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Aucone E, Kirchgeorg S, Valentini A, Pellissier L, Deiner K, Mintchev S. Drone-assisted collection of environmental DNA from tree branches for biodiversity monitoring. Sci Robot 2023; 8:eadd5762. [PMID: 36652506 DOI: 10.1126/scirobotics.add5762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The protection and restoration of the biosphere is crucial for human resilience and well-being, but the scarcity of data on the status and distribution of biodiversity puts these efforts at risk. DNA released into the environment by organisms, i.e., environmental DNA (eDNA), can be used to monitor biodiversity in a scalable manner if equipped with the appropriate tool. However, the collection of eDNA in terrestrial environments remains a challenge because of the many potential surfaces and sources that need to be surveyed and their limited accessibility. Here, we propose to survey biodiversity by sampling eDNA on the outer branches of tree canopies with an aerial robot. The drone combines a force-sensing cage with a haptic-based control strategy to establish and maintain contact with the upper surface of the branches. Surface eDNA is then collected using an adhesive surface integrated in the cage of the drone. We show that the drone can autonomously land on a variety of branches with stiffnesses between 1 and 103 newton/meter without prior knowledge of their structural stiffness and with robustness to linear and angular misalignments. Validation in the natural environment demonstrates that our method is successful in detecting animal species, including arthropods and vertebrates. Combining robotics with eDNA sampling from a variety of unreachable aboveground substrates can offer a solution for broad-scale monitoring of biodiversity.
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Affiliation(s)
- Emanuele Aucone
- Environmental Robotics Laboratory, Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland.,Swiss Federal Institute for Forest, Snow, and Landscape Research WSL, Birmensdorf, Switzerland
| | - Steffen Kirchgeorg
- Environmental Robotics Laboratory, Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland.,Swiss Federal Institute for Forest, Snow, and Landscape Research WSL, Birmensdorf, Switzerland
| | | | - Loïc Pellissier
- Swiss Federal Institute for Forest, Snow, and Landscape Research WSL, Birmensdorf, Switzerland.,Ecosystems and Landscape Evolution Group, Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland
| | - Kristy Deiner
- Environmental DNA Group, Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland
| | - Stefano Mintchev
- Environmental Robotics Laboratory, Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland.,Swiss Federal Institute for Forest, Snow, and Landscape Research WSL, Birmensdorf, Switzerland
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2
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Keck F, Hürlemann S, Locher N, Stamm C, Deiner K, Altermatt F. A triad of kicknet sampling, eDNA metabarcoding, and predictive modeling to assess richness of mayflies, stoneflies and caddisflies in rivers. MBMG 2022. [DOI: 10.3897/mbmg.6.79351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Monitoring biodiversity is essential to understand the impacts of human activities and for effective management of ecosystems. Thereby, biodiversity can be assessed through direct collection of targeted organisms, through indirect evidence of their presence (e.g. signs, environmental DNA, camera trap, etc.), or through extrapolations from species distribution and species richness models. Differences in approaches used in biodiversity assessment, however, may come with individual challenges and hinder cross-study comparability. In the context of rapidly developing techniques, we compared three different approaches in order to better understand assessments of aquatic macroinvertebrate diversity. Specifically, we compared the community composition and species richness of three orders of aquatic macroinvertebrates (mayflies, stoneflies, and caddisflies, hereafter EPT) obtained via eDNA metabarcoding and via traditional in situ kicknet sampling to catchment-level based predictions of a species richness model. We used kicknet data from 24 sites in Switzerland and compared taxonomic lists to those obtained using eDNA amplified with two different primer sets. Richness detected by these methods was compared to the independent predictions made by a statistical species richness model, that is, a generalized linear model using landscape-level features to estimate EPT diversity. Despite the ability of eDNA to consistently detect some EPT species found by traditional sampling, we found important discrepancies in community composition between the kicknet and eDNA approaches, particularly at a local scale. We found the EPT-specific primer set fwhF2/EPTDr2n, detected a greater number of targeted EPT species compared to the more general primer set mlCOIintF/HCO2198. Moreover, we found that the species richness measured by eDNA from either primer set was poorly correlated to the richness measured by kicknet sampling (Pearson correlation = 0.27) and that the richness estimated by eDNA and kicknet were poorly correlated with the prediction of the species richness model (Pearson correlation = 0.30 and 0.44, respectively). The weak relationships between the traditional kicknet sampling and eDNA with this model indicates inherent limitations in upscaling species richness estimates, and possibly a limited ability of the model to meet real world expectations. It is also possible that the number of replicates was not sufficient to detect ambiguous correlations. Future challenges include improving the accuracy and sensitivity of each approach individually, yet also acknowledging their respective limitations, in order to best meet stakeholder demands and address the biodiversity crisis we are facing.
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3
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Mauvisseau Q, Harper LR, Sander M, Hanner RH, Kleyer H, Deiner K. The Multiple States of Environmental DNA and What Is Known about Their Persistence in Aquatic Environments. Environ Sci Technol 2022; 56:5322-5333. [PMID: 35435663 PMCID: PMC9069692 DOI: 10.1021/acs.est.1c07638] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Increased use of environmental DNA (eDNA) analysis for indirect species detection has spurred the need to understand eDNA persistence in the environment. Understanding the persistence of eDNA is complex because it exists in a mixture of different states (e.g., dissolved, particle adsorbed, intracellular, and intraorganellar), and each state is expected to have a specific decay rate that depends on environmental parameters. Thus, improving knowledge about eDNA conversion rates between states and the reactions that degrade eDNA in different states is needed. Here, we focus on eukaryotic extraorganismal eDNA, outline how water chemistry and suspended mineral particles likely affect conversion among each eDNA state, and indicate how environmental parameters affect persistence of states in the water column. On the basis of deducing these controlling parameters, we synthesized the eDNA literature to assess whether we could already derive a general understanding of eDNA states persisting in the environment. However, we found that these parameters are often not being measured or reported when measured, and in many cases very few experimental data exist from which to draw conclusions. Therefore, further study of how environmental parameters affect eDNA state conversion and eDNA decay in aquatic environments is needed. We recommend analytic controls that can be used during the processing of water to assess potential losses of different eDNA states if all were present in a water sample, and we outline future experimental work that would help determine the dominant eDNA states in water.
