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Meier R, Hartop E, Pylatiuk C, Srivathsan A. Towards holistic insect monitoring: species discovery, description, identification and traits for all insects. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230120. [PMID: 38705187 PMCID: PMC11070263 DOI: 10.1098/rstb.2023.0120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 01/25/2024] [Indexed: 05/07/2024] Open
Abstract
Holistic insect monitoring needs scalable techniques to overcome taxon biases, determine species abundances, and gather functional traits for all species. This requires that we address taxonomic impediments and the paucity of data on abundance, biomass and functional traits. We here outline how these data deficiencies could be addressed at scale. The workflow starts with large-scale barcoding (megabarcoding) of all specimens from mass samples obtained at biomonitoring sites. The barcodes are then used to group the specimens into molecular operational taxonomic units that are subsequently tested/validated as species with a second data source (e.g. morphology). New species are described using barcodes, images and short diagnoses, and abundance data are collected for both new and described species. The specimen images used for species discovery then become the raw material for training artificial intelligence identification algorithms and collecting trait data such as body size, biomass and feeding modes. Additional trait data can be obtained from vouchers by using genomic tools developed by molecular ecologists. Applying this pipeline to a few samples per site will lead to greatly improved insect monitoring regardless of whether the species composition of a sample is determined with images, metabarcoding or megabarcoding. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.
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Affiliation(s)
- Rudolf Meier
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
- Institute of Biology, Humboldt University, 10115 Berlin, Germany
| | - Emily Hartop
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
| | - Christian Pylatiuk
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Amrita Srivathsan
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
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2
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Samreen KB, Manzoor F. Assessing arthropod biodiversity with DNA barcoding in Jinnah Garden, Lahore, Pakistan. PeerJ 2024; 12:e17420. [PMID: 38832046 PMCID: PMC11146329 DOI: 10.7717/peerj.17420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 04/28/2024] [Indexed: 06/05/2024] Open
Abstract
Previous difficulties in arthropod taxonomy (such as limitations in conventional morphological approaches, the possibility of cryptic species and a shortage of knowledgeable taxonomists) has been overcome by the powerful tool of DNA barcoding. This study presents a thorough analysis of DNA barcoding in regards to Pakistani arthropods, which were collected from Lahore's Jinnah Garden. The 88 % (9,451) of the 10,792 specimens that were examined were able to generate DNA barcodes and 83% (8,974) of specimens were assigned 1,361 barcode index numbers (BINs). However, the success rate differed significantly between the orders of arthropods, from 77% for Thysanoptera to an astounding 93% for Diptera. Through morphological exams, DNA barcoding, and cross-referencing with the Barcode of Life Data system (BOLD), the Barcode Index Numbers (BINs) were assigned with a high degree of accuracy, both at the order (100%) and family (98%) levels. Though, identifications at the genus (37%) and species (15%) levels showed room for improvement. This underscores the ongoing need for enhancing and expanding the DNA barcode reference library. This study identified 324 genera and 191 species, underscoring the advantages of DNA barcoding over traditional morphological identification methods. Among the 17 arthropod orders identified, Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera from the class Insecta dominated, collectively constituting 94% of BINs. Expected malaise trap Arthropod fauna in Jinnah Garden could contain approximately 2,785 BINs according to Preston log-normal species distribution, yet the Chao-1 Index predicts 2,389.74 BINs. The Simpson Index of Diversity (1-D) is 0.989, signaling high species diversity, while the Shannon Index is 5.77, indicating significant species richness and evenness. These results demonstrated that in Pakistani arthropods, DNA barcoding and BOLD are an invaluable tool for improving taxonomic understanding and biodiversity assessment, opening the door for further eDNA and metabarcoding research.
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Affiliation(s)
- Khush Bakhat Samreen
- Department of Zoology, Lahore College for Women University, Lahore, Lahore, Pakistan
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3
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Hussain A, Kakar A, Naseem M, Kamran K, Ullah Z, Shehla S, Obaid MK, Ahmed N, Khan Q, Liaqat I. Molecular identification of Hymenopteran insects collected by using Malaise traps from Hazarganji Chiltan National Park Quetta, Pakistan. PLoS One 2024; 19:e0300903. [PMID: 38598453 PMCID: PMC11006193 DOI: 10.1371/journal.pone.0300903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 03/05/2024] [Indexed: 04/12/2024] Open
Abstract
The order Hymenoptera holds great significance for humans, particularly in tropical and subtropical regions, due to its role as a pollinator of wild and cultivated flowering plants, parasites of destructive insects and honey producers. Despite this importance, limited attention has been given to the genetic diversity and molecular identification of Hymenopteran insects in most protected areas. This study provides insights into the first DNA barcode of Hymenopteran insects collected from Hazarganji Chiltan National Park (HCNP) and contributes to the global reference library of DNA barcodes. A total of 784 insect specimens were collected using Malaise traps, out of which 538 (68.62%) specimens were morphologically identified as Hymenopteran insects. The highest abundance of species of Hymenoptera (133/538, 24.72%) was observed during August and least in November (16/538, 2.97%). Genomic DNA extraction was performed individually from 90/538 (16.73%) morphologically identified specimens using the standard phenol-chloroform method, which were subjected separately to the PCR for their molecular confirmation via the amplification of cytochrome c oxidase subunit 1 (cox1) gene. The BLAST analyses of obtained sequences showed 91.64% to 100% identities with related sequences and clustered phylogenetically with their corresponding sequences that were reported from Australia, Bulgaria, Canada, Finland, Germany, India, Israel, and Pakistan. Additionally, total of 13 barcode index numbers (BINs) were assigned by Barcode of Life Data Systems (BOLD), out of which 12 were un-unique and one was unique (BOLD: AEU1239) which was assigned for Anthidium punctatum. This indicates the potential geographical variation of Hymenopteran population in HCNP. Further comprehensive studies are needed to molecularly confirm the existing insect species in HCNP and evaluate their impacts on the environment, both as beneficial (for example, pollination, honey producers and natural enemies) and detrimental (for example, venomous stings, crop damage, and pathogens transmission).
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Affiliation(s)
- Abid Hussain
- Department of Zoology, Faculty of Life Sciences, University of Balochistan, Balochistan, Pakistan
| | - Asmatullah Kakar
- Department of Zoology, Faculty of Life Sciences, University of Balochistan, Balochistan, Pakistan
| | - Mahrukh Naseem
- Department of Zoology, Faculty of Life Sciences, University of Balochistan, Balochistan, Pakistan
| | - Kashif Kamran
- Department of Zoology, Faculty of Life Sciences, University of Balochistan, Balochistan, Pakistan
| | - Zafar Ullah
- Department of Zoology, University of Loralai, Balochistan, Pakistan
| | - Shehla Shehla
- Department of Zoology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Kashif Obaid
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Nazeer Ahmed
- Balochistan University of Information Technology, Engineering and Management Sciences, Balochistan, Pakistan
| | - Qaiser Khan
- Department of Zoology, Faculty of Life Sciences, University of Balochistan, Balochistan, Pakistan
| | - Iram Liaqat
- Department of Zoology, Government College University, Lahore, Punjab, Pakistan
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Khan Q, Kakar A, Kamran K. New faunistic data on Diptera (Hexapoda, Insecta) from the Ziarat Juniperus forest ecosystem (Pakistan). Biodivers Data J 2024; 12:e114414. [PMID: 38566888 PMCID: PMC10985402 DOI: 10.3897/bdj.12.e114414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/08/2024] [Indexed: 04/04/2024] Open
Abstract
Background This study presents the first faunistic record and DNA barcoding for some Diptera species recorded from the Juniperus forest ecosystem of Balochistan, Pakistan. DNA barcoding was used to explore species diversity of Dipterans and collections carried out using a Malaise trap between December 2018 to December 2019. This process involved sequencing the 658 bp Cytochrome Oxidase I (COI) gene. New information Amongst the collected Diptera specimens, nine families were identified, representing 13 genera. These species include Atherigonasoccata (Rondani, 1871), Atherigonavaria (Schiner, 1868), Chironomusdorsalis (Meigen, 1818), Eupeodescorollae (Linnaeus, 1758), Eristalistenax (Linnaeus,1758), Goniaornata (Meigen, 1826), Luciliasericata (Meigen, 1826), Paragusquadrifasciatus (Linnaeus, 1758), Polleniarudis (Fabricius, 1794), Raviniapernix (Thompson, 1869), Sarcophagadux (Thompson, 1869), Trupaneaamoena (Schiner, 1868) and Wohlfahrtiabella (Linnaeus, 1758). The families Syrphidae and Sarcophagidae exhibited the highest representation, each comprising three genera and three species. They were followed by the family Muscidae, which had a single genus and two species. Anthomyiidae, Chironomidae, Calliphoridae, Polleniidae, Tachinidae and Tephritidae were represented by only one genus and one species. A nique Barcode Index Number (BIN) was allotted to Tachinidae (specie i.e Goniaornata). The results indicated that barcoding through cytochrome oxidase I is an effective approach for the accurate identification and genetic studies of Diptera species. This discovery highlights the significant diversity of this insect order in study region. Furthermore, a comprehensive list of other Diptera species remains elusive because of difficulties in distinguishing them, based on morphology and a lack of professional entomological knowledge.
