153 results on '"Deiner, Kristy"'
Search Results
2. Environmental DNA Methods for Ecological Monitoring and Biodiversity Assessment in Estuaries
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Nagarajan, Raman P, Bedwell, Mallory, Holmes, Ann E, Sanches, Thiago, Acuña, Shawn, Baerwald, Melinda, Barnes, Matthew A, Blankenship, Scott, Connon, Richard E, Deiner, Kristy, Gille, Daphne, Goldberg, Caren S, Hunter, Margaret E, Jerde, Christopher L, Luikart, Gordon, Meyer, Rachel S, Watts, Alison, and Schreier, Andrea
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Biodiversity ,Environmental DNA ,Estuary ,Invasive species ,Monitoring ,San Francisco Estuary ,Earth Sciences ,Environmental Sciences ,Biological Sciences ,Marine Biology & Hydrobiology - Abstract
Environmental DNA (eDNA) detection methods can complement traditional biomonitoring to yield new ecological insights in aquatic systems. However, the conceptual and methodological frameworks for aquatic eDNA detection and interpretation were developed primarily in freshwater environments and have not been well established for estuaries and marine environments that are by nature dynamic, turbid, and hydrologically complex. Environmental context and species life history are critical for successful application of eDNA methods, and the challenges associated with eDNA detection in estuaries were the subject of a symposium held at the University of California Davis on January 29, 2020 (https://marinescience.ucdavis.edu/engagement/past-events/edna). Here, we elaborate upon topics addressed in the symposium to evaluate eDNA methods in the context of monitoring and biodiversity studies in estuaries. We first provide a concise overview of eDNA science and methods, and then examine the San Francisco Estuary (SFE) as a case study to illustrate how eDNA detection can complement traditional monitoring programs and provide regional guidance on future potential eDNA applications. Additionally, we offer recommendations for enhancing communication between eDNA scientists and natural resource managers, which is essential for integrating eDNA methods into existing monitoring programs. Our intent is to create a resource that is accessible to those outside the field of eDNA, especially managers, without oversimplifying the challenges or advantages of these methods.
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- 2022
3. Calibrating Environmental DNA Metabarcoding to Conventional Surveys for Measuring Fish Species Richness
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McElroy, Mary E, Dressler, Terra L, Titcomb, Georgia C, Wilson, Emily A, Deiner, Kristy, Dudley, Tom L, Eliason, Erika J, Evans, Nathan T, Gaines, Steven D, Lafferty, Kevin D, Lamberti, Gary A, Li, Yiyuan, Lodge, David M, Love, Milton S, Mahon, Andrew R, Pfrender, Michael E, Renshaw, Mark A, Selkoe, Kimberly A, and Jerde, Christopher L
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bland-altman analysis ,Lin's concordance correlation coefficient ,high-throughput sequencing ,marine ,freshwater ,eDNA ,Ecology ,Evolutionary Biology - Published
- 2020
4. Improving the recovery for dissolved eDNA state: A comparative analysis of isopropanol precipitation, magnetic bead extraction, and centrifugal dialysis
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Kirtane, Anish, primary and Deiner, Kristy, additional
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- 2024
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5. Acidity promotes degradation of multi-species environmental DNA in lotic mesocosms.
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Seymour, Mathew, Durance, Isabelle, Cosby, Bernard J, Ransom-Jones, Emma, Deiner, Kristy, Ormerod, Steve J, Colbourne, John K, Wilgar, Gregory, Carvalho, Gary R, de Bruyn, Mark, Edwards, François, Emmett, Bridget A, Bik, Holly M, and Creer, Simon
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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.
