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Brydegaard M, Pedales RD, Feng V, Yamoa ASD, Kouakou B, Månefjord H, Wührl L, Pylatiuk C, Amorim DDS, Meier R. Towards global insect biomonitoring with frugal methods. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230103. [PMID: 38705174 PMCID: PMC11070255 DOI: 10.1098/rstb.2023.0103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/24/2024] [Indexed: 05/07/2024] Open
Abstract
None of the global targets for protecting nature are currently met, although humanity is critically dependent on biodiversity. A significant issue is the lack of data for most biodiverse regions of the planet where the use of frugal methods for biomonitoring would be particularly important because the available funding for monitoring is insufficient, especially in low-income countries. We here discuss how three approaches to insect biomonitoring (computer vision, lidar, DNA sequences) could be made more frugal and urge that all biomonitoring techniques should be evaluated for global suitability before becoming the default in high-income countries. This requires that techniques popular in high-income countries should undergo a phase of 'innovation through simplification' before they are implemented more broadly. We predict that techniques that acquire raw data at low cost and are suitable for analysis with AI (e.g. images, lidar-signals) will be particularly suitable for global biomonitoring, while techniques that rely heavily on patented technologies may be less promising (e.g. DNA sequences). We conclude the opinion piece by pointing out that the widespread use of AI for data analysis will require a global strategy for providing the necessary computational resources and training. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.
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Affiliation(s)
- Mikkel Brydegaard
- Dept. Physics, Lund University, Sölvegatan 14c, 22362 Lund, Sweden
- Dept. Biology, Lund University, Sölvegatan 35, 22362 Lund, Sweden
- Norsk Elektro Optikk, Østensjøveien 34, 0667 Oslo, Norge
- FaunaPhotonics, Støberi Støberigade 14, 2450 København, Denmark
| | - Ronniel D. Pedales
- Institute of Biology, University of the Philippines Diliman, Quezon City, Philippines 1101
- 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
| | - Vivian Feng
- 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
| | - Assoumou saint-doria Yamoa
- Instrumentation, Imaging and Spectroscopy Laboratory, Felix Houphouet-Boigny Institute, BP1093 Yamoussoukro, Ivory Coast
| | - Benoit Kouakou
- Instrumentation, Imaging and Spectroscopy Laboratory, Felix Houphouet-Boigny Institute, BP1093 Yamoussoukro, Ivory Coast
| | - Hampus Månefjord
- Dept. Physics, Lund University, Sölvegatan 14c, 22362 Lund, Sweden
| | - Lorenz Wührl
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Christian Pylatiuk
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Dalton de Souza Amorim
- Departamento de Biologia, FFCLRP, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil
| | - 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
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Smith CD, Cornman RS, Fike JA, Kraus JM, Oyler-McCance SJ, Givens CE, Hladik ML, Vandever MW, Kolpin DW, Smalling KL. Comparing modern identification methods for wild bees: Metabarcoding and image-based morphological taxonomic assignment. PLoS One 2024; 19:e0301474. [PMID: 38564614 PMCID: PMC10986983 DOI: 10.1371/journal.pone.0301474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
With the decline of bee populations worldwide, studies determining current wild bee distributions and diversity are increasingly important. Wild bee identification is often completed by experienced taxonomists or by genetic analysis. The current study was designed to compare two methods of identification including: (1) morphological identification by experienced taxonomists using images of field-collected wild bees and (2) genetic analysis of composite bee legs (multiple taxa) using metabarcoding. Bees were collected from conservation grasslands in eastern Iowa in summer 2019 and identified to the lowest taxonomic unit using both methods. Sanger sequencing of individual wild bee legs was used as a positive control for metabarcoding. Morphological identification of bees using images resulted in 36 unique taxa among 22 genera, and >80% of Bombus specimens were identified to species. Metabarcoding was limited to genus-level assignments among 18 genera but resolved some morphologically similar genera. Metabarcoding did not consistently detect all genera in the composite samples, including kleptoparasitic bees. Sanger sequencing showed similar presence or absence detection results as metabarcoding but provided species-level identifications for cryptic species (i.e., Lasioglossum). Genus-specific detections were more frequent with morphological identification than metabarcoding, but certain genera such as Ceratina and Halictus were identified equally well with metabarcoding and morphology. Genera with proportionately less tissue in a composite sample were less likely to be detected using metabarcoding. Image-based methods were limited by image quality and visible morphological features, while genetic methods were limited by databases, primers, and amplification at target loci. This study shows how an image-based identification method compares with genetic techniques, and how in combination, the methods provide valuable genus- and species-level information for wild bees while preserving tissue for other analyses. These methods could be improved and transferred to a field setting to advance our understanding of wild bee distributions and to expedite conservation research.
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Affiliation(s)
- Cassandra D. Smith
- Oregon Water Science Center, U.S. Geological Survey, Bend, Oregon, United States of America
| | - Robert S. Cornman
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, United States of America
| | - Jennifer A. Fike
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, United States of America
| | - Johanna M. Kraus
- Columbia Environmental Research Center, U.S. Geological Survey, Columbia, Missouri, United States of America
| | - Sara J. Oyler-McCance
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, United States of America
| | - Carrie E. Givens
- Upper Midwest Water Science Center, U.S. Geological Survey, Lansing, Michigan, United States of America
| | - Michelle L. Hladik
- California Water Science Center, U.S. Geological Survey, Sacramento, California, United States of America
| | - Mark W. Vandever
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, United States of America
| | - Dana W. Kolpin
- Central Midwest Water Science Center, U.S. Geological Survey, Iowa City, Iowa, United States of America
| | - Kelly L. Smalling
- New Jersey Water Science Center, U.S. Geological Survey, Lawrenceville, New Jersey, United States of America
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Gajski D, Wolff JO, Melcher A, Weber S, Prost S, Krehenwinkel H, Kennedy SR. Facilitating taxonomy and phylogenetics: An informative and cost-effective protocol integrating long amplicon PCRs and third-generation sequencing. Mol Phylogenet Evol 2024; 192:107988. [PMID: 38072140 DOI: 10.1016/j.ympev.2023.107988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/22/2023] [Accepted: 12/07/2023] [Indexed: 12/31/2023]
Abstract
Phylogenetic inference has become a standard technique in integrative taxonomy and systematics, as well as in biogeography and ecology. DNA barcodes are often used for phylogenetic inference, despite being strongly limited due to their low number of informative sites. Also, because current DNA barcodes are based on a fraction of a single, fast-evolving gene, they are highly unsuitable for resolving deeper phylogenetic relationships due to saturation. In recent years, methods that analyse hundreds and thousands of loci at once have improved the resolution of the Tree of Life, but these methods require resources, experience and molecular laboratories that most taxonomists do not have. This paper introduces a PCR-based protocol that produces long amplicons of both slow- and fast-evolving unlinked mitochondrial and nuclear gene regions, which can be sequenced by the affordable and portable ONT MinION platform with low infrastructure or funding requirements. As a proof of concept, we inferred a phylogeny of a sample of 63 spider species from 20 families using our proposed protocol. The results were overall consistent with the results from approaches based on hundreds and thousands of loci, while requiring just a fraction of the cost and labour of such approaches, making our protocol accessible to taxonomists worldwide.
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Affiliation(s)
- Domagoj Gajski
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno 611 37, Czech Republic
| | - Jonas O Wolff
- Evolutionary Biomechanics, Zoological Institute and Museum, University of Greifswald, Loitzer Str. 26, Greifswald 17489, Germany; School of Natural Sciences, Macquarie University, NSW 2109, Sydney, Australia
| | - Anja Melcher
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Sven Weber
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Stefan Prost
- Ecology and Genetics Research Unit, University of Oulu, Pentti Kaiteran katu 1, Linnanmaa, Finland
| | - Henrik Krehenwinkel
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Susan R Kennedy
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany.
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Emerson BC, Borges PAV, Cardoso P, Convey P, deWaard JR, Economo EP, Gillespie RG, Kennedy S, Krehenwinkel H, Meier R, Roderick GK, Strasberg D, Thébaud C, Traveset A, Creedy TJ, Meramveliotakis E, Noguerales V, Overcast I, Morlon H, Papadopoulou A, Vogler AP, Arribas P, Andújar C. Collective and harmonized high throughput barcoding of insular arthropod biodiversity: Toward a Genomic Observatories Network for islands. Mol Ecol 2023; 32:6161-6176. [PMID: 36156326 DOI: 10.1111/mec.16683] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 08/11/2022] [Accepted: 08/19/2022] [Indexed: 12/01/2022]
Abstract
Current understanding of ecological and evolutionary processes underlying island biodiversity is heavily shaped by empirical data from plants and birds, although arthropods comprise the overwhelming majority of known animal species, and as such can provide key insights into processes governing biodiversity. Novel high throughput sequencing (HTS) approaches are now emerging as powerful tools to overcome limitations in the availability of arthropod biodiversity data, and hence provide insights into these processes. Here, we explored how these tools might be most effectively exploited for comprehensive and comparable inventory and monitoring of insular arthropod biodiversity. We first reviewed the strengths, limitations and potential synergies among existing approaches of high throughput barcode sequencing. We considered how this could be complemented with deep learning approaches applied to image analysis to study arthropod biodiversity. We then explored how these approaches could be implemented within the framework of an island Genomic Observatories Network (iGON) for the advancement of fundamental and applied understanding of island biodiversity. To this end, we identified seven island biology themes at the interface of ecology, evolution and conservation biology, within which collective and harmonized efforts in HTS arthropod inventory could yield significant advances in island biodiversity research.
