The Use of DNA Barcoding in Identification and Conservation of Rosewood (Dalbergia spp.)
The genus Dalbergia contains many valuable timber species threatened by illegal logging and deforestation, but knowledge on distributions and threats is often limited and accurate species identification difficult. The aim of this study was to apply DNA barcoding methods to support conservation effor...
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| creator | Hartvig, Ida Czako, Mihaly Kjær, Erik Dahl Nielsen, Lene Rostgaard Theilade, Ida |
| description | The genus Dalbergia contains many valuable timber species threatened by illegal logging and deforestation, but knowledge on distributions and threats is often limited and accurate species identification difficult. The aim of this study was to apply DNA barcoding methods to support conservation efforts of Dalbergia species in Indochina. We used the recommended rbcL, matK and ITS barcoding markers on 95 samples covering 31 species of Dalbergia, and tested their discrimination ability with both traditional distance-based as well as different model-based machine learning methods. We specifically tested whether the markers could be used to solve taxonomic confusion concerning the timber species Dalbergia oliveri, and to identify the CITES-listed Dalbergia cochinchinensis. We also applied the barcoding markers to 14 samples of unknown identity. In general, we found that the barcoding markers discriminated among Dalbergia species with high accuracy. We found that ITS yielded the single highest discrimination rate (100%), but due to difficulties in obtaining high-quality sequences from degraded material, the better overall choice for Dalbergia seems to be the standard rbcL+matK barcode, as this yielded discrimination rates close to 90% and amplified well. The distance-based method TaxonDNA showed the highest identification rates overall, although a more complete specimen sampling is needed to conclude on the best analytic method. We found strong support for a monophyletic Dalbergia oliveri and encourage that this name is used consistently in Indochina. The CITES-listed Dalbergia cochinchinensis was successfully identified, and a species-specific assay can be developed from the data generated in this study for the identification of illegally traded timber. We suggest that the use of DNA barcoding is integrated into the work flow during floristic studies and at national herbaria in the region, as this could significantly increase the number of identified specimens and improve knowledge about species distributions. |
| doi_str_mv | 10.1371/journal.pone.0138231 |
| format | Article |
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The aim of this study was to apply DNA barcoding methods to support conservation efforts of Dalbergia species in Indochina. We used the recommended rbcL, matK and ITS barcoding markers on 95 samples covering 31 species of Dalbergia, and tested their discrimination ability with both traditional distance-based as well as different model-based machine learning methods. We specifically tested whether the markers could be used to solve taxonomic confusion concerning the timber species Dalbergia oliveri, and to identify the CITES-listed Dalbergia cochinchinensis. We also applied the barcoding markers to 14 samples of unknown identity. In general, we found that the barcoding markers discriminated among Dalbergia species with high accuracy. We found that ITS yielded the single highest discrimination rate (100%), but due to difficulties in obtaining high-quality sequences from degraded material, the better overall choice for Dalbergia seems to be the standard rbcL+matK barcode, as this yielded discrimination rates close to 90% and amplified well. The distance-based method TaxonDNA showed the highest identification rates overall, although a more complete specimen sampling is needed to conclude on the best analytic method. We found strong support for a monophyletic Dalbergia oliveri and encourage that this name is used consistently in Indochina. The CITES-listed Dalbergia cochinchinensis was successfully identified, and a species-specific assay can be developed from the data generated in this study for the identification of illegally traded timber. We suggest that the use of DNA barcoding is integrated into the work flow during floristic studies and at national herbaria in the region, as this could significantly increase the number of identified specimens and improve knowledge about species distributions.