGISA project in the case of Golfo Nuevo rocky shore
invertebrates. The only available, detailed and integrative compilation of reported
marine invertebrate species was restricted to environments shallower than 50 m and
was of limited geographical scope (Uruguayan shelf; <xref ref-type="bibr" rid="pone.0014631-Scarabino2">[48]</xref>). There are no similar
studies on the much larger and presumably more diverse Argentinean coast. It should
be taken into account that the data presented here do not represent a revision of
the identifications. Species must be evaluated through the material deposited in
museum collections or by searching the species in the locality or area in which they
were reported <xref ref-type="bibr" rid="pone.0014631-Scarabino2">[48]</xref>. However, and although data presented must be verified by
experts of each group, our results should reflect the current knowledge of marine
invertebrate biodiversity in the area. Finally, data on algae, and the validity of
seaweed taxa reported were checked with Algae Base <xref ref-type="bibr" rid="pone.0014631-Guiry1">[45]</xref> to update species names or
higher taxonomic levels. Plankton were included in the different invertebrates
groups (1,000 species were cited for Brazil and Argentina, <xref ref-type="bibr" rid="pone.0014631-Boltovskoy1">[49]</xref>) (See <xref ref-type="supplementary-material" rid="pone.0014631.s002">Table S2</xref> for a
list of the main organizations in the Patagonian region that have contributed to
knowledge of biodiversity on the regional scale and provided data sources for this
revision). For the Brazilian shelf region, besides OBIS, the information was
gathered with the assistance of several taxonomic specialists, and also taken from
the available literature in both national and international journals, as well as
many sources found in the gray literature (dissertations and theses) from major
university libraries. Also, the National Council for the Development of Science and
Technology (CNPq) Lattes Platform was accessed to assemble information based on
Brazilian scientists' publications. Lattes Platform is a database where all
Brazilian scientists are required to deposit their curriculum to gain funding for
their research work. For the Tropical West Atlantic region, the data were compiled
from OBIS and from a few literature sources. On the other hand, most information on
threats and conservation was assembled from documents produced by the various
national ministries of environment and from available scientific texts.</p><p>Information regarding microorganisms such as bacteria and phytoplankton is provided
for the overall continent and is not separated by subregions.</p></sec><sec id="s4"><title>Results</title><sec id="s4a"><title>Subregion 1: The Tropical East Pacific – Colombia, Ecuador, and the
Pacific Coasts of Panama and Costa Rica</title><p>The Tropical East Pacific (TEP) coastline is about 5,100 km long, extending from
the Nicaragua-Costa Rica border (11°04′34″N,
85°41′55″W) to the Ecuador–Peru border
(3°24′34″S, 80°18′25″W). According to Briggs
<xref ref-type="bibr" rid="pone.0014631-Briggs1">[50]</xref>, this
area, including the corresponding 45,000 km<sup>2</sup> of continental shelf,
belongs to the TEP Biogeographic Region, which encompasses the continental
shoreline and shelf that extends south of the lower end of the Gulf of
California along the continental coastline down to about Cabo Blanco near the
Ecuador–Peru border. It also includes several oceanic islands and
archipelagos, such as Galapagos, Malpelo, Cocos, and Clipperton <xref ref-type="bibr" rid="pone.0014631-Briggs1">[50]</xref>. More
specifically within the TEP, this subregion represents the southern half of the
Panamanian Province, which extends from the Gulf of Tehuantepec in Mexico
(22°N) to Cabo Blanco (4°S), Peru <xref ref-type="bibr" rid="pone.0014631-Briggs1">[50]</xref>. The boundaries and extent
of the Panamanian Province almost coincide with those of the Pacific
Central-American Coastal Large Marine Ecosystem <xref ref-type="bibr" rid="pone.0014631-Bakun1">[51]</xref>. According to the
bioregionalization scheme of the world's coasts and shelf areas <xref ref-type="bibr" rid="pone.0014631-Spalding1">[52]</xref>, <xref ref-type="bibr" rid="pone.0014631-SullivanSealey1">[53]</xref>,
the Pacific coasts of Costa Rica and western Panama fall within the Nicoya
Ecoregion, whereas the eastern half of the Pacific coast of Panama, the
Colombian coast, and the northern half of the Ecuadorian mainland coast
correspond to the Panama Bight Ecoregion, and the southern Ecuadorian coast and
the northernmost Peruvian coast fall within the Guayaquil Ecoregion. These three
ecoregions are in any case part of the TEP <xref ref-type="bibr" rid="pone.0014631-Spalding1">[52]</xref>.</p><p>The morphology of the coast throughout this region is highly variable and
heterogeneous, as are the features of the coastal masses. Much of the shoreline
includes high cliffs with alternating pocket beaches. This pattern dominates the
shorelines of northern and southern Costa Rica, central Panama, northern
Colombia, and norther Ecuador. By contrast, low coasts are made of ample
alluvial plains or deltas, backed by estuarine lagoons, tidal channels, and
extensive mangrove swamps on mudflats <xref ref-type="bibr" rid="pone.0014631-SullivanSealey1">[53]</xref>–<xref ref-type="bibr" rid="pone.0014631-Correa1">[57]</xref>.</p><p>The Pacific coasts of Panama, Colombia, and northern Ecuador are covered mostly
by mangroves and dense rainforest vegetation. This is one of the wettest places
in the world, with local rainfall of more than 10,000 mm/year on the northern
Pacific coast of Colombia and very high river discharges. These conditions lead
to the largest concentration of estuarine systems with high freshwater outflows
of the South American Pacific, including the San Juan-Buenaventura,
Patía, Mira, Cayapas, and Gulf of Guayaquil estuaries. The predominant
dry climate in northern Costa Rica gradually changes toward the southeast to
rainy, humid conditions in eastern Panama-Colombia and then, to the south, again
to dryer climate in southern Ecuador and to arid conditions in northern Peru,
where less than 100 mm/year of rainfall is recorded <xref ref-type="bibr" rid="pone.0014631-West1">[55]</xref>, <xref ref-type="bibr" rid="pone.0014631-Chatwin1">[58]</xref>, <xref ref-type="bibr" rid="pone.0014631-Ecuador1">[59]</xref>.</p><p>Oceanic currents are rather complex in this region, with the North Equatorial
Counter Current entering from the Central Pacific and a branch of the Humboldt
Current, called the Colombia Current, coming in from the south. These currents
create a large anticlockwise gyre in the Panama Bight and generate the Panama
Current, which flows southwest toward the Galapagos (<xref ref-type="fig" rid="pone-0014631-g002">Figure 2</xref>). The northernmost coastal waters of
Costa Rica are seasonally influenced by an upwelling system at the Gulf of
Papagayo as well as the Gulf of Panama and adjacent areas, and the southern edge
of the Ecuadorian coast is affected by the huge upwelling system along the
shores of Peru <xref ref-type="bibr" rid="pone.0014631-Fiedler1">[60]</xref>. The region is greatly affected by El Niño
events, which occur at about four- to nine-year intervals and widely change
climatic and oceanographic conditions (<xref ref-type="fig" rid="pone-0014631-g003">Figures 3</xref> and <xref ref-type="fig" rid="pone-0014631-g004">4</xref>). During El Niño the North
Equatorial Counter Current strengthens and widens, producing a surge of
relatively hot water from the central Pacific that hits the coast and
substantially reduces the influence of the upwelling systems <xref ref-type="bibr" rid="pone.0014631-Fiedler1">[60]</xref>, <xref ref-type="bibr" rid="pone.0014631-Strub1">[61]</xref>.</p><fig id="pone-0014631-g002" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0014631.g002</object-id><label>Figure 2</label><caption><title>Map showing currents and bathymetry around the South American
continent.</title><p>Bathymetry scale in meters.</p></caption><graphic xlink:href="pone.0014631.g002"></graphic></fig><fig id="pone-0014631-g003" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0014631.g003</object-id><label>Figure 3</label><caption><title>Map showing the sea surface temperature (SST) around the South
American continent.</title><p>A: Austral winter, B: Austral summer.</p></caption><graphic xlink:href="pone.0014631.g003"></graphic></fig><fig id="pone-0014631-g004" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0014631.g004</object-id><label>Figure 4</label><caption><title>Map showing primary production measured as chlorophyll a (Chl a)
around the South American continent.</title><p>A: Austral winter, B: Austral summer.</p></caption><graphic xlink:href="pone.0014631.g004"></graphic></fig><p>The continental shelf is variably narrow in Costa Rica, western Panama and
northern Colombia (less than 20 km wide). The only places where the width
exceeds 100 km are off the gulfs of Panama and Guayaquil. Roughly one-third of
the coastline consists of stretches of mangroves on mudflats, with major
concentrations along the southern half of the Colombian and northern Ecuadorian
coast and in the gulfs of Guayaquil, San Miguel, Chiriquí, and Nicoya
<xref ref-type="bibr" rid="pone.0014631-Cruz1">[1]</xref>, <xref ref-type="bibr" rid="pone.0014631-West1">[55]</xref>, <xref ref-type="bibr" rid="pone.0014631-Chatwin1">[58]</xref>. There are
substantial stretches of rocky shores scattered throughout the coast; the
longest uninterrupted sections occur at the northwesternmost coast of Costa
Rica, along the Nicoya and Osa Peninsulas, at the northernmost edge of the
Colombian shoreline, and in the central coast of Ecuador. Long stretches of
sandy beaches are mostly concentrated along the Costa Rican, central Panamanian,
central Colombian and northern-central Ecuadorian shorelines <xref ref-type="bibr" rid="pone.0014631-Cruz1">[1]</xref>, <xref ref-type="bibr" rid="pone.0014631-Clapperton1">[56]</xref>–<xref ref-type="bibr" rid="pone.0014631-Chatwin1">[58]</xref>. Coral reef development in
this region is limited by the regular impact of El Niño events and
unfavorable conditions that result from freshwater input from river runoff,
siltation, nutrient enrichment, and upwelling influences <xref ref-type="bibr" rid="pone.0014631-Glynn1">[62]</xref>. The overwhelming majority
of reef habitat in this region consists of rocky reefs. More suitable conditions
for coral development are found around islands and rocky promontories located
away from the mainland shoreline such as Isla del Caño (Costa Rica), Isla
Coiba, the Pearl Islands (Panama), Isla Gorgona (southwestern Colombia), Isla La
Plata, Isla Salango, and Bajo Montañita (central mainland coast of
Ecuador) <xref ref-type="bibr" rid="pone.0014631-Corts1">[63]</xref>–<xref ref-type="bibr" rid="pone.0014631-Glynn2">[66]</xref>.</p><sec id="s4a1"><title>Marine biodiversity in the Tropical East Pacific: Ecuador, Colombia,
Panama, and Costa Rica</title><p>At least 6,714 species-level taxa have been reported in the Pacific coastal
waters of Costa Rica, Panama, Colombia, and Ecuador (<xref ref-type="table" rid="pone-0014631-t001">Table 1</xref>, <xref ref-type="supplementary-material" rid="pone.0014631.s003">Table
S3</xref>), from four Protista groups, (Foraminifera, Radiolaria,
Tintinnida, Dinoflagelata), two plant phyla (algae, angiospermae), and 30
animal phyla. The quality of information was different for each of the taxa,
and no information was available on bacteria, fungi, Gastrotricha, and
Rotifera. This species number is constantly increasing, as new species are
described every year or are recorded for the first time in the region.
Knowing the taxonomic background (availability and expertise) of the region,
we did not expect to be able to produce species accounts of the same quality
for all the taxonomic groups. For most of the groups, the review can be
considered satisfactory, but several of these counts would greatly benefit
from further taxonomic review. At the phylum level, no species were reported
from five phyla, and this is probably because of a lack of taxomomic
attention rather than the absolute absence of these groups from the region,
which is highly unlikely. Not a single species of the phyla Placozoa,
Gnathostomulida, Micrognathozoa, Loricifera, and Nematomorpha has been
recorded from the entire TEP region. The most diverse taxa in the region are
the Polychaeta (1,894 species), fishes (1,212 species), Crustacea (863
species), and Mollusca (875 species), which together account for
47.3% of the total known biota.</p><table-wrap id="pone-0014631-t001" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0014631.t001</object-id><label>Table 1</label><caption><title>Summary of the diversity, state of knowledge, and expertise of
the main taxonomic groups within the Tropical East Pacific subregion
of South America.</title></caption><alternatives><graphic id="pone-0014631-t001-1" xlink:href="pone.0014631.t001"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col></colgroup><thead><tr><td align="left" rowspan="1" colspan="1">Taxonomic group</td><td align="left" rowspan="1" colspan="1">No. species<xref ref-type="table-fn" rid="nt101">1</xref></td><td align="left" rowspan="1" colspan="1">State of knowledge</td><td align="left" rowspan="1" colspan="1">No. introduced species</td><td align="left" rowspan="1" colspan="1">No. experts</td><td align="left" rowspan="1" colspan="1">No. ID guides<xref ref-type="table-fn" rid="nt102">2</xref></td></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1"><bold>Domain Archaea</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Domain Bacteria (including Cyanobacteria)</bold></td><td align="left" rowspan="1" colspan="1">18</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">ND</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Domain Eukarya</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Kingdom Chromista</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Phaeophyta</td><td align="left" rowspan="1" colspan="1">40</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">ND</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Kingdom Plantae</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Chlorophyta</td><td align="left" rowspan="1" colspan="1">84</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">ND</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1">Rhodophyta</td><td align="left" rowspan="1" colspan="1">183</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">ND</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1">Angiospermae</td><td align="left" rowspan="1" colspan="1">10</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">ND</td><td align="left" rowspan="1" colspan="1">15</td><td align="left" rowspan="1" colspan="1">3</td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Kingdom Protista (Protozoa)</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Dinomastigota (Dinoflagellata)</td><td align="left" rowspan="1" colspan="1">132</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">ND</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1">Foraminifera</td><td align="left" rowspan="1" colspan="1">164</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">ND</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Kingdom Animalia</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Porifera</td><td align="left" rowspan="1" colspan="1">42</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">ND</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1">Cnidaria</td><td align="left" rowspan="1" colspan="1">110</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">ND</td><td align="left" rowspan="1" colspan="1">10</td><td align="left" rowspan="1" colspan="1">2</td></tr><tr><td align="left" rowspan="1" colspan="1">Platyhelminthes</td><td align="left" rowspan="1" colspan="1">29</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">ND</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1">Mollusca</td><td align="left" rowspan="1" colspan="1">875</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">3</td></tr><tr><td align="left" rowspan="1" colspan="1">Annelida</td><td align="left" rowspan="1" colspan="1">1894</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1">Crustacea</td><td align="left" rowspan="1" colspan="1">863</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">ND</td><td align="left" rowspan="1" colspan="1">8</td><td align="left" rowspan="1" colspan="1">2</td></tr><tr><td align="left" rowspan="1" colspan="1">Bryozoa</td><td align="left" rowspan="1" colspan="1">45</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">ND</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1">Echinodermata</td><td align="left" rowspan="1" colspan="1">223</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">1</td></tr><tr><td align="left" rowspan="1" colspan="1">Urochordata (Tunicata)</td><td align="left" rowspan="1" colspan="1">18</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">ND</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1">Other invertebrates</td><td align="left" rowspan="1" colspan="1">61</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">ND</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">1</td></tr><tr><td align="left" rowspan="1" colspan="1">Vertebrata (Pisces)</td><td align="left" rowspan="1" colspan="1">1212</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">10</td><td align="left" rowspan="1" colspan="1">20</td><td align="left" rowspan="1" colspan="1">6</td></tr><tr><td align="left" rowspan="1" colspan="1">Other vertebrates</td><td align="left" rowspan="1" colspan="1">89</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">71</td><td align="left" rowspan="1" colspan="1">17</td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>SUBTOTAL</bold></td><td align="left" rowspan="1" colspan="1">6092</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>TOTAL REGIONAL DIVERSITY</bold><xref ref-type="table-fn" rid="nt103">3</xref></td><td align="left" rowspan="1" colspan="1">6714</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr></tbody></table></alternatives><table-wrap-foot><fn id="nt101"><label>1</label><p>Sources of the reports: databases, scientific literature, books,
field guides, technical reports.</p></fn><fn id="nt102"><label>2</label><p>Identification guides cited in Text S1.</p></fn><fn id="nt103"><label>3</label><p>Total regional diversity, including all taxonomic groups as
reported in <xref ref-type="supplementary-material" rid="pone.0014631.s003">Table S3</xref>.</p></fn></table-wrap-foot></table-wrap><p>A few of the species recorded from this region do not have resident
populations in the area or in the entire TPE, but are vagrant species that
reside in the Peruvian or Galapagos provinces. These include the Humboldt
penguin (<italic>Spheniscus humboldtii</italic>) and three species of
otariid pinnipeds that have been regularly recorded in Ecuador and southern
Colombia <xref ref-type="bibr" rid="pone.0014631-Salaman1">[67]</xref>, <xref ref-type="bibr" rid="pone.0014631-Capella1">[68]</xref>. In addition, under
certain anomalous oceanographic conditions (e.g., strong El Niño
events), the pelagic larvae of some Indo-West Pacific or Central Pacific
species seem able to cross the eastern Pacific zoogeographic barrier and can
succesfully settle in suitable places in the TEP. In this way the occasional
records of the Indo-West Pacific crown-of-thorns starfish
(<italic>Acanthaster planci</italic>) in Panamanian reefs <xref ref-type="bibr" rid="pone.0014631-Glynn3">[69]</xref> and the
Indo-West Pacific gastropods <italic>Mitra mitra</italic> and
<italic>Erosaria caputserpentis</italic> around Gorgona Island in
Colombia <xref ref-type="bibr" rid="pone.0014631-Cosel1">[70]</xref>, <xref ref-type="bibr" rid="pone.0014631-Cantera1">[71]</xref> can be explained.</p><p>Estimation of the number of endemic species could be accomplished with
relatively high confidence for only 21 of the 68 taxa groups (31%),
because information was simply not available for the remaining groups. The
total number of endemic species in the region for the 21 taxa is 122, which
represents only 2.18% of the species for these groups. The seemingly
low number of endemics in this region is a consequence of the widespread
distribution of the great majority of species beyond the Central-American
Coastal region. However, at a global scale, endemism in the TEP is among the
highest of any of the world's marine biogeographic regions <xref ref-type="bibr" rid="pone.0014631-Briggs1">[50]</xref>. For
example, of the nearly 1,300 species of fish recorded in the TEP, about
71% are endemic <xref ref-type="bibr" rid="pone.0014631-Zapata2">[72]</xref>.</p><p>With the exception of mangroves, seagrasses, mammals, birds, and reptiles, we
can expect that the number of species recorded in this region will increase
in the future particularly for those groups scored 1–3 (least well
known) in the column “state of knowledge” in <xref ref-type="table" rid="pone-0014631-t001">Table 1</xref> and <xref ref-type="supplementary-material" rid="pone.0014631.s003">Table
S3</xref>. However, even for relatively well known groups such as
mollusks, echinoderms, and fishes, the inventories have by no means been
completed, and further discoveries ought to be expected. The marine biota of
the coastal waters in this region is far from being well known. Indeed, the
Colombian and Ecuadorian coastal waters have been recognized as the least
explored in the TEP region <xref ref-type="bibr" rid="pone.0014631-Cruz1">[1]</xref>, <xref ref-type="bibr" rid="pone.0014631-Daz1">[2]</xref>, <xref ref-type="bibr" rid="pone.0014631-Glynn2">[66]</xref>, <xref ref-type="bibr" rid="pone.0014631-Zapata2">[72]</xref>. The 6,700 species of marine taxa recorded at
present are clearly an underestimate. The lack of comprehensive regional
identification guides for most taxa is a major handicap to carrying out more
accurate species inventories, and most of those that are available need
thorough revisions. The OBIS database for the TEP region reports a total of
3,446 species, which is about 51% of the actual number of species
reported in this review (<xref ref-type="table" rid="pone-0014631-t002">Table 2</xref>).</p><table-wrap id="pone-0014631-t002" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0014631.t002</object-id><label>Table 2</label><caption><title>Comparison of the number of species per 100 kilometers of coast
in the five subregions of South America contained in the OBIS
database and in the present update (OBIS has a total of 13,656
species for the five subregions combined).</title></caption><alternatives><graphic id="pone-0014631-t002-2" xlink:href="pone.0014631.t002"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col></colgroup><thead><tr><td align="left" rowspan="1" colspan="1">Subregion</td><td align="left" rowspan="1" colspan="1">Number of species Present review</td><td align="left" rowspan="1" colspan="1">Number of species in OBIS</td><td align="left" rowspan="1" colspan="1">Species/100 km of coast Present review</td><td align="left" rowspan="1" colspan="1">Species/100 km of coast OBIS</td><td align="left" rowspan="1" colspan="1">% of species in OBIS</td></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">Tropical East Pacific</td><td align="left" rowspan="1" colspan="1">6714</td><td align="left" rowspan="1" colspan="1">3446</td><td align="left" rowspan="1" colspan="1">132</td><td align="left" rowspan="1" colspan="1">68</td><td align="left" rowspan="1" colspan="1">51</td></tr><tr><td align="left" rowspan="1" colspan="1">Humboldt Current</td><td align="left" rowspan="1" colspan="1">10201</td><td align="left" rowspan="1" colspan="1">3894</td><td align="left" rowspan="1" colspan="1">140</td><td align="left" rowspan="1" colspan="1">53</td><td align="left" rowspan="1" colspan="1">38</td></tr><tr><td align="left" rowspan="1" colspan="1">Tropical West Atlantic</td><td align="left" rowspan="1" colspan="1">2743</td><td align="left" rowspan="1" colspan="1">2095</td><td align="left" rowspan="1" colspan="1">146</td><td align="left" rowspan="1" colspan="1">112</td><td align="left" rowspan="1" colspan="1">76</td></tr><tr><td align="left" rowspan="1" colspan="1">Brazilian Shelves</td><td align="left" rowspan="1" colspan="1">9103</td><td align="left" rowspan="1" colspan="1">5474</td><td align="left" rowspan="1" colspan="1">122</td><td align="left" rowspan="1" colspan="1">73</td><td align="left" rowspan="1" colspan="1">60</td></tr><tr><td align="left" rowspan="1" colspan="1">Patagonian Shelf</td><td align="left" rowspan="1" colspan="1">3776</td><td align="left" rowspan="1" colspan="1">3171</td><td align="left" rowspan="1" colspan="1">67</td><td align="left" rowspan="1" colspan="1">56</td><td align="left" rowspan="1" colspan="1">84</td></tr></tbody></table></alternatives></table-wrap><p>A total of 19 alien species belonging to six of the 68 taxa groups were
registered (<xref ref-type="table" rid="pone-0014631-t001">Table 1</xref>).
The most important introduced taxa in numbers of species are the Pisces (10
species). The absence of recorded introductions of more species from other
groups is indicative of the poor level of taxonomic knowledge for these
groups, rather than a lack of actual introductions. The Panama Canal has
provided opportunities for partial reconnection of the shallow-water faunas
of the TEP and the Caribbean since 1914, particularly by freshwater-tolerant
species. However, only two of the six Caribbean fishes that have entered the
TEP by this method, but only one or two species (a pipefish and the Western
Atlantic tarpon) seem to have successfully become resident populations there
<xref ref-type="bibr" rid="pone.0014631-Robertson1">[73]</xref>. In addition, for the majority of invertebrate
groups, there is often difficulty in deciding whether newly reported marine
species are introduced aliens, native species that had not been formerly
recorded, or cryptogenic species.</p><p>Taxonomic expertise in the region provides limited coverage. For many groups,
the only currently active taxonomists work outside the region. Current local
expertise is completely absent or inadequate for many important taxa,
particularly those with small body sizes and little economic significance.
The taxa best covered by local expertise are Angiospermae, Aves, Reptilia,
Pisces, Algae, Echinodermata, and some groups of Cnidaria, Crustacea, and
Mollusca. Moreover, only a small fraction of the local experts are employed
as full-time systematists or taxonomists. For several groups, the coverage
of available guides and identification keys is relatively good (fishes,
turtles, birds, reef corals, mollusks, decapod crustaceans), although some
are outdated. For all the other groups, such guides are either inadequate or
completely lacking. An outstanding, collective effort for cataloging the
known marine biota of Costa Rica has recently been published <xref ref-type="bibr" rid="pone.0014631-Wehrtmann1">[74]</xref>.</p><p>Inevitably, given the limited number of active taxonomists in the region,
certain taxa (e.g., fish, mollusks, corals, and some crustacean groups) have
received far more attention than others, whereas many others have even been
completely neglected. Sampling effort has also been strongly biased toward
specific locations and habitats in coastal and shallow waters (mangroves,
sand beaches, coral and rocky reefs), with scarce collecting of demersal and
benthic organisms in waters deeper than 100 m.</p></sec><sec id="s4a2"><title>Threats and conservation strategies in the Tropical East Pacific</title><p>The major threats to marine biodiversity in this region are fisheries, global
climate change, habitat destruction or alteration, invasive species,
pollution, and human overpopulation along the coastal zone <xref ref-type="bibr" rid="pone.0014631-Cruz1">[1]</xref>, <xref ref-type="bibr" rid="pone.0014631-Chatwin1">[58]</xref>. The
eastern Panamanian and northern Colombian Pacific are in this sense not
severely affected, considering that human settlements in this area are
small. However, the marine ecosystems are moderately influenced by
terrestrial runoff, which has significantly increased in the last 20 years.