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Affiliation(s)
- Brent C Emerson
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), San Cristóbal de la Laguna, Spain
| | - Paulo A V Borges
- Centre for Ecology, Evolution and Environmental Changes (cE3c)/Azorean Biodiversity Group, Faculty of Agricultural Sciences and Environment, CHANGE - Global Change and Sustainability Institute, University of the Azores, Angra do Heroísmo, Portugal
| | - Pedro Cardoso
- Centre for Ecology, Evolution and Environmental Changes (cE3c)/Azorean Biodiversity Group, Faculty of Agricultural Sciences and Environment, CHANGE - Global Change and Sustainability Institute, University of the Azores, Angra do Heroísmo, Portugal
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History Luomus, University of Helsinki, Helsinki, Finland
| | - Peter Convey
- British Antarctic Survey, NERC, Cambridge, UK
- Department of Zoology, University of Johannesburg, Auckland Park, South Africa
| | - Jeremy R deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
- School of Environmental Sciences, University of Guelph, Guelph, Canada
| | - Evan P Economo
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, Massachusetts, USA
| | - Rosemary G Gillespie
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, California, USA
| | - Susan Kennedy
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | | | - 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 City, Singapore
| | - George K Roderick
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, California, USA
| | | | - Christophe Thébaud
- UMR 5174 EDB Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier Toulouse III, CNRS, IRD, Toulouse, France
| | - Anna Traveset
- Global Change Research Group, Mediterranean Institut of Advanced Studies (CSIC-UIB), Mallorca, Spain
| | - Thomas J Creedy
- Department of Life Sciences, Natural History Museum, London, UK
| | | | - Víctor Noguerales
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), San Cristóbal de la Laguna, Spain
| | - Isaac Overcast
- Département de Biologie, École normale supérieure, Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, Université PSL, Paris, France
| | - Hélène Morlon
- Département de Biologie, École normale supérieure, Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, Université PSL, Paris, France
| | - Anna Papadopoulou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Life Sciences, Imperial College London, London, UK
| | - Paula Arribas
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), San Cristóbal de la Laguna, Spain
| | - Carmelo Andújar
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), San Cristóbal de la Laguna, Spain
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Bailey RC, Reynoldson TB. Can datasets from long-term biomonitoring programs detect climate change effects on stream benthos? Sci Prog 2023; 106:368504231219335. [PMID: 38105549 PMCID: PMC10729632 DOI: 10.1177/00368504231219335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
We analyzed datasets from a long-term monitoring program of stream ecosystems in British Columbia, Canada, to determine whether or not it could detect climate change effects. In the Fraser River Basin (monitoring timespan 1994-2019), there was a marked (∼50%) increase in alpha diversity in reference streams, while BC North Coast (2004-2021) streams showed a modest trend of decreasing diversity and Columbia River Basin (2003-2018) and Vancouver Island (2001-2019) streams showed modestly increasing diversity. In all four regions, diversity across all sites in a specific period was primarily a function of sampling effort during this period rather than a temporal trend. Across all the regions, only three of 21 groups of faunally similar sites defined by Reference Condition Approach predictive modeling showed a suggestion of a directional change in community structure over time. Only 1 of 15 reference sites that were repeatedly sampled over several years showed a pattern that may indicate a response to changing climate. Three, not mutually exclusive, reasons why we did not see a clear effect of climate change on BC stream ecosystems were: 1) Little or no effect of climate change relative to other, potentially interacting biotic and abiotic factors, 2) The timespan of monitoring was too short to detect cumulative effects of climate change, and, most importantly, 3) The sampling design and protocol were unable to detect climate change effects. To better detect and characterize the effects of climate change on streams in monitoring programs, we recommend annual re-sampling of a few reference sites and detailed analysis of the natural and human environment of the sites along with better characterization of the benthic community (e.g. with eDNA) at all monitored sites.
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Affiliation(s)
- Robert C Bailey
- Ontario Tech University, Faculty of Science, Oshawa, Ontario, Canada
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6
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Aunins AA, Mueller SJ, Fike JA, Cornman RS. Assessing arthropod diversity metrics derived from stream environmental DNA: spatiotemporal variation and paired comparisons with manual sampling. PeerJ 2023; 11:e15163. [PMID: 37020852 PMCID: PMC10069422 DOI: 10.7717/peerj.15163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/13/2023] [Indexed: 04/03/2023] Open
Abstract
Background Benthic invertebrate (BI) surveys have been widely used to characterize freshwater environmental quality but can be challenging to implement at desired spatial scales and frequency. Environmental DNA (eDNA) allows an alternative BI survey approach, one that can potentially be implemented more rapidly and cheaply than traditional methods. Methods We evaluated eDNA analogs of BI metrics in the Potomac River watershed of the eastern United States. We first compared arthropod diversity detected with primers targeting mitochondrial 16S (mt16S) and cytochrome c oxidase 1 (cox1 or COI) loci to that detected by manual surveys conducted in parallel. We then evaluated spatial and temporal variation in arthropod diversity metrics with repeated sampling in three focal parks. We also investigated technical factors such as filter type used to capture eDNA and PCR inhibition treatment. Results Our results indicate that genus-level assessment of eDNA compositions is achievable at both loci with modest technical noise, although database gaps remain substantial at mt16S for regional taxa. While the specific taxa identified by eDNA did not strongly overlap with paired manual surveys, some metrics derived from eDNA compositions were rank-correlated with previously derived biological indices of environmental quality. Repeated sampling revealed statistical differences between high- and low-quality sites based on taxonomic diversity, functional diversity, and tolerance scores weighted by taxon proportions in transformed counts. We conclude that eDNA compositions are efficient and informative of stream condition. Further development and validation of scoring schemes analogous to commonly used biological indices should allow increased application of the approach to management needs.
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Affiliation(s)
- Aaron A. Aunins
- Eastern Ecological Research Center, U.S. Geological Survey, Kearneysville, West Virginia, United States
| | - Sara J. Mueller
- Wildlife and Fisheries Sciences Program, The Pennsylvania State College, State College, Pennsylvania, United States
| | - Jennifer A. Fike
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, United States
| | - Robert S. Cornman
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, United States
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7
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Robinson CV, Porter TM, McGee KM, McCusker M, Wright MTG, Hajibabaei M. Multi-marker DNA metabarcoding detects suites of environmental gradients from an urban harbour. Sci Rep 2022; 12:10556. [PMID: 35732669 PMCID: PMC9217803 DOI: 10.1038/s41598-022-13262-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/25/2022] [Indexed: 11/18/2022] Open
Abstract
There is increasing need for biodiversity monitoring, especially in places where potential anthropogenic disturbance may significantly impact ecosystem health. We employed a combination of traditional morphological and bulk macroinvertebrate metabarcoding analyses to benthic samples collected from Toronto Harbour (Ontario, Canada) to compare taxonomic and functional diversity of macroinvertebrates and their responses to environmental gradients. At the species rank, sites assessed using COI metabarcoding showed more variation than sites assessed using morphological methods. Depending on the assessment method, we detected gradients in magnesium (morphological taxa), ammonia (morphological taxa, COI sequence variants), pH (18S sequence variants) as well as gradients in contaminants such as metals (COI & 18S sequence variants) and organochlorines (COI sequence variants). Observed responses to contaminants such as aromatic hydrocarbons and metals align with known patchy distributions in harbour sediments. We determined that the morphological approach may limit the detection of macroinvertebrate responses to lake environmental conditions due to the effort needed to obtain fine level taxonomic assignments necessary to investigate responses. DNA metabarcoding, however, need not be limited to macroinvertebrates, can be automated, and taxonomic assignments are associated with a certain level of accuracy from sequence variants to named taxonomic groups. The capacity to detect change using a scalable approach such as metabarcoding is critical for addressing challenges associated with biodiversity monitoring and ecological investigations.
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Affiliation(s)
- Chloe V Robinson
- Centre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Whales Initiative, Ocean Wise Conservation Association, Victoria, BC, V8V 4Z9, Canada
| | - Teresita M Porter
- Centre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Katie M McGee
- Centre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Megan McCusker
- Environment and Climate Change Canada, Burlington, ON, L7S 1A1, Canada
| | - Michael T G Wright
- Centre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Mehrdad Hajibabaei
- Centre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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8
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A Comparison of eDNA and Visual Survey Methods for Detection of Longnose Darter Percina nasuta in Missouri. FISHES 2022. [DOI: 10.3390/fishes7020070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
The longnose darter Percina nasuta is a rare and cryptic fish that recently disappeared from much of its historic range. We developed and used an environmental DNA (eDNA) assay for longnose darter paired with visual surveys to better determine the species’ range and compare detection probability between sampling approaches in an occupancy modeling framework. We detected longnose darter eDNA further upstream in the mainstem St. Francis River than previously reported and in a tributary for the first time. Our multi-scale occupancy approach compared models where detection was constant against a model that allowed detection to vary by survey method. The constant model received the most support indicating survey method was not a strong predictor and detection was estimated at 0.70 (0.45–0.86; 95% CI) across both methods. Our study produced effective longnose darter eDNA primers and demonstrated the application of eDNA for sampling small-bodied, cryptic fish. We detected longnose darter eDNA 27 km upstream of their known range and determined that snorkel surveys are the most efficient sampling method if water clarity allows. We recommend target sample sizes to achieve various detection goals for both sample methods and our results inform future design of distributional and monitoring efforts.
