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Seymour M, Roslin T, deWaard JR, Perez KHJ, D'Souza ML, Ratnasingham S, Ashfaq M, Levesque-Beaudin V, Blagoev GA, Bukowski B, Cale P, Crosbie D, Decaëns T, deWaard SL, Ekrem T, El-Ansary HO, Evouna Ondo F, Fraser D, Geiger MF, Hajibabaei M, Hallwachs W, Hanisch PE, Hausmann A, Heath M, Hogg ID, Janzen DH, Kinnaird M, Kohn JR, Larrivée M, Lees DC, León-Règagnon V, Liddell M, Lijtmaer DA, Lipinskaya T, Locke SA, Manjunath R, Martins DJ, Martins MB, Mazumdar S, McKeown JTA, Anderson-Teixeria K, Miller SE, Milton MA, Miskie R, Morinière J, Mutanen M, Naik S, Nichols B, Noguera FA, Novotny V, Penev L, Pentinsaari M, Quinn J, Ramsay L, Rochefort R, Schmidt S, Smith MA, Sobel CN, Somervuo P, Sones JE, Staude HS, St Jaques B, Stur E, Telfer AC, Tubaro PL, Wardlaw TJ, Worcester R, Yang Z, Young MR, Zemlak T, Zakharov EV, Zlotnick B, Ovaskainen O, Hebert PDN. Global arthropod beta-diversity is spatially and temporally structured by latitude. Commun Biol 2024; 7:552. [PMID: 38720028 PMCID: PMC11078949 DOI: 10.1038/s42003-024-06199-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
Global biodiversity gradients are generally expected to reflect greater species replacement closer to the equator. However, empirical validation of global biodiversity gradients largely relies on vertebrates, plants, and other less diverse taxa. Here we assess the temporal and spatial dynamics of global arthropod biodiversity dynamics using a beta-diversity framework. Sampling includes 129 sampling sites whereby malaise traps are deployed to monitor temporal changes in arthropod communities. Overall, we encountered more than 150,000 unique barcode index numbers (BINs) (i.e. species proxies). We assess between site differences in community diversity using beta-diversity and the partitioned components of species replacement and richness difference. Global total beta-diversity (dissimilarity) increases with decreasing latitude, greater spatial distance and greater temporal distance. Species replacement and richness difference patterns vary across biogeographic regions. Our findings support long-standing, general expectations of global biodiversity patterns. However, we also show that the underlying processes driving patterns may be regionally linked.
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Affiliation(s)
- Mathew Seymour
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
| | - Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), Ulls väg 18B, Uppsala, 75651, Sweden
- Department of Agricultural Sciences, Faculty of Agriculture and Forestry, University of Helsinki, PO Box 27, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, Helsinki, 00014, Finland
| | - Jeremy R deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Kate H J Perez
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Michelle L D'Souza
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Muhammad Ashfaq
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Gergin A Blagoev
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Belén Bukowski
- División Ornitología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | - Peter Cale
- Australian Landscape Trust, Renmark, SA, SA5341, Australia
| | | | - Thibaud Decaëns
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | - Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
| | - Hosam O El-Ansary
- Plant Production Department, College of Food & Agriculture Sciences, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Fidèle Evouna Ondo
- Agence Nationale des Parcs Nationaux, Departement de la Recherche Scientifique, Libreville, Gabon
| | - David Fraser
- BC Conservation Data Centre, Ministry of Environment, Box 9338, Station Prov Govt, Victoria, BC, V8W 9M1, Canada
| | - Matthias F Geiger
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 160, 53113, Bonn, Germany
| | - Mehrdad Hajibabaei
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Winnie Hallwachs
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Priscila E Hanisch
- División Ornitología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
- Department of Animal Ecology and Tropical Biology, Biocenter - University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Axel Hausmann
- SNSB-Zoologische Staatssammlung München, Munich, Germany
| | | | - Ian D Hogg
- Canadian High Arctic Research Station, Polar Knowledge Canada, Cambridge Bay, NU, Canada
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Daniel H Janzen
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - Joshua R Kohn
- Section of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0116, USA
| | - Maxim Larrivée
- Insectarium, Montréal Space for Life, Montréal, QC, Canada
| | - David C Lees
- Department of Science, Natural History Museum, South Kensington, London, United Kingdom
| | - Virginia León-Règagnon
- Estación de Biología Chamela, Instituto de Biología, Universidad Nacional Autónoma de México, A. P. 21, C.P, 48980, San Patricio, Jalisco, Mexico
| | - Michael Liddell
- Centre for Tropical, Environmental, and Sustainability Sciences, James Cook University, Cairns, Queensland, Australia
| | - Darío A Lijtmaer
- División Ornitología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | - Tatsiana Lipinskaya
- Laboratory of Hydrobiology, Scientific and Practical Center for Bioresources, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Sean A Locke
- Departamento de Biología, University of Puerto Rico at Mayagüez, Mayagüez, 00680, Puerto Rico
| | - Ramya Manjunath
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Dino J Martins
- Mpala Research Centre and Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Marlúcia B Martins
- Laboratório de Ecologia de Invertebrados, Coordenação de Zoologia, Museu Paraense Emilio Goeldi, Avenida Perimetral 1901, Terra Firma, CEP, 66077 530, Belém, Pará, Brazil
| | - Santosh Mazumdar
- Department of Zoology, University of Chittagong, 4331, Chittagong, Bangladesh
| | - Jaclyn T A McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Scott E Miller
- National Museum of Natural History, Smithsonian Institution, Washington, WA, USA
| | - Megan A Milton
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Renee Miskie
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, 90014, Oulu, Finland
| | - Suresh Naik
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Becky Nichols
- US National Park Service, 1316 Cherokee Orchard Road, Great Smoky Mountains National Park, Gatlinburg, TN, USA
| | - Felipe A Noguera
- Estación de Biología Chamela, Instituto de Biología, Universidad Nacional Autónoma de México, A. P. 21, C.P, 48980, San Patricio, Jalisco, Mexico
| | - Vojtech Novotny
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Lyubomir Penev
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Gagarin Street, 1113, Sofia, Bulgaria
| | - Mikko Pentinsaari
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Jenna Quinn
- Rare Charitable Research Reserve, Cambridge, ON, Canada
| | - Leah Ramsay
- BC Conservation Data Centre, Ministry of Environment, Box 9338, Station Prov Govt, Victoria, BC, V8W 9M1, Canada
| | - Regina Rochefort
- North Cascades National Park Service Complex, 810 State Route 20, Sedro-Woolley, WA, 98284, USA
| | - Stefan Schmidt
- SNSB-Zoologische Staatssammlung München, Munich, Germany
| | - M Alex Smith
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Crystal N Sobel
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Panu Somervuo
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, Helsinki, 00014, Finland
| | - Jayme E Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Brianne St Jaques
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Elisabeth Stur
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
| | - Angela C Telfer
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Pablo L Tubaro
- División Ornitología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | - Tim J Wardlaw
- ARC Centre for Forest Values, University of Tasmania, Hobart, TAS, Australia
| | - Robyn Worcester
- Stanley Park Ecology Society, P.O. Box 5167, Vancouver, BC, V6B 4B2, Canada
| | - Zhaofu Yang
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Entomological Museum, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Monica R Young
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Tyler Zemlak
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Evgeny V Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, Helsinki, 00014, Finland
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35 (Survontie 9C), FI-40014, Jyväskylä, Finland
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Ratnasingham S, Wei C, Chan D, Agda J, Agda J, Ballesteros-Mejia L, Boutou HA, El Bastami ZM, Ma E, Manjunath R, Rea D, Ho C, Telfer A, McKeowan J, Rahulan M, Steinke C, Dorsheimer J, Milton M, Hebert PDN. BOLD v4: A Centralized Bioinformatics Platform for DNA-Based Biodiversity Data. Methods Mol Biol 2024; 2744:403-441. [PMID: 38683334 DOI: 10.1007/978-1-0716-3581-0_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
BOLD, the Barcode of Life Data System, supports the acquisition, storage, validation, analysis, and publication of DNA barcodes, activities requiring the integration of molecular, morphological, and distributional data. Its pivotal role in curating the reference library of DNA barcodes, coupled with its data management and analysis capabilities, makes it a central resource for biodiversity science. It enables rapid, accurate identification of specimens and also reveals patterns of genetic diversity and evolutionary relationships among taxa.Launched in 2005, BOLD has become an increasingly powerful tool for advancing the understanding of planetary biodiversity. It currently hosts 17 million specimen records and 14 million barcodes that provide coverage for more than a million species from every continent and ocean. The platform has the long-term goal of providing a consistent, accurate system for identifying all species of eukaryotes.BOLD's integrated analytical tools, full data lifecycle support, and secure collaboration framework distinguish it from other biodiversity platforms. BOLD v4 brought enhanced data management and analysis capabilities as well as novel functionality for data dissemination and publication. Its next version will include features to strengthen its utility to the research community, governments, industry, and society-at-large.
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Affiliation(s)
| | - Catherine Wei
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Dean Chan
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Jireh Agda
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Josh Agda
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Hamza Ait Boutou
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Eddie Ma
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Ramya Manjunath
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Dana Rea
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Chris Ho
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Angela Telfer
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Jaclyn McKeowan
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Miduna Rahulan
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Claudia Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Justin Dorsheimer
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Megan Milton
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Paul D N Hebert
- College of Biological Science, University of Guelph, Guelph, ON, Canada
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Leroy BML, Rabl D, Püls M, Hochrein S, Bae S, Müller J, Hebert PDN, Kuzmina ML, Zakharov EV, Lemme H, Hahn WA, Hilmers T, Jacobs M, Kienlein S, Pretzsch H, Heidrich L, Seibold S, Roth N, Vogel S, Kriegel P, Weisser WW. Trait-mediated responses of caterpillar communities to spongy moth outbreaks and subsequent tebufenozide treatments. Ecol Appl 2023; 33:e2890. [PMID: 37212374 DOI: 10.1002/eap.2890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 03/14/2023] [Accepted: 05/17/2023] [Indexed: 05/23/2023]
Abstract
Outbreaks of the spongy moth Lymantria dispar can have devastating impacts on forest resources and ecosystems. Lepidoptera-specific insecticides, such as Bacillus thuringiensis var. kurstaki (BTK) and tebufenozide, are often deployed to prevent heavy defoliation of the forest canopy. While it has been suggested that using BTK poses less risk to non-target Lepidoptera than leaving an outbreak untreated, in situ testing of this assumption has been impeded by methodological challenges. The trade-offs between insecticide use and outbreaks have yet to be addressed for tebufenozide, which is believed to have stronger side effects than BTK. We investigated the short-term trade-offs between tebufenozide treatments and no-action strategies for the non-target herbivore community in forest canopies. Over 3 years, Lepidoptera and Symphyta larvae were sampled by canopy fogging in 48 oak stands in southeast Germany during and after a spongy moth outbreak. Half of the sites were treated with tebufenozide and changes in canopy cover were monitored. We contrasted the impacts of tebufenozide and defoliator outbreaks on the abundance, diversity, and functional structure of chewing herbivore communities. Tebufenozide treatments strongly reduced Lepidoptera up to 6 weeks after spraying. Populations gradually converged back to control levels after 2 years. Shelter-building species dominated caterpillar assemblages in treated plots in the post-spray weeks, while flight-dimorphic species were slow to recover and remained underrepresented in treated stands 2 years post-treatment. Spongy moth outbreaks had minor effects on leaf chewer communities. Summer Lepidoptera decreased only when severe defoliation occurred, whereas Symphyta declined 1 year after defoliation. Polyphagous species with only partial host plant overlap with the spongy moth were absent from heavily defoliated sites, suggesting greater sensitivity of generalists to defoliation-induced plant responses. These results demonstrate that both tebufenozide treatments and spongy moth outbreaks alter canopy herbivore communities. Tebufenozide had a stronger and longer lasting impact, but it was restricted to Lepidoptera, whereas the outbreak affected both Lepidoptera and Symphyta. These results are tied to the fact that only half of the outbreak sites experienced severe defoliation. This highlights the limited accuracy of current defoliation forecast methods, which are used as the basis for the decision to spray insecticides.
