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D’Ercole J, Dapporto L, Opler P, Schmidt CB, Ho C, Menchetti M, Zakharov EV, Burns JM, Hebert PDN. A genetic atlas for the butterflies of continental Canada and United States. PLoS One 2024; 19:e0300811. [PMID: 38568891 PMCID: PMC10990199 DOI: 10.1371/journal.pone.0300811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/05/2024] [Indexed: 04/05/2024] Open
Abstract
Multi-locus genetic data for phylogeographic studies is generally limited in geographic and taxonomic scope as most studies only examine a few related species. The strong adoption of DNA barcoding has generated large datasets of mtDNA COI sequences. This work examines the butterfly fauna of Canada and United States based on 13,236 COI barcode records derived from 619 species. It compiles i) geographic maps depicting the spatial distribution of haplotypes, ii) haplotype networks (minimum spanning trees), and iii) standard indices of genetic diversity such as nucleotide diversity (π), haplotype richness (H), and a measure of spatial genetic structure (GST). High intraspecific genetic diversity and marked spatial structure were observed in the northwestern and southern North America, as well as in proximity to mountain chains. While species generally displayed concordance between genetic diversity and spatial structure, some revealed incongruence between these two metrics. Interestingly, most species falling in this category shared their barcode sequences with one at least other species. Aside from revealing large-scale phylogeographic patterns and shedding light on the processes underlying these patterns, this work also exposed cases of potential synonymy and hybridization.
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Affiliation(s)
- Jacopo D’Ercole
- Centre for Biodiversity Genomics, Guelph, Ontario, Canada
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Leonardo Dapporto
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Paul Opler
- Colorado State University, Fort Collins, Colorado, United States of America
| | - Christian B. Schmidt
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Chris Ho
- Centre for Biodiversity Genomics, Guelph, Ontario, Canada
| | | | | | - John M. Burns
- Department of Entomology, Smithsonian Institution, Washington, DC, United States of America
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Guelph, Ontario, Canada
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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2
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Schmidt BC. Confirmed occurrence of the tribe Apameini (Lepidoptera, Noctuidae, Noctuinae) in the Neotropical region: a new genus endemic to Costa Rican montane forests. Zookeys 2022; 1114:121-130. [PMID: 36761704 PMCID: PMC9848747 DOI: 10.3897/zookeys.1114.84361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/18/2022] [Indexed: 11/12/2022] Open
Abstract
The genus Nublapamea gen. nov. is described (type species: Tracheaaltivolans Schaus), here determined to belong to the primarily temperate Holarctic tribe Apameini (Noctuidae: Noctuinae). Currently known only from mid- to upper elevation montane forests of Costa Rica, Nublapamea is a disjunct southern extension of a largely northern hemisphere temperate region fauna. The life history of Nublapameaaltivolans is unknown; it may be associated with chusquea bamboo (Chusquea Kunth), as most Apameini are dietary specialists on graminoids.
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Affiliation(s)
- B. Christian Schmidt
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, K.W. Neatby Bldg., 960 Carling Ave., Ottawa, ON, K1A 0C6, CanadaCanadian National Collection of InsectsOttawaCanada
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3
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Ashfaq M, Khan AM, Rasool A, Akhtar S, Nazir N, Ahmed N, Manzoor F, Sones J, Perez K, Sarwar G, Khan AA, Akhter M, Saeed S, Sultana R, Tahir HM, Rafi MA, Iftikhar R, Naseem MT, Masood M, Tufail M, Kumar S, Afzal S, McKeown J, Samejo AA, Khaliq I, D’Souza ML, Mansoor S, Hebert PDN. A DNA barcode survey of insect biodiversity in Pakistan. PeerJ 2022; 10:e13267. [PMID: 35497186 PMCID: PMC9048642 DOI: 10.7717/peerj.13267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/23/2022] [Indexed: 01/15/2023] Open
Abstract
Although Pakistan has rich biodiversity, many groups are poorly known, particularly insects. To address this gap, we employed DNA barcoding to survey its insect diversity. Specimens obtained through diverse collecting methods at 1,858 sites across Pakistan from 2010-2019 were examined for sequence variation in the 658 bp barcode region of the cytochrome c oxidase 1 (COI) gene. Sequences from nearly 49,000 specimens were assigned to 6,590 Barcode Index Numbers (BINs), a proxy for species, and most (88%) also possessed a representative image on the Barcode of Life Data System (BOLD). By coupling morphological inspections with barcode matches on BOLD, every BIN was assigned to an order (19) and most (99.8%) were placed to a family (362). However, just 40% of the BINs were assigned to a genus (1,375) and 21% to a species (1,364). Five orders (Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera) accounted for 92% of the specimens and BINs. More than half of the BINs (59%) are so far only known from Pakistan, but others have also been reported from Bangladesh (13%), India (12%), and China (8%). Representing the first DNA barcode survey of the insect fauna in any South Asian country, this study provides the foundation for a complete inventory of the insect fauna in Pakistan while also contributing to the global DNA barcode reference library.
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Affiliation(s)
- Muhammad Ashfaq
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, Canada
| | - Arif M. Khan
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | - Akhtar Rasool
- Centre for Animal Sciences and Fisheries, University of Swat, Mingora, Pakistan
| | - Saleem Akhtar
- Directorate of Entomology, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Naila Nazir
- Department of Entomology, University of Poonch, Rawalakot, Azad Kashmir, Pakistan
| | - Nazeer Ahmed
- Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan
| | - Farkhanda Manzoor
- Department of Zoology, Lahore College for Women University, Lahore, Pakistan
| | - Jayme Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
| | - Kate Perez
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
| | - Ghulam Sarwar
- Institute of Zoology, University of the Punjab, Lahore, Pakistan
| | - Azhar A. Khan
- College of Agriculture, Bahauddin Zakariya University Bahadur Campus, Layyah, Pakistan
| | - Muhammad Akhter
- Pulses Research Institute, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Shafqat Saeed
- Faculty of Agriculture and Environmental Sciences, MNS University of Agriculture, Multan, Pakistan
| | - Riffat Sultana
- Department of Zoology, University of Sindh, Jamshoro, Pakistan
| | | | - Muhammad A. Rafi
- National Insect Museum, National Agricultural Research Center, Islamabad, Pakistan
| | - Romana Iftikhar
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | | | - Mariyam Masood
- Government College Women University Faisalabad, Faisalabad, Pakistan
| | | | - Santosh Kumar
- Department of Zoology, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Sabila Afzal
- Department of Zoology, University of Narowal, Narowal, Pakistan
| | - Jaclyn McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
| | | | | | | | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, Canada
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4
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Young MR, Hebert PDN. Unearthing soil arthropod diversity through DNA metabarcoding. PeerJ 2022; 10:e12845. [PMID: 35178296 PMCID: PMC8815377 DOI: 10.7717/peerj.12845] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/06/2022] [Indexed: 01/10/2023] Open
Abstract
DNA metabarcoding has the potential to greatly advance understanding of soil biodiversity, but this approach has seen limited application for the most abundant and species-rich group of soil fauna-the arthropods. This study begins to address this gap by comparing information on species composition recovered from metabarcoding two types of bulk samples (specimens, soil) from a temperate zone site and from bulk soil samples collected at eight sites in the Arctic. Analysis of 22 samples (3 specimen, 19 soil) revealed 410 arthropod OTUs belonging to 112 families, 25 orders, and nine classes. Studies at the temperate zone site revealed little overlap in species composition between soil and specimen samples, but more overlap at higher taxonomic levels (families, orders) and congruent patterns of α- and β-diversity. Expansion of soil analyses to the Arctic revealed locally rich, highly dissimilar, and spatially structured assemblages compatible with dispersal limited and environmentally driven assembly. The current study demonstrates that DNA metabarcoding of bulk soil enables rapid, large-scale assessments of soil arthropod diversity. However, deep sequence coverage is required to adequately capture the species present in these samples, and expansion of the DNA barcode reference library is necessary to improve taxonomic resolution of the sequences recovered through this approach.