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9
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Bruno A, Casiraghi M, Bautista M, Hajibabaei M. Editorial: Stressors Acting on Aquatic Ecosystems: High-Throughput Sequencing Approaches to Shed Light on Human-Nature Interactions. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.763442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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10
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Combining DNA and people power for healthy rivers: Implementing the STREAM community-based approach for global freshwater monitoring. Perspect Ecol Conserv 2021. [DOI: 10.1016/j.pecon.2021.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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11
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Hirohara T, Tsuri K, Miyagawa K, Paine RTR, Yamanaka H. The Application of PMA (Propidium Monoazide) to Different Target Sequence Lengths of Zebrafish eDNA: A New Approach Aimed Toward Improving Environmental DNA Ecology and Biological Surveillance. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.632973] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Environmental DNA (eDNA) analysis has enabled more sensitive and efficient biological monitoring than traditional methods. However, since the target species is not directly observed, interpretation of results cannot preclude process Type I errors. Specifically, there may be a spatial or temporal gap between the target eDNA and the eDNA source in the sampled area. Moreover, eDNA surveillance lacks the ability to distinguish whether eDNA originated from a living or non-living source. This kind of Type I error is difficult to control for, in part, because the relationship between the state of eDNA (i.e., intracellular or extracellular) and the degradation rate is still unclear. Here, we applied PMA (Propidium monoazide) to eDNA analysis which enabled us to differentiate “intact cells” from “disrupted cells.” PMA is a dye that has a high affinity for double-stranded DNA and forms a covalent bond with double-stranded DNA and inhibits amplification of the bonded DNA molecules by PCR. Since PMA is impermeable to the cell membrane, DNA protected by an intact cell membrane can be selectively detected. In this study, we investigated the workability of PMA on vertebrate eDNA using zebrafish, Danio rerio. Aquarium water was incubated for 1 week to monitor the eDNA degradation process of both intracellular and extracellular eDNA. We developed ten species-specific quantitative PCR assays for D. rerio with different amplification lengths that enabled independent quantification of total eDNA (sum of intracellular and extracellular eDNA, commonly measured in other studies) and intracellular eDNA (DNA in intact cells) and allow for analyses of sequence length-dependent eDNA degradation in combination with PMA. We confirmed that PMA is effective at differentiating “intact” and “disrupted” fish cells. We found that total eDNA and intracellular eDNA have different degradation processes that are dependent on the length of target sequence. For future conservation efforts using eDNA analyses, it is necessary to increase the reliability of the analysis results. The research presented here provides new analysis tools that expand our understanding of the ecology of eDNA, so that more accurate and reliable conclusions can be determined.
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12
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Nugent CM, Elliott TA, Ratnasingham S, Hebert PDN, Adamowicz SJ. Debar: A sequence-by-sequence denoiser for COI-5P DNA barcode data. Mol Ecol Resour 2021; 21:2832-2846. [PMID: 33749132 DOI: 10.1111/1755-0998.13384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 03/05/2021] [Indexed: 12/14/2022]
Abstract
DNA barcoding and metabarcoding are now widely used to advance species discovery and biodiversity assessments. High-throughput sequencing (HTS) has expanded the volume and scope of these analyses, but elevated error rates introduce noise into sequence records that can inflate estimates of biodiversity. Denoising -the separation of biological signal from instrument (technical) noise-of barcode and metabarcode data currently employs abundance-based methods which do not capitalize on the highly conserved structure of the cytochrome c oxidase subunit I (COI) region employed as the animal barcode. This manuscript introduces debar, an R package that utilizes a profile hidden Markov model to denoise indel errors in COI sequences introduced by instrument error. In silico studies demonstrated that debar recognized 95% of artificially introduced indels in COI sequences. When applied to real-world data, debar reduced indel errors in circular consensus sequences obtained with the Sequel platform by 75%, and those generated on the Ion Torrent S5 by 94%. The false correction rate was less than 0.1%, indicating that debar is receptive to the majority of true COI variation in the animal kingdom. In conclusion, the debar package improves DNA barcode and metabarcode workflows by aiding the generation of more accurate sequences aiding the characterization of species diversity.
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Affiliation(s)
- Cameron M Nugent
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada.,Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Tyler A Elliott
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Sarah J Adamowicz
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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13
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Lin X, Mo L, Bu W, Wang X. The first comprehensive DNA barcode reference library of Chinese
Tanytarsus
(Diptera: Chironomidae) for environmental DNA metabarcoding. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13209] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Xiao‐Long Lin
- College of Life Sciences Nankai University Tianjin China
- Department of Natural History NTNU University Museum Norwegian University of Science and Technology Trondheim Norway
| | - Lidong Mo
- Institute of Integrative Biology ETH Zurich (Swiss Federal Institute of Technology) Zurich Switzerland
| | - Wen‐Jun Bu
- College of Life Sciences Nankai University Tianjin China
| | - Xin‐Hua Wang
- College of Life Sciences Nankai University Tianjin China
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14
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Compson ZG, McClenaghan B, Singer GAC, Fahner NA, Hajibabaei M. Metabarcoding From Microbes to Mammals: Comprehensive Bioassessment on a Global Scale. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.581835] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Global biodiversity loss is unprecedented, and threats to existing biodiversity are growing. Given pervasive global change, a major challenge facing resource managers is a lack of scalable tools to rapidly and consistently measure Earth's biodiversity. Environmental genomic tools provide some hope in the face of this crisis, and DNA metabarcoding, in particular, is a powerful approach for biodiversity assessment at large spatial scales. However, metabarcoding studies are variable in their taxonomic, temporal, or spatial scope, investigating individual species, specific taxonomic groups, or targeted communities at local or regional scales. With the advent of modern, ultra-high throughput sequencing platforms, conducting deep sequencing metabarcoding surveys with multiple DNA markers will enhance the breadth of biodiversity coverage, enabling comprehensive, rapid bioassessment of all the organisms in a sample. Here, we report on a systematic literature review of 1,563 articles published about DNA metabarcoding and summarize how this approach is rapidly revolutionizing global bioassessment efforts. Specifically, we quantify the stakeholders using DNA metabarcoding, the dominant applications of this technology, and the taxonomic groups assessed in these studies. We show that while DNA metabarcoding has reached global coverage, few studies deliver on its promise of near-comprehensive biodiversity assessment. We then outline how DNA metabarcoding can help us move toward real-time, global bioassessment, illustrating how different stakeholders could benefit from DNA metabarcoding. Next, we address barriers to widespread adoption of DNA metabarcoding, highlighting the need for standardized sampling protocols, experts and computational resources to handle the deluge of genomic data, and standardized, open-source bioinformatic pipelines. Finally, we explore how technological and scientific advances will realize the promise of total biodiversity assessment in a sample—from microbes to mammals—and unlock the rich information genomics exposes, opening new possibilities for merging whole-system DNA metabarcoding with (1) abundance and biomass quantification, (2) advanced modeling, such as species occupancy models, to improve species detection, (3) population genetics, (4) phylogenetics, and (5) food web and functional gene analysis. While many challenges need to be addressed to facilitate widespread adoption of environmental genomic approaches, concurrent scientific and technological advances will usher in methods to supplement existing bioassessment tools reliant on morphological and abiotic data. This expanded toolbox will help ensure that the best tool is used for the job and enable exciting integrative techniques that capitalize on multiple tools. Collectively, these new approaches will aid in addressing the global biodiversity crisis we now face.
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15
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Antich A, Palacín C, Cebrian E, Golo R, Wangensteen OS, Turon X. Marine biomonitoring with eDNA: Can metabarcoding of water samples cut it as a tool for surveying benthic communities? Mol Ecol 2020; 30:3175-3188. [PMID: 32974967 DOI: 10.1111/mec.15641] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/06/2020] [Accepted: 09/07/2020] [Indexed: 12/21/2022]
Abstract
In the marine realm, biomonitoring using environmental DNA (eDNA) of benthic communities requires destructive direct sampling or the setting-up of settlement structures. Comparatively much less effort is required to sample the water column, which can be accessed remotely. In this study we assess the feasibility of obtaining information from the eukaryotic benthic communities by sampling the adjacent water layer. We studied two different rocky-substrate benthic communities with a technique based on quadrat sampling. We also took replicate water samples at four distances (0, 0.5, 1.5, and 20 m) from the benthic habitat. Using broad range primers to amplify a ca. 313 bp fragment of the cytochrome oxidase subunit I gene, we obtained a total of 3,543 molecular operational taxonomic units (MOTUs). The structure obtained in the two environments was markedly different, with Metazoa, Archaeplastida and Stramenopiles being the most diverse groups in benthic samples, and Hacrobia, Metazoa and Alveolata in the water. Only 265 MOTUs (7.5%) were shared between benthos and water samples and, of these, 180 (5.1%) were identified as benthic taxa that left their DNA in the water. Most of them were found immediately adjacent to the benthos, and their number decreased as we moved apart from the benthic habitat. It was concluded that water eDNA, even in the close vicinity of the benthos, was a poor proxy for the analysis of benthic structure, and that direct sampling methods are required for monitoring these complex communities via metabarcoding.
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Affiliation(s)
- Adrià Antich
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
| | - Cruz Palacín
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, and Research Institute of Biodiversity (IRBIO), Barcelona, Spain
| | - Emma Cebrian
- Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Raül Golo
- Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Owen S Wangensteen
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Xavier Turon
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
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16
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Nugent CM, Adamowicz SJ. Alignment-free classification of COI DNA barcode data with the Python package Alfie. METABARCODING AND METAGENOMICS 2020. [DOI: 10.3897/mbmg.4.55815] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Characterization of biodiversity from environmental DNA samples and bulk metabarcoding data is hampered by off-target sequences that can confound conclusions about a taxonomic group of interest. Existing methods for isolation of target sequences rely on alignment to existing reference barcodes, but this can bias results against novel genetic variants. Effectively parsing targeted DNA barcode data from off-target noise improves the quality of biodiversity estimates and biological conclusions by limiting subsequent analyses to a relevant subset of available data. Here, we present Alfie, a Python package for the alignment-free classification of cytochrome c oxidase subunit I (COI) DNA barcode sequences to taxonomic kingdoms. The package determines k-mer frequencies of DNA sequences, and the frequencies serve as input for a neural network classifier that was trained and tested using ~58,000 publicly available COI sequences. The classifier was designed and optimized through a series of tests that allowed for the optimal set of DNA k-mer features and optimal machine learning algorithm to be selected. The neural network classifier rapidly assigns COI sequences of varying lengths to kingdoms with greater than 99% accuracy and is shown to generalize effectively and make accurate predictions about data from previously unseen taxonomic classes. The package contains an application programming interface that allows the Alfie package’s functionality to be extended to different DNA sequence classification tasks to suit a user’s need, including classification of different genes and barcodes, and classification to different taxonomic levels. Alfie is free and publicly available through GitHub (https://github.com/CNuge/alfie) and the Python package index (https://pypi.org/project/alfie/).