Reefs in this area also share some common threats such as bleaching, and the
live coral cover has decreased because of temperature increases of at least
1°C–2°C associated with the ENSO effect <xref ref-type="bibr" rid="pone.0014631-Daz2">[75]</xref>. Other threats identified
in this region are fisheries and occasional oil spills from ships <xref ref-type="bibr" rid="pone.0014631-Chatwin1">[58]</xref>, <xref ref-type="bibr" rid="pone.0014631-Zapata3">[76]</xref>.
Fisheries not only pose a threat to fish and benthic invertebrate species
such as shrimp, but have also proved to have detrimental effects on sea
turtles, particularly on the species <italic>Lepidochelys olivacea</italic>and <italic>Chelonia agassizii</italic>, which are incidentally captured by
shrimp trawling nets <xref ref-type="bibr" rid="pone.0014631-Amorocho1">[77]</xref>. There are 33 Marine Protected Areas, or MPAs, in
this region, including nature reserves, narional parks, and coastal wetlands
of international importance, 6 in Costa Rica, 19 in Panama, 5 in Colombia,
and 9 in Ecuador.</p></sec></sec><sec id="s4b"><title>Subregion 2: The Humboldt Current - Chile and Peru</title><p>The Humboldt Current Large region (HC) extends about 7,280 km along the west
coast of South America from northern Peru (3°24′34″S,
80°18′25″W) to the southern tip of Chile
(54°55′39″S, 64°52′12″W) <xref ref-type="bibr" rid="pone.0014631-McGinley1">[78]</xref>, <xref ref-type="bibr" rid="pone.0014631-Heileman1">[79]</xref>. It has a surface area of
2.5 million square kilometers, containing 0.42% of the world's
seamounts and 24 major estuaries <xref ref-type="bibr" rid="pone.0014631-Heileman1">[79]</xref>. The HC is one of the
major upwelling systems of the world, with moderate to extremely high primary
productivity (150–300 gC/m<sup>2</sup>/yr, <xref ref-type="fig" rid="pone-0014631-g004">Figure 4</xref>) and highly productive fisheries
(e.g., in 1994, fish captures of Peru and Chile amounted to 12 million tons)
accounting for 16%–20% of global fish captures <xref ref-type="bibr" rid="pone.0014631-Heileman1">[79]</xref>–<xref ref-type="bibr" rid="pone.0014631-Hill1">[81]</xref>. This current system is characterized by cold waters
that flow toward the equator, with offshore Ekman transport and coastal
upwelling of cold, nutrient-rich subsurface water (<xref ref-type="fig" rid="pone-0014631-g002">Figures 2</xref> and <xref ref-type="fig" rid="pone-0014631-g003">3</xref>). The current system is complex and marked
by coastal currents that can export waters up to 1,000 km offshore <xref ref-type="bibr" rid="pone.0014631-Heileman1">[79]</xref>, <xref ref-type="bibr" rid="pone.0014631-Marn1">[82]</xref> with
subsequent effects on biological populations of species with planktonic
dispersal <xref ref-type="bibr" rid="pone.0014631-Thiel1">[80]</xref>.
While the northern part of the HC is affected by ENSO events, characterized by
influx of warm (e.g., temperature anomaly in northern Chile 2.5°C to
5.5°C; Sielfeld et al. 2002), nutrient-depleted equatorial waters and
consequent shifts in species composition <xref ref-type="bibr" rid="pone.0014631-Thiel1">[80]</xref>, these events are of short
duration. In fact, over the last 25 years the overall tendency of the HC has
been slight cooling (−0.10°C SST; <xref ref-type="bibr" rid="pone.0014631-Belkin1">[83]</xref>).</p><p>The HC has traditionally been divided into two principal biogeographic provinces:
the Peruvian Province north of 30°S, which is under subtropical influence,
and the Magellanic Province south of 41°S, which is under subantarctic
influence <xref ref-type="bibr" rid="pone.0014631-Brattstrm1">[25]</xref>, <xref ref-type="bibr" rid="pone.0014631-Dahl1">[84]</xref>. Between these zones (30°–41°S)
researchers distinguish a transition zone <xref ref-type="bibr" rid="pone.0014631-Brattstrm1">[25]</xref>, <xref ref-type="bibr" rid="pone.0014631-Balech1">[85]</xref>–<xref ref-type="bibr" rid="pone.0014631-Viviani1">[87]</xref>. In a review of 27
biogeographic classifications proposed for the southeastern Pacific coast, Camus
<xref ref-type="bibr" rid="pone.0014631-Camus1">[88]</xref>identified three consistent spatial units: a Northern Area (north of 30°S)
containing a warm temperate biota (the Peruvian Province), a Southern Area
(41°–43°S to 56°S) with an austral biota (the Magellanic
Province), and an extensive Intermediate Area (30°S to
41°–43°S) lacking transitional elements and containing a mixed
biota without a distinguishing character. In spite of the numerous efforts made
to describe patterns on the Chilean coast (<xref ref-type="bibr" rid="pone.0014631-Hernndez1">[89]</xref> and see reviews by Camus
<xref ref-type="bibr" rid="pone.0014631-Camus1">[88]</xref>;
Fernández et al. <xref ref-type="bibr" rid="pone.0014631-Fernndez1">[90]</xref>; Thiel et al. <xref ref-type="bibr" rid="pone.0014631-Thiel1">[80]</xref>), there are few studies
focused on understanding the macroscale patterns of the HC, and no studies have
been conducted using an explicit two-dimensional spatial analysis of
biodiversity in this subregion.</p><p>Historically, the lack of studies based on georeferenced data of marine
biodiversity was due to a lack of macroscale databases compiling this kind of
information. However, since 2002 the Ocean Biogeographic Information System
(OBIS) <xref ref-type="bibr" rid="pone.0014631-ODor1">[91]</xref>,
<xref ref-type="bibr" rid="pone.0014631-Costello1">[92]</xref> has
begun to provide georeferenced data of marine biodiversity from all oceans, with
access through a Web portal (<ext-link ext-link-type="uri" xlink:href="http://www.iobis.org">www.iobis.org</ext-link>).</p><sec id="s4b1"><title>Marine biodiversity in the Humboldt Current: Chile and Peru</title><p>Analysis of the compiled data indicates three zones of high richness for this
region (<xref ref-type="fig" rid="pone-0014631-g005">Figure 5</xref>): (a)
the northern Peruvian coast between 5° and 8°S, with 501 species,
270 genera, and 193 families at the point of maximum diversity; (b) the
northern Chilean coast between 22° and 24°S, with 431 species, 273
genera, and 159 families at the point of maximum diversity; and (c) the
southern Chilean coast between 52° and 56°S, with 522 species, 324
genera, and 188 families at the point of maximum diversity. The richness
distribution was only consistent with the biogeographical limit between the
previously described Peruvian Province and Intermediate Area (30°S).
This limit is characterized by an area of low richness between 25° and
29°S. This pattern separates the Peruvian Province to the north, with
two areas of high richness (northern Peru and northern Chile), and the
Intermediate Area and Magellanic Province to the south, with one area of
high richness in the southern Magellanic Province (southern Chile).</p><fig id="pone-0014631-g005" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0014631.g005</object-id><label>Figure 5</label><caption><title>Species richness in the Humboldt Current subregion.</title><p>Scale represents number of species.</p></caption><graphic xlink:href="pone.0014631.g005"></graphic></fig><p>The current diversity of the HC includes 10,201 species (<xref ref-type="table" rid="pone-0014631-t003">Table 3</xref>, <xref ref-type="supplementary-material" rid="pone.0014631.s004">Table
S4</xref>). Amphipoda, Gastropoda, and Polychaeta are the taxa with the
greatest number of described species, while 18 taxa do not have reliable
taxonomic information (e.g., Oomycota, Loricifera). The best state of
taxonomic knowledge is for Mammalia, Aves, Reptilia, Pisces, Echinodermata,
and Mollusca. All of the other taxa had few, or very old, identification
guides and few experts currently working in the field until very recently,
when a comprehensive illustrated guide of marine benthic fauna of the
Chilean Patagonian fjords was published <xref ref-type="bibr" rid="pone.0014631-Hussermann1">[93]</xref>. In this book, the
authors point out that the Chilean fjord region is one of the most diverse
in terms of marine fauna but also the least studied. This field guide
represents a 10 year unprecedented collective taxonomic effort in South
America in which nearly 50 specialists from 28 institutions and 14 countries
all over the world participated. The book provides identification keys for
nearly 500 species from 32 taxonomic groups within 13 phyla, and reports
more than 1800 species for this region.</p><table-wrap id="pone-0014631-t003" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0014631.t003</object-id><label>Table 3</label><caption><title>Summary of the diversity, state of knowledge, and expertise of
the main taxonomic groups within the Humboldt Current subregion of
South America.</title></caption><alternatives><graphic id="pone-0014631-t003-3" xlink:href="pone.0014631.t003"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col></colgroup><thead><tr><td align="left" rowspan="1" colspan="1">Taxonomic group</td><td align="left" rowspan="1" colspan="1">No. species<xref ref-type="table-fn" rid="nt104">1</xref></td><td align="left" rowspan="1" colspan="1">State of knowledge</td><td align="left" rowspan="1" colspan="1">No. introduced species</td><td align="left" rowspan="1" colspan="1">No. experts</td><td align="left" rowspan="1" colspan="1">No. ID guides<xref ref-type="table-fn" rid="nt105">2</xref></td></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1"><bold>Domain Archaea</bold></td><td align="left" rowspan="1" colspan="1">—</td><td align="left" rowspan="1" colspan="1">—</td><td align="left" rowspan="1" colspan="1">—</td><td align="left" rowspan="1" colspan="1">—</td><td align="left" rowspan="1" colspan="1">—</td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Domain Bacteria (including Cyanobacteria)</bold></td><td align="left" rowspan="1" colspan="1">≫15</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">ND</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Domain Eukarya</bold></td><td align="left" rowspan="1" colspan="1">—</td><td align="left" rowspan="1" colspan="1">—</td><td align="left" rowspan="1" colspan="1">—</td><td align="left" rowspan="1" colspan="1">—</td><td align="left" rowspan="1" colspan="1">—</td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Kingdom Chromista</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Phaeophyta</td><td align="left" rowspan="1" colspan="1">118</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">6</td><td align="left" rowspan="1" colspan="1">3</td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Kingdom Plantae</bold></td><td align="left" rowspan="1" colspan="1">—</td><td align="left" rowspan="1" colspan="1">—</td><td align="left" rowspan="1" colspan="1">—</td><td align="left" rowspan="1" colspan="1">—</td><td align="left" rowspan="1" colspan="1">—</td></tr><tr><td align="left" rowspan="1" colspan="1">Chlorophyta</td><td align="left" rowspan="1" colspan="1">97</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">6</td><td align="left" rowspan="1" colspan="1">3</td></tr><tr><td align="left" rowspan="1" colspan="1">Rhodophyta</td><td align="left" rowspan="1" colspan="1">320</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">10</td><td align="left" rowspan="1" colspan="1">6</td><td align="left" rowspan="1" colspan="1">3</td></tr><tr><td align="left" rowspan="1" colspan="1">Angiospermae</td><td align="left" rowspan="1" colspan="1">ND</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Kingdom Protista (Protozoa)</bold></td><td align="left" rowspan="1" colspan="1">—</td><td align="left" rowspan="1" colspan="1">—</td><td align="left" rowspan="1" colspan="1">—</td><td align="left" rowspan="1" colspan="1">—</td><td align="left" rowspan="1" colspan="1">—</td></tr><tr><td align="left" rowspan="1" colspan="1">Dinomastigota (Dinoflagellata)</td><td align="left" rowspan="1" colspan="1">≫2</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">ND</td><td align="left" rowspan="1" colspan="1">12</td><td align="left" rowspan="1" colspan="1">3</td></tr><tr><td align="left" rowspan="1" colspan="1">Foraminifera</td><td align="left" rowspan="1" colspan="1">500</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">ND</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Kingdom Animalia</bold></td><td align="left" rowspan="1" colspan="1">—</td><td align="left" rowspan="1" colspan="1">—</td><td align="left" rowspan="1" colspan="1">—</td><td align="left" rowspan="1" colspan="1">—</td><td align="left" rowspan="1" colspan="1">—</td></tr><tr><td align="left" rowspan="1" colspan="1">Porifera</td><td align="left" rowspan="1" colspan="1">159</td><td align="left" rowspan="1" colspan="1">1 to 2</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td></tr><tr><td align="left" rowspan="1" colspan="1">Cnidaria</td><td align="left" rowspan="1" colspan="1">517</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">3</td></tr><tr><td align="left" rowspan="1" colspan="1">Platyhelminthes</td><td align="left" rowspan="1" colspan="1">210</td><td align="left" rowspan="1" colspan="1">1 to 3</td><td align="left" rowspan="1" colspan="1">ND</td><td align="left" rowspan="1" colspan="1">8</td><td align="left" rowspan="1" colspan="1">1</td></tr><tr><td align="left" rowspan="1" colspan="1">Mollusca</td><td align="left" rowspan="1" colspan="1">1203</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">7</td><td align="left" rowspan="1" colspan="1">16</td><td align="left" rowspan="1" colspan="1">19</td></tr><tr><td align="left" rowspan="1" colspan="1">Annelida</td><td align="left" rowspan="1" colspan="1">649</td><td align="left" rowspan="1" colspan="1">2 to 5</td><td align="left" rowspan="1" colspan="1">8</td><td align="left" rowspan="1" colspan="1">8</td><td align="left" rowspan="1" colspan="1">6</td></tr><tr><td align="left" rowspan="1" colspan="1">Crustacea</td><td align="left" rowspan="1" colspan="1">3136</td><td align="left" rowspan="1" colspan="1">2 to 5</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">8</td><td align="left" rowspan="1" colspan="1">33</td></tr><tr><td align="left" rowspan="1" colspan="1">Bryozoa</td><td align="left" rowspan="1" colspan="1">401</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2</td></tr><tr><td align="left" rowspan="1" colspan="1">Echinodermata</td><td align="left" rowspan="1" colspan="1">364</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">2</td></tr><tr><td align="left" rowspan="1" colspan="1">Urochordata (Tunicata)</td><td align="left" rowspan="1" colspan="1">109</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">9</td></tr><tr><td align="left" rowspan="1" colspan="1">Other invertebrates</td><td align="left" rowspan="1" colspan="1">776</td><td align="left" rowspan="1" colspan="1">1 to 5</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">12</td><td align="left" rowspan="1" colspan="1">19</td></tr><tr><td align="left" rowspan="1" colspan="1">Vertebrata (Pisces)</td><td align="left" rowspan="1" colspan="1">1167</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">35</td><td align="left" rowspan="1" colspan="1">9</td><td align="left" rowspan="1" colspan="1">4</td></tr><tr><td align="left" rowspan="1" colspan="1">Other vertebrates</td><td align="left" rowspan="1" colspan="1">209</td><td align="left" rowspan="1" colspan="1">1 to 5</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">37</td><td align="left" rowspan="1" colspan="1">11</td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>SUBTOTAL</bold></td><td align="left" rowspan="1" colspan="1"><bold>9935</bold></td><td align="left" rowspan="1" colspan="1"><bold>1 to 5</bold></td><td align="left" rowspan="1" colspan="1"><bold>77</bold></td><td align="left" rowspan="1" colspan="1"><bold>145</bold></td><td align="left" rowspan="1" colspan="1"><bold>122</bold></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>TOTAL REGIONAL DIVERSITY</bold><xref ref-type="table-fn" rid="nt106">3</xref></td><td align="left" rowspan="1" colspan="1"><bold>10201</bold></td><td align="left" rowspan="1" colspan="1"><bold>1 to 5</bold></td><td align="left" rowspan="1" colspan="1"><bold>77</bold></td><td align="left" rowspan="1" colspan="1"><bold>151</bold></td><td align="left" rowspan="1" colspan="1"><bold>127</bold></td></tr></tbody></table></alternatives><table-wrap-foot><fn id="nt104"><label>1</label><p>Sources of the reports: databases, scientific literature, books,
field guides, technical reports.</p></fn><fn id="nt105"><label>2</label><p>Identification guides cited in References.</p></fn><fn id="nt106"><label>3</label><p>Total regional diversity, including all taxonomic groups as
reported in <xref ref-type="supplementary-material" rid="pone.0014631.s004">Table S4</xref>.</p></fn></table-wrap-foot></table-wrap><p>As for endemicity and alien species in the HC region, only Polychaeta, Aves,
and Mammalia have records of endemic species, while 31 taxa report
introduced species. Rhodophyta, Salmoniforme, and Polychaeta have the
greatest number of reported introduced species. The greatest number of
experts is concentrated in Mammalia, Aves, and Mollusca, while some highly
diverse groups have few taxonomic experts (e.g., Polychaeta) and other
groups lack taxonomic experts altogether (e.g., Nematoda, Rotifera). The
taxa with the greatest number of identification guides are Decapoda and
Amphipoda, while 49 taxa have only one (n = 23) or no
(n = 26) published identification guides. Of these
total number of described species for the HC, only 1.5% are used as
fishery resources, nine of them being commercial fish species which
constitute the greatest part of annual captures in the study area (i.e.,
<italic>Engraulis ringens</italic>, <italic>Sardinops sagax</italic>,
<italic>Trachurus murphyi</italic>, <italic>Strangomera
bentincki</italic>, <italic>Scomber japonicus</italic>,
<italic>Merluccius gayi gayi</italic>, <italic>Macruronus
magellanicus</italic>, <italic>Sarda chiliensis</italic>, and
<italic>Merluccius australis</italic><xref ref-type="bibr" rid="pone.0014631-SeaAroundUs1">[94]</xref>). The OBIS database for the HC region reports of
3,894 species, which is about 38% of the actual number reported in
this review (<xref ref-type="table" rid="pone-0014631-t002">Table 2</xref>).
Despite the fact that the OBIS database for the HC needs to be completed
considering the existing knowledge of biodiversity in this region (<xref ref-type="table" rid="pone-0014631-t003">Table 3</xref> and <xref ref-type="supplementary-material" rid="pone.0014631.s003">S3</xref>), it
shows patterns consistent with previously described biogeographic limits and
with the potential processes (e.g., ENSO, OMZ, historical glacial events)
that could explain the observed differences in biodiversity between the
Peruvian and Magellanic provinces. An improvement of the OBIS database will
only be possible with an increase in the number of taxonomic experts to
cover underrepresented taxa, together with the widespread incorporation of
molecular approaches for species recognition. Nevertheless, OBIS has an
advantage over other available electronic datasets given that data are
georeferenced, which increases potential for the analysis of patterns and
underlying processes. The incorporation of revised taxonomic data, and the
investment in new coastal and oceanic expeditions will help to improve OBIS
with better georeferenced data which will allow us to reevaluate the HC
regional biodiversity patterns.</p></sec><sec id="s4b2"><title>Threats and conservation strategies in the Humboldt Current</title><p>Currently, the governments of Peru and Chile have made efforts to protect the
biodiversity contained in the HC through declared Coastal Marine Protected
Areas <xref ref-type="bibr" rid="pone.0014631-Fernndez2">[95]</xref>, <xref ref-type="bibr" rid="pone.0014631-CPPS1">[96]</xref>. In Chile there are 74 areas subject to some form
of marine conservation (22 officially protected areas and 52 proposals). The
currently protected areas in Chile cover over 30,000 km<sup>2</sup> and
include five marine reserves, one marine park, six natural sanctuaries,
eight coastal marine protected areas, one biosphere reserve, and one RAMSAR
site. In Peru there are 14 marine and coastal protected areas comprising
over 3,000 km<sup>2</sup>, including six natural protected marine and
coastal areas, two natural sanctuaries, two national reserves, one wildlife
refuge, one reserved zone, and two areas of regional conservation. These
different designations translate into different degrees of protection, which
vary from regulated take (e.g. regulated fishing activities) to highly
restricted extraction <xref ref-type="bibr" rid="pone.0014631-CPPS1">[96]</xref>. In total, only about 1.4% of the HC is
currently under some degree of protection (this value is based on the most
current report of Coastal Marine Protected Areas of the Southeastern
Pacific, and increases the percentage reported by Heileman et al., <xref ref-type="bibr" rid="pone.0014631-Heileman1">[79]</xref> more
than twelvefold). In spite of these conservation efforts, Fernández
and Castilla <xref ref-type="bibr" rid="pone.0014631-Fernndez2">[95]</xref> indicate that the apparently disparate goals for
conservation (i.e., exploitation of marine resources vs. preservation of
marine species) pose a challenge and constraint for the formation of a
network of marine protected areas.</p><p>Threats to the biodiversity of the HC include contamination and
overexploitation of resources. However, while such activities can have
important impacts on marine biodiversity at the local scale, the wide
distibution of many species and their spatial structure as metapopulations
may protect the diversity of species' populations at the regional and
global scales, where these threats could cause local, but not global,
extinction. Furthermore, at the global level, species invasions have been
identified as an important cause of biodiversity decline <xref ref-type="bibr" rid="pone.0014631-DAntonio1">[97]</xref>.
Although there are few reports of highly invasive or aggressive
nonindigenous species in the HC <xref ref-type="bibr" rid="pone.0014631-Castilla1">[47]</xref>, we believe that the
introduction of nonnative species represents a large risk to native
biodiversity. The rise in the aquaculture of exotic species (mostly
introduced salmonid species) and of international maritime transport in this
ecosystem, coupled with deficient taxonomic and biogeographical information
about native species, and the lack of explicit studies evaluating species
introductions in nonpristine areas such as ports and aquaculture centers,
leaves the door wide open for a potential disaster. In spite of this threat,
there have been few efforts to recognize and map endemic flora and fauna of
the HC and the biogeographical regions within this study area (<xref ref-type="table" rid="pone-0014631-t003">Table 3</xref>). As mentioned
above, this deficiency makes it difficult to identify nonindigenous species.
A case in point is the mussel <italic>Mytilus galloprovincialis</italic> in
Chile <xref ref-type="bibr" rid="pone.0014631-Castilla1">[47]</xref>, which is a recognized invader around the world,
but because of the lack of taxonomic expertise and georeferenced data, the
date of introduction and current distribution in Chile is unknown. The
internationally recognized problem of nonindigenous species introductions
has recently been addressed in the HC where researchers and policymakers of
Chile and Peru have begun to try to generate practical solutions through
organizations such as Globallast and I3N-IABIN (Invasive Species Information
Network – Interamerican Biodiversity Information Network).</p></sec></sec><sec id="s4c"><title>Subregion 3: The Patagonian Shelf - Uruguay and Argentina</title><p>The Patagonian Shelf (PS) extends for about 5,649 km along the Atlantic coast of
South America from northern Uruguay (33°51′21″S,
53°11′43″W) to the southern tip of Argentina, bordering with
Chile (54°55′39″S, 64°52′12″W). The area of the
Patagonian Shelf extends more than 3 million square kilometers in Uruguayan and
Argentinean territories and comprises coastal environments, the continental
shelf and slope, and ocean basins. Its continental shelf is generally up to 100
m in depth, and is the largest and one of the most productive ecosystems in the
Southern Hemisphere <xref ref-type="bibr" rid="pone.0014631-FCMPAI1">[98]</xref>. In the PS, two major marine currents coexists: the
cold Malvinas and the warm Brazil currents (<xref ref-type="fig" rid="pone-0014631-g002">Figure 2</xref>). The former originates in the
Antarctic circumpolar current and carries a high nutrient load north along the
Argentine coast. The nutrient-poor waters of the Brazil current meet the
Malvinas current as it moves southward along the edge of the slope <xref ref-type="bibr" rid="pone.0014631-Piola1">[99]</xref>, <xref ref-type="bibr" rid="pone.0014631-Piola2">[100]</xref>. In the
confluence or transition zone (from 30° to 46°S), a series of
oceanographic phenomena (eddies, marine fronts, etc.) allow for high biological
production <xref ref-type="bibr" rid="pone.0014631-Acha1">[101]</xref>(<xref ref-type="fig" rid="pone-0014631-g003">Figures 3</xref> and <xref ref-type="fig" rid="pone-0014631-g004">4</xref>). Together, the coastline
extension of Uruguay and Argentina measures about 5,649 km of coastline <xref ref-type="bibr" rid="pone.0014631-Barragn1">[102]</xref>–<xref ref-type="bibr" rid="pone.0014631-Defeo1">[104]</xref> and span approximately
24° in latitude; consequently, the region exhibits large topographical
changes and climatic heterogeneity. Tidal regime is semidiurnal and the mean
tidal amplitude varies from 0.5 m in Uruguay to over 8.2 m in the southern
Argentinean Patagonia <xref ref-type="bibr" rid="pone.0014631-SHN1">[105]</xref>. Air temperature changes seasonally in response to
variations in solar radiation, cloud cover, winds, and marine currents <xref ref-type="bibr" rid="pone.0014631-Piola2">[100]</xref>. The
minimum and maximum air temperatures are −10.5°C and 39.4°C,
respectively, while maximum and minimum average ranges from 3.9°C to
20.9°C. Mean wind speed varies from 14.5 to 30.0 km/h <xref ref-type="bibr" rid="pone.0014631-SMN1">[106]</xref>.</p><p>The Río de la Plata estuary represents the greatest freshwater inflow to
the region, discharging on average 2.4×10<sup>4</sup> m<sup>3</sup>/s
<xref ref-type="bibr" rid="pone.0014631-Defeo1">[104]</xref>, and
is one of the few geographical features (i.e., Valdés Península,
the Northpatagonic Gulfs, and the Magallanes Strait) that influence water
circulation at a regional scale <xref ref-type="bibr" rid="pone.0014631-Piola3">[107]</xref>. Thus, the confluence of the Malvinas and Brazil
currents, together with the abundant terrestrial runoff of Río de la
Plata, and the relatively shallow waters of the area, combine to produce a
singular hydrographic system <xref ref-type="bibr" rid="pone.0014631-SullivanSealey1">[53]</xref>.</p><p>Biogeographically, the PS is divided into two zoogeographical provinces, the
Argentinian and the Magellanic, that join around Valdés Península.