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Affiliation(s)
- Monica R. Young
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada,Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada,Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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D'Ercole J, Dincă V, Opler PA, Kondla N, Schmidt C, Phillips JD, Robbins R, Burns JM, Miller SE, Grishin N, Zakharov EV, DeWaard JR, Ratnasingham S, Hebert PDN. A DNA barcode library for the butterflies of North America. PeerJ 2021; 9:e11157. [PMID: 33976967 PMCID: PMC8061581 DOI: 10.7717/peerj.11157] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 03/04/2021] [Indexed: 12/14/2022] Open
Abstract
Although the butterflies of North America have received considerable taxonomic attention, overlooked species and instances of hybridization continue to be revealed. The present study assembles a DNA barcode reference library for this fauna to identify groups whose patterns of sequence variation suggest the need for further taxonomic study. Based on 14,626 records from 814 species, DNA barcodes were obtained for 96% of the fauna. The maximum intraspecific distance averaged 1/4 the minimum distance to the nearest neighbor, producing a barcode gap in 76% of the species. Most species (80%) were monophyletic, the others were para- or polyphyletic. Although 15% of currently recognized species shared barcodes, the incidence of such taxa was far higher in regions exposed to Pleistocene glaciations than in those that were ice-free. Nearly 10% of species displayed high intraspecific variation (>2.5%), suggesting the need for further investigation to assess potential cryptic diversity. Aside from aiding the identification of all life stages of North American butterflies, the reference library has provided new perspectives on the incidence of both cryptic and potentially over-split species, setting the stage for future studies that can further explore the evolutionary dynamics of this group.
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Affiliation(s)
- Jacopo D'Ercole
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada.,Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Vlad Dincă
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Paul A Opler
- Colorado State University, Fort Collins, CO, United States of America
| | | | - Christian Schmidt
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food, Guelph, Ontario, Canada
| | - Jarrett D Phillips
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada.,School of Computer Science, University of Guelph, Guelph, Ontario, Canada
| | - Robert Robbins
- Department of Entomology, Smithsonian Institution, Washington DC, United States of America
| | - John M Burns
- Department of Entomology, Smithsonian Institution, Washington DC, United States of America
| | - Scott E Miller
- Department of Entomology, Smithsonian Institution, Washington DC, United States of America
| | - Nick Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, United States of America.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States of America
| | - Evgeny V Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Jeremy R DeWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | - Paul D N Hebert
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada.,Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
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6
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Dincă V, Dapporto L, Somervuo P, Vodă R, Cuvelier S, Gascoigne-Pees M, Huemer P, Mutanen M, Hebert PDN, Vila R. High resolution DNA barcode library for European butterflies reveals continental patterns of mitochondrial genetic diversity. Commun Biol 2021; 4:315. [PMID: 33750912 PMCID: PMC7943782 DOI: 10.1038/s42003-021-01834-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 02/11/2021] [Indexed: 11/09/2022] Open
Abstract
The study of global biodiversity will greatly benefit from access to comprehensive DNA barcode libraries at continental scale, but such datasets are still very rare. Here, we assemble the first high-resolution reference library for European butterflies that provides 97% taxon coverage (459 species) and 22,306 COI sequences. We estimate that we captured 62% of the total haplotype diversity and show that most species possess a few very common haplotypes and many rare ones. Specimens in the dataset have an average 95.3% probability of being correctly identified. Mitochondrial diversity displayed elevated haplotype richness in southern European refugia, establishing the generality of this key biogeographic pattern for an entire taxonomic group. Fifteen percent of the species are involved in barcode sharing, but two thirds of these cases may reflect the need for further taxonomic research. This dataset provides a unique resource for conservation and for studying evolutionary processes, cryptic species, phylogeography, and ecology.
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Affiliation(s)
- Vlad Dincă
- Ecology and Genetics Research Unit, PO Box 3000, University of Oulu, 90014, Oulu, Finland.
- Institut de Biologia Evolutiva (CSIC-UPF), 03008, Barcelona, Spain.