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- 2018
6. Molecular Population Genetics of the Northern Elephant Seal Mirounga angustirostris.
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Abadía-Cardoso, Alicia, Freimer, Nelson B, Deiner, Kristy, and Garza, John Carlos
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Genetics ,Life on Land ,Alleles ,Animals ,Base Sequence ,California ,Gene Frequency ,Genetic Variation ,Genetics ,Population ,Mexico ,Microsatellite Repeats ,Mutation Rate ,Population Density ,Seals ,Earless ,Sequence Analysis ,DNA ,bottleneck ,genetic variation ,microsatellites ,Mirounga ,mutation rate ,pinniped ,Evolutionary Biology - 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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- 2017
7. Range-wide phylogeographic structure of the vernal pool fairy shrimp (Branchinecta lynchi)
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Deiner, Kristy, Hull, Joshua M, and May, Bernie
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Biological Sciences ,Ecology ,Evolutionary Biology ,Genetics ,Life on Land ,Animals ,Crustacea ,Geography ,Phylogeny ,General Science & Technology - 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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- 2017
8. The ecologist's field guide to sequence‐based identification of biodiversity
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Creer, Simon, Deiner, Kristy, Frey, Serita, Porazinska, Dorota, Taberlet, Pierre, Thomas, W Kelley, Potter, Caitlin, and Bik, Holly M
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Human Genome ,Biotechnology ,Genetics ,Generic health relevance ,biodiversity ,DNA sequencing ,metabarcoding ,metagenomics ,metatranscriptomics ,molecular ecology ,Environmental Science and Management ,Ecology ,Evolutionary Biology - Abstract
The past 100 years of ecological research has seen substantial progress in understanding the natural world and likely effects of change, whether natural or anthropogenic. Traditional ecological approaches underpin such advances, but would additionally benefit from recent developments in the sequence-based quantification of biodiversity from the fields of molecular ecology and genomics. By building on a long and rich history of molecular taxonomy and taking advantage of the new generation of DNA sequencing technologies, we are gaining previously impossible insights into alpha and beta diversity from all domains of life, irrespective of body size. While a number of complementary reviews are available in specialist journals, our aim here is to succinctly describe the different technologies available within the omics toolbox and showcase the opportunities available to contemporary ecologists to advance our understanding of biodiversity and its potential roles in ecosystems. Starting in the field, we walk the reader through sampling and preservation of genomic material, including typical taxonomy marker genes used for species identification. Moving on to the laboratory, we cover nucleic acid extraction approaches and highlight the principal features of using marker gene assessment, metagenomics, metatranscriptomics, single-cell genomics and targeted genome sequencing as complementary approaches to assess the taxonomic and functional characteristics of biodiversity. We additionally provide clear guidance on the forms of DNA found in the environmental samples (e.g. environmental vs. ancient DNA) and highlight a selection of case studies, including the investigation of trophic relationships/food webs. Given the maturity of sequence-based identification of prokaryotes and microbial eukaryotes, more exposure is given to macrobial communities. We additionally illustrate current approaches to genomic data analysis and highlight the exciting prospects of the publicly available data underpinning published sequence-based studies. Given that ecology ‘has to count’, we identify the impact that molecular genetic analyses have had on stakeholders and end-users and predict future developments for the fields of biomonitoring. Furthermore, we conclude by highlighting future opportunities in the field of systems ecology afforded by effective engagement between the fields of traditional and molecular ecology.
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- 2016
9. Introduction to special issue: Advancing disease ecology through eDNA monitoring of infectious agents
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Childress, Jasmine, primary, Faust, Christina L., additional, and Deiner, Kristy, additional
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- 2023
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10. Introduction to special issue: Advancing disease ecology through eDNA monitoring of infectious agents.
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Childress, Jasmine, Faust, Christina L., and Deiner, Kristy
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- 2024
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11. Sorting states of environmental DNA: Effects of isolation method and water matrix on the recovery of membrane‐bound, dissolved, and adsorbed states of eDNA
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Kirtane, Anish, primary, Kleyer, Hannah, additional, and Deiner, Kristy, additional
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- 2023
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12. From Barcodes to Biomes: Special issues from the 6th International Barcode of Life Conference
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Adamowicz, Sarah J., Chain, Frederic J.J., Clare, Elizabeth L., Deiner, Kristy, Dinca, Vlad, Elias-Gutierrez, Manuel, Hausmann, Axel, Hogg, Ian D., Kekkonen, Mari, Lijtmaer, Dario A., Naaum, Amanda, Steinke, Dirk, Valdez-Moreno, Martha, Van der Bank, Michelle, Wilson, John-James, and Xu, Jianping
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Genetic research -- Conferences, meetings and seminars ,Biological sciences - Abstract
The two special issues--Barcodes to Biomes--mark the one-year anniversary of the 6th International Barcode of Life Conference held in Guelph, Canada. The 6th Conference brought together 601 delegates from 51 [...]