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0138231</identifier><identifier>PMID: 26375850</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Biodiversity ; Biological research ; Conservation ; Conservation biology ; Conservation of Natural Resources ; Dalbergia ; Dalbergia - genetics ; Dalbergia - growth & development ; Dalbergia cochinchinensis ; Dalbergia oliveri ; Deforestation ; Deoxyribonucleic acid ; DNA ; DNA Barcoding, Taxonomic - methods ; DNA, Plant - genetics ; Endangered & extinct species ; Fabaceae ; Flowers & plants ; Gene sequencing ; Genetic aspects ; Genetic markers ; Genotypes ; Identification and classification ; Learning algorithms ; Logging ; Machine learning ; Markers ; Phylogeny ; Rosewoods ; Sequence Analysis, DNA - methods ; Species ; Species Specificity ; Threatened species ; Wildlife conservation ; Workflow</subject><ispartof>PloS one, 2015-09, Vol.10 (9), p.e0138231</ispartof><rights>COPYRIGHT 2015 Public Library of Science</rights><rights>2015 Hartvig 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>2015 Hartvig et al 2015 Hartvig et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-1bf25712763ddc35bce7b43d689a51de9213985407a76ba924d60d0fbbcbdb2c3</citedby><cites>FETCH-LOGICAL-c692t-1bf25712763ddc35bce7b43d689a51de9213985407a76ba924d60d0fbbcbdb2c3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4573973/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4573973/$$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/26375850$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Lumbsch, Helge Thorsten</contributor><creatorcontrib>Hartvig, Ida</creatorcontrib><creatorcontrib>Czako, Mihaly</creatorcontrib><creatorcontrib>Kjær, Erik Dahl</creatorcontrib><creatorcontrib>Nielsen, Lene Rostgaard</creatorcontrib><creatorcontrib>Theilade, Ida</creatorcontrib><title>The Use of DNA Barcoding in Identification and Conservation of Rosewood (Dalbergia spp.)</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The genus Dalbergia contains many valuable timber species threatened by illegal logging and deforestation, but knowledge on distributions and threats is often limited and accurate species identification difficult. The aim of this study was to apply DNA barcoding methods to support conservation efforts of Dalbergia species in Indochina. We used the recommended rbcL, matK and ITS barcoding markers on 95 samples covering 31 species of Dalbergia, and tested their discrimination ability with both traditional distance-based as well as different model-based machine learning methods. We specifically tested whether the markers could be used to solve taxonomic confusion concerning the timber species Dalbergia oliveri, and to identify the CITES-listed Dalbergia cochinchinensis. We also applied the barcoding markers to 14 samples of unknown identity. In general, we found that the barcoding markers discriminated among Dalbergia species with high accuracy. We found that ITS yielded the single highest discrimination rate (100%), but due to difficulties in obtaining high-quality sequences from degraded material, the better overall choice for Dalbergia seems to be the standard rbcL+matK barcode, as this yielded discrimination rates close to 90% and amplified well. The distance-based method TaxonDNA showed the highest identification rates overall, although a more complete specimen sampling is needed to conclude on the best analytic method. We found strong support for a monophyletic Dalbergia oliveri and encourage that this name is used consistently in Indochina. The CITES-listed Dalbergia cochinchinensis was successfully identified, and a species-specific assay can be developed from the data generated in this study for the identification of illegally traded timber. We suggest that the use of DNA barcoding is integrated into the work flow during floristic studies and at national herbaria in the region, as this could significantly increase the number of identified specimens and improve knowledge about species distributions.</description><subject>Biodiversity</subject><subject>Biological research</subject><subject>Conservation</subject><subject>Conservation biology</subject><subject>Conservation of Natural Resources</subject><subject>Dalbergia</subject><subject>Dalbergia - genetics</subject><subject>Dalbergia - growth & development</subject><subject>Dalbergia cochinchinensis</subject><subject>Dalbergia oliveri</subject><subject>Deforestation</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA Barcoding, Taxonomic - methods</subject><subject>DNA, Plant - genetics</subject><subject>Endangered & extinct species</subject><subject>Fabaceae</subject><subject>Flowers & plants</subject><subject>Gene sequencing</subject><subject>Genetic aspects</subject><subject>Genetic markers</subject><subject>Genotypes</subject><subject>Identification and classification</subject><subject>Learning algorithms</subject><subject>Logging</subject><subject>Machine learning</subject><subject>Markers</subject><subject>Phylogeny</subject><subject>Rosewoods</subject><subject>Sequence