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Morinière J, Hendrich L, Balke M, Beermann AJ, König T, Hess M, Koch S, Müller R, Leese F, Hebert PDN, Hausmann A, Schubart CD, Haszprunar G. A DNA barcode library for Germany′s mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and Trichoptera). Mol Ecol Resour 2017; 17:1293-1307. [DOI: 10.1111/1755-0998.12683] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 04/07/2017] [Accepted: 04/19/2017] [Indexed: 02/02/2023]
Affiliation(s)
- Jérôme Morinière
- Bavarian State Collection of Zoology (SNSB - ZSM); München Germany
| | - Lars Hendrich
- Bavarian State Collection of Zoology (SNSB - ZSM); München Germany
| | - Michael Balke
- Bavarian State Collection of Zoology (SNSB - ZSM); München Germany
- Department Biology II and GeoBioCenter; Ludwig-Maximilians-University; München Germany
| | - Arne J. Beermann
- Aquatic Ecosystem Research; University of Duisburg-Essen; Essen Germany
| | - Tobias König
- Bavarian State Collection of Zoology (SNSB - ZSM); München Germany
| | - Monika Hess
- Büro H2 Ökologische Gutachten, Hess & Heckes GbR; München Germany
| | | | | | - Florian Leese
- Aquatic Ecosystem Research; University of Duisburg-Essen; Essen Germany
- Center for Water and Environmental Research (ZWU); University of Duisburg-Essen; Essen Germany
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics; University of Guelph; Guelph ON Canada
| | - Axel Hausmann
- Bavarian State Collection of Zoology (SNSB - ZSM); München Germany
- Department Biology II and GeoBioCenter; Ludwig-Maximilians-University; München Germany
| | | | - Gerhard Haszprunar
- Bavarian State Collection of Zoology (SNSB - ZSM); München Germany
- Department Biology II and GeoBioCenter; Ludwig-Maximilians-University; München Germany
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52
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Hernández-Triana LM, Montes De Oca F, Prosser SW, Hebert PD, Gregory TR, McMurtrie S. DNA barcoding as an aid for species identification in austral black flies (Insecta: Diptera: Simuliidae). Genome 2017; 60:348-357. [DOI: 10.1139/gen-2015-0168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this paper, the utility of a partial sequence of the COI gene, the DNA barcoding region, for the identification of species of black flies in the austral region was assessed. Twenty-eight morphospecies were analyzed: eight of the genus Austrosimulium (four species in the subgenus Austrosimulium s. str., three species in the subgenus Novaustrosimulium, and one species unassigned to subgenus), two of the genus Cnesia, eight of Gigantodax, three of Paracnephia, one of Paraustrosimulium, and six of Simulium (subgenera Morops, Nevermannia, and Pternaspatha). The neighbour-joining tree derived from the DNA barcode sequences grouped most specimens according to species or species groups recognized by morphotaxonomic studies. Intraspecific sequence divergences within morphologically distinct species ranged from 0% to 1.8%, while higher divergences (2%–4.2%) in certain species suggested the presence of cryptic diversity. The existence of well-defined groups within S. simile revealed the likely inclusion of cryptic diversity. DNA barcodes also showed that specimens identified as C. dissimilis, C. nr. pussilla, and C. ornata might be conspecific, suggesting possible synonymy. DNA barcoding combined with a sound morphotaxonomic framework would provide an effective approach for the identification of black flies in the region.