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- 2016
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13. Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys
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Grey, Erin K., Bernatchez, Louis, Cassey, Phillip, Deiner, Kristy, Deveney, Marty, Howland, Kimberly L., Lacoursière-Roussel, Anaïs, Leong, Sandric Chee Yew, Li, Yiyuan, Olds, Brett, Pfrender, Michael E., Prowse, Thomas A. A., Renshaw, Mark A., and Lodge, David M.
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- 2018
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14. Plant–animal interactions in the era of environmental DNA ( eDNA )—A review
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Banerjee, Pritam, primary, Stewart, Kathryn A., additional, Antognazza, Caterina M., additional, Bunholi, Ingrid V., additional, Deiner, Kristy, additional, Barnes, Matthew A., additional, Saha, Santanu, additional, Verdier, Héloïse, additional, Doi, Hideyuki, additional, Maity, Jyoti Prakash, additional, Chan, Michael W. Y., additional, and Chen, Chien Yen, additional
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- 2022
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15. A triad of kicknet sampling, eDNA metabarcoding, and predictive modeling to assess richness of mayflies, stoneflies and caddisflies in rivers
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Keck, François, primary, Hürlemann, Samuel, additional, Locher, Nadine, additional, Stamm, Christian, additional, Deiner, Kristy, additional, and Altermatt, Florian, additional
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- 2022
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16. Graduate Student's Guide to Necessary Skills for Nonacademic Conservation Careers
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BLICKLEY, JESSICA L., DEINER, KRISTY, GARBACH, KELLY, LACHER, IARA, MEEK, MARIAH H., PORENSKY, LAUREN M., WILKERSON, MARIT L., WINFORD, ERIC M., and SCHWARTZ, MARK W.
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- 2013
17. A triad of kicknet sampling, eDNA metabarcoding, and predictive modeling to assess richness of mayflies, stoneflies and caddisflies in rivers
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Keck, François, Hürlemann, Samuel, Locher, Nadine, Stamm, Christian, Deiner, Kristy, Altermatt, Florian, University of Zurich, Keck, François, and Altermatt, Florian
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1109 Insect Science ,UFSP13-8 Global Change and Biodiversity ,Trichoptera ,Ephemeroptera ,Metabarcoding ,Plecoptera ,Water DNA ,2309 Nature and Landscape Conservation ,10127 Institute of Evolutionary Biology and Environmental Studies ,1105 Ecology, Evolution, Behavior and Systematics ,1311 Genetics ,1110 Plant Science ,1312 Molecular Biology ,Genetics ,570 Life sciences ,biology ,590 Animals (Zoology) ,Animal Science and Zoology ,1103 Animal Science and Zoology ,Molecular Biology ,Nature and Landscape Conservation - 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., Metabarcoding and Metagenomics, 6, ISSN:2534-9708
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- 2022
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18. Effects of Temperature on Physiology and Reproductive Success of a Montane Leaf Beetle: Implications for Persistence of Native Populations Enduring Climate Change
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Dahlhoff, Elizabeth P., Fearnley, Shannon L., Bruce, Douglas A., Gibbs, Allen G., Stoneking, Robin, McMillan, David M., Deiner, Kristy, Smiley, John T., and Rank, Nathan E.