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Affiliation(s)
- Quentin Mauvisseau
- Natural
History Museum, University of Oslo, Sars’ gate 1, 0562 Oslo, Norway
| | - Lynsey R. Harper
- Nature
Metrics Ltd, CABI Site, Bakeham Lane, Egham, Surrey TW20 9TY, United Kingdom
| | - Michael Sander
- Department
of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, CH-8092 Zurich, Switzerland
| | - Robert H. Hanner
- Department
of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Hannah Kleyer
- Department
of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, CH-8092 Zurich, Switzerland
| | - Kristy Deiner
- Department
of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, CH-8092 Zurich, Switzerland
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4
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Rodriguez-Ezpeleta N, Morissette O, Bean CW, Manu S, Banerjee P, Lacoursière-Roussel A, Beng KC, Alter SE, Roger F, Holman LE, Stewart KA, Monaghan MT, Mauvisseau Q, Mirimin L, Wangensteen OS, Antognazza CM, Helyar SJ, de Boer H, Monchamp ME, Nijland R, Abbott CL, Doi H, Barnes MA, Leray M, Hablützel PI, Deiner K. Trade-offs between reducing complex terminology and producing accurate interpretations from environmental DNA: Comment on "Environmental DNA: What's behind the term?" by Pawlowski et al., (2020). Mol Ecol 2021; 30:4601-4605. [PMID: 34036646 PMCID: PMC8698002 DOI: 10.1111/mec.15942] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/31/2021] [Accepted: 04/28/2021] [Indexed: 12/12/2022]
Abstract
In a recent paper, “Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring,” Pawlowski et al. argue that the term eDNA should be used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra‐organismal DNA from macro‐organisms. We agree with this view. However, we are concerned that their proposed two‐level terminology specifying sampling environment and targeted taxa is overly simplistic and might hinder rather than improve clear communication about environmental DNA and its use in biomonitoring. This terminology is based on categories that are often difficult to assign and uninformative, and it overlooks a fundamental distinction within eDNA: the type of DNA (organismal or extra‐organismal) from which ecological interpretations are derived.
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Affiliation(s)
| | - Olivier Morissette
- Direction de l'expertise sur la Faune Aquatique, Ministère des Forêt de la Faune et des Parcs, Québec, QC, Canada
| | - Colin W Bean
- Scottish Centre for Ecology and the Natural Environment, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Shivakumara Manu
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Pritam Banerjee
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan.,Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Anaïs Lacoursière-Roussel
- Government of Canada, Department of Fisheries and Oceans, St. Andrews Biological Station, St. Andrews, NB, Canada
| | - Kingsly C Beng
- Department of Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - S Elizabeth Alter
- Department of Biology and Chemistry, California State University Monterey Bay, Seaside, CA, USA
| | - Fabian Roger
- Centre for Environmental and Climate Research (CEC), Lund University, Lund, Sweden
| | - Luke E Holman
- School of Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, UK
| | - Kathryn A Stewart
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, the Netherlands
| | - Michael T Monaghan
- Department of Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.,Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | | | - Luca Mirimin
- Department of Natural Sciences, School of Science and Computing, Galway-Mayo Institute of Technology, Galway, Ireland
| | - Owen S Wangensteen
- Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø, Norway
| | - Caterina M Antognazza
- Department of Theoretical and Applied Sciences, University of Insubria, Varese, Italy
| | - Sarah J Helyar
- Institute of Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Hugo de Boer
- Natural History Museum, University of Oslo, Oslo, Norway
| | | | - Reindert Nijland
- Marine Animal Ecology Group, Wageningen University, Wageningen, The Netherlands
| | - Cathryn L Abbott
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Hideyuki Doi
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Japan
| | - Matthew A Barnes
- Department of Natural Resources Management, Texas Tech University, Lubbock, TX, USA
| | - Matthieu Leray
- Smithsonian Tropical Research Institute, Smithsonian Institution, Panama City, Panama
| | | | - Kristy Deiner
- Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
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5
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Lacoursière-Roussel A, Deiner K. Environmental DNA is not the tool by itself. J Fish Biol 2021; 98:383-386. [PMID: 31644816 DOI: 10.1111/jfb.14177] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 10/22/2019] [Indexed: 05/19/2023]
Affiliation(s)
- Anaïs Lacoursière-Roussel
- St. Andrews Biological Station (SABS), Fisheries and Oceans Canada (DFO), St. Andrews, New Brunswick, Canada
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6
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Sales NG, Wangensteen OS, Carvalho DC, Deiner K, Præbel K, Coscia I, McDevitt AD, Mariani S. Space-time dynamics in monitoring neotropical fish communities using eDNA metabarcoding. Sci Total Environ 2021; 754:142096. [PMID: 32898783 DOI: 10.1016/j.scitotenv.2020.142096] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/24/2020] [Accepted: 08/29/2020] [Indexed: 06/11/2023]
Abstract
The biodiverse Neotropical ecoregion remains insufficiently assessed, poorly managed, and threatened by unregulated human activities. Novel, rapid and cost-effective DNA-based approaches are valuable to improve understanding of the biological communities and for biomonitoring in remote areas. Here, we evaluate the potential of environmental DNA (eDNA) metabarcoding for assessing the structure and distribution of fish communities by analysing water and sediment from 11 locations along the Jequitinhonha River catchment (Brazil). Each site was sampled twice, before and after a major rain event in a five-week period and fish diversity was estimated using high-throughput sequencing of 12S rRNA amplicons. In total, 252 Molecular Operational Taxonomic Units (MOTUs) and 34 fish species were recovered, including endemic, introduced, and previously unrecorded species for this basin. Spatio-temporal variation of eDNA from fish assemblages was observed and species richness was nearly twice as high before the major rain event compared to afterwards. Yet, peaks of diversity were primarily associated with only four of the locations. No correlation between β-diversity and longitudinal distance or presence of dams was detected, but low species richness observed at sites located near dams might that these anthropogenic barriers may have an impact on local fish diversity. Unexpectedly high α-diversity levels recorded at the river mouth suggest that these sections should be further evaluated as putative "eDNA reservoirs" for rapid monitoring. By uncovering spatio-temporal changes, unrecorded biodiversity components, and putative anthropogenic impacts on fish assemblages, we further strengthen the potential of eDNA metabarcoding as a biomonitoring tool, especially in regions often neglected or difficult to access.
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Affiliation(s)
- Naiara Guimarães Sales
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, UK; CESAM - Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal.
| | - Owen Simon Wangensteen
- Norwegian College of Fishery Science, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Daniel Cardoso Carvalho
- Programa de Pós-graduação em Biologia de Vertebrados, Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, Brazil
| | | | - Kim Præbel
- Norwegian College of Fishery Science, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Ilaria Coscia
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, UK
| | - Allan D McDevitt
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, UK
| | - Stefano Mariani
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, UK; School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK
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7
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McElroy ME, Dressler TL, Titcomb GC, Wilson EA, Deiner K, Dudley TL, Eliason EJ, Evans NT, Gaines SD, Lafferty KD, Lamberti GA, Li Y, Lodge DM, Love MS, Mahon AR, Pfrender ME, Renshaw MA, Selkoe KA, Jerde CL. Calibrating Environmental DNA Metabarcoding to Conventional Surveys for Measuring Fish Species Richness. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00276] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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8
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Mansfeldt C, Deiner K, Mächler E, Fenner K, Eggen RIL, Stamm C, Schönenberger U, Walser JC, Altermatt F. Microbial community shifts in streams receiving treated wastewater effluent. Sci Total Environ 2020; 709:135727. [PMID: 31887504 DOI: 10.1016/j.scitotenv.2019.135727] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 10/22/2019] [Accepted: 11/22/2019] [Indexed: 05/17/2023]
Abstract
Wastewater treatment plant (WWTP) effluents release not only chemical constituents in watersheds, but also contain microorganisms. Thus, an understanding of what microorganisms are released and how they change microbial communities within natural streams is needed. To characterize the community shifts in streams receiving WWTP effluent, we sampled water-column microorganisms from upstream, downstream, and the effluent of WWTPs located on 23 headwater streams in which no other effluent was released upstream. We characterized the bacterial community by sequencing the V3-V4 region of the 16S rRNA gene. We hypothesized that the downstream community profile would be a hydraulic mixture between the two sources (i.e., upstream and effluent). In ordination analyses, the downstream bacterial community profile was a mixture between the upstream and effluent. For 14 of the sites, the main contribution (>50%) to the downstream community originated from bacteria in the WWTP effluent and significant shifts in relative abundance of specific sequence variants were detected. These shifts in sequence variants may serve as general bioindicators of wastewater-effluent influenced streams, with a human-gut related Ruminococcus genus displaying the highest shift (30-fold higher abundances downstream). However, not all taxa composition changes were predicted based on hydraulic mixing alone. Specifically, the decrease of Cyanobacteria/Chloroplast reads was not adequately described by hydraulic mixing. The potential alteration of stream microbial communities via a high inflow of human-gut related bacteria and a decrease in autotrophic functional groups resulting from WWTP effluent creates the potential for general shifts in stream ecosystem function.