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Affiliation(s)
- Qaiser Khan
- Department of Zoology, University of Balochistan, Quetta, PakistanDepartment of Zoology, University of BalochistanQuettaPakistan
| | - Asmathullah Kakar
- Department of Zoology, University of Balochistan, Quetta, PakistanDepartment of Zoology, University of BalochistanQuettaPakistan
| | - Kashif Kamran
- Department of Zoology, University of Balochistan, Quetta, PakistanDepartment of Zoology, University of BalochistanQuettaPakistan
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Srivathsan A, Ang Y, Heraty JM, Hwang WS, Jusoh WFA, Kutty SN, Puniamoorthy J, Yeo D, Roslin T, Meier R. Convergence of dominance and neglect in flying insect diversity. Nat Ecol Evol 2023; 7:1012-1021. [PMID: 37202502 PMCID: PMC10333119 DOI: 10.1038/s41559-023-02066-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 04/06/2023] [Indexed: 05/20/2023]
Abstract
Most of arthropod biodiversity is unknown to science. Consequently, it has been unclear whether insect communities around the world are dominated by the same or different taxa. This question can be answered through standardized sampling of biodiversity followed by estimation of species diversity and community composition with DNA barcodes. Here this approach is applied to flying insects sampled by 39 Malaise traps placed in five biogeographic regions, eight countries and numerous habitats (>225,000 specimens belonging to >25,000 species in 458 families). We find that 20 insect families (10 belonging to Diptera) account for >50% of local species diversity regardless of clade age, continent, climatic region and habitat type. Consistent differences in family-level dominance explain two-thirds of variation in community composition despite massive levels of species turnover, with most species (>97%) in the top 20 families encountered at a single site only. Alarmingly, the same families that dominate insect diversity are 'dark taxa' in that they suffer from extreme taxonomic neglect, with little signs of increasing activities in recent years. Taxonomic neglect tends to increase with diversity and decrease with body size. Identifying and tackling the diversity of 'dark taxa' with scalable techniques emerge as urgent priorities in biodiversity science.
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Affiliation(s)
- Amrita Srivathsan
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany
| | - Yuchen Ang
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore
| | - John M Heraty
- Department of Entomology, University of California, Riverside, CA, USA
| | - Wei Song Hwang
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore
| | - Wan F A Jusoh
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore
- School of Science, Monash University Malaysia, Subang Jaya, Malaysia
| | - Sujatha Narayanan Kutty
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Jayanthi Puniamoorthy
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Darren Yeo
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Rudolf Meier
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany.
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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Renkema JM, McFadden-Smith W, Chen S. Semi-Quantitative Detection of Drosophila suzukii (Diptera: Drosophilidae) From Bulk Trap Samples Using PCR Technology. JOURNAL OF ECONOMIC ENTOMOLOGY 2022; 115:990-998. [PMID: 35178553 DOI: 10.1093/jee/toab258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Indexed: 06/14/2023]
Abstract
Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) is a ubiquitous global pest of several fruit crops. Trapped adult numbers are used to monitor populations and make control decisions, but differentiating D. suzukii from other trapped Drosophila spp. is laborious. We developed a real-time PCR method for specific detection and semi-quantification of D. suzukii from trap samples. The PCR assay did not amplify DNA from 29 other Drosophilidae species tested. Drosophila suzukii was detected from ≥0.96 pg target DNA and from laboratory samples containing one D. suzukii in 2000 other Drosophila spp. flies. We tested DNA stability of one D. suzukii in 100 Drosophila spp. flies in water or ethanol at 20, 25, or 30°C for 1, 4, or 7 d. Only water at 30°C for 7 d fully impaired D. suzukii DNA detectability. Substituting mouthwash for water resulted in D. suzukii detection in all samples held for 7 d at 30°C or daily fluctuating temperatures of 33/23°C. Traps with mouthwash as a drowning liquid had D. suzukii captures equal to traps with water. A calibration curve was established using samples in mouthwash containing 1/1,000-100/1,000 D. suzukii/total Drosophila spp. flies and incubated at 25°C for 7 d. The curve had a coefficient of determination (R2) of 0.9279 between D. suzukii numbers from the PCR and the true D. suzukii numbers in samples prepared in 70% ethanol. Collecting samples in mouthwash is expected to improve detection accuracy, and the qPCR method can be a useful tool to support D. suzukii monitoring and management.
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Affiliation(s)
- Justin M Renkema
- London Research and Development Centre-Vineland Campus, Agriculture and Agri-Food Canada, Vineland Station, ON, Canada
| | - Wendy McFadden-Smith
- Vineland Resource Centre, Ontario Ministry of Agriculture Food and Rural Affairs, Vineland Station, ONCanada
| | - Shu Chen
- Agriculture and Food Laboratory, Laboratory Services Division, University of Guelph, Guelph, ON, Canada
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Arribas P, Andújar C, Bohmann K, deWaard JR, Economo EP, Elbrecht V, Geisen S, Goberna M, Krehenwinkel H, Novotny V, Zinger L, Creedy TJ, Meramveliotakis E, Noguerales V, Overcast I, Morlon H, Papadopoulou A, Vogler AP, Emerson BC. Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods. Gigascience 2022; 11:6646445. [PMID: 35852418 PMCID: PMC9295367 DOI: 10.1093/gigascience/giac065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 05/04/2022] [Accepted: 06/02/2022] [Indexed: 11/12/2022] Open
Abstract
Metazoan metabarcoding is emerging as an essential strategy for inventorying biodiversity, with diverse projects currently generating massive quantities of community-level data. The potential for integrating across such data sets offers new opportunities to better understand biodiversity and how it might respond to global change. However, large-scale syntheses may be compromised if metabarcoding workflows differ from each other. There are ongoing efforts to improve standardization for the reporting of inventory data. However, harmonization at the stage of generating metabarcode data has yet to be addressed. A modular framework for harmonized data generation offers a pathway to navigate the complex structure of terrestrial metazoan biodiversity. Here, through our collective expertise as practitioners, method developers, and researchers leading metabarcoding initiatives to inventory terrestrial biodiversity, we seek to initiate a harmonized framework for metabarcode data generation, with a terrestrial arthropod module. We develop an initial set of submodules covering the 5 main steps of metabarcode data generation: (i) sample acquisition; (ii) sample processing; (iii) DNA extraction; (iv) polymerase chain reaction amplification, library preparation, and sequencing; and (v) DNA sequence and metadata deposition, providing a backbone for a terrestrial arthropod module. To achieve this, we (i) identified key points for harmonization, (ii) reviewed the current state of the art, and (iii) distilled existing knowledge within submodules, thus promoting best practice by providing guidelines and recommendations to reduce the universe of methodological options. We advocate the adoption and further development of the terrestrial arthropod module. We further encourage the development of modules for other biodiversity fractions as an essential step toward large-scale biodiversity synthesis through harmonization.