| | - Leonardo Dapporto
- ZEN lab, Dipartimento di Biologia, University of Florence, 50019, Sesto Fiorentino, Italy
| | - Panu Somervuo
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, FI-00014, Helsinki, Finland
| | | | - Sylvain Cuvelier
- VVE Workgroup Butterflies, Diamantstraat 4, 8900, Ieper, Belgium
| | | | - Peter Huemer
- Naturwissenschaftliche Sammlungen, Sammlungs- und Forschungszentrum, Tiroler Landesmuseen, 6060, Hall in Tirol, Austria
| | - Marko Mutanen
- Ecology and Genetics Research Unit, PO Box 3000, University of Oulu, 90014, Oulu, Finland
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), 03008, Barcelona, Spain
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7
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Marín MA, López-Rubio A, Clavijo A, Pyrcz TW, Freitas AVL, Uribe SI, Álvarez CF. Use of species delimitation approaches to tackle the cryptic diversity of an assemblage of high Andean butterflies (Lepidoptera: Papilionoidea). Genome 2021; 64:937-949. [PMID: 33596120 DOI: 10.1139/gen-2020-0100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cryptic biological diversity has generated ambiguity in taxonomic and evolutionary studies. Single-locus methods and other approaches for species delimitation are useful for addressing this challenge, enabling the practical processing of large numbers of samples for identification and inventory purposes. This study analyzed an assemblage of high Andean butterflies using DNA barcoding and compared the identifications based on the current morphological taxonomy with three methods of species delimitation (automatic barcode gap discovery, generalized mixed Yule coalescent model, and Poisson tree processes). Sixteen potential cryptic species were recognized using these three methods, representing a net richness increase of 11.3% in the assemblage. A well-studied taxon of the genus Vanessa, which has a wide geographical distribution, appeared with the potential cryptic species that had a higher genetic differentiation at the local level than at the continental level. The analyses were useful for identifying the potential cryptic species in Pedaliodes and Forsterinaria complexes, which also show differentiation along altitudinal and latitudinal gradients. This genetic assessment of an entire assemblage of high Andean butterflies (Papilionoidea) provides baseline information for future research in a region characterized by high rates of endemism and population isolation.
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Affiliation(s)
- Mario Alejandro Marín
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, São Paulo (SP), Brazil.,Grupo de Investigación en Sistemática Molecular, Universidad Nacional de Colombia, Medellín, Antioquia, Colombia
| | - Andrés López-Rubio
- Grupo de Investigación en Sistemática Molecular, Universidad Nacional de Colombia, Medellín, Antioquia, Colombia
| | - Alejandra Clavijo
- Grupo de Investigación en Sistemática Molecular, Universidad Nacional de Colombia, Medellín, Antioquia, Colombia
| | - Tomasz Wilhelm Pyrcz
- Department of Invertebrate Evolution, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa, Kraków, Poland.,Nature Education Centre, Jagiellonian University, Gronostajowa, Kraków, Poland
| | - André Victor Lucci Freitas
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, São Paulo (SP), Brazil.,Museu de Diversidade Biológica, Instituto de Biologia, Universidade Estadual de Campinas, São Paulo, Brazil
| | - Sandra Inés Uribe
- Grupo de Investigación en Sistemática Molecular, Universidad Nacional de Colombia, Medellín, Antioquia, Colombia
| | - Carlos Federico Álvarez
- Grupo de Investigación en Sistemática Molecular, Universidad Nacional de Colombia, Medellín, Antioquia, Colombia
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8
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Camacho-Sánchez FY, Aguirre AA, Narváez-Zapata JA, Zavala-Norzagaray AA, Ley-Quiñónez CP, Acosta-Sánchez HH, Rodriguez-González H, Delgado-Trejo C, Reyes-López MA. DNA barcode analysis of the endangered green turtle ( Chelonia mydas) in Mexico 1. Genome 2021; 64:879-891. [PMID: 33555972 DOI: 10.1139/gen-2019-0213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Technological and analytical advances to study evolutionary biology, ecology, and conservation of green turtles (Chelonia mydas) are realized through molecular approaches including DNA barcoding. We characterized the usefulness of COI DNA barcodes in green turtles in Mexico to better understand genetic divergence and other genetic parameters of this species. We analyzed 63 sequences, including 25 from green turtle field specimens collected from the Gulf of Mexico and from the Mexican Pacific and 38 already present in the Barcode of Life Data Systems (BOLD). A total of 13 haplotypes were identified with four novel haplotypes from the Pacific Ocean and three novel haplotypes from the Atlantic Ocean. Intraspecific distance values among COI gene sequences by two different models were 0.01, demonstrating that there is not a subdivision for green turtle species. Otherwise, the interspecific distance interval ranged from 0.07 to 0.13, supporting a clear subdivision among all sea turtle species. Haplotype and total nucleotide diversity values of the COI gene reflect a medium genetic diversity average. Green turtles of the Mexican Pacific showed common haplotypes to some Australian and Chinese turtles, but different from the haplotypes of the Mexican Atlantic. COI analysis revealed new haplotypes and confirmed that DNA barcodes were useful for evaluation of the population diversity of green turtles in Mexico.
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Affiliation(s)
- Fátima Yedith Camacho-Sánchez
- Conservation Medicine Lab, Centro de Biotecnología Genómica-Instituto Politécnico Nacional, Reynosa, Tamaulipas, Mexico.,Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
| | - A Alonso Aguirre
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
| | - José Alberto Narváez-Zapata
- Laboratorio de Biotecnología Industrial, Centro de Biotecnología Genómica-Instituto Politécnico Nacional, Reynosa, Tamaulipas, Mexico
| | - Alan A Zavala-Norzagaray
- Laboratorio de Vida Silvestre, Departamento de Medio Ambiente, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional, Unidad Sinaloa, Instituto Politécnico Nacional, Guasave, Sinaloa, Mexico
| | - Cesar P Ley-Quiñónez
- Laboratorio de Vida Silvestre, Departamento de Medio Ambiente, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional, Unidad Sinaloa, Instituto Politécnico Nacional, Guasave, Sinaloa, Mexico
| | - H Hugo Acosta-Sánchez
- United Nations Development Programme-Comisión Nacional de Áreas Naturales Protegidas, Ciudad Victoria, Tamaulipas, Mexico
| | - Hervey Rodriguez-González
- Laboratorio Nutrición Acuícola, Departamento de Acuacultura, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional, Unidad Sinaloa, Instituto Politécnico Nacional, Guasave, Sinaloa, Mexico
| | - Carlos Delgado-Trejo
- Departamento de Ecología Marina, Proyecto Tortuga Negra, Instituto de Investigaciones sobre los Recursos Naturales, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Miguel Angel Reyes-López
- Conservation Medicine Lab, Centro de Biotecnología Genómica-Instituto Politécnico Nacional, Reynosa, Tamaulipas, Mexico
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9
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Wöger R, Wöger R, Nuss M. DNA barcodes for Aotearoa New Zealand Pyraloidea (Lepidoptera). Biodivers Data J 2020; 8:e58841. [PMID: 33293886 PMCID: PMC7718215 DOI: 10.3897/bdj.8.e58841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/09/2020] [Indexed: 11/24/2022] Open
Abstract
Identification of pyraloid species is often hampered by highly similar external morphology requiring microscopic dissection of genitalia. This becomes especially obvious when mass samples from ecological studies or insect monitoring have to be analysed. DNA barcode sequences could accelerate identification, but are not available for most pyraloid species from New Zealand. Hence, we are presenting a first DNA-barcode library for this group, providing 440 COI barcodes (cytochrome C oxidase I sequences) for 73 morphologically-identified species, which is 29% of Pyraloidea known from New Zealand. Results are analysed using the Barcode Index Number system (BIN) of BOLD and the Automatic Barcode Gap Discovery method (ABGD). Using BIN, the 440 barcodes reveal 82 clusters. A perfect match between BIN assignment and morphological identification was found for 63 species (86.3%). Four species (5.5%) share BINs, each with two species in one BIN, of which Glaucocharis epiphaea and Glaucocharis harmonica even share the same barcode. In contrast, six species (8.2%) split into two or more BINs, with the highest number of five BINs for Orocrambus ramosellus. The interspecific variation of all collected specimens of New Zealand Pyraloidea averages 12.54%. There are deep intraspecific divergences (> 2%) in seven species, for instance Orocrambus vulgaris with up to 6.6% and Scoparia ustimacula with 5.5%. Using ABGD, the 440 barcodes reveal 71 or 88 operational taxonomic units (OTUs), depending on the preferred partition. A perfect match between OTU and morphological identification was found for 56 species (76.7%) or 62 species (84.9%). ABGD delivers four or seven species sharing OTUs and four or ten species split into more than one OTU. Morphological re-examination, as well as the analysis of a concatenated dataset of COI and the nuclear markers EF1α and GADPH for species split into more than one BIN or OTU, do not support a higher number of species. Likewise, there is no evidence for Wolbachia infection as a trigger for these sequence variations.