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Affiliation(s)
- Cresten Mansfeldt
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Kristy Deiner
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland; Natural History Museum London, London, UK.
| | - Elvira Mächler
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland; Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Kathrin Fenner
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland; Department of Environmental Systems Science, ETH, Zürich, Switzerland; Chemistry Department, University of Zürich, Zürich, Switzerland
| | - Rik I L Eggen
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland; Department of Environmental Systems Science, ETH, Zürich, Switzerland
| | - Christian Stamm
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Urs Schönenberger
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | | | - Florian Altermatt
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland; Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
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9
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Blackman R, Mächler E, Altermatt F, Arnold A, Beja P, Boets P, Egeter B, Elbrecht V, Filipe AF, Jones J, Macher J, Majaneva M, Martins F, Múrria C, Meissner K, Pawlowski J, Schmidt Yáñez P, Zizka V, Leese F, Price B, Deiner K. Advancing the use of molecular methods for routine freshwater macroinvertebrate biomonitoring – the need for calibration experiments. MBMG 2019. [DOI: 10.3897/mbmg.3.34735] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Over the last decade, steady advancements have been made in the use of DNA-based methods for detection of species in a wide range of ecosystems. This progress has culminated in molecular monitoring methods being employed for the detection of several species for enforceable management purposes of endangered, invasive, and illegally harvested species worldwide. However, the routine application of DNA-based methods to monitor whole communities (typically a metabarcoding approach) in order to assess the status of ecosystems continues to be limited. In aquatic ecosystems, the limited use is particularly true for macroinvertebrate communities. As part of the DNAqua-Net consortium, a structured discussion was initiated with the aim to identify potential molecular methods for freshwater macroinvertebrate community assessment and identify important knowledge gaps for their routine application. We focus on three complementary DNA sources that can be metabarcoded: 1) DNA from homogenised samples (bulk DNA), 2) DNA extracted from sample preservative (fixative DNA), and 3) environmental DNA (eDNA) from water or sediment. We provide a brief overview of metabarcoding macroinvertebrate communities from each DNA source and identify challenges for their application to routine monitoring. To advance the utilisation of DNA-based monitoring for macroinvertebrates, we propose an experimental design template for a series of methodological calibration tests. The template compares sources of DNA with the goal of identifying the effects of molecular processing steps on precision and accuracy. Furthermore, the same samples will be morphologically analysed, which will enable the benchmarking of molecular to traditional processing approaches. In doing so we hope to highlight pathways for the development of DNA-based methods for the monitoring of freshwater macroinvertebrates.
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10
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Deiner K, Lopez J, Bourne S, Holman L, Seymour M, Grey EK, Lacoursière A, Li Y, Renshaw MA, Pfrender ME, Rius M, Bernatchez L, Lodge DM. Optimising the detection of marine taxonomic richness using environmental DNA metabarcoding: the effects of filter material, pore size and extraction method. MBMG 2018. [DOI: 10.3897/mbmg.2.28963] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The analysis of environmental DNA (eDNA) using metabarcoding has increased in use as a method for tracking biodiversity of ecosystems. Little is known about eDNA in marine human-modified environments, such as commercial ports, which are key sites to monitor for anthropogenic impacts on coastal ecosystems. To optimise an eDNA metabarcoding protocol in these environments, seawater samples were collected in a commercial port and methodologies for concentrating and purifying eDNA were tested for their effect on eukaryotic DNA yield and subsequent richness of Operational Taxonomic Units (OTUs). Different filter materials [Cellulose Nitrate (CN) and Glass Fibre (GF)], with different pore sizes (0.5 µm, 0.7 µm and 1.2 µm) and three previously published liquid phase extraction methods were tested. The number of eukaryotic OTUs detected differed by a factor of three amongst the method combinations. The combination of CN filters with phenol-chloroform-isoamyl alcohol extractions recovered a higher amount of eukaryotic DNA and OTUs compared to GF filters and the chloroform-isoamyl alcohol extraction method. Pore size was not independent of filter material but did affect the yield of eukaryotic DNA. For the OTUs assigned to a highly successful non-indigenous species, Styelaclava, the two extraction methods with phenol significantly outperformed the extraction method without phenol; other experimental treatments did not contribute significantly to detection. These results highlight that careful consideration of methods is warranted because choice of filter material and extraction method create false negative detections of marine eukaryotic OTUs and underestimate taxonomic richness from environmental samples.
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11
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Lacoursière‐Roussel A, Howland K, Normandeau E, Grey EK, Archambault P, Deiner K, Lodge DM, Hernandez C, Leduc N, Bernatchez L. eDNA metabarcoding as a new surveillance approach for coastal Arctic biodiversity. Ecol Evol 2018; 8:7763-7777. [PMID: 30250661 PMCID: PMC6144963 DOI: 10.1002/ece3.4213] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/20/2018] [Accepted: 04/23/2018] [Indexed: 12/21/2022] Open
Abstract
Because significant global changes are currently underway in the Arctic, creating a large-scale standardized database for Arctic marine biodiversity is particularly pressing. This study evaluates the potential of aquatic environmental DNA (eDNA) metabarcoding to detect Arctic coastal biodiversity changes and characterizes the local spatio-temporal distribution of eDNA in two locations. We extracted and amplified eDNA using two COI primer pairs from ~80 water samples that were collected across two Canadian Arctic ports, Churchill and Iqaluit, based on optimized sampling and preservation methods for remote regions surveys. Results demonstrate that aquatic eDNA surveys have the potential to document large-scale Arctic biodiversity change by providing a rapid overview of coastal metazoan biodiversity, detecting nonindigenous species, and allowing sampling in both open water and under the ice cover by local northern-based communities. We show that DNA sequences of ~50% of known Canadian Arctic species and potential invaders are currently present in public databases. A similar proportion of operational taxonomic units was identified at the species level with eDNA metabarcoding, for a total of 181 species identified at both sites. Despite the cold and well-mixed coastal environment, species composition was vertically heterogeneous, in part due to river inflow in the estuarine ecosystem, and differed between the water column and tide pools. Thus, COI-based eDNA metabarcoding may quickly improve large-scale Arctic biomonitoring using eDNA, but we caution that aquatic eDNA sampling needs to be standardized over space and time to accurately evaluate community structure changes.