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Affiliation(s)
- Paula Arribas
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206 San Cristóbal de la Laguna, Spain
| | - Carmelo Andújar
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206 San Cristóbal de la Laguna, Spain
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Jeremy R deWaard
- Centre for Biodiversity Genomics, University of Guelph, N1G2W1 Guelph, Canada.,School of Environmental Sciences, University of Guelph, N1G2W1 Guelph, Canada
| | - Evan P Economo
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, 904-0495 Japan
| | - Vasco Elbrecht
- Centre for Biodiversity Monitoring (ZBM), Zoological Research Museum Alexander Koenig,D-53113 Bonn, Germany
| | - Stefan Geisen
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Marta Goberna
- Department of Environment and Agronomy, INIA-CSIC, 28040 Madrid, Spain
| | | | - Vojtech Novotny
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, 37005 Ceske Budejovice, Czech Republic.,Faculty of Science, University of South Bohemia, 37005 Ceske Budejovice, Czech Republic
| | - Lucie Zinger
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France.,Naturalis Biodiversity Center, 2300 RA Leiden, The Netherlands
| | - Thomas J Creedy
- Department of Life Sciences, Natural History Museum, SW7 5BD London, UK
| | | | - Víctor Noguerales
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206 San Cristóbal de la Laguna, Spain
| | - Isaac Overcast
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Hélène Morlon
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Anna Papadopoulou
- Department of Biological Sciences, University of Cyprus, 1678 Nicosia, Cyprus
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, SW7 5BD London, UK.,Department of Life Sciences, Imperial College London, SW7 2AZ London, UK
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206 San Cristóbal de la Laguna, Spain
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Geissmann Q, Abram PK, Wu D, Haney CH, Carrillo J. Sticky Pi is a high-frequency smart trap that enables the study of insect circadian activity under natural conditions. PLoS Biol 2022; 20:e3001689. [PMID: 35797311 PMCID: PMC9262196 DOI: 10.1371/journal.pbio.3001689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 05/26/2022] [Indexed: 11/18/2022] Open
Abstract
In the face of severe environmental crises that threaten insect biodiversity, new technologies are imperative to monitor both the identity and ecology of insect species. Traditionally, insect surveys rely on manual collection of traps, which provide abundance data but mask the large intra- and interday variations in insect activity, an important facet of their ecology. Although laboratory studies have shown that circadian processes are central to insects' biological functions, from feeding to reproduction, we lack the high-frequency monitoring tools to study insect circadian biology in the field. To address these issues, we developed the Sticky Pi, a novel, autonomous, open-source, insect trap that acquires images of sticky cards every 20 minutes. Using custom deep learning algorithms, we automatically and accurately scored where, when, and which insects were captured. First, we validated our device in controlled laboratory conditions with a classic chronobiological model organism, Drosophila melanogaster. Then, we deployed an array of Sticky Pis to the field to characterise the daily activity of an agricultural pest, Drosophila suzukii, and its parasitoid wasps. Finally, we demonstrate the wide scope of our smart trap by describing the sympatric arrangement of insect temporal niches in a community, without targeting particular taxa a priori. Together, the automatic identification and high sampling rate of our tool provide biologists with unique data that impacts research far beyond chronobiology, with applications to biodiversity monitoring and pest control as well as fundamental implications for phenology, behavioural ecology, and ecophysiology. We released the Sticky Pi project as an open community resource on https://doc.sticky-pi.com.
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Affiliation(s)
- Quentin Geissmann
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver (Unceded xʼməθkʼəýəm Musqueam Territory), British Columbia, Canada
- * E-mail:
| | - Paul K. Abram
- Agriculture and Agri-Food Canada, Agassiz, British Columbia, Canada
| | - Di Wu
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver (Unceded xʼməθkʼəýəm Musqueam Territory), British Columbia, Canada
| | - Cara H. Haney
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Juli Carrillo
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver (Unceded xʼməθkʼəýəm Musqueam Territory), British Columbia, Canada
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9
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Kaczmarek M, Entling MH, Hoffmann C. Using Malaise Traps and Metabarcoding for Biodiversity Assessment in Vineyards: Effects of Weather and Trapping Effort. INSECTS 2022; 13:insects13060507. [PMID: 35735844 PMCID: PMC9224819 DOI: 10.3390/insects13060507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/16/2022]
Abstract
Metabarcoding is a powerful tool for ecological studies and monitoring that might provide a solution to the time-consuming taxonomic identification of the vast diversity of insects. Here, we assess how ambient weather conditions during Malaise trap exposure and the effort of trapping affect biomass and taxa richness in vineyards. Biomass varied by more than twofold with weather conditions. It increased with warmer and drier weather but was not significantly related with wind or precipitation. Taxa richness showed a saturating relationship with increasing trapping duration and was influenced by environmental and seasonal effects. Taxa accumulation was high, increasing fourfold from three days of monthly trap exposure compared to continuous trapping and nearly sixfold from sampling at a single site compared to 32 sites. The limited saturation was mainly due to a large number of singletons, such as rare species, in the metabarcoding dataset. Metabarcoding can be key for long-term insect monitoring. We conclude that single traps operated for up to ten days per month are suitable to monitor the presence of common species. However, more intensive trapping is necessary for a good representation of rare species in biodiversity monitoring. The data collected here can potentially guide the design of monitoring studies.
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Affiliation(s)
- Marvin Kaczmarek
- Julius Kühn Institute—Federal Research Institute for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Geilweilerhof, D-76833 Siebeldingen, Germany;
- Institute for Environmental Sciences—iES Landau, University of Koblenz-Landau, Fortstraße 7, D-76829 Landau in der Pfalz, Germany;
- Correspondence:
| | - Martin H. Entling
- Institute for Environmental Sciences—iES Landau, University of Koblenz-Landau, Fortstraße 7, D-76829 Landau in der Pfalz, Germany;
| | - Christoph Hoffmann
- Julius Kühn Institute—Federal Research Institute for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Geilweilerhof, D-76833 Siebeldingen, Germany;
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10
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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] [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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11
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DNA barcodes reveal striking arthropod diversity and unveil seasonal patterns of variation in the southern Atlantic Forest. PLoS One 2022; 17:e0267390. [PMID: 35482734 PMCID: PMC9049551 DOI: 10.1371/journal.pone.0267390] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 04/07/2022] [Indexed: 11/19/2022] Open
Abstract
The Atlantic Forest harbors 7% of global biodiversity and possesses high levels of endemism, but many of its component taxa remain unstudied. Due to the importance of tropical forests and the urgency to protect them, there is a compelling need to address this knowledge gap. To provide more information on its arthropod fauna, a Malaise trap was deployed for 12 months in a semi-degraded area of the southern Upper Paraná ecoregion of the Atlantic Forest. All specimens were DNA barcoded and the Barcode Index Number (BIN) system was employed to assign each specimen to a species proxy. DNA barcodes were obtained from 75,500 arthropods that included representatives of 8,651 BINs. Nearly 81% of these BINs were first records, highlighting the high rates of endemism and lack of study of arthropods from the Atlantic Forest. Diptera was the most abundant order, followed by Hemiptera, Lepidoptera and Hymenoptera. Diptera was also the most species-rich order, followed by Hymenoptera, Lepidoptera, and Coleoptera, a result consistent with studies in other biogeographic regions. Insects were most abundant in winter and most diverse in autumn and winter. This pattern, however, was caused mainly by the dynamics of dipteran diversity as other orders differed in their seasonal variation. The BIN composition of the insect community varied sharply through the year and also differed between the two consecutive summers included in the sampling period. The study of the 38 commonest BINs showed that seasonal patterns of abundance were not order-specific. Temperature had the strongest impact on seasonal abundance variation. Our results highlight the striking and understudied arthropod diversity of the highly fragmented Atlantic Forest, the predominance of dipterans, and the fact that abundance and richness in this insect community peak in the coolest months. Standardized studies like this generate fast and reliable biodiversity inventories and unveil ecological patterns, thus providing valuable information for conservation programs.
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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] [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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Boucher S, Savage J. DNA barcoding of the leaf-miner flies (Diptera, Agromyzidae) of Mitaraka, French Guiana. Zookeys 2022; 1083:147-168. [PMID: 35115876 PMCID: PMC8807582 DOI: 10.3897/zookeys.1083.76651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 01/05/2022] [Indexed: 11/17/2022] Open
Abstract
Species level identification of Agromyzidae based on morphology is often challenging due to their small size and morphological homogeneity. DNA barcoding has been used regularly to assist with the identification of economically important species of Agromyzidae, but rarely as a tool for species delineation or identification in biodiversity surveys. The main objective of this study was to investigate whether DNA barcoding and the BIN (Barcoding Index) system could assist with species identification, species delineation, male/ female association, and diversity assessment of Agromyzidae material previously determined to morphospecies from Mitaraka, French Guiana. Amplification success was low, with sequences over 400 bp recovered for only 24 (48%) of the selected specimens. Sequences assigned to 17 morphospecies formed 16 distinct branches or clusters separated by very high (minimum of 10%) sequence divergence. Following the reassessment and subsequent reassignment of one specimen, congruence between morphology and DNA barcodes was high with a single instance of two morphospecies sharing identical sequences. While DNA barcoding did not assist with identification (none of our sequences matched those of named taxa in BOLD or GenBank), it did provide support for most of our morphospecies concepts, including male/female associations. The BIN system also provided access to information about the distribution and habitat preferences of several taxa. We conclude that DNA barcoding was a useful approach to study the species diversity of our samples but that much work remains to be done before it can be used as an identification tool for the Agromyzidae fauna of Mitaraka and the rest of the Neotropical region.