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Affiliation(s)
- Benjamin M L Leroy
- Terrestrial Ecology Research Group, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Dominik Rabl
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Marcel Püls
- Terrestrial Ecology Research Group, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Sophia Hochrein
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Soyeon Bae
- Terrestrial Ecology Research Group, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jörg Müller
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
- Bavarian Forest National Park, Grafenau, Germany
| | - Paul D N Hebert
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Maria L Kuzmina
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Evgeny V Zakharov
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Hannes Lemme
- Department of Forest Protection, Bavarian State Institute of Forestry, Freising, Germany
| | - W Andreas Hahn
- Department of Forest Protection, Bavarian State Institute of Forestry, Freising, Germany
| | - Torben Hilmers
- Chair of Forest Growth and Yield Science, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Martin Jacobs
- Chair of Forest Growth and Yield Science, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Sebastian Kienlein
- Terrestrial Ecology Research Group, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Hans Pretzsch
- Chair of Forest Growth and Yield Science, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Lea Heidrich
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Sebastian Seibold
- Terrestrial Ecology Research Group, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
- Ecosystem Dynamics and Forest Management Research Group, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
- Berchtesgaden National Park, Berchtesgaden, Germany
| | - Nicolas Roth
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Sebastian Vogel
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Peter Kriegel
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Wolfgang W Weisser
- Terrestrial Ecology Research Group, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
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Quicke DLJ, Ranjith AP, Priyadarsanan DR, Nasser M, Hebert PDN, Butcher BA. Two new genera and one new species of the tribe Adeshini (Hymenoptera, Braconidae, Braconinae) from India and South Africa. Zookeys 2023; 1166:235-259. [PMID: 37346769 PMCID: PMC10280206 DOI: 10.3897/zookeys.1166.105589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 05/14/2023] [Indexed: 06/23/2023] Open
Abstract
Two new genera and one new species of the Braconinae tribe Adeshini are described and illustrated: Crenuladesha Ranjith & Quicke, gen. nov., type species Adeshanarendrani Ranjith, 2017, comb. nov. from India, and Protadesha Quicke & Butcher, gen. nov., type species Protadeshaintermedia Quicke & Butcher, sp. nov. from South Africa. The former lacks the mid-longitudinal propodeal carina characteristic of the tribe, and the latter displays less derived fore wing venation with two distinct abscissae of vein 2CU. A molecular phylogenetic analysis is included to confirm their correct placement. Since neither of the two new genera displays all of the characters given in the original diagnosis of the Adeshini a revised diagnosis is provided, as well as an illustrated key to the genera.
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Affiliation(s)
- Donald L. J. Quicke
- Integrative Ecology Laboratory, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, ThailandChulalongkorn UniversityBangkokThailand
| | - Avunjikkattu Parambil Ranjith
- Ashoka Trust for Research in Ecology and the Environment (ATREE), Royal Enclave, Srirampura, Jakkur Post, Bangalore 560064, IndiaAshoka Trust for Research in Ecology and the Environment (ATREE)BangaloreIndia
| | - Dharma Rajan Priyadarsanan
- Ashoka Trust for Research in Ecology and the Environment (ATREE), Royal Enclave, Srirampura, Jakkur Post, Bangalore 560064, IndiaAshoka Trust for Research in Ecology and the Environment (ATREE)BangaloreIndia
| | - Mannankadiyan Nasser
- Insect Ecology and Ethology Laboratory, Department of Zoology, University of Calicut, Kerala, Pin: 673635, IndiaUniversity of CalicutCalicutIndia
| | - Paul D. N. Hebert
- Department of Integrative Biology, University of Guelph, Biodiversity Institute of Ontario, Guelph, CanadaUniversity of GuelphGuelphCanada
| | - Buntika A. Butcher
- Integrative Ecology Laboratory, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, ThailandChulalongkorn UniversityBangkokThailand
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Hebert PDN, Bock DG, Prosser SWJ. Interrogating 1000 insect genomes for NUMTs: A risk assessment for estimates of species richness. PLoS One 2023; 18:e0286620. [PMID: 37289794 PMCID: PMC10249859 DOI: 10.1371/journal.pone.0286620] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/22/2023] [Indexed: 06/10/2023] Open
Abstract
The nuclear genomes of most animal species include NUMTs, segments of the mitogenome incorporated into their chromosomes. Although NUMT counts are known to vary greatly among species, there has been no comprehensive study of their frequency/attributes in the most diverse group of terrestrial organisms, insects. This study examines NUMTs derived from a 658 bp 5' segment of the cytochrome c oxidase I (COI) gene, the barcode region for the animal kingdom. This assessment is important because unrecognized NUMTs can elevate estimates of species richness obtained through DNA barcoding and derived approaches (eDNA, metabarcoding). This investigation detected nearly 10,000 COI NUMTs ≥ 100 bp in the genomes of 1,002 insect species (range = 0-443). Variation in nuclear genome size explained 56% of the mitogenome-wide variation in NUMT counts. Although insect orders with the largest genome sizes possessed the highest NUMT counts, there was considerable variation among their component lineages. Two thirds of COI NUMTs possessed an IPSC (indel and/or premature stop codon) allowing their recognition and exclusion from downstream analyses. The remainder can elevate species richness as they showed 10.1% mean divergence from their mitochondrial homologue. The extent of exposure to "ghost species" is strongly impacted by the target amplicon's length. NUMTs can raise apparent species richness by up to 22% when a 658 bp COI amplicon is examined versus a doubling of apparent richness when 150 bp amplicons are targeted. Given these impacts, metabarcoding and eDNA studies should target the longest possible amplicons while also avoiding use of 12S/16S rDNA as they triple NUMT exposure because IPSC screens cannot be employed.
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Affiliation(s)
- Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Dan G. Bock
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Sean W. J. Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
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7
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Toro-Delgado E, Hernández-Roldán J, Dincă V, Vicente JC, Shaw MR, Quicke DL, Vodă R, Albrecht M, Fernández-Triana J, Vidiella B, Valverde S, Dapporto L, Hebert PDN, Talavera G, Vila R. Butterfly–parasitoid–hostplant interactions in Western Palaearctic Hesperiidae: a DNA barcoding reference library. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The study of ecological interactions between plants, phytophagous insects and their natural enemies is an essential but challenging component for understanding ecosystem dynamics. Molecular methods such as DNA barcoding can help elucidate these interactions. In this study, we employed DNA barcoding to establish hostplant and parasitoid interactions with hesperiid butterflies, using a complete reference library for Hesperiidae of continental Europe and north-western Africa (53 species, 100% of those recorded) based on 2934 sequences from 38 countries. A total of 233 hostplant and parasitoid interactions are presented, some recovered by DNA barcoding larval remains or parasitoid cocoons. Combining DNA barcode results with other lines of evidence allowed 94% species-level identification for Hesperiidae, but success was lower for parasitoids, in part due to unresolved taxonomy. Potential cases of cryptic diversity, both in Hesperiidae and Microgastrinae, are discussed. We briefly analyse the resulting interaction networks. Future DNA barcoding initiatives in this region should focus attention on north-western Africa and on parasitoids, because in these cases barcode reference libraries and taxonomy are less well developed.
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Affiliation(s)
| | - Juan Hernández-Roldán
- Institut de Biologia Evolutiva (CSIC-UPF) , 03008 Barcelona , Spain
- Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid , c/ Darwin, 2, ES - 28049 Madrid , Spain
| | - Vlad Dincă
- Ecology and Genetics Research Unit, PO Box 3000, University of Oulu , 90014 Oulu , Finland
- Research Institute of the University of Bucharest (ICUB), University of Bucharest , Bucharest , Romania
| | | | - Mark R Shaw
- National Museums of Scotland , Edinburgh , UK
| | - Donald Lj Quicke
- Department of Biology, Faculty of Life Sciences, Chulalongkorn University , Bangkok , Thailand
| | | | | | | | - Blai Vidiella
- Centre de Recerca Matemàtica , Edifici C , Campus de Bellaterra, Barcelona , Spain
| | - Sergi Valverde
- Institut de Biologia Evolutiva (CSIC-UPF) , 03008 Barcelona , Spain
- European Centre for Living Technology , Venice , Italy
| | - Leonardo Dapporto
- Dipartimento di Biologia, University of Florence , 50019 Sesto Fiorentino , Italy
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph , Guelph, ON N1G 2W1 , Canada
| | - Gerard Talavera
- Institut Botànic de Barcelona (IBB), CSIC-Ajuntament de Barcelona , Passeig del Migdia s/n, 08038 Barcelona , Spain
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF) , 03008 Barcelona , Spain
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8
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Schultz JA, Hebert PDN. Do pseudogenes pose a problem for metabarcoding marine animal communities? Mol Ecol Resour 2022; 22:2897-2914. [PMID: 35700118 DOI: 10.1111/1755-0998.13667] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 06/01/2022] [Indexed: 11/30/2022]
Abstract
Because DNA metabarcoding typically employs sequence diversity among mitochondrial amplicons to estimate species composition, nuclear mitochondrial pseudogenes (NUMTs) can inflate diversity. This study quantifies the incidence and attributes of NUMTs derived from the 658 bp barcode region of cytochrome c oxidase I (COI) in 156 marine animal genomes. NUMTs were examined to ascertain if they could be recognized by their possession of indels or stop codons. In total, 309 NUMTs ≥ 150 bp were detected, with an average of 1.98 per species (range = 0-33) and a mean length of 391 bp ± 200 bp. Among this total, 75 (24.3 %) lacked indels or stop codons. NUMTs appear to pose the greatest interpretational risk when short (< 313 bp) amplicons are used, such as in eDNA studies, dietary analyses, or processed fish identification. Employing the standard amplicon length (313 bp) for marine metabarcoding, NUMTs could potentially inflate the OTU count by 21% above the true species count while also raising intraspecific variation at COI by 15%. However, when both amplicon length and position are considered, inflation in OTU counts and in barcode variation were just 9% and 10%, respectively, suggesting NUMTs will not seriously distort biodiversity assessments. There was a weak positive correlation between genome size and NUMT count but no variation among phyla or trophic groups. Until bioinformatic advances improve NUMT detection, the best defense involves targeting long amplicons and developing reference databases that include both mitochondrial sequences and their NUMT derivatives.
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Affiliation(s)
- Jessica A Schultz
- Department of Integrative Biology, University of Guelph, Guelph, ON, CANADA.,Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, CANADA
| | - Paul D N Hebert
- Department of Integrative Biology, University of Guelph, Guelph, ON, CANADA.,Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, CANADA
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9
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González MA, Goiri F, Prosser SWJ, Cevidanes A, Hernández-Triana LM, Barandika JF, Hebert PDN, García-Pérez AL. Culicoides species community composition and feeding preferences in two aquatic ecosystems in northern Spain. Parasit Vectors 2022; 15:199. [PMID: 35690834 PMCID: PMC9188056 DOI: 10.1186/s13071-022-05297-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/21/2022] [Indexed: 11/15/2022] Open
Abstract
Background Aquatic ecosystems provide breeding sites for blood-sucking insects such as Culicoides biting midges (Diptera: Ceratopogonidae), but factors affecting their distribution and host choice are poorly understood. A study was undertaken at two nature reserves in northern Spain to examine the abundance, species composition, population dynamics and feeding patterns of biting midges between 2018 and 2019. Methods Culicoides were captured by light suction traps baited with CO2 and by sweep netting vegetation. Blood meals and species identification of blood-fed specimens were determined using cytochrome c oxidase I subunit (COI) DNA barcoding. Multivariate generalized linear models were used to evaluate the associations between the abundance of Culicoides, the species richness and other parameters. Results The 4973 identified specimens comprised 28 species of Culicoides. These included two species reported for the first time in northern Spain, thus raising to 54 the number of Culicoides species described in the region. Specimens of all 28 species and 99.6% of the total specimens collected were caught in suction traps, while sweep netting vegetation revealed just 11 species and 0.4% of the total specimens. Midge abundance peaked in June/early July, with five species comprising > 80% of the captures: Culicoides alazanicus (24.9%), Culicoides griseidorsum (20.3%), Culicoides poperinghensis (16.2%), Culicoides kibunensis (10.7%) and Culicoides clastrieri (9.6%). DNA barcode analysis of blood meals from eight Culicoides species revealed that they fed on 17 vertebrate species (3 mammals and 14 birds). Species in the subgenus Avaritia were primarily ornithophilic, except for C. griseidorsum and C. poperinghensis. Host DNA from blood meals was successfully amplified from 75% of blood-fed females. A pictorial blood meal digestion scale is provided to accurately assess the blood-fed status of female Culicoides. Conclusions The large number of different blood meal sources identified in the midges captured in this study signals the likely importance of wild birds and mammals (e.g. red deer and wild boar) as reservoir/amplifying hosts for pathogens. Available hosts are more exposed to being bitten by biting midge populations in aquatic ecosystems in late spring and early summer. Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05297-5.
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Affiliation(s)
- Mikel A González
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain.,Applied Zoology and Animal Conservation Research Group, Department of Biology, University of the Balearic Islands (UIB), Palma de Mallorca, Spain
| | - Fátima Goiri
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Sean W J Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Aitor Cevidanes
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Luis M Hernández-Triana
- Vector-Borne Diseases Research Group, Virology Department-Animal and Plant Health Agency, Addlestone, UK
| | - Jesús F Barandika
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Ana L García-Pérez
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain.
