DNA barcode data accurately assign higher spider taxa
The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfe...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2016-07-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/2201.pdf |
| _version_ | 1797419289612910592 |
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| author | Jonathan A. Coddington Ingi Agnarsson Ren-Chung Cheng Klemen Čandek Amy Driskell Holger Frick Matjaž Gregorič Rok Kostanjšek Christian Kropf Matthew Kweskin Tjaša Lokovšek Miha Pipan Nina Vidergar Matjaž Kuntner |
| author_facet | Jonathan A. Coddington Ingi Agnarsson Ren-Chung Cheng Klemen Čandek Amy Driskell Holger Frick Matjaž Gregorič Rok Kostanjšek Christian Kropf Matthew Kweskin Tjaša Lokovšek Miha Pipan Nina Vidergar Matjaž Kuntner |
| author_sort | Jonathan A. Coddington |
| collection | DOAJ |
| description | The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios “barcodes” (whether single or multiple, organelle or nuclear, loci) clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families—taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level assignment. We used BLAST queries of each sequence against the entire library and got the top ten hits. The percent sequence identity was reported from these hits (PIdent, range 75–100%). Accurate assignment of higher taxa (PIdent above which errors totaled less than 5%) occurred for genera at PIdent values >95 and families at PIdent values ≥ 91, suggesting these as heuristic thresholds for accurate generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all higher taxon assignments were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However, the quality of the underlying database impacts accuracy of results; many outliers in our dataset could be attributed to taxonomic and/or sequencing errors in BOLD and GenBank. It seems that an accurate and complete reference library of families and genera of life could provide accurate higher level taxonomic identifications cheaply and accessibly, within years rather than decades. |
| first_indexed | 2024-03-09T06:46:15Z |
| format | Article |
| id | doaj.art-51705e40038641519d49f15ebb76650d |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:46:15Z |
| publishDate | 2016-07-01 |
| publisher | PeerJ Inc. |
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| spelling | doaj.art-51705e40038641519d49f15ebb76650d2023-12-03T10:35:09ZengPeerJ Inc.PeerJ2167-83592016-07-014e220110.7717/peerj.2201DNA barcode data accurately assign higher spider taxaJonathan A. Coddington0Ingi Agnarsson1Ren-Chung Cheng2Klemen Čandek3Amy Driskell4Holger Frick5Matjaž Gregorič6Rok Kostanjšek7Christian Kropf8Matthew Kweskin9Tjaša Lokovšek10Miha Pipan11Nina Vidergar12Matjaž Kuntner13National Museum of Natural History, Smithsonian Institution, Washington, D.C., United StatesNational Museum of Natural History, Smithsonian Institution, Washington, D.C., United StatesEZ Lab, Institute of Biology, Research Centre of the Slovenian Academy of Sciences and Arts, Ljubljana, SloveniaEZ Lab, Institute of Biology, Research Centre of the Slovenian Academy of Sciences and Arts, Ljubljana, SloveniaNational Museum of Natural History, Smithsonian Institution, Washington, D.C., United StatesDepartment of Invertebrates, Natural History Museum Bern, Bern, SwitzerlandEZ Lab, Institute of Biology, Research Centre of the Slovenian Academy of Sciences and Arts, Ljubljana, SloveniaDepartment of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, SloveniaDepartment of Invertebrates, Natural History Museum Bern, Bern, SwitzerlandNational Museum of Natural History, Smithsonian Institution, Washington, D.C., United StatesEZ Lab, Institute of Biology, Research Centre of the Slovenian Academy of Sciences and Arts, Ljubljana, SloveniaEZ Lab, Institute of Biology, Research Centre of the Slovenian Academy of Sciences and Arts, Ljubljana, SloveniaEZ Lab, Institute of Biology, Research Centre of the Slovenian Academy of Sciences and Arts, Ljubljana, SloveniaNational Museum of Natural History, Smithsonian Institution, Washington, D.C., United StatesThe use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios “barcodes” (whether single or multiple, organelle or nuclear, loci) clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families—taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level assignment. We used BLAST queries of each sequence against the entire library and got the top ten hits. The percent sequence identity was reported from these hits (PIdent, range 75–100%). Accurate assignment of higher taxa (PIdent above which errors totaled less than 5%) occurred for genera at PIdent values >95 and families at PIdent values ≥ 91, suggesting these as heuristic thresholds for accurate generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all higher taxon assignments were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However, the quality of the underlying database impacts accuracy of results; many outliers in our dataset could be attributed to taxonomic and/or sequencing errors in BOLD and GenBank. It seems that an accurate and complete reference library of families and genera of life could provide accurate higher level taxonomic identifications cheaply and accessibly, within years rather than decades.https://peerj.com/articles/2201.pdfTaxonomic impedimentFamilyGenusGlobal Genome InitiativeGenomeDNA barcoding |
| spellingShingle | Jonathan A. Coddington Ingi Agnarsson Ren-Chung Cheng Klemen Čandek Amy Driskell Holger Frick Matjaž Gregorič Rok Kostanjšek Christian Kropf Matthew Kweskin Tjaša Lokovšek Miha Pipan Nina Vidergar Matjaž Kuntner DNA barcode data accurately assign higher spider taxa PeerJ Taxonomic impediment Family Genus Global Genome Initiative Genome DNA barcoding |
| title | DNA barcode data accurately assign higher spider taxa |
| title_full | DNA barcode data accurately assign higher spider taxa |
| title_fullStr | DNA barcode data accurately assign higher spider taxa |
| title_full_unstemmed | DNA barcode data accurately assign higher spider taxa |
| title_short | DNA barcode data accurately assign higher spider taxa |
| title_sort | dna barcode data accurately assign higher spider taxa |
| topic | Taxonomic impediment Family Genus Global Genome Initiative Genome DNA barcoding |
| url | https://peerj.com/articles/2201.pdf |
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