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Affiliation(s)
- Renate Wöger
- Senckenberg Museum of Zoology, Dresden, GermanySenckenberg Museum of ZoologyDresdenGermany
| | - Roland Wöger
- Senckenberg Museum of Zoology, Dresden, GermanySenckenberg Museum of ZoologyDresdenGermany
| | - Matthias Nuss
- Senckenberg Museum of Zoology, Dresden, GermanySenckenberg Museum of ZoologyDresdenGermany
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10
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Huemer P, Karsholt O, Aarvik L, Berggren K, Bidzilya O, Junnilainen J, Landry JF, Mutanen M, Nupponen K, Segerer A, Šumpich J, Wieser C, Wiesmair B, Hebert PDN. DNA barcode library for European Gelechiidae (Lepidoptera) suggests greatly underestimated species diversity. Zookeys 2020; 921:141-157. [PMID: 32256152 PMCID: PMC7109146 DOI: 10.3897/zookeys.921.49199] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 02/06/2020] [Indexed: 11/12/2022] Open
Abstract
For the first time, a nearly complete barcode library for European Gelechiidae is provided. DNA barcode sequences (COI gene – cytochrome c oxidase 1) from 751 out of 865 nominal species, belonging to 105 genera, were successfully recovered. A total of 741 species represented by specimens with sequences ≥ 500bp and an additional ten species represented by specimens with shorter sequences were used to produce 53 NJ trees. Intraspecific barcode divergence averaged only 0.54% whereas distance to the Nearest-Neighbour species averaged 5.58%. Of these, 710 species possessed unique DNA barcodes, but 31 species could not be reliably discriminated because of barcode sharing or partial barcode overlap. Species discrimination based on the Barcode Index System (BIN) was successful for 668 out of 723 species which clustered from minimum one to maximum 22 unique BINs. Fifty-five species shared a BIN with up to four species and identification from DNA barcode data is uncertain. Finally, 65 clusters with a unique BIN remained unidentified to species level. These putative taxa, as well as 114 nominal species with more than one BIN, suggest the presence of considerable cryptic diversity, cases which should be examined in future revisionary studies.
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Affiliation(s)
- Peter Huemer
- Naturwissenschaftliche Sammlungen, Tiroler Landesmuseen Betriebsges.m.b.H., Innsbruck, Austria Tiroler Landesmuseen Betriebsges.m.b.H. Innsbruck Austria
| | - Ole Karsholt
- Zoological Museum, Natural History Museum of Denmark, Copenhagen, Denmark Natural History Museum of Denmark Copenhagen Denmark
| | - Leif Aarvik
- Natural History Museum, University of Oslo, Oslo, Norway University of Oslo Oslo Norway
| | - Kai Berggren
- Kristiansand, Norway Unaffiliated Kristiansand Norway
| | - Oleksiy Bidzilya
- Institute for Evolutionary Ecology of the National Academy of Sciences of Ukraine, Kiev, Ukraine Institute for Evolutionary Ecology, National Academy of Sciences of Ukraine Kiev Ukraine
| | - Jari Junnilainen
- Finnish Museum of Natural History, Zoology Unit, Helsinki, Finland Finnish Museum of Natural History Helsinki Finland
| | - Jean-François Landry
- Canadian National Collection of Insects, Arachnids, and Nematodes, Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Canada Agriculture and Agri-Food Canada Ottawa Canada
| | - Marko Mutanen
- Department of Ecology and Genetics, University of Oulu, Finland University of Oulu Oulu Finland
| | | | - Andreas Segerer
- SNSB-Zoological State Collection, Munich, Germany Zoological State Collection Munich Germany
| | - Jan Šumpich
- National Museum, Natural History Museum, Department of Entomology, Praha, Czech Republic Natural History Museum Prague Czech Republic
| | - Christian Wieser
- Landesmuseum Kärnten, Klagenfurt, Austria Landesmuseum Kärnten Klagenfurt am Wörthersee Austria
| | - Benjamin Wiesmair
- Naturwissenschaftliche Sammlungen, Tiroler Landesmuseen Betriebsges.m.b.H., Innsbruck, Austria Tiroler Landesmuseen Betriebsges.m.b.H. Innsbruck Austria
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada University of Guelph Guelph Canada
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11
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Cognato AI, Sari G, Smith SM, Beaver RA, Li Y, Hulcr J, Jordal BH, Kajimura H, Lin CS, Pham TH, Singh S, Sittichaya W. The Essential Role of Taxonomic Expertise in the Creation of DNA Databases for the Identification and Delimitation of Southeast Asian Ambrosia Beetle Species (Curculionidae: Scolytinae: Xyleborini). Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00027] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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12
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Capacity of United States federal government and its partners to rapidly and accurately report the identity (taxonomy) of non-native organisms intercepted in early detection programs. Biol Invasions 2019. [DOI: 10.1007/s10530-019-02147-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AbstractThe early detection of and rapid response to invasive species (EDRR) depends on accurate and rapid identification of non-native species. The 2016–2018 National Invasive Species Council Management Plan called for an assessment of US government (federal) capacity to report on the identity of non-native organisms intercepted through early detection programs. This paper serves as the response to that action item. Here we summarize survey-based findings and make recommendations for improving the federal government’s capacity to identify non-native species authoritatively in a timely manner. We conclude with recommendations to improve accurate identification within the context of EDRR by increasing coordination, maintaining taxonomic expertise, creating an identification tools clearinghouse, developing and using taxonomic standards for naming and identification protocols, expanding the content of DNA and DNA Barcode libraries, ensuring long-term sustainability of biological collections, and engaging and empowering citizens and citizen science groups.