The Argentine Biogeographic Province extends from 36° to 43°S,
encompassing coastal or relatively shallow shelf areas off Uruguay, and the
provinces of Buenos Aires, Río Negro, and Chubut in Argentina. The
Magellanic Biogeographic Province, extending from 43°to 56°S, includes
the coasts of southern Patagonia and the Malvinas/ Falkland Islands <xref ref-type="bibr" rid="pone.0014631-LpezGappa1">[108]</xref>, as
well as deep waters in the outer Uruguayan shelf and slope <xref ref-type="bibr" rid="pone.0014631-Carranza1">[109]</xref> and in outer Buenos
Aires province. The coastal transition between both faunistic assemblages occurs
around 43°–44°S. On the continental shelf, it follows a
southwest–northeast direction around 70–100 m depth. In some benthic
taxa (e.g., Amphipods) only 15.3% of marine benthic species known to
Brazil have also been found in Argentina, suggesting that the Río de la
Plata estuary may act as a biogeographic barrier for many warm-temperate and
subtropical species. However, most Magellanic species that occur in southern
Chile extend to the southwest Atlantic <xref ref-type="bibr" rid="pone.0014631-LpezGappa1">[108]</xref>, <xref ref-type="bibr" rid="pone.0014631-Carranza2">[110]</xref>.</p><sec id="s4c1"><title>Marine biodiversity in the Patagonian Shelf: Argentina and
Uruguay</title><p>Total marine biodiversity of Argentina and Uruguay is 3,776 species,
invertebrates accounting for nearly 75% of total records. Mollusca
(22.5%), Crustacea (16.2%), and Pisces (14.3%) were the
most diverse taxa, and together with the echinoderms, cnidarians, and
macroalgae account for 65.3% of the total (<xref ref-type="table" rid="pone-0014631-t004">Table 4</xref> and <xref ref-type="supplementary-material" rid="pone.0014631.s005">S5</xref>).
The number of species listed in the OBIS database is nearly 3,200 (<xref ref-type="table" rid="pone-0014631-t002">Table 2</xref>), meaning that
important efforts have been carried out in this region by incorporating data
into the georeferenced format of OBIS. For most taxonomic groups, species
records in this region need thorough revision, however, the estimated number
of taxonomists devoted to invertebrates in this region is low, and most are
focused on mollusks and crustaceans.</p><table-wrap id="pone-0014631-t004" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0014631.t004</object-id><label>Table 4</label><caption><title>Summary of the diversity, state of knowledge, and expertise of
the main taxonomic groups within the Patagonian Shelf subregion of
South America.</title></caption><alternatives><graphic id="pone-0014631-t004-4" xlink:href="pone.0014631.t004"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col></colgroup><thead><tr><td align="left" rowspan="1" colspan="1">Taxonomic group</td><td align="left" rowspan="1" colspan="1">No. species<xref ref-type="table-fn" rid="nt107">1</xref></td><td align="left" rowspan="1" colspan="1">State of knowledge</td><td align="left" rowspan="1" colspan="1">No. introduced species</td><td align="left" rowspan="1" colspan="1">No. experts</td><td align="left" rowspan="1" colspan="1">No. ID guides<xref ref-type="table-fn" rid="nt108">2</xref></td></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1"><bold>Domain Archaea</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Domain Bacteria (including Cyanobacteria)</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Domain Eukarya</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Kingdom Chromista</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Phaeophyta</td><td align="left" rowspan="1" colspan="1">59</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1"><5</td><td align="left" rowspan="1" colspan="1"><10</td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Kingdom Plantae</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Chlorophyta</td><td align="left" rowspan="1" colspan="1">59</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1"><5</td><td align="left" rowspan="1" colspan="1"><10</td></tr><tr><td align="left" rowspan="1" colspan="1">Rhodophyta</td><td align="left" rowspan="1" colspan="1">145</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Angiospermae</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Kingdom Protista (Protozoa)</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Dinomastigota (Dinoflagellata)</td><td align="left" rowspan="1" colspan="1">-</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Foraminifera</td><td align="left" rowspan="1" colspan="1">15</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Kingdom Animalia</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Porifera</td><td align="left" rowspan="1" colspan="1">252</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Cnidaria</td><td align="left" rowspan="1" colspan="1">258</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Platyhelminthes</td><td align="left" rowspan="1" colspan="1">36</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Mollusca</td><td align="left" rowspan="1" colspan="1">849</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Annelida</td><td align="left" rowspan="1" colspan="1">205</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">>30</td><td align="left" rowspan="1" colspan="1">>10</td></tr><tr><td align="left" rowspan="1" colspan="1">Crustacea</td><td align="left" rowspan="1" colspan="1">611</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">9</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Bryozoa</td><td align="left" rowspan="1" colspan="1">143</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Echinodermata</td><td align="left" rowspan="1" colspan="1">207</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Urochordata (Tunicata)</td><td align="left" rowspan="1" colspan="1">20</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">6</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Other invertebrates</td><td align="left" rowspan="1" colspan="1">181</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Vertebrata (Pisces)</td><td align="left" rowspan="1" colspan="1">539</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">>10</td><td align="left" rowspan="1" colspan="1">>5</td></tr><tr><td align="left" rowspan="1" colspan="1">Other vertebrates</td><td align="left" rowspan="1" colspan="1">197</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>SUBTOTAL</bold></td><td align="left" rowspan="1" colspan="1"><bold>3776</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><bold>33</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>TOTAL REGIONAL DIVERSITY</bold><xref ref-type="table-fn" rid="nt109">3</xref></td><td align="left" rowspan="1" colspan="1"><bold>3776</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr></tbody></table></alternatives><table-wrap-foot><fn id="nt107"><label>1</label><p>Sources of the reports: databases, scientific literature, books,
field guides, technical reports.</p></fn><fn id="nt108"><label>2</label><p>Identification guides cited in Text S2.</p></fn><fn id="nt109"><label>3</label><p>Total regional diversity, including all taxonomic groups as
reported in <xref ref-type="supplementary-material" rid="pone.0014631.s005">Table S5</xref>.</p></fn></table-wrap-foot></table-wrap><p>Globally, 129 species of marine mammals have been described, and 44 of those
occur in the southwestern Atlantic. These include members of three families
of Misticeti (seven species of whales) and five families of Odontoceti (27
species). From 36 known species of pinnipeds, 10 were reported for the
Patagonian Shelf. Four breed in Uruguayan and Patagonian coasts, and six
species have frequent or occasional presence while migrating beyond
Antarctic waters. Sixteen percent of the marine mammals occurring in the
southwest Atlantic Ocean are endemic or limited in distribution (La Plata
River dolphin, Austral dolphin, and Commerson dolphin). Some are
representatives of distant populations in the Southern Hemisphere, such as
the Commerson dolphin observed in the mouth of rivers and bays in Patagonia.
The southern right whale breeds in waters of the north Patagonian gulfs, the
second most important reproductive area after South Africa in terms of
number of animals. Species with relatively small populations but high
aesthetic value, such as the killer whale, are also commonly observed in
Patagonia, with only some dozens of individuals. The most important
biodiversity of marine mammals has been recorded around Cabo Polonio in
Uruguay and from Río Negro Province to Beagle channel in Argentina.
In Río Negro the sea lions breed under the cliffs at Islote Lobos and
San Matías Gulf.</p><p>Marine and coastal birds are relatively well known in the Patagonian Shelf
region, where there are 147 recorded species belonging to nine orders and 24
families. Seabirds comprise over 60 species, of which penguins represent the
largest biomass. This group includes 18 species that breed and feed in the
shelf waters, and the rest breed in other regions, such as Antarctica or New
Zealand, and use the area as feeding grounds <xref ref-type="bibr" rid="pone.0014631-Favero1">[111]</xref>. The breeding
distribution of seabirds along the Patagonian coast of Argentina and the
Uruguayan coast is relatively well known, totaling close to 300 colonies of
between one and eight species each <xref ref-type="bibr" rid="pone.0014631-Escalante1">[112]</xref>, <xref ref-type="bibr" rid="pone.0014631-Yorio1">[113]</xref>.
Highest species diversity and abundance of breeding seabirds is found in
central and southern Patagonia (Chubut and Santa Cruz Provinces) and the
Malvinas/Falkland Islands <xref ref-type="bibr" rid="pone.0014631-Yorio1">[113]</xref>, <xref ref-type="bibr" rid="pone.0014631-Woods1">[114]</xref>. Less is known about their distribution at sea,
although surveys have been conducted in waters of the Malvinas/Falkland
Islands <xref ref-type="bibr" rid="pone.0014631-White1">[115]</xref> and several studies have tracked seabirds during
their feeding and migration trips <xref ref-type="bibr" rid="pone.0014631-BirdLife1">[116]</xref>, <xref ref-type="bibr" rid="pone.0014631-Falabella1">[117]</xref>.
The coasts of this region are also important feeding and resting sites for
close to 20 nearctic and Patagonian migratory shorebirds, and the migratory
patterns of some of them are well known. Little is known, however, about the
distribution and abundance patterns of the rest of the coastal bird species.
Twenty-five of the birds recorded in this PS are listed as threatened by
Birdlife International.</p><p>Marine invertebrate groups from Argentina and Uruguay present great diversity
and have not been studied in their totality. For example, the molluscan
fauna (0–50 m) from Uruguay is composed of more than 380 marine and
estuarine species <xref ref-type="bibr" rid="pone.0014631-Scarabino1">[21]</xref>, <xref ref-type="bibr" rid="pone.0014631-Scarabino3">[118]</xref>. In front of
Río de la Plata (Banco Inglés), 25 macroinvertebrate taxa were
registered, including 1 ophiurid, 1 bryozoan, 4 crustaceans, and 4
polychaetes, of which the mollusks are the dominant group: 15 species, 1
Polyplacophora, 8 Bivalvia, 6 Gastropoda (1 invasive), represented by 11
families and 11 genera <xref ref-type="bibr" rid="pone.0014631-Carranza3">[119]</xref>. Exposed sites on the rocky shores of the Cabo
Dos Bahias protected area (Chubut Province, Argentina), harbor a great
diversity of species <xref ref-type="bibr" rid="pone.0014631-Bertness1">[120]</xref>. In San Sebastián Bay (Tierra del Fuego)
113 macroinvertebrate benthic taxa were recorded, representing 12 phyla
typical of the Magellanic Biogeographic Province, <xref ref-type="bibr" rid="pone.0014631-LpezGappa2">[121]</xref>. In a study of the
macrozoobenthos of the Beagle Channel, 32,500 organisms from 34 taxa were
recorded; of which Bivalvia and Polychaeta were the most abundant, while
Asteroidea and Decapoda dominated in biomass <xref ref-type="bibr" rid="pone.0014631-Diez1">[122]</xref>. A survey on the
amphipod biodiversity showed a total of 43 families, 118 genera, and 212
species registered in the Argentina and Magellanic biogeographic provinces
(including Malvinas Islands) from 36° to 56°S <xref ref-type="bibr" rid="pone.0014631-LpezGappa1">[108]</xref>. Some 15 species of
Volutid snails are endemic to the Atlantic Patagonian shelf and adjacent
areas <xref ref-type="bibr" rid="pone.0014631-Bigatti2">[123]</xref>. The Burwood Bank (east of Isla de los Estados)
has great abundance and diversity of endemic species, including 22 species
of isopods and 12 species of bivalves <xref ref-type="bibr" rid="pone.0014631-Scarabino1">[21]</xref>, <xref ref-type="bibr" rid="pone.0014631-Scarabino3">[118]</xref>,
<xref ref-type="bibr" rid="pone.0014631-Bigatti2">[123]</xref>, <xref ref-type="bibr" rid="pone.0014631-Zelaya1">[124]</xref>.</p><p>Concerning regional flora, about 45% of the species occurring in the
Uruguayan coast represent a southern extension of the subtropical
distribution, and about 38% are a northern extension of the
warm-temperate flora with several cosmopolitan species. Therefore, typical
representatives of a tropical or temperate flora are equally absent in the
region <xref ref-type="bibr" rid="pone.0014631-Coll1">[125]</xref>. More information is required to gain a better
understanding of seaweed diversity along the coast of the southwestern
Atlantic. At present there are few taxonomists in Argentina and in Uruguay.
To have good, reliable taxonomic information, it is necessary that young
researchers incorporating new techniques (including environmental genetics)
advance the exploration of poorly studied areas.</p></sec><sec id="s4c2"><title>Threats and conservation strategies in the Patagonian Shelf</title><p>Within the the Patagonian Shelf region, Sullivan and Bustamante <xref ref-type="bibr" rid="pone.0014631-SullivanSealey1">[53]</xref>ranked the Uruguay–Buenos Aires Shelf ecoregion high in biological
importance and need for conservation actions, because the area presents high
biological productivity, abundant populations of finfish, and numerous
marine mammals and seabirds that feed upon those fish. Intensive fisheries
in the Patagonian region are limited to a few species of fishes and
invertebrates, and 10 species (seven fish, one squid, one shrimp, and one
bivalve) represent 85% of the catch <xref ref-type="bibr" rid="pone.0014631-FCMPAI1">[98]</xref>, <xref ref-type="bibr" rid="pone.0014631-Defeo1">[104]</xref>, <xref ref-type="bibr" rid="pone.0014631-Caete1">[126]</xref>. At least 15 species
that inhabit this region, mainly birds and mammals, provide some of the
greatest examples of marine fauna on the planet <xref ref-type="bibr" rid="pone.0014631-Falabella1">[117]</xref>. As top predators,
these species play key and varied roles in the marine ecosystem.
Albatrosses, petrels, penguins, sea lions, and elephant seals require large
areas and abundant food supplies for their survival. The International Union
for Conservation of Nature (IUCN) has evaluated 223 species from the
Patagonian region, and of these, 65 species are actually endangered, 39 of
them fishes, 5 mammals, 16 birds, and 5 turtles <xref ref-type="bibr" rid="pone.0014631-FCMPAI1">[98]</xref>.</p><p>In general, major threats to marine biodiversity include fisheries
overexploitation, habitat deterioration, and invasion of exotic species. The
most serious threats to vertebrates are overfishing, bycatch of seabirds,
marine mammals, and turtles, as well as degradation of coastal and marine
environments, urban pollution, and pollution from industrial activities such
as fishing and oil exploration, exploitation, and transport. Threats to
marine invertebrates biodiversity include degradation and disturbance of
environments, urban development in coastal areas, dredging, resuspension of
sediment, establishment and operation of ports, presence of exotic species,
tourist use, global and local aquatic contamination, fisheries targeting for
invertebrate species or bycatch resulting from dredging <xref ref-type="bibr" rid="pone.0014631-Bigatti2">[123]</xref>.
Activities carried out with bottom nets are also responsible for
modifications in the communities, which are generally slow to recover, even
after the activities stop. Bottom trawling dominates coastal and deep-sea
fishing and produces large amounts of discards of benthic invertebrates,
equivalent to 80% of the catch <xref ref-type="bibr" rid="pone.0014631-OrensanzLobo1">[127]</xref>. Bycatch affects
at least four species of marine turtles, some 20 species of birds, and seven
species of mammals (sea lions, elephant seals, and dolphins) as well as fish
and marine invertebrates. For example, an estimated 7,000 albatrosses and
petrels belonging to 12 species were killed as a result of interaction with
longline fishing vessels between 1999 and 2001. In the hake fishery, 37
species of fish, crustaceans, and mollusks (including the Argentine squid,
<italic>Illex argentinus</italic>) are caught and discarded. Between
35,900 and 42,000 tons of hake were caught in 2002 as bycatch in the trawl
fishery targeting the Argentine red shrimp, <italic>Pleoticus
muelleri</italic><xref ref-type="bibr" rid="pone.0014631-Caete1">[126]</xref>. In
Uruguay, 55 species of macroinvertebrates were recorded in the fisheries of
the volutid <italic>Zidona dufresnei</italic>. The fishery targeting for the
scallops <italic>Psichrochlamys patagonica</italic> and <italic>Aequipecten
tehuelchus</italic> is the largest scallop fishery in the world, with
catches of more than 11,000 tons in 2006, exploiting banks with a total area
of 11,250 km<sup>2</sup><xref ref-type="bibr" rid="pone.0014631-OrensanzLobo1">[127]</xref>.</p><p>In recent years, a series of biological invasions including algae, mollusks,
hydroids, bryozoans, ascidiaceans, and crustaceans occurred in marine
environments because of involuntary transport or voluntary introduction,
always with severe consequences not only for the local biodiversity but also
from an economical perspective <xref ref-type="bibr" rid="pone.0014631-Bigatti2">[123]</xref>, <xref ref-type="bibr" rid="pone.0014631-OrensanzLobo2">[128]</xref>–<xref ref-type="bibr" rid="pone.0014631-Schwindt1">[130]</xref>. This problem
constitutes a serious threat to biological diversity in the area. At least
41 non-native species have been recorded, especially invertebrates and algae
<xref ref-type="bibr" rid="pone.0014631-OrensanzLobo2">[128]</xref>. <italic>Undaria pinnatifida</italic> is a
successful invasive seaweed widespread along a large area of the coast of
Patagonia. Its presence is associated with a dramatic decrease in species
richness and diversity of native seaweeds. This impact should be considered
not only from a biodiversity point of view but also from an economic
perspective <xref ref-type="bibr" rid="pone.0014631-Casas1">[131]</xref>. <italic>Undaria</italic> has been found
widespread in populations of the agar-producing red alga
<italic>Gracilaria</italic> and recently was reported settled on
shellfish commercial beds (M.L. Piriz, personal communication). Even when
native sea urchins feed on <italic>Undaria</italic>, they are unlikely to
play a role in the control of this kelp <xref ref-type="bibr" rid="pone.0014631-Teso1">[132]</xref>.</p><p>In Argentina, there are currently 45 coastal and marine protected areas aimed
at protecting marine or coastal resources <xref ref-type="bibr" rid="pone.0014631-Sapoznikow1">[133]</xref>, <xref ref-type="bibr" rid="pone.0014631-Yorio2">[134]</xref>. The
strong interest in coastal resources has resulted in the designation of
protected areas in which the extension of marine environments is in general
relatively small or simply lacking <xref ref-type="bibr" rid="pone.0014631-Yorio2">[134]</xref>. Thus, only 16 of these
protected areas include adjacent waters, while the rest protect exclusively
terrestrial environments on the coast. However, these coastal protected
areas include marine organisms, such as seabirds and marine mammals, among
their main conservation targets. Recent initiatives, led mainly by the
National Parks Administration of Argentina, are focusing on the designation
of new marine parks that include larger areas of marine waters. In the
Malvinas Islands, there are 17 natural reserves with significant coastal
habitat <xref ref-type="bibr" rid="pone.0014631-FCMPAI1">[98]</xref>.</p><p>In Uruguay, there is an incipient process to implement the first Marine
Protected Areas. The newly developed National System of Protected Areas is
responsible for this process, and there are currently three coastal areas
considered (Santa Lucía, Cabo Polonio, and Cerro Verde). In addition,
there are proposals for a network of marine protected areas <xref ref-type="bibr" rid="pone.0014631-Defeo1">[104]</xref>. The
banning of hunting in the 1960s was the first national strategy for the
conservation of marine mammals in Argentina. Then, emblematic species such
as the southern right whale prompted specific protective initiatives such as
National Natural Monuments (Law 23.094/84). Uruguay (1998) also adopted the
protection and conservation of cetaceans and pinnipeds. Relevant actions for
conservation are aimed at the creation of more protected areas, development
management, and mitigation plans, including education and scientific
research. For benthic species, the most important feature requiring urgent
conservation is the habitat, which can be done by avoiding or minimizing the
effects of the dredging nets. Recently, ecosystem-based fishery management
and Marine Protected Areas are emerging as promising tools to conserve
marine environments, in view of declining fisheries indicators in the region
<xref ref-type="bibr" rid="pone.0014631-Defeo1">[104]</xref>,
<xref ref-type="bibr" rid="pone.0014631-Mugetti1">[135]</xref>, <xref ref-type="bibr" rid="pone.0014631-Milessi1">[136]</xref>. In this sense, the Secretary of Environment and
Sustainable Development and the Federal Fishery Council of Argentina
recently (2009) banned “totally and permanently” fisheries
activities in the Burwood Bank (<ext-link ext-link-type="uri" xlink:href="http://www.ambiente.gov.ar">www.ambiente.gov.ar</ext-link>).
This zone presents high biodiversity and endemism, and the policy is in
agreement with the conservation of marine bottom environments in relation to
Argentine commitments with UN Food and Agriculture Organization. An
international, ecoregional conservation program will contribute to the
continuity of the ecological processes supporting the rich biodiversity of
this subregion. This will be critical to ensure ecosystem resilience and
adaptation to a changing environment, maintaining ecosystem processes and
sustainable use of marine resources.</p></sec></sec><sec id="s4d"><title>Subregion 4: The Brazilian Shelves - North, South, and East</title><p>Brazil has the longest coastline in South America, extending 7,491 km on the
Atlantic coast of South America from Brazil's border with French Guiana in
the north at Cape Orange (4°20′20″S, 51°22′12″W)
to its southern border with Uruguay at Chuí (33°51′21″S,
53°11′43″W). Its territorial sea includes the 12 nautical miles
from the coastline, the maritime zone that begins in the coastal region,
including the marine continental shelf and the exclusive economic zone that
extends 200 nautical miles from the coast. Besides this area, Brazil has
successfully pleaded to the United Nations for an addition of 900 km<sup>2</sup>where the continental shelf extends beyond the 200 nautical miles based on the
UN Convention on the Law of the Sea. This means that the Brazilian
jurisdictional waters now comprise 4.5 million km<sup>2</sup> and have been
designated by the Interministerial Committee on the Sea Resources (CIRM, acronym
in Portuguese) as the “Blue Amazon.”</p><p>The Brazilian continental shelf and margin are very heterogeneous. The shelf is
narrowest in the Northeast Region (8 km off Recife) and widest both off the
Amazon River in the north (∼300 km), and in the south off Rio Grande do Sul
(246 km). Apart from the Amazon, there are other important river outflows such
as the São Francisco in the Northeast Region, the Pardo, Doce, and
Jequitinhonha in the central part of the country, Paraíba do Sul, and the
combination of the La Plata and Patos Lagoon outflows in the South Region <xref ref-type="bibr" rid="pone.0014631-Castro1">[137]</xref>. Also, the
continental shelf breaks at different depths depending on the region:
80–100 m in the North Region; 60–70 m in the Northeast and northern
Southeast regions from the Vitória-Trindade ridge to the north;
160–200 m in the southern part of the Southeast and South regions. Around
70% of the Brazilian exclusive economic zone defined between 12 and 200
miles off the coast is within the slope and abyssal zones. The slope is much
steeper in the Northeast and Southeast regions than in the North and South
regions and also comprises a variety of deep-sea canyons, cold corals, and cold
seeps.</p><p>The western South Atlantic including its seamounts and topographic ridges has
been formed since the opening of the Atlantic Ocean around 110 million years
ago. The northern Brazilian margin has several major topographic highs that form
the North Brazilian Ridge and several scattered seamounts rising from the ocean
floor. These constrain the North Atlantic Deep Water flow, causing turbulence
and upwelling due to the seamounts topography <xref ref-type="bibr" rid="pone.0014631-Campos1">[138]</xref>. Large erosional and
accretionary forces in the Amazon River mouth, caused by water boils,
crosscurrents, eddies, and tides, result in unstable channels and banks with few
stable points <xref ref-type="bibr" rid="pone.0014631-Agard1">[139]</xref>–<xref ref-type="bibr" rid="pone.0014631-Gibbs1">[141]</xref>. Fluid muds occur on the
inner shelf north of the river mouth. However, south of the Amazon mouth, the
lack of sediment influx has resulted in a complexly embayed erosional coastline
<xref ref-type="bibr" rid="pone.0014631-Torres1">[142]</xref>. The
Amazon Fan area is stable tectonically, with subsidance rates of 5–20 cm
in a thousand years, but it is not quiescent. Numerous earthquakes within the
last 20 years have recorded magnitudes of 3.0 to 4.8 <xref ref-type="bibr" rid="pone.0014631-Nittrouer1">[163]</xref>. Besides earthquake
activity, near-surface faults and large methane gas deposits also create
unstable seabed conditions <xref ref-type="bibr" rid="pone.0014631-Damuth1">[143]</xref>. High-resolution seismic profiles near the shelf
edge show evidence of near-surface slumps and faulting 20–50 m in the
subsurface and concentrations (about 500 m<sup>2</sup>) of methane gas <xref ref-type="bibr" rid="pone.0014631-Damuth1">[143]</xref>. Several
studies (e.g., Amazon Shelf Study—AMASEDS, LEPLAC, REMAC, GLORIA, Ocean
Drilling Program—ODP) indicate that there is evidence for gas seepage on
the slope off the Amazon fan based on the incidence of bottom-simulating
reflections (BSRs), mud volcanoes, pock marks, gas in sediments, and deeper
hydrocarbon occurrences. The existence of methane at relatively shallow depths
and extensive areas of gas hydrates have been mapped in this region. Also, gas
chimneys have been reported, and exploratory wells have discovered subcommercial
gas accumulations and pock marks along fault planes. A sound geological and
geophysical understanding of the Foz do Amazonas Basin is already available and
used by the energy companies.</p><p>A major oceanic plateau occurs off the eastern boundary of the Amazon cone: the
Ceara Rise. The Fernando de Noronha Ridge formed by a seamount ridge and
basement highs occurs at the western extremity of the Romanche Trench off the
Northeast Region of Brazil. Along this ridge, the Atol das Rocas is on the
western side of the flat top of a seamount, and oceanic basalt outcrops form the
Fernando de Noronha Island at the eastern extreme of this ridge. Basaltic rocks
are close to the surface at the Atol das Rocas, but only shallow-water
carbonates outcrop <xref ref-type="bibr" rid="pone.0014631-Kikuchi1">[144]</xref>. This is one of the first marine protected areas
created in Brazil because of the intense bird and turtle activities and also
rich marine life <xref ref-type="bibr" rid="pone.0014631-Kikuchi1">[144]</xref>. Many other seamounts, such as the Pernambuco and
Bahia seamounts, occur along fracture zone lines farther south.</p><p>The Victoria-Trindade Ridge comprises seamounts arising from the Brazilian
continental margin toward the Mid-Atlantic Ridge, with volcanic rock
outcroppings at Trindade and Martin Vaz oceanic islands at the eastern extremity
of this chain, about 1,050 km from the continent. Between the continental margin
and Trindade, the other seamounts on this ridge rise from around 5,000 m in the
southwest Atlantic abyssal plain, but have fairly shallow summits at depths of
34–76 m. Along the eastern Brazilian continental margin, several plateaus
can be found, but the major ones are the Abrolhos Bank and Pernambuco Plateau,
and smaller ones such as João Pessoa and Rio Grande do Norte
Plateaus.</p><p>The large Sao Paulo Plateau is in the southern region off Brazil, and its
southern edge is formed by a sharp volcanic ridge with more than 2,000 m relief
and with several seamounts at its eastern boundary <xref ref-type="bibr" rid="pone.0014631-Jinno1">[145]</xref>. According to these
authors, a broad aseismic ridge occurs to the southeast of the São Paulo
plateau. These topographic features also form a major barrier to the Antarctic
Atlantic Bottom Water (AABW), which flows northward through the Vema channel
<xref ref-type="bibr" rid="pone.0014631-Gamboa1">[146]</xref>,
<xref ref-type="bibr" rid="pone.0014631-Gamboa2">[147]</xref>.