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Affiliation(s)
- Stéphanie Boucher
- Department of Natural Resource Sciences, McGill University, Macdonald Campus, Ste-Anne-de-Bellevue, H9X 3V9, Quebec, CanadaMcGill UniversityQuebecCanada
| | - Jade Savage
- Bishop’s University, Sherbrooke, J1M 1Z7, Quebec, CanadaBishop’s UniversitySherbrookeCanada
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14
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Schneider S, Taylor GW, Kremer SC, Burgess P, McGroarty J, Mitsui K, Zhuang A, deWaard JR, Fryxell JM. Bulk arthropod abundance, biomass and diversity estimation using deep learning for computer vision. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13769] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | | | - Kyomi Mitsui
- Integrative Biology University of Guelph Guelph ON Canada
| | - Alex Zhuang
- Computer Science University of Toronto Toronto ON Canada
| | - Jeremy R. deWaard
- Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
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15
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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] [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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16
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Creedy TJ, Andújar C, Meramveliotakis E, Noguerales V, Overcast I, Papadopoulou A, Morlon H, Vogler AP, Emerson BC, Arribas P. Coming of age for COI metabarcoding of whole organism community DNA: Towards bioinformatic harmonisation. Mol Ecol Resour 2021; 22:847-861. [PMID: 34496132 PMCID: PMC9292290 DOI: 10.1111/1755-0998.13502] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/28/2021] [Accepted: 08/23/2021] [Indexed: 11/26/2022]
Abstract
Metabarcoding of DNA extracted from community samples of whole organisms (whole organism community DNA, wocDNA) is increasingly being applied to terrestrial, marine and freshwater metazoan communities to provide rapid, accurate and high resolution data for novel molecular ecology research. The growth of this field has been accompanied by considerable development that builds on microbial metabarcoding methods to develop appropriate and efficient sampling and laboratory protocols for whole organism metazoan communities. However, considerably less attention has focused on ensuring bioinformatic methods are adapted and applied comprehensively in wocDNA metabarcoding. In this study we examined over 600 papers and identified 111 studies that performed COI metabarcoding of wocDNA. We then systematically reviewed the bioinformatic methods employed by these papers to identify the state‐of‐the‐art. Our results show that the increasing use of wocDNA COI metabarcoding for metazoan diversity is characterised by a clear absence of bioinformatic harmonisation, and the temporal trends show little change in this situation. The reviewed literature showed (i) high heterogeneity across pipelines, tasks and tools used, (ii) limited or no adaptation of bioinformatic procedures to the nature of the COI fragment, and (iii) a worrying underreporting of tasks, software and parameters. Based upon these findings we propose a set of recommendations that we think the metabarcoding community should consider to ensure that bioinformatic methods are appropriate, comprehensive and comparable. We believe that adhering to these recommendations will improve the long‐term integrative potential of wocDNA COI metabarcoding for biodiversity science.
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Affiliation(s)
- Thomas J Creedy
- Department of Life Sciences, Natural History Museum, London, UK
| | - Carmelo Andújar
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), S.C. La Laguna, Spain
| | | | - Victor Noguerales
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), S.C. La Laguna, Spain.,Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Isaac Overcast
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieur, CNRS, INSERM, Université PSL, Paris, France
| | - Anna Papadopoulou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Hélène Morlon
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieur, CNRS, INSERM, Université PSL, Paris, France
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK.,Department of Life Sciences, Imperial College London Silwood Park Campus, Ascot, UK
| | - Brent C Emerson
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), S.C. La Laguna, Spain
| | - Paula Arribas
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), S.C. La Laguna, Spain
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Pantoja C, Faltýnková A, O'Dwyer K, Jouet D, Skírnisson K, Kudlai O. Diversity of echinostomes (Digenea: Echinostomatidae) in their snail hosts at high latitudes. ACTA ACUST UNITED AC 2021; 28:59. [PMID: 34319230 PMCID: PMC8336728 DOI: 10.1051/parasite/2021054] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/24/2021] [Indexed: 11/14/2022]
Abstract
The biodiversity of freshwater ecosystems globally still leaves much to be discovered, not least in the trematode parasite fauna they support. Echinostome trematode parasites have complex, multiple-host life-cycles, often involving migratory bird definitive hosts, thus leading to widespread distributions. Here, we examined the echinostome diversity in freshwater ecosystems at high latitude locations in Iceland, Finland, Ireland and Alaska (USA). We report 14 echinostome species identified morphologically and molecularly from analyses of nad1 and 28S rDNA sequence data. We found echinostomes parasitising snails of 11 species from the families Lymnaeidae, Planorbidae, Physidae and Valvatidae. The number of echinostome species in different hosts did not vary greatly and ranged from one to three species. Of these 14 trematode species, we discovered four species (Echinoparyphium sp. 1, Echinoparyphium sp. 2, Neopetasiger sp. 5, and Echinostomatidae gen. sp.) as novel in Europe; we provide descriptions for the newly recorded species and those not previously associated with DNA sequences. Two species from Iceland (Neopetasiger islandicus and Echinoparyphium sp. 2) were recorded in both Iceland and North America. All species found in Ireland are new records for this country. Via an integrative taxonomic approach taken, both morphological and molecular data are provided for comparison with future studies to elucidate many of the unknown parasite life cycles and transmission routes. Our reports of species distributions spanning Europe and North America highlight the need for parasite biodiversity assessments across large geographical areas.
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Affiliation(s)
- Camila Pantoja
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic - Institute of Ecology, Nature Research Centre, Akademijos 2, 08412 Vilnius, Lithuania
| | - Anna Faltýnková
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Katie O'Dwyer
- Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, H91 T8NW Galway, Ireland
| | - Damien Jouet
- BioSpecT EA7506, Faculty of Pharmacy, University of Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51096 Reims Cedex, France
| | - Karl Skírnisson
- Laboratory of Parasitology, Institute for Experimental Pathology, Keldur, University of Iceland, IS-112 Reykjavík, Iceland
| | - Olena Kudlai
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic - Institute of Ecology, Nature Research Centre, Akademijos 2, 08412 Vilnius, Lithuania
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Elbrecht V, Lindner A, Manerus L, Steinke D. A bright idea-metabarcoding arthropods from light fixtures. PeerJ 2021; 9:e11841. [PMID: 34395083 PMCID: PMC8320520 DOI: 10.7717/peerj.11841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/01/2021] [Indexed: 11/28/2022] Open
Abstract
Arthropod communities in buildings have not been extensively studied, although humans have always shared their homes with them. In this study we explored if arthropod DNA can be retrieved and metabarcoded from indoor environments through the collection of dead specimens in light fixtures to better understand what shapes arthropod diversity in our homes. Insects were collected from 45 light fixtures at the Centre for Biodiversity Genomics (CBG, Guelph, Canada), and by community scientists at 12 different residential homes in Southern Ontario. The CBG ground floor of the CBG showed the greatest arthropod diversity, especially in light fixtures that were continuously illuminated. The community scientist samples varied strongly by light fixture type, lightbulb used, time passed since lamp was last cleaned, and specimen size. In all cases, the majority of OTUs was not shared between samples even within the same building. This study demonstrates that light fixtures might be a useful resource to determine arthropod diversity in our homes, but individual samples are likely not representative of the full diversity.
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Affiliation(s)
- Vasco Elbrecht
- Department of Environmental Systems Science Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zurich, Zurich, Switzerland
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Angie Lindner
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Laura Manerus
- 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
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Steinke D, Braukmann TWA, Manerus L, Woodhouse A, Elbrecht V. Effects of Malaise trap spacing on species richness and composition of terrestrial arthropod bulk samples. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.59201] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Malaise trap is a popular device for assessing diverse terrestrial arthropod communities because it collects large samples with modest effort. A number of factors influence its collection efficiency, placement being one of them. For instance, when designing larger biotic surveys using arrays of Malaise traps we need to know the optimal distance between individual traps that maximises observable species richness and community composition. We examined the influence of spacing between Malaise traps by metabarcoding samples from two field experiments at a site in Waterloo, Ontario, Canada. For one experiment, we used two trap pairs deployed at weekly increasing distances (3 m increments from 3 to 30 m). The second experiment involved a total of 10 traps set up in a row at 3 m distance intervals for three consecutive weeks.