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13
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deWaard JR, Ratnasingham S, Zakharov EV, Borisenko AV, Steinke D, Telfer AC, Perez KHJ, Sones JE, Young MR, Levesque-Beaudin V, Sobel CN, Abrahamyan A, Bessonov K, Blagoev G, deWaard SL, Ho C, Ivanova NV, Layton KKS, Lu L, Manjunath R, McKeown JTA, Milton MA, Miskie R, Monkhouse N, Naik S, Nikolova N, Pentinsaari M, Prosser SWJ, Radulovici AE, Steinke C, Warne CP, Hebert PDN. A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples. Sci Data 2019; 6:308. [PMID: 31811161 PMCID: PMC6897906 DOI: 10.1038/s41597-019-0320-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/11/2019] [Indexed: 01/08/2023] Open
Abstract
The reliable taxonomic identification of organisms through DNA sequence data requires a well parameterized library of curated reference sequences. However, it is estimated that just 15% of described animal species are represented in public sequence repositories. To begin to address this deficiency, we provide DNA barcodes for 1,500,003 animal specimens collected from 23 terrestrial and aquatic ecozones at sites across Canada, a nation that comprises 7% of the planet's land surface. In total, 14 phyla, 43 classes, 163 orders, 1123 families, 6186 genera, and 64,264 Barcode Index Numbers (BINs; a proxy for species) are represented. Species-level taxonomy was available for 38% of the specimens, but higher proportions were assigned to a genus (69.5%) and a family (99.9%). Voucher specimens and DNA extracts are archived at the Centre for Biodiversity Genomics where they are available for further research. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, and the Global Genome Biodiversity Network Data Portal.
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Affiliation(s)
- Jeremy R deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | - Evgeny V Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Alex V Borisenko
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Dirk Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Angela C Telfer
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Kate H J Perez
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Jayme E Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Monica R Young
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | - Crystal N Sobel
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Arusyak Abrahamyan
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Kyrylo Bessonov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
- Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Gergin Blagoev
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Stephanie L deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Chris Ho
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Natalia V Ivanova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Kara K S Layton
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
- Ocean Frontier Institute, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Liuqiong Lu
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Ramya Manjunath
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Jaclyn T A McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Megan A Milton
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Renee Miskie
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Norm Monkhouse
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Suresh Naik
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Nadya Nikolova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Mikko Pentinsaari
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Sean W J Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | - Claudia Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Connor P Warne
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada.
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14
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Prous M, Lee KM, Mutanen M. Cross-contamination and strong mitonuclear discordance in Empria sawflies (Hymenoptera, Tenthredinidae) in the light of phylogenomic data. Mol Phylogenet Evol 2019; 143:106670. [PMID: 31706020 DOI: 10.1016/j.ympev.2019.106670] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 11/02/2019] [Accepted: 11/04/2019] [Indexed: 10/25/2022]
Abstract
In several sawfly taxa strong mitonuclear discordance has been observed, with nuclear genes supporting species assignments based on morphology, whereas the barcode region of the mitochondrial COI gene suggests different relationships. As previous studies were based on only a few nuclear genes, the causes and the degree of mitonuclear discordance remain ambiguous. Here, we obtained genomic-scale ddRAD data together with Sanger sequences of mitochondrial COI and two to three nuclear protein coding genes to investigate species limits and mitonuclear discordance in two closely related species groups of the sawfly genus Empria. As found previously based on nuclear ITS and mitochondrial COI sequences, species are in most cases supported as monophyletic based on new nuclear data reported here, but not based on mitochondrial COI. This mitonuclear discordance can be explained by occasional mitochondrial introgression with little or no nuclear gene flow, a pattern that might be common in haplodiploid taxa with slowly evolving mitochondrial genomes. Some species in the E. immersa group are not recovered as monophyletic according to either mitochondrial or nuclear data, but this could partly be because of unresolved taxonomy. Preliminary analyses of ddRAD data did not recover monophyly of E. japonica within the E. longicornis group (three Sanger sequenced nuclear genes strongly supported monophyly), but closer examination of the data and additional Sanger sequencing suggested that both specimens were substantially (possibly 10-20% of recovered loci) cross-contaminated. A reason could be specimen identification tag jumps during sequencing library preparation that in previous studies have been shown to affect up to 2.5% of the sequenced reads. We provide an R script to examine patterns of identical loci among the specimens and estimate that the cross-contamination rate is not unusually high for our ddRAD dataset as a whole (based on counting of identical sequences in the immersa and longicornis groups, which are well separated from each other and probably do not hybridise). The high rate of cross-contamination for both E. japonica specimens might be explained by the small number of recovered loci (~1000) compared to most other specimens (>10 000 in some cases) because of poor sequencing results. We caution against drawing unexpected biological conclusions when closely related specimens are pooled before sequencing and tagged only at one end of the molecule or at both ends using a unique combination of limited number of tags (less than the number of specimens).
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Affiliation(s)
- Marko Prous
- Senckenberg Deutsches Entomologisches Institut, Eberswalder Straße 90, 15374 Müncheberg, Germany; Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014 Tartu, Estonia.
| | - Kyung Min Lee
- Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, FI-90014, University of Oulu, Finland
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, FI-90014, University of Oulu, Finland
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15
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Dincă V, Lee KM, Vila R, Mutanen M. The conundrum of species delimitation: a genomic perspective on a mitogenetically super-variable butterfly. Proc Biol Sci 2019; 286:20191311. [PMID: 31530141 PMCID: PMC6784721 DOI: 10.1098/rspb.2019.1311] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Palaearctic butterfly Melitaea didyma stands out as one of the most striking cases of intraspecific genetic differentiation detected in Lepidoptera: 11 partially sympatric mitochondrial lineages have been reported, displaying levels of divergence of up to 7.4%. To better understand the evolutionary processes underlying the diversity observed in mtDNA, we compared mtDNA and genome-wide SNP data using double-digest restriction site-associated DNA sequencing (ddRADseq) results from 93 specimens of M. didyma ranging from Morocco to eastern Kazakhstan. We found that, between ddRADseq and mtDNA results, there is a match only in populations that probably remained allopatric for long periods of time. Other mtDNA lineages may have resulted from introgression events and were probably affected by Wolbachia infection. The five main ddRADseq clades supported by STRUCTURE were parapatric or allopatric and showed high pairwise FST values, but some were also estimated to display various levels of gene flow. Melitaea didyma represents one of the first cases of deep mtDNA splits among European butterflies assessed by a genome-wide DNA analysis and reveals that the interpretation of patterns remains challenging even when a high amount of genomic data is available. These findings actualize the ongoing debate of species delimitation in allopatry, an issue probably of relevance to a significant proportion of global biodiversity.