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10
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Sharkey MJ, Baker A, Manjunath R, Hebert PDN. Description of Chilearinus Sharkey gen. nov. and status of Nearctic Earinus Wesmael, 1837 (Braconidae, Agathidinae) with the description of new species. Zookeys 2022; 1099:57-86. [PMID: 36761440 PMCID: PMC9848775 DOI: 10.3897/zookeys.1099.81473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/14/2022] [Indexed: 11/12/2022] Open
Abstract
The Neotropical members formerly included in Earinus Wesmael, 1837 are transferred to a new genus, Chilearinus Sharkey gen. nov. Presently three Nearctic species of Earinus are recognized, i.e., Earinuserythropoda Cameron, 1887, Earinuslimitaris Say,1835, and Earinuszeirapherae Walley, 1935, and these are retained in Earinus. Earinuschubuquensis Berta, 2000 and Earinusscitus Enderlein, 1920 are transferred to Chilearinus, i.e., C.chubuquensis, and C.scitus, comb. nov. One other species is transferred to Chilearinus, i.e., Microgasterrubricollis Spinola, 1851, Chilearinusrubricollis, comb. nov. Two other Neotropical species, Earinushubrechtae Braet, 2002 and Earinusbourguignoni Braet, 2002 were described under the genus Earinus but are here transferred to Lytopylus, L.hubrechtae, and L.bourguignoni comb. nov. Two new species of Chilearinus are described, C.covidchronos and C.janbert spp. nov. The status of Agathislaevithorax Spinola,1851, Agathisrubricata Spinola,1851, and Agathisareolata Spinola, 1851 is discussed. A neotype is designated for Earinuslimitaris (Say, 1835) and diagnosed with a COI barcode. Earinusaustinbakeri and Earinuswalleyi spp. nov. are described. The status of both Earinus and Chilearinus in the Americas is discussed. A revised key to the genera of Agathidinae of the Americas is presented.
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Affiliation(s)
- Michael J. Sharkey
- The Hymenoptera Institute, 116 Franklin Ave., Redlands, CA, 92373, USAThe Hymenoptera InstituteRedlandsUnited States of America
| | - Austin Baker
- Department of Biological Sciences and Center for Biodiversity Research, University of Memphis, TN, USAUniversity of MemphisMemphisUnited States of America
| | - Ramya Manjunath
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, CanadaUniversity of GuelphGuelphCanada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, CanadaUniversity of GuelphGuelphCanada
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11
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Steinke D, deWaard SL, Sones JE, Ivanova NV, Prosser SWJ, Perez K, Braukmann TWA, Milton M, Zakharov EV, deWaard JR, Ratnasingham S, Hebert PDN. Message in a Bottle-Metabarcoding enables biodiversity comparisons across ecoregions. Gigascience 2022; 11:6575387. [PMID: 35482490 PMCID: PMC9049109 DOI: 10.1093/gigascience/giac040] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 01/24/2022] [Accepted: 03/29/2022] [Indexed: 12/31/2022] Open
Abstract
Background Traditional biomonitoring approaches have delivered a basic understanding of biodiversity, but they cannot support the large-scale assessments required to manage and protect entire ecosystems. This study used DNA metabarcoding to assess spatial and temporal variation in species richness and diversity in arthropod communities from 52 protected areas spanning 3 Canadian ecoregions. Results This study revealed the presence of 26,263 arthropod species in the 3 ecoregions and indicated that at least another 3,000–5,000 await detection. Results further demonstrate that communities are more similar within than between ecoregions, even after controlling for geographical distance. Overall α-diversity declined from east to west, reflecting a gradient in habitat disturbance. Shifts in species composition were high at every site, with turnover greater than nestedness, suggesting the presence of many transient species. Conclusions Differences in species composition among their arthropod communities confirm that ecoregions are a useful synoptic for biogeographic patterns and for structuring conservation efforts. The present results also demonstrate that metabarcoding enables large-scale monitoring of shifts in species composition, making it possible to move beyond the biomass measurements that have been the key metric used in prior efforts to track change in arthropod communities.
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Affiliation(s)
- D Steinke
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - S L deWaard
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - J E Sones
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - N V Ivanova
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - S W J Prosser
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - K Perez
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - T W A Braukmann
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - M Milton
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - E V Zakharov
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - J R deWaard
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada.,School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - S Ratnasingham
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - P D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
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12
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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Yin Y, Yao LF, Hu Y, Shao ZK, Hong XY, Hebert PDN, Xue XF. DNA barcoding uncovers cryptic diversity in minute herbivorous mites (Acari, Eriophyoidea). Mol Ecol Resour 2022; 22:1986-1998. [PMID: 35178894 DOI: 10.1111/1755-0998.13599] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 11/29/2022]
Abstract
Eriophyoid mites (Acari: Eriophyoidea) are among the smallest of terrestrial arthropods and the most species-rich group of herbivorous mites with a high host specificity. However, knowledge of their species diversity has been impeded by the difficulty of their morphological differentiation. This study assembles a DNA barcode reference library that includes 1,850 mitochondrial COI sequences which provides coverage for 45% of the 930 species of eriophyoid mites known from China, and for 37 North American species. Sequence analysis showed a clear barcode gap in nearly all species, reflecting the fact that intraspecific divergences averaged 0.97% versus a mean of 18.51% for interspecific divergences (minimum nearest-neighbor distances) in taxa belonging to three families. Based on these results, we used DNA barcoding to explore the species diversity of eriophyoid mites as well as their host interactions. The 1,850 sequences were assigned to 531 Barcode Index Numbers (BINs). Analyses examining the correspondence between these BINs and species identifications based on morphology revealed that members of 45 species were assigned to two or more BINs, resulting in 1.16 times more BINs than morphospecies. Richness projections suggest that over 2,345 BINs occurred at the sampled locations. Host plant analysis showed that 89% of these mites (BINs) attack only one or two congeneric host species, but the others have several hosts. Furthermore, host-mite network analyses demonstrate that eriophyoid mites are high host-specific, and modularity is high in plant-mite networks. By creating a highly effective identification system for eriophyoid mites in BOLD, DNA barcoding will advance our understanding of the diversity of eriophyoid mites and their host interactions.
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Affiliation(s)
- Yue Yin
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China.,Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada
| | - Liang-Fei Yao
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yue Hu
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zi-Kai Shao
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada
| | - Xiao-Feng Xue
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
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14
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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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15
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Chimeno C, Hausmann A, Schmidt S, Raupach MJ, Doczkal D, Baranov V, Hübner J, Höcherl A, Albrecht R, Jaschhof M, Haszprunar G, Hebert PDN. Peering into the Darkness: DNA Barcoding Reveals Surprisingly High Diversity of Unknown Species of Diptera (Insecta) in Germany. Insects 2022; 13:insects13010082. [PMID: 35055925 PMCID: PMC8779287 DOI: 10.3390/insects13010082] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/16/2021] [Accepted: 01/05/2022] [Indexed: 02/01/2023]
Abstract
Determining the size of the German insect fauna requires better knowledge of several megadiverse families of Diptera and Hymenoptera that are taxonomically challenging. This study takes the first step in assessing these “dark taxa” families and provides species estimates for four challenging groups of Diptera (Cecidomyiidae, Chironomidae, Phoridae, and Sciaridae). These estimates are based on more than 48,000 DNA barcodes (COI) from Diptera collected by Malaise traps that were deployed in southern Germany. We assessed the fraction of German species belonging to 11 fly families with well-studied taxonomy in these samples. The resultant ratios were then used to estimate the species richness of the four “dark taxa” families (DT families hereafter). Our results suggest a surprisingly high proportion of undetected biodiversity in a supposedly well-investigated country: at least 1800–2200 species await discovery in Germany in these four families. As this estimate is based on collections from one region of Germany, the species count will likely increase with expanded geographic sampling.
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Affiliation(s)
- Caroline Chimeno
- SNSB-Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 München, Germany; (A.H.); (S.S.); (M.J.R.); (D.D.); (J.H.); (A.H.); (R.A.); (G.H.)
- Correspondence:
| | - Axel Hausmann
- SNSB-Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 München, Germany; (A.H.); (S.S.); (M.J.R.); (D.D.); (J.H.); (A.H.); (R.A.); (G.H.)
| | - Stefan Schmidt
- SNSB-Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 München, Germany; (A.H.); (S.S.); (M.J.R.); (D.D.); (J.H.); (A.H.); (R.A.); (G.H.)
| | - Michael J. Raupach
- SNSB-Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 München, Germany; (A.H.); (S.S.); (M.J.R.); (D.D.); (J.H.); (A.H.); (R.A.); (G.H.)
| | - Dieter Doczkal
- SNSB-Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 München, Germany; (A.H.); (S.S.); (M.J.R.); (D.D.); (J.H.); (A.H.); (R.A.); (G.H.)
| | - Viktor Baranov
- Department Biology II, Ludwig-Maximilians-University of Munich (LMU), Großhaderner Str. 2, Martinsried, 82152 Planegg, Germany;
| | - Jeremy Hübner
- SNSB-Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 München, Germany; (A.H.); (S.S.); (M.J.R.); (D.D.); (J.H.); (A.H.); (R.A.); (G.H.)
| | - Amelie Höcherl
- SNSB-Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 München, Germany; (A.H.); (S.S.); (M.J.R.); (D.D.); (J.H.); (A.H.); (R.A.); (G.H.)
| | - Rosa Albrecht
- SNSB-Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 München, Germany; (A.H.); (S.S.); (M.J.R.); (D.D.); (J.H.); (A.H.); (R.A.); (G.H.)
| | | | - Gerhard Haszprunar
- SNSB-Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 München, Germany; (A.H.); (S.S.); (M.J.R.); (D.D.); (J.H.); (A.H.); (R.A.); (G.H.)
- Department Biology II, Ludwig-Maximilians-University of Munich (LMU), Großhaderner Str. 2, Martinsried, 82152 Planegg, Germany;
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada;
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16
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Roslin T, Somervuo P, Pentinsaari M, Hebert PDN, Agda J, Ahlroth P, Anttonen P, Aspi J, Blagoev G, Blanco S, Chan D, Clayhills T, deWaard J, deWaard S, Elliot T, Elo R, Haapala S, Helve E, Ilmonen J, Hirvonen P, Ho C, Itämies J, Ivanov V, Jakovlev J, Juslén A, Jussila R, Kahanpää J, Kaila L, Jari-PekkaKaitila, Kakko A, Kakko I, Karhu A, Karjalainen S, Kjaerandsen J, Koskinen J, Laasonen EM, Laasonen L, Laine E, Lampila P, Levesque-Beaudin V, Lu L, Lähteenaro M, Majuri P, Malmberg S, Manjunath R, Martikainen P, Mattila J, McKeown J, Metsälä P, Miklasevskaja M, Miller M, Miskie R, Muinonen A, Veli-MattiMukkala, Naik S, Nikolova N, Nupponen K, Ovaskainen O, Österblad I, Paasivirta L, Pajunen T, Parkko P, Paukkunen J, Penttinen R, Perez K, Pohjoismäki J, Prosser S, Raekunnas M, Rahulan M, Rannisto M, Ratnasingham S, Raukko P, Rinne A, Rintala T, Miranda Romo S, Salmela J, Salokannel J, Savolainen R, Schulman L, Sihvonen P, Soliman D, Sones J, Steinke C, Ståhls G, Tabell J, Tiusanen M, Várkonyi G, Vesterinen EJ, Viitanen E, Vikberg V, Viitasaari M, Vilen J, Warne C, Wei C, Winqvist K, Zakharov E, Mutanen M. A molecular-based identification resource for the arthropods of Finland. Mol Ecol Resour 2021; 22:803-822. [PMID: 34562055 DOI: 10.1111/1755-0998.13510] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species. To quantify the improvement in identification accuracy enabled by the current reference library, we ran 1000 Finnish insect and spider species through the Barcode of Life Data system (BOLD) identification engine. Of these, 91% were correctly assigned to a unique species when compared to the new reference library alone, 85% were correctly identified when compared to BOLD with the new material included, and 75% with the new material excluded. To capitalize on this resource, we used the new reference material to train a probabilistic taxonomic assignment tool, FinPROTAX, scoring high success. For the full-length barcode region, the accuracy of taxonomic assignments at the level of classes, orders, families, subfamilies, tribes, genera, and species reached 99.9%, 99.9%, 99.8%, 99.7%, 99.4%, 96.8%, and 88.5%, respectively. The FinBOL arthropod reference library and FinPROTAX are available through the Finnish Biodiversity Information Facility (www.laji.fi) at https://laji.fi/en/theme/protax. Overall, the FinBOL investment represents a massive capacity-transfer from the taxonomic community of Finland to all sectors of society.