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Affiliation(s)
| | - Kimberly Howland
- Central and Arctic RegionFisheries and Oceans CanadaFreshwater InstituteWinnipegMBCanada
| | - Eric Normandeau
- Department of BiologyInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Erin K. Grey
- Division of Science, Mathematics and TechnologyGovernors State UniversityUniversity ParkILUSA
| | | | - Kristy Deiner
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZürichSwitzerland
| | - David M. Lodge
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNYUSA
| | - Cecilia Hernandez
- Department of BiologyInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Noémie Leduc
- Department of BiologyInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Louis Bernatchez
- Department of BiologyInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
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12
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Li Y, Evans NT, Renshaw MA, Jerde CL, Olds BP, Shogren AJ, Deiner K, Lodge DM, Lamberti GA, Pfrender ME. Estimating fish alpha- and beta-diversity along a small stream with environmental DNA metabarcoding. MBMG 2018. [DOI: 10.3897/mbmg.2.24262] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Environmental DNA (eDNA) metabarcoding has been increasingly applied to biodiversity surveys in stream ecosystems. In stream networks, the accuracy of eDNA-based biodiversity assessment depends on whether the upstream eDNA influx affects downstream detection. Biodiversity assessment in low-discharge streams should be less influenced by eDNA transport than in high-discharge streams. We estimated α- and β-diversity of the fish community from eDNA samples collected in a small Michigan (USA) stream from its headwaters to its confluence with a larger river. We found that α-diversity increased from upstream to downstream and, as predicted, we found a significant positive correlation between β-diversity and physical distance (stream length) between locations indicating species turnover along the longitudinal stream gradient. Sample replicates and different genetic markers showed similar species composition, supporting the consistency of the eDNA metabarcoding approach to estimate α- and β-diversity of fishes in low-discharge streams.
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13
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Seymour M, Durance I, Cosby BJ, Ransom-Jones E, Deiner K, Ormerod SJ, Colbourne JK, Wilgar G, Carvalho GR, de Bruyn M, Edwards F, Emmett BA, Bik HM, Creer S. Acidity promotes degradation of multi-species environmental DNA in lotic mesocosms. Commun Biol 2018; 1:4. [PMID: 30271891 PMCID: PMC6123786 DOI: 10.1038/s42003-017-0005-3] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/26/2017] [Indexed: 01/12/2023] Open
Abstract
Accurate quantification of biodiversity is fundamental to understanding ecosystem function and for environmental assessment. Molecular methods using environmental DNA (eDNA) offer a non-invasive, rapid, and cost-effective alternative to traditional biodiversity assessments, which require high levels of expertise. While eDNA analyses are increasingly being utilized, there remains considerable uncertainty regarding the dynamics of multispecies eDNA, especially in variable systems such as rivers. Here, we utilize four sets of upland stream mesocosms, across an acid–base gradient, to assess the temporal and environmental degradation of multispecies eDNA. Sampling included water column and biofilm sampling over time with eDNA quantified using qPCR. Our findings show that the persistence of lotic multispecies eDNA, sampled from water and biofilm, decays to non-detectable levels within 2 days and that acidic environments accelerate the degradation process. Collectively, the results provide the basis for a predictive framework for the relationship between lotic eDNA degradation dynamics in spatio-temporally dynamic river ecosystems. Mathew Seymour et al. investigate the persistence of environmental DNA (eDNA) in river systems in environments of varying pH. Using four sets of upland stream mesocosms, they find that eDNA degrades to non-detectable levels within two days and this degradation is accelerated in acidic environments.
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Affiliation(s)
- Mathew Seymour
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK.
| | - Isabelle Durance
- Water Research Institute and Cardiff School of Biosciences, Cardiff, CF10 3AX, UK
| | - Bernard J Cosby
- NERC Centre for Ecology & Hydrology, Environment Centre Wales, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK
| | - Emma Ransom-Jones
- School of Biological Sciences and Natural Resources and Geography, Bangor University, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK
| | - Kristy Deiner
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Steve J Ormerod
- Water Research Institute and Cardiff School of Biosciences, Cardiff, CF10 3AX, UK
| | - John K Colbourne
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Gregory Wilgar
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Gary R Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Mark de Bruyn
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | | | - Bridget A Emmett
- NERC Centre for Ecology & Hydrology, Environment Centre Wales, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK
| | - Holly M Bik
- Department of Nematology, University of California-Riverside, Riverside, CA, 92521, USA
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK.
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14
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Deiner K, Bik HM, Mächler E, Seymour M, Lacoursière-Roussel A, Altermatt F, Creer S, Bista I, Lodge DM, de Vere N, Pfrender ME, Bernatchez L. Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Mol Ecol 2017; 26:5872-5895. [PMID: 28921802 DOI: 10.1111/mec.14350] [Citation(s) in RCA: 583] [Impact Index Per Article: 83.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 08/31/2017] [Accepted: 09/05/2017] [Indexed: 12/14/2022]
Abstract
The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing ("HTS") platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed "environmental DNA" or "eDNA"). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called "eDNA metabarcoding" and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education.
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Affiliation(s)
- Kristy Deiner
- Atkinson Center for a Sustainable Future, Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Holly M Bik
- Department of Nematology, University of California, Riverside, CA, USA
| | - Elvira Mächler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Mathew Seymour
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales Building, Bangor University, Bangor, Gwynedd, UK
| | | | - Florian Altermatt
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales Building, Bangor University, Bangor, Gwynedd, UK
| | - Iliana Bista
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales Building, Bangor University, Bangor, Gwynedd, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - David M Lodge
- Atkinson Center for a Sustainable Future, Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Natasha de Vere
- Conservation and Research Department, National Botanic Garden of Wales, Llanarthne, Carmarthenshire, UK.,Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Michael E Pfrender
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, Notre Dame, IN, USA
| | - Louis Bernatchez
- IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Québec, QC, Canada
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15
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Abadía-Cardoso A, Freimer NB, Deiner K, Garza JC. Molecular Population Genetics of the Northern Elephant Seal Mirounga angustirostris. J Hered 2017; 108:618-627. [PMID: 28821186 PMCID: PMC5892393 DOI: 10.1093/jhered/esx053] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 06/21/2017] [Indexed: 11/13/2022] Open
Abstract
The northern elephant seal, Mirounga angustirostris, was heavily hunted and declared extinct in the 19th century. However, a colony remained on remote Guadalupe Island, Mexico and the species has since repopulated most of its historical distribution. Here, we present a comprehensive evaluation of genetic variation in the species. First, we assess the effect of the demographic bottleneck on microsatellite variability and compare it with that found in other pinnipeds, demonstrating levels of variation similar to that in species that continue to be threatened with extinction. Next, we use sequence data from these markers to demonstrate that some of the limited polymorphism predates the bottleneck. However, most contemporary variation appears to have arisen recently and persisted due to exponential growth. We also describe how we use the range in allele size of microsatellites to estimate ancestral effective population size before the bottleneck, demonstrating a large reduction in effective size. We then employ a classical method for bacteria to estimate the microsatellite mutation rate in the species, deriving an estimate that is extremely similar to that estimated for a similar set of loci in humans, indicating consistency of microsatellite mutation rates in mammals. Finally, we find slight significant structure between some geographically separated colonies, although its biological significance is unclear. This work demonstrates that genetic analysis can be useful for evaluating the population biology of the northern elephant seal, in spite of the bottleneck that removed most genetic variation from the species.