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Affiliation(s)
- Vlad Dincă
- Department of Ecology and Genetics, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Kyung Min Lee
- Department of Ecology and Genetics, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta, 37, 08003 Barcelona, Spain
| | - Marko Mutanen
- Department of Ecology and Genetics, University of Oulu, PO Box 3000, 90014 Oulu, Finland
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16
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17
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Linking morphological and molecular taxonomy for the identification of poultry house, soil, and nest dwelling mites in the Western Palearctic. Sci Rep 2019; 9:5784. [PMID: 30962473 PMCID: PMC6453913 DOI: 10.1038/s41598-019-41958-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 03/20/2019] [Indexed: 01/03/2023] Open
Abstract
Because of its ability to expedite specimen identification and species delineation, the barcode index number (BIN) system presents a powerful tool to characterize hyperdiverse invertebrate groups such as the Acari (mites). However, the congruence between BINs and morphologically recognized species has seen limited testing in this taxon. We therefore apply this method towards the development of a barcode reference library for soil, poultry litter, and nest dwelling mites in the Western Palearctic. Through analysis of over 600 specimens, we provide DNA barcode coverage for 35 described species and 70 molecular taxonomic units (BINs). Nearly 80% of the species were accurately identified through this method, but just 60% perfectly matched (1:1) with BINs. High intraspecific divergences were found in 34% of the species examined and likely reflect cryptic diversity, highlighting the need for revision in these taxa. These findings provide a valuable resource for integrative pest management, but also highlight the importance of integrating morphological and molecular methods for fine-scale taxonomic resolution in poorly-known invertebrate lineages.
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18
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Pohl GR, andry JF, Schmidt BC, deWaard JR. Lepidoptera of Canada. Zookeys 2019; 819:463-505. [PMID: 30713459 PMCID: PMC6355748 DOI: 10.3897/zookeys.819.27259] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/20/2018] [Indexed: 11/21/2022] Open
Abstract
The known Lepidoptera (moths and butterflies) of the provinces and territories of Canada are summarised, and current knowledge is compared to the state of knowledge in 1979. A total of 5405 species are known to occur in Canada in 81 families, and a further 50 species have been reported but are unconfirmed. This represents an increase of 1348 species since 1979. The DNA barcodes available for Canadian Lepidoptera are also tabulated, based on a dataset of 148,314 specimens corresponding to 5842 distinct clusters. A further yet-undiscovered 1400 species of Lepidoptera are estimated to occur in Canada. The Gelechioidea are the most poorly known major lineage of Lepidoptera in Canada. Nunavut, Prince Edward Island, and British Columbia are thought to show the greatest deficit in our knowledge of Lepidoptera. The unglaciated portions of the Yukon (Beringia), and the Pacific Maritime, Montane Cordillera, and Western Interior Basin ecozones of British Columbia are also identified as hotbeds of undescribed biodiversity.
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Affiliation(s)
- Gregory R. Pohl
- Natural Resources Canada, Canadian Forest Service, 5320 – 122 St., Edmonton, Alberta, T6H 3S5, CanadaNatural Resources CanadaEdmontonCanada
| | - Jean-François andry
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, CanadaAgriculture and Agri-Food CanadaOttawaCanada
| | - B. Chris Schmidt
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, CanadaAgriculture and Agri-Food CanadaOttawaCanada
| | - Jeremy R. deWaard
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, CanadaUniversity of GuelphGuelphCanada
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19
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Abstract
Based on data presented in 29 papers published in the Biota of Canada Special Issue of ZooKeys and data provided herein about Zygentoma, more than 44,100 described species of terrestrial arthropods (Arachnida, Myriapoda, Insecta, Entognatha) are now known from Canada. This represents more than a 34% increase in the number of described species reported 40 years ago (Danks 1979a). The most speciose groups are Diptera (9620 spp.), Hymenoptera (8757), and Coleoptera (8302). Less than 5% of the fauna has a natural Holarctic distribution and an additional 5.1% are non-native species. A conservatively estimated 27,000-42,600 additional species are expected to be eventually discovered in Canada, meaning that the total national species richness is ca. 71,100-86,700 and that currently 51-62% of the fauna is known. Of the most diverse groups, those that are least known, in terms of percent of the Canadian fauna that is documented, are Acari (31%), Thysanoptera (37%), Hymenoptera (46%), and Diptera (32-65%). All groups but Pauropoda have DNA barcodes based on Canadian material. More than 75,600 Barcode Index Numbers have been assigned to Canadian terrestrial arthropods, 63.5% of which are Diptera and Hymenoptera. Much work remains before the Canadian fauna is fully documented, and this will require decades to achieve. In particular, greater and more strategic investment in surveys and taxonomy (including DNA barcoding) is needed to adequately document the fauna.
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Affiliation(s)
- David W. Langor
- Natural Resources Canada, Canadian Forest Service, 5320 – 122 St. NW, Edmonton, Alberta, T6H 3S5, CanadaNatural Resources Canada, Canadian Forest ServiceEdmontonCanada
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20
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Huemer P, Hebert PDN, Mutanen M, Wieser C, Wiesmair B, Hausmann A, Yakovlev R, Möst M, Gottsberger B, Strutzenberger P, Fiedler K. Large geographic distance versus small DNA barcode divergence: Insights from a comparison of European to South Siberian Lepidoptera. PLoS One 2018; 13:e0206668. [PMID: 30388147 PMCID: PMC6214556 DOI: 10.1371/journal.pone.0206668] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/17/2018] [Indexed: 12/16/2022] Open
Abstract
Spanning nearly 13,000 km, the Palearctic region provides an opportunity to examine the level of geographic coverage required for a DNA barcode reference library to be effective in identifying species with broad ranges. This study examines barcode divergences between populations of 102 species of Lepidoptera from Europe and South Siberia, sites roughly 6,000 km apart. While three-quarters of these species showed divergence between their Asian and European populations, these divergence values ranged between 0-1%, distinctly less than the distance to the Nearest-Neighbor species in all but a few cases. Our results suggest that further taxonomic studies may be required for 16 species that showed either extremely low interspecific or high intraspecific variation. For example, seven species pairs showed low or no barcode divergence, but four of these cases are likely to reflect taxonomic over-splitting while the others involve species pairs that are either young or show evidence for introgression. Conversely, some of the nine species with deep intraspecific divergence at varied spatial levels may include overlooked species. Although these 16 cases require further investigation, our overall results indicate that barcode reference libraries based on records from one locality can be very effective in identifying specimens across an extensive geographic area.