Results show that community similarity of samples decreases over distance between traps. The amount of species shared between trap pairs drops considerably at about 18 m trap-to-trap distance. This change can be observed across all major taxonomic groups and for two different habitat types (grassland and forest). Large numbers of OTUs found only once within samples cause rather large dissimilarity between distance pairs even at close proximity. This could be caused by a large number of transient species from adjacent habitats which arrive at the trap through passive transport, as well as capture of rare taxa, which end up in different traps by chance.
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20
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Orta-Pineda G, Abella-Medrano CA, Suzán G, Serrano-Villagrana A, Ojeda-Flores R. Effects of landscape anthropization on sylvatic mosquito assemblages in a rainforest in Chiapas, Mexico. Acta Trop 2021; 216:105849. [PMID: 33524383 DOI: 10.1016/j.actatropica.2021.105849] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 01/22/2021] [Accepted: 01/23/2021] [Indexed: 12/14/2022]
Abstract
Global change and ecosystem transformation at regional and local scales during recent decades have facilitated the exponential increase of outbreaks of mosquito-borne diseases. Mosquito-borne pathogens are responsible for millions of infections, mainly in tropical regions where marginalized human populations are located, and where in recent years processes of landscape anthropization have occurred. Anthropogenic landscape transformation is known to change species assemblages. However, the magnitude of these effects is largely unknown, and the effects of anthropogenic landscape transformation on sylvatic mosquito assemblages are poorly known in Mexican ecosystems. We evaluate how mosquito abundance, richness, and diversity change along a gradient of three human-modified landscapes-one highly anthropized, one moderately anthropized, and one slightly anthropized-within a tropical forest matrix in a Protected Natural Area in Chiapas. A total of 4 538 mosquitoes belonging to 23 species were captured and identified at the three sites. We found differences in the structure and abundance of the three mosquito assemblages. The species assemblage of the highly anthropized site was significantly different from the other sites, and the relative abundance of the assemblages increased with landscape anthropization. Our results suggest that landscape anthropization alters the composition and structure of mosquito assemblages, modifying the abundance and species richness of mosquitoes associated with sylvatic ecosystems. This could support the hypothesis of intermediate disturbance that suggests the diversity is maximized when late and early successional species coexist in these ecosystems. This information is essential to understand the ecology of potential sylvatic vectors and the environmental factors that are involved in the emergence and re-emergence of mosquito-borne diseases.
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Magoga G, Fontaneto D, Montagna M. Factors affecting the efficiency of molecular species delimitation in a species-rich insect family. Mol Ecol Resour 2021; 21:1475-1489. [PMID: 33565247 DOI: 10.1111/1755-0998.13352] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/19/2021] [Accepted: 02/03/2021] [Indexed: 11/28/2022]
Abstract
In the context of global biodiversity loss, molecular species delimitation approaches can be very useful for accelerating species discovery through DNA taxonomy and inventory through DNA metabarcoding. In this study, the effect of some intrinsic factors on the efficiency of various single-marker species delimitation methods (fixed and variable nucleotide distance thresholds, ABGD, ASAP, GMYC, mPTP) was tested on more than 90 empirical data sets, derived from a set of 7,237 COI sequences attributed to 542 leaf beetles species (Coleoptera: Chrysomelidae). The considered factors were: (i) the number of haplotypes per species (as a proxy for genetic diversity), (ii) the geographic distance among conspecific collection localities (as a proxy of sampling width), (iii) the difficulty related to morphological identification of species, and (iv) the taxonomic rank. Distance-based methods, with on average more than 70% of match with morphological identification, outperformed those relying on phylogenetic trees, with less than 59%. A high number of haplotypes per species was found to have a negative effect on delimitation efficiency, whereas large geographic distances within species had a positive effect. All methods delimitations (except for GMYC) were significantly affected by the presence of species that are difficult to be identified, decreasing their efficiency. Finally, the only method influenced by the taxonomic rank of the data set was GMYC, showing lower efficiency in data sets at the genus than at higher levels. The observed biases we highlighted affecting efficiency could be accounted for when developing input data sets for species delimitation analyses to obtain a more reliable representation of biological diversity.
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Affiliation(s)
- Giulia Magoga
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Diego Fontaneto
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Ricerca Sulle Acque (IRSA), Molecular Ecology Group (MEG), Verbania, Italy
| | - Matteo Montagna
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milano, Italy.,BAT Center - Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Napoli "Federico II", Portici, Italy
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22
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Arribas P, Andújar C, Bidartondo MI, Bohmann K, Coissac É, Creer S, deWaard JR, Elbrecht V, Ficetola GF, Goberna M, Kennedy S, Krehenwinkel H, Leese F, Novotny V, Ronquist F, Yu DW, Zinger L, Creedy TJ, Meramveliotakis E, Noguerales V, Overcast I, Morlon H, Vogler AP, Papadopoulou A, Emerson BC. Connecting high-throughput biodiversity inventories: Opportunities for a site-based genomic framework for global integration and synthesis. Mol Ecol 2021; 30:1120-1135. [PMID: 33432777 PMCID: PMC7986105 DOI: 10.1111/mec.15797] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 12/21/2020] [Accepted: 01/05/2021] [Indexed: 01/03/2023]
Abstract
High-throughput sequencing (HTS) is increasingly being used for the characterization and monitoring of biodiversity. If applied in a structured way, across broad geographical scales, it offers the potential for a much deeper understanding of global biodiversity through the integration of massive quantities of molecular inventory data generated independently at local, regional and global scales. The universality, reliability and efficiency of HTS data can potentially facilitate the seamless linking of data among species assemblages from different sites, at different hierarchical levels of diversity, for any taxonomic group and regardless of prior taxonomic knowledge. However, collective international efforts are required to optimally exploit the potential of site-based HTS data for global integration and synthesis, efforts that at present are limited to the microbial domain. To contribute to the development of an analogous strategy for the nonmicrobial terrestrial domain, an international symposium entitled "Next Generation Biodiversity Monitoring" was held in November 2019 in Nicosia (Cyprus). The symposium brought together evolutionary geneticists, ecologists and biodiversity scientists involved in diverse regional and global initiatives using HTS as a core tool for biodiversity assessment. In this review, we summarize the consensus that emerged from the 3-day symposium. We converged on the opinion that an effective terrestrial Genomic Observatories network for global biodiversity integration and synthesis should be spatially led and strategically united under the umbrella of the metabarcoding approach. Subsequently, we outline an HTS-based strategy to collectively build an integrative framework for site-based biodiversity data generation.