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Affiliation(s)
- Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Panu Somervuo
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Mikko Pentinsaari
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Jireh Agda
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Petri Ahlroth
- Finnish Environment Institute (SYKE), Helsinki, Finland
| | - Perttu Anttonen
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Jouni Aspi
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Gergin Blagoev
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Santiago Blanco
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Dean Chan
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Jeremy deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Stephanie deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Tyler Elliot
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Riikka Elo
- Zoological Museum, Biodiversity Unit, University of Turku, Turku, Finland.,Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | | | | | - Jari Ilmonen
- Metsähallitus, Parks & Wildlife Finland, Vantaa, Finland
| | | | - Chris Ho
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Vladislav Ivanov
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | | | - Aino Juslén
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | | | - Jere Kahanpää
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Lauri Kaila
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | | | | | - Iiro Kakko
- Forssa Museum of Natural History, Forssa, Finland
| | | | | | - Jostein Kjaerandsen
- The Arctic University Museum of Norway, UiT -The Arctic University of Norway, Langnes, Tromsø, Norway
| | - Janne Koskinen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.,Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | | | | | | | | | | | - Liuqiong Lu
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Meri Lähteenaro
- Division of Systematics, Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Entomology, Swedish Museum of Natural History, Stockholm, Sweden
| | | | | | - Ramya Manjunath
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | | | - Jaclyn McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | | | - Meredith Miller
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Renee Miskie
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | | | - Suresh Naik
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Nadia Nikolova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.,Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | | | | | - Timo Pajunen
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | | | - Juho Paukkunen
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Ritva Penttinen
- Zoological Museum, Biodiversity Unit, University of Turku, Turku, Finland.,Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Kate Perez
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Jaakko Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Sean Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Miduna Rahulan
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Meeri Rannisto
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | | | | | | | | | | | - Jukka Salmela
- Regional Museum of Lapland, Arktikum, Rovaniemi, Finland.,Arctic Centre, University of Lapland, Rovaniemi, Finland
| | | | - Riitta Savolainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Leif Schulman
- Finnish Environment Institute (SYKE), Helsinki, Finland.,Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | - Pasi Sihvonen
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | - Dina Soliman
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Jayme Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Claudia Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Gunilla Ståhls
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | | | - Mikko Tiusanen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Gergely Várkonyi
- Biodiversity Centre, Finnish Environment Institute SYKE, Kuhmo, Finland
| | - Eero J Vesterinen
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Biology, University of Turku, Turku, Finland
| | | | | | | | | | - Connor Warne
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Catherine Wei
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Evgeny Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
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17
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Attiná N, Núñez Bustos EO, Lijtmaer DA, Hebert PDN, Tubaro PL, Lavinia PD. Genetic variation in neotropical butterflies is associated with sampling scale, species distributions, and historical forest dynamics. Mol Ecol Resour 2021; 21:2333-2349. [PMID: 34097821 DOI: 10.1111/1755-0998.13441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 11/26/2022]
Abstract
Previous studies of butterfly diversification in the Neotropics have focused on Amazonia and the tropical Andes, while southern regions of the continent have received little attention. To address the gap in knowledge about the Lepidoptera of temperate South America, we analysed over 3000 specimens representing nearly 500 species from Argentina for a segment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Representing 42% of the country's butterfly fauna, collections targeted species from the Atlantic and Andean forests, and biodiversity hotspots that were previously connected but are now isolated. We assessed COI effectiveness for species discrimination and identification and how its performance was affected by geographic distances and taxon coverage. COI data also allowed to study patterns of genetic variation across Argentina, particularly between populations in the Atlantic and Andean forests. Our results show that COI discriminates species well, but that identification success is reduced on average by ~20% as spatial and taxonomic coverage rises. We also found that levels of genetic variation are associated with species' spatial distribution type, a pattern which might reflect differences in their dispersal and colonization abilities. In particular, intraspecific distance between populations in the Atlantic and Andean forests was significantly higher in species with disjunct distributions than in those with a continuous range. All splits between lineages in these forests dated to the Pleistocene, but divergence dates varied considerably, suggesting that historical connections between the Atlantic and Andean forests have differentially affected their shared butterfly fauna. Our study supports the fact that large-scale assessments of mitochondrial DNA variation are a powerful tool for evolutionary studies.
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Affiliation(s)
- Natalí Attiná
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | - Ezequiel O Núñez Bustos
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | - Darío A Lijtmaer
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Pablo L Tubaro
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | - Pablo D Lavinia
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina.,Universidad Nacional de Río Negro. CIT Río Negro (UNRN-CONICET). Sede Atlántica, Viedma, Río Negro, Viedma, Argentina
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18
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Hleap JS, Littlefair JE, Steinke D, Hebert PDN, Cristescu ME. Assessment of current taxonomic assignment strategies for metabarcoding eukaryotes. Mol Ecol Resour 2021; 21:2190-2203. [PMID: 33905615 DOI: 10.1111/1755-0998.13407] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 03/08/2021] [Accepted: 04/19/2021] [Indexed: 01/04/2023]
Abstract
The effective use of metabarcoding in biodiversity science has brought important analytical challenges due to the need to generate accurate taxonomic assignments. The assignment of sequences to genus or species level is critical for biodiversity surveys and biomonitoring, but it is particularly challenging as researchers must select the approach that best recovers information on species composition. This study evaluates the performance and accuracy of seven methods in recovering the species composition of mock communities by using COI barcode fragments. The mock communities varied in species number and specimen abundance, while upstream molecular and bioinformatic variables were held constant, and using a set of COI fragments. We evaluated the impact of parameter optimization on the quality of the predictions. Our results indicate that BLAST top hit competes well with more complex approaches if optimized for the mock community under study. For example, the two machine learning methods that were benchmarked proved more sensitive to reference database heterogeneity and completeness than methods based on sequence similarity. The accuracy of assignments was impacted by both species and specimen counts (query compositional heterogeneity) which ultimately influence the selection of appropriate software. We urge researchers to: (i) use realistic mock communities to allow optimization of parameters, regardless of the taxonomic assignment method employed; (ii) carefully choose and curate the reference databases including completeness; and (iii) use QIIME, BLAST or LCA methods, in conjunction with parameter tuning to better assign taxonomy to diverse communities, especially when information on species diversity is lacking for the area under study.
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Affiliation(s)
- Jose S Hleap
- Department of Biology, McGill University, Montreal, QC, Canada.,SHARCNET, University of Guelph, Guelph, ON, Canada.,Fundacion SQUALUS, Cali, Colombia
| | - Joanne E Littlefair
- Department of Biology, McGill University, Montreal, QC, Canada.,Queen Mary University of London, London, UK
| | - Dirk Steinke
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Paul D N Hebert
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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19
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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: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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Nugent CM, Elliott TA, Ratnasingham S, Hebert PDN, Adamowicz SJ. Debar: A sequence-by-sequence denoiser for COI-5P DNA barcode data. Mol Ecol Resour 2021; 21:2832-2846. [PMID: 33749132 DOI: 10.1111/1755-0998.13384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 03/05/2021] [Indexed: 12/14/2022]
Abstract
DNA barcoding and metabarcoding are now widely used to advance species discovery and biodiversity assessments. High-throughput sequencing (HTS) has expanded the volume and scope of these analyses, but elevated error rates introduce noise into sequence records that can inflate estimates of biodiversity. Denoising -the separation of biological signal from instrument (technical) noise-of barcode and metabarcode data currently employs abundance-based methods which do not capitalize on the highly conserved structure of the cytochrome c oxidase subunit I (COI) region employed as the animal barcode. This manuscript introduces debar, an R package that utilizes a profile hidden Markov model to denoise indel errors in COI sequences introduced by instrument error. In silico studies demonstrated that debar recognized 95% of artificially introduced indels in COI sequences. When applied to real-world data, debar reduced indel errors in circular consensus sequences obtained with the Sequel platform by 75%, and those generated on the Ion Torrent S5 by 94%. The false correction rate was less than 0.1%, indicating that debar is receptive to the majority of true COI variation in the animal kingdom. In conclusion, the debar package improves DNA barcode and metabarcode workflows by aiding the generation of more accurate sequences aiding the characterization of species diversity.
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Affiliation(s)
- Cameron M Nugent
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada.,Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Tyler A Elliott
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Sarah J Adamowicz
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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21
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Hernández-Triana LM, Garza-Hernández JA, Ortega Morales AI, Prosser SWJ, Hebert PDN, Nikolova NI, Barrero E, de Luna-Santillana EDJ, González-Alvarez VH, Mendez-López R, Chan-Chable RJ, Fooks AR, Rodríguez-Pérez MA. An Integrated Molecular Approach to Untangling Host-Vector-Pathogen Interactions in Mosquitoes (Diptera: Culicidae) From Sylvan Communities in Mexico. Front Vet Sci 2021; 7:564791. [PMID: 33778029 PMCID: PMC7988227 DOI: 10.3389/fvets.2020.564791] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 12/18/2020] [Indexed: 11/23/2022] Open
Abstract
There are ~240 species of Culicidae in Mexico, of which some are vectors of arthropod-borne viruses such as Zika virus, dengue virus, chikungunya virus, and West Nile virus. Thus, the identification of mosquito feeding preferences is paramount to understanding of vector–host–pathogen interactions that, in turn, can aid the control of disease outbreaks. Typically, DNA and RNA are extracted separately for animal (insects and blood meal hosts) and viral identification, but this study demonstrates that multiple organisms can be analyzed from a single RNA extract. For the first time, residual DNA present in standard RNA extracts was analyzed by DNA barcoding in concert with Sanger and next-generation sequencing (NGS) to identify both the mosquito species and the source of their meals in blood-fed females caught in seven sylvan communities in Chiapas State, Mexico. While mosquito molecular identification involved standard barcoding methods, the sensitivity of blood meal identification was maximized by employing short primers with NGS. In total, we collected 1,634 specimens belonging to 14 genera, 25 subgenera, and 61 morphospecies of mosquitoes. Of these, four species were new records for Mexico (Aedes guatemala, Ae. insolitus, Limatus asulleptus, Trichoprosopon pallidiventer), and nine were new records for Chiapas State. DNA barcode sequences for >300 bp of the COI gene were obtained from 291 specimens, whereas 130 bp sequences were recovered from another 179 specimens. High intraspecific divergence values (>2%) suggesting cryptic species complexes were observed in nine taxa: Anopheles eiseni (5.39%), An. pseudopunctipennis (2.79%), Ae. podographicus (4.05%), Culex eastor (4.88%), Cx. erraticus (2.28%), Toxorhynchites haemorrhoidalis (4.30%), Tr. pallidiventer (4.95%), Wyeomyia adelpha/Wy. guatemala (7.30%), and Wy. pseudopecten (4.04%). The study increased the number of mosquito species known from 128 species to 138 species for Chiapas State, and 239 for Mexico as a whole. Blood meal analysis showed that Aedes angustivittatus fed on ducks and chicken, whereas Psorophora albipes fed on humans. Culex quinquefasciatus fed on diverse hosts including chicken, human, turkey, and Mexican grackle. No arbovirus RNA was detected by reverse transcriptase–polymerase chain reaction in the surveyed specimens. This study demonstrated, for the first time, that residual DNA present in RNA blood meal extracts can be used to identify host vectors, highlighting the important role of molecular approaches in both vector identification and revealing host–vector–pathogen interactions.
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Affiliation(s)
- Luis M Hernández-Triana
- Animal and Plant Health Agency, Virology Department, Rabies and Wildlife Zoonoses Research Group, Addlestone, United Kingdom
| | | | - Aldo I Ortega Morales
- Departamento de Parasitología, Universidad Autónoma Agraria Antonio Narro, Unidad Laguna, Periférico Raúl López Sánchez y Carretera a Santa Fe, Torreón, Mexico
| | - Sean W J Prosser
- Center for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Paul D N Hebert
- Center for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Nadya I Nikolova
- Center for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Elsa Barrero
- Animal and Plant Health Agency, Virology Department, Rabies and Wildlife Zoonoses Research Group, Addlestone, United Kingdom
| | | | | | - Ramón Mendez-López
- Departamento de Parasitología, Universidad Autónoma Agraria Antonio Narro, Unidad Laguna, Periférico Raúl López Sánchez y Carretera a Santa Fe, Torreón, Mexico
| | - Rahuel J Chan-Chable
- Departamento de Parasitología, Universidad Autónoma Agraria Antonio Narro, Unidad Laguna, Periférico Raúl López Sánchez y Carretera a Santa Fe, Torreón, Mexico
| | - Anthony R Fooks
- Animal and Plant Health Agency, Virology Department, Rabies and Wildlife Zoonoses Research Group, Addlestone, United Kingdom
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22
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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D'Ercole J, Prosser SWJ, Hebert PDN. A SMRT approach for targeted amplicon sequencing of museum specimens (Lepidoptera)-patterns of nucleotide misincorporation. PeerJ 2021; 9:e10420. [PMID: 33520432 PMCID: PMC7811786 DOI: 10.7717/peerj.10420] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 11/02/2020] [Indexed: 12/28/2022] Open
Abstract
Natural history collections are a valuable resource for molecular taxonomic studies and for examining patterns of evolutionary diversification, particularly in the case of rare or extinct species. However, the recovery of sequence information is often complicated by DNA degradation. This article describes use of the Sequel platform (Pacific Biosciences) to recover the 658 bp barcode region of the mitochondrial cytochrome c oxidase I (COI) gene from 380 butterflies with an average age of 50 years. Nested multiplex PCR was employed for library preparation to facilitate sequence recovery from extracts with low concentrations of highly degraded DNA. By employing circular consensus sequencing (CCS) of short amplicons (circa 150 bp), full-length barcodes could be assembled without a reference sequence, an important advance from earlier protocols which required reference sequences to guide contig assembly. The Sequel protocol recovered COI sequences (499 bp on average) from 318 of 380 specimens (84%), much higher than for Sanger sequencing (26%). Because each read derives from a single molecule, it was also possible to quantify the incidence of substitutions arising from DNA damage. In agreement with past work on sequence changes induced by DNA degradation, the transition C/G → T/A was the most prevalent category of change, but its rate of occurrence (4.58E−4) was so low that it did not impede the recovery of reliable sequences. Because the current protocol recovers COI sequence from most museum specimens, and because sequence fidelity is unaffected by nucleotide misincorporations, large-scale sequence characterization of museum specimens is feasible.
