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A Ranking system for reference libraries of DNA Barcodes: application to marine fish species from Portugal

2012-04Journal article Open access
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dc.contributor.authorCosta, Filipe O.
dc.contributor.authorLandi, Monica
dc.contributor.authorMartins, Rogelia
dc.contributor.authorCosta, Maria H.
dc.contributor.authorLima Costa, Maria Emília
dc.contributor.authorCarneiro, Miguel
dc.contributor.authorAlves, Maria J.
dc.contributor.authorSteinke, Dirk
dc.contributor.authorCarvalho, Gary R.
dc.date.accessioned2018-12-07T14:52:34Z
dc.date.available2018-12-07T14:52:34Z
dc.date.issued2012-04
dc.description.abstractBackground: The increasing availability of reference libraries of DNA barcodes (RLDB) offers the opportunity to the screen the level of consistency in DNA barcode data among libraries, in order to detect possible disagreements generated from taxonomic uncertainty or operational shortcomings. We propose a ranking system to attribute a confidence level to species identifications associated with DNA barcode records from a RLDB. Here we apply the proposed ranking system to a newly generated RLDB for marine fish of Portugal. Methodology/Principal Findings: Specimens (n = 659) representing 102 marine fish species were collected along the continental shelf of Portugal, morphologically identified and archived in a museum collection. Samples were sequenced at the barcode region of the cytochrome oxidase subunit I gene (COI-5P). Resultant DNA barcodes had average intra-specific and inter-specific Kimura-2-parameter distances (0.32% and 8.84%, respectively) within the range usually observed for marine fishes. All specimens were ranked in five different levels (A-E), according to the reliability of the match between their species identification and the respective diagnostic DNA barcodes. Grades A to E were attributed upon submission of individual specimen sequences to BOLD-IDS and inspection of the clustering pattern in the NJ tree generated. Overall, our study resulted in 73.5% of unambiguous species IDs (grade A), 7.8% taxonomically congruent barcode clusters within our dataset, but awaiting external confirmation (grade B), and 18.7% of species identifications with lower levels of reliability (grades C/E). Conclusion/Significance: We highlight the importance of implementing a system to rank barcode records in RLDB, in order to flag taxa in need of taxonomic revision, or reduce ambiguities of discordant data. With increasing DNA barcode records publicly available, this cross-validation system would provide a metric of relative accuracy of barcodes, while enabling the continuous revision and annotation required in taxonomic work.
dc.description.sponsorshipFEDER through POFC-COMPETE; national funds from "Fundacao para a Ciencia e a Tecnologia (FCT)" [FCOMP-01-0124-FEDER-007381, FCOMP-01-0124-FEDER-010596, PEst-C/BIA/UI4050/2011]; Marie Curie Fellowship [MEIF-CT-2005-024966]; European Reintegration Grant by European Commission [PERG02-GA-2007-224890]; FCT [SFRH/BPD/45246/2008]; Canadian Centre for DNA Barcoding from Ontario Genomics Institute [2008-OGI-ICI-03]; Genome Canada; Ontario Ministry of Research and Innovation; Natural Sciences and Engineering Research Council of Canada; Alfred P. Sloan Foundation
dc.description.versioninfo:eu-repo/semantics/publishedVersion
dc.identifier.doi10.1371/journal.pone.0035858
dc.identifier.issn1932-6203
dc.identifier.urihttp://hdl.handle.net/10400.1/11127
dc.language.isoeng
dc.peerreviewedyes
dc.publisherPublic Library of Science
dc.relationMOLECULAR BIODIVERSITY AND META-SPECIES PHYLOGEOGRAPHY OF FISH FROM THE NE ATLANTIC AND MEDITERRANEAN
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectDivergence
dc.subjectSequences
dc.subjectAustralia
dc.subjectTaxonomy
dc.subjectLife
dc.titleA Ranking system for reference libraries of DNA Barcodes: application to marine fish species from Portugal
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleMOLECULAR BIODIVERSITY AND META-SPECIES PHYLOGEOGRAPHY OF FISH FROM THE NE ATLANTIC AND MEDITERRANEAN
oaire.awardURIinfo:eu-repo/grantAgreement/FCT//SFRH%2FBPD%2F45246%2F2008/PT
oaire.citation.issue4
oaire.citation.startPagee35858
oaire.citation.titlePLoS ONE
oaire.citation.volume7
person.familyNameLima Costa
person.givenNameMaria Emília
person.identifier.orcid0000-0002-4433-5756
person.identifier.scopus-author-id7003633118
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.rightsopenAccess
rcaap.typearticle
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relation.isAuthorOfPublication.latestForDiscovery6eb9b8a6-dd51-4ace-809b-7d7de9cdfe36
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