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Affiliation(s)
- Paula Arribas
- Island Ecology and Evolution Research GroupInstituto de Productos Naturales y Agrobiología (IPNA‐CSIC)San Cristóbal de la LagunaSpain
| | - Carmelo Andújar
- Island Ecology and Evolution Research GroupInstituto de Productos Naturales y Agrobiología (IPNA‐CSIC)San Cristóbal de la LagunaSpain
| | - Martin I. Bidartondo
- Department of Life SciencesImperial College LondonLondonUK
- Comparative Plant and Fungal BiologyRoyal Botanic GardensLondonUK
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Éric Coissac
- Université Grenoble Alpes, CNRS, Université Savoie Mont BlancLECA, Laboratoire d’Ecologie AlpineGrenobleFrance
| | - Simon Creer
- School of Natural SciencesBangor UniversityGwyneddUK
| | - Jeremy R. deWaard
- Centre for Biodiversity GenomicsUniversity of GuelphGuelphCanada
- School of Environmental SciencesUniversity of GuelphGuelphCanada
| | - Vasco Elbrecht
- Centre for Biodiversity Monitoring (ZBM)Zoological Research Museum Alexander KoenigBonnGermany
| | - Gentile F. Ficetola
- Université Grenoble Alpes, CNRS, Université Savoie Mont BlancLECA, Laboratoire d’Ecologie AlpineGrenobleFrance
- Department of Environmental Sciences and PolicyUniversity of MilanoMilanoItaly
| | - Marta Goberna
- Department of Environment and AgronomyINIAMadridSpain
| | - Susan Kennedy
- Biodiversity and Biocomplexity UnitOkinawa Institute of Science and Technology Graduate UniversityOnna‐sonJapan
- Department of BiogeographyTrier UniversityTrierGermany
| | | | - Florian Leese
- Aquatic Ecosystem Research, Faculty of BiologyUniversity of Duisburg‐EssenEssenGermany
- Centre for Water and Environmental Research (ZWU) EssenUniversity of Duisburg‐EssenEssenGermany
| | - Vojtech Novotny
- Biology Centre, Institute of EntomologyCzech Academy of SciencesCeske BudejoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaCeske BudejoviceCzech Republic
| | - Fredrik Ronquist
- Department of Bioinformatics and GeneticsSwedish Museum of Natural HistoryStockholmSweden
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | - Lucie Zinger
- Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERMUniversité PSLParisFrance
| | | | | | | | - Isaac Overcast
- Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERMUniversité PSLParisFrance
- Division of Vertebrate ZoologyAmerican Museum of Natural HistoryNew YorkUSA
| | - Hélène Morlon
- Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERMUniversité PSLParisFrance
| | - Alfried P. Vogler
- Department of Life SciencesImperial College LondonLondonUK
- Department of Life SciencesNatural History MuseumLondonUK
| | | | - Brent C. Emerson
- Island Ecology and Evolution Research GroupInstituto de Productos Naturales y Agrobiología (IPNA‐CSIC)San Cristóbal de la LagunaSpain
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Pumkaeo P, Takahashi J, Iwahashi H. Detection and monitoring of insect traces in bioaerosols. PeerJ 2021; 9:e10862. [PMID: 33614291 PMCID: PMC7879950 DOI: 10.7717/peerj.10862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/08/2021] [Indexed: 11/20/2022] Open
Abstract
Studies on bioaerosols have primarily focused on their chemical and biological compositions and their impact on public health and the ecosystem. However, most bioaerosol studies have only focused on viruses, bacteria, fungi, and pollen. To assess the diversity and composition of airborne insect material in particulate matter (PM) for the first time, we attempted to detect DNA traces of insect origin in dust samples collected over a two-year period. These samples were systematically collected at one-month intervals and categorized into two groups, PM2.5 and PM10, based on the aerodynamic diameter of the aerosol particles. Cytochrome-c oxidase I (COI) was the barcoding region used to identify the origins of the extracted DNA. The airborne insect community in these samples was analyzed using the Illumina MiSeq platform. The most abundant insect sequences belonged to the order Hemiptera (true bugs), whereas order Diptera were also detected in both PM2.5 and PM10 samples. Additionally, we inferred the presence of particulates of insect origin, such as brochosomes and integument particles, using scanning electron microscopy (SEM). This provided additional confirmation of the molecular results. In this study, we demonstrated the benefits of detection and monitoring of insect information in bioaerosols for understanding the source and composition. Our results suggest that the PM2.5 and PM10 groups are rich in insect diversity. Lastly, the development of databases can improve the identification accuracy of the analytical results.
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Affiliation(s)
- Panyapon Pumkaeo
- Division of Science of Biological Resources, United Graduate School of Agricultural Science, Gifu University, Gifu, 1-1 Yanagido, Japan
| | - Junko Takahashi
- National Institute of Advanced Industrial Science and Technology (AIST), Health and Medical Research Institute, Tsukuba, Ibaraki, Japan
| | - Hitoshi Iwahashi
- Department of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Gifu, 1-1 Yanagido, Japan
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Young RG, Milián‐García Y, Yu J, Bullas‐Appleton E, Hanner RH. Biosurveillance for invasive insect pest species using an environmental DNA metabarcoding approach and a high salt trap collection fluid. Ecol Evol 2021; 11:1558-1569. [PMID: 33613989 PMCID: PMC7882945 DOI: 10.1002/ece3.7113] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/05/2020] [Accepted: 11/13/2020] [Indexed: 12/27/2022] Open
Abstract
With the increase in global trade and warming patterns, the movement, introduction, and establishment of non-native insect species has increased. A rapid and effective early detection biosurveillance program to identify species of concern is needed to reduce future impacts and costs associated with introduced non-native species. One of the challenges facing insect surveillance trapping methods is the sheer volume of individual specimens in the collections. Although molecular identification methods are improving, they currently have limitations (e.g., destructive processing of specimens) and a protocol addressing these limitations can support regulatory applications that need morphological evidence to corroborate molecular data.The novel protocol presented here uses a metabarcoding approach to amplify environmental DNA from a saturated salt solution trap fluid, which retains trap specimens for downstream morphological identifications. The use of a saturated salt solution to preserve specimens in traps addresses issues with the high evaporation rate of ethanol in traps, and public safety concerns with other fluid preservation options with unattended traps in public settings.Using a metabarcoding approach, a 407-nucleotide segment of the cytochrome c oxidase subunit 1 (COI) animal barcode region was successfully amplified from Lindgren funnel trap collection fluids. These traps were placed in forested areas to survey for wood-boring beetles of regulatory concern. Our results displayed successful amplification of target taxa, including the molecular identification of the Japanese Beetle Popillia japonica, a species regulated in Canada. A second species, Anisandrus maiche, recently introduced to North America, was identified in every trap. The genus Lymantria, which contains numerous species of concern to North American woodlands, was also detected. Also, there were six other species identified of interest due to their potential impacts on native and crop flora and fauna.Our results show how this protocol can be used as an efficient method for the surveillance of insects using a trap with a saturated salt solution and eDNA metabarcoding to detect species of regulatory concern.
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Affiliation(s)
- Robert G. Young
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | | | - Jaeju Yu
- Animal BiosciencesUniversity of GuelphGuelphONCanada
| | | | - Robert H. Hanner
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
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25
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Basset Y, Donoso DA, Hajibabaei M, Wright MTG, Perez KHJ, Lamarre GPA, De León LF, Palacios-Vargas JG, Castaño-Meneses G, Rivera M, Perez F, Bobadilla R, Lopez Y, Ramirez JA, Barrios H. Methodological considerations for monitoring soil/litter arthropods in tropical rainforests using DNA metabarcoding, with a special emphasis on ants, springtails and termites. METABARCODING AND METAGENOMICS 2020. [DOI: 10.3897/mbmg.4.58572] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Robust data to refute or support claims of global insect decline are currently lacking, particularly for the soil fauna in the tropics. DNA metabarcoding represents a powerful approach for rigorous spatial and temporal monitoring of the taxonomically challenging soil fauna. Here, we provide a detailed field protocol, which was successfully applied in Barro Colorado Island (BCI) in Panama, to collect soil samples and arthropods in a tropical rainforest, to be later processed with metabarcoding. We also estimate the proportion of soil/litter ant, springtail and termite species from the local fauna that can be detected by metabarcoding samples obtained either from Berlese-Tullgren (soil samples), Malaise or light traps. Each collecting method detected a rather distinct fauna. Soil and Malaise trap samples detected 213 species (73%) of all target species. Malaise trap samples detected many ant species, whereas soil samples were more efficient at detecting springtail and termite species. With respect to long-term monitoring of soil-dwelling and common species (more amenable to statistical trends), the best combination of two methods were soil and light trap samples, detecting 94% of the total of common species. A protocol including 100 soil, 40 Malaise and 80 light trap samples annually processed by metabarcoding would allow the long-term monitoring of at least 11%, 18% and 16% of species of soil/litter ants, springtails and termites, respectively, present on BCI, and a high proportion of the total abundance (up to 80% of all individuals) represented by these taxa.