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- 2008
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19. Microbial community shifts in streams receiving treated wastewater effluent
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Mansfeldt, Cresten, Deiner, Kristy, Mächler, Elvira, Fenner, Kathrin, Eggen, Rik I L, Stamm, Christian, Schönenberger, Urs, Walser, Jean-Claude, Altermatt, Florian, University of Zurich, and Deiner, Kristy
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10120 Department of Chemistry ,2305 Environmental Engineering ,2304 Environmental Chemistry ,2310 Pollution ,540 Chemistry ,2311 Waste Management and Disposal - Published
- 2020
20. Diversification and biodiversity dynamics of hot and cold spots
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Melián, Carlos J., Seehausen, Ole, Eguíluz, Víctor M., Fortuna, Miguel A., and Deiner, Kristy
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- 2015
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21. A practical guide to DNA-based methods for biodiversity assessment
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Bruce, Kat, Blackman, Rosetta C., Bourlat, Sarah J., Hellström, Micaela, Bakker, Judith, Bista, Iliana, Bohmann, Kristine, Bouchez, Agnès, Brys, Rein, Clark, Katie, Elbrecht, Vasco, Fazi, Stefano, Fonseca, Vera G., Hänfling, Bernd, Leese, Florian, Mächler, Elvira, Mahon, Andrew R., Meissner, Kristian, Panksep, Kristel, Pawlowski, Jan, Schmidt Yáñez, Paul Luis, Seymour, Mathew, Thalinger, Bettina, Valentini, Alice, Woodcock, Paul, Traugott, Michael, Vasselon, Valentin, and Deiner, Kristy
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Data processing ,DNA based methods ,Biodiversity ,Biota composition ,Species identification - Abstract
This book represents a synthesis of knowledge and best practice in the field of DNA-based biomonitoring at the time of writing. It has been written with end-users of molecular tools in mind, as well as those who are new to the field in research settings and are looking to gain an overall grounding in the subject area. For each of the main types of sample (water, soil / sediment, bulk invertebrates and diatoms), and for each stage of the field and laboratory processes, we outline key considerations, decisions that need to be made, factors that might influence those decisions, and trade-offs inherent in the choices made. We hope that this will help users, practitioners, and those commissioning DNA-based monitoring programmes to navigate this large field and critically evaluate the strengths and weaknesses of different analysis workflows based on context, project aims and available resources. DNA-based methods for species detection and identification have revolutionised our ability to assess biodiversity in terrestrial, freshwater and marine ecosystems. Starting from the seminal study that used eDNA to detect invasive american bullfrogs in France (Ficetola et al. 2008), research conducted over the last decade has demonstrated the power of these approaches for surveying a wide range of species and groups. Early applications included the use of eDNA to monitor Asian Carp in the USA (Jerde et al. 2013). Following heavy scrutiny, the method was eventually adopted, and is still employed today by the United States Geological Survey (USGS). A flurry of research followed, with tests designed for many threatened and invasive species including New zealand mudsnails (Goldberg et al. 2013), american crayfish (Geerts et al. 2018), gammarids (Blackman et al. 2017), and great crested newts (Biggs et al. 2015). The great crested newt eDNA test has been employed for regulatory monitoring in the UK since 2014. During the same time period, there was a proliferation of research studies that used high-throughput sequencing approaches to describe whole communities of organisms from mixed species and environmental samples, using an approach termed DNA metabarcoding (Taberlet et al. 2012c). As the field developed fast and the approaches were applied to a wide range of research and monitoring objectives, a high level of methodological variation was introduced at all stages of the workflow (Seymour 2019). Thus, while a significant level of consensus on scientific best-practice now exists in many areas, this may not be readily discerned from the now-extensive body of research literature. As environmental