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17
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Taylor CL, Barker NP, Barber-James HM, Villet MH, Pereira-da-Conceicoa LL. Habitat requirements affect genetic variation in three species of mayfly (Ephemeroptera, Baetidae) from South Africa. Zookeys 2020; 936:1-24. [PMID: 32547291 PMCID: PMC7272479 DOI: 10.3897/zookeys.936.38587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 11/04/2019] [Indexed: 12/23/2022] Open
Abstract
This study investigates genetic diversity in three species of Ephemeroptera, one eurytopic and therefore widespread (Afroptilumsudafricanum) and two stenotopic and thus endemic (Demoreptusnatalensis and Demoreptuscapensis) species, all of which co-occur in the southern Great Escarpment, South Africa. Mitochondrial DNA was analysed to compare the genetic diversity between the habitat generalist and the two habitat specialists. Afroptilumsudafricanum showed no indication of population genetic structure due to geographic location, while both Demoreptus species revealed clear genetic differentiation between geographic localities and catchments, evident from phylogenetic analyses and high FST values from AMOVA. In addition, the phylogenetic analyses indicate some deeper haplotype divergences within A.sudafricanum and Demoreptus that merit taxonomic attention. These results give important insight into evolutionary processes occurring through habitat specialisation and population isolation. Further research and sampling across a wider geographic setting that includes both major mountain blocks of the Escarpment and lowland non-Escarpment sites will allow for refined understanding of biodiversity and associated habitat preferences, and illuminate comparative inferences into gene flow and cryptic speciation.
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Affiliation(s)
- Chantal L Taylor
- Department of Zoology and Entomology, Rhodes University, Somerset Street, Makhanda (Grahamstown), 6140, South Africa
| | - Nigel P Barker
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, 0028, South Africa
| | - Helen M Barber-James
- Department of Zoology and Entomology, Rhodes University, Somerset Street, Makhanda (Grahamstown), 6140, South Africa.,Department of Freshwater Invertebrates, Albany Museum, Somerset Street, Makhanda (Grahamstown), 6140, South Africa
| | - Martin H Villet
- Department of Zoology and Entomology, Rhodes University, Somerset Street, Makhanda (Grahamstown), 6140, South Africa
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18
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DNA metabarcoding reveals metacommunity dynamics in a threatened boreal wetland wilderness. Proc Natl Acad Sci U S A 2020; 117:8539-8545. [PMID: 32217735 PMCID: PMC7165428 DOI: 10.1073/pnas.1918741117] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The complexity and natural variability of ecosystems present a challenge for reliable detection of change due to anthropogenic influences. This issue is exacerbated by necessary trade-offs that reduce the quality and resolution of survey data for assessments at large scales. The Peace-Athabasca Delta (PAD) is a large inland wetland complex in northern Alberta, Canada. Despite its geographic isolation, the PAD is threatened by encroachment of oil sands mining in the Athabasca watershed and hydroelectric dams in the Peace watershed. Methods capable of reliably detecting changes in ecosystem health are needed to evaluate and manage risks. Between 2011 and 2016, aquatic macroinvertebrates were sampled across a gradient of wetland flood frequency, applying both microscope-based morphological identification and DNA metabarcoding. By using multispecies occupancy models, we demonstrate that DNA metabarcoding detected a much broader range of taxa and more taxa per sample compared to traditional morphological identification and was essential to identifying significant responses to flood and thermal regimes. We show that family-level occupancy masks high variation among genera and quantify the bias of barcoding primers on the probability of detection in a natural community. Interestingly, patterns of community assembly were nearly random, suggesting a strong role of stochasticity in the dynamics of the metacommunity. This variability seriously compromises effective monitoring at local scales but also reflects resilience to hydrological and thermal variability. Nevertheless, simulations showed the greater efficiency of metabarcoding, particularly at a finer taxonomic resolution, provided the statistical power needed to detect change at the landscape scale.
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19
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The Chironomidae (Diptera) of Svalbard and Jan Mayen. INSECTS 2020; 11:insects11030183. [PMID: 32183077 PMCID: PMC7143642 DOI: 10.3390/insects11030183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 02/26/2020] [Accepted: 03/03/2020] [Indexed: 11/27/2022]
Abstract
Non-biting midges of the fly family Chironomidae are extremely abundant and diverse in Arctic regions and are essential components of Arctic ecosystems. Modern identification tools based on documented records of Arctic chironomid species are therefore important for ecological research and environmental monitoring in the region. Here, we provide an updated review of the chironomid fauna of the Svalbard archipelago and the island of Jan Mayen, Norway. Our results show that a total of 73 species distributed across 24 genera in four subfamilies are known from these areas. Our review treats 109 taxa, including nomina dubia and misidentifications. It includes morphological identification keys to all known species as well as photographs of most taxa and DNA barcodes of 66 species. Taxonomic remarks are given for selected taxa, including previous misidentifications and erroneous records. Chironomus islandicus, Tvetenia bavarica, Limnophyes schnelli, Metriocnemus brusti and Metriocnemus fuscipes as well as the genera Allocladius, Corynoneura and Bryophaenocladius are reported from Svalbard for the first time, while Procladius (Holotanypus) frigidus, Stictochironomus psilopterus, Chaetocladius incertus, Orthocladius (Orthocladius) mixtus and Smittia longicosta, previously considered as junior synonyms or nomina dubia, are revived as valid species based on examination of type material or literature. Twenty species within eleven genera are introduced with interim names. Metriocnemus similis is regarded as a junior synonym of Metriocnemus ursinus, and Smittia incerta, Smittia flexinervis and Smittia spitzbergensis are regarded as nomina dubia. Valid taxa no longer considered as part of the Svalbard fauna are Parochlus kiefferi, Arctopelopia barbitarsis, Procladius (Holotanypus) crassinervis, Diamesa lindrothi, Diamesa incallida, Diamesa lundstromi, Chironomus hyperboreus, Sergentia coracina, Camptocladius stercorarius, Chaetocladius dissipatus, Chaetocladius dentiforceps, Chaetocladius laminatus, Chaetocladius perennis, Cricotopus (Cricotopus) humeralis, Cricotopus (Cricotopus) polaris, Hydrosmittia ruttneri, Limnophyes edwardsi, Metriocnemus picipes, Metriocnemus tristellus, Orthocladius (Eudactylocladius) gelidus, Orthocladius (Euorthocladius) thienemanni, Orthocladius (Orthocladius) obumbratus, Orthocladius (Orthocladius) rhyacobius, Paralimnophyes, Paraphaenocladius impensus, Psectrocladius (Monopsectrocladius) calcaratus, Psectrocladius (Psectrocladius) psilopterus, Psectrocladius (Psectrocladius) ventricosus, Smittia lasiophthalma, Smittia lasiops and Zalutschia tatrica.
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20
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Turon X, Antich A, Palacín C, Præbel K, Wangensteen OS. From metabarcoding to metaphylogeography: separating the wheat from the chaff. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2020; 30:e02036. [PMID: 31709684 PMCID: PMC7078904 DOI: 10.1002/eap.2036] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/31/2019] [Accepted: 10/03/2019] [Indexed: 05/31/2023]
Abstract
Metabarcoding is by now a well-established method for biodiversity assessment in terrestrial, freshwater, and marine environments. Metabarcoding data sets are usually used for α- and β-diversity estimates, that is, interspecies (or inter-MOTU [molecular operational taxonomic unit]) patterns. However, the use of hypervariable metabarcoding markers may provide an enormous amount of intraspecies (intra-MOTU) information-mostly untapped so far. The use of cytochrome oxidase (COI) amplicons is gaining momentum in metabarcoding studies targeting eukaryote richness. COI has been for a long time the marker of choice in population genetics and phylogeographic studies. Therefore, COI metabarcoding data sets may be used to study intraspecies patterns and phylogeographic features for hundreds of species simultaneously, opening a new field that we suggest to name metaphylogeography. The main challenge for the implementation of this approach is the separation of erroneous sequences from true intra-MOTU variation. Here, we develop a cleaning protocol based on changes in entropy of the different codon positions of the COI sequence, together with co-occurrence patterns of sequences. Using a data set of community DNA from several benthic littoral communities in the Mediterranean and Atlantic seas, we first tested by simulation on a subset of sequences a two-step cleaning approach consisting of a denoising step followed by a minimal abundance filtering. The procedure was then applied to the whole data set. We obtained a total of 563 MOTUs that were usable for phylogeographic inference. We used semiquantitative rank data instead of read abundances to perform AMOVAs and haplotype networks. Genetic variability was mainly concentrated within samples, but with an important between seas component as well. There were intergroup differences in the amount of variability between and within communities in each sea. For two species, the results could be compared with traditional Sanger sequence data available for the same zones, giving similar patterns. Our study shows that metabarcoding data can be used to infer intra- and interpopulation genetic variability of many species at a time, providing a new method with great potential for basic biogeography, connectivity and dispersal studies, and for the more applied fields of conservation genetics, invasion genetics, and design of protected areas.