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Affiliation(s)
| | - Fernanda Montes De Oca
- Program of Applied Studies for the Conservation of Nahuel Huapi National Park, Fagnano 244, CP 8400 Bariloche, Argentina
| | - Sean W.J. Prosser
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Paul D.N. Hebert
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - T. Ryan Gregory
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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Colorado-Garzón FA, Adler PH, García LF, Muñoz de Hoyos P, Bueno ML, Matta NE. Estimating Diversity of Black Flies in theSimulium ignescensandSimulium tunjaComplexes in Colombia: Chromosomal Rearrangements as the Core of Integrative Taxonomy. J Hered 2016; 108:12-24. [DOI: 10.1093/jhered/esw063] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 10/03/2016] [Indexed: 11/13/2022] Open
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54
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Hausmann A, Miller SE, Holloway JD, deWaard JR, Pollock D, Prosser SW, Hebert PD. Calibrating the taxonomy of a megadiverse insect family: 3000 DNA barcodes from geometrid type specimens (Lepidoptera, Geometridae). Genome 2016; 59:671-84. [DOI: 10.1139/gen-2015-0197] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
It is essential that any DNA barcode reference library be based upon correctly identified specimens. The Barcode of Life Data Systems (BOLD) requires information such as images, geo-referencing, and details on the museum holding the voucher specimen for each barcode record to aid recognition of potential misidentifications. Nevertheless, there are misidentifications and incomplete identifications (e.g., to a genus or family) on BOLD, mainly for species from tropical regions. Unfortunately, experts are often unavailable to correct taxonomic assignments due to time constraints and the lack of specialists for many groups and regions. However, considerable progress could be made if barcode records were available for all type specimens. As a result of recent improvements in analytical protocols, it is now possible to recover barcode sequences from museum specimens that date to the start of taxonomic work in the 18th century. The present study discusses success in the recovery of DNA barcode sequences from 2805 type specimens of geometrid moths which represent 1965 species, corresponding to about 9% of the 23 000 described species in this family worldwide and including 1875 taxa represented by name-bearing types. Sequencing success was high (73% of specimens), even for specimens that were more than a century old. Several case studies are discussed to show the efficiency, reliability, and sustainability of this approach.
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Affiliation(s)
- Axel Hausmann
- Staatliche Naturwissenschaftliche Sammlungen Bayerns – Zoologische Staatssammlung München, Münchhausenstr. 21, D-81247 Munich, Germany
| | - Scott E. Miller
- National Museum of Natural History, Smithsonian Institution, Box 37012, Washington, DC 20013-7012, USA
| | - Jeremy D. Holloway
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Jeremy R. deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - David Pollock
- National Museum of Natural History, Smithsonian Institution, Box 37012, Washington, DC 20013-7012, USA
| | - Sean W.J. Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Paul D.N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
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Prosser SWJ, deWaard JR, Miller SE, Hebert PDN. DNA barcodes from century-old type specimens using next-generation sequencing. Mol Ecol Resour 2015; 16:487-97. [PMID: 26426290 DOI: 10.1111/1755-0998.12474] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 09/14/2015] [Accepted: 09/25/2015] [Indexed: 02/05/2023]
Abstract
Type specimens have high scientific importance because they provide the only certain connection between the application of a Linnean name and a physical specimen. Many other individuals may have been identified as a particular species, but their linkage to the taxon concept is inferential. Because type specimens are often more than a century old and have experienced conditions unfavourable for DNA preservation, success in sequence recovery has been uncertain. This study addresses this challenge by employing next-generation sequencing (NGS) to recover sequences for the barcode region of the cytochrome c oxidase 1 gene from small amounts of template DNA. DNA quality was first screened in more than 1800 century-old type specimens of Lepidoptera by attempting to recover 164-bp and 94-bp reads via Sanger sequencing. This analysis permitted the assignment of each specimen to one of three DNA quality categories--high (164-bp sequence), medium (94-bp sequence) or low (no sequence). Ten specimens from each category were subsequently analysed via a PCR-based NGS protocol requiring very little template DNA. It recovered sequence information from all specimens with average read lengths ranging from 458 bp to 610 bp for the three DNA categories. By sequencing ten specimens in each NGS run, costs were similar to Sanger analysis. Future increases in the number of specimens processed in each run promise substantial reductions in cost, making it possible to anticipate a future where barcode sequences are available from most type specimens.