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Affiliation(s)
- Alicia Abadía-Cardoso
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada Km 103, Pedregal Playitas, 22860 Ensenada, BC, Mexico; University of California, Santa Cruz, 110 McAllister Way, Santa Cruz, CA 95060; Southwest Fisheries Science Center, National Marine Fisheries Service, 110 McAllister Way, Santa Cruz, CA 95060; Center for Neurobehavioral Genetics, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095. Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Rd., Ithaca, NY 14850
| | - Nelson B Freimer
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada Km 103, Pedregal Playitas, 22860 Ensenada, BC, Mexico; University of California, Santa Cruz, 110 McAllister Way, Santa Cruz, CA 95060; Southwest Fisheries Science Center, National Marine Fisheries Service, 110 McAllister Way, Santa Cruz, CA 95060; Center for Neurobehavioral Genetics, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095. Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Rd., Ithaca, NY 14850
| | - Kristy Deiner
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada Km 103, Pedregal Playitas, 22860 Ensenada, BC, Mexico; University of California, Santa Cruz, 110 McAllister Way, Santa Cruz, CA 95060; Southwest Fisheries Science Center, National Marine Fisheries Service, 110 McAllister Way, Santa Cruz, CA 95060; Center for Neurobehavioral Genetics, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095. Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Rd., Ithaca, NY 14850
| | - John Carlos Garza
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada Km 103, Pedregal Playitas, 22860 Ensenada, BC, Mexico; University of California, Santa Cruz, 110 McAllister Way, Santa Cruz, CA 95060; Southwest Fisheries Science Center, National Marine Fisheries Service, 110 McAllister Way, Santa Cruz, CA 95060; Center for Neurobehavioral Genetics, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095. Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Rd., Ithaca, NY 14850
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16
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Deiner K, Renshaw MA, Li Y, Olds BP, Lodge DM, Pfrender ME. Long‐range PCR allows sequencing of mitochondrial genomes from environmental DNA. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12836] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kristy Deiner
- Department of Biological Sciences Environmental Change Initiative University of Notre Dame Notre Dame IN USA
| | - Mark A. Renshaw
- Department of Biological Sciences Environmental Change Initiative University of Notre Dame Notre Dame IN USA
| | - Yiyuan Li
- Department of Biological Sciences Environmental Change Initiative University of Notre Dame Notre Dame IN USA
| | - Brett P. Olds
- Department of Biological Sciences Environmental Change Initiative University of Notre Dame Notre Dame IN USA
| | - David M. Lodge
- Department of Biological Sciences Environmental Change Initiative University of Notre Dame Notre Dame IN USA
| | - Michael E. Pfrender
- Department of Biological Sciences Environmental Change Initiative University of Notre Dame Notre Dame IN USA
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17
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Abstract
Wetland habitats across the world are experiencing rapid modification and loss due to accelerating habitat conversion. Impacts to wetland habitats are particularly acute in California where up to 90% of wetland habitats have been modified or lost. Vernal pool ecosystems have therefore undergone a dramatic loss in habitat and along with them an entire endemic fauna is under threat of extinction. Recent efforts to conserve vernal pool habitat and associated species have involved restoration and creation of vernal pools as well as translocations of threatened species. The vernal pool fairy shrimp, Branchinecta lynchi, is one of several endemic and federally listed species being targeted for translocations. To guide reintroduction and conservation, detailed information on range-wide population structure and diversity is needed. We collected genetic data from two mitochondrial genes throughout the known extant range of B. lynchi to elucidate population structure and diversity of the species. We found support for phylogeographic structure throughout the range of B. lynch associated with isolated watersheds and vernal pool regions previously identified in the recovery plan for the species. The underlying mechanisms responsible for this broad pattern of genetic structure have yet to be identified. However, the evidence of only a few haplotypes being shared across the species range and patterns of isolation by distance within vernal pool regions suggests dispersal limitation may play a role. These results stress that conservation programs, at a minimum, should consider using individuals from regional populations as sources for reintroductions to maintain historical patterns of genetic differentiation. Additionally, because genetic structure is associated with vernal pool regions which are based on local hydrology and geology, translocations should proceed considering the distance between donor and recipient sites.
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Affiliation(s)
- Kristy Deiner
- Department of Animal Science, University of California Davis, Davis, California, United States of America
- * E-mail:
| | - Joshua M. Hull
- Sacramento Fish and Wildlife Office, U.S. Fish and Wildlife Service, Sacramento, California, United States of America
| | - Bernie May
- Department of Animal Science, University of California Davis, Davis, California, United States of America
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18
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Leese F, Altermatt F, Bouchez A, Ekrem T, Hering D, Meissner K, Mergen P, Pawlowski J, Piggott J, Rimet F, Steinke D, Taberlet P, Weigand A, Abarenkov K, Beja P, Bervoets L, Björnsdóttir S, Boets P, Boggero A, Bones A, Borja Á, Bruce K, Bursić V, Carlsson J, Čiampor F, Čiamporová-Zatovičová Z, Coissac E, Costa F, Costache M, Creer S, Csabai Z, Deiner K, DelValls Á, Drakare S, Duarte S, Eleršek T, Fazi S, Fišer C, Flot JF, Fonseca V, Fontaneto D, Grabowski M, Graf W, Guðbrandsson J, Hellström M, Hershkovitz Y, Hollingsworth P, Japoshvili B, Jones J, Kahlert M, Kalamujic Stroil B, Kasapidis P, Kelly M, Kelly-Quinn M, Keskin E, Kõljalg U, Ljubešić Z, Maček I, Mächler E, Mahon A, Marečková M, Mejdandzic M, Mircheva G, Montagna M, Moritz C, Mulk V, Naumoski A, Navodaru I, Padisák J, Pálsson S, Panksep K, Penev L, Petrusek A, Pfannkuchen M, Primmer C, Rinkevich B, Rotter A, Schmidt-Kloiber A, Segurado P, Speksnijder A, Stoev P, Strand M, Šulčius S, Sundberg P, Traugott M, Tsigenopoulos C, Turon X, Valentini A, van der Hoorn B, Várbíró G, Vasquez Hadjilyra M, Viguri J, Vitonytė I, Vogler A, Vrålstad T, Wägele W, Wenne R, Winding A, Woodward G, Zegura B, Zimmermann J. DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe. RIO 2016. [DOI: 10.3897/rio.2.e11321] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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19
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Adamowicz SJ, Chain FJJ, Clare EL, Deiner K, Dincă V, Elías-Gutiérrez M, Hausmann A, Hogg ID, Kekkonen M, Lijtmaer DA, Naaum A, Steinke D, Valdez-Moreno M, Van der Bank M, Wilson JJ, Xu J. From Barcodes to Biomes: Special Issues from the 6th International Barcode of Life Conference. Genome 2016; 59:v-ix. [PMID: 27829307 DOI: 10.1139/gen-2016-0195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Sarah J Adamowicz
- a Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Frédéric J J Chain
- b Department of Biology, McGill University, 1205 Docteur Penfield, Montreal, QC H3A 1B1, Canada
| | - Elizabeth L Clare
- c School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, U.K
| | - Kristy Deiner
- d Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall A406A, 215 Tower Rd., Ithaca, NY 14850, USA
| | - Vlad Dincă
- e Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada; Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, 08003, Barcelona, Spain
| | - Manuel Elías-Gutiérrez
- f El Colegio de la Frontera Sur, Av. Centenario Km 5.5, Chetumal, Quintana Roo 77014, Mexico
| | - Axel Hausmann
- g SNSB - Zoologische Staatssammlung München, Münchhausenstr. 21, D-81247 Munich, Germany
| | - Ian D Hogg