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Affiliation(s)
- Jacopo D'Ercole
- Centre for Biodiversity Genomics, Guelph, ON, Canada.,Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | | | - Paul D N Hebert
- Centre for Biodiversity Genomics, Guelph, ON, Canada.,Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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24
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Estrada-Franco JG, Fernández-Santos NA, Adebiyi AA, López-López MDJ, Aguilar-Durán JA, Hernández-Triana LM, Prosser SWJ, Hebert PDN, Fooks AR, Hamer GL, Xue L, Rodríguez-Pérez MA. Vertebrate-Aedes aegypti and Culex quinquefasciatus (Diptera)-arbovirus transmission networks: Non-human feeding revealed by meta-barcoding and next-generation sequencing. PLoS Negl Trop Dis 2020; 14:e0008867. [PMID: 33382725 PMCID: PMC7806141 DOI: 10.1371/journal.pntd.0008867] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 01/13/2021] [Accepted: 10/09/2020] [Indexed: 01/06/2023] Open
Abstract
Background Aedes aegypti mosquito-borne viruses including Zika (ZIKV), dengue (DENV), yellow fever (YFV), and chikungunya (CHIKV) have emerged and re-emerged globally, resulting in an elevated burden of human disease. Aedes aegypti is found worldwide in tropical, sub-tropical, and temperate areas. The characterization of mosquito blood meals is essential to understand the transmission dynamics of mosquito-vectored pathogens. Methodology/principal findings Here, we report Ae. aegypti and Culex quinquefasciatus host feeding patterns and arbovirus transmission in Northern Mexico using a metabarcoding-like approach with next-generation deep sequencing technology. A total of 145 Ae. aegypti yielded a blood meal analysis result with 107 (73.8%) for a single vertebrate species and 38 (26.2%) for two or more. Among the single host blood meals for Ae. aegypti, 28.0% were from humans, 54.2% from dogs, 16.8% from cats, and 1.0% from tortoises. Among those with more than one species present, 65.9% were from humans and dogs. For Cx. quinquefasciatus, 388 individuals yielded information with 326 (84%) being from a single host and 63 (16.2%) being from two or more hosts. Of the single species blood meals, 77.9% were from dogs, 6.1% from chickens, 3.1% from house sparrows, 2.4% from humans, while the remaining 10.5% derived from other 12 host species. Among those which had fed on more than one species, 11% were from dogs and humans, and 89% of other host species combinations. Forage ratio analysis revealed dog as the most over-utilized host by Ae. aegypti (= 4.3) and Cx. quinquefasciatus (= 5.6) and the human blood index at 39% and 4%, respectively. A total of 2,941 host-seeking female Ae. aegypti and 3,536 Cx. quinquefasciatus mosquitoes were collected in the surveyed area. Of these, 118 Ae. aegypti pools and 37 Cx. quinquefasciatus pools were screened for seven arboviruses (ZIKV, DENV 1–4, CHIKV, and West Nile virus (WNV)) using qRT-PCR and none were positive (point prevalence = 0%). The 95%-exact upper limit confidence interval was 0.07% and 0.17% for Ae. aegypti and Cx. quinquefasciatus, respectively Conclusions/significance The low human blood feeding rate in Ae. aegypti, high rate of feeding on mammals by Cx. quinquefasciatus, and the potential risk to transmission dynamics of arboviruses in highly urbanized areas of Northern Mexico is discussed. Elucidating arbovirus-vector-host contact networks is critical to understand and control mosquito-borne virus transmission, including pathogens such as ZIKV, DENV 1–4, CHIKV, and WNV. Here, we report the results of metabarcoding of blood meals of two primary pathogen mosquito vectors, Aedes aegypti and Culex quinquefasciatus. We found limited human blood feeding by Ae. aegypti and high preference for feeding on mammals by Cx. quinquefasciatus. Interestingly, blood meal analysis revealed dogs as the most utilized host for both vector species suggesting the potential for zooprophylaxis for human-amplified urban arboviruses. Pools of these vector species were tested for seven arboviruses and all were negative. We calculated vectorial capacity to discuss the potential risk and transmission dynamics of pathogens transmitted by these two important vectors in an urban location in Northern Mexico.
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Affiliation(s)
| | - Nadia A. Fernández-Santos
- Instituto Politécnico Nacional, Centro de Biotecnología Genómica, Ciudad Reynosa, Tamaulipas, México
| | - Adeniran A. Adebiyi
- Instituto Politécnico Nacional, Centro de Biotecnología Genómica, Ciudad Reynosa, Tamaulipas, México
| | - María de J. López-López
- Instituto Politécnico Nacional, Centro de Biotecnología Genómica, Ciudad Reynosa, Tamaulipas, México
| | - Jesús A. Aguilar-Durán
- Instituto Politécnico Nacional, Centro de Biotecnología Genómica, Ciudad Reynosa, Tamaulipas, México
| | | | | | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Ontario, Canada
| | - Anthony R. Fooks
- Animal and Plant Health Agency, Woodham Lane, Addlestone, Surrey, United Kingdom
| | - Gabriel L. Hamer
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
| | - Ling Xue
- College of Mathematical Sciences, Harbin Engineering University, Harbin, Heilongjiang, P.R. China
| | - Mario A. Rodríguez-Pérez
- Instituto Politécnico Nacional, Centro de Biotecnología Genómica, Ciudad Reynosa, Tamaulipas, México
- * E-mail: ,
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25
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González MA, Prosser SW, Hernández-Triana LM, Alarcón-Elbal PM, Goiri F, López S, Ruiz-Arrondo I, Hebert PDN, García-Pérez AL. Avian Feeding Preferences of Culex pipiens and Culiseta spp. Along an Urban-to-Wild Gradient in Northern Spain. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.568835] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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26
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Floren A, von Rintelen T, Hebert PDN, de Araujo BC, Schmidt S, Balke M, Narakusumo RP, Peggie D, Ubaidillah R, von Rintelen K, Müller T. Integrative ecological and molecular analysis indicate high diversity and strict elevational separation of canopy beetles in tropical mountain forests. Sci Rep 2020; 10:16677. [PMID: 33028881 PMCID: PMC7541450 DOI: 10.1038/s41598-020-73519-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 09/16/2020] [Indexed: 11/18/2022] Open
Abstract
Tropical mountain forests contribute disproportionately to terrestrial biodiversity but little is known about insect diversity in the canopy and how it is distributed between tree species. We sampled tree-specific arthropod communities from 28 trees by canopy fogging and analysed beetle communities which were first morphotyped and then identified by their DNA barcodes. Our results show that communities from forests at 1100 and 1700 m a.s.l. are almost completely distinct. Diversity was much lower in the upper forest while community structure changed from many rare, less abundant species to communities with a pronounced dominance structure. We also found significantly higher beta-diversity between trees at the lower than higher elevation forest where community similarity was high. Comparisons on tree species found at both elevations reinforced these results. There was little species overlap between sites indicating limited elevational ranges. Furthermore, we exploited the advantage of DNA barcodes to patterns of haplotype diversity in some of the commoner species. Our results support the advantage of fogging and DNA barcodes for community studies and underline the need for comprehensive research aimed at the preservation of these last remaining pristine forests.
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Affiliation(s)
- Andreas Floren
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Hans-Martin-Weg 5, 97074, Würzburg, Germany. .,Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247, Munich, Germany. .,Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.
| | - Thomas von Rintelen
- Museum für Naturkunde-Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115, Berlin, Germany
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | | | - Stefan Schmidt
- Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247, Munich, Germany
| | - Michael Balke
- Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247, Munich, Germany
| | - Raden Pramesa Narakusumo
- Zoology Division (Museum Zoologicum Bogoriense), Research Center for Biology, Indonesian Institute of Sciences, Jl. Raya Jakarta-Bogor KM 46, Cibinong, Bogor, 16911, Indonesia.,Museum of Natural History Karlsruhe, Erbprinzenstr. 13, 76133, Karlsruhe, Germany
| | - Djunijanti Peggie
- Zoology Division (Museum Zoologicum Bogoriense), Research Center for Biology, Indonesian Institute of Sciences, Jl. Raya Jakarta-Bogor KM 46, Cibinong, Bogor, 16911, Indonesia
| | - Rosichon Ubaidillah
- Zoology Division (Museum Zoologicum Bogoriense), Research Center for Biology, Indonesian Institute of Sciences, Jl. Raya Jakarta-Bogor KM 46, Cibinong, Bogor, 16911, Indonesia
| | - Kristina von Rintelen
- Museum für Naturkunde-Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115, Berlin, Germany
| | - Tobias Müller
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
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27
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Kocić K, Petrović A, Čkrkić J, Kavallieratos NG, Rakhshani E, Arnó J, Aparicio Y, Hebert PDN, Tomanović Ž. Resolving the Taxonomic Status of Potential Biocontrol Agents Belonging to the Neglected Genus Lipolexis Förster (Hymenoptera, Braconidae, Aphidiinae) with Descriptions of Six New Species. Insects 2020; 11:insects11100667. [PMID: 33003457 PMCID: PMC7650595 DOI: 10.3390/insects11100667] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/23/2020] [Accepted: 09/23/2020] [Indexed: 11/16/2022]
Abstract
Simple Summary Lipolexis is small but widely distributed genus across Europe and Asia. Nevertheless, its taxonomic distinctiveness was subsequently questioned by some authors who considered it as a synonym of the genus Diaeretus. Although Lipolexis is widely distributed and one species (Lipolexis oregmae Gahan) is an important biological control agent, the last taxonomic study on it was conducted more than 50 years ago. Our study employs an integrative approach (morphology and molecular analysis (COI barcode region)), to examine Lipolexis specimens that were sampled worldwide, including specimens from BOLD database. It led to the description of six new species. Each of the new species possesses clear morphological characters that distinguishes it from its congeners. Our findings suggest that two groups can be differentiated within the genus—oregmae and gracilis. Furthermore, we present a key for the identification to all known Lipolexis species of the world. Abstract Lipolexis is a small genus in the subfamily Aphidiinae represented by one species in Europe (Lipolexis gracilis Förster) and by four in Asia (Lipolexis wuyiensis Chen, L. oregmae Gahan, L. myzakkaiae Pramanik and Raychaudhuri and L. pseudoscutellaris Pramanik and Raychaudhuri). Although L. oregmae is employed in biological control programs against pest aphids, the last morphological study on the genus was completed over 50 years ago. This study employs an integrative approach (morphology and molecular analysis (COI barcode region)), to examine Lipolexis specimens that were sampled worldwide, including specimens from BOLD database. These results establish that two currently recognized species of Lipolexis (L. gracilis, L. oregmae) are actually a species complex and also reveal phylogenetic relationships within the genus. Six new species are described and a global key for the identification of Lipolexis species is provided.
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Affiliation(s)
- Korana Kocić
- Institute of Zoology, Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (K.K.); (A.P.); (J.Č.); (Ž.T.)
| | - Andjeljko Petrović
- Institute of Zoology, Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (K.K.); (A.P.); (J.Č.); (Ž.T.)
| | - Jelisaveta Čkrkić
- Institute of Zoology, Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (K.K.); (A.P.); (J.Č.); (Ž.T.)
| | - Nickolas G. Kavallieratos
- Laboratory of Agricultural Zoology and Entomology, Department of Crop Science, Agricultural University of Athens, 75 Iera Odos str., 11885 Athens, Greece
- Correspondence:
| | - Ehsan Rakhshani
- Department of Plant Protection, College of Agriculture, University of Zabol, Zabol 98615-538, Iran;
| | - Judit Arnó
- IRTA Cabrils, 08348 Cabrils, Spain; (J.A.); (Y.A.)
| | | | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road, East Guelph, ON N1G 2W1, Canada;
| | - Željko Tomanović
- Institute of Zoology, Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (K.K.); (A.P.); (J.Č.); (Ž.T.)