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Salvi D, Berrilli E, D'Alessandro P, Biondi M. Sharpening the DNA barcoding tool through a posteriori taxonomic validation: The case of Longitarsus flea beetles (Coleoptera: Chrysomelidae). PLoS One 2020; 15:e0233573. [PMID: 32437469 PMCID: PMC7241800 DOI: 10.1371/journal.pone.0233573] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/07/2020] [Indexed: 11/30/2022] Open
Abstract
The accuracy of the DNA barcoding tool depends on the existence of a comprehensive archived library of sequences reliably determined at species level by expert taxonomists. However, misidentifications are not infrequent, especially following large-scale DNA barcoding campaigns on diverse and taxonomically complex groups. In this study we used the species-rich flea beetle genus Longitarsus, that requires a high level of expertise for morphological species identification, as a case study to assess the accuracy of the DNA barcoding tool following several optimization procedures. We built a cox1 reference database of 1502 sequences representing 78 Longitarsus species, among which 117 sequences (32 species) were newly generated using a non-invasive DNA extraction method that allows keeping reference voucher specimens. Within this dataset we identified 69 taxonomic inconsistencies using barcoding gap analysis and tree topology methods. Threshold optimisation and a posteriori taxonomic revision based on newly generated reference sequences and metadata allowed resolving 44 sequences with ambiguous and incorrect identification and provided a significant improvement of the DNA barcoding accuracy and identification efficacy. Unresolved taxonomic uncertainties, due to overlapping intra- and inter-specific levels of divergences, mainly regards the Longitarsus pratensis species complex and polyphyletic groups L. melanocephalus, L. nigrofasciatus and L. erro. Such type of errors indicates either poorly established taxonomy or any biological processes that make mtDNA groups poorly predictive of species boundaries (e.g. recent speciation or interspecific hybridisation), thus providing directions for further integrative taxonomic and evolutionary studies. Overall, this study underlines the importance of reference vouchers and high-quality metadata associated to sequences in reference databases and corroborates, once again, the key role of taxonomists in any step of the DNA barcoding pipeline in order to generate and maintain a correct and functional reference library.
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Affiliation(s)
- Daniele Salvi
- Department of Health, Life and Environmental Sciences, University of L'Aquila, Coppito, L'Aquila, Italy
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Emanuele Berrilli
- Department of Health, Life and Environmental Sciences, University of L'Aquila, Coppito, L'Aquila, Italy
| | - Paola D'Alessandro
- Department of Health, Life and Environmental Sciences, University of L'Aquila, Coppito, L'Aquila, Italy
| | - Maurizio Biondi
- Department of Health, Life and Environmental Sciences, University of L'Aquila, Coppito, L'Aquila, Italy
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27
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Tan MH, Gan HM, Lee YP, Grandjean F, Croft LJ, Austin CM. A Giant Genome for a Giant Crayfish ( Cherax quadricarinatus) With Insights Into cox1 Pseudogenes in Decapod Genomes. Front Genet 2020; 11:201. [PMID: 32211032 PMCID: PMC7069360 DOI: 10.3389/fgene.2020.00201] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 02/20/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Mun Hua Tan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, VIC, Australia
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Han Ming Gan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, VIC, Australia
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Yin Peng Lee
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, VIC, Australia
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Frederic Grandjean
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267 Equipe Ecologie Evolution Symbiose, Poitiers, France
| | - Laurence J. Croft
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, VIC, Australia
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Christopher M. Austin
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, VIC, Australia
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
- School of Science, Monash University Malaysia, Petaling Jaya, Malaysia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Petaling Jaya, Malaysia
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Garces JM, Sartori M, Freitag H. Integrative taxonomy of the genus Dudgeodes Sartori, 2008 (Insecta, Ephemeroptera, Teloganodidae) from the Philippines with description of new species and supplementary descriptions of Southeast Asian species. Zookeys 2020; 910:93-129. [PMID: 32099517 PMCID: PMC7026199 DOI: 10.3897/zookeys.910.48659] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 01/05/2020] [Indexed: 11/12/2022] Open
Abstract
COI sequences were used as an initial clustering method to delimit putative species of the genus Dudgeodes in the Philippines. An overview of the diagnostic characters of Philippine species and characters with high intraspecific variability are given. Six new species of Dudgeodes are described and illustrated: D. bauernfeindi Garces & Sartori, sp. nov., D. freitagi Garces & Sartori, sp. nov., D. luntian Garces & Sartori, sp. nov., D. pangantihoni Garces & Sartori, sp. nov., D. tabang Garces & Sartori, sp. nov., and D. vonrinteleni Garces & Sartori, sp. nov., all known from the nymphal stage. Supplementary descriptions are provided for D. pescadori Sartori, 2008, D. hutanis Sartori, 2008, D. stephani Sartori, 2008, D. ulmeri Sartori, 2008, and D. celebensis Sartori, 2008. A key to the nymphs of Philippine Dudgeodes species is proposed.
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Affiliation(s)
- Jhoana M. Garces
- Department of Biology, School of Science and Engineering, Ateneo de Manila University, Quezon City, PhilippinesAteneo de Manila UniversityQuezon CityPhilippines
| | - Michel Sartori
- Museum of Zoology, Palais de Rumine, Place Riponne 6, CH-1014 Lausanne, SwitzerlandMuseum of ZoologyLausanneSwitzerland
- Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, SwitzerlandUniversity of LausanneLausanneSwitzerland
| | - Hendrik Freitag
- Department of Biology, School of Science and Engineering, Ateneo de Manila University, Quezon City, PhilippinesAteneo de Manila UniversityQuezon CityPhilippines
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A DNA Barcoding Survey of an Arctic Arthropod Community: Implications for Future Monitoring. INSECTS 2020; 11:insects11010046. [PMID: 31936447 PMCID: PMC7023425 DOI: 10.3390/insects11010046] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 12/20/2019] [Accepted: 01/06/2020] [Indexed: 12/02/2022]
Abstract
Accurate and cost-effective methods for tracking changes in arthropod communities are needed to develop integrative environmental monitoring programs in the Arctic. To date, even baseline data on their species composition at established ecological monitoring sites are severely lacking. We present the results of a pilot assessment of non-marine arthropod diversity in a middle arctic tundra area near Ikaluktutiak (Cambridge Bay), Victoria Island, Nunavut, undertaken in 2018 using DNA barcodes. A total of 1264 Barcode Index Number (BIN) clusters, used as a proxy for species, were recorded. The efficacy of widely used sampling methods was assessed. Yellow pan traps captured 62% of the entire BIN diversity at the study sites. When complemented with soil and leaf litter sifting, the coverage rose up to 74.6%. Combining community-based data collection with high-throughput DNA barcoding has the potential to overcome many of the logistic, financial, and taxonomic obstacles for large-scale monitoring of the Arctic arthropod fauna.
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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] [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] [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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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] [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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33
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Avigliano E, Rosso JJ, Lijtmaer D, Ondarza P, Piacentini L, Izquierdo M, Cirigliano A, Romano G, Nuñez Bustos E, Porta A, Mabragaña E, Grassi E, Palermo J, Bukowski B, Tubaro P, Schenone N. Biodiversity and threats in non-protected areas: A multidisciplinary and multi-taxa approach focused on the Atlantic Forest. Heliyon 2019; 5:e02292. [PMID: 31497670 PMCID: PMC6722266 DOI: 10.1016/j.heliyon.2019.e02292] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/04/2019] [Accepted: 08/08/2019] [Indexed: 01/15/2023] Open
Abstract
Along many decades, protected environments were targeted by the scientific community for ecological research and for the collection of scientific information related to environmental aspects and biodiversity. However, most of the territory in hotspot regions with weak or even non legal protection has been left aside. These non-protected areas (NPA) could host high biodiversity values. This paper addresses how scientific effort on a NPA (CIAR) of 700 ha from the Atlantic Rain Forest, generates new information and tools for large-scale environmental and biodiversity management in NPAs. Information published during the last decade was summarized and complemented with subsequent novel data about biodiversity (new species, first records, DNA and chemical analyses, etc.). The results showed: 1 new genus (arachnid), 6 new species and several putative new species (fish and arthropod), 6 vulnerable species (bird and mammal) and 36 first records for Argentina (fish, arthropod, platyhelminth and fungi). When compared with protected natural areas of the same biome, the CIAR showed highly valuable aspects for fauna and environment conservation, positioning this NPA as a worldwide hotspot for some taxa. Indeed, when compared to international hotspots in a coordinated Malaise trap program, the CIAR showed 8,651 different barcode index numbers (∼species) of arthropods, 80% of which had not been previously barcoded. Molecules like Inoscavin A, with antifungal activity against phytopathogens, was isolated for the first time in Phellinus merrillii fungi. The study of major threats derived from anthropic activities measured 20 trace elements, 18 pesticides (i.e. endosulfans, chlorpyrifos, DDTs, HCHs) and 27 pharmaceuticals and drugs (i.e. benzoylecgonine and norfluoxetine) in different biotic and abiotic matrices (water, sediment, fish and air biomonitors). This integrated data analysis shows that biodiversity research in NPA is being undervalued and how multidisciplinary and multi-taxa surveys creates a new arena for research and a pathway towards sustainable development in emerging countries with biodiversity hotspots.
