DNA barcoding in the Southeast Pacific marine realm: Low coverage and geographic representation despite high diversity
The Southeast Pacific comprises two Large Marine Ecosystems, the Pacific Central-American Coastal and the Humboldt Current System; and is one of the less well known in the tropical subregions in terms of biodiversity. To address this, we compared DNA barcoding repositories with the marine biodiversi...
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| creator | Ramirez, Jorge L Rosas-Puchuri, Ulises Cañedo, Rosa Maria Alfaro-Shigueto, Joanna Ayon, Patricia Zelada-Mázmela, Eliana Siccha-Ramirez, Raquel Velez-Zuazo, Ximena |
| description | The Southeast Pacific comprises two Large Marine Ecosystems, the Pacific Central-American Coastal and the Humboldt Current System; and is one of the less well known in the tropical subregions in terms of biodiversity. To address this, we compared DNA barcoding repositories with the marine biodiversity species for the Southeast Pacific. We obtained a checklist of marine species in the Southeast Pacific (i.e. Colombia, Ecuador, Chile, and Peru) from the Ocean Biodiversity Information System (OBIS) database and compared it with species available at the Barcoding of Life Data System (BOLD) repository. Of the 5504 species records retrieved from OBIS, 42% of them had at least one registered specimen in BOLD (including specimens around the world); however, only 4.5% of records corresponded to publicly available DNA barcodes including specimens collected from a Southeast Pacific country. The low representation of barcoded species does not vary much across the different taxonomic groups or within countries, but we observed an asymmetric distribution of DNA barcoding records for taxonomic groups along the coast, being more abundant for the Humboldt Current System than the Pacific Central-American Coastal. We observed high-level of barcode records with Barcode Index Number (BIN) incongruences, particularly for fishes (Actinopterygii = 30.27% and Elasmobranchii = 24.71%), reflecting taxonomic uncertainties for fishes, whereas for Invertebrates and Mammalia more than 85% of records were classified as data deficient or inadequate procedure for DNA barcoding. DNA barcoding is a powerful tool to study biodiversity, with a great potential to increase the knowledge of the Southeast Pacific marine biodiversity. Our results highlight the critical need for increasing taxonomic sampling effort, the number of trained taxonomic specialists, laboratory facilities, scientific collections, and genetic reference libraries. |
| doi_str_mv | 10.1371/journal.pone.0244323 |
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To address this, we compared DNA barcoding repositories with the marine biodiversity species for the Southeast Pacific. We obtained a checklist of marine species in the Southeast Pacific (i.e. Colombia, Ecuador, Chile, and Peru) from the Ocean Biodiversity Information System (OBIS) database and compared it with species available at the Barcoding of Life Data System (BOLD) repository. Of the 5504 species records retrieved from OBIS, 42% of them had at least one registered specimen in BOLD (including specimens around the world); however, only 4.5% of records corresponded to publicly available DNA barcodes including specimens collected from a Southeast Pacific country. The low representation of barcoded species does not vary much across the different taxonomic groups or within countries, but we observed an asymmetric distribution of DNA barcoding records for taxonomic groups along the coast, being more abundant for the Humboldt Current System than the Pacific Central-American Coastal. We observed high-level of barcode records with Barcode Index Number (BIN) incongruences, particularly for fishes (Actinopterygii = 30.27% and Elasmobranchii = 24.71%), reflecting taxonomic uncertainties for fishes, whereas for Invertebrates and Mammalia more than 85% of records were classified as data deficient or inadequate procedure for DNA barcoding. DNA barcoding is a powerful tool to study biodiversity, with a great potential to increase the knowledge of the Southeast Pacific marine biodiversity. Our results highlight the critical need for increasing taxonomic sampling effort, the number of trained taxonomic specialists, laboratory facilities, scientific collections, and genetic reference libraries.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0244323</identifier><identifier>PMID: 33370342</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Animals ; Aquatic Organisms - classification ; Aquatic Organisms - genetics ; Bar codes ; Biodiversity ; Biology and life sciences ; Caretta caretta ; Computer and information sciences ; Conservation biology ; Deoxyribonucleic acid ; Dermochelys coriacea ; DNA ; DNA barcoding ; DNA Barcoding, Taxonomic - methods ; Earth Sciences ; Ecology and Environmental Sciences ; Ecosystem ; Ecosystem biology ; Endangered & extinct species ; Extinction ; Fishes - classification ; Fishes - genetics ; Gene Library ; Gene sequencing ; Invertebrates ; Invertebrates - classification ; Invertebrates - genetics ; Marine biology ; Marine ecosystems ; Names ; Pacific Ocean - epidemiology ; Phylogeny ; Repositories ; Representations ; Research and analysis methods ; Skewed distributions ; South America ; Species ; Taxonomy</subject><ispartof>PloS one, 2020-12, Vol.15 (12), p.e0244323-e0244323</ispartof><rights>COPYRIGHT 2020 Public Library of Science</rights><rights>2020 Ramirez et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2020 Ramirez et al 2020 Ramirez