According to Campos et al. <xref ref-type="bibr" rid="pone.0014631-Campos1">[138]</xref>, major upwelling and turbulent submarine flows are
likely to occur on the flanks of these topographic highs, and the occurrence of
cobalt crusts and manganese nodules can be expected in the abyssal areas.</p><p>The climate of the Brazilian coast generally depends on the South Atlantic
tropical and polar anticyclones, the latter with its cold air mass originating
in southern Argentina <xref ref-type="bibr" rid="pone.0014631-Valentin1">[148]</xref>, or in the Weddell Sea in the Antarctic region
(Aquino personal communication). Over the last few centuries, the wind regime
oscillation has been the major factor causing water temperature variability
<xref ref-type="bibr" rid="pone.0014631-Mahiques1">[149]</xref>.
This also greatly influences the displacement of water masses and the occurrence
of eddies and upwellings of seawater in the subantarctic (South Atlantic Central
Water) especially in the Southeast and South regions of Brazil <xref ref-type="bibr" rid="pone.0014631-Valentin1">[148]</xref>.</p><p>Meridional temperature gradients characterize the South Atlantic, where the sea
surface temperature increases with latitude and decreases toward the southern
region <xref ref-type="bibr" rid="pone.0014631-RossiWongtschowski1">[150]</xref>. Warmer temperatures from the South Equatorial
Current dominate the margin north of the Vitória-Trindade Ridge at the
north-northeastern border where they meet cooler waters from the North
Equatorial Current. South of the Vitória-Trindade Ridge, water masses are
more stratified as the southward flow of the Brazil Current encounters the
subtropical gyre south of Rio de Janeiro <xref ref-type="bibr" rid="pone.0014631-Silveira1">[151]</xref>. Each year, during the
first semester, five water masses are dominant at 20°S: (1) the Tropical
Water (TW) from surface to 200 m (22°C–27°C and salinity
36.5–37); (2) the SACW from 200 to 660 m (6°C–18.5°C and
salinity 34.5–36.4); (3) the Antarctic Intermediate Waters (AIW) from 700
to 1,200 (4°C–10°C and salinity 34.2–34.8); (4) the North
Atlantic Deep Water (NADW) from 1,200 to 2,000 m (3°C–4°C and
salinity 34.6–35); and (5) the Atlantic Antarctic Bottom Water (AABW) at
abyssal depths (0.5°C and salinity 34.60) <xref ref-type="bibr" rid="pone.0014631-Silveira1">[151]</xref>–<xref ref-type="bibr" rid="pone.0014631-Pedrosa1">[154]</xref> (<xref ref-type="fig" rid="pone-0014631-g003">Figure 3</xref>).</p><p>The Brazilian continental margin is strongly influenced by the western contour
currents. There are two major contour currents detected at the surface: the
Brazil Current (BC) flowing southward and the Brazilian Northern Current (BNC)
flowing northward <xref ref-type="bibr" rid="pone.0014631-Castro1">[137]</xref>. The BC, which is shallowest between 15° and
20°S, transports saline, oligotrophic tropical waters, and as it reaches the
Vitória-Trindade Ridge, it receives additional contribution from the
South Atlantic Central Waters (SACW), reaching a vertical extension of about 500
m, and continues to flow southward toward the Subtropical Convergence
(33°–38°S) where it merges with the Malvinas Current and then
flows away from the coast to the east <xref ref-type="bibr" rid="pone.0014631-Gordon1">[155]</xref> (<xref ref-type="fig" rid="pone-0014631-g002">Figure 2</xref>).</p><p>The BC changes direction near Cabo Frio in the state of Rio de Janeiro as a
wind-driven process following the continental margin to the southwest and
causing eddies throughout the year <xref ref-type="bibr" rid="pone.0014631-Podesta1">[156]</xref>. This process promotes
the upwelling of the SACW, which is rich in nutrients <xref ref-type="bibr" rid="pone.0014631-MoreiraDaSilva1">[157]</xref>, <xref ref-type="bibr" rid="pone.0014631-Valentin2">[158]</xref>,
enhancing fisheries biodiversity and biomass in the region <xref ref-type="bibr" rid="pone.0014631-Brandini1">[159]</xref>. The BC increases in
volume as it reaches the south of Cape Santa Marta Grande because of the
intermediate portion of the subtropical gyre circulation (500–1,200 m).
The AIW is transported at this depth range, and the BC becomes more than 1,000 m
thick as it flows through the South American Atlantic southern continental
margin <xref ref-type="bibr" rid="pone.0014631-Silveira3">[160]</xref>. The AIW receives the Intermediate Contour Current (ICC)
at intermediate levels around 28°S. The ICC flows northward, contours the
Vitória-Trindade Ridge, and receives a contribution at the level of the
Southern Equatorial Current branch at 19°S, forming the Brazilian Northern
Subcurrent (BNS). This transports the SACW and AIW toward the equator, and it
strengthens toward the northern part of Cape Branco in Paraíba as a
result of its fusion with the BNC and equatorial branches of the South
Equatorial Current <xref ref-type="bibr" rid="pone.0014631-Vink1">[161]</xref>. This allows the BNC to cross the equator moving
away from South America at 10°N. According to Vink et al. <xref ref-type="bibr" rid="pone.0014631-Vink1">[161]</xref>, the
Brazilian North and Northeast regions are strongly influenced by the BNC.</p><p>The BNC reaches speeds of 1–2 m/s, forcing the Amazon River water and
sediments to the northwest. The Amazon shelf in itself is a dynamic region, and
dominated by the effluent of the Amazon River, which has a mean annual transport
of approximately 1.8×10<sup>5</sup> m<sup>3</sup>/s of freshwater flowing
into the Atlantic Ocean <xref ref-type="bibr" rid="pone.0014631-Curtin1">[162]</xref> and depositing a daily average of 3 million tons of
sediment near its mouth <xref ref-type="bibr" rid="pone.0014631-Torres1">[142]</xref>, <xref ref-type="bibr" rid="pone.0014631-Nittrouer1">[163]</xref>. The annual outflow from the river accounts for
20% of all the freshwater that drains into the oceans of the world <xref ref-type="bibr" rid="pone.0014631-Moore1">[164]</xref>. Waters
from the Amazon River can migrate as far north as Barbados and as far as 320 km
offshore.</p><p>The South Atlantic is possibly a major corridor to the deep Atlantic oceanic
circulation with the northward flow of the AABW, which originates especially in
the Weddell Sea, and the southward flow of the NADW above it <xref ref-type="bibr" rid="pone.0014631-Boltovskoy2">[152]</xref>. The
latter greatly contributes to the circulation toward the east and upwells at the
Antarctic Divergence at 60°S. The circulation of water masses, especially
the deep-water circulation, is greatly influenced by all topographic features
along the Brazilian continental margin and the presence of adjacent seamounts.
The southwest Atlantic thermocline is well marked with its upper limit between
50 and 100 m, but its depth varies depending on latitude and season, being
deeper in the winter at highest latitudes. Near the seamounts with shallow
summits (e.g., those at the Vitória-Trindade Ridge or at the North
Brazilian Ridge), local turbulence because of the upwelling effects disturbs the
thermocline <xref ref-type="bibr" rid="pone.0014631-RossiWongtschowski1">[150, and authors therein]</xref>.</p><p>Considering the heterogeneity of the Brazilian continental shelf, margin,
adjacent seamounts, and abyssal plain, the very large Brazilian marine ecosystem
<xref ref-type="bibr" rid="pone.0014631-Prescott1">[165]</xref>–<xref ref-type="bibr" rid="pone.0014631-McGlinley2">[168]</xref> is hydrologically and
topographically complex. In fact, it has contrasting dominant ecosystems of
unique features, including mangroves, coral reefs, dunes, sand banks, sandy
beaches, rocky shores, lagoons, estuaries, and salt marshes, all of which host
an uncountable number of flora and fauna species with high levels of endemism.
Some species are in danger of extinction, while others are detected as being
invasive. Despite its low productivity (less than 150 gC/m<sup>2</sup>/y, based
on SeaWiFS global primary productivity estimates) (<xref ref-type="fig" rid="pone-0014631-g004">Figure 4</xref>), this whole “Blue
Amazon” has a high marine biodiversity <xref ref-type="bibr" rid="pone.0014631-McGlinley1">[167]</xref>, and its deep seas
include a variety of ecosystems such as canyons, gregarious kelp, coralline and
sponge systems, pock marks, seamounts, and abyssal plains with manganese nodules
and other mineral resources <xref ref-type="bibr" rid="pone.0014631-Campos1">[138]</xref>, <xref ref-type="bibr" rid="pone.0014631-Viana1">[169]</xref>–<xref ref-type="bibr" rid="pone.0014631-Hovland1">[174]</xref>.</p><sec id="s4d1"><title>Marine biodiversity in the Brazilian Shelf</title><p>A total of 9,103 species have been reported in Brazilian waters (<xref ref-type="table" rid="pone-0014631-t005">Tables 5</xref> and <xref ref-type="supplementary-material" rid="pone.0014631.s006">S6</xref>).
The most diverse taxa in the region's marine coastal waters are the
crustaceans (1,966 species), followed by the mollusks (1,833 species), the
fishes (1,294), and the polychaetes (987 species), which together account
for 66.79% of the total known biota. While most of the available
information on marine biodiversity is about the continental shelf, Brazil
also has a number of significant publications on the slope, the seamounts
and oceanic islands, and the abyssal plains (<xref ref-type="supplementary-material" rid="pone.0014631.s007">Table
S7</xref>). These publications derive from many cruises along the
Brazilian coast, deeper stations mainly at the southeast offshore, but also
deep-sea fishing in the North and Northeast regions (<xref ref-type="supplementary-material" rid="pone.0014631.s008">Table
S8</xref>). Most of the deep-sea research has been relatively recent
(since 1986) and focused on fish, macrobenthic invertebrates, and
zooplankton, while the best-studied areas have been the Campos Basin, the
North Brazilian Ridge, Fernando de Noronha, and Vitória-Trindade
Ridge. As for the continental shelf, most of the knowledge on marine
biodiversity has been gathered from the north of Brazil, part of the
northeastern coast, and those from the southern regions derive from the
continental shelf shallow waters. The Brazilian continental shelf, like most
shelves around the world, is subject to growing pressure from human
activities and holds the majority of fisheries resources <xref ref-type="bibr" rid="pone.0014631-PiresVanin1">[175]</xref>.
There are several articles on the taxonomy, phylogeny, biogeography,
biology, and ecology of many marine organisms, and also community data
available from major national programs such as the REVIZEE (Assessment of
the Sustainable Potential of Living Resources of the Brazilian Exclusive
Economic Zone), which encompassed the whole of the Brazilian coast. Some
examples are provided in <xref ref-type="supplementary-material" rid="pone.0014631.s008">Table S8</xref>. Also, many studies are regional
and include several topics from taxonomy to marine communities, oceanography
studies, and conservation. An example of a comprehensive study is the OPISS
(Oceanografia da Plataforma Interna de Sao Sebastiao), which was carried out
at the Sao Sebastiao Continental Shelf on the northern coast of Sao Paulo
State <xref ref-type="bibr" rid="pone.0014631-PiresVanin1">[175]</xref>. This region is subject to a complex
hydrological regime with physiographic features determined by its proximity
to the Serra do Mar (mountains dominated by Atlantic Forest), the presence
of Sao Sebastiao Island, and the development of one of the most important
oil and gas terminals in Brazil <xref ref-type="bibr" rid="pone.0014631-PiresVanin1">[175]</xref>. Other fairly well
studied areas are the Guanabara Bay in Rio de Janeiro State <xref ref-type="bibr" rid="pone.0014631-Gomes1">[176]</xref>–<xref ref-type="bibr" rid="pone.0014631-Areas1">[188]</xref>; Ubatuba <xref ref-type="bibr" rid="pone.0014631-Fransozo1">[189]</xref>–<xref ref-type="bibr" rid="pone.0014631-Burone1">[192]</xref>, Cananéia in
São Paulo State <xref ref-type="bibr" rid="pone.0014631-Saul1">[193]</xref>, <xref ref-type="bibr" rid="pone.0014631-Cergole1">[194]</xref>; and Paranagua Bay in
Parana State <xref ref-type="bibr" rid="pone.0014631-Netto1">[195]</xref>–<xref ref-type="bibr" rid="pone.0014631-Lana2">[201]</xref>.</p><table-wrap id="pone-0014631-t005" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0014631.t005</object-id><label>Table 5</label><caption><title>Summary of the diversity, state of knowledge, and expertise of
the main taxonomic groups within the Brazilian Shelves subregion of
South America.</title></caption><alternatives><graphic id="pone-0014631-t005-5" xlink:href="pone.0014631.t005"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col></colgroup><thead><tr><td align="left" rowspan="1" colspan="1">Taxonomic group</td><td align="left" rowspan="1" colspan="1">No. species<xref ref-type="table-fn" rid="nt110">1</xref></td><td align="left" rowspan="1" colspan="1">State of knowledge</td><td align="left" rowspan="1" colspan="1">No. introduced species</td><td align="left" rowspan="1" colspan="1">No. experts</td><td align="left" rowspan="1" colspan="1">No. ID guides<xref ref-type="table-fn" rid="nt111">2</xref></td></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1"><bold>Domain Archaea</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Domain Bacteria (including Cyanobacteria)</bold></td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Domain Eukarya</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Kingdom Chromista</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Phaeophyta</td><td align="left" rowspan="1" colspan="1">106</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">8</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Kingdom Plantae</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Chlorophyta</td><td align="left" rowspan="1" colspan="1">201</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">8</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Rhodophyta</td><td align="left" rowspan="1" colspan="1">488</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">8</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Angiospermae</td><td align="left" rowspan="1" colspan="1">14</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Kingdom Protista (Protozoa)</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Dinomastigota (Dinoflagellata)</td><td align="left" rowspan="1" colspan="1">49</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Foraminifera</td><td align="left" rowspan="1" colspan="1">15</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Kingdom Animalia</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Porifera</td><td align="left" rowspan="1" colspan="1">400</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">15</td><td align="left" rowspan="1" colspan="1">2</td></tr><tr><td align="left" rowspan="1" colspan="1">Cnidaria</td><td align="left" rowspan="1" colspan="1">535</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">35</td><td align="left" rowspan="1" colspan="1">10</td></tr><tr><td align="left" rowspan="1" colspan="1">Platyhelminthes</td><td align="left" rowspan="1" colspan="1">45</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Mollusca</td><td align="left" rowspan="1" colspan="1">1833</td><td align="left" rowspan="1" colspan="1">2 to 4</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">36</td><td align="left" rowspan="1" colspan="1">7</td></tr><tr><td align="left" rowspan="1" colspan="1">Annelida</td><td align="left" rowspan="1" colspan="1">987</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">8</td><td align="left" rowspan="1" colspan="1">23</td><td align="left" rowspan="1" colspan="1">5+1 in prep.</td></tr><tr><td align="left" rowspan="1" colspan="1">Crustacea</td><td align="left" rowspan="1" colspan="1">1966</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">6</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Bryozoa</td><td align="left" rowspan="1" colspan="1">133</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Echinodermata</td><td align="left" rowspan="1" colspan="1">254</td><td align="left" rowspan="1" colspan="1">3 to 4</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">13</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Urochordata (Tunicata)</td><td align="left" rowspan="1" colspan="1">70</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Other invertebrates</td><td align="left" rowspan="1" colspan="1">308</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Vertebrata (Pisces)</td><td align="left" rowspan="1" colspan="1">1294</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">4+</td><td align="left" rowspan="1" colspan="1">3</td></tr><tr><td align="left" rowspan="1" colspan="1">Other vertebrates</td><td align="left" rowspan="1" colspan="1">178</td><td align="left" rowspan="1" colspan="1">4 to 5</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">40</td><td align="left" rowspan="1" colspan="1">2</td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>SUBTOTAL</bold></td><td align="left" rowspan="1" colspan="1"><bold>8878</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><bold>10</bold></td><td align="left" rowspan="1" colspan="1"><bold>196</bold></td><td align="left" rowspan="1" colspan="1"><bold>29</bold></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>TOTAL REGIONAL DIVERSITY</bold><xref ref-type="table-fn" rid="nt112">3</xref></td><td align="left" rowspan="1" colspan="1"><bold>9103</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr></tbody></table></alternatives><table-wrap-foot><fn id="nt110"><label>1</label><p>Sources of the reports: databases, scientific literature, books,
field guides, technical reports.</p></fn><fn id="nt111"><label>2</label><p>Identification guides cited in References and in <xref ref-type="supplementary-material" rid="pone.0014631.s007">Table S7</xref>.</p></fn><fn id="nt112"><label>3</label><p>Total regional diversity, including all taxonomic groups as
reported in <xref ref-type="supplementary-material" rid="pone.0014631.s006">Table S6</xref>.</p></fn></table-wrap-foot></table-wrap><p>Collections of marine organisms exist at several important institutions
throughout Brazil, such as Museu Emilio Goeldi (North Region); LABOMar (a
marine laboratory at the Universidade Federal do Ceará), Universidade
Federal de Pernambuco and Universidade Federal Rural de Pernambuco,
Universidade de Mossoró (Paraíba), all in the Northeast
Region; Museu Nacional and Instituto de Biologia at the Universidade Federal
do Rio de Janeiro; Museu de Zoologia, Departamento de Ecologia Geral
(Instituto de Biociências), Instituto Oceanográfico at the
Universidade de São Paulo, SP, and Museu de Zoologia da Universidade
Estadual de Campinas “Adão Jose Cardoso” (Southeast
Region); Departamento de Zoologia at the Universidade Federal do
Paraná, and the Museu Oceanográfico (Fundação
Universidade do Rio Grande, Rio Grande do Sul) in the South Region. Also,
several species lists and illustrated guides and manuals have been produced
recently including reviews on the biodiversity of the ecosystems in the
continental shelf <xref ref-type="bibr" rid="pone.0014631-Falco1">[202]</xref>–<xref ref-type="bibr" rid="pone.0014631-Hazin1">[221]</xref>.</p><p>According to the REVIZEE program, the Brazilian continental shelf and slope
(down to 2,076 m depth) have been divided into four sectors called
“scores”: North, Northeast, Central, and South. In each of these
scores, extensive surveys have been carried out to estimate the diversity
and abundance of planktonic, nectonic and benthic organisms and their
sustainable exploitation potential <xref ref-type="bibr" rid="pone.0014631-Amaral3">[212]</xref>, <xref ref-type="bibr" rid="pone.0014631-Lavrado2">[215]</xref>, <xref ref-type="bibr" rid="pone.0014631-Costa2">[222]</xref>, <xref ref-type="bibr" rid="pone.0014631-Costa3">[223]</xref>.</p><p>In the Brazilian North score, the freshwater from the Amazon River, rich in
nutrients, is responsible for the highest primary production in the country
(more than 300 gC/m<sup>2</sup>/yr, based on SeaWiFS global primary
productivity estimates) <xref ref-type="bibr" rid="pone.0014631-McGlinley2">[168]</xref>, <xref ref-type="bibr" rid="pone.0014631-McGlinley1">[167]</xref>. Most of what is
known about marine biodiversity in the north is related to fishing, mangrove
habitats, and data obtained through the REVIZEE program. About 30% of
Brazilian fishing takes place in the North Region, where Pará is the
country's second-largest landing port <xref ref-type="bibr" rid="pone.0014631-Isaac1">[224]</xref>–<xref ref-type="bibr" rid="pone.0014631-Pinheiro1">[226]</xref>.
Harvested species include catfish, corvina, sawfish, red porgy, lobsters,
and prawns. The region includes one of the main shrimp banks in the world,
extending from Tutóia in Maranhão to Orinoco in the Guiana,
mainly because of its extensive mangrove areas <xref ref-type="bibr" rid="pone.0014631-Isaac2">[227]</xref>, <xref ref-type="bibr" rid="pone.0014631-Coelho1">[228]</xref>. The mangroves sustain
high biodiversity of estuarine and marine organisms and represent important
nurseries for many species of fish, feeding grounds for some marine mammals
such as the manitees, and a nesting place for many species of seabirds <xref ref-type="bibr" rid="pone.0014631-AbreuJunior1">[229]</xref>,
<xref ref-type="bibr" rid="pone.0014631-Rosas1">[203]</xref>.</p><p>The Northeast score accounts for about 12% of the national fishing
(about 70,000 tons per year) and this fishing can be divided into two
groups: coastal fishing mainly on the continental shelf, and fishing near
islands and oceanic banks <xref ref-type="bibr" rid="pone.0014631-Ferreira1">[230]</xref>–<xref ref-type="bibr" rid="pone.0014631-Vaske2">[235]</xref>. The oceanic fishing is
dedicated to tunas <xref ref-type="bibr" rid="pone.0014631-Viana1">[169]</xref>, <xref ref-type="bibr" rid="pone.0014631-Pedrosa2">[236]</xref>–<xref ref-type="bibr" rid="pone.0014631-Vras1">[243]</xref>. Dog
snaper, dentex, sawfish, red porgy, flying fish, mackerel, and dorado are
among the most important fish landed by artisanal fisherman in the region
<xref ref-type="bibr" rid="pone.0014631-Ferreira1">[230]</xref>. Shrimps, prawns, and lobsters are captured in
trawling nets and are exploited to the sustainable limit <xref ref-type="bibr" rid="pone.0014631-Santos1">[178]</xref>, <xref ref-type="bibr" rid="pone.0014631-Coelho2">[244]</xref>–<xref ref-type="bibr" rid="pone.0014631-SilvaJr1">[246]</xref>. <italic>Panulirus
argus</italic>, <italic>P. laevicauda</italic>, <italic>P.
echinatus</italic>, <italic>Syllarides brasiliensis</italic>, and
<italic>S. delfosi</italic> are economically important, but only the
first two have fishing restrictions. Crustaceans and mollusks are considered
important resources in the Northeast Region. According to Alves and Nishida
<xref ref-type="bibr" rid="pone.0014631-Alves1">[247]</xref>,
the crab <italic>Ucides cordatus</italic> (Linnaeus, 1763) or
“caranguejo-uçá,” as it is known in Brazil, is one
of the most conspicuous and abundant components of the Brazilian mangrove
ecosystems epibenthic macrofauna, and the most exploited resource by
artisanal fisheries, especially in the Northeast Region. The scientific
interest in other marine organisms, which inhabit different ecosystems in
the region, is supported by local federal universities and research
centers.</p><p>The Central score is characterized by the presence of coral reefs and
calcareous algae. The Abrolhos Bank on the southern coast of Bahia State is
the largest coral bank in the South Atlantic (70,000 km<sup>2</sup>) with
more than 16 stony corals recorded <xref ref-type="bibr" rid="pone.0014631-Castro3">[248]</xref>. Edged by Atlantic
forest, the bank comprises a mosaic of coastal marine environments,
including coral reefs, algae bottoms, mangroves, beaches, and sand banks
<xref ref-type="bibr" rid="pone.0014631-Castro2">[170]</xref>,
<xref ref-type="bibr" rid="pone.0014631-Maida1">[249]</xref>,
<xref ref-type="bibr" rid="pone.0014631-Figueiredo1">[250]</xref>. The highest biodiversity in the South Atlantic
is found in this area; Abrolhos shelters not only many endemic species such
as the brain coral, but also crustaceans, mollusks, sea turtles, and marine
mammals (especially cetaceans) <xref ref-type="bibr" rid="pone.0014631-Siciliano1">[251]</xref>–<xref ref-type="bibr" rid="pone.0014631-Morete1">[253]</xref>.