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28
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Quicke DLJ, Sharkey MJ, Janzen D, Hallwachs W, Hebert PDN, Butcher BA. A new genus and species of Neotropical gregarious braconine parasitoid (Hymenoptera: Braconidae) of a caterpillar (Lepidoptera: Hesperiidae). Zootaxa 2020; 4816:zootaxa.4816.3.7. [PMID: 33055695 DOI: 10.11646/zootaxa.4816.3.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Indexed: 11/04/2022]
Abstract
A new genus of braconine parasitoid wasp, Acgorium Sharkey Quicke gen. nov., based on a new species from Costa Rica, Acgorium felipechavarriai Sharkey sp. nov., is described and illustrated, based on specimens reared from wild-caught hesperiid caterpillars of Dyscophellus phraxanor (Hewitson). Acgorium felipechavarriai is the first known braconine gregarious ectoparasitoid of a butterfly caterpillar.
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Affiliation(s)
- Donald L J Quicke
- Integrative Ecology Laboratory, Department of Biology, Faculty of Science, Chulalongkorn University, Pathumwan, Thailand Center of Excellence in Entomology: Bee Biology, Diversity of Insects and Mites, Chulalongkorn University, Pathumwan, Thailand..
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29
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Janzen DH, Hallwachs W, Pereira G, Blanco R, Masis A, Chavarria MM, Chavarria F, Guadamuz A, Araya M, Smith MA, Valerio J, Guido H, Sanchez E, Bermudez S, Perez K, Manjunath R, Ratnasingham S, St Jacques B, Milton M, DeWaard JR, Zakharov E, Naik S, Hajibabaei M, Hebert PDN, Hasegawa M. Using DNA-barcoded Malaise trap samples to measure impact of a geothermal energy project on the biodiversity of a Costa Rican old-growth rain forest. Genome 2020; 63:407-436. [PMID: 32579871 DOI: 10.1139/gen-2020-0002] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We report one year (2013-2014) of biomonitoring an insect community in a tropical old-growth rain forest, during construction of an industrial-level geothermal electricity project. This is the first-year reaction by the species-rich insect biodiversity; six subsequent years are being analyzed now. The site is on the margin of a UNESCO Natural World Heritage Site, Área de Conservación Guanacaste (ACG), in northwestern Costa Rica. This biomonitoring is part of Costa Rica's ongoing efforts to sustainably retain its wild biodiversity through biodevelopmental integration with its societies. Essential tools are geothermal engineering needs, entomological knowledge, insect species-rich forest, government-NGO integration, common sense, DNA barcoding for species-level identification, and Malaise traps. This research is tailored for integration with its society at the product level. We combine an academic view with on-site engineering decisions. This biomonitoring requires alpha-level DNA barcoding combined with centuries of morphology-based entomological taxonomy and ecology. Not all desired insect community analyses are performed; they are for data from subsequent years combined with this year. We provide enough analysis to be used by both guilds now. This biomonitoring has shown, for the first year, that the geothermal project impacts only the biodiversity within a zone less than 50 m from the project margin.
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Affiliation(s)
- Daniel H Janzen
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Winnie Hallwachs
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Guillermo Pereira
- Programa Parataxónomos, Area de Conservacion Guanacaste, Apdo. 69-5000, Liberia, Costa Rica
| | - Roger Blanco
- Programa de Investigacion, Area de Conservacion Guanacaste, Apdo. 69-5000, Liberia, Costa Rica
| | - Alejandro Masis
- Director, Area de Conservacion Guanacaste, Apdo. 69-5000, Liberia, Costa Rica
| | | | - Felipe Chavarria
- Area de Conservacion Guanacaste, Apdo. 69-5000, Liberia, Costa Rica
| | - Adrian Guadamuz
- Programa Parataxónomos, Area de Conservacion Guanacaste, Apdo. 69-5000, Liberia, Costa Rica
| | - Magaly Araya
- Programa Parataxónomos, Area de Conservacion Guanacaste, Apdo. 69-5000, Liberia, Costa Rica
| | - M Alex Smith
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | | | | | | | | | - Kate Perez
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Ramya Manjunath
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada
| | | | - Brianne St Jacques
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Megan Milton
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Jeremy R DeWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Evgeny Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Suresh Naik
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Mehrdad Hajibabaei
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada
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30
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Affiliation(s)
- W John Kress
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012;
| | - Jonna A K Mazet
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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31
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Hardulak LA, Morinière J, Hausmann A, Hendrich L, Schmidt S, Doczkal D, Müller J, Hebert PDN, Haszprunar G. DNA metabarcoding for biodiversity monitoring in a national park: Screening for invasive and pest species. Mol Ecol Resour 2020; 20:1542-1557. [PMID: 32559020 DOI: 10.1111/1755-0998.13212] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 06/03/2020] [Accepted: 06/09/2020] [Indexed: 01/09/2023]
Abstract
DNA metabarcoding was utilized for a large-scale, multiyear assessment of biodiversity in Malaise trap collections from the Bavarian Forest National Park (Germany, Bavaria). Principal component analysis of read count-based biodiversities revealed clustering in concordance with whether collection sites were located inside or outside of the National Park. Jaccard distance matrices of the presences of barcode index numbers (BINs) at collection sites in the two survey years (2016 and 2018) were significantly correlated. Overall similar patterns in the presence of total arthropod BINs, as well as BINs belonging to four major arthropod orders across the study area, were observed in both survey years, and are also comparable with results of a previous study based on DNA barcoding of Sanger-sequenced specimens. A custom reference sequence library was assembled from publicly available data to screen for pest or invasive arthropods among the specimens or from the preservative ethanol. A single 98.6% match to the invasive bark beetle Ips duplicatus was detected in an ethanol sample. This species has not previously been detected in the National Park.
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Affiliation(s)
- Laura A Hardulak
- SNSB-Zoologische Staatssammlung München, Munich, Germany.,Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Axel Hausmann
- SNSB-Zoologische Staatssammlung München, Munich, Germany
| | - Lars Hendrich
- SNSB-Zoologische Staatssammlung München, Munich, Germany
| | - Stefan Schmidt
- SNSB-Zoologische Staatssammlung München, Munich, Germany
| | - Dieter Doczkal
- SNSB-Zoologische Staatssammlung München, Munich, Germany
| | - Jörg Müller
- National Park Bavarian Forest, Grafenau, Germany.,Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, University of Würzburg, Biocenter, Rauhenebrach, Germany
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
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32
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Quicke DLJ, Belokobylskij SA, Braet Y, van Achterberg C, Hebert PDN, Prosser SWJ, Austin AD, Fagan-Jeffries EP, Ward DF, Shaw MR, Butcher BA. Phylogenetic reassignment of basal cyclostome braconid parasitoid wasps (Hymenoptera) with description of a new, enigmatic Afrotropical tribe with a highly anomalous 28S D2 secondary structure. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa037] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
A new tribe of braconid wasps provisionally included in the Rhyssalinae, Laibaleini trib. nov., type genus Laibalea gen. nov. (type species Laibalea enigmatica sp. nov.), from Kenya and the Central African Republic, is described. A molecular dataset, with emphasis on basally derived taxa based on four gene fragments (28S D2–D3 expansion region, COI barcode, elongation factor 1-alpha and 16S ribosomal DNA), was analysed both alone and in combination with a morphological dataset. Molecular phylogenetic placement of the new species into an existing subfamily is complicated by the extreme sequence divergence of the three sequences obtained for Laibalea. In both the combined sequence analysis and the combined DNA plus morphological tree, Laibalea is recovered as a sister group to the Rhyssalinae plus all non-cyclostome lineage braconids excluding Mesostoinae, Maxfischeriinae and Aphidiinae. A consensus of morphological characters and molecular analyses suggests inclusion of Laibalea either in the otherwise principally Holarctic subfamily Rhyssalinae or perhap more basally, in the principally Gondwanan Mesostoinae s.l., although we cannot exclude the possibility that it might represent a separate basal lineage. We place Laibalea in its own tribe, provisionally included in Rhyssalinae. The DNA sequence data are presented for several genera for the first time. Avga, the type genus of Avgini, is shown not to belong to Mesostoinae s.l. or Hormiinae, but its exact relationships remain uncertain. The generic compositions of Rhyssalinae and Mesostoinae s.l. are revised. Anachyra, Apoavga, Neptihormius, Neoavga and Opiopterus are shown to belong to Mesostoinae s.s. A key to the tribes of Rhyssalinae is provided.
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Affiliation(s)
- Donald L J Quicke
- Integrative Ecology Laboratory, Department of Biology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, BKK, Thailand
- Center of Excellence in Entomology: Bee Biology, Diversity of Insects and Mites, Chulalongkorn University, Phayathai Road, Pathumwan, BKK, Thailand
| | - Sergey A Belokobylskij
- Zoological Institute, Russian Academy of Sciences, St Petersburg, Russia
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
| | - Yves Braet
- Royal Belgian Institute of Natural Sciences, O.D. Phylogeny and Taxonomy, Entomology, Brussels, Belgium
- Unité d’Entomologie fonctionnelle et évolutive, Gembloux Agro-Bio Tech, Université de Liège, Passage des Déportés 2, Gembloux, Belgium
| | | | - Paul D N Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Sean W J Prosser
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Andrew D Austin
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Erinn P Fagan-Jeffries
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Darren F Ward
- New Zealand Arthropod Collection, Landcare Research, Auckland, New Zealand
| | | | - Buntika A Butcher
- Integrative Ecology Laboratory, Department of Biology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, BKK, Thailand
- Center of Excellence in Entomology: Bee Biology, Diversity of Insects and Mites, Chulalongkorn University, Phayathai Road, Pathumwan, BKK, Thailand
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33
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Pentinsaari M, Ratnasingham S, Miller SE, Hebert PDN. BOLD and GenBank revisited - Do identification errors arise in the lab or in the sequence libraries? PLoS One 2020; 15:e0231814. [PMID: 32298363 PMCID: PMC7162515 DOI: 10.1371/journal.pone.0231814] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 03/30/2020] [Indexed: 11/23/2022] Open
Abstract
Applications of biological knowledge, such as forensics, often require the determination of biological materials to a species level. As such, DNA-based approaches to identification, particularly DNA barcoding, are attracting increased interest. The capacity of DNA barcodes to assign newly encountered specimens to a species relies upon access to informatics platforms, such as BOLD and GenBank, which host libraries of reference sequences and support the comparison of new sequences to them. As parameterization of these libraries expands, DNA barcoding has the potential to make valuable contributions in diverse applied contexts. However, a recent publication called for caution after finding that both platforms performed poorly in identifying specimens of 17 common insect species. This study follows up on this concern by asking if the misidentifications reflected problems in the reference libraries or in the query sequences used to test them. Because this reanalysis revealed that missteps in acquiring and analyzing the query sequences were responsible for most misidentifications, a workflow is described to minimize such errors in future investigations. The present study also revealed the limitations imposed by the lack of a polished species-level taxonomy for many groups. In such cases, applications can be strengthened by mapping the geographic distributions of sequence-based species proxies rather than waiting for the maturation of formal taxonomic systems based on morphology.
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Affiliation(s)
- Mikko Pentinsaari
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | - Scott E. Miller
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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35
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Mutanen M, Ovaskainen O, Várkonyi G, Itämies J, Prosser SWJ, Hebert PDN, Hanski I. Dynamics of a host-parasitoid interaction clarified by modelling and DNA sequencing. Ecol Lett 2020; 23:851-859. [PMID: 32207239 PMCID: PMC7187309 DOI: 10.1111/ele.13486] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/14/2019] [Accepted: 02/14/2020] [Indexed: 11/28/2022]
Abstract
It has been hypothesised that the 2-year oscillations in abundance of Xestia moths are mediated by interactions with 1-year Ophion parasitoid wasps. We tested this hypothesis by modelling a 35-year time series of Xestia and Ophion from Northern Finland. Additionally, we used DNA barcoding to ascertain the species diversity of Ophion and targeted amplicon sequencing of their gut contents to confirm their larval hosts. Modelling of the time-series data strongly supported the hypothesised host-parasitoid dynamics and that periodic occurrence of Xestia moths is mediated by Ophion. DNA barcodes revealed that Ophion included five species rather than just one while targeted amplicon sequencing verified that Ophion does parasitise Xestia. At least one Ophion species employs 1-year Syngrapha interrogationis as an alternate host, but it did not detectably affect Xestia-Ophion dynamics. We also demonstrate the previously unrecognised complexity of this system due to cryptic parasitoid diversity.