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Affiliation(s)
- Esteban Avigliano
- Centro de Investigaciones Antonia Ramos (CIAR), Fundación Bosques Nativos Argentinos, Camino Balneario s/n, Villa Bonita, Misiones, Argentina
- Instituto de Investigaciones en Producción Animal (INPA-CONICET-UBA), Universidad de Buenos Aires, Av. Chorroarín 280, (C1427CWO), Buenos Aires, Argentina
| | - Juan Jose Rosso
- Grupo de Biotaxonomía Morfológica y Molecular de Peces (BIMOPE), Instituto de Investigaciones Marinas y Costeras, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata (CONICET), Dean Funes 3350, (B7600), Mar del Plata, Argentina
| | - Dario Lijtmaer
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN-CONICET), Av. Angel Gallardo 470, (C1405DJR), Buenos Aires, Argentina
| | - Paola Ondarza
- Laboratorio de Ecotoxicología y Contaminación Ambiental, Instituto de Investigaciones Marinas y Costeras, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata (CONICET), Dean Funes 3350, (B7600), Mar del Plata, Argentina
| | - Luis Piacentini
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN-CONICET), Av. Angel Gallardo 470, (C1405DJR), Buenos Aires, Argentina
| | - Matías Izquierdo
- Laboratorio de Biología Reproductiva y Evolución, Instituto de Diversidad y Ecología Animal (IDEA-UNC-CONICET), Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba. Av. Velez Sarsfield 299 (X5000 JJC), Córdoba, Argentina
| | - Adriana Cirigliano
- Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, (1428), Buenos Aires, Argentina
| | - Gonzalo Romano
- Departamento de Biología, Facultad de Ciencias Naturales, Universidad Nacional de la Patagonia San Juan Bosco (CONICET), Ruta 259 km 16.4, (9000), Esquel, Chubut, Argentina
| | - Ezequiel Nuñez Bustos
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN-CONICET), Av. Angel Gallardo 470, (C1405DJR), Buenos Aires, Argentina
| | - Andres Porta
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN-CONICET), Av. Angel Gallardo 470, (C1405DJR), Buenos Aires, Argentina
| | - Ezequiel Mabragaña
- Grupo de Biotaxonomía Morfológica y Molecular de Peces (BIMOPE), Instituto de Investigaciones Marinas y Costeras, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata (CONICET), Dean Funes 3350, (B7600), Mar del Plata, Argentina
| | - Emanuel Grassi
- Instituto Misionero de Biodiversidad (IMiBio), Ruta N12 km 5, (N3370), Puerto Iguazú, Misiones, Argentina
| | - Jorge Palermo
- Departamento de Biología, Facultad de Ciencias Naturales, Universidad Nacional de la Patagonia San Juan Bosco (CONICET), Ruta 259 km 16.4, (9000), Esquel, Chubut, Argentina
- Unidad de Microanálisis y Métodos Físicos en Química Orgánica (UMYMFOR-CONICET), Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, (1428), Buenos Aires, Argentina
| | - Belen Bukowski
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN-CONICET), Av. Angel Gallardo 470, (C1405DJR), Buenos Aires, Argentina
| | - Pablo Tubaro
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN-CONICET), Av. Angel Gallardo 470, (C1405DJR), Buenos Aires, Argentina
| | - Nahuel Schenone
- Centro de Investigaciones Antonia Ramos (CIAR), Fundación Bosques Nativos Argentinos, Camino Balneario s/n, Villa Bonita, Misiones, Argentina
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Morinière J, Balke M, Doczkal D, Geiger MF, Hardulak LA, Haszprunar G, Hausmann A, Hendrich L, Regalado L, Rulik B, Schmidt S, Wägele JW, Hebert PDN. A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding-based biomonitoring. Mol Ecol Resour 2019; 19:900-928. [PMID: 30977972 PMCID: PMC6851627 DOI: 10.1111/1755-0998.13022] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 11/29/2022]
Abstract
This study summarizes results of a DNA barcoding campaign on German Diptera, involving analysis of 45,040 specimens. The resultant DNA barcode library includes records for 2,453 named species comprising a total of 5,200 barcode index numbers (BINs), including 2,700 COI haplotype clusters without species‐level assignment, so called “dark taxa.” Overall, 88 out of 117 families (75%) recorded from Germany were covered, representing more than 50% of the 9,544 known species of German Diptera. Until now, most of these families, especially the most diverse, have been taxonomically inaccessible. By contrast, within a few years this study provided an intermediate taxonomic system for half of the German Dipteran fauna, which will provide a useful foundation for subsequent detailed, integrative taxonomic studies. Using DNA extracts derived from bulk collections made by Malaise traps, we further demonstrate that species delineation using BINs and operational taxonomic units (OTUs) constitutes an effective method for biodiversity studies using DNA metabarcoding. As the reference libraries continue to grow, and gaps in the species catalogue are filled, BIN lists assembled by metabarcoding will provide greater taxonomic resolution. The present study has three main goals: (a) to provide a DNA barcode library for 5,200 BINs of Diptera; (b) to demonstrate, based on the example of bulk extractions from a Malaise trap experiment, that DNA barcode clusters, labelled with globally unique identifiers (such as OTUs and/or BINs), provide a pragmatic, accurate solution to the “taxonomic impediment”; and (c) to demonstrate that interim names based on BINs and OTUs obtained through metabarcoding provide an effective method for studies on species‐rich groups that are usually neglected in biodiversity research projects because of their unresolved taxonomy.
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Affiliation(s)
| | | | | | - Matthias F Geiger
- Zoological Research Museum Alexander Koenig - Leibniz Institute for Animal Biodiversity, Bonn, Germany
| | | | | | | | | | | | - Björn Rulik
- Zoological Research Museum Alexander Koenig - Leibniz Institute for Animal Biodiversity, Bonn, Germany
| | | | - Johann-Wolfgang Wägele
- Zoological Research Museum Alexander Koenig - Leibniz Institute for Animal Biodiversity, Bonn, Germany
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
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Abstract
In 1979 nearly 1400 spider species in 32 families either had been recorded (1249) or were believed to occur (~140) in Canada. Twenty years later, although significant progress had been made in survey efforts in some regions, Canada's spider inventory had only increased by approximately 7% to roughly 1500 species known or expected to occur. The family count had increased to 38 but only two additions were truly novel (five family additions and one family deletion were the result of advances in family-level systematics). The first comprehensive taxonomic checklist of Canadian spider species was published in 2010 documenting the regional distributions of 1376 species representing 42 families (three novel since 1999). From 2010 through 2017 new national records steadily accumulated resulting in the current (2018) Canadian inventory of 1477 species classified in 45 families (one novel since 2010). Although there has been close to a 20% increase in the number of spider species recorded in Canada since 1979, much greater increases have occurred in some of the regional species checklists, indicating increasing knowledge of the regional distribution of species previously recorded elsewhere in Canada. For example the regional checklists for Newfoundland, British Columbia, and Prince Edward Island have increased by 69%, 339%, and 520%, respectively. The national and regional increases reflect significant advances in the first two decades of the 21st Century in spider faunistics research in previously under-sampled habitats and regions and the development of molecular techniques and consequent barcoding of spiders. Of the 1477 species recorded in Canada, 92% have been successfully DNA barcoded resulting in 1623 unique Barcode Index Numbers (BINs). At least 25 of the BINs are associated with relatively easily distinguished but undescribed morpho-species. The majority, however, appear to indicate the existence of many cryptic species within Canada's known spider fauna. These data, coupled with the fact that novel Canadian or even Nearctic spider species records (including of undescribed species) continue to accumulate annually (especially in habitat-diverse regions such as British Columbia), suggest that Canada's tally of spider species may approach or even exceed 1800.
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Affiliation(s)
- Robb Bennett
- Department of Entomology, Natural History Section, Royal British Columbia Museum, 675 Belleville Street, Victoria, British Columbia, V8W 9W2, CanadaRoyal British Columbia MuseumVictoriaCanada
| | - Gergin Blagoev
- Centre for Biodiversity Genomics, University of Guelph, 579 Gordon Street, Guelph, Ontario, N1G 2W1, CanadaUniversity of GuelphGuelphCanada
| | - Claudia Copley
- Department of Entomology, Natural History Section, Royal British Columbia Museum, 675 Belleville Street, Victoria, British Columbia, V8W 9W2, CanadaRoyal British Columbia MuseumVictoriaCanada
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