practitioners and policy makers are now increasingly starting to integrate DNAbased methods into routine monitoring applications including protected species licensing1, statutory monitoring2 (Hänfling et al. 2016) and environmental impact assessment3, various national and international efforts have been undertaken to standardise methods and integrate them into monitoring frameworks (Pilliod et al. 2019, Loeza-Quintana et al. 2020, Minamoto et al. 2021, Pawlowski et al. 2020a4). In Europe, the EU COST Action DNAqua-Net (Leese et al. 2018) has been working towards incorporating molecular monitoring tools for Biological Quality Elements (BQEs, e.g., fish, macroinvertebrates and phytoplankton- benthos) into the Water Framework Directive (WFD, 2000/60/EC)5 and the Marine Strategy Framework Directive (MSFD, 2008/56/EC)6. Thus, emphasis now shifts from fundamental research to robust and efficient application of DNAbased methods for operational use at large scales. This requires that scientific robustness is balanced with consideration of the practical realities faced by environmental managers. Moreover, there is increased need for strong quality assurance in a setting where non-expert field samplers and commercial laboratories are involved with the generation of data that non-specialist decision-makers then rely on to inform potentially costly action (or non-action). This places increased emphasis on robustness, replicability, traceability and ease-of-use, which may not always be the central focus of studies carried out in the academic research environment. This document aims to summarise the scientific consensus relating to every step of the field and laboratory workflows involved in the most common types of samples and analyses. We do not go into great detail regarding bioinformatics (computational processing of sequence data) and data analysis since these are extensive topics in their own right. We uniquely set the field and lab steps in the context of the practical and logistical constraints faced by environmental managers in terms of cost, logistics, safety, ease-of-use, and quality assurance, highlighting key decisions to be made and the inherent trade-offs associated with the various options. We hope that this will support non-experts, and those new to the field, to navigate the key considerations associated with planning or evaluating monitoring programmes using DNA-based monitoring methods. Additionally, it will aid decision-makers in writing and evaluating tenders and proposals, ensuring that the methods used for a given project are fit-for-purpose and that results are correctly interpreted. Alongside the many areas of emerging consensus, there remain some areas where further research is still required to balance scientific best-practice with the constraints and priorities of end-users. We hope that by shining a light on the importance of these issues, the research community will be encouraged to address them. More generally, we hope to inspire researchers in this now highly-applied scientific field to consider end-user constraints when designing and implementing research projects. This will help to accelerate uptake by users and maximise the impact of research. DNA-based bioassessment methods continue to evolve, and there are several emerging technologies that show exciting promise to move beyond even what is possible today. Examples include in-field sequencing using the MinION device from Oxford Nanopore Technologies (Pomerantz et al. 2018, Davidov et al. 2020, Hatfield et al. 2020), PCR-free metagenomic approaches (Bista et al. 2018, Giebner et al. 2020) and CRISPR for rapid detection of species, which is particularly relevant for invasive an non-native species monitoring (Williams et al. 2019, 2020). We recognise the potential of these methods, but do not consider them in detail here, since they are not yet far enough developed for routine application. EU COST Action DNAqua-Net (CA 15219 a COST (European Cooperation in Science and Technology). DNAqua-Net, European Union Horizon 2020 Published Refereed Current 14.a Mature Multi-organisational International Genetic differentiation Species distributions Method
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- 2021
22. An urban Blitz with a twist : rapid biodiversity assessment using aquatic environmental DNA