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Affiliation(s)
- Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, FI-90014, Finland, Oulu
| | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, FI-00014, Finland, Helsinki.,Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Gergely Várkonyi
- Friendship Park Research Centre, Finnish Environment Institute, FI-88900, Kuhmo, Finland
| | | | - Sean W J Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Ilkka Hanski
- Department of Biosciences, Metapopulation Research Center, University of Helsinki, Helsinki, Finland
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36
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Čkrkić J, Petrović A, Kocić K, Mitrović M, Kavallieratos NG, van Achterberg C, Hebert PDN, Tomanović Ž. Phylogeny of the Subtribe Monoctonina (Hymenoptera, Braconidae, Aphidiinae). Insects 2020; 11:insects11030160. [PMID: 32121620 PMCID: PMC7143268 DOI: 10.3390/insects11030160] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 11/23/2022]
Abstract
Members of the Monoctonina subtribe have long been neglected in applied studies of the subfamily Aphidiinae, due to their low economic importance, as they do not parasitize pests of cultivated plants. Consequently, data about this group are scarce, including its taxonomy and phylogeny. In the present study, we explore inter- and intraspecific genetic variation of Monoctonina species, including genera Monoctonus Haliday 1833, Monoctonia Starý 1962, Falciconus Mackauer 1959 and Harkeria Cameron 1900. We employ two molecular markers, the barcode region of the mitochondrial cytochrome c oxidase subunit I (COI) and the D2 region of the 28S nuclear gene (28S rDNA), to analyze genetic structuring and phylogeny of all available Monoctonina species, and combine them with morphological data for an integrative approach. We report one new species, and three potentially new species which can be formally described when further specimens are available. Analysis of phylogenetic relationships within the subtribe shows a basal position for the genera Falciconus and Monoctonia, and the close relatedness of Harkeria and Monoctonus.
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Affiliation(s)
- Jelisaveta Čkrkić
- Institute of Zoology, Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (A.P.); (K.K.); (Ž.T.)
- Correspondence:
| | - Andjeljko Petrović
- Institute of Zoology, Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (A.P.); (K.K.); (Ž.T.)
| | - Korana Kocić
- Institute of Zoology, Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (A.P.); (K.K.); (Ž.T.)
| | - Milana Mitrović
- Institute for Plant Protection and Environment, Department of Plant Pests, Banatska 33, 11000 Belgrade, Serbia;
| | - Nickolas G. Kavallieratos
- Laboratory of Agricultural Zoology and Entomology, Department of Crop Science, Agricultural University of Athens, 75 Iera Odos str., 11885 Athens, Attica, Greece;
| | | | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada;
| | - Željko Tomanović
- Institute of Zoology, Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (A.P.); (K.K.); (Ž.T.)
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Ovaskainen O, Abrego N, Somervuo P, Palorinne I, Hardwick B, Pitkänen JM, Andrew NR, Niklaus PA, Schmidt NM, Seibold S, Vogt J, Zakharov EV, Hebert PDN, Roslin T, Ivanova NV. Monitoring Fungal Communities With the Global Spore Sampling Project. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2019.00511] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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38
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Yin Y, Yao LF, Zhang Q, Hebert PDN, Xue XF. Using multiple lines of evidence to delimit protogynes and deutogynes of four-legged mites: a case study on Epitrimerus sabinae s.l. (Acari : Eriophyidae). INVERTEBR SYST 2020. [DOI: 10.1071/is20014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Accurate species delimitation is essential for the study of biodiversity, but morphological approaches often provide a limited ability to connect different life stages, sexes or other phenotypic variants in eriophyoid mites because many species possess two phenotypically distinct forms: protogynes and deutogynes. In this study, we analysed the morphological variation in 26 populations of the eriophyoid mite, Epitrimerus sabinae Xue & Hong, 2005 s.l., from sites across its entire known distribution and revealed three morphotypes (LNS: large, normal palp seta d; MBS: medium, bifurcated palp seta d; SBS: small, bifurcated palp seta d) distinguished by body size and structure of dorsal pedipalp genual seta. Five lines of evidence (morphometrics, DNA-based species delimitation, phylogenetics, haplotype network, mitochondrial genome architecture) indicated that the MBS and SBS groups were very distinct from LNS (E. sabinae s.s.). In fact, the MBS and SBS morphotypes are properly placed in the genus Leipothrix with the MBS lineage representing the protogyne of L. juniperensis, sp. nov., whereas the SBS lineage is its deutogyne. By expanding the approaches used to link protogynes and deutogynes of eriophyoid mites, this study provides a way to accelerate the delineation of species boundaries in this important group of plant pests.
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39
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Naseem MT, Ashfaq M, Khan AM, Rasool A, Asif M, Hebert PDN. BIN overlap confirms transcontinental distribution of pest aphids (Hemiptera: Aphididae). PLoS One 2019; 14:e0220426. [PMID: 31821347 PMCID: PMC6903727 DOI: 10.1371/journal.pone.0220426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/24/2019] [Indexed: 11/25/2022] Open
Abstract
DNA barcoding is highly effective for identifying specimens once a reference sequence library is available for the species assemblage targeted for analysis. Despite the great need for an improved capacity to identify the insect pests of crops, the use of DNA barcoding is constrained by the lack of a well-parameterized reference library. The current study begins to address this limitation by developing a DNA barcode reference library for the pest aphids of Pakistan. It also examines the affinities of these species with conspecific populations from other geographic regions based on both conventional taxonomy and Barcode Index Numbers (BINs). A total of 809 aphids were collected from a range of plant species at sites across Pakistan. Morphological study and DNA barcoding allowed 774 specimens to be identified to one of 42 species while the others were placed to a genus or subfamily. Sequences obtained from these specimens were assigned to 52 BINs whose monophyly were supported by neighbor-joining (NJ) clustering and Bayesian inference. The 42 species were assigned to 41 BINs with 38 showing BIN concordance. These species were represented on BOLD by 7,870 records from 69 countries. Combining these records with those from Pakistan produced 60 BINs with 12 species showing a BIN split and three a BIN merger. Geo-distance correlations showed that intraspecific divergence values for 49% of the species were not affected by the distance between populations. Forty four of the 52 BINs from Pakistan had counterparts in 73 countries across six continents, documenting the broad distributions of pest aphids.
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Affiliation(s)
- Muhammad Tayyib Naseem
- National institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Muhammad Ashfaq
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
- * E-mail:
| | - Arif Muhammad Khan
- National institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | - Akhtar Rasool
- National institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Zoology, University of Swat, Swat, Pakistan
| | - Muhammad Asif
- 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, ON, Canada
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40
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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: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Pentinsaari M, Anderson R, Borowiec L, Bouchard P, Brunke A, Douglas H, Smith ABT, Hebert PDN. DNA barcodes reveal 63 overlooked species of Canadian beetles (Insecta, Coleoptera). Zookeys 2019; 894:53-150. [PMID: 31844409 PMCID: PMC6906170 DOI: 10.3897/zookeys.894.37862] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 10/25/2019] [Indexed: 11/12/2022] Open
Abstract
This study demonstrates the power of DNA barcoding to detect overlooked and newly arrived taxa. Sixty-three species of Coleoptera representing 25 families are studied based on DNA barcode data and morphological analysis of the barcoded specimens. Three of the species involve synonymies or previous taxonomic confusion in North America, while the first Canadian records are published for 60 species. Forty-two species are adventive in North America, and 40 of these adventive species originate from the Palaearctic region. Three genera are recorded from the Nearctic region for the first time: Coelostoma Brullé, 1835 (Hydrophilidae), Scydmoraphes Reitter, 1891 (Staphylinidae), and Lythraria Bedel, 1897 (Chrysomelidae). Two new synonymies are established: Mycetoporus triangulatus Campbell, 1991 (Staphylinidae) is a junior synonym of Mycetoporus reichei Pandellé, 1869, syn. nov. while Bledius philadelphicus Fall, 1919 (Staphylinidae) is a junior synonym of Bledius gallicus (Gravenhorst, 1806), syn. nov. The previously suggested move of Ctenicera tigrina (Fall, 1901) to the genus Pseudanostirus Dolin, 1964 (Elateridae) is formalized, resulting in Pseudanostirus tigrinus (Fall, 1901), comb. nov.
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Affiliation(s)
- Mikko Pentinsaari
- Centre for Biodiversity Genomics, 50 Stone Road East University of Guelph, Guelph, ON, N1G 2W1, Canada Centre for Biodiversity Genomics, University of Guelph Guelph Canada
| | - Robert Anderson
- Canadian Museum of Nature, P.O. Box 3443, Station D, Ottawa, ON, K1P 6P4, Canada Canadian Museum of Nature Ottawa Canada
| | - Lech Borowiec
- Department of Biodiversity and Evolutionary Taxonomy, University of Wrocław, Przybyszewskiego 65, 51-148 Wrocław, Poland University of Wroclaw Wroclaw Poland
| | - Patrice Bouchard
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada Agriculture and Agri-Food Canada Ottawa Canada
| | - Adam Brunke
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada Agriculture and Agri-Food Canada Ottawa Canada
| | - Hume Douglas
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada Agriculture and Agri-Food Canada Ottawa Canada
| | - Andrew B T Smith
- Canadian Museum of Nature, P.O. Box 3443, Station D, Ottawa, ON, K1P 6P4, Canada Canadian Museum of Nature Ottawa Canada
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, 50 Stone Road East University of Guelph, Guelph, ON, N1G 2W1, Canada Centre for Biodiversity Genomics, University of Guelph Guelph Canada
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Handy SM, Deeds JR, Ivanova NV, Hebert PDN, Hanner RH, Ormos A, Weigt LA, Moore MM, Yancy HF. A Single-Laboratory Validated Method for the Generation of DNA Barcodes for the Identification of Fish for Regulatory Compliance. J AOAC Int 2019. [DOI: 10.1093/jaoac/94.1.201] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The U.S. Food and Drug Administration is responsible for ensuring that the nation's food supply is safe and accurately labeled. This task is particularly challenging in the case of seafood where a large variety of species are marketed, most of this commodity is imported, and processed product is difficult to identify using traditional morphological methods. Reliable species identification is critical for both foodborne illness investigations and for prevention of deceptive practices, such as those where species are intentionally mislabeled to circumvent import restrictions or for resale as species of higher value. New methods that allow accurate and rapid species identifications are needed, but any new methods to be used for regulatory compliance must be both standardized and adequately validated. "DNA barcoding" is a process by which species discriminations are achieved through the use of short, standardized gene fragments. For animals, a fragment (655 base pairs starting near the 5′ end) of the cytochrome c oxidase subunit 1 mitochondrial gene has been shown to provide reliable species level discrimination in most cases. We provide here a protocol with single-laboratory validation for the generation of DNA barcodes suitable for the identification of seafood products, specifically fish, in a manner that is suitable for FDA regulatory use.
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Affiliation(s)
- Sara M Handy
- U.S. Food and Drug Administration, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, College Park, MD 20740, USA
| | - Jonathan R Deeds
- U.S. Food and Drug Administration, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, College Park, MD 20740, USA
| | - Natalia V Ivanova
- Canadian Centre for DNA Barcoding, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Rd East, Guelph, ON, Canada, N1G 2W1
| | - Paul D N Hebert
- Canadian Centre for DNA Barcoding, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Rd East, Guelph, ON, Canada, N1G 2W1
| | - Robert H Hanner
- University of Guelph, Department of Integrative Biology, 50 Stone Rd East, Guelph, ON, Canada, N1G 2W1
| | - Andrea Ormos
- Smithsonian Institution, National Museum of Natural History, Laboratories of Analytical Biology, MRC 534, Washington, DC 20013-7012, USA
| | - Lee A Weigt
- Smithsonian Institution, National Museum of Natural History, Laboratories of Analytical Biology, MRC 534, Washington, DC 20013-7012, USA
| | - Michelle M Moore
- U.S. Food and Drug Administration, Office of Regulatory Affairs, Pacific Regional Laboratory Northwest, Applied Technology Center, 22201 23rd Dr SE, Bothell, WA 98021-4421, USA
| | - Haile F Yancy
- U.S. Food and Drug Administration, Office of Research, Center for Veterinary Medicine, 8401 Muirkirk Rd, Laurel, MD 20708
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Young MR, Proctor HC, deWaard JR, Hebert PDN. DNA barcodes expose unexpected diversity in Canadian mites. Mol Ecol 2019; 28:5347-5359. [DOI: 10.1111/mec.15292] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/17/2019] [Accepted: 10/21/2019] [Indexed: 01/24/2023]
Affiliation(s)
- Monica R. Young
- Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
- Department of Integrative Biology University of Guelph Guelph ON Canada
| | - Heather C. Proctor
- Department of Biological Sciences University of Alberta Edmonton AB Canada
| | - Jeremy R. deWaard
- Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
- Department of Integrative Biology University of Guelph Guelph ON Canada
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Arias-Penna DC, Whitfield JB, Janzen DH, Winifred Hallwachs, Dyer LA, Smith MA, Hebert PDN, Fernández-Triana JL. A species-level taxonomic review and host associations of Glyptapanteles (Hymenoptera, Braconidae, Microgastrinae) with an emphasis on 136 new reared species from Costa Rica and Ecuador. Zookeys 2019; 890:1-685. [PMID: 31798309 PMCID: PMC6881475 DOI: 10.3897/zookeys.890.35786] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 07/15/2019] [Indexed: 01/01/2023] Open
Abstract
The descriptive taxonomic study reported here is focused on Glyptapanteles, a species-rich genus of hymenopteran parasitoid wasps. The species were found within the framework of two independent long-term Neotropical caterpillar rearing projects: northwestern Costa Rica (Área de Conservación Guanacaste, ACG) and eastern Andes, Ecuador (centered on Yanayacu Biological Station, YBS). One hundred thirty-six new species of Glyptapanteles Ashmead are described and all of them are authored by Arias-Penna. None of them was recorded in both countries; thus, 78 are from Costa Rica and the remaining 58 from Ecuador. Before this revision, the number of Neotropical described Glyptapanteles did not reach double digits. Reasonable boundaries among species were generated by integrating three datasets: Cytochrome Oxidase I (COI) gene sequencing data, natural history (host records), and external morphological characters. Each species description is accompanied by images and known geographical distribution. Characteristics such as shape, ornamentation, and location of spun Glyptapanteles cocoons were imaged as well. Host-parasitoid associations and food plants are also here published for the first time. A total of 88 species within 84 genera in 15 Lepidoptera families was encountered as hosts in the field. With respect to food plants, these wild-caught parasitized caterpillars were reared on leaves of 147 species within 118 genera in 60 families. The majority of Glyptapanteles species appeared to be relatively specialized on one family of Lepidoptera or even on some much lower level of taxonomic refinement. Those herbivores in turn are highly food-plant specialized, and once caterpillars were collected, early instars (1-3) yielded more parasitoids than later instars. Glyptapanteles jimmilleri Arias-Penna, sp. nov. is the first egg-larval parasitoid recorded within the genus, though there may be many more since such natural history requires a more focused collection of eggs. The rate of hyperparasitoidism within the genus was approximately 4% and was represented by Mesochorus spp. (Ichneumonidae). A single case of multiparasitoidism was reported, Copidosoma floridanum Ashmead (Encyrtidae) and Glyptapanteles ilarisaaksjarvi Arias-Penna, sp. nov. both parasitoid species emerged from the caterpillar of Noctuidae: Condica cupienta (Cramer). Bodyguard behavior was observed in two Glyptapanteles species: G. howelldalyi Arias-Penna, sp. nov. and G. paulhansoni Arias-Penna, sp. nov. A dichotomous key for all the new species is provided. The numerous species described here, and an equal number already reared but not formally described, signal a far greater Glyptapanteles species richness in the Neotropics than suggested by the few described previously.