- h Centre for Biodiversity and Ecology Research, Department of Biological Sciences, University of Waikato, Private Bag 3105, Hamilton, New Zealand
| | - Mari Kekkonen
- i Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Darío A Lijtmaer
- j División Ornitología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Buenos Aires, Argentina
| | - Amanda Naaum
- i Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Dirk Steinke
- i Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Martha Valdez-Moreno
- f El Colegio de la Frontera Sur, Av. Centenario Km 5.5, Chetumal, Quintana Roo 77014, Mexico
| | - Michelle Van der Bank
- k African Centre for DNA Barcoding, University of Johannesburg, PO Box 524, APK Campus, 2006 Johannesburg, South Africa
| | - John-James Wilson
- l Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Jianping Xu
- m Department of Biology, McMaster University, 12809 Main St. West, Hamilton, ON L8S 4K1, Canada
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20
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Adamowicz SJ, Chain FJJ, Clare EL, Deiner K, Dincă V, Elías-Gutiérrez M, Hausmann A, Hogg ID, Kekkonen M, Lijtmaer DA, Naaum A, Steinke D, Valdez-Moreno M, Van der Bank M, Wilson JJ, Xu J. From Barcodes to Biomes: Special Issues from the 6th International Barcode of Life Conference. Genome 2016; 59:v-ix. [PMID: 27611699 DOI: 10.1139/gen-2016-0159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Sarah J Adamowicz
- a Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Frédéric J J Chain
- b Department of Biology, McGill University, 1205 Docteur Penfield, Montreal, QC H3A 1B1, Canada
| | - Elizabeth L Clare
- c School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, U.K
| | - Kristy Deiner
- d Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall A406A, 215 Tower Rd., Ithaca, NY 14850, USA
| | - Vlad Dincă
- e Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada; Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, 08003, Barcelona, Spain
| | - Manuel Elías-Gutiérrez
- f El Colegio de la Frontera Sur, Av. Centenario Km 5.5, Chetumal, Quintana Roo 77014, Mexico
| | - Axel Hausmann
- g SNSB - Zoologische Staatssammlung München, Münchhausenstr. 21, D-81247 Munich, Germany
| | - Ian D Hogg
- h Centre for Biodiversity and Ecology Research, Department of Biological Sciences, University of Waikato, Private Bag 3105, Hamilton, New Zealand
| | - Mari Kekkonen
- i Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Darío A Lijtmaer
- j División Ornitología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Buenos Aires, Argentina
| | - Amanda Naaum
- i Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Dirk Steinke
- i Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Martha Valdez-Moreno
- f El Colegio de la Frontera Sur, Av. Centenario Km 5.5, Chetumal, Quintana Roo 77014, Mexico
| | - Michelle Van der Bank
- k African Centre for DNA Barcoding, University of Johannesburg, PO Box 524, APK Campus, 2006 Johannesburg, South Africa
| | - John-James Wilson
- l Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Jianping Xu
- m Department of Biology, McMaster University, 12809 Main St. West, Hamilton, ON L8S 4K1, Canada
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21
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Deiner K, Fronhofer EA, Mächler E, Walser JC, Altermatt F. Environmental DNA reveals that rivers are conveyer belts of biodiversity information. Nat Commun 2016; 7:12544. [PMID: 27572523 PMCID: PMC5013555 DOI: 10.1038/ncomms12544] [Citation(s) in RCA: 200] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 07/12/2016] [Indexed: 01/07/2023] Open
Abstract
DNA sampled from the environment (eDNA) is a useful way to uncover biodiversity patterns. By combining a conceptual model and empirical data, we test whether eDNA transported in river networks can be used as an integrative way to assess eukaryotic biodiversity for broad spatial scales and across the land-water interface. Using an eDNA metabarcode approach, we detect 296 families of eukaryotes, spanning 19 phyla across the catchment of a river. We show for a subset of these families that eDNA samples overcome spatial autocorrelation biases associated with the classical community assessments by integrating biodiversity information over space. In addition, we demonstrate that many terrestrial species are detected; thus suggesting eDNA in river water also incorporates biodiversity information across terrestrial and aquatic biomes. Environmental DNA transported in river networks offers a novel and spatially integrated way to assess the total biodiversity for whole landscapes and will transform biodiversity data acquisition in ecology.
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Affiliation(s)
- Kristy Deiner
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland.,Department of Biological Sciences, University of Notre Dame, 290B Galvin Life Sciences, Notre Dame, Indiana 46556, USA
| | - Emanuel A Fronhofer
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Elvira Mächler
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Jean-Claude Walser
- Swiss Federal Institute of Technology (ETH), Zürich, Genetic Diversity Centre, CHN E 55 Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Florian Altermatt
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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22
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Goldberg CS, Turner CR, Deiner K, Klymus KE, Thomsen PF, Murphy MA, Spear SF, McKee A, Oyler‐McCance SJ, Cornman RS, Laramie MB, Mahon AR, Lance RF, Pilliod DS, Strickler KM, Waits LP, Fremier AK, Takahara T, Herder JE, Taberlet P. Critical considerations for the application of environmental
DNA
methods to detect aquatic species. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12595] [Citation(s) in RCA: 497] [Impact Index Per Article: 62.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Caren S. Goldberg
- School of the Environment Washington State University 100 Dairy Rd. Pullman WA 99164 USA
| | - Cameron R. Turner
- Department of Biological Sciences University of Notre Dame Notre Dame IN 46556 USA
| | - Kristy Deiner
- Department of Biological Sciences University of Notre Dame Notre Dame IN 46556 USA
| | - Katy E. Klymus
- Lake Erie Center University of Toledo 6200 Bayshore Rd. Oregon OH 43616 USA
| | - Philip Francis Thomsen
- Centre for GeoGenetics Natural History Museum of Denmark University of Copenhagen Øster Voldgade 5‐7 DK‐1350 Copenhagen Denmark
| | - Melanie A. Murphy
- Department of Ecosystem Science andManagement Program in Ecology University of Wyoming Department 3354 1000 E University Ave Laramie WY 82071 USA
| | | | - Anna McKee
- U.S. Geological Survey South Atlantic Water Science Center 1770 Corporate Drive Suite 500 Norcross GA 30093 USA
| | - Sara J. Oyler‐McCance
- U.S. Geological Survey Fort Collins Science Center 2150 Centre Ave, Building C Fort Collins CO 80526 USA
| | - Robert Scott Cornman
- U.S. Geological Survey Fort Collins Science Center 2150 Centre Ave, Building C Fort Collins CO 80526 USA
| | - Matthew B. Laramie
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center Boise ID 83706 USA
| | - Andrew R. Mahon
- Department of Biology Institute for Great Lakes Research Central Michigan University Mount Pleasant MI 48859 USA
| | - Richard F. Lance
- Environmental Laboratory US Army Engineer Research & Development Center Vicksburg MS 39180 USA
| | - David S. Pilliod
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center Boise ID 83706 USA
| | - Katherine M. Strickler
- School of the Environment Washington State University 100 Dairy Rd. Pullman WA 99164 USA
| | - Lisette P. Waits
- Fish and Wildlife Sciences University of Idaho Moscow ID 83844‐1136 USA
| | - Alexander K. Fremier
- School of the Environment Washington State University 100 Dairy Rd. Pullman WA 99164 USA
| | - Teruhiko Takahara
- Faculty of Life and Environmental Science Shimane University 1060 Nishikawatsu Matsue Shimane 690‐8504 Japan
| | - Jelger E. Herder
- Reptile, Amphibian and Fish Conservation Netherlands (RAVON) P.O. Box 1413 6501 BK Nijmegen The Netherlands
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine Université Grenoble Alpes F‐38000 Grenoble France
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23