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Affiliation(s)
- Xavier Turon
- Department of Marine EcologyCentre for Advanced Studies of Blanes (CEAB, CSIC)BlanesCataloniaSpain
| | - Adrià Antich
- Department of Marine EcologyCentre for Advanced Studies of Blanes (CEAB, CSIC)BlanesCataloniaSpain
| | - Creu Palacín
- Department of Evolutionary Biology, Ecology and Environmental Sciences, and Institute of Biodiversity Research (IRBio)University of BarcelonaBarcelonaCataloniaSpain
| | - Kim Præbel
- Norwegian College of Fishery ScienceUiT the Arctic University of NorwayTromsøNorway
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21
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Bowser ML, Brassfield R, Dziergowski A, Eskelin T, Hester J, Magness DR, McInnis M, Melvin T, Morton JM, Stone J. Towards conserving natural diversity: A biotic inventory by observations, specimens, DNA barcoding and high-throughput sequencing methods. Biodivers Data J 2020; 8:e50124. [PMID: 32165853 PMCID: PMC7058680 DOI: 10.3897/bdj.8.e50124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 02/15/2020] [Indexed: 11/12/2022] Open
Abstract
The Kenai National Wildlife Refuge has been given a broad conservation mandate to conserve natural diversity. A prerequisite for fulfilling this purpose is to be able to identify the species and communities that make up that biodiversity. We tested a set of varied methods for inventory and monitoring of plants, birds and terrestrial invertebrates on a grid of 40 sites in a 938 ha study area in the Slikok Creek watershed, Kenai Peninsula, Alaska. We sampled plants and lichens through observation and specimen-based methods. We surveyed birds using bird call surveys on variable circular plots. We sampled terrestrial arthropods by sweep net sampling, processing samples with High Throughput Sequencing methods. We surveyed for earthworms, using the hot mustard extraction method and identified worm specimens by morphology and DNA barcoding. We examined community membership using clustering methods and Nonmetric Multidimensional Scaling. We documented a total of 4,764 occurrences of 984 species and molecular operational taxonomic units: 87 vascular plants, 51 mosses, 12 liverworts, 111 lichens, 43 vertebrates, 663 arthropods, 9 molluscs and 8 annelid worms. Amongst these records, 102 of the arthropod species appeared to be new records for Alaska. We found three non-native species: Deroceras agreste (Linnaeus, 1758) (Stylommatophora: Agriolimacidae), Dendrobaena octaedra (Savigny, 1826) (Crassiclitellata: Lumbricidae) and Heterarthrus nemoratus (Fallén, 1808) (Hymenoptera: Tenthredinidae). Both D. octaedra and H. nemoratus were found at sites distant from obvious human disturbance. The 40 sites were grouped into five community groups: upland mixed forest, black spruce forest, open deciduous forest, shrub-sedge bog and willow. We demonstrated that, at least for a subset of species that could be detected using these methods, we were able to document current species distributions and assemblages in a way that could be efficiently repeated for the purposes of biomonitoring. While our methods could be improved and additional methods and groups could be added, our combination of techniques yielded a substantial portion of the data necessary for fulfilling Kenai National Wildlife Refuge's broad conservation purposes.
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Affiliation(s)
- Matthew Lewis Bowser
- U.S. Fish & Wildlife Service, Kenai National Wildlife Refuge, Soldotna, Alaska, United States of AmericaU.S. Fish & Wildlife Service, Kenai National Wildlife RefugeSoldotna, AlaskaUnited States of America
| | - Rebekah Brassfield
- Salish Kootenai College, Pablo, Montana, United States of AmericaSalish Kootenai CollegePablo, MontanaUnited States of America
| | - Annie Dziergowski
- U.S. Fish & Wildlife Service, North Florida Ecological Services Office, Jacksonville, Florida, United States of AmericaU.S. Fish & Wildlife Service, North Florida Ecological Services OfficeJacksonville, FloridaUnited States of America
| | - Todd Eskelin
- U.S. Fish & Wildlife Service, Kenai National Wildlife Refuge, Soldotna, Alaska, United States of AmericaU.S. Fish & Wildlife Service, Kenai National Wildlife RefugeSoldotna, AlaskaUnited States of America
| | - Jennifer Hester
- City of Soldotna, Planning and Zoning Commision, Soldotna, Alaska, United States of AmericaCity of Soldotna, Planning and Zoning CommisionSoldotna, AlaskaUnited States of America
| | - Dawn Robin Magness
- U.S. Fish & Wildlife Service, Kenai National Wildlife Refuge, Soldotna, Alaska, United States of AmericaU.S. Fish & Wildlife Service, Kenai National Wildlife RefugeSoldotna, AlaskaUnited States of America
| | - Mariah McInnis
- Auburn University, School of Forestry & Wildlife Sciences, Auburn, Alabama, United States of AmericaAuburn University, School of Forestry & Wildlife SciencesAuburn, AlabamaUnited States of America
| | - Tracy Melvin
- Michigan State University, College of Agriculture & Natural Resources, Department of Fisheries and Wildlife, East Lansing, Michigan, United States of AmericaMichigan State University, College of Agriculture & Natural Resources, Department of Fisheries and WildlifeEast Lansing, MichiganUnited States of America
| | - John M. Morton
- U.S. Fish & Wildlife Service (retired), Soldotna, Alaska, United States of AmericaU.S. Fish & Wildlife Service (retired)Soldotna, AlaskaUnited States of America
| | - Joel Stone
- University of Alaska Fairbanks, Fairbanks, Alaska, United States of AmericaUniversity of Alaska FairbanksFairbanks, AlaskaUnited States of America
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22
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Hajibabaei M, Porter TM, Robinson CV, Baird DJ, Shokralla S, Wright MTG. Watered-down biodiversity? A comparison of metabarcoding results from DNA extracted from matched water and bulk tissue biomonitoring samples. PLoS One 2019; 14:e0225409. [PMID: 31830042 PMCID: PMC6907778 DOI: 10.1371/journal.pone.0225409] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/31/2019] [Indexed: 12/31/2022] Open
Abstract
Biomonitoring programs have evolved beyond the sole use of morphological identification to determine the composition of invertebrate species assemblages in an array of ecosystems. The application of DNA metabarcoding in freshwater systems for assessing benthic invertebrate communities is now being employed to generate biological information for environmental monitoring and assessment. A possible shift from the extraction of DNA from net-collected bulk benthic samples to its extraction directly from water samples for metabarcoding has generated considerable interest based on the assumption that taxon detectability is comparable when using either method. To test this, we studied paired water and benthos samples from a taxon-rich wetland complex, to investigate differences in the detection of arthropod taxa from each sample type. We demonstrate that metabarcoding of DNA extracted directly from water samples is a poor surrogate for DNA extracted from bulk benthic samples, focusing on key bioindicator groups. Our results continue to support the use of bulk benthic samples as a basis for metabarcoding-based biomonitoring, with nearly three times greater total richness in benthic samples compared to water samples. We also demonstrated that few arthropod taxa are shared between collection methods, with a notable lack of key bioindicator EPTO taxa in the water samples. Although species coverage in water could likely be improved through increased sample replication and/or increased sequencing depth, benthic samples remain the most representative, cost-effective method of generating aquatic compositional information via metabarcoding.
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Affiliation(s)
- Mehrdad Hajibabaei
- Centre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
| | - Teresita M. Porter
- Centre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada
| | - Chloe V. Robinson
- Centre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Donald J. Baird
- Environment and Climate Change Canada @ Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Shadi Shokralla
- Centre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Michael T. G. Wright
- Centre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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23
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Porter TM, Morris DM, Basiliko N, Hajibabaei M, Doucet D, Bowman S, Emilson EJS, Emilson CE, Chartrand D, Wainio-Keizer K, Séguin A, Venier L. Variations in terrestrial arthropod DNA metabarcoding methods recovers robust beta diversity but variable richness and site indicators. Sci Rep 2019; 9:18218. [PMID: 31796780 PMCID: PMC6890670 DOI: 10.1038/s41598-019-54532-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 11/13/2019] [Indexed: 11/09/2022] Open
Abstract
Terrestrial arthropod fauna have been suggested as a key indicator of ecological integrity in forest systems. Because phenotypic identification is expert-limited, a shift towards DNA metabarcoding could improve scalability and democratize the use of forest floor arthropods for biomonitoring applications. The objective of this study was to establish the level of field sampling and DNA extraction replication needed for arthropod biodiversity assessments from soil. Processing 15 individually collected soil samples recovered significantly higher median richness (488-614 sequence variants) than pooling the same number of samples (165-191 sequence variants) prior to DNA extraction, and we found no significant richness differences when using 1 or 3 pooled DNA extractions. Beta diversity was robust to changes in methodological regimes. Though our ability to identify taxa to species rank was limited, we were able to use arthropod COI metabarcodes from forest soil to assess richness, distinguish among sites, and recover site indicators based on unnamed exact sequence variants. Our results highlight the need to continue DNA barcoding local taxa during COI metabarcoding studies to help build reference databases. All together, these sampling considerations support the use of soil arthropod COI metabarcoding as a scalable method for biomonitoring.
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Affiliation(s)
- Teresita M Porter
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, ON, P6A 2E5, Canada.