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Affiliation(s)
- Diana Carolina Arias-Penna
- Department of Entomology, University of Illinois, 320 Morrill Hall, 505 S. Goodwin Ave., Urbana, IL 61801, USA
| | - James B Whitfield
- Department of Entomology, University of Illinois, 320 Morrill Hall, 505 S. Goodwin Ave., Urbana, IL 61801, USA
| | - Daniel H Janzen
- Department of Biology, University of Pennsylvania, 102 Leidy Laboratories, 433 S. University Ave., Philadelphia, PA 19104, USA
| | - Winifred Hallwachs
- Department of Biology, University of Pennsylvania, 3400 Chestnut St, Philadelphia, PA 19104, USA
| | - Lee A Dyer
- Department of Biology, University of Nevada, 1664 N. Virginia Street, Reno, NV 89557, USA
| | - M Alex Smith
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
| | - Paul D N Hebert
- Biodiversity Institute of Ontario, University of Guelph, 579 Gordon St., Guelph, Ontario, N1G 1Y2, Canada
| | - José L Fernández-Triana
- Canadian National Collection of Insects, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
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Quicke DLJ, Austin AD, Fagan‐Jeffries EP, Hebert PDN, Butcher BA. Molecular phylogeny places the enigmatic subfamily Masoninae within the Ichneumonidae, not the Braconidae. ZOOL SCR 2019. [DOI: 10.1111/zsc.12390] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Donald L. J. Quicke
- Integrative Ecology Laboratory Department of Biology Faculty of Science Chulalongkorn University Bangkok Thailand
- Center of Excellence in Entomology: Bee Biology Diversity of Insects and Mites Chulalongkorn University Bangkok Thailand
| | - Andrew D. Austin
- Australian Centre for Evolutionary Biology and Biodiversity School of Biological Sciences The University of Adelaide Adelaide SA Australia
| | - Erinn P. Fagan‐Jeffries
- Australian Centre for Evolutionary Biology and Biodiversity School of Biological Sciences The University of Adelaide Adelaide SA Australia
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics Biodiversity Institute of OntarioUniversity of Guelph Guelph ON Canada
| | - Buntika A. Butcher
- Integrative Ecology Laboratory Department of Biology Faculty of Science Chulalongkorn University Bangkok Thailand
- Center of Excellence in Entomology: Bee Biology Diversity of Insects and Mites Chulalongkorn University Bangkok Thailand
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Čkrkić J, Petrović A, Kocić K, Kavallieratos NG, Hebert PDN, Tomanović Ž. Review of the world Monoctonina Mackauer 1961 (Hymenoptera, Braconidae, Aphidiinae): key for their identification and descriptions of five new species. Zootaxa 2019; 4691:zootaxa.4691.4.3. [PMID: 31719387 DOI: 10.11646/zootaxa.4691.4.3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Indexed: 11/04/2022]
Abstract
The subtribe Monoctonina has long been overlooked when it comes to morphological studies, probably due to the low economic importance of its members. Mainly distributed in high montane areas and forest ecosystems, species of Monoctonina are not often found in large populations and do not parasitize pests of cultivated plants. Our research uncovered five new species belonging to this subtribe (Monoctonus brachyradius sp. n., M. canadensis sp. n., M. inexpectatus sp. n., M. luteus sp. n., and M. parvipalpus sp. n.). We also redescribe species originally described over a century ago, and discuss the utility of certain morphological characters, as well as status of some species within Monoctonina.
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Affiliation(s)
- Jelisaveta Čkrkić
- Institute of Zoology, Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia.
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Abstract
Abstract
Given that species is the fundamental unit in systematic biology, rigorous species delimitation is crucial for taxonomic studies, yet routine species delimitation remains an ongoing challenge in the taxonomic practice of insects. The two-horned scorpionfly Dicerapanorpa is a small genus in Panorpidae (Mecoptera) endemic to the Qinling-Bashan and Hengduan mountains, a biodiversity hotspot. However, species of Dicerapanorpa are difficult to delineate owing to marked intraspecific variation and interspecific similarity. Here, we investigate the diversity and species boundaries of Dicerapanorpa using an integrative approach based on DNA barcoding, morphological, geometric morphometric and molecular phylogenetic analyses. This integrative analyses confirmed the 13 described species of Dicerapanorpa and revealed three new species: Dicerapanorpa lativalva sp. nov., Dicerapanorpa hualongshana sp. nov. and Dicerapanorpa minshana sp. nov. Most molecular operational taxonomic units are in congruence with morphological clusters. Possible reasons for several discordances in Dicerapanorpa are tentatively discussed.
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Affiliation(s)
- Gui-Lin Hu
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Kai Gao
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Ji-Shen Wang
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Bao-Zhen Hua
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
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Huemer P, Wieser C, Stark W, Hebert PDN, Wiesmair B. DNA barcode library of megadiverse Austrian Noctuoidea (Lepidoptera) - a nearly perfect match of Linnean taxonomy. Biodivers Data J 2019; 7:e37734. [PMID: 31423084 PMCID: PMC6694074 DOI: 10.3897/bdj.7.e37734] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 07/23/2019] [Indexed: 01/14/2023] Open
Abstract
The aim of the study was to establish a nationwide barcode library for the most diverse group of Austrian Lepidoptera, the Noctuoidea, with 5 families (Erebidae, Euteliidae, Noctuidae, Nolidae, Notodontidae) and around 690 species. Altogether, 3431 DNA barcode sequences from COI gene (cytochrome c oxidase 1) belonging to 671 species were gathered, with 3223 sequences >500 bp. The intraspecific divergence with a mean of only 0.17% is low in most species whereas interspecific distances to the Nearest Neighbour are significantly higher with an average of 4.95%. Diagnostic DNA barcodes were obtained for 658 species. Only 13 species (1.9% of the Austrian Noctuoidea) cannot be reliably identified from their DNA barcode (Setina aurita/Setina irrorella, Conisania leineri/Conisania poelli, Photedes captiuncula/Photedes minima, Euxoa obelisca/Euxoa vitta/Euxoa tritici, Mesapamaea secalella/Mesapamea secalis, Amphipoea fucosa/Amphipoea lucens). A similarly high identification performance was achieved by the Barcode Index (BIN) system. 671 species of Austrian Noctuoidea, representing 3202 records with BINs, are assigned to a total of 678 BINs. The vast majority of 649 species is placed into a single BIN, with only 13 species recognised as BIN-sharing (including the barcode sharing species above). Twenty-one species were assigned to more than one BIN and have to be checked for cryptic diversity in the future.
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Affiliation(s)
- Peter Huemer
- Tiroler Landesmuseen Betriebsges.m.b.H., Innsbruck, Austria Tiroler Landesmuseen Betriebsges.m.b.H. Innsbruck Austria
| | - Christian Wieser
- Landesmuseum Kärnten, Klagenfurt am Wörthersee, Austria Landesmuseum Kärnten Klagenfurt am Wörthersee Austria
| | | | - Paul D N Hebert
- Biodiversity Institute of Ontario, Guelph, Canada Biodiversity Institute of Ontario Guelph Canada
| | - Benjamin Wiesmair
- Tiroler Landesmuseen Betriebsges.m.b.H., Innsbruck, Austria Tiroler Landesmuseen Betriebsges.m.b.H. Innsbruck Austria
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Braukmann TWA, Ivanova NV, Prosser SWJ, Elbrecht V, Steinke D, Ratnasingham S, de Waard JR, Sones JE, Zakharov EV, Hebert PDN. Metabarcoding a diverse arthropod mock community. Mol Ecol Resour 2019; 19:711-727. [PMID: 30779309 PMCID: PMC6850013 DOI: 10.1111/1755-0998.13008] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 02/13/2019] [Indexed: 12/31/2022]
Abstract
Although DNA metabarcoding is an attractive approach for monitoring biodiversity, it is often difficult to detect all the species present in a bulk sample. In particular, sequence recovery for a given species depends on its biomass and mitome copy number as well as the primer set employed for PCR. To examine these variables, we constructed a mock community of terrestrial arthropods comprised of 374 species. We used this community to examine how species recovery was impacted when amplicon pools were constructed in four ways. The first two protocols involved the construction of bulk DNA extracts from different body segments (Bulk Abdomen, Bulk Leg). The other protocols involved the production of DNA extracts from single legs which were then merged prior to PCR (Composite Leg) or PCR‐amplified separately (Single Leg) and then pooled. The amplicons generated by these four treatments were then sequenced on three platforms (Illumina MiSeq, Ion Torrent PGM and Ion Torrent S5). The choice of sequencing platform did not substantially influence species recovery, although the Miseq delivered the highest sequence quality. As expected, species recovery was most efficient from the Single Leg treatment because amplicon abundance varied little among taxa. Among the three treatments where PCR occurred after pooling, the Bulk Abdomen treatment produced a more uniform read abundance than the Bulk Leg or Composite Leg treatment. Primer choice also influenced species recovery and evenness. Our results reveal how variation in protocols can have substantial impacts on perceived diversity unless sequencing coverage is sufficient to reach an asymptote.
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Affiliation(s)
| | - Natalia V Ivanova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Sean W J Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Vasco Elbrecht
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Dirk Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada.,Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | | | - Jeremy R de Waard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada.,School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Jayme E Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Evgeny V Zakharov
- Centre for Biodiversity Genomics, 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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50
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Ashfaq M, Blagoev G, Tahir HM, Khan AM, Mukhtar MK, Akhtar S, Butt A, Mansoor S, Hebert PDN. Assembling a DNA barcode reference library for the spiders (Arachnida: Araneae) of Pakistan. PLoS One 2019; 14:e0217086. [PMID: 31116764 PMCID: PMC6530854 DOI: 10.1371/journal.pone.0217086] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/04/2019] [Indexed: 01/16/2023] Open
Abstract
Morphological study of 1,795 spiders from sites across Pakistan placed these specimens in 27 families and 202 putative species. COI sequences >400 bp recovered from 1,782 specimens were analyzed using neighbor-joining trees, Bayesian inference, barcode gap, and Barcode Index Numbers (BINs). Specimens of 109 morphological species were assigned to 123 BINs with ten species showing BIN splits, while 93 interim species included representatives of 98 BINs. Maximum conspecific divergences ranged from 0–5.3% while congeneric distances varied from 2.8–23.2%. Excepting one species pair (Oxyopes azhari–Oxyopes oryzae), the maximum intraspecific distance was always less than the nearest-neighbor (NN) distance. Intraspecific divergence values were not significantly correlated with geographic distance. Most (75%) BINs detected in this study were new to science, while those shared with other nations mainly derived from India. The discovery of many new, potentially endemic species and the low level of BIN overlap with other nations highlight the importance of constructing regional DNA barcode reference libraries.
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Affiliation(s)
- Muhammad Ashfaq
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- * E-mail:
| | - Gergin Blagoev
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Arif M. Khan
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | | | - Saleem Akhtar
- Directorate of Entomology, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Abida Butt
- Department of Zoology, University of the Punjab, Lahore, Pakistan
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
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