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Affiliation(s)
- Sean W J Prosser
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada
| | - Jeremy R deWaard
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada
| | - Scott E Miller
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Paul D N Hebert
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada
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56
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Jordaens K, Goergen G, Virgilio M, Backeljau T, Vokaer A, De Meyer M. DNA Barcoding to Improve the Taxonomy of the Afrotropical Hoverflies (Insecta: Diptera: Syrphidae). PLoS One 2015; 10:e0140264. [PMID: 26473612 PMCID: PMC4608823 DOI: 10.1371/journal.pone.0140264] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 09/22/2015] [Indexed: 11/19/2022] Open
Abstract
The identification of Afrotropical hoverflies is very difficult because of limited recent taxonomic revisions and the lack of comprehensive identification keys. In order to assist in their identification, and to improve the taxonomy of this group, we constructed a reference dataset of 513 COI barcodes of 90 of the more common nominal species from Ghana, Togo, Benin and Nigeria (W Africa) and added ten publically available COI barcodes from nine nominal Afrotropical species to this (total: 523 COI barcodes; 98 nominal species; 26 genera). The identification accuracy of this dataset was evaluated with three methods (K2P distance-based, Neighbor-Joining (NJ) / Maximum Likelihood (ML) analysis, and using SpeciesIdentifier). Results of the three methods were highly congruent and showed a high identification success. Nine species pairs showed a low (< 0.03) mean interspecific K2P distance that resulted in several incorrect identifications. A high (> 0.03) maximum intraspecific K2P distance was observed in eight species and barcodes of these species not always formed single clusters in the NJ / ML analayses which may indicate the occurrence of cryptic species. Optimal K2P thresholds to differentiate intra- from interspecific K2P divergence were highly different among the three subfamilies (Eristalinae: 0.037, Syrphinae: 0.06, Microdontinae: 0.007-0.02), and among the different general suggesting that optimal thresholds are better defined at the genus level. In addition to providing an alternative identification tool, our study indicates that DNA barcoding improves the taxonomy of Afrotropical hoverflies by selecting (groups of) taxa that deserve further taxonomic study, and by attributing the unknown sex to species for which only one of the sexes is known.
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Affiliation(s)
- Kurt Jordaens
- Department of Biology–Invertebrate Section and Joint Experimental Molecular Unit (JEMU), Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium
| | - Georg Goergen
- Department of Biology, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Massimiliano Virgilio
- Department of Biology–Invertebrate Section and Joint Experimental Molecular Unit (JEMU), Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium
| | - Thierry Backeljau
- International Institute of Tropical Agriculture, 08 BP 0932 Tri Postal, Cotonou, Republic of Benin
- Royal Belgian Institute of Natural Sciences–OD Taxonomy and Phylogeny and Joint Experimental Molecular Unit (JEMU), Vautierstraat 29, B-1000 Brussels, Belgium
| | - Audrey Vokaer
- Department of Biology–Invertebrate Section and Joint Experimental Molecular Unit (JEMU), Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium
| | - Marc De Meyer
- Department of Biology–Invertebrate Section and Joint Experimental Molecular Unit (JEMU), Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium
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Shokralla S, Porter TM, Gibson JF, Dobosz R, Janzen DH, Hallwachs W, Golding GB, Hajibabaei M. Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform. Sci Rep 2015; 5:9687. [PMID: 25884109 PMCID: PMC4401116 DOI: 10.1038/srep09687] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/16/2015] [Indexed: 01/26/2023] Open
Abstract
Genetic information is a valuable component of biosystematics, especially specimen identification through the use of species-specific DNA barcodes. Although many genomics applications have shifted to High-Throughput Sequencing (HTS) or Next-Generation Sequencing (NGS) technologies, sample identification (e.g., via DNA barcoding) is still most often done with Sanger sequencing. Here, we present a scalable double dual-indexing approach using an Illumina Miseq platform to sequence DNA barcode markers. We achieved 97.3% success by using half of an Illumina Miseq flowcell to obtain 658 base pairs of the cytochrome c oxidase I DNA barcode in 1,010 specimens from eleven orders of arthropods. Our approach recovers a greater proportion of DNA barcode sequences from individuals than does conventional Sanger sequencing, while at the same time reducing both per specimen costs and labor time by nearly 80%. In addition, the use of HTS allows the recovery of multiple sequences per specimen, for deeper analysis of genetic variation in target gene regions.