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Hupało, Kamil, Majaneva, Markus, Czachur, Molly Victoria, Sire, Lucas, Marquina, Daniel, Lijtmaer, Darío A., Ivanov, Vladislav, Leidenberger, Sonja, Čiampor, Fedor, Jr, Čiamporová-Zaťovičová, Zuzana, Mendes, Izabela S., Desiderato, Andrea, Topstad, Lasse, Meganck, Kenny, Hariz Z. A., Danial, Kjærstad, Gaute, Lin, Xiao‐Long, Price, Benjamin, Stevens, Mark, Ekrem, Torbjørn, Deiner, Kristy, Hupało, Kamil, Majaneva, Markus, Czachur, Molly Victoria, Sire, Lucas, Marquina, Daniel, Lijtmaer, Darío A., Ivanov, Vladislav, Leidenberger, Sonja, Čiampor, Fedor, Jr, Čiamporová-Zaťovičová, Zuzana, Mendes, Izabela S., Desiderato, Andrea, Topstad, Lasse, Meganck, Kenny, Hariz Z. A., Danial, Kjærstad, Gaute, Lin, Xiao‐Long, Price, Benjamin, Stevens, Mark, Ekrem, Torbjørn, and Deiner, Kristy
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As global biodiversity declines, there is an increasing need to create an educated and engaged society. Having people of all ages participate in measuring biodiversity where they live helps to create awareness. Recently, the use of environmental DNA (eDNA) for biodiversity surveys has gained momentum. Here, we explore whether sampling eDNA and sequencing it can be used as a means of rapidly surveying urban biodiversity for educational purposes. We sampled 2 × 1 L of water from each of 15 locations in the city of Trondheim, Norway, including a variety of freshwater, marine, and brackish habitats. DNA was extracted, amplified in triplicate targeting the barcoding fragment of COI gene, and sequenced. The obtained data were analyzed on the novel mBRAVE platform, an online open‐access software and computing resource. The water samples were collected in 2 days by two people, and the laboratory analysis was completed in 5 days by one person. Overall, we detected the presence of 506 BINs identified as belonging to 435 taxa, representing at least 265 putative species. On average, only 5.4% of the taxa were shared among six replicates per site. Based on the observed diversity, three distinct clusters were detected and related to the geographic distribution of sites. There were some taxa shared between the habitats, with a substantial presence of terrestrial biota. Here we propose a new form of BioBlitz, where with noninvasive sampling effort combined with swift processing and straightforward online analyses, hundreds of species can be detected. Thus, using eDNA analysis of water is useful for rapid biodiversity surveys and valuable for educational purposes. We show that rapid eDNA surveys, combined with openly available services and software, can be used as an educational tool to raise awareness about the importance of biodiversity., CC BY 4.0
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- 2021
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23. 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)
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Rodriguez‐Ezpeleta, Naiara, Morissette, Olivier, Bean, Colin W., Manu, Shivakumara, Banerjee, Pritam, Lacoursière‐Roussel, Anaïs, Beng, Kingsly C., Alter, S. Elizabeth, Roger, Fabian, Holman, Luke E., Stewart, Kathryn A., Monaghan, Michael T., Mauvisseau, Quentin, Mirimin, Luca, Wangensteen, Owen S., Antognazza, Caterina M., Helyar, Sarah J., Boer, Hugo, Monchamp, Marie‐Eve, Nijland, Reindert, Abbott, Cathryn L., Doi, Hideyuki, Barnes, Matthew A., Leray, Matthieu, Hablützel, Pascal I., Deiner, Kristy, Rodriguez‐Ezpeleta, Naiara, Morissette, Olivier, Bean, Colin W., Manu, Shivakumara, Banerjee, Pritam, Lacoursière‐Roussel, Anaïs, Beng, Kingsly C., Alter, S. Elizabeth, Roger, Fabian, Holman, Luke E., Stewart, Kathryn A., Monaghan, Michael T., Mauvisseau, Quentin, Mirimin, Luca, Wangensteen, Owen S., Antognazza, Caterina M., Helyar, Sarah J., Boer, Hugo, Monchamp, Marie‐Eve, Nijland, Reindert, Abbott, Cathryn L., Doi, Hideyuki, Barnes, Matthew A., Leray, Matthieu, Hablützel, Pascal I., and Deiner, Kristy
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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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- 2021
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24. 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)