- Biodiversity Institute of Ontario, Centre for Biodiversity Genomics & Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada.
| | - Dave M Morris
- Ministry of Natural Resources and Forestry, Centre for Northern Forest Ecosystem Research, Thunder Bay, ON, P7E 2V6, Canada
| | - Nathan Basiliko
- Laurentian University, Department of Biology and the Vale Living with Lakes Centre, Sudbury, ON, P3E 2C6, Canada
| | - Mehrdad Hajibabaei
- Biodiversity Institute of Ontario, Centre for Biodiversity Genomics & Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Daniel Doucet
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, ON, P6A 2E5, Canada
| | - Susan Bowman
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, ON, P6A 2E5, Canada
| | - Erik J S Emilson
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, ON, P6A 2E5, Canada
| | - Caroline E Emilson
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, ON, P6A 2E5, Canada
| | - Derek Chartrand
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, ON, P6A 2E5, Canada
| | - Kerrie Wainio-Keizer
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, ON, P6A 2E5, Canada
| | - Armand Séguin
- Laurentian Forestry Centre, Natural Resources Canada, Québec, QC, G1V 4C7, Canada
| | - Lisa Venier
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, ON, P6A 2E5, Canada
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Christodoulou M, O'Hara TD, Hugall AF, Arbizu PM. Dark Ophiuroid Biodiversity in a Prospective Abyssal Mine Field. Curr Biol 2019; 29:3909-3912.e3. [PMID: 31630951 DOI: 10.1016/j.cub.2019.09.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/04/2019] [Accepted: 09/05/2019] [Indexed: 01/30/2023]
Abstract
The seafloor contains valuable mineral resources, including polymetallic (or manganese) nodules that form on offshore abyssal plains. The largest and most commercially attractive deposits are located in the Clarion Clipperton Fracture Zone (CCZ), in the eastern Pacific Ocean (EP) between Hawaii and Mexico, where testing of a mineral collection system is set to start soon [1]. The requirement to establish pre-mining environmental management plans has prompted numerous recent biodiversity and DNA barcoding surveys across these remote regions. Here we map DNA sequences from sampled ophiuroids (brittle stars, including post-larvae) of the CCZ and Peru Basin onto a substantial tree of life to show unprecedented levels of abyssal ophiuroid phylogenetic diversity including at least three ancient (>70 Ma), previously unknown clades. While substantial dark (unobserved) biodiversity has been reported from various microbial meta-barcoding projects [2, 3], our data show that we have considerably under-estimated the biodiversity of even the most conspicuous mega-faunal invertebrates [4] of the EP abyssal plain.
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Affiliation(s)
- Magdalini Christodoulou
- German Centre for Marine Biodiversity Research, Senckenberg am Meer, Südstrand 44, 26382 Wilhelmshaven, Germany
| | - Timothy D O'Hara
- Museums Victoria, Sciences Department, 11 Nicholson Street, Carlton 3054, VIC, Australia.
| | - Andrew F Hugall
- Museums Victoria, Sciences Department, 11 Nicholson Street, Carlton 3054, VIC, Australia
| | - Pedro Martinez Arbizu
- German Centre for Marine Biodiversity Research, Senckenberg am Meer, Südstrand 44, 26382 Wilhelmshaven, Germany
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Gauthier M, Konecny‐Dupré L, Nguyen A, Elbrecht V, Datry T, Douady C, Lefébure T. Enhancing DNA metabarcoding performance and applicability with bait capture enrichment and DNA from conservative ethanol. Mol Ecol Resour 2019; 20:79-96. [DOI: 10.1111/1755-0998.13088] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Mailys Gauthier
- CNRS UMR 5023 ENTPE Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés Univ Lyon Université Claude Bernard Lyon 1 Villeurbanne France
- IRSTEA UR‐RiverLy Centre de Lyon‐Villeurbanne Villeurbanne Cedex France
| | - Lara Konecny‐Dupré
- CNRS UMR 5023 ENTPE Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés Univ Lyon Université Claude Bernard Lyon 1 Villeurbanne France
| | | | - Vasco Elbrecht
- Centre for Biodiversity Genomics University of Guelph Guelph Ontario Canada
| | - Thibault Datry
- IRSTEA UR‐RiverLy Centre de Lyon‐Villeurbanne Villeurbanne Cedex France
| | - Christophe Douady
- CNRS UMR 5023 ENTPE Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés Univ Lyon Université Claude Bernard Lyon 1 Villeurbanne France
| | - Tristan Lefébure
- CNRS UMR 5023 ENTPE Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés Univ Lyon Université Claude Bernard Lyon 1 Villeurbanne France
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McGee KM, Robinson CV, Hajibabaei M. Gaps in DNA-Based Biomonitoring Across the Globe. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00337] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Sun Z, Majaneva M, Sokolova E, Rauch S, Meland S, Ekrem T. DNA metabarcoding adds valuable information for management of biodiversity in roadside stormwater ponds. Ecol Evol 2019; 9:9712-9722. [PMID: 31534687 PMCID: PMC6745668 DOI: 10.1002/ece3.5503] [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: 02/25/2019] [Revised: 07/01/2019] [Accepted: 07/05/2019] [Indexed: 12/25/2022] Open
Abstract
ABSTRACT Stormwater ponds are used to compensate for the adverse effects that road runoff might have on the natural environment. Depending on their design and placement, stormwater ponds can act as both refugia and traps for local biodiversity. To evaluate the impact of stormwater ponds on biodiversity, it is critical to use effective and precise methods for identification of life associated with the water body. DNA metabarcoding has recently become a promising tool for identification and assessment of freshwater biodiversity.Using both morphology and DNA metabarcoding, we analyze species richness and biological composition of samples from 12 stormwater ponds and investigate the impact of pond size and pollution levels in the sediments and water column on the macroinvertebrate community structure.DNA metabarcoding captured and identified more than twice the number of taxa compared to morphological identification. The (dis)similarity of macroinvertebrate community composition in different ponds showed that the ponds appear better separated in the results obtained by DNA metabarcoding, but that the explained variation is higher for the results obtained by morphologically identification, since it provides abundance data.The reliance on morphological methods has limited our perception of the aquatic biodiversity in response to anthropogenic stressors, thereby providing inaccurate information for appropriate design and management of stormwater ponds; these drawbacks can be overcome by DNA metabarcoding. Synthesis and applications. The results indicate that DNA metabarcoding is a useful tool in identifying species, especially Diptera, which are difficult to determine. Application of DNA metabarcoding greatly increases the number of species identified at each sampling site, thereby providing a more accurate information regarding the way the ponds function and how they are affected by management. OPEN PRACTICES This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://www.ebi.ac.uk/ena/data/view/PRJEB30841.
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Affiliation(s)
- Zhenhua Sun
- Architecture and Civil Engineering, Water Environment Technology, Chalmers University of TechnologyGothenburgSweden
| | - Markus Majaneva
- Department of Natural HistoryNorwegian University of Science and Technology, NTNU University MuseumTrondheimNorway
| | - Ekaterina Sokolova
- Architecture and Civil Engineering, Water Environment Technology, Chalmers University of TechnologyGothenburgSweden
| | - Sebastien Rauch
- Architecture and Civil Engineering, Water Environment Technology, Chalmers University of TechnologyGothenburgSweden
| | - Sondre Meland
- Faculty of Environmental Sciences and Natural Resource ManagementNorwegian University of Life SciencesÅsNorway
- Norwegian Institute for Water Research (NIVA)OsloNorway
| | - Torbjørn Ekrem
- Department of Natural HistoryNorwegian University of Science and Technology, NTNU University MuseumTrondheimNorway
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Singer GAC, Fahner NA, Barnes JG, McCarthy A, Hajibabaei M. Comprehensive biodiversity analysis via ultra-deep patterned flow cell technology: a case study of eDNA metabarcoding seawater. Sci Rep 2019; 9:5991. [PMID: 30979963 PMCID: PMC6461652 DOI: 10.1038/s41598-019-42455-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/01/2019] [Indexed: 11/09/2022] Open
Abstract
The characterization of biodiversity is a crucial element of ecological investigations as well as environmental assessment and monitoring activities. Increasingly, amplicon-based environmental DNA metabarcoding (alternatively, marker gene metagenomics) is used for such studies given its ability to provide biodiversity data from various groups of organisms simply from analysis of bulk environmental samples such as water, soil or sediments. The Illumina MiSeq is currently the most popular tool for carrying out this work, but we set out to determine whether typical studies were reading enough DNA to detect rare organisms (i.e., those that may be of greatest interest such as endangered or invasive species) present in the environment. We collected sea water samples along two transects in Conception Bay, Newfoundland and analyzed them on the MiSeq with a sequencing depth of 100,000 reads per sample (exceeding the 60,000 per sample that is typical of similar studies). We then analyzed these same samples on Illumina's newest high-capacity platform, the NovaSeq, at a depth of 7 million reads per sample. Not surprisingly, the NovaSeq detected many more taxa than the MiSeq thanks to its much greater sequencing depth. However, contrary to our expectations this pattern was true even in depth-for-depth comparisons. In other words, the NovaSeq can detect more DNA sequence diversity within samples than the MiSeq, even at the exact same sequencing depth. Even when samples were reanalyzed on the MiSeq with a sequencing depth of 1 million reads each, the MiSeq's ability to detect new sequences plateaued while the NovaSeq continued to detect new sequence variants. These results have important biological implications. The NovaSeq found 40% more metazoan families in this environment than the MiSeq, including some of interest such as marine mammals and bony fish so the real-world implications of these findings are significant. These results are most likely associated to the advances incorporated in the NovaSeq, especially a patterned flow cell, which prevents similar sequences that are neighbours on the flow cell (common in metabarcoding studies) from being erroneously merged into single spots by the sequencing instrument. This study sets the stage for incorporating eDNA metabarcoding in comprehensive analysis of oceanic samples in a wide range of ecological and environmental investigations.