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Affiliation(s)
- Shadi Shokralla
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, Canada N1G 2W1
| | - Teresita M Porter
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S 4K1
| | - Joel F Gibson
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, Canada N1G 2W1
| | - Rafal Dobosz
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, Canada N1G 2W1
| | - Daniel H Janzen
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA 19104
| | - Winnie Hallwachs
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA 19104
| | - G Brian Golding
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S 4K1
| | - Mehrdad Hajibabaei
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, Canada N1G 2W1
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58
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Price BW, Henry CS, Hall AC, Mochizuki A, Duelli P, Brooks SJ. Singing from the grave: DNA from a 180 year old type specimen confirms the identity of Chrysoperla carnea (Stephens). PLoS One 2015; 10:e0121127. [PMID: 25853856 PMCID: PMC4390323 DOI: 10.1371/journal.pone.0121127] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 02/11/2015] [Indexed: 11/28/2022] Open
Abstract
Historically serving as repositories for morphologically-based taxonomic research, natural history collections are now increasingly being targeted in studies utilizing DNA data. The development of advanced molecular techniques has facilitated extraction of useable DNA from old specimens, including type material. Sequencing diagnostic molecular markers from type material enables accurate species designation, especially where modern taxonomic hypotheses confirm morphologically cryptic species complexes. One such example is Chrysoperla carnea (Stephens), which belongs to a complex of about 20 cryptic species, most of which can only be reliably distinguished by their pre-mating courtship songs or by DNA analysis. The subtle morphological variation in the group has led to disagreement over the previous designation of the lectotype for C. carnea, an issue that has been further compounded because Chrysoperla carnea is a highly valued biological control agent in arable crops. Archival DNA extraction and sequencing from the 180 year old lectotype specimen, combined with Bayesian and Likelihood based phylogenetic analyses of modern specimens from the entire complex, were used to establish unambiguously the true identity of Chrysoperla carnea.
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Affiliation(s)
- Ben W. Price
- Life Sciences Department, Natural History Museum, London, England
| | - Charles S. Henry
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, United States of America
- * E-mail:
| | - Andie C. Hall
- Core Research Laboratories, Natural History Museum, London, England
| | - Atsushi Mochizuki
- National Institute for Agro-Environmental Sciences, Tsukuba City, Ibaraki, Japan
| | - Peter Duelli
- WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
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59
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Mitchell A. Collecting in collections: a PCR strategy and primer set for DNA barcoding of decades-old dried museum specimens. Mol Ecol Resour 2015; 15:1102-11. [PMID: 25644663 DOI: 10.1111/1755-0998.12380] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 01/10/2015] [Accepted: 01/13/2015] [Indexed: 11/27/2022]
Abstract
Natural history museums are vastly underutilized as a source of material for DNA analysis because of perceptions about the limitations of DNA degradation in older specimens. Despite very few exceptions, most DNA barcoding projects, which aim to obtain sequence data from all species, generally use specimens collected specifically for that purpose, instead of the wealth of identified material in museums, constrained by the lack of suitable PCR methods. Any techniques that extend the utility of museum specimens for DNA analysis therefore are highly valuable. This study first tested the effects of specimen age and PCR amplicon size on PCR success rates in pinned insect specimens, then developed a PCR primer set and amplification strategy allowing greatly increased utilization of older museum specimens for DNA barcoding. PCR success rates compare favourably with the few published studies utilizing similar aged specimens, and this new strategy has the advantage of being easily automated for high-throughput laboratory workflows. The strategy uses hemi-nested, degenerate, M13-tailed PCR primers to amplify two overlapping amplicons, using two PCRs per amplicon (i.e. four PCRs per DNA sample). Initial PCR products are reamplified using an internal primer and a M13 primer. Together the two PCR amplicons yield 559 bp of the COI gene from Coleoptera, Lepidoptera, Diptera, Hemiptera, Odonata and presumably also other insects. BARCODE standard-compliant data were recovered from 67% (56 of 84) of specimens up to 25 years old, and 51% (102 of 197) of specimens up to 55 years old. Given the time, cost and specialist expertise required for fieldwork and identification, 'collecting in collections' is a viable alternative allowing researchers to capitalize on the knowledge captured by curation work in decades past.
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Affiliation(s)
- Andrew Mitchell
- Australian Museum Research Institute, Australian Museum, 6 College Street, Sydney, NSW, 2010, Australia
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