How effective are DNA barcodes in the identification of African rainforest trees?

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cg.contributor.affiliationBioversity Internationalen
cg.contributor.crpForests, Trees and Agroforestry
cg.coverage.regionAfrica
cg.identifier.doihttps://doi.org/10.1371/journal.pone.0054921en
cg.isijournalISI Journalen
cg.issn1932-6203en
cg.issue4en
cg.journalPLOS ONEen
cg.reviewStatusPeer Reviewen
cg.subject.bioversityDNAen
cg.subject.bioversityIDENTIFICATIONen
cg.subject.bioversityRAIN FORESTSen
cg.subject.bioversityTAXONOMYen
cg.volume8en
dc.contributor.authorParmentier, I.en
dc.contributor.authorDuminil, J.en
dc.contributor.authorKuzmina, M.en
dc.contributor.authorPhilippe, M.en
dc.contributor.authorThomas, D.W.en
dc.contributor.authorDuncan, T.en
dc.contributor.authorKenfack, D.en
dc.contributor.authorChuyong, G.B.en
dc.contributor.authorHardy, Olivier J.en
dc.date.accessioned2014-05-05T08:44:25Zen
dc.date.available2014-05-05T08:44:25Zen
dc.identifier.urihttps://hdl.handle.net/10568/35565
dc.titleHow effective are DNA barcodes in the identification of African rainforest trees?en
dcterms.abstractDNA barcoding of rain forest trees could potentially help biologists identify species and discover new ones. However, DNA barcodes cannot always distinguish between closely related species, and the size and completeness of barcode databases are key parameters for their successful application. We test the ability of rbcL, matK and trnH-psbA plastid DNA markers to identify rain forest trees at two sites in Atlantic central Africa under the assumption that a database is exhaustive in terms of species content, but not necessarily in terms of haplotype diversity within species. We assess the accuracy of identification to species or genus using a genetic distance matrix between samples either based on a global multiple sequence alignment (GD) or on a basic local alignment search tool (BLAST). Where a local database is available (within a 50 ha plot), barcoding was generally reliable for genus identification (95–100% success), but less for species identification (71–88%). Using a single marker, best results for species identification were obtained with trnH-psbA. There was a significant decrease of barcoding success in species-rich clades. When the local database was used to identify the genus of trees from another region and did include all genera from the query individuals but not all species, genus identification success decreased to 84–90%. The GD method performed best but a global multiple sequence alignment is not applicable on trnH-psbA. Barcoding is a useful tool to assign unidentified African rain forest trees to a genus, but identification to a species is less reliable, especially in species-rich clades, even using an exhaustive local database. Combining two markers improves the accuracy of species identification but it would only marginally improve genus identification. Finally, we highlight some limitations of the BLAST algorithm as currently implemented and suggest possible improvements for barcoding applications.en
dcterms.accessRightsOpen Access
dcterms.available2013-04-02
dcterms.bibliographicCitationParmentier, I.; Duminil, J.; Kuzmina, M.; Philippe, M.; Thomas, D.W.; Duncan, T.; Kenfack, D.; Chuyong, G.B.; Hardy, O.J. -2013-How effective are DNA barcodes in the identification of African rainforest trees?-PLoS ONE 8(4)-e54921en
dcterms.extente54921en
dcterms.issued2013
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.publisherPublic Library of Scienceen
dcterms.subjectdnaen
dcterms.subjectidentificationen
dcterms.subjectrain forestsen
dcterms.subjecttaxonomyen
dcterms.subjecttreesen
dcterms.typeJournal Article

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