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Affiliation(s)
- G A C Singer
- Centre for Environmental Genomics Applications, eDNAtec Inc., St. John's, NL, Canada
| | - N A Fahner
- Centre for Environmental Genomics Applications, eDNAtec Inc., St. John's, NL, Canada
| | - J G Barnes
- Centre for Environmental Genomics Applications, eDNAtec Inc., St. John's, NL, Canada
| | - A McCarthy
- Centre for Environmental Genomics Applications, eDNAtec Inc., St. John's, NL, Canada
| | - M Hajibabaei
- Centre for Environmental Genomics Applications, eDNAtec Inc., St. John's, NL, Canada.
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, ON, Canada.
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Creedy TJ, Ng WS, Vogler AP. Toward accurate species-level metabarcoding of arthropod communities from the tropical forest canopy. Ecol Evol 2019; 9:3105-3116. [PMID: 30962884 PMCID: PMC6434547 DOI: 10.1002/ece3.4839] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 09/28/2018] [Accepted: 10/05/2018] [Indexed: 01/13/2023] Open
Abstract
Metabarcoding of arthropod communities can be used for assessing species diversity in tropical forests but the methodology requires validation for accurate and repeatable species occurrences in complex mixtures. This study investigates how the composition of ecological samples affects the accuracy of species recovery.Starting with field-collected bulk samples from the tropical canopy, the recovery of specimens was tested for subsets of different body sizes and major taxa, by assembling these subsets into increasingly complex composite pools. After metabarcoding, we track whether richness, diversity, and most importantly composition of any size class or taxonomic subset are affected by the presence of other subsets in the mixture.Operational taxonomic units (OTUs) greatly exceeded the number of morphospecies in most taxa, even under very stringent sequencing read filtering. There was no significant effect on the recovered OTU richness of small and medium-sized arthropods when metabarcoded alongside larger arthropods, despite substantial biomass differences in the mixture. The recovery of taxonomic subsets was not generally influenced by the presence of other taxa, although with some exceptions likely due to primer mismatches. Considerable compositional variation within size and taxon-based subcommunities was evident resulting in high beta-diversity among samples from within a single tree canopy, but this beta-diversity was not affected by experimental manipulation.We conclude that OTU recovery in complex arthropod communities, with sufficient sequencing depth and within reasonable size ranges, is not skewed by variable biomass of the constituent species. This could remove the need for time-intensive manual sorting prior to metabarcoding. However, there remains a chance of taxonomic bias, which may be primer-dependent. There will never be a panacea primer; instead, metabarcoding studies should carefully consider whether the aim is broadscale turnover, in which case these biases may not be important, or species lists, in which case separate PCRs and sequencing might be necessary. OTU number inflation remains an issue in metabarcoding and requires bioinformatic development, particularly in read filtering and OTU clustering, and/or greater use of species-identifying sequences generated outside of bulk sequencing.
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Affiliation(s)
- Thomas J. Creedy
- Department of Life SciencesNatural History MuseumLondonUK
- Department of Life SciencesImperial College LondonSilwood Park CampusAscotUK
| | - Wui Shen Ng
- Department of Life SciencesNatural History MuseumLondonUK
- Department of Life SciencesImperial College LondonSilwood Park CampusAscotUK
| | - Alfried P. Vogler
- Department of Life SciencesNatural History MuseumLondonUK
- Department of Life SciencesImperial College LondonSilwood Park CampusAscotUK
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30
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Majaneva M, Diserud OH, Eagle SH, Hajibabaei M, Ekrem T. Choice of DNA extraction method affects DNA metabarcoding of unsorted invertebrate bulk samples. METABARCODING AND METAGENOMICS 2018. [DOI: 10.3897/mbmg.2.26664] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Characterisation of freshwater benthic biodiversity using DNA metabarcoding may allow more cost-effective environmental assessments than the current morphological-based assessment methods. DNA metabarcoding methods where sorting or pre-sorting of samples are avoided altogether are especially interesting, since the time between sampling and taxonomic identification is reduced. Due to the presence of non-target material like plants and sediments in crude samples, DNA extraction protocols become important for maximising DNA recovery and sample replicability. We sampled freshwater invertebrates from six river and lake sites and extracted DNA from homogenised bulk samples in quadruplicate subsamples, using a published method and two commercially available kits: HotSHOT approach, Qiagen DNeasy Blood & Tissue Kit and Qiagen DNeasy PowerPlant Pro Kit. The performance of the selected extraction methods was evaluated by measuring DNA yield and applying DNA metabarcoding to see if the choice of DNA extraction method affects DNA yield and metazoan diversity results. The PowerPlant Kit extractions resulted in the highest DNA yield and a strong significant correlation between sample weight and DNA yield, while the DNA yields of the Blood & Tissue Kit and HotSHOT method did not correlate with the sample weights. Metazoan diversity measures were more repeatable in samples extracted with the PowerPlant Kit compared to those extracted with the HotSHOT method or the Blood & Tissue Kit. Subsampling using Blood & Tissue Kit and HotSHOT extraction failed to describe the same community in the lake samples. Our study exemplifies that the choice of DNA extraction protocol influences the DNA yield as well as the subsequent community analysis. Based on our results, low specimen abundance samples will likely provide more stable results if specimens are sorted prior to DNA extraction and DNA metabarcoding, but the repeatability of the DNA extraction and DNA metabarcoding results was close to ideal in high specimen abundance samples.
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Zhang X, Xia P, Wang P, Yang J, Baird DJ. Omics Advances in Ecotoxicology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:3842-3851. [PMID: 29481739 DOI: 10.1021/acs.est.7b06494] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Toxic substances in the environment generate adverse effects at all levels of biological organization from the molecular level to community and ecosystem. Given this complexity, it is not surprising that ecotoxicologists have struggled to address the full consequences of toxic substance release at ecosystem level, due to the limits of observational and experimental tools to reveal the changes in deep structure at different levels of organization. -Omics technologies, consisting of genomics and ecogenomics, have the power to reveal, in unprecedented detail, the cellular processes of an individual or biodiversity of a community in response to environmental change with high sample/observation throughput. This represents a historic opportunity to transform the way we study toxic substances in ecosystems, through direct linkage of ecological effects with the systems biology of organisms. Three recent examples of -omics advance in the assessment of toxic substances are explored here: (1) the use of functional genomics in the discovery of novel molecular mechanisms of toxicity of chemicals in the environment; (2) the development of laboratory pipelines of dose-dependent, reduced transcriptomics to support high-throughput chemical testing at the biological pathway level; and (3) the use of eDNA metabarcoding approaches for assessing chemical effects on biological communities in mesocosm experiments and through direct observation in field monitoring. -Omics advances in ecotoxicological studies not only generate new knowledge regarding mechanisms of toxicity and environmental effect, improving the relevance and immediacy of laboratory toxicological assessment, but can provide a wholly new paradigm for ecotoxicology by linking ecological models to mechanism-based, systems biology approaches.
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Affiliation(s)
- Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment , Nanjing University , Nanjing 210023 , China
| | - Pu Xia
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment , Nanjing University , Nanjing 210023 , China
| | - Pingping Wang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment , Nanjing University , Nanjing 210023 , China
| | - Jianghu Yang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment , Nanjing University , Nanjing 210023 , China
| | - Donald J Baird
- Environment & Climate Change Canada @ Canadian Rivers Institute, Department of Biology , University of New Brunswick , Fredericton , New Brunswick E3B 5A3 , Canada
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Stubbington R, Chadd R, Cid N, Csabai Z, Miliša M, Morais M, Munné A, Pařil P, Pešić V, Tziortzis I, Verdonschot RCM, Datry T. Biomonitoring of intermittent rivers and ephemeral streams in Europe: Current practice and priorities to enhance ecological status assessments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 618:1096-1113. [PMID: 29074240 DOI: 10.1016/j.scitotenv.2017.09.137] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 09/13/2017] [Accepted: 09/14/2017] [Indexed: 06/07/2023]
Abstract
Intermittent rivers and ephemeral streams (IRES) are common across Europe and dominate some Mediterranean river networks. In all climate zones, IRES support high biodiversity and provide ecosystem services. As dynamic ecosystems that transition between flowing, pool, and dry states, IRES are typically poorly represented in biomonitoring programmes implemented to characterize EU Water Framework Directive ecological status. We report the results of a survey completed by representatives from 20 European countries to identify current challenges to IRES status assessment, examples of best practice, and priorities for future research. We identify five major barriers to effective ecological status classification in IRES: 1. the exclusion of IRES from Water Framework Directive biomonitoring based on their small catchment size; 2. the lack of river typologies that distinguish between contrasting IRES; 3. difficulties in defining the 'reference conditions' that represent unimpacted dynamic ecosystems; 4. classification of IRES ecological status based on lotic communities sampled using methods developed for perennial rivers; and 5. a reliance on taxonomic characterization of local communities. Despite these challenges, we recognize examples of innovative practice that can inform modification of current biomonitoring activity to promote effective IRES status classification. Priorities for future research include reconceptualization of the reference condition approach to accommodate spatiotemporal fluctuations in community composition, and modification of indices of ecosystem health to recognize both taxon-specific sensitivities to intermittence and dispersal abilities, within a landscape context.