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Olds BP, Jerde CL, Renshaw MA, Li Y, Evans NT, Turner CR, Deiner K, Mahon AR, Brueseke MA, Shirey PD, Pfrender ME, Lodge DM, Lamberti GA. Estimating species richness using environmental DNA. Ecol Evol 2016; 6:4214-26. [PMID: 27516876 PMCID: PMC4972244 DOI: 10.1002/ece3.2186] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/21/2016] [Accepted: 04/26/2016] [Indexed: 12/03/2022] Open
Abstract
The foundation for any ecological study and for the effective management of biodiversity in natural systems requires knowing what species are present in an ecosystem. We assessed fish communities in a stream using two methods, depletion‐based electrofishing and environmental DNA metabarcoding (eDNA) from water samples, to test the hypothesis that eDNA provides an alternative means of determining species richness and species identities for a natural ecosystem. In a northern Indiana stream, electrofishing yielded a direct estimate of 12 species and a mean estimated richness (Chao II estimator) of 16.6 species with a 95% confidence interval from 12.8 to 42.2. eDNA sampling detected an additional four species, congruent with the mean Chao II estimate from electrofishing. This increased detection rate for fish species between methods suggests that eDNA sampling can enhance estimation of fish fauna in flowing waters while having minimal sampling impacts on fish and their habitat. Modern genetic approaches therefore have the potential to transform our ability to build a more complete list of species for ecological investigations and inform management of aquatic ecosystems.
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Affiliation(s)
- Brett P Olds
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana; Shrimp Department Oceanic Institute at Hawai'i Pacific University Waimanalo Hawaii
| | - Christopher L Jerde
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana; Biology Department University of Nevada Reno Nevada
| | - Mark A Renshaw
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana
| | - Yiyuan Li
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana
| | - Nathan T Evans
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana
| | - Cameron R Turner
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana
| | - Kristy Deiner
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana
| | - Andrew R Mahon
- Department of Biology Institute for Great Lakes Research Central Michigan University Mount Pleasant Michigan
| | - Michael A Brueseke
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana
| | - Patrick D Shirey
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana
| | - Michael E Pfrender
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana
| | - David M Lodge
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana
| | - Gary A Lamberti
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana
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24
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Creer S, Deiner K, Frey S, Porazinska D, Taberlet P, Thomas WK, Potter C, Bik HM. The ecologist's field guide to sequence‐based identification of biodiversity. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12574] [Citation(s) in RCA: 234] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory School of Biological Sciences Environment Centre Wales Building Bangor University Deiniol Road Bangor Gwynedd LL57 2UW UK
| | - Kristy Deiner
- Eawag: Aquatic Ecology Überlandstrasse 133 8600 Dübendorf Switzerland
| | - Serita Frey
- Natural Resources and the Environment University of New Hampshire Durham NH 03824 USA
| | - Dorota Porazinska
- Department of Ecology and Evolutionary Biology University of Colorado at Boulder Boulder CO 80309 USA
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine CNRS UMR 5553 Université Joseph Fourier BP 43 F‐38041 Grenoble Cedex 9 France
| | - W. Kelley Thomas
- Department of Molecular, Cellular, & Biomedical Sciences University of New Hampshire Durham NH 03824 USA
| | - Caitlin Potter
- Molecular Ecology and Fisheries Genetics Laboratory School of Biological Sciences Environment Centre Wales Building Bangor University Deiniol Road Bangor Gwynedd LL57 2UW UK
| | - Holly M. Bik
- Center for Genomics and Systems Biology Department of Biology New York University, New York NY 10003 USA
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25
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Mächler E, Deiner K, Spahn F, Altermatt F. Fishing in the Water: Effect of Sampled Water Volume on Environmental DNA-Based Detection of Macroinvertebrates. Environ Sci Technol 2016; 50:305-312. [PMID: 26560432 DOI: 10.1021/acs.est.5b04188] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Accurate detection of organisms is crucial for the effective management of threatened and invasive species because false detections directly affect the implementation of management actions. The use of environmental DNA (eDNA) as a species detection tool is in a rapid development stage; however, concerns about accurate detections using eDNA have been raised. We evaluated the effect of sampled water volume (0.25 to 2 L) on the detection rate for three macroinvertebrate species. Additionally, we tested (depending on the sampled water volume) what amount of total extracted DNA should be screened to reduce uncertainty in detections. We found that all three species were detected in all volumes of water. Surprisingly, however, only one species had a positive relationship between an increased sample volume and an increase in the detection rate. We conclude that the optimal sample volume might depend on the species-habitat combination and should be tested for the system where management actions are warranted. Nevertheless, we minimally recommend sampling water volumes of 1 L and screening at least 14 μL of extracted eDNA for each sample to reduce uncertainty in detections when studying macroinvertebrates in rivers and using our molecular workflow.
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Affiliation(s)
- Elvira Mächler
- Swiss Federal Institute of Aquatic Science and Technology (Eawag) , 8600 Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich , Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Kristy Deiner
- Swiss Federal Institute of Aquatic Science and Technology (Eawag) , 8600 Dübendorf, Switzerland
- Department of Biological Sciences, University of Notre Dame , 180 Galvin Life Sciences, Notre Dame, Indiana 46556 United States
| | - Fabienne Spahn
- Department of Biology, ETH Zurich , 8093 Zürich, Switzerland
| | - Florian Altermatt
- Swiss Federal Institute of Aquatic Science and Technology (Eawag) , 8600 Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich , Winterthurerstrasse 190, 8057 Zürich, Switzerland
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26
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Abstract
Environmental DNA (eDNA) monitoring is a novel molecular technique to detect species in natural habitats. Many eDNA studies in aquatic systems have focused on lake or ponds, and/or on large vertebrate species, but applications to invertebrates in river systems are emerging. A challenge in applying eDNA monitoring in flowing waters is that a species' DNA can be transported downstream. Whether and how far eDNA can be detected due to downstream transport remains largely unknown. In this study we tested for downstream detection of eDNA for two invertebrate species, Daphnia longispina and Unio tumidus, which are lake dwelling species in our study area. The goal was to determine how far away from the source population in a lake their eDNA could be detected in an outflowing river. We sampled water from eleven river sites in regular intervals up to 12.3 km downstream of the lake, developed new eDNA probes for both species, and used a standard PCR and Sanger sequencing detection method to confirm presence of each species' eDNA in the river. We detected D. longispina at all locations and across two time points (July and October); whereas with U. tumidus, we observed a decreased detection rate and did not detect its eDNA after 9.1 km. We also observed a difference in detection for this species at different times of year. The observed movement of eDNA from the source amounting to nearly 10 km for these species indicates that the resolution of an eDNA sample can be large in river systems. Our results indicate that there may be species' specific transport distances for eDNA and demonstrate for the first time that invertebrate eDNA can persist over relatively large distances in a natural river system.