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Affiliation(s)
- Peter Huemer
- Naturwissenschaftliche Sammlungen, Tiroler Landesmuseen Betriebsges.m.b.H., Innsbruck, Austria
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | | | - Benjamin Wiesmair
- Naturwissenschaftliche Sammlungen, Tiroler Landesmuseen Betriebsges.m.b.H., Innsbruck, Austria
| | - Axel Hausmann
- Section Lepidoptera, Bavarian State Collection of Zoology, Munich, Germany
| | - Roman Yakovlev
- Ecology Department, Altai State University, Barnaul, Russia
- Tomsk State University, Tomsk, Russia
| | - Markus Möst
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Brigitte Gottsberger
- Department of Botany & Biodiversity Research, University of Vienna, Vienna, Austria
| | | | - Konrad Fiedler
- Department of Botany & Biodiversity Research, University of Vienna, Vienna, Austria
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21
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Ekrem T, Stur E, Orton MG, Adamowicz SJ. DNA barcode data reveal biogeographic trends in Arctic non-biting midges. Genome 2018; 61:787-796. [DOI: 10.1139/gen-2018-0100] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chironomid flies (non-biting midges) are among the most abundant and diverse animals in Arctic regions, but detailed analyses of species distributions and biogeographical patterns are hampered by challenging taxonomy and reliance on morphology for species-level identification. Here we take advantage of available DNA barcode data of Arctic Chironomidae in BOLD to analyse similarities in species distributions across a northern Nearctic – West Palearctic gradient. Using more than 260 000 barcodes representing 4666 BINs (Barcode Index Numbers) and 826 named species (some with interim names) from a combination of public and novel data, we show that the Greenland chironomid fauna shows affinities to both the Nearctic and the West Palearctic regions. While raw taxon counts indicate a strong Greenland – North American affinity, comparisons using Chao’s dissimilarity metric support a slightly higher similarity between Greenland and West Palearctic chironomid communities. Results were relatively consistent across different definitions of species taxonomic units, including morphologically determined species, BINs, and superBINs based on a ∼4.5% threshold. While most taxa found in Greenland are shared with at least one other region, reflecting circum-Arctic dispersal, our results also reveal that Greenland harbours a small endemic biodiversity. Our exploratory study showcases how DNA barcoding efforts using standardized gene regions contribute to an understanding of broad-scale patterns in biogeography by enabling joint analysis of public DNA sequence data derived from diverse prior studies.
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Affiliation(s)
- Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Elisabeth Stur
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Matthew G. Orton
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Sarah J. Adamowicz
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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22
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Schmidt BC, Sullivan JB. Three species in one: a revision of Clemensiaalbata Packard (Erebidae, Arctiinae, Lithosiini). Zookeys 2018:39-55. [PMID: 30337822 PMCID: PMC6189222 DOI: 10.3897/zookeys.788.26048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 06/11/2018] [Indexed: 11/12/2022] Open
Abstract
Clemensiaalbata Packard, previously thought to be a single, widely distributed North American species, is here shown to consist of three distinct, primarily parapatric species: Clemensiaalbata Packard, C.umbrata Packard, stat. rev., and Clemensiaochreata Schmidt & Sullivan, sp. n. Adults and genitalic structures of the three species are illustrated.
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Affiliation(s)
- B Christian Schmidt
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, K.W. Neatby Bldg., 960 Carling Ave., Ottawa, ON, Canada K1A 0C6200 Canadian National Collection of Insects, Arachnids, and Nematodes Ottawa Canada
| | - J Bolling Sullivan
- Craven St., Beaufort, North Carolina 28516, USA Unaffiliated Beaufort United States of America
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23
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Adams JK, Schmidt BC. A new species of Sympistis Hübner from Sapelo Island, Georgia, USA (Lepidoptera, Noctuidae, Oncocnemidinae). Zookeys 2018:79-86. [PMID: 30337825 PMCID: PMC6189225 DOI: 10.3897/zookeys.788.26484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/04/2018] [Indexed: 11/12/2022] Open
Abstract
A new species of the Sympistisbadistriga species-group, Sympistiseleaner Adams, sp. n. is described from Sapelo Island, a back-barrier island in coastal Georgia, United States of America. Adults and genitalia of S.eleaner are illustrated, in addition to adults of similar species in the Sympistisbadistriga species-group. The composition of this species-group is discussed.
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Affiliation(s)
- James K Adams
- Department of Biology, Dalton State College, Dalton, Georgia 30720, USA Dalton State College Dalton United States of America
| | - B Christian Schmidt
- Canadian National Collection of Insects, Arachnids, and Nematodes, Agriculture and Agri-Food Canada, KW Neatby Bldg., 960 Carling Ave., Ottawa, Ontario K1A 0C6, Canada Canadian National Collection of Insects, Arachnids, and Nematodes Ottawa Canada
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24
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Palting JD, Ferguson DC, Moore W. A new species of Hypoprepia from the mountains of central Arizona (Lepidoptera, Erebidae, Arctiinae, Lithosiini). Zookeys 2018:19-38. [PMID: 30337821 PMCID: PMC6189220 DOI: 10.3897/zookeys.788.26885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/09/2018] [Indexed: 11/20/2022] Open
Abstract
A new firefly-mimicking lichen moth of the genus Hypoprepia, H.lampyroides Palting & Ferguson, sp. n., is described from the mountains of east-central Arizona and the Sierra Madre Occidental of Mexico. Hypoprepia Hübner, 1831 is a North American genus of lithosiine tiger moths, previously consisting of five species: H.fucosa Hübner, 1831 and H.miniata (Kirby, 1837), both of eastern and central North America; H.cadaverosa Strecker, 1878 from the Rocky Mountains into New Mexico and west Texas; H.inculta H. Edwards, 1882, a widespread western USA species and H.muelleri Dyar, 1907 from the vicinity of Mexico City. The latter is herein synonymized under H.inculta (= H.muellerisyn. n.), resulting in the total number of taxa in the genus unchanged at five.