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Rodriguez-Ezpeleta, Naiara, Morissette, Olivier, Bean, Colin W., Manu, Shivakumara, Banerjee, Pritam, Lacoursière-Roussel, Anaïs, Beng, Kingsly C., Alter, Elizabeth, Roger, Fabian, Holman, Luke E., Stewart, Kathryn A., Monaghan, Michael T., Mauvisseau, Quentin, Mirimin, Luca, Wangensteen, Owen S., Antognazza, Caterina M., Helyar, Sarah J., de Boer, Hugo, Monchamp, Marie Eve, Nijland, Reindert, Abbott, Cathryn L., Doi, Hideyuki, Barnes, Matthew A., Leray, Matthieu, Hablützel, Pascal I., Deiner, Kristy, Rodriguez-Ezpeleta, Naiara, Morissette, Olivier, Bean, Colin W., Manu, Shivakumara, Banerjee, Pritam, Lacoursière-Roussel, Anaïs, Beng, Kingsly C., Alter, Elizabeth, Roger, Fabian, Holman, Luke E., Stewart, Kathryn A., Monaghan, Michael T., Mauvisseau, Quentin, Mirimin, Luca, Wangensteen, Owen S., Antognazza, Caterina M., Helyar, Sarah J., de Boer, Hugo, Monchamp, Marie Eve, Nijland, Reindert, Abbott, Cathryn L., Doi, Hideyuki, Barnes, Matthew A., Leray, Matthieu, Hablützel, Pascal I., and Deiner, Kristy
- 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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- 2021
25. Trade-offs between reducing complex terminology and producing accurate interpretations from environmental DNA
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Manu, Shivakumara, Holman, Luke, Nijland, Reindert, Hablützel, Pascal, Monchamp, Marie-Eve, Barnes, Matthew, Banerjee, Pritam, Abbott, Cathryn, Roger, Fabian, Stewart, Kathryn, Deiner, Kristy, Monaghan, Michael, Wangensteen, Owen, Helyar, Sarah, Beng, Kingsly, Morissette, Olivier, Mauvisseau, Quentin, Leray, Matthieu, de Boer, Hugo, Mirimin, Luca, Doi, Hideyuki, Alter, S., Lacoursière-Roussel, Anaïs, Rodriguez-Ezpeleta, Naiara, Bean, Colin, and Antognazza, Caterina
- Subjects
bepress|Life Sciences ,bepress|Life Sciences|Biodiversity - 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. Not only is this terminology based on categories that are often difficult to assign and uninformative, but it ignores what is in our opinion the most important distinction within eDNA: the type of DNA (organismal or extra-organismal) from which ecological interpretations are derived.
- Published
- 2020
26. A validation scale to determine the readiness of environmental DNA assays for routine species monitoring
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Thalinger, Bettina, primary, Deiner, Kristy, additional, Harper, Lynsey R., additional, Rees, Helen C., additional, Blackman, Rosetta C., additional, Sint, Daniela, additional, Traugott, Michael, additional, Goldberg, Caren S., additional, and Bruce, Kat, additional
- Published
- 2021
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27. The future of biodiversity monitoring and conservation utilizing environmental DNA
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Deiner, Kristy, primary, Yamanaka, Hiroki, additional, and Bernatchez, Louis, additional
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- 2020
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28. An urban Blitz with a twist: rapid biodiversity assessment using aquatic environmental DNA
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Hupało, Kamil, primary, Majaneva, Markus, additional, Czachur, Molly Victoria, additional, Sire, Lucas, additional, Marquina, Daniel, additional, Lijtmaer, Darío A., additional, Ivanov, Vladislav, additional, Leidenberger, Sonja, additional, Čiampor, Fedor, additional, Čiamporová‐Zaťovičová, Zuzana, additional, Mendes, Izabela S., additional, Desiderato, Andrea, additional, Topstad, Lasse, additional, Meganck, Kenny, additional, Hariz Z. A., Danial, additional, Kjærstad, Gaute, additional, Lin, Xiao‐Long, additional, Price, Benjamin, additional, Stevens, Mark, additional, Ekrem, Torbjørn, additional, and Deiner, Kristy, additional
- Published
- 2020
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29. Calibrating Environmental DNA Metabarcoding to Conventional Surveys for Measuring Fish Species Richness
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McElroy, Mary E., primary, Dressler, Terra L., additional, Titcomb, Georgia C., additional, Wilson, Emily A., additional, Deiner, Kristy, additional, Dudley, Tom L., additional, Eliason, Erika J., additional, Evans, Nathan T., additional, Gaines, Steven D., additional, Lafferty, Kevin D., additional, Lamberti, Gary A., additional, Li, Yiyuan, additional, Lodge, David M., additional, Love, Milton S., additional, Mahon, Andrew R., additional, Pfrender, Michael E., additional, Renshaw, Mark A., additional, Selkoe, Kimberly A., additional, and Jerde, Christopher L., additional