et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-220c38fe9f4415661a70c9b779f29125995dc579bc93c17fa36cae253b37192d3</citedby><cites>FETCH-LOGICAL-c692t-220c38fe9f4415661a70c9b779f29125995dc579bc93c17fa36cae253b37192d3</cites><orcidid>0000-0003-0529-2623 ; 0000-0001-8138-9203</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7769448/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7769448/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33370342$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Pardo-Pérez, Judith</contributor><creatorcontrib>Ramirez, Jorge L</creatorcontrib><creatorcontrib>Rosas-Puchuri, Ulises</creatorcontrib><creatorcontrib>Cañedo, Rosa Maria</creatorcontrib><creatorcontrib>Alfaro-Shigueto, Joanna</creatorcontrib><creatorcontrib>Ayon, Patricia</creatorcontrib><creatorcontrib>Zelada-Mázmela, Eliana</creatorcontrib><creatorcontrib>Siccha-Ramirez, Raquel</creatorcontrib><creatorcontrib>Velez-Zuazo, Ximena</creatorcontrib><title>DNA barcoding in the Southeast Pacific marine realm: Low coverage and geographic representation despite high diversity</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The Southeast Pacific comprises two Large Marine Ecosystems, the Pacific Central-American Coastal and the Humboldt Current System; and is one of the less well known in the tropical subregions in terms of biodiversity. 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We observed high-level of barcode records with Barcode Index Number (BIN) incongruences, particularly for fishes (Actinopterygii = 30.27% and Elasmobranchii = 24.71%), reflecting taxonomic uncertainties for fishes, whereas for Invertebrates and Mammalia more than 85% of records were classified as data deficient or inadequate procedure for DNA barcoding. DNA barcoding is a powerful tool to study biodiversity, with a great potential to increase the knowledge of the Southeast Pacific marine biodiversity. 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To address this, we compared DNA barcoding repositories with the marine biodiversity species for the Southeast Pacific. We obtained a checklist of marine species in the Southeast Pacific (i.e. Colombia, Ecuador, Chile, and Peru) from the Ocean Biodiversity Information System (OBIS) database and compared it with species available at the Barcoding of Life Data System (BOLD) repository. Of the 5504 species records retrieved from OBIS, 42% of them had at least one registered specimen in BOLD (including specimens around the world); however, only 4.5% of records corresponded to publicly available DNA barcodes including specimens collected from a Southeast Pacific country. The low representation of barcoded species does not vary much across the different taxonomic groups or within countries, but we observed an asymmetric distribution of DNA barcoding records for taxonomic groups along the coast, being more abundant for the Humboldt Current System than the Pacific Central-American Coastal. We observed high-level of barcode records with Barcode Index Number (BIN) incongruences, particularly for fishes (Actinopterygii = 30.27% and Elasmobranchii = 24.71%), reflecting taxonomic uncertainties for fishes, whereas for Invertebrates and Mammalia more than 85% of records were classified as data deficient or inadequate procedure for DNA barcoding. DNA barcoding is a powerful tool to study biodiversity, with a great potential to increase the knowledge of the Southeast Pacific marine biodiversity. Our results highlight the critical need for increasing taxonomic sampling effort, the number of trained taxonomic specialists, laboratory facilities, scientific collections, and genetic reference libraries.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>33370342</pmid><doi>10.1371/journal.pone.0244323</doi><tpages>e0244323</tpages><orcidid>https://orcid.org/0000-0003-0529-2623</orcidid><orcidid>https://orcid.org/0000-0001-8138-9203</orcidid><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2020-12, Vol.15 (12), p.e0244323-e0244323 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_2473448497 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Analysis Animals Aquatic Organisms - classification Aquatic Organisms - genetics Bar codes Biodiversity Biology and life sciences Caretta caretta Computer and information sciences Conservation biology Deoxyribonucleic acid Dermochelys coriacea DNA DNA barcoding DNA Barcoding, Taxonomic - methods Earth Sciences Ecology and Environmental Sciences Ecosystem Ecosystem biology Endangered & extinct species Extinction Fishes - classification Fishes - genetics Gene Library Gene sequencing Invertebrates Invertebrates - classification Invertebrates - genetics Marine biology Marine ecosystems Names Pacific Ocean - epidemiology Phylogeny Repositories Representations Research and analysis methods Skewed distributions South America Species Taxonomy |
| title | DNA barcoding in the Southeast Pacific marine realm: Low coverage and geographic representation despite high diversity |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-27T19%3A50%3A26IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=DNA%20barcoding%20in%20the%20Southeast%20Pacific%20marine%20realm:%20Low%20coverage%20and%20geographic%20representation%20despite%20high%20diversity&rft.jtitle=PloS%20one&rft.au=Ramirez,%20Jorge%20L&rft.date=2020-12-28&rft.volume=15&rft.issue=12&rft.spage=e0244323&rft.epage=e0244323&rft.pages=e0244323-e0244323&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0244323&rft_dat=%3Cgale_plos_%3EA646874254%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2473448497&rft_id=info:pmid/33370342&rft_galeid=A646874254&rft_doaj_id=oai_doaj_org_article_a1ba57afc38a4bf699f3793b0002f617&rfr_iscdi=true |