Nonarticulated calcareous algae found in this region attach to various
substrates. As this region is generally oligotrophic and has different water
masses including that of the Atlantic Central Waters, which are coldest and
rich in nutrients, a rich diversity of macroalgae benefit from these
hydrological conditions. These macroalgae include mainly the tropical orders
Cladophorales, Bryopsidales, Dyctiotales, Fucales, and Ceramiales, among
others <xref ref-type="bibr" rid="pone.0014631-YoneshigueValentin1">[254]</xref>, which are also usually found in the Caribbean
Sea <xref ref-type="bibr" rid="pone.0014631-Littler1">[255]</xref>. Conversely, many species with temperate affinities
and found only in areas under the influence of the subantarctic-originated
Atlantic Central Waters, such as the kelp <italic>Laminaria
abyssalis</italic><xref ref-type="bibr" rid="pone.0014631-Joly1">[256]</xref>, the
geographic distribution of which extends from the northern part of Cabo Frio
in Rio de Janeiro State to the mouth of Rio Doce River in Espírito
Santo State <xref ref-type="bibr" rid="pone.0014631-OliveiraFilho1">[257]</xref>, [Yoneshigue-Valentin personal
observation]. The region is also characterized by endemic species of
the kelp <italic>Laminaria abyssalis</italic> and the agariferous
<italic>Gracilaria abyssalis</italic> and is abundant in economically
important rhodolites formed by calcareous algae. About 774 infrageneric taxa
of marine macroalgae (482 Rodophyta, 191 Chlorophyta, 101 Heterokontophyta)
are so far known for the whole Brazilian coast. Regarding fisheries,
Serraniids, groupers, and other species of fish that live in reefs and rock
bottoms, and also pelagic fish are often caught in the shores of southern
Bahia and also Espírito Santo State. Cabo Frio, Niterói, and
Angra dos Reis in Rio de Janeiro State are other important landing ports in
the Central score. The artisanal fishing is significant for prawns, corvine,
mullet, and cutlass in certain areas such as the Guanabara Bay, Sepetiba
Bay, Ilha Grande, and Parati in Rio de Janeiro State.</p><p>About 185 species of fish have been identified from the Southern score. There
are many landing ports (Rio Grande, Itajaí and Navegantes, Santos and
Guarujá) in the South Region, and fishing control is harder in this
region. In contrast to the Northeast Region, artisanal fishing in the South
represents only about 15% of the regional production <xref ref-type="bibr" rid="pone.0014631-Haimovici1">[258]</xref>,
<xref ref-type="bibr" rid="pone.0014631-Borzone1">[259]</xref>. But artisanal fishing with bottom trawling is
common in São Paulo, Paraná, and Santa Catarina states, where
the main fishing targets are prawns, corvinas, hakes, soles, engrauliids,
and mullet <xref ref-type="bibr" rid="pone.0014631-Arajo1">[260]</xref>, <xref ref-type="bibr" rid="pone.0014631-Pezzuto1">[261]</xref>. Prawns and crabs are
heavily fished in Patos Lagoon in Rio Grande do Sul State, and at its
coastline the fishing industry aims at corvinas, hake, anchovies, sardines,
shark, skate, and dogfish, among others <xref ref-type="bibr" rid="pone.0014631-Haimovici1">[258]</xref>. There are several
important field guides and manuals related not only to pelagic organisms but
also to benthic ones (e.g., sponges <xref ref-type="bibr" rid="pone.0014631-Silva2">[262]</xref>, <xref ref-type="bibr" rid="pone.0014631-Silva3">[263]</xref>, <xref ref-type="bibr" rid="pone.0014631-Lazoski1">[264]</xref>, polychaetes <xref ref-type="bibr" rid="pone.0014631-Lana4">[265]</xref>, <xref ref-type="bibr" rid="pone.0014631-DiDomenico1">[266]</xref>).</p></sec><sec id="s4d2"><title>Threats and conservation strategies in the Brazilian Shelf</title><p>Over the years, the vast extent of the coastline and the variety of coastal
marine ecosystems in Brazil gave rise to the public perception of
inexhaustible sea resources. This perception led to policies that encouraged
unsustainable use of resources. As a result, although marine fisheries
contribute 63% of the total fish production in Brazil, over
80% of the resources are currently overexploited <xref ref-type="bibr" rid="pone.0014631-MMA1">[267]</xref>, <xref ref-type="bibr" rid="pone.0014631-MMA2">[268]</xref>. On the
other hand, the fishing industry in Brazil is responsible for generating
approximately 800,000 jobs, apart from providing animal protein for human
consumption. This means the fishing industry has enormous social and
economic importance affecting some 4 million people who depend directly or
indirectly on this sector <xref ref-type="bibr" rid="pone.0014631-BRASIL1">[269]</xref>. Brazilian legislation defines the coastal zone
as a national patrimony that includes also the 12 nautical miles of
territorial sea. Coastal management is conducted by a national plan legally
enforced, complemented by state and county plans, and by coastal
ecologic-economic zoning limited to small portions of the coastal zone <xref ref-type="bibr" rid="pone.0014631-Jablonski1">[270]</xref>.
However, only a small portion of the enormous Brazilian coastline is under
some form of protection or management, and there are large areas under
anthropogenic pressures <xref ref-type="bibr" rid="pone.0014631-Amaral4">[271]</xref>. Considering the high levels of endemism of
Brazilian marine organisms, and the likelihood that the growing population
will exert even higher anthropogenic pressures such as fishing, large-scale
conservation and management plans are urgently needed. Some efforts have
been undertaken with management from different societal sectors and with
background information provided by the scientific community <xref ref-type="bibr" rid="pone.0014631-Floeter2">[272]</xref>–<xref ref-type="bibr" rid="pone.0014631-Perez1">[274]</xref>.</p><p>Considering all the factors mentioned above, Brazil faces the difficult tasks
of identifying, inventorying, and scientifically studying all its biological
diversity (terrestrial and marine), as well as developing and implementing
management and sustainable use mechanisms <xref ref-type="bibr" rid="pone.0014631-MMA1">[267]</xref>, <xref ref-type="bibr" rid="pone.0014631-MMA2">[268]</xref>. The government's
primary formal mechanism for guaranteeing the conservation of Brazilian
biodiversity is the Convention on Biological Diversity. This convention was
adopted and approved during the United Nations Conference on Environment and
Development, held in Rio de Janeiro in June 1992. As a prime mover in these
negotiations, Brazil was the first signatory of the convention, and on
December 29, 1994, the Brazilian Federal Government established the National
Programme of Biological Diversity (PRONABIO) <xref ref-type="bibr" rid="pone.0014631-MMA1">[267]</xref>, <xref ref-type="bibr" rid="pone.0014631-MMA2">[268]</xref>. This program has been
modified since that time to coordinate implementation of Brazil's
commitments to the convention, and the Brazilian Ministry of Environment has
played a key role in this process, which includes the formulation of the
National Biodiversity Policy (Política Nacional de Biodiversidade,
PNB). The PNB was prepared in consultation with the federal and states'
governmental officials, nongovernmental organizations, scientific,
indigenous and local communities, and entrepeneurs. As part of this process,
the ministry has coordinated a series of baseline studies, such as an
evaluation of the adequacy of the Brazilian legislation in relation to the
Convention on Biological Diversity, a state-of-the-art synthesis of the
knowledge of the Brazilian biodiversity, a comparative analysis of national
biodiversity strategies from 46 countries, and a synthesis of records of
traditional knowledge associated with biodiversity <xref ref-type="bibr" rid="pone.0014631-Gerhardinger1">[275]</xref>. Also, parallel
to the national consultancy, the ministry has promoted a general evaluation
of seven major biomes in Brazil, including that on the coastal zone and
marine environment <xref ref-type="bibr" rid="pone.0014631-MMA1">[267]</xref>, <xref ref-type="bibr" rid="pone.0014631-MMA2">[268]</xref>. Currently, despite existing policies, there is
an intensification of conflict between small-scale and industrial fishermen,
shrimp farming and mangrove crab harvesting, resorts installation and native
communities, NGOs and activities of oil and gas companies, and between
federal and state governmental agencies in Brazil over environmental permits
<xref ref-type="bibr" rid="pone.0014631-Jablonski1">[270]</xref>. The major challenge for PRONABIO has been to
demonstrate the direct benefits of conserving biodiversity and to promote
the public action required to increase and guarantee the sustainable use of
biodiversity.</p><p>Even though Brazil has implemented conservation practices in coastal and
maritime zones (Marine Protected Areas, Marine Reserves, and Marine National
Parks), these efforts represent less than 0.4% of the total area
within the territorial sea and EEZ (<xref ref-type="fig" rid="pone-0014631-g006">Figure 6</xref>) <xref ref-type="bibr" rid="pone.0014631-BRASIL1">[269]</xref>. Several initiatives
have been put in place to change the way people think. These initiatives
include teaching the concept of conservation units through the demonstration
of case studies, implementation of participative shared management of
resources, capacity building aimed at technicians and managers, and outreach
to decision makers <xref ref-type="bibr" rid="pone.0014631-Prates2">[276]</xref>. Some of these coastal and marine conservation
units have been set in the northern coast of Paraná and south of
São Paulo, as well as in the south of Bahía, Rio de Janeiro,
and Santa Catarina <xref ref-type="bibr" rid="pone.0014631-Prates2">[276]</xref>. Today Brazil has 16 Marine Protected Areas
mostly over coral reef ecosystems, including three recognized by
international acts (RAMSAR and Natural World Heritage sites) <xref ref-type="bibr" rid="pone.0014631-Prates2">[276]</xref>.</p><fig id="pone-0014631-g006" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0014631.g006</object-id><label>Figure 6</label><caption><title>Map of the Marine Protected Areas (MPAs) of Brazil.</title></caption><graphic xlink:href="pone.0014631.g006"></graphic></fig><p>Shallow-water reefs (those occurring on the continental shelf), are an
important physiographic feature of the coast of Brazil and occur along at
least one-third of the coastline (about 3,000 km, from Maranhão to
south of Bahia). Coral reefs prevail northward (0°52′N to
19°S) and rocky reefs southward (20° to 28°S) <xref ref-type="bibr" rid="pone.0014631-Castro2">[170]</xref>, <xref ref-type="bibr" rid="pone.0014631-Castro3">[248]</xref>, <xref ref-type="bibr" rid="pone.0014631-Floeter4">[277]</xref>,
<xref ref-type="bibr" rid="pone.0014631-Rangel1">[278]</xref>.
These extensive areas encompass diverse reef fish and invertebrate
communities, in many places overexploited, where only recently have studies
related to the impacts of fisheries on these ecosystems provided the basis
for implementing management and conservation actions (<xref ref-type="bibr" rid="pone.0014631-Prates2">[276]</xref>–<xref ref-type="bibr" rid="pone.0014631-Frdou1">[280]</xref> and
authors therein). Around 18 million people depend directly or indirectly on
reef ecosystems in Brazil <xref ref-type="bibr" rid="pone.0014631-Maida1">[249]</xref>. As coral reefs are recognized as areas within
the Convention, several actions with regard to these environments have been
motivated in Brazil. The “Atlas dos Recifes de Coral nas Unidades de
Conservação Brasileiras” (Atlas of the Coral Reefs
within the Brazilian Conservation Units) published in 2003 was the first
initiative to map the corals in the South Atlantic, not included in world
maps before. There is a campaign for the Conscious Conduct in Reef
Environments, outreach activity on conservation aimed at tourists. A
monitoring program of Brazilian coral reefs (Reef Check Brazil, <ext-link ext-link-type="uri" xlink:href="http://reefcheck.org">http://reefcheck.org</ext-link>) aims to establish the baselines for
the conservation units national monitoring program that protect these
ecosystems (this has now more than five years of sampling data). The
Ministry has established partnerships with projects such as the Coral Vivo
Project (Live Coral, <ext-link ext-link-type="uri" xlink:href="http://www.coralvivo.org.br">www.coralvivo.org.br</ext-link>) in which several techniques for coral
reproduction have been used, besides the country's enrollment in the
International Coral Reef Initiative. Other projects associated with reefs
are worth mentioning. The Institute Chico Mendes of Biodiversity
Conservation (ICMBio – <ext-link ext-link-type="uri" xlink:href="http://www.icmbio.gov.br">http://www.icmbio.gov.br</ext-link>), an organization responsible for
conservation and management of threatened species in Brazil, is leading a
national initiative to assess the status of conservation of species,
including coral reef species, in partnership with IUCN and the Global Marine
Species Assessment. The Goliath Grouper Project (<ext-link ext-link-type="uri" xlink:href="http://merosdobrasil.org">http://merosdobrasil.org</ext-link>) benefits the goliath grouper
<italic>Epinephelus itajara</italic>, the largest Atlantic grouper,
which is considered a critically endangered species according to IUCN
criteria and has been protected by the Brazilian Federal Law since 2002. The
Marine Management Areas Science Program is an international program of
Conservation International that is evaluating the effects of different
management regimes to devise the best actions for the future. Within this
context, the Abrolhos Shelf is part of a network attempting a similar
experiment in parallel, which includes four intensive study areas around the
globe (Brazil, Fiji, Belize, and Panama). Also in Abrolhos, the mesophotic
reefs, holding unique “twilight zone” assemblages, have been
revealed through a multidisciplinary and multi-institutional project in
which remotely operated vehicles have been used unveiling the potential of
the area for a variety of ecosystem services.</p><p>The established Brazilian Marine Protected Areas, Marine Reserves, and Marine
Parks are fairly recent, the majority implemented with the intention to
conserve biodiversity and sustain the natural habitats of marine organisms
from all realms <xref ref-type="bibr" rid="pone.0014631-McGlinley1">[167]</xref>, <xref ref-type="bibr" rid="pone.0014631-McGlinley2">[168]</xref>, <xref ref-type="bibr" rid="pone.0014631-Prates2">[276]</xref>. The
Marine State Park Parcel Manoel Luis, for instance, includes three coral
banks off the northern coast of Maranhão State, at the northern
distribution limit of several fish species that are endemic to the Brazilian
coast <xref ref-type="bibr" rid="pone.0014631-McGlinley1">[167]</xref>, <xref ref-type="bibr" rid="pone.0014631-McGlinley2">[168]</xref>. Also, a complex
estuarine system of islands, bays, coves, and mangrove forests make up the
Reentrancias Maranhenses in the same state and is designated as a RAMSAR
site (<ext-link ext-link-type="uri" xlink:href="http://www.mma.gov.br">http://www.mma.gov.br</ext-link>) because of its great importance for
numerous species of fish, shellfish, migratory birds, and manatees <xref ref-type="bibr" rid="pone.0014631-McGlinley1">[167]</xref>,
<xref ref-type="bibr" rid="pone.0014631-McGlinley2">[168]</xref>. Other examples include Atol das Rocas and
Fernando de Noronha Marine National Park, both off the northeastern coast.
Apart from being a Marine Reserve, Atol das Rocas is also considered a
Natural World Heritage Site. It is the second largest reproductive area for
the sea turtle <italic>Chelonia mydas</italic> and the main reproductive
area for the seabird species <italic>Sterna fuscata</italic>, <italic>Sula
dactylatra</italic>, <italic>Sula leucogaster</italic>, <italic>Anous
stolidus</italic>, and <italic>Anous minutus</italic>. In the southern
coast, the Arvoredo Biological Marine Reserve (Reserva Biológica
Marinha do Arvoredo, RBMA) (27°17′7″S and
48°25′30″W) is an important nursery for many fish and other
marine invertebrates <xref ref-type="bibr" rid="pone.0014631-Bouzon1">[281]</xref>. All these and other conservation units have
also been seen as a way of managing fisheries, especially where
multispecific techniques are used and conventional management tools do not
have any effect <xref ref-type="bibr" rid="pone.0014631-Prates2">[276]</xref>. But several specialists have been pointing out
the need for the establishment of no-fishing zones, including in the deep
sea, as mechanisms for recovery and conservation of fish stocks <xref ref-type="bibr" rid="pone.0014631-Floeter2">[272]</xref>–<xref ref-type="bibr" rid="pone.0014631-Perez1">[274]</xref>.</p><p>Mangrove ecosystems cover 16 of the 17 Brazilian coastal states, representing
85% of the coastline (about 7,300 km), and are therefore crucial to
local communities but also subject to huge pressures and human impacts.
Mangrove ecosystems are among the most productive and have been considered
essential to a variety of natural resources and environmental services, as
they support economic activities and secure the environmental integrity in
tropical coastal areas. In recognition of the importance of these
ecosystems, the challenges of consolidatoffing and maintaining Mangrove
Conservation Units, the Ministry of Environment, in partnership with the
Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais
Renováveis – IBAMA (Brazilian Renewable Natural Resources and
Environmental Institute) and the United Nations Development Program (UNDP),
has submitted a proposal to the Global Environment Facility called
“Project on the Conservation and Effective Sustainable Usage of
Brazilian Mangroves” (known as Projeto GEF Mangue). This project is to
raise funds to establish a network of protected areas that would allow the
conservation and sustainable use of this country's 13,400
km<sup>2</sup> of mangroves (equivalent to 9% of the total
mangrove area worldwide) (<ext-link ext-link-type="uri" xlink:href="http://www.mma.gov.br">http://www.mma.gov.br</ext-link>).</p><p>Apart from these economically important ecosystems, marine mammals, seabirds,
and reptiles (mainly turtles) also receive special attention from NGOs and
environmental agencies in Brazil. Projeto TAMAR-IBAMA (National Sea Turtle
Conservation Program of Brazil), for instance, has a successful history of
conservation with a joint governmental and nongovernmental administration,
where local communities are involved <xref ref-type="bibr" rid="pone.0014631-Marcovaldi1">[282]</xref>. Turtles have long
lives and grow slowly to adulthood over 20 to 50 years. They have complex
life cycles and use a variety of ecosystems, including the land where they
lay their eggs as well as coastal and oceanic waters where they feed,
develop, and mate <xref ref-type="bibr" rid="pone.0014631-Marcovaldi1">[282]</xref>, <xref ref-type="bibr" rid="pone.0014631-Bellini1">[283]</xref>. Five species of
turtles occur in the Brazilian coast: <italic>Caretta caretta</italic>,
<italic>Chelonia myda</italic>s, <italic>Eretmochelys
imbricata</italic>, <italic>Lepidochelys olivacea</italic>, and
<italic>Dermochelys coriacea</italic><xref ref-type="bibr" rid="pone.0014631-Marcovaldi1">[282]</xref>.
Former egg poachers have been employed through the TAMAR Project to patrol
the beaches and protect the nests, and this together with an education
program and ecotourism have promoted the conservation of endangered sea
turtles. Additionally, the project contributes to community festivals,
supports local schools and health care facilities, and assists in developing
alternative sources of income for residents who once had relied only on the
exploitation of sea turtles <xref ref-type="bibr" rid="pone.0014631-Marcovaldi1">[282]</xref>. The project has
established 18 conservation stations covering 1,100 km of the Brazilian
mainland coast. Like birds, however, turtles face other threats such as
plastic debris and hook-and-line fishing bycatch <xref ref-type="bibr" rid="pone.0014631-Bugoni1">[284]</xref>–<xref ref-type="bibr" rid="pone.0014631-Mascarenhas1">[286]</xref>,
and there is a need for further monitoring and to develop mitigation
measures <xref ref-type="bibr" rid="pone.0014631-Bugoni2">[285]</xref>.</p><p>Generally, Brazil is considered relatively poor in seabirds as a result of
the low productivity of its tropical waters <xref ref-type="bibr" rid="pone.0014631-Sick1">[287]</xref>. But about 130 coastal
and marine species can be found throughout the coast and oceanic islands
<xref ref-type="bibr" rid="pone.0014631-Marini1">[288]</xref>. The great majority of these birds come from the Northern Hemisphere
between September and May, and from the meridional extreme between May and
August <xref ref-type="bibr" rid="pone.0014631-Marini1">[288]</xref><xref ref-type="bibr" rid="pone.0014631-Bellini1">[283]</xref>, to
mate and reproduce in marine protected areas such as the Atol das Rocas, are
crucial for the maintenance of these populations.</p><p>Cetaceans are commonly sighted in along the Brazilian coast, and most studies
have been related to their occurrence <xref ref-type="bibr" rid="pone.0014631-Gomes2">[289]</xref>–<xref ref-type="bibr" rid="pone.0014631-Hassel1">[297]</xref>,
abundance and distribution <xref ref-type="bibr" rid="pone.0014631-Kinas1">[252]</xref>, <xref ref-type="bibr" rid="pone.0014631-Morete1">[253]</xref>, <xref ref-type="bibr" rid="pone.0014631-Zerbini3">[298]</xref>, diversity <xref ref-type="bibr" rid="pone.0014631-Pinedo1">[204]</xref>, <xref ref-type="bibr" rid="pone.0014631-Parente1">[299]</xref>,
ecology <xref ref-type="bibr" rid="pone.0014631-Siciliano1">[251]</xref>, <xref ref-type="bibr" rid="pone.0014631-Pizzorno1">[300]</xref>, <xref ref-type="bibr" rid="pone.0014631-DiBeneditto2">[301]</xref>,
behavior and reproductive biology <xref ref-type="bibr" rid="pone.0014631-SilvaJr1">[246]</xref>, <xref ref-type="bibr" rid="pone.0014631-Ramos1">[302]</xref>,
stranding <xref ref-type="bibr" rid="pone.0014631-Pinedo2">[303]</xref>, <xref ref-type="bibr" rid="pone.0014631-Ramos2">[304]</xref> and accidental capture <xref ref-type="bibr" rid="pone.0014631-Lodi2">[305]</xref>–<xref ref-type="bibr" rid="pone.0014631-DiBeneditto3">[307]</xref>.
Parente et al. <xref ref-type="bibr" rid="pone.0014631-Parente1">[299]</xref> have evaluated the relationship between seismic
surveys, oceanographic data, and diversity of cetaceans in Brazil since the
increase in seismic survey activities. This study suggests that there is a
decrease in the diversity of species over time, uncorrelated with changes in
oceanographic patterns, but rather associated with the increasing number of
seismic surveys. Nonetheless the authors recognize the need for further
observations and improved methodologies to analyze the cetaceans'
behavioral patterns. Apart from cetaceans, other mammals occur along the
Brazilian coast and deserve protection, including manatees that are commonly
found in mangrove areas in the North and Northeast regions and and fur seals
that occur in the southern part of the country near Chuí. Manatees
(<italic>Trichechus manatus</italic>) were hunted in the past for their
meat and skin and were at risk of extinction, but they are currently
protected by the Brazilian government. A dedicated center for the study and
protection of manatees (Centro Nacional de Pesquisa,
Conservação e Manejo de Mamíferos Aquáticos or
Centro Mamíferos Aquáticos/IBAMA) was created in 1980. At that
time, an extensive survey was carried out, areas of protection were
established, and regional executive bases were implemented especially in the
North and Northeast regions. This way, the animals have been rehabilitated;
some reproduce in captivity and their young are maintained until they are
ready for reintroduction to their natural environment.</p><p>There are only two refuges for pinnipids along the whole Brazilian coastline,
and these are in Rio Grande do Sul state in the south. The South American
sea lion (<italic>Otaria flavescens</italic>) is the most anthropogenically
affected species, mainly because of its fishing interactions <xref ref-type="bibr" rid="pone.0014631-Silva1">[214]</xref>, <xref ref-type="bibr" rid="pone.0014631-Pinedo3">[308]</xref> and
other authors therein). A program for the conservation and management of
pinnipids in Brazil (Programa de Conservação e Manejo dos
Pinípedes – NEMA/IBAMA) was implemented from 1993 to 2004 for
the protection of pinniped species that use the Rio Grande do Sul state
seashore, and two conservation units exist in the south, but further efforts
are necessary to promote environmental education, monitoring, and
appropriate handling of these animals <xref ref-type="bibr" rid="pone.0014631-Silva1">[214]</xref>.</p><p>Ferreira et al. <xref ref-type="bibr" rid="pone.0014631-Ferreira2">[309]</xref> have compiled information on the threat of
invasive species for Brazil. They have considered that Brazil is undoubtedly
a major receptor and donor of tropical and subtropical organisms in the
world's oceans, taking into account the enormous variety of its marine
ecosystems and the extent of its coastline. Currently, 66 invasive species
have been recorded for the marine environment in Brazil from the following
groups: phytoplankton (3); macroalgae (10), zooplankton (10), zoobenthos
(38), fish (4), and pelagic bacteria (1) <xref ref-type="bibr" rid="pone.0014631-Coradin1">[310]</xref>–<xref ref-type="bibr" rid="pone.0014631-Bardi1">[312]</xref>.</p><p>A trend toward increasing bioinvasion events in regional coastal ecosystems
may exist, but data are still sparse and locally produced <xref ref-type="bibr" rid="pone.0014631-Ferreira2">[309]</xref>.