- Published
- 2020
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30. Environmental DNA metabarcoding: Transforming how we survey animal and plant communities
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Deiner, Kristy, Bik, Holly M, Mächler, Elvira, Seymour, Mathew, Lacoursière-Roussel, Anaïs, Altermatt, Florian, Creer, Simon, Bista, Iliana, Lodge, David M, de Vere, Natasha, Pfrender, Michael E, Bernatchez, Louis, University of Zurich, and Deiner, Kristy
- Subjects
bioinformatic pipeline ,conservation ,invasive species ,10127 Institute of Evolutionary Biology and Environmental Studies ,1105 Ecology, Evolution, Behavior and Systematics ,1311 Genetics ,biomonitoring ,citizen science ,570 Life sciences ,biology ,590 Animals (Zoology) ,macro ,ecology ,eDNA ,species richness ,organism - 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. ISSN:0962-1083 ISSN:1365-294X
- Published
- 2017
31. Advancing the use of molecular methods for routine freshwater macroinvertebrate biomonitoring – the need for calibration experiments
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Blackman, Rosetta C, Mächler, Elvira; https://orcid.org/0000-0003-0430-6173, Altermatt, Florian, Arnold, Amanda, Beja, Pedro, Boets, Pieter, Egeter, Bastian, Elbrecht, Vasco, Filipe, Ana Filipa, Jones, J Iwan, Macher, Jan, Majaneva, Markus, Martins, Filipa M S, Murria, Cesc, Meissner, Kristian, Pawlowski, Jan, Schmidt Yanez, Paul L, Zizka, Vera M A, Leese, Florian, Price, Benjamin W, Deiner, Kristy, Blackman, Rosetta C, Mächler, Elvira; https://orcid.org/0000-0003-0430-6173, Altermatt, Florian, Arnold, Amanda, Beja, Pedro, Boets, Pieter, Egeter, Bastian, Elbrecht, Vasco, Filipe, Ana Filipa, Jones, J Iwan, Macher, Jan, Majaneva, Markus, Martins, Filipa M S, Murria, Cesc, Meissner, Kristian, Pawlowski, Jan, Schmidt Yanez, Paul L, Zizka, Vera M A, Leese, Florian, Price, Benjamin W, and Deiner, Kristy
- 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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- 2019
32. Author Correction: Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys
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Grey, Erin K., primary, Bernatchez, Louis, additional, Cassey, Phillip, additional, Deiner, Kristy, additional, Deveney, Marty, additional, Howland, Kimberly L., additional, Lacoursière-Roussel, Anaïs, additional, Leong, Sandric Chee Yew, additional, Li, Yiyuan, additional, Olds, Brett, additional, Pfrender, Michael E., additional, Prowse, Thomas A. A., additional, Renshaw, Mark A., additional, and Lodge, David M., additional
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- 2019
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33. Advancing the use of molecular methods for routine freshwater macroinvertebrate biomonitoring – the need for calibration experiments
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Blackman, Rosetta, primary, Mächler, Elvira, additional, Altermatt, Florian, additional, Arnold, Amanda, additional, Beja, Pedro, additional, Boets, Pieter, additional, Egeter, Bastian, additional, Elbrecht, Vasco, additional, Filipe, Ana Filipa, additional, Jones, John, additional, Macher, Jan, additional, Majaneva, Markus, additional, Martins, Filipa, additional, Múrria, Cesc, additional, Meissner, Kristian, additional, Pawlowski, Jan, additional, Schmidt Yáñez, Paul, additional, Zizka, Vera, additional, Leese, Florian, additional, Price, Benjamin, additional, and Deiner, Kristy, additional
- Published
- 2019
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34. Optimising the detection of marine taxonomic richness using environmental DNA metabarcoding: the effects of filter material, pore size and extraction method
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Deiner, Kristy, primary, Lopez, Jacqueline, additional, Bourne, Steve, additional, Holman, Luke, additional, Seymour, Mathew, additional, Grey, Erin K., additional, Lacoursière, Anaïs, additional, Li, Yiyuan, additional, Renshaw, Mark A., additional, Pfrender, Michael E., additional, Rius, Marc, additional, Bernatchez, Louis, additional, and Lodge, David M., additional
- Published
- 2018
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35. eDNA metabarcoding as a new surveillance approach for coastal Arctic