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Affiliation(s)
- Kristy Deiner
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
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27
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Deiner K, Knapp RA, Boiano DM, May B. Increased accuracy of species lists developed for alpine lakes using morphology and cytochrome oxidase I for identification of specimens. Mol Ecol Resour 2013; 13:820-31. [PMID: 23773698 DOI: 10.1111/1755-0998.12130] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 05/03/2013] [Accepted: 05/09/2013] [Indexed: 12/17/2022]
Abstract
The first step in many community ecology studies is to produce a species list from a sample of individuals. Community ecologists now have two viable ways of producing a species list: morphological and barcode identification. In this study, we compared the taxonomic resolution gained by a combined use of both methods and tested whether a change in taxonomic resolution significantly impacted richness estimates for benthic macroinvertebrates sampled from ten lakes in Sequoia National Park, USA. Across all lakes, 77 unique taxa were identified and 42% (32) were reliably identified to species using both barcode and morphological identification. Of the 32 identified to species, 63% (20) were identified solely by comparing the barcode sequence from cytochrome oxidase I to the Barcode of Life reference library. The increased resolution using a combined identification approach compared to identifications based solely on morphology resulted in a significant increase in estimated richness within a lake at the order, family, genus and species levels of taxonomy (P < 0.05). Additionally, young or damaged individuals that could not be identified using morphology were identified using their COI sequences to the genus or species level on average 75% of the time. Our results demonstrate that a combined identification approach improves accuracy of benthic macroinvertebrate species lists in alpine lakes and subsequent estimates of richness. We encourage the use of barcodes for identification purposes and specifically when morphology is insufficient, as in the case of damaged and early life stage specimens of benthic macroinvertebrates.
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Affiliation(s)
- Kristy Deiner
- Department of Animal Science, University of California-Davis, One Shields Ave, Davis, CA 95616, USA.
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28
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Blickley JL, Deiner K, Garbach K, Lacher I, Meek MH, Porensky LM, Wilkerson ML, Winford EM, Schwartz MW. Graduate student's guide to necessary skills for nonacademic conservation careers. Conserv Biol 2013; 27:24-34. [PMID: 23140555 DOI: 10.1111/j.1523-1739.2012.01956.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 07/09/2011] [Indexed: 06/01/2023]
Abstract
Graduate education programs in conservation science generally focus on disciplinary training and discipline-specific research skills. However, nonacademic conservation professionals often require an additional suite of skills. This discrepancy between academic training and professional needs can make it difficult for graduate students to identify the skills and experiences that will best prepare them for the conservation job market. We analyzed job advertisements for conservation-science positions and interviewed conservation professionals with experience hiring early-career conservation scientists to determine what skills employers of conservation professionals seek; whether the relative importance of skills varies by job sector (government, nonprofit, and private); and how graduate students interested in careers in conservation science might signal competency in key skills to potential employers. In job advertisements, disciplinary, interpersonal, and project-management skills were in the top 5 skills mentioned across all job sectors. Employers' needs for additional skills, like program leadership, conflict resolution and negotiation, and technical and information technology skills, varied across sectors. Our interview results demonstrated that some skills are best signaled to employers via experiences obtained outside thesis or dissertation work. Our findings suggest that graduate students who wish to be competitive in the conservation job market can benefit by gaining skills identified as important to the job sector in which they hope to work and should not necessarily expect to be competent in these skills simply by completing their chosen degree path.
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Affiliation(s)
- Jessica L Blickley
- Graduate Group in Ecology, University of California, One Shields Avenue, Davis, CA 95616, USA
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29
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Deiner K, Lemmon AR, Mack AL, Fleischer RC, Dumbacher JP. A Passerine Bird's evolution corroborates the geologic history of the island of New Guinea. PLoS One 2011; 6:e19479. [PMID: 21573115 PMCID: PMC3089620 DOI: 10.1371/journal.pone.0019479] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2010] [Accepted: 04/07/2011] [Indexed: 11/18/2022] Open
Abstract
New Guinea is a biologically diverse island, with a unique geologic history and topography that has likely played a role in the evolution of species. Few island-wide studies, however, have examined the phylogeographic history of lowland species. The objective of this study was to examine patterns of phylogeographic variation of a common and widespread New Guinean bird species (Colluricincla megarhyncha). Specifically, we test the mechanisms hypothesized to cause geographic and genetic variation (e.g., vicariance, isolation by distance and founder-effect with dispersal). To accomplish this, we surveyed three regions of the mitochondrial genome and a nuclear intron and assessed differences among 23 of the 30 described subspecies from throughout their range. We found support for eight highly divergent lineages within C. megarhyncha. Genetic lineages were found within continuous lowland habitat or on smaller islands, but all individuals within clades were not necessarily structured by predicted biogeographic barriers. There was some evidence of isolation by distance and potential founder-effects. Mitochondrial DNA sequence divergence among lineages was at a level often observed among different species or even genera of birds (5-11%), suggesting lineages within regions have been isolated for long periods of time. When topographical barriers were associated with divergence patterns, the estimated divergence date for the clade coincided with the estimated time of barrier formation. We also found that dispersal distance and range size are positively correlated across lineages. Evidence from this research suggests that different phylogeographic mechanisms concurrently structure lineages of C. megarhyncha and are not mutually exclusive. These lineages are a result of evolutionary forces acting at different temporal and spatial scales concordant with New Guinea's geological history.
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Affiliation(s)
- Kristy Deiner
- Department of Vertebrate Zoology and Anthropology and Center for Comparative Genomics, California Academy of Sciences, San Francisco, California, United States of America
- Genomic Variation Lab, University of California Davis, Davis, California, United States of America
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, Florida, United States of America
| | - Andrew L. Mack
- Powdermill Nature Reserve, Carnegie Museum of Natural History, Pittsburgh, Pennsylvania, United States of America
| | - Robert C. Fleischer
- Center for Conservation and Evolutionary Genetics, National Zoological Park, Smithsonian Institution, Washington, D.C., United States of America
| | - John P. Dumbacher
- Department of Vertebrate Zoology and Anthropology and Center for Comparative Genomics, California Academy of Sciences, San Francisco, California, United States of America
- Center for Conservation and Evolutionary Genetics, National Zoological Park, Smithsonian Institution, Washington, D.C., United States of America
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30
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Dahlhoff E, Fearnley S, Bruce D, Gibbs A, Stoneking R, McMillan D, Deiner K, Smiley J, Rank N. Effects of Temperature on Physiology and Reproductive Success of a Montane Leaf Beetle: Implications for Persistence of Native Populations Enduring Climate Change. Physiol Biochem Zool 2008; 81:718-32. [DOI: 10.1086/590165] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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