According to these authors, there might be a bias in actual invasion rates
as a result of different research efforts in the recent past. As this is a
relatively new topic in Brazil, the first comprehensive lists of introduced
and invasive species are just beginning to be compiled, and the patterns of
invasion are not well understood <xref ref-type="bibr" rid="pone.0014631-Ferreira2">[309]</xref>, <xref ref-type="bibr" rid="pone.0014631-Junqueira1">[313]</xref>.</p></sec></sec><sec id="s4e"><title>Subregion 5: The Tropical West Atlantic - Venezuelan Atlantic, Guyana,
Suriname, and French Guiana</title><p>The Tropical West Atlantic region is bounded by the non-Caribbean section of the
coast of Venezuela as well as by Guyana (formerly British Guyana), Suriname, and
French Guiana, and defined by Longhurst <xref ref-type="bibr" rid="pone.0014631-Longhurst1">[314]</xref> as the “Guianas
Coastal Province.” It extends for about 1,877 km along the Atlantic coast
of South America from the Brazilian border with French Guiana
(4°20′20″S, 51°22′12″W) to the northern section
of the Venezuelan Atlantic (10°39′22″N,
61°39′52″W). In the northern sector, the deltaic plains of the
Orinoco and the Gulf of Paria in the north Atlantic coast of South America cover
2,763,000 ha and constitute one of the major wetlands in South America as well
as one of the best preserved ecosystems in the world. The productivity of this
area is significant and one of the highest among neighboring areas in the
adjacent Caribbean <xref ref-type="bibr" rid="pone.0014631-PDVSA1">[315]</xref> (<xref ref-type="fig" rid="pone-0014631-g004">Figure
4</xref>). These wetlands were formed by the combined action of sediment and
freshwater discharges from the Orinoco, one of the longest rivers in South
America (2,140 km) along with the tides on a flat alluvial plain <xref ref-type="bibr" rid="pone.0014631-Lasso1">[316]</xref>. The
physical and chemical characteristics as well as the ecosystems that develop in
this area are therefore defined by these factors <xref ref-type="bibr" rid="pone.0014631-Colonnello1">[317]</xref>. The surface sea
temperature is relatively constant throughout the year
(27°C–28°C), and temperature drops to 12°C at 200 m depth
(<xref ref-type="fig" rid="pone-0014631-g003">Figure 3</xref>). During the
dry season, salinity at the Gulf of Paria is about 35–35‰, while
during the rainy season it may drop to 10‰ with variations in the
vertical gradient corresponding to an estuarine environment. Predominant winds
in this area are the northeast trade winds, with a mean speed of 6.6 m/s in the
Atlantic Front and 2 m/s in the Gulf of Paria. Winds show a seasonal pattern in
which the highest speeds are observed in January, February, and March (monthly
mean: 7.5 m/s), and the lowest in July, August, and September (monthly mean: 5.7
m/s). In most of the continental portion of Venezuela and many coastal areas,
wind intensity is also associated with cumulonimbus cloud systems, which are
often observed during the rainy season. The Venezuelan coast is not often
affected by hurricanes or tropical storms. However, these events can occur, and
hurricanes have at times reached the Venezuelan coast at a frequency of one
every 36 years. In these cases, wind speeds have increased to almost 40 m/s.
Wave pattern is also mostly determined by the northeast trade winds, although
this pattern may be altered by changes in wind intensity and by extratropical
cyclonic depressions that occur in the North Atlantic, generating waves that
reach the Venezuelan coasts as swells. Waves are usually 1–6.25 m in
height and frequently more than 4 m in May, November, and December. Offshore the
Orinoco Delta, currents are dominated by the Guayana Current, which flows mainly
toward the northwest at about 150 cm/s, significantly affecting the entire
region because of the large amounts of water it transports (<xref ref-type="fig" rid="pone-0014631-g002">Figure 2</xref>). On the other hand, the Orinoco
River discharges also affect the circulation pattern of the oceanic water mass
seasonally throughout the year (rainy and dry seasons). The Orinoco has the
world's third-largest flow (average discharge of 5.4×10<sup>11</sup>m<sup>3</sup>/year), which, combined with that of the Amazon River, accounts
for 25% of all the freshwater discharged to the world's oceans.
Tides are usually semidiurnal and vary from 1.7 to 4.5 m depending on the zone
<xref ref-type="bibr" rid="pone.0014631-INTECMARUSB1">[318]</xref>.</p><p>In the southern sector of this region, the climate in French Guiana is typically
wet equatorial, driven by the Intertropical Convergence Zone. Rainy season is
mainly between May and June, but there is a secondary rainy season in January
and February. Both periods greatly influence the Amazon River discharge, making
the waters extremely turbid. Tides are semidiurnal with an amplitude of up to
2.5 m. The main currents are the North Brazil Current becoming the Guianas
Current, which flows to the northwest and carries low-salinity waters rich in
nutrients and sediment from the Amazon (<xref ref-type="fig" rid="pone-0014631-g002">Figure 2</xref>). Upwelling is also characteristic
of this sector, providing more nutrients to the water but not decreasing
significantly its temperature <xref ref-type="bibr" rid="pone.0014631-Artigas1">[18]</xref> (<xref ref-type="fig" rid="pone-0014631-g003">Figures
3</xref> and <xref ref-type="fig" rid="pone-0014631-g004">4</xref>).</p><p>From an ecological point of view, the coastal marine habitats in the northern
sector of this region can be divided into several subareas: (1) the coastal
fringe south of the Paria Peninsula, dominated by rocky shores, (2) the coastal
fringe of the Gulf of Paria and the Atlantic Ocean, dominated by mangroves, and
(3) the Atlantic coasts, dominated by soft bottoms and sandy beaches. All of
these are part of the “Gulf of Paria and Atlantic Front” ecoregion
as defined by Miloslavich et al. <xref ref-type="bibr" rid="pone.0014631-Miloslavich3">[319]</xref>. Each of these
subareas has ecologically distinct features that are determined by the
particular physiography, hydrodynamism, tides, sediments, physics, and chemistry
of the area. These conditions allow the development of distinct ecosystems along
this “variably stable” continental fringe that are characterized by
a total interdependency between biotic and abiotic components <xref ref-type="bibr" rid="pone.0014631-PDVSA1">[315]</xref>. In the
southern sector, the coastal habitats are mainly mudflats, extensive mangrove
swamps, narrow sandy beaches, and brackish water creeks <xref ref-type="bibr" rid="pone.0014631-Artigas1">[18]</xref>.</p><sec id="s4e1"><title>Marine biodiversity in the Tropical West Atlantic</title><p>A total of 2,743 species have been reported in this region (<xref ref-type="table" rid="pone-0014631-t006">Tables 6</xref> and <xref ref-type="supplementary-material" rid="pone.0014631.s009">S9</xref>).
The most diverse groups were the fish (32%), followed by the
crustaceans (19%), the mollusks (16%), and the polychaetes
(6%). Despite having a large coastal extension, neither the Gulf of
Paria nor the Venezuelan Atlantic Front including the Orinoco Delta has been
well studied. Knowledge of the marine biodiversity of the area is scarce and
mostly reported in gray literature. The first studies of benthic communities
in the Gulf of Paria and the Venezuelan Atlantic Front were carried out in
the 1960s and 1970s, mostly focused on crustaceans <xref ref-type="bibr" rid="pone.0014631-Flores1">[320]</xref>, gastropods <xref ref-type="bibr" rid="pone.0014631-Altena1">[321]</xref>–<xref ref-type="bibr" rid="pone.0014631-Flores2">[328]</xref>. In the late 1990s and
early 2000s, baseline studies were carried out in the area in response to
the interest of oil and gas companies in establishing both offshore and
coastal developments. Such studies produced some species lists, but because
of the lack of taxonomic expertise, these are incomplete and do not reflect
well the actual biodiversity <xref ref-type="bibr" rid="pone.0014631-Lasso1">[316]</xref>, <xref ref-type="bibr" rid="pone.0014631-Martn2">[329]</xref>. Recently, more extensive biodiversity and
environmental impact studies have been developed <xref ref-type="bibr" rid="pone.0014631-Lasso1">[316]</xref>, <xref ref-type="bibr" rid="pone.0014631-INTECMARUSB1">[318]</xref>, <xref ref-type="bibr" rid="pone.0014631-Bone1">[330]</xref>, <xref ref-type="bibr" rid="pone.0014631-Klein1">[331]</xref> and a
complete environmental baseline is compiled in Martín et al. <xref ref-type="bibr" rid="pone.0014631-Martn2">[329]</xref>.</p><table-wrap id="pone-0014631-t006" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0014631.t006</object-id><label>Table 6</label><caption><title>Summary of the diversity, state of knowledge, and expertise of
the main taxonomic groups within the Tropical West Atlantic
subregion of South America.</title></caption><alternatives><graphic id="pone-0014631-t006-6" xlink:href="pone.0014631.t006"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col></colgroup><thead><tr><td align="left" rowspan="1" colspan="1">Taxonomic group</td><td align="left" rowspan="1" colspan="1">No. species<xref ref-type="table-fn" rid="nt113">1</xref></td><td align="left" rowspan="1" colspan="1">State of knowledge</td><td align="left" rowspan="1" colspan="1">No. introduced species</td><td align="left" rowspan="1" colspan="1">No. experts</td><td align="left" rowspan="1" colspan="1">No. ID guides<xref ref-type="table-fn" rid="nt114">2</xref></td></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1"><bold>Domain Archaea</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Domain Bacteria (including Cyanobacteria)</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Domain Eukarya</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Kingdom Chromista</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Phaeophyta</td><td align="left" rowspan="1" colspan="1">12</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Kingdom Plantae</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Chlorophyta</td><td align="left" rowspan="1" colspan="1">24</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Rhodophyta</td><td align="left" rowspan="1" colspan="1">98</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Angiospermae</td><td align="left" rowspan="1" colspan="1">7</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Kingdom Protista (Protozoa)</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Dinomastigota (Dinoflagellata)</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Foraminifera</td><td align="left" rowspan="1" colspan="1">48</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Kingdom Animalia</bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Porifera</td><td align="left" rowspan="1" colspan="1">23</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Cnidaria</td><td align="left" rowspan="1" colspan="1">131</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Platyhelminthes</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Mollusca</td><td align="left" rowspan="1" colspan="1">431</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Annelida</td><td align="left" rowspan="1" colspan="1">172</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Crustacea</td><td align="left" rowspan="1" colspan="1">519</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">12</td><td align="left" rowspan="1" colspan="1">23</td></tr><tr><td align="left" rowspan="1" colspan="1">Bryozoa</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Echinodermata</td><td align="left" rowspan="1" colspan="1">107</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Urochordata (Tunicata)</td><td align="left" rowspan="1" colspan="1">16</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Other invertebrates</td><td align="left" rowspan="1" colspan="1">43</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Vertebrata (Pisces)</td><td align="left" rowspan="1" colspan="1">889</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2</td></tr><tr><td align="left" rowspan="1" colspan="1">Other vertebrates</td><td align="left" rowspan="1" colspan="1">223</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">1</td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>SUBTOTAL</bold></td><td align="left" rowspan="1" colspan="1">2743</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">11</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>TOTAL REGIONAL DIVERSITY</bold><xref ref-type="table-fn" rid="nt115">3</xref></td><td align="left" rowspan="1" colspan="1">2743</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">11</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr></tbody></table></alternatives><table-wrap-foot><fn id="nt113"><label>1</label><p>Sources of the reports: databases, scientific literature, books,
field guides, technical reports.</p></fn><fn id="nt114"><label>2</label><p>Identification guides cited in References.</p></fn><fn id="nt115"><label>3</label><p>Total regional diversity, including all taxonomic groups as
reported in <xref ref-type="supplementary-material" rid="pone.0014631.s009">Table S9</xref>.</p></fn></table-wrap-foot></table-wrap><p>The OBIS database currently lists 2,095 species in the Tropical West
Atlantic, which represents 76% of the total as updated in this paper
(<xref ref-type="table" rid="pone-0014631-t002">Table 2</xref>). Even
though most of these species are not new descriptions, a significant number
of them were not reported in this area until recently, particularly in the
Venezuelan Atlantic Front area. In this particular area, of the 1,561
species that have their collection date registered in OBIS (since 1884),
50% were collected between 2001 and 2004, and 47% between 1950
and 1980. In general, the best-known taxonomic groups are fish and
crustaceans, both important as fisheries resources, which account for about
51% of the total known biodiversity. The mollusks, for example,
usually the most diverse group, account for only about 15% of total
biodiversity, and the other major groups such as macroalgae, sponges,
cnidarians, and polychaetes account for less than 20% of the
total.</p><p>The most recent review of decapod crustaceans of the lower Orinoco Delta
reports 30 species (23 genera and 12 families), of which the most abundant
were the shrimps <italic>Litopenaeus schmitti</italic>,
<italic>Macrobrachium amazonicum</italic>, and <italic>Xiphopenaeus
kroyeri</italic><xref ref-type="bibr" rid="pone.0014631-Pereira1">[332]</xref>. In
the Gulf of Paria, about 300 species have been reported, and of these, the
gastropods are the most diverse group (200 species), followed by the
crustaceans (22 species) and polychaetes (11 species) <xref ref-type="bibr" rid="pone.0014631-Capelo1">[333]</xref>. In the Atlantic
Front, sampling between 2001 and 2002, collected macrofauna of 11 phyla:
Protozoa, Porifera, Cnidaria, Nematoda, Nemertea, Annelida, Sipuncula,
Echiura, Mollusca, Crustacea, and Echinodermata. Of these, annelids (mainly
of the families Pilargidae, Spionidae, and Paraonidae) were the most
abundant group, representing 60.7% of total abundance, followed by
crustaceans (mainly peracarids) and bivalves with 15.4% and
9.3%, respectively, The most diverse polychaete famlies were
Onuphidae and Syllidae, followed by Paraonidae. The shallow zone (less than
200 m) had higher abundances than the deeper zones for all groups <xref ref-type="bibr" rid="pone.0014631-Bone1">[330]</xref>. Other
important groups are the peracarid crustaceans, which were collected in
42% of the samples, amongst which the amphipods were the most
abundant group (57.8%), followed by the isopods (20.7%),
cumaceans (12.1%), and tanaidaceans (9.5%). Sampling was
carried out up to 200 m in depth and higher abundances were found in the
shallower zone, above 200 m (86%) <xref ref-type="bibr" rid="pone.0014631-Martn3">[334]</xref>. Bone et al. <xref ref-type="bibr" rid="pone.0014631-Bone2">[335]</xref> reviewed
the taxonomic composition of the Orinoco Delta benthic community and
reported a total biodiversity of 31 species belonging to four phyla
(Nematoda, Annelida, Mollusca, and Arthropoda), one subphyllum (Crustacea),
four classes (Polychaeta, Gasteropoda, Maxilopoda, and Malacostraca), two
subclasses (Ostracoda and Copepoda), one suborder (Peracarida), two orders
(Decapoda and Mysidacea), and 22 families.</p><p>Few studies of the planktonic community have been made. A total of 367
species of marine and estuarine phytoplankton and 182 species of zooplankton
have been reported for the Orinoco Delta and its zone of influence in the
Atlantic Ocean. These communities are strongly influenced by rain and tidal
regimes <xref ref-type="bibr" rid="pone.0014631-Bone2">[335]</xref>–<xref ref-type="bibr" rid="pone.0014631-Zoppi1">[341]</xref>. The nektonic community
is also affected by rain seasonality, both in biodiversity and in biomass.
During the rainy season, fish diversity and biomass (29,318 t) are higher
and dominated by estuarine species. During the dry season, both fish
diversity and biomass (10,611 t) are lower and dominated by marine species.
This region has a great potential for future research and species discovery.
Few taxonomic groups are well known, while most of the groups are either
poorly known or almost unknown.</p></sec><sec id="s4e2"><title>Threats and conservation strategies in the Tropical West Atlantic</title><p>The Tropical West Atlantic is heavily fished by local populations, and many
species, primarily fish and decapod crustaceans, have commercial value. For
some of these species, there is information about their biology
(reproduction, fecundity), ecology and fisheries <xref ref-type="bibr" rid="pone.0014631-Marcano1">[342]</xref>–<xref ref-type="bibr" rid="pone.0014631-Lpez3">[359]</xref>. The
impact of such fisheries on biodiversity is poorly known. Fisheries focus on
catching shrimp, scienid fish, and catfish, which are abundant in estuarine
habitats, and snappers and groupers, abundant in deeper waters and on rocky
bottoms. Historical data on industrial trawling fisheries have shown six
species of catfish, scienids, carangids, and lutjanids (snappers). The most
important species for longline artisanal fisheries have been the red snapper
(<italic>Lutjanus purpureus</italic>), the grouper <italic>Epinephelus
flavolimbatus</italic>, and the snapper <italic>Rhomboplites
aurorubens</italic>. The most important species captured with lines are
the “carite sierra” (<italic>Scomberomorus cavalla</italic>),
the barracuda (<italic>Sphyraena barracuda</italic>), the
“dorado” (<italic>Coryphaena hippurus</italic>), and the
“peto” (<italic>Acanthocybium solandri</italic>) <xref ref-type="bibr" rid="pone.0014631-Molinet1">[360]</xref>.</p><p>Major threats to biodiversity in this region are industrial (trawling) and
artisanal (line and longline) fishing, urban development, agriculture
development, dredging and flow navigation, water pollution (runoff from the
Orinoco and Amazon basins), mangrove deforestation, activities related to
oil and gas exploitation, port activities, and maritime shipping <xref ref-type="bibr" rid="pone.0014631-Klein1">[331]</xref>. These
authors assigned values to each of these threats according to their level of
menace on a scale from 1 to 8 (from least to highest impact). By this
measure, the most threatening activities are those related to oil and gas
exploitation, industrial fisheries, dredging, and mangrove deforestation. In
regard to industrial fishing, a new Fisheries and Aquaculture Law (article
23) has prohibited industrial shrimp trawl activities within
Venezuela's ocean territory and exclusive maritime economic zone,
starting on March 14, 2009. It is expected that the impact of this activity
will cease to be a problem in the near future at least within Venezuelan
waters. The impact of oil- and gas-related activities depends in great
measure on whether these activities are offshore or at the coastline. The
impact of offshore activities, when carried out within strict safety
parameters, are usually limited to the area surrounding the platforms. This
cannot be said of activities on the coast, where the impact is much greater
and is spread over a much larger area. Environmental catastrophes such as
the British Petroleum Deepwater Horizon in the Gulf of Mexico, despite being
extremely atypical, dramatically alert on the risks of carrying out such
environmentally risky activities in off shore areas without the proper
security measures.</p><p>The Tropical West Atlantic region includes several MPAs within the different
countries covering nearly 10,900 km<sup>2</sup> overall (land and sea). In
Venezuela, the Orinoco Delta and Gulf of Paria region have two protected
areas under special conservation regulations. These are the Turuépano
National Park in the Gulf of Paria, and the Orinoco Delta National Park. Of
these, the most impressive is the Orinoco Delta National Park, which is also
a Biosphere Reserve of mainly land and estuarine areas <xref ref-type="bibr" rid="pone.0014631-Miloslavich3">[319]</xref>. Recently, Klein
et al. <xref ref-type="bibr" rid="pone.0014631-Klein1">[331]</xref> engaged in a conservation study in this area
carried out by the Universidad Simón Bolívar and the Nature
Conservancy to suggest and establish, based on conservation objects, marine
areas to be declared under protection. The conservation objects chosen for
this area were the rocky shores, the sandy beaches, and the soft bottoms.
One of the recommendations given by these authors for conservation is to
expand the Orinoco Delta National Park farther into the oceanic area to
protect the marine environments as well. In Guyana, there are no formally
established MPAs, but the 140 km long “Shell Beach,” a nesting
site for at least four species of marine turtles, is protected directly and
indirectly by conservation activities involving local communities. In
Suriname, there are seven MPAs, of which four are Nature Reserves and two
are multiple-use management areas. In French Guiana, there is only one
Nature Reserve of about 78 km<sup>2</sup> of marine areas.</p></sec><sec id="s4e3"><title>Microorganisms in South America: Bacteria and Phytoplankton</title><p>The best-known marine phytoplankton taxonomic groups are diatoms and
dinoflagellates. As an example, in Mexican marine waters, the number of taxa
recorded is about 1,400 <xref ref-type="bibr" rid="pone.0014631-HernndezBecerril1">[361]</xref>. Recent
studies on phytoplankton dynamics complete this picture in South American
estuarine systems, including those of Gómez et al. <xref ref-type="bibr" rid="pone.0014631-Gmez1">[362]</xref>,
Calliari et al. <xref ref-type="bibr" rid="pone.0014631-Calliari2">[363]</xref>, Licursi et al. <xref ref-type="bibr" rid="pone.0014631-Licursi1">[364]</xref>, and Carreto et al.
<xref ref-type="bibr" rid="pone.0014631-Carreto1">[365]</xref>in the Río de la Plata and of Popovich and Marcovecchio <xref ref-type="bibr" rid="pone.0014631-Popovich1">[366]</xref> in
the Bahia Blanca estuary, as well as in littoral tropical systems <xref ref-type="bibr" rid="pone.0014631-Villac2">[367]</xref>. On
the other hand, phytoplankton studies, together with food web and
biogeochemical flux estimations, have intensively been carried out in the
upwelling system off Chile <xref ref-type="bibr" rid="pone.0014631-Anabaln1">[368]</xref>–<xref ref-type="bibr" rid="pone.0014631-Gonzlez1">[372]</xref> and in southern
Chilean fjords <xref ref-type="bibr" rid="pone.0014631-AlvesdeSouza1">[373]</xref>. Phyto- and bacterioplankton dynamics are also
studied in French Guiana coastal and shelf systems under direct Amazon
influence <xref ref-type="bibr" rid="pone.0014631-Artigas2">[43]</xref>, as well as in subtropical lagoons in southern
Brazil, focusing in phytoplankton dynamics and trophic fate <xref ref-type="bibr" rid="pone.0014631-Abreu1">[374]</xref>, <xref ref-type="bibr" rid="pone.0014631-Abreu2">[375]</xref>, and in
South Atlantic oceanographic frontal systems <xref ref-type="bibr" rid="pone.0014631-Brandini3">[376]</xref>–<xref ref-type="bibr" rid="pone.0014631-Santoferrara1">[378]</xref>.
The diversity of picoeukarya and cyanobacteria was investigated at
intermediate shelf stations in the Patagonian system <xref ref-type="bibr" rid="pone.0014631-Artigas2">[43]</xref><xref ref-type="bibr" rid="pone.0014631-Sellanes2">[40]</xref>.
Microbial dynamics (Eukarya and Eubacteria) are intensively explored in
central Chile <xref ref-type="bibr" rid="pone.0014631-Graco1">[379]</xref>–<xref ref-type="bibr" rid="pone.0014631-Levipan1">[383]</xref> and in the Peruvian
upwelling system <xref ref-type="bibr" rid="pone.0014631-Hamersley1">[384]</xref>, related to the oxygen minimum zone and big
upwelling productivity and remineralization patterns. Biogeographical issues
are also considered in a recent survey on bacterial assemblages (phylum
level) in surface waters from the Gulf of Mexico to the southeastern
tropical Pacific <xref ref-type="bibr" rid="pone.0014631-Falcn1">[385]</xref>. Bacterial dynamics and diversity are studied in
coastal lagoons in Uruguay <xref ref-type="bibr" rid="pone.0014631-Piccini1">[386]</xref>, in sediments of fluid mud in French Guiana
<xref ref-type="bibr" rid="pone.0014631-Madrid1">[387]</xref>,
in waters and sediments of the oxygen minimum zone off the South American
Pacific coast <xref ref-type="bibr" rid="pone.0014631-Gallardo4">[388]</xref>, and in anoxic waters of the Cariaco Basin
(<xref ref-type="bibr" rid="pone.0014631-Lin1">[389]</xref>,
Chistoserdov et al., upublished), where novel Eukarya are also studied <xref ref-type="bibr" rid="pone.0014631-Stoeck1">[390]</xref>.</p><p>In polluted coastal systems, bacteria with ability to degrade pesticides and
hydrocarbons are currently monitored. In coastal areas of the Colombian
Caribbean, 64 native marine bacterial strains were isolated from sediment
samples <xref ref-type="bibr" rid="pone.0014631-Gmez2">[391]</xref>. The oil-degrading bacteria are also studied in
the Orinoco Delta, which has been subject to intensive oil exploitation.