Analysis, DNA - 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genetics</topic><topic>Dalbergia - growth & development</topic><topic>Dalbergia cochinchinensis</topic><topic>Dalbergia oliveri</topic><topic>Deforestation</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA Barcoding, Taxonomic - methods</topic><topic>DNA, Plant - genetics</topic><topic>Endangered & extinct species</topic><topic>Fabaceae</topic><topic>Flowers & plants</topic><topic>Gene sequencing</topic><topic>Genetic aspects</topic><topic>Genetic markers</topic><topic>Genotypes</topic><topic>Identification and classification</topic><topic>Learning algorithms</topic><topic>Logging</topic><topic>Machine learning</topic><topic>Markers</topic><topic>Phylogeny</topic><topic>Rosewoods</topic><topic>Sequence Analysis, DNA - methods</topic><topic>Species</topic><topic>Species Specificity</topic><topic>Threatened species</topic><topic>Wildlife conservation</topic><topic>Workflow</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Hartvig, Ida</creatorcontrib><creatorcontrib>Czako, Mihaly</creatorcontrib><creatorcontrib>Kjær, Erik Dahl</creatorcontrib><creatorcontrib>Nielsen, Lene Rostgaard</creatorcontrib><creatorcontrib>Theilade, Ida</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hartvig, Ida</au><au>Czako, Mihaly</au><au>Kjær, Erik Dahl</au><au>Nielsen, Lene Rostgaard</au><au>Theilade, Ida</au><au>Lumbsch, Helge Thorsten</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The Use of DNA Barcoding in Identification and Conservation of Rosewood (Dalbergia spp.)</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2015-09-16</date><risdate>2015</risdate><volume>10</volume><issue>9</issue><spage>e0138231</spage><pages>e0138231-</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The genus Dalbergia contains many valuable timber species threatened by illegal logging and deforestation, but knowledge on distributions and threats is often limited and accurate species identification difficult. The aim of this study was to apply DNA barcoding methods to support conservation efforts of Dalbergia species in Indochina. We used the recommended rbcL, matK and ITS barcoding markers on 95 samples covering 31 species of Dalbergia, and tested their discrimination ability with both traditional distance-based as well as different model-based machine learning methods. We specifically tested whether the markers could be used to solve taxonomic confusion concerning the timber species Dalbergia oliveri, and to identify the CITES-listed Dalbergia cochinchinensis. We also applied the barcoding markers to 14 samples of unknown identity. In general, we found that the barcoding markers discriminated among Dalbergia species with high accuracy. We found that ITS yielded the single highest discrimination rate (100%), but due to difficulties in obtaining high-quality sequences from degraded material, the better overall choice for Dalbergia seems to be the standard rbcL+matK barcode, as this yielded discrimination rates close to 90% and amplified well. The distance-based method TaxonDNA showed the highest identification rates overall, although a more complete specimen sampling is needed to conclude on the best analytic method. We found strong support for a monophyletic Dalbergia oliveri and encourage that this name is used consistently in Indochina. The CITES-listed Dalbergia cochinchinensis was successfully identified, and a species-specific assay can be developed from the data generated in this study for the identification of illegally traded timber. We suggest that the use of DNA barcoding is integrated into the work flow during floristic studies and at national herbaria in the region, as this could significantly increase the number of identified specimens and improve knowledge about species distributions.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>26375850</pmid><doi>10.1371/journal.pone.0138231</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Biodiversity Biological research Conservation Conservation biology Conservation of Natural Resources Dalbergia Dalbergia - genetics Dalbergia - growth & development Dalbergia cochinchinensis Dalbergia oliveri Deforestation Deoxyribonucleic acid DNA DNA Barcoding, Taxonomic - methods DNA, Plant - genetics Endangered & extinct species Fabaceae Flowers & plants Gene sequencing Genetic aspects Genetic markers Genotypes Identification and classification Learning algorithms Logging Machine learning Markers Phylogeny Rosewoods Sequence Analysis, DNA - methods Species Species Specificity Threatened species Wildlife conservation Workflow |
| title | The Use of DNA Barcoding in Identification and Conservation of Rosewood (Dalbergia spp.) |
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