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Affiliation(s)
- John Douglas Palting
- Graduate Interdisciplinary Program in Entomology and Insect Science, University of Arizona, Tucson, Arizona, 85721-0036, USA.,Department of Entomology, University of Arizona, Forbes 410, Tucson, Arizona, 85721-0036, USA
| | - Douglas C Ferguson
- Systematic Entomology Laboratory, PSI, Agricultural Research Service, U.S. Department of Agriculture, c/o Smithsonian Institution, Washington, D.C., 20013-7012, USA
| | - Wendy Moore
- Department of Entomology, University of Arizona, Forbes 410, Tucson, Arizona, 85721-0036, USA
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Crabo LG, Schmidt BC. A revision of Admetovis Grote, with the description of a new species from western North America (Noctuidae, Noctuinae, Hadenini). Zookeys 2018:167-181. [PMID: 30337828 PMCID: PMC6189219 DOI: 10.3897/zookeys.788.26480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/06/2018] [Indexed: 11/16/2022] Open
Abstract
The genus Admetovis Grote is revised. Admetovisicarussp. n. is described from the mountains of western North America. A lectotype of Admetovisoxymorus Grote is designated. Illustrations of the adults, male and female genitalia, and distribution maps are presented, together with an identification key. The classification of the genus is reviewed resulting in its reassignment to the tribe Hadenini from Orthosiini.
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Affiliation(s)
- Lars G Crabo
- 724 14th Street, Bellingham, Washington 98225, USA.,Adjunct faculty: Washington State University, Pullman, Washington, USA
| | - B Christian Schmidt
- Canadian National Collection of Insects, Arachnids, and Nematodes, Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada K1A 0C6
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26
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Nagle RB, Schmidt BC. A new species of Euchaetes Harris from southern Arizona (Erebidae, Arctiinae). Zookeys 2018:69-77. [PMID: 30337824 PMCID: PMC6189226 DOI: 10.3897/zookeys.788.26310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/10/2018] [Indexed: 11/22/2022] Open
Abstract
Euchaetesnancyaesp. n. is described from southeastern Arizona. Although superficially similar to species of Pygarctia Grote, structural and molecular variation shows it to be most closely related to Euchaeteshelena (Cassino). Adults, genitalic structure, eggs, and first instar larvae are described and illustrated. The larval host plant remains unknown. Euchaeteshelena is confirmed as occurring in Mexico.
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Affiliation(s)
- Raymond B Nagle
- Department of Pathology, University of Arizona, Tucson, AZ, USA University of Arizona Tucson United States of America
| | - B Christian Schmidt
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, K.W. Neatby Bldg., 960 Carling Ave., Ottawa, ON, Canada K1A 0C6, USA Canadian National Collection of Insects, Arachnids and Nematodes Ottawa Canada
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27
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deWaard JR, Levesque-Beaudin V, deWaard SL, Ivanova NV, McKeown JTA, Miskie R, Naik S, Perez KHJ, Ratnasingham S, Sobel CN, Sones JE, Steinke C, Telfer AC, Young AD, Young MR, Zakharov EV, Hebert PDN. Expedited assessment of terrestrial arthropod diversity by coupling Malaise traps with DNA barcoding 1. Genome 2018; 62:85-95. [PMID: 30257096 DOI: 10.1139/gen-2018-0093] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Monitoring changes in terrestrial arthropod communities over space and time requires a dramatic increase in the speed and accuracy of processing samples that cannot be achieved with morphological approaches. The combination of DNA barcoding and Malaise traps allows expedited, comprehensive inventories of species abundance whose cost will rapidly decline as high-throughput sequencing technologies advance. Aside from detailing protocols from specimen sorting to data release, this paper describes their use in a survey of arthropod diversity in a national park that examined 21 194 specimens representing 2255 species. These protocols can support arthropod monitoring programs at regional, national, and continental scales.
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Affiliation(s)
- Jeremy R deWaard
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Valerie Levesque-Beaudin
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Stephanie L deWaard
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Natalia V Ivanova
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Jaclyn T A McKeown
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Renee Miskie
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Suresh Naik
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Kate H J Perez
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Sujeevan Ratnasingham
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Crystal N Sobel
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Jayme E Sones
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Claudia Steinke
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Angela C Telfer
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Andrew D Young
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada.,b Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Monica R Young
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Evgeny V Zakharov
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Paul D N Hebert
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
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Insect diversity in the Saharo-Arabian region: Revealing a little-studied fauna by DNA barcoding. PLoS One 2018; 13:e0199965. [PMID: 29985924 PMCID: PMC6037371 DOI: 10.1371/journal.pone.0199965] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/18/2018] [Indexed: 11/19/2022] Open
Abstract
Although insects dominate the terrestrial fauna, sampling constraints and the poor taxonomic knowledge of many groups have limited assessments of their diversity. Passive sampling techniques and DNA-based species assignments now make it possible to overcome these barriers. For example, Malaise traps collect specimens with minimal intervention while the Barcode Index Number (BIN) system automates taxonomic assignments. The present study employs Malaise traps and DNA barcoding to extend understanding of insect diversity in one of the least known zoogeographic regions, the Saharo-Arabian. Insects were collected at four sites in three countries (Egypt, Pakistan, Saudi Arabia) by deploying Malaise traps. The collected specimens were analyzed by sequencing 658 bp of cytochrome oxidase I (DNA barcode) and assigning BINs on the Barcode of Life Data Systems. The year-long deployment of a Malaise trap in Pakistan and briefer placements at two Egyptian sites and at one in Saudi Arabia collected 53,092 specimens. They belonged to 17 insect orders with Diptera and Hymenoptera dominating the catch. Barcode sequences were recovered from 44,432 (84%) of the specimens, revealing the occurrence of 3,682 BINs belonging to 254 families. Many of these taxa were uncommon as 25% of the families and 50% of the BINs from Pakistan were only present in one sample. Family and BIN counts varied significantly through the year, but diversity indices did not. Although more than 10,000 specimens were analyzed from each nation, just 2% of BINs were shared by Pakistan and Saudi Arabia, 4% by Egypt and Pakistan, and 7% by Egypt and Saudi Arabia. The present study demonstrates how the BIN system can circumvent the barriers imposed by limited access to taxonomic specialists and by the fact that many insect species in the Saharo-Arabian region are undescribed.
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