Furthermore, the Microbial Observatory of Rio de Janeiro (MoRio) <xref ref-type="bibr" rid="pone.0014631-Vieira1">[392]</xref>, <xref ref-type="bibr" rid="pone.0014631-Vieira2">[393]</xref>established in Guanabara Bay (Brazil), by exploring microbial biodiversity
in different coastal systems (including unpolluted sites) constitutes a
model for the study of threatened tropical coastal systems. The activity and
diversity of hydrocarbon- and oil-degrading bacteria are assessed also in
temperate waters and sediments of coastal systems of Argentina <xref ref-type="bibr" rid="pone.0014631-Cubitto1">[394]</xref>,
<xref ref-type="bibr" rid="pone.0014631-Lozada1">[395]</xref>;
Dionisi et al., unpublished). Finally, symbionts and pathogenic microbes are
currently assessed in coral reefs of the Caribbean and South America <xref ref-type="bibr" rid="pone.0014631-Rohwer1">[396]</xref>, as
well as in mangroves <xref ref-type="bibr" rid="pone.0014631-SotoRamirez1">[397]</xref> and extreme environments <xref ref-type="bibr" rid="pone.0014631-DazMuoz1">[398]</xref>.</p></sec></sec></sec><sec id="s5"><title>Discussion</title><sec id="s5a"><title>Analysis of latitudinal trends in biodiversity and species richness</title><p>The regional analysis of South American marine biodiversity showed tremendous
heterogeneity not only in physical environments, including size and conditions,
but also in research capacity, history of exploration, and conservation actions.
Threats to biodiversity seem to be more or less common to all the subregions,
varying probably in the level of intensity from one subregion to another. South
American marine biodiversity is least well known in the Tropical East Pacific
(with the exception of Costa Rica and Panama) and the Tropical West Atlantic,
although the latter subregion has a slightly higher diversity when the total
number of species is standardized by coastal length—nearly 150 species in
100 km of coast (<xref ref-type="table" rid="pone-0014631-t007">Table 7</xref>).
In the Tropical West Atlantic, particularly in the Venezuelan Atlantic Front,
sampling of marine biodiversity has intensified in recent years <xref ref-type="bibr" rid="pone.0014631-Lasso1">[316]</xref>, <xref ref-type="bibr" rid="pone.0014631-Pereira1">[332]</xref>, <xref ref-type="bibr" rid="pone.0014631-Capelo1">[333]</xref>, <xref ref-type="bibr" rid="pone.0014631-Bone2">[335]</xref>, <xref ref-type="bibr" rid="pone.0014631-Spiniello1">[339]</xref>, <xref ref-type="bibr" rid="pone.0014631-ZoppiDeRoa1">[340]</xref>,
significantly increasing our knowledge, but there are still many gaps and
unknowns. One of the major limits to the knowledge of marine biodiversity in
this region is the shortage of taxonomic expertise. As reported in <xref ref-type="table" rid="pone-0014631-t006">Table 6</xref>, there are 2,743
species known to this region, of which 2,475 (90.2%) are from only five
major groups: fish and other vertebrates (birds being highly diverse),
crustaceans, mollusks, polychaetes, echinoderms, and macroalgae. This means that
overall diversity is probably highly underestimated, especially in less-known
taxonomic groups.</p><table-wrap id="pone-0014631-t007" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0014631.t007</object-id><label>Table 7</label><caption><title>Number of species of cnidarians, mollusks, crustaceans, echinoderms,
and fish per kilometer of coast and per South American
subregion.</title></caption><alternatives><graphic id="pone-0014631-t007-7" xlink:href="pone.0014631.t007"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col></colgroup><thead><tr><td align="left" rowspan="1" colspan="1">Subregion</td><td align="left" rowspan="1" colspan="1">Taxonomic group</td><td align="left" rowspan="1" colspan="1">Number of species by taxonomic group</td><td align="left" rowspan="1" colspan="1">% of total species</td><td align="left" rowspan="1" colspan="1">Species/100 km of coast</td></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1"><bold>Tropical East Pacific</bold></td><td align="left" rowspan="1" colspan="1">Fish</td><td align="left" rowspan="1" colspan="1">1212</td><td align="left" rowspan="1" colspan="1">18.1</td><td align="left" rowspan="1" colspan="1">23.8</td></tr><tr><td align="left" rowspan="1" colspan="1">Coastal length: 5100 km</td><td align="left" rowspan="1" colspan="1">Crustaceans</td><td align="left" rowspan="1" colspan="1">863</td><td align="left" rowspan="1" colspan="1">12.9</td><td align="left" rowspan="1" colspan="1">16.9</td></tr><tr><td align="left" rowspan="1" colspan="1">Total species: 6714</td><td align="left" rowspan="1" colspan="1">Mollusks</td><td align="left" rowspan="1" colspan="1">875</td><td align="left" rowspan="1" colspan="1">13.0</td><td align="left" rowspan="1" colspan="1">17.2</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">Echinoderms</td><td align="left" rowspan="1" colspan="1">223</td><td align="left" rowspan="1" colspan="1">3.3</td><td align="left" rowspan="1" colspan="1">4.4</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">Cnidarians</td><td align="left" rowspan="1" colspan="1">110</td><td align="left" rowspan="1" colspan="1">1.6</td><td align="left" rowspan="1" colspan="1">2.2</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><bold>TOTAL</bold></td><td align="left" rowspan="1" colspan="1"><bold>3283</bold></td><td align="left" rowspan="1" colspan="1"><bold>48.9</bold></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Humboldt Current system</bold></td><td align="left" rowspan="1" colspan="1">Fish</td><td align="left" rowspan="1" colspan="1">1167</td><td align="left" rowspan="1" colspan="1">11.4</td><td align="left" rowspan="1" colspan="1">16.0</td></tr><tr><td align="left" rowspan="1" colspan="1">Coastal length: 7280 km</td><td align="left" rowspan="1" colspan="1">Crustaceans</td><td align="left" rowspan="1" colspan="1">3136</td><td align="left" rowspan="1" colspan="1">30.7</td><td align="left" rowspan="1" colspan="1">43.1</td></tr><tr><td align="left" rowspan="1" colspan="1">Total species: 10201</td><td align="left" rowspan="1" colspan="1">Mollusks</td><td align="left" rowspan="1" colspan="1">1203</td><td align="left" rowspan="1" colspan="1">11.8</td><td align="left" rowspan="1" colspan="1">16.5</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">Echinoderms</td><td align="left" rowspan="1" colspan="1">364</td><td align="left" rowspan="1" colspan="1">3.6</td><td align="left" rowspan="1" colspan="1">5.0</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">Cnidarians</td><td align="left" rowspan="1" colspan="1">517</td><td align="left" rowspan="1" colspan="1">5.1</td><td align="left" rowspan="1" colspan="1">7.1</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><bold>TOTAL</bold></td><td align="left" rowspan="1" colspan="1"><bold>6387</bold></td><td align="left" rowspan="1" colspan="1"><bold>62.6</bold></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Patagonian Shelf</bold></td><td align="left" rowspan="1" colspan="1">Fish</td><td align="left" rowspan="1" colspan="1">539</td><td align="left" rowspan="1" colspan="1">14.3</td><td align="left" rowspan="1" colspan="1">9.5</td></tr><tr><td align="left" rowspan="1" colspan="1">Coastal length: 5649 km</td><td align="left" rowspan="1" colspan="1">Crustaceans</td><td align="left" rowspan="1" colspan="1">611</td><td align="left" rowspan="1" colspan="1">16.2</td><td align="left" rowspan="1" colspan="1">10.8</td></tr><tr><td align="left" rowspan="1" colspan="1">Total species: 3776</td><td align="left" rowspan="1" colspan="1">Mollusks</td><td align="left" rowspan="1" colspan="1">849</td><td align="left" rowspan="1" colspan="1">22.5</td><td align="left" rowspan="1" colspan="1">15.0</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">Echinoderms</td><td align="left" rowspan="1" colspan="1">207</td><td align="left" rowspan="1" colspan="1">5.5</td><td align="left" rowspan="1" colspan="1">3.7</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">Cnidarians</td><td align="left" rowspan="1" colspan="1">258</td><td align="left" rowspan="1" colspan="1">6.8</td><td align="left" rowspan="1" colspan="1">4.6</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><bold>TOTAL</bold></td><td align="left" rowspan="1" colspan="1"><bold>2464</bold></td><td align="left" rowspan="1" colspan="1"><bold>65.3</bold></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Brazilian Shelf</bold></td><td align="left" rowspan="1" colspan="1">Fish</td><td align="left" rowspan="1" colspan="1">1294</td><td align="left" rowspan="1" colspan="1">14.2</td><td align="left" rowspan="1" colspan="1">17.3</td></tr><tr><td align="left" rowspan="1" colspan="1">Coastal length: 7491 km</td><td align="left" rowspan="1" colspan="1">Crustaceans</td><td align="left" rowspan="1" colspan="1">1966</td><td align="left" rowspan="1" colspan="1">21.6</td><td align="left" rowspan="1" colspan="1">26.2</td></tr><tr><td align="left" rowspan="1" colspan="1">Total species: 9103</td><td align="left" rowspan="1" colspan="1">Mollusks</td><td align="left" rowspan="1" colspan="1">1833</td><td align="left" rowspan="1" colspan="1">20.1</td><td align="left" rowspan="1" colspan="1">24.5</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">Echinoderms</td><td align="left" rowspan="1" colspan="1">254</td><td align="left" rowspan="1" colspan="1">2.8</td><td align="left" rowspan="1" colspan="1">3.4</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">Cnidarians</td><td align="left" rowspan="1" colspan="1">535</td><td align="left" rowspan="1" colspan="1">5.9</td><td align="left" rowspan="1" colspan="1">7.1</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><bold>TOTAL</bold></td><td align="left" rowspan="1" colspan="1"><bold>5882</bold></td><td align="left" rowspan="1" colspan="1"><bold>64.6</bold></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Tropical West Atlantic</bold></td><td align="left" rowspan="1" colspan="1">Fish</td><td align="left" rowspan="1" colspan="1">889</td><td align="left" rowspan="1" colspan="1">32.4</td><td align="left" rowspan="1" colspan="1">47.4</td></tr><tr><td align="left" rowspan="1" colspan="1">Coastal length: 1877 km</td><td align="left" rowspan="1" colspan="1">Crustaceans</td><td align="left" rowspan="1" colspan="1">519</td><td align="left" rowspan="1" colspan="1">18.9</td><td align="left" rowspan="1" colspan="1">27.7</td></tr><tr><td align="left" rowspan="1" colspan="1">Total species: 2743</td><td align="left" rowspan="1" colspan="1">Mollusks</td><td align="left" rowspan="1" colspan="1">431</td><td align="left" rowspan="1" colspan="1">15.7</td><td align="left" rowspan="1" colspan="1">23.0</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">Echinoderms</td><td align="left" rowspan="1" colspan="1">107</td><td align="left" rowspan="1" colspan="1">3.9</td><td align="left" rowspan="1" colspan="1">5.7</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">Cnidarians</td><td align="left" rowspan="1" colspan="1">131</td><td align="left" rowspan="1" colspan="1">4.8</td><td align="left" rowspan="1" colspan="1">7.0</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><bold>TOTAL</bold></td><td align="left" rowspan="1" colspan="1"><bold>2077</bold></td><td align="left" rowspan="1" colspan="1"><bold>75.7</bold></td><td align="left" rowspan="1" colspan="1"></td></tr></tbody></table></alternatives></table-wrap><p>From a biodiversity perspective, globally, coastal and shelf waters not only
present the greatest species richness (but see Gray, <xref ref-type="bibr" rid="pone.0014631-Gray1">[399]</xref>) and highest productivity
<xref ref-type="bibr" rid="pone.0014631-Cusson1">[400]</xref> of
the world's oceans, but they also are biogeographically distinct from the
adjacent high seas and deep benthic environments <xref ref-type="bibr" rid="pone.0014631-Briggs1">[50]</xref>, <xref ref-type="bibr" rid="pone.0014631-Ekman1">[401]</xref>. In the South American
continent, deep-sea exploration is relatively recent, and most efforts have been
concentrated in the southern countries, mainly Brazil (<xref ref-type="supplementary-material" rid="pone.0014631.s007">Table
S7</xref>).</p><p>In general, the best-known taxonomic groups in the marine environments worldwide
are the cnidarians, mollusks, crustaceans, and echinoderms among the
invertebrates, and the fishes <xref ref-type="bibr" rid="pone.0014631-Bouchet1">[402]</xref>. These groups together usually account for
50%–60% of the known marine biodiversity. In the global
analysis carried out by the National and Regional Committees of the Census of
Marine Life (see PLoS ONE collection “Marine Biodiversity and Biogeography
– Regional Comparisons of Global Issues”: <ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.1371/issue.pcol.v02.i09">http://dx.doi.org/10.1371/issue.pcol.v02.i09</ext-link>), the crustaceans,
molluscs, and fishes comprised approximately 50% of all known species
across the 25 regions studied <xref ref-type="bibr" rid="pone.0014631-Costello2">[403]</xref>. In the OBIS database, for instance, which is the
largest marine biodiversity database in the world with nearly 25 million species
distribution records, from over 100,000 different species and 750 datasets (by
April 2010), these groups combined account for 69.7% of all species
(9.0% cnidarians, 11.4% mollusks, 23.0% crustaceans,
5.3% echinoderms, and 21.1% fishes). In the South American
subregions, these taxonomic groups account for 54.2% in the Tropical East
Pacific, 62.6% in the Humboldt Current, 65.3% in the Patagonian
Shelf, 64.6% in the Brazilian Shelves, and 75.7% in the Tropical
West Atlantic (<xref ref-type="table" rid="pone-0014631-t007">Table 7</xref>).
The fact that their proportion in the Tropical East Pacific is much lower than
expected indicates that even for these well-known groups, there is still much to
discover.</p><p>Data show important differences in total biodiversity between the Atlantic and
Pacific oceans at the same latitude. In this sense, as mentioned earlier, in the
north of the continent, the Tropical East Pacific is richer in total number of
species than the Tropical West Atlantic (a difference which is not so evident
when standardized by kilometers of coast), and in the south, the Humboldt
Current system is much richer than the Patagonian Shelf.</p><p>It has been proposed that in marine environments, biodiversity is greatest in
tropical regions, decreasing gradually toward higher latitudes <xref ref-type="bibr" rid="pone.0014631-Rosenzweig1">[404]</xref>–<xref ref-type="bibr" rid="pone.0014631-Engle1">[407]</xref>. This trend has been
observed at the regional level in mollusks and isopods <xref ref-type="bibr" rid="pone.0014631-Roy1">[405]</xref>–<xref ref-type="bibr" rid="pone.0014631-Rex1">[408]</xref>, but not in the local
patterns of intertidal macrobenthic fauna <xref ref-type="bibr" rid="pone.0014631-Coates1">[409]</xref>. On the other hand,
intertidal assemblages of echinoderms at the global level have been reported to
peak in high northern latitudes and clearly decline with latitude, while
subtidal assemblages of echinoderms show no latitudinal trends but rather seem
to have regional diversity hotspots <xref ref-type="bibr" rid="pone.0014631-Iken1">[410]</xref>. Empirical studies <xref ref-type="bibr" rid="pone.0014631-Willig1">[411]</xref> and
meta-analysis <xref ref-type="bibr" rid="pone.0014631-Hillebrand1">[412]</xref> have shown that this relationship between latitude
and species richness is based on the decline of regional biodiversity (gamma
biodiversity) toward the poles, and not on the variation of the local community
richness (alpha biodiversity). Boltovskoy et al. <xref ref-type="bibr" rid="pone.0014631-Boltovskoy3">[413]</xref> suggested that the
trend toward decreasing biodiversity with increasing latitude seemed to be
balanced by a higher biomass and endemism at higher latitudes. However, there
has been little systematic effort to document these patterns in the southwestern
Atlantic, and most existing efforts are almost exclusively focused on
invertebrates <xref ref-type="bibr" rid="pone.0014631-LpezGappa1">[108]</xref>, <xref ref-type="bibr" rid="pone.0014631-Astorga1">[414]</xref>–<xref ref-type="bibr" rid="pone.0014631-Griffiths1">[416]</xref>. On the other hand,
Gray <xref ref-type="bibr" rid="pone.0014631-Gray1">[399]</xref>,
<xref ref-type="bibr" rid="pone.0014631-Gray2">[417]</xref>reported that species richness in the Antarctic is high, questioning the
validity of the proposed latitudinal pattern. To test whether this pattern is
valid or not, it is necessary to review as much information as possible
regarding local and regional species richness <xref ref-type="bibr" rid="pone.0014631-Clarke1">[9]</xref>. In this sense, the above
mentioned global analysis <xref ref-type="bibr" rid="pone.0014631-Costello2">[403]</xref>, showed that the most diverse coastal areas in the
world are within Japanese and Australian waters (about 33,000 species each)
followed by Chinese waters (about 22,000 species). A recent analysis carried out
with about 11,500 species across 13 separate taxonomic groups of coastal and
oceanic environments, showed that there are different diversity patterns for
coastal and oceanic species, with coastal species being more diverse in the
equatorial West Pacific, and the oceanic species being more diverse in mid
latitudes. For all groups studied, sea surface temperature was identified as a
significant driver for these patterns, while habitat availability was
significant for most, however not all, of the groups <xref ref-type="bibr" rid="pone.0014631-Tittensor1">[418]</xref>.</p><p>In the north of the South American continent, the tropical Caribbean region, has
about 12,000 marine species, a number which is certainly higher than for any of
the subregions in this paper <xref ref-type="bibr" rid="pone.0014631-Miloslavich1">[20]</xref>.The data reviewed here
shows that for the Atlantic Ocean, the tropical region has higher biodiversity
than the temperate region, varying from 146 species per 100 km of coast in the
Tropical West Atlantic to 122 species per 100 km of coast in Brazil, and to 67
species per 100 km of coast in the Patagonian Shelf (<xref ref-type="table" rid="pone-0014631-t002">Table 2</xref>). On the other hand, this trend is
not evident in the Pacific Ocean, as the diversity in the Tropical East Pacific
is 132 species per 100 km of coast and a little higher in the Humboldt Current
system (140 species per 100 km of coast). When these comparisons are made within
particular taxonomic groups, the latitudinal trends mentioned earlier for total
biodiversity in the Atlantic Ocean can only be observed for fish and crustaceans
(<xref ref-type="fig" rid="pone-0014631-g007">Figure 7</xref>). Regional
“hot spots” of biodiversity for the best-known taxonomic groups seem
to be in the Tropical West Atlantic for fishes, in the Humboldt Current for
crustaceans, in Brazil and the Tropical West Atlantic for mollusks, and in
Brazil for macroalgae.</p><fig id="pone-0014631-g007" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0014631.g007</object-id><label>Figure 7</label><caption><title>Number of species per 100 km of coast for the major taxonomic groups
(macroalgae, cnidarians, mollusks, crustaceans, echinoderms, and fishes)
for the five South American subregions studied.</title></caption><graphic xlink:href="pone.0014631.g007"></graphic></fig><p>There is not a clear relationship between increasing latitudes and increasing
species richness for macroalgae, and it has been stated that temperate regions
can achieve species numbers at least as high as those in the tropics <xref ref-type="bibr" rid="pone.0014631-Bolton1">[419]</xref>. In the
northern hemisphere, latitudinal macroalgal trends in species density and
biomass have been reported for some strata within the intertidal and shallow
subtidal zones, with more taxa and biomass at higher latitudes <xref ref-type="bibr" rid="pone.0014631-Konar2">[420]</xref>. In the
southern hemisphere, the floras of the Patagonian coast, Tierra del Fuego, and
Malvinas are recorded among the most species diverse in the Southern Ocean <xref ref-type="bibr" rid="pone.0014631-John1">[421]</xref>. The data
presented in this paper show that macroalgae are an important group for the
species richness of all regions, varying from 4.9% to 8.7% of
total species biodiversity. In regional trends, the highest biodiversity of
macroalgal species was found in the Brazilian region (10.6 species per 100 km of
coast), followed by the Humboldt Current system (7.3 species per 100 km of
coast), the Tropical West Atlantic (7.1 species per 100 km of coast), and the
Tropical East Pacific (6.0 species per 100 km of coast). The lowest diversity
was found for the Patagonian Shelf (4.7 species per 100 km of coast), which
could seem contradictory to the previous statement by John et al. <xref ref-type="bibr" rid="pone.0014631-John1">[421]</xref>, but this
could be because the relatively small hot spots of macroalgal diversity found in
the scarse rocky shores of the Patagonian Shelf are being “diluted”
among hundreds of kilometers of sandy coasts with no macroalgae.</p><p>The trends discussed here, however, both for fauna and macroalgae, may not truly
reflect real patterns, as sampling has not been equal throughout the continent,
and taxonomic capacity is very uneven from one country to another as is the case
in the Caribbean <xref ref-type="bibr" rid="pone.0014631-Miloslavich1">[20]</xref>. These patterns are based on analysis of a thoroughly
updated biodiversity review as was carried out in each of the South American
subregions in this paper. But the patterns cannot be visualized correctly
because we do not know all the localities for all the species compiled here. To
visualize marine diversity distribution patterns in South America, we relied in
the OBIS database, which has more than 50% of the species for four of the
subregions (between 51% and 84%), and about 38% for the
Humboldt Current system (<xref ref-type="table" rid="pone-0014631-t002">Table
2</xref>, <xref ref-type="fig" rid="pone-0014631-g008">Figure 8</xref>).
From this figure it is evident that all regions as reviewed in this paper have a
higher number of species than the number reported in OBIS (all dots above the
diagonal line), and that the biodiversity in some regions is well represented in
the OBIS database (e.g. Patagonian shelf) while in others, this is not the case
(e.g. Humboldt current). Strictly with OBIS data, the patterns of biodiversity
along the latitudinal gradient of the Atlantic Ocean are the same as those we
report with updated data, but that was not the case for the Pacific Ocean, where
the tropical zones show more diversity than the temperate zones (<xref ref-type="fig" rid="pone-0014631-g009">Figure 9</xref>). This difference is
probably because the Humboldt Current system is poorly represented in the OBIS
database. Based on this observed inconsistency, we tested for this particular
region, which has the largest latitudinal variation in the continent, whether
the expected pattern of biodiversity would have been different from the observed
pattern given a homogeneous sampling effort. To test for this, we used the
rarefaction technique to estimate the number of species that would have been
recorded in a given number of observations (e.g., Magurran, <xref ref-type="bibr" rid="pone.0014631-Magurran1">[422]</xref>). In
this analysis, we used a conservative number of 10 observations, which
corresponds to the standardized sample size used to estimate the richness per
cell using the rarefaction technique. An <italic>a posteriori</italic>neighborhood operation was conducted to improve the detection of biogeographical
patterns. Using this function, we recalculated the values of each grid cell
using the mean, according to the values of the cells in a 3×3 neighborhood
around that cell. Later, the expected geographic pattern in biodiversity was
compared with the observed biogeographic pattern from this study, and the
provinces previously described for the southeastern Pacific coast by Camus <xref ref-type="bibr" rid="pone.0014631-Camus1">[88]</xref>.</p><fig id="pone-0014631-g008" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0014631.g008</object-id><label>Figure 8</label><caption><title>Number of species in the OBIS database versus the number of species
in the present review.</title><p>A: Total number of species. B: Species per 100 km of coast. The largest
the length of the dashed line (deviation from the diagonal), the largest
the difference between the two datasets (OBIS and the present
review).</p></caption><graphic xlink:href="pone.0014631.g008"></graphic></fig><fig id="pone-0014631-g009" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0014631.g009</object-id><label>Figure 9</label><caption><title>Map showing the distribution of marine biodiversity around the South
American continent using data from the OBIS database.</title><p>Richness scale represents number of species. Bathymetry scale in
meters.</p></caption><graphic xlink:href="pone.0014631.g009"></graphic></fig><p>The analysis of the distribution of patterns of richness along the Humboldt
Current system observed in the OBIS database showed three zones of high richness
(<xref ref-type="fig" rid="pone-0014631-g010">Figure 10</xref>) with the
highest values found in the Strait of Magellan. This zone of maximum diversity
is in accordance with previously described patterns of mollusk diversity on the
southern Pacific coast <xref ref-type="bibr" rid="pone.0014631-Valdovinos1">[423]</xref>, as well as with the observed pattern for marine
invertebrates on the Chilean coast described by Lancellotti and Vásquez
<xref ref-type="bibr" rid="pone.0014631-Lancellotti1">[424]</xref>, <xref ref-type="bibr" rid="pone.0014631-Lancellotti2">[425]</xref> and polychaetes by Hernández et al. <xref ref-type="bibr" rid="pone.0014631-Hernndez1">[89]</xref>. This
zone of maximum diversity has historically experienced the combined effects of
climatic processes, tectonic activity, and glaciers, provoking the formation of
a large system of archipelagos, with an abundance of gulfs, fjords, and canals
<xref ref-type="bibr" rid="pone.0014631-Camus1">[88]</xref>. This
zone has been associated with changes in local conditions (i.e., substrate
types, tidal amplitude, temperature, and salinity) <xref ref-type="bibr" rid="pone.0014631-Santelices1">[426]</xref>, which would generate
a highly diversified mosaic of different biotopes <xref ref-type="bibr" rid="pone.0014631-Mariani1">[427]</xref>, which would act as
refuges during repeated glacial advances over the last 40 million years <xref ref-type="bibr" rid="pone.0014631-Crame1">[428]</xref>. The sum of
these factors would favor the local radiation of taxa, leading to the current
area of high taxonomic diversity in the Strait of Magellan
(52°–56°S) as reported in our study, and secondarily causing low
faunistic affinity with taxa from the Antarctic Peninsula <xref ref-type="bibr" rid="pone.0014631-Caete2">[429]</xref>.</p><fig id="pone-0014631-g010" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0014631.g010</object-id><label>Figure 10</label><caption><title>Expected species richness in the Humboldt Current subregion using the
rarefaction technique to estimate the number of species that would have
been observed given a standard number of 10 observations.</title><p>Scale represents expected number of species.</p></caption><graphic xlink:href="pone.0014631.g010"></graphic></fig><p>In the northern zone, the bands of lowest diversity (off southern Peru between
15°–19°S and northern Chile between 25°–29°S, <xref ref-type="fig" rid="pone-0014631-g005">Figure 5</xref>) are strongly
influenced by the large-scale low-frequency spatial disturbances called El
Niño/Southern Oscillation (ENSO). This phenomenon provokes a series of
alterations in the structure of the current system and, consequently, the
coastal biota of the region, with regional-scale influences up to
30°–36°S <xref ref-type="bibr" rid="pone.0014631-Camus2">[430]</xref>, <xref ref-type="bibr" rid="pone.0014631-Gutirrez1">[431]</xref>. Since the appearance of ENSO about 5,000 years ago
<xref ref-type="bibr" rid="pone.0014631-Rollins1">[432]</xref>,
the southeastern Pacific biota has experienced a continued disturbing influence,
and now ENSO is a critical component of regional dynamics, having played an
important role in defining the current biogeography of the area <xref ref-type="bibr" rid="pone.0014631-Fernndez1">[90]</xref>.