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Affiliation(s)
- Rachel Stubbington
- School of Science and Technology, Nottingham Trent University, NG11 8NS, UK.
| | - Richard Chadd
- Environment Agency of England, Spalding, PE11 1DA, UK
| | - Núria Cid
- Freshwater Ecology and Management (FEM) Research Group, Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Catalonia, Spain
| | - Zoltán Csabai
- Department of Hydrobiology, Faculty of Sciences, University of Pécs, Ifjúság útja 6, H-7624 Pécs, Hungary
| | - Marko Miliša
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb, Croatia
| | - Manuela Morais
- Department of Biology, Institute of Earth Sciences, Universidade de Évora, Largo dos Colegiais, 7000 Évora, Portugal
| | - Antoni Munné
- Catalan Water Agency, c/Provença, 204-208, 08036 Barcelona, Catalonia, Spain
| | - Petr Pařil
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Vladimir Pešić
- Department of Biology, University of Montenegro, Cetinjski put b.b., 81000 Podgorica, Montenegro
| | - Iakovos Tziortzis
- Water Development Department, Ministry of Agriculture, Rural Development and Environment, Kennedy Avenue 100-110, Palouriotissa, 1047 Nicosia, Cyprus
| | - Ralf C M Verdonschot
- Wageningen Environmental Research, Wageningen University & Research, P.O. Box 47, 6700 AA, Wageningen, The Netherlands
| | - Thibault Datry
- Irstea, UR MALY, Centre de Lyon-Villeurbanne, 5 rue de la Doua CS70077, 69626 Villeurbanne Cedex, France
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Why We Need Sustainable Networks Bridging Countries, Disciplines, Cultures and Generations for Aquatic Biomonitoring 2.0: A Perspective Derived From the DNAqua-Net COST Action. ADV ECOL RES 2018. [DOI: 10.1016/bs.aecr.2018.01.001] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Andújar C, Arribas P, Gray C, Bruce C, Woodward G, Yu DW, Vogler AP. Metabarcoding of freshwater invertebrates to detect the effects of a pesticide spill. Mol Ecol 2017; 27:146-166. [DOI: 10.1111/mec.14410] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 10/09/2017] [Accepted: 10/16/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Carmelo Andújar
- Department of Life Sciences; Natural History Museum; London UK
- Department of Life Sciences; Imperial College London; Ascot UK
- Grupo de Ecología y Evolución en Islas; Instituto de Productos Naturales y Agrobiología (IPNA-CSIC); San Cristóbal de la Laguna Spain
| | - Paula Arribas
- Department of Life Sciences; Natural History Museum; London UK
- Department of Life Sciences; Imperial College London; Ascot UK
- Grupo de Ecología y Evolución en Islas; Instituto de Productos Naturales y Agrobiología (IPNA-CSIC); San Cristóbal de la Laguna Spain
| | - Clare Gray
- Department of Life Sciences; Imperial College London; Ascot UK
| | | | - Guy Woodward
- Department of Life Sciences; Imperial College London; Ascot UK
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution; Kunming Institute of Zoology; Chinese Academy of Sciences; Kunming Yunnan China
- School of Biological Sciences; University of East Anglia; Norwich Norfolk UK
| | - Alfried P. Vogler
- Department of Life Sciences; Natural History Museum; London UK
- Department of Life Sciences; Imperial College London; Ascot UK
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Collet A, Durand JD, Desmarais E, Cerqueira F, Cantinelli T, Valade P, Ponton D. DNA barcoding post-larvae can improve the knowledge about fish biodiversity: an example from La Reunion, SW Indian Ocean. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:905-918. [PMID: 28984152 DOI: 10.1080/24701394.2017.1383406] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The aim of this study was to demonstrate that fish larvae identified using their COI sequences offer a unique opportunity for improving the knowledge of local fish richness. Fish larvae were sampled at the end of their pelagic phase using light-traps set off the West Coast of La Reunion Island, southwestern Indian Ocean, once per month from October 2014 to March 2015. Among the 5174 larvae caught, 214 morphologically different specimens were selected, 196 successfully barcoded, giving a total of 101 different Barcode Index Numbers (BINs). Among these BINs, 55 had never been recorded in La Reunion exclusive economic zone (EEZ), and 13 were new for the BOLD database. Even if the sampling effort for collecting fish post-larvae during this study was relatively low, it allowed adding at least nine new species to an updated checklist of fishes of La Reunion EEZ.
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Affiliation(s)
| | - Jean-Dominique Durand
- b UMR 9190 MARBEC, IRD-CNRS-IFREMER-UM, Department of Ecology , Evolutionary Biology University of Science, VNUHCM , Ho Chi Minh City , Vietnam
| | - Eric Desmarais
- c ISEM, CNRS , University of Montpellier, IRD, EPHE , Montpellier , France
| | | | - Thomas Cantinelli
- c ISEM, CNRS , University of Montpellier, IRD, EPHE , Montpellier , France
| | | | - Dominique Ponton
- d ENTROPIE, IRD , Université de La Réunion, CNRS, Laboratoire d'Excellence CORAIL , La Réunion , France
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Parker J, Helmstetter AJ, Devey D, Wilkinson T, Papadopulos AST. Field-based species identification of closely-related plants using real-time nanopore sequencing. Sci Rep 2017; 7:8345. [PMID: 28827531 PMCID: PMC5566789 DOI: 10.1038/s41598-017-08461-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 07/12/2017] [Indexed: 01/04/2023] Open
Abstract
Advances in DNA sequencing and informatics have revolutionised biology over the past four decades, but technological limitations have left many applications unexplored. Recently, portable, real-time, nanopore sequencing (RTnS) has become available. This offers opportunities to rapidly collect and analyse genomic data anywhere. However, generation of datasets from large, complex genomes has been constrained to laboratories. The portability and long DNA sequences of RTnS offer great potential for field-based species identification, but the feasibility and accuracy of these technologies for this purpose have not been assessed. Here, we show that a field-based RTnS analysis of closely-related plant species (Arabidopsis spp.) has many advantages over laboratory-based high-throughput sequencing (HTS) methods for species level identification and phylogenomics. Samples were collected and sequenced in a single day by RTnS using a portable, “al fresco” laboratory. Our analyses demonstrate that correctly identifying unknown reads from matches to a reference database with RTnS reads enables rapid and confident species identification. Individually annotated RTnS reads can be used to infer the evolutionary relationships of A. thaliana. Furthermore, hybrid genome assembly with RTnS and HTS reads substantially improved upon a genome assembled from HTS reads alone. Field-based RTnS makes real-time, rapid specimen identification and genome wide analyses possible.
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Affiliation(s)
- Joe Parker
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, UK, TW9 3AB.
| | | | - Dion Devey
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, UK, TW9 3AB
| | - Tim Wilkinson
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, UK, TW9 3AB
| | - Alexander S T Papadopulos
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, UK, TW9 3AB. .,Molecular Ecology and Fisheries Genetics Laboratory, Environment Centre Wales, School of Biological Sciences, Bangor University, Bangor, UK, LL57 2UW.
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Horn T, Häser A. Bamboo tea: reduction of taxonomic complexity and application of DNA diagnostics based on rbcL and matK sequence data. PeerJ 2016; 4:e2781. [PMID: 27957401 PMCID: PMC5149056 DOI: 10.7717/peerj.2781] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 11/10/2016] [Indexed: 11/30/2022] Open
Abstract
Background Names used in ingredient lists of food products are trivial and in their nature rarely precise. The most recent scientific interpretation of the term bamboo (Bambusoideae, Poaceae) comprises over 1,600 distinct species. In the European Union only few of these exotic species are well known sources for food ingredients (i.e., bamboo sprouts) and are thus not considered novel foods, which would require safety assessments before marketing of corresponding products. In contrast, the use of bamboo leaves and their taxonomic origin is mostly unclear. However, products containing bamboo leaves are currently marketed. Methods We analysed bamboo species and tea products containing bamboo leaves using anatomical leaf characters and DNA sequence data. To reduce taxonomic complexity associated with the term bamboo, we used a phylogenetic framework to trace the origin of DNA from commercially available bamboo leaves within the bambusoid subfamily. For authentication purposes, we introduced a simple PCR based test distinguishing genuine bamboo from other leaf components and assessed the diagnostic potential of rbcL and matK to resolve taxonomic entities within the bamboo subfamily and tribes. Results Based on anatomical and DNA data we were able to trace the taxonomic origin of bamboo leaves used in products to the genera Phyllostachys and Pseudosasa from the temperate “woody” bamboo tribe (Arundinarieae). Currently available rbcL and matK sequence data allow the character based diagnosis of 80% of represented bamboo genera. We detected adulteration by carnation in four of eight tea products and, after adapting our objectives, could trace the taxonomic origin of the adulterant to Dianthus chinensis (Caryophyllaceae), a well known traditional Chinese medicine with counter indications for pregnant women.
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Affiliation(s)
- Thomas Horn
- Molecular Cellbiology, Karlsruhe Institute of Technology , Karlsruhe , Germany
| | - Annette Häser
- Molecular Cellbiology, Karlsruhe Institute of Technology , Karlsruhe , Germany
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Hebert PDN, Hollingsworth PM, Hajibabaei M. From writing to reading the encyclopedia of life. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150321. [PMID: 27481778 PMCID: PMC4971178 DOI: 10.1098/rstb.2015.0321] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2016] [Indexed: 11/12/2022] Open
Abstract
Prologue 'As the study of natural science advances, the language of scientific description may be greatly simplified and abridged. This has already been done by Linneaus and may be carried still further by other invention. The descriptions of natural orders and genera may be reduced to short definitions, and employment of signs, somewhat in the manner of algebra, instead of long descriptions. It is more easy to conceive this, than it is to conceive with what facility, and in how short a time, a knowledge of all the objects of natural history may ultimately be acquired; and that which is now considered learning and science, and confined to a few specially devoted to it, may at length be universally possessed in every civilized country and in every rank of life'. J. C. Louden 1829. Magazine of natural history, vol. 1: This article is part of the themed issue 'From DNA barcodes to biomes'.
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Affiliation(s)
- Paul D N Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | | | - Mehrdad Hajibabaei
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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