According to Camus <xref ref-type="bibr" rid="pone.0014631-Camus2">[430]</xref>, the characteristics of ENSO probably subjected
local populations to frequent bottlenecks and nonselective extinctions, which
could generate high interpopulational variability and even provoke founder
effects. These population-level processes, together with ENSO should have
produced increases in local diversity; however, while our results do not support
this hypothesis, they do support the ENSO hypothesis as a cause of extinctions
and low diversity in the zone. The low diversity of benthic polychaetes observed
in the northern zone can probably also be attributed to a low speciation rate,
due to the low differentiation of niches (i.e., low diversity of microhabitats)
observed in this zone with respect to the zone south of 41°S, which would
function as a biological mechanism determining local-scale diversity <xref ref-type="bibr" rid="pone.0014631-Shmida1">[433]</xref>.
Additionally, as was proposed by Moreno et al. <xref ref-type="bibr" rid="pone.0014631-Moreno1">[434]</xref>, the northern latitude
benthic richness of the HC potentially is controlled by the development of a
shallow oxygen minimum zone during the Neogene <xref ref-type="bibr" rid="pone.0014631-MartinezPardo1">[435]</xref>. This phenomenon,
which is observed on the Peruvian and northern Chilean coasts, occurs at less
than 50 m depth <xref ref-type="bibr" rid="pone.0014631-Morales2">[436]</xref>–<xref ref-type="bibr" rid="pone.0014631-Helly1">[438]</xref> and strongly influences the
distribution and diversity of benthic marine species <xref ref-type="bibr" rid="pone.0014631-Levin1">[439]</xref>.</p><p>The rarefaction technique, used to evaluate the expected pattern of biodiversity,
showed a consistent pattern of increase in the richness of marine species toward
tropical latitudes (<xref ref-type="fig" rid="pone-0014631-g010">Figure
10</xref>). These results allow us to predict that a homogeneous sampling
effort will improve the OBIS database and provide more accurate patterns of
biodiversity. This expected pattern is a hypothetical scenario—constructed
on a conservative number of 10 observations—that can only be evaluated if
the OBIS database continues to grow, using new georeferenced data made available
not only from new studies of marine biodiversity in the HC, but also by
uploading in the OBIS system information that is already either in the
literature or in local databases.</p><p>Research capacity is stronger in the southern countries of the continent, in
Brazil, Argentina, and Chile, which also have a longer history in marine
research. For example, contrary to what is generally stated abroad, the
southwest Atlantic has had many oceanographic and biological studies for many
years, but most past literature was mainly in Brazilian regional scientific
journals in Portuguese. Many molecular tools have been used to study latitudinal
gradients, identify cryptic and endemic species, and consider other questions
related to biodiversity <xref ref-type="bibr" rid="pone.0014631-Nobrega1">[440]</xref>–<xref ref-type="bibr" rid="pone.0014631-Valderrama1">[444]</xref>. In the last seven
years, a great effort has been made to incorporate data into open-access
databases such as OBIS, especially from Brazil and Argentina through their OBIS
nodes. However, there is still much information available locally that has to be
incorporated into the system, as was demonstrated for the Humboldt Current
system. On the other hand, it is true that even in the best-studied areas along
the vast South American coastline, there is still much to be done and
discovered, both in the continental shelf and especially in deep-sea
environments.</p><sec id="s5a1"><title>Species discovery and analysis of endemism</title><p>Description of South American species began as early as the mid-1700s with
several peaks of discovery around 1850, 1900, and 1970 (<xref ref-type="fig" rid="pone-0014631-g011">Figure 11a</xref>). Since then, new species have
been added to the total every year exponentially (<xref ref-type="fig" rid="pone-0014631-g011">Figure 11b</xref>). A total of 13,656 species
are reported in OBIS for the five subregions considered in this paper. As
mentioned, this number could represent about half of the known species of
South America. As stated in <xref ref-type="table" rid="pone-0014631-t001">tables 1</xref>, <xref ref-type="table" rid="pone-0014631-t003">3</xref>, <xref ref-type="table" rid="pone-0014631-t004">4</xref>,
<xref ref-type="table" rid="pone-0014631-t005">5</xref>, and <xref ref-type="table" rid="pone-0014631-t006">6</xref>, the best known groups
in the region (those ranked mostly between 4 and 5 in the “state of
knowledge” category) are fish, mollusks, crustaceans, echinoderms,
cnidarians, and macroalgae. The rate of discovery for these best-known
taxonomic groups has been variable, and the number of fish, mollusk, and
crustacean species is continuously increasing. However, this is not true of
cnidarians, echinoderms, and macroalgae, which seem to have reached a
relatively stable number, with few new additions (<xref ref-type="fig" rid="pone-0014631-g012">Figure 12</xref>). This stability certainly
indicates that these groups have been neglected in the region, probably the
consequence of a combination of factors, including lack of taxonomic
expertise, limited funding for research, lack of collecting effort, and
limited access to sampling sites. However, these curves are based in OBIS
data which has an iconsistent subset of data for the region, with some
regions (e.g. Brazil) better represented than others (e.g. Humboldt
Current), so a full species inventory is needed to confirm if these patterns
are valid. On the other hand, given the richness of these three groups in
the world context (Bouchet, <xref ref-type="bibr" rid="pone.0014631-Bouchet1">[402]</xref> has reported a total
of 9,795 cnidarians, 7,000 echinoderms, and 10,300 macroalgae), it seems
unlikely that such low numbers represent the total regional biodiversity of
these groups for such a vast area as South America. While it is true that
new descriptions of some well-known groups such as vertebrates have
decreased in the last decade, the application of new molecular methods at a
broader global scale, together with the exploration of the less explored
environments will undoubtedly help to improve and refine the knowledge on
marine biodiversity. In addition, shifts in species distribution associated
with climate change are expected to increase in frequency in the near
future.</p><fig id="pone-0014631-g011" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0014631.g011</object-id><label>Figure 11</label><caption><title>Species description in South America.</title><p>A: Number of species described per year for all taxonomic groups. B:
Species-description accumulation curves for marine species taking
into account all taxonomic groups. Period: 1750–2000. Data
from OBIS database (using only “valid names” which
corrects for synonyms).</p></caption><graphic xlink:href="pone.0014631.g011"></graphic></fig><fig id="pone-0014631-g012" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0014631.g012</object-id><label>Figure 12</label><caption><title>Species-description accumulation curves for South American marine
species by taxonomic group (macroalgae, cnidarians, mollusks,
crustaceans, echinoderms, and fishes).</title><p>Data from OBIS database (using only “valid names” which
corrects for synonyms).</p></caption><graphic xlink:href="pone.0014631.g012"></graphic></fig><p>Two interesting questions can be asked about the 13,656 species that compose
about half of the known biodiversity of South America. The first is, how
many of them are exclusive to one subregion or are shared by two or more
subregions, and in which proportion? This is a question of endemism within
regions of South America. The second question is, how many of these species
are exclusive to South America and in which taxonomic groups? This is a
question of South American endemism within a global context. To answer the
first question, we sorted the number of species in the OBIS database that
are present in one, two, three, four, and five subregions, and how they were
distributed (<xref ref-type="table" rid="pone-0014631-t008">Table 8</xref>).
A total of 10,311 species are reported to exist exclusively in only one
South American subregion, that is, 75.5% of the total species
reported for the region. Among the subregions, this endemism within South
America represents 71.2% of the species for the Tropical East Pacific
(2,452 species), 43.4% for the Humboldt Current (1,691 species),
48.2% for the Tropical West Atlantic (896 species), 71.6% for
Brazil (3,921 species), and 42.6% for the Patagonian Shelf (1,351
species). On the other hand, the number of species shared by two or more
subregions decreased as the number of subregions involved increased; with 28
species shared by all five subregions (comprising mainly protists, a few
cnidarians, and the killer whale, <italic>Orcinus orca</italic>).</p><table-wrap id="pone-0014631-t008" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0014631.t008</object-id><label>Table 8</label><caption><title>Number of species reported exclusively for the five subregions of
South America from the OBIS database.</title></caption><alternatives><graphic id="pone-0014631-t008-8" xlink:href="pone.0014631.t008"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col></colgroup><thead><tr><td align="left" rowspan="1" colspan="1">SUBREGION</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">5</td></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">Tropical East Pacific</td><td align="left" rowspan="1" colspan="1">2452</td><td align="left" rowspan="1" colspan="1">674</td><td align="left" rowspan="1" colspan="1">218</td><td align="left" rowspan="1" colspan="1">74</td><td align="left" rowspan="1" colspan="1">28</td></tr><tr><td align="left" rowspan="1" colspan="1">Humboldt Current</td><td align="left" rowspan="1" colspan="1">1691</td><td align="left" rowspan="1" colspan="1">1540</td><td align="left" rowspan="1" colspan="1">453</td><td align="left" rowspan="1" colspan="1">182</td><td align="left" rowspan="1" colspan="1">28</td></tr><tr><td align="left" rowspan="1" colspan="1">Tropical West Atlantic</td><td align="left" rowspan="1" colspan="1">896</td><td align="left" rowspan="1" colspan="1">642</td><td align="left" rowspan="1" colspan="1">372</td><td align="left" rowspan="1" colspan="1">157</td><td align="left" rowspan="1" colspan="1">28</td></tr><tr><td align="left" rowspan="1" colspan="1">Brazilian Shelves</td><td align="left" rowspan="1" colspan="1">3921</td><td align="left" rowspan="1" colspan="1">995</td><td align="left" rowspan="1" colspan="1">358</td><td align="left" rowspan="1" colspan="1">173</td><td align="left" rowspan="1" colspan="1">28</td></tr><tr><td align="left" rowspan="1" colspan="1">Patagonian Shelf</td><td align="left" rowspan="1" colspan="1">1351</td><td align="left" rowspan="1" colspan="1">1167</td><td align="left" rowspan="1" colspan="1">459</td><td align="left" rowspan="1" colspan="1">166</td><td align="left" rowspan="1" colspan="1">28</td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>TOTAL</bold></td><td align="left" rowspan="1" colspan="1"><bold>10311</bold></td><td align="left" rowspan="1" colspan="1"><bold>2509</bold></td><td align="left" rowspan="1" colspan="1"><bold>620</bold></td><td align="left" rowspan="1" colspan="1"><bold>188</bold></td><td align="left" rowspan="1" colspan="1"><bold>28</bold></td></tr></tbody></table></alternatives></table-wrap><p>To answer the second question, we filtered from the global database the
species that are only found around South America, that is, the species that
have not been reported elsewhere in the world. The total number of species
that are “endemic” to South America within the global context
according to the data in OBIS is 3,065 species, which represents
22.4% of the total reported for the region. These species represent
several phyla, of which the most abundant were the mollusks (42%),
followed by the arthropods (mainly crustaceans: 23%), and the
chordates (fish and other vertebrates: 12%). Polychaetes, cnidarians,
sponges, echinoderms, and nematodes accounted altogether for 19% of
these “endemic” species. Although this is a good estimate of
endemism for the region, the numbers could change as new data are
incorporated into the OBIS database. For instance, it is possible that a
species considered as “endemic” to South America could have been
observed outside the region but that these records have not been published
in OBIS. Moreover, with new exploration, species considered to be endemic to
South America could appear elsewhere, and would no longer be considered
endemic. The total number of endemic species as reviewed in this paper was
886 (67 for the Tropical East Pacific, 197 for the Humboldt Current system,
4 for the Tropical West Atlantic, 446 for Brazil, and 172 for the Patagonian
Shelf). These low numbers in relation to what is reported in OBIS as
exclusive of South America indicate that regional knowledge about which
species are endemic is generally poor, especially for tropical areas, both
Pacific and Atlantic. Other regions of extremely high endemism are New
Zealand and Antarctica with about 48% of endemic species <xref ref-type="bibr" rid="pone.0014631-Gordon2">[445]</xref>, <xref ref-type="bibr" rid="pone.0014631-Griffiths2">[446]</xref>,
followed by Australia and South Africa with about 28% of endemic
species <xref ref-type="bibr" rid="pone.0014631-Butler1">[447]</xref>, <xref ref-type="bibr" rid="pone.0014631-Griffiths3">[448]</xref> all of which are
located in the Southern Hemisphere as is most of South America. Griffiths et
al. <xref ref-type="bibr" rid="pone.0014631-Griffiths3">[448]</xref> reported high levels of species endemism for
South African waters (around 4,233 species), a number that is subject to
change as some species are being reported in other countries. Among these
endemic species, the bryozoans and the mollusks showed high levels of
endemism (64% and 56%, respectively), while echinoderms and
sponges had much lower levels of endemism (3.6% and 8.8%,
respectively). Assuming our estimate of endemism is valid, then South
America could be considered as a region of high endemism for mollusks, as
has been reported for some localities in Brazil <xref ref-type="bibr" rid="pone.0014631-Leal1">[449]</xref>. In New Zealand <xref ref-type="bibr" rid="pone.0014631-Gordon2">[445]</xref>, there
are 6,741 endemic species, of which nearly 3,000 are mollusks. In this
sense, both New Zealand and South Africa have good knowledge of their
species richness and endemism, and South America has yet to attain it. For
instance, it has been discussed that seamounts in Brazil seem to be highly
endemic (see Bouchet & Leal, <xref ref-type="bibr" rid="pone.0014631-Bouchet2">[450]</xref> for reports on the
gastropod fauna of Brazilian seamounts and their reproductive modes, as well
as Vaske Jr et al., <xref ref-type="bibr" rid="pone.0014631-Vaske2">[235]</xref> on deep-water scorpion fish). This raises
interesting questions related to reproductive and developpmental strategies,
endemism, and faunistic relationships between the Brazilian continental
margin and other parts of the Atlantic: Would Brazilian seamounts function
as stepping stones in the Atlantic Ocean? How much more endemism do they
hold, and what is the relationship between species found on seamounts and
those found on the continental margin? Would seamounts act as a gene source
or sink? Increasing our knowledge of seamounts would allow us a better
understanding of how they function, and provide better baselines for
management and conservation, especially if seamounts are repositories of
unique biodiversity.</p><p>As mentioned earlier, the heterogeneity and vast extent of the South American
coast and the diversity of habitats and oceanographic conditions there have
important implications for biodiversity. We have discussed the state of
knowledge of marine biodiversity, observed latitudinal trends, the potential
endemism of the region, and the limits of our knowledge. South America is
certainly in a good position to improve its expertise and is likely to
advance in some regions, such as Brazil, sooner than in others. National and
regional initiatives in new exploration, especially to unknown areas and
ecosystems, as well as collaboration between the different countries is
fundamental to achieving the goal of completing inventories of species
diversity and distribution that will allow accurate interpretation of the
biogeography of the continent, latitudinal trends, and differences between
its two oceanic coasts. Spalding et al. <xref ref-type="bibr" rid="pone.0014631-Spalding1">[52]</xref> proposed a
bioregionalization of the coastal and shelf areas of the world based in
ecoregions. These ecoregions extend beyond national borders and even beyond
continents. It would had been interesting to make the same analysis we have
done here but comparing among ecoregions instead of the regions used in this
paper. However, this is not possible with the present state of knowledge,
because most of the data compiled here relate to a specific country rather
than to geographic coordinates, as can be found in OBIS. Thus, an extra
effort to compile all species records in the literature, validate the
taxonomy of these records, and make them available through open-source
databases such as OBIS is of outmost importance and must be encouraged and
supported by local governments through biodiversity policies. In this paper,
we have attempted such a compilation, and in doing so, we have become even
more aware of the magnitude of the work still to be done to move on to the
next level of knowledge and understanding.</p></sec></sec></sec><sec sec-type="supplementary-material" id="s6"><title>Supporting Information</title><supplementary-material content-type="local-data" id="pone.0014631.s001"><label>Table S1</label><caption><p>Sources of information used to estimate total number of marine species for
different taxa of the Tropical East Pacific region of South America.</p><p>(0.05 MB DOC)</p></caption><media xlink:href="pone.0014631.s001.doc" mimetype="application" mime-subtype="msword"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="pone.0014631.s002"><label>Table S2</label><caption><p>Sources of information used to estimate total number of marine species for
different taxa of the Patagonian Shelf region of South America.</p><p>(0.06 MB DOC)</p></caption><media xlink:href="pone.0014631.s002.doc" mimetype="application" mime-subtype="msword"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="pone.0014631.s003"><label>Table S3</label><caption><p>Diversity, state of knowledge, and expertise of all taxonomic groups within
the Tropical East Pacific region of South America. Sources of the reports:
databases, scientific literature, books, field guides, technical reports.
State of knowledge classified as: 5 = very well known
(>80% described, identification guides <20 years old, and
current taxonomic expertise); 4 = well known
(>70% described, identification guides <50 years old, some
taxonomic expertise); 3 = poorly known (<50%
species described, identification guides old or incomplete, no present
expertise within region); 2 = very poorly known (only
few species recorded, no identification guides, no expertise);
1 = unknown (no species recorded, no identification
guides, no expertise). Taxonomic experts were defined as people with
expertise in the description and identification of particular groups of
marine species (i.e., taxa).</p><p>(0.03 MB XLS)</p></caption><media xlink:href="pone.0014631.s003.xls" mimetype="application" mime-subtype="vnd.ms-excel"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="pone.0014631.s004"><label>Table S4</label><caption><p>Diversity, state of knowledge, and expertise of all taxonomic groups within
the Humboldt Current region of South America. Sources of the reports:
databases, scientific literature, books, field guides, technical reports.
State of knowledge classified as: 5 = very well known
(>80% described, identification guides <20 years old, and
current taxonomic expertise); 4 = well known
(>70% described, identification guides <50 years old, some
taxonomic expertise); 3 = poorly known (<50%
species described, identification guides old or incomplete, no present
expertise within region); 2 = very poorly known (only
few species recorded, no identification guides, no expertise);
1 = unknown (no species recorded, no identification
guides, no expertise). Taxonomic experts were defined as people with
expertise in the description and identification of particular groups of
marine species (i.e., taxa).</p><p>(0.05 MB XLS)</p></caption><media xlink:href="pone.0014631.s004.xls" mimetype="application" mime-subtype="vnd.ms-excel"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="pone.0014631.s005"><label>Table S5</label><caption><p>Diversity, state of knowledge, and expertise of all taxonomic groups within
the Patagonian Shelf region of South America. Sources of the reports:
databases, scientific literature, books, field guides, technical reports.
State of knowledge classified as: 5 = very well known
(>80% described, identification guides <20 years old, and
current taxonomic expertise); 4 = well known
(>70% described, identification guides <50 years old, some
taxonomic expertise); 3 = poorly known (<50%
species described, identification guides old or incomplete, no present
expertise within region); 2 = very poorly known (only
few species recorded, no identification guides, no expertise);
1 = unknown (no species recorded, no identification
guides, no expertise). Taxonomic experts were defined as people with
expertise in the description and identification of particular groups of
marine species (i.e., taxa).</p><p>(0.03 MB XLS)</p></caption><media xlink:href="pone.0014631.s005.xls" mimetype="application" mime-subtype="vnd.ms-excel"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="pone.0014631.s006"><label>Table S6</label><caption><p>Diversity, state of knowledge, and expertise of all taxonomic groups within
the Brazilian region of South America. Sources of the reports: databases,
scientific literature, books, field guides, technical reports. State of
knowledge classified as: 5 = very well known
(>80% described, identification guides <20 years old, and
current taxonomic expertise); 4 = well known
(>70% described, identification guides <50 years old, some
taxonomic expertise); 3 = poorly known (<50%
species described, identification guides old or incomplete, no present
expertise within region); 2 = very poorly known (only
few species recorded, no identification guides, no expertise);
1 = unknown (no species recorded, no identification
guides, no expertise). Taxonomic experts were defined as people with
expertise in the description and identification of particular groups of
marine species (i.e., taxa).</p><p>(0.04 MB XLS)</p></caption><media xlink:href="pone.0014631.s006.xls" mimetype="application" mime-subtype="vnd.ms-excel"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="pone.0014631.s007"><label>Table S7</label><caption><p>Summary of literature sources on marine biodiversity for the non-coastal
Brazilian deep-sea marine realms: (1) slope, (2) seamounts and oceanic
islands, and (3) abyssal plains.</p><p>(0.09 MB DOC)</p></caption><media xlink:href="pone.0014631.s007.doc" mimetype="application" mime-subtype="msword"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="pone.0014631.s008"><label>Table S8</label><caption><p>Major Brazilian cruises that have taken samples in the deep sea, including
seamounts and abyssal plains.</p><p>(0.06 MB DOC)</p></caption><media xlink:href="pone.0014631.s008.doc" mimetype="application" mime-subtype="msword"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="pone.0014631.s009"><label>Table S9</label><caption><p>Diversity, state of knowledge, and expertise of all taxonomic groups within
the Tropical West Atlantic region of South America. Sources of the reports:
databases, scientific literature, books, field guides, technical reports.
State of knowledge classified as: 5 = very well known
(>80% described, identification guides <20 years old, and
current taxonomic expertise); 4 = well known
(>70% described, identification guides <50 years old, some
taxonomic expertise); 3 = poorly known (<50%
species described, identification guides old or incomplete, no present
expertise within region); 2 = very poorly known (only
few species recorded, no identification guides, no expertise);
1 = unknown (no species recorded, no identification
guides, no expertise). Taxonomic experts were defined as people with
expertise in the description and identification of particular groups of
marine species (i.e., taxa).</p><p>(0.03 MB XLS)</p></caption><media xlink:href="pone.0014631.s009.xls" mimetype="application" mime-subtype="vnd.ms-excel"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material></sec></body><back><ack><p>We are grateful to Alvaro Sanhueza, Bryan Morales and Sofia Paz for help in
compilation of databases of the Humboldt Current system and Olivia Paz
Hernández for her valuable comments. Special thanks to J.M. Lobo Orensanz for
generous contribution with bibliography on marine invertebrates. Andrés
Averbuj, Mariano Cumplido, Federico del Brío and Maria Emilia Rechimont
helped in the database preparation of the Patagonian Shelf region. Yusbelly
Díaz, Sandra López and Iliana Ortega helped in the database
compilation of the Tropical West Atlantic region.</p><p>Flávio Dias Passos, André Morgado Esteves, Denise R. Tenenbaum, Eduardo
C.M. Hajdu, Inácio Domingos da Silva Neto, Manuela Bassoi, Michelle Klautau,
Monica V. Petti, Priscila A. Grohmann, Ricardo da Silva Absalão, provided
data for the compilation of the marine biodiversity of Brazil for different
taxonomic groups, as well as the Brazilian CNPq Lattes database. Monica V Petti is
specially thanked for her useful suggestions.</p><p>We thank Fabio Lang and Rubens M. Lopes for their assistance in accessing the OBIS
Brazilian information. Ana Paula Prates from the Ministry of Environment is thanked
for her support to the work of the Census of Marine Life in Brazil and for providing
us with useful information on Government conservation strategies. Maria Cordelia
Machado is thanked for her constant support to Census work in Brazil. The
Interministerial Secretariat for the Sea Resources (SECIRM) and Petrobras have
played a major role in all Brazilian marine studies including those related to
biodiversity. Rafael Bendayan de Moura is thanked for his assistance in compiling
the Brazilian map with the marine conservation areas based on the Ministry of
Environment information.</p><p>We acknowledge César Paz for assistance with the bibliographic format, Emanuel
Valero for assistance in <xref ref-type="fig" rid="pone-0014631-g007">figures
7</xref> and <xref ref-type="fig" rid="pone-0014631-g008">8</xref>, and Michele
DuRand, Charles Griffiths, and Dale Langford for editorial comments.</p></ack><fn-group><fn fn-type="conflict"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="financial-disclosure"><p><bold>Funding: </bold>A grant was received from the Alfred P. Sloan Foundation. The funders had no role
in study design, data collection and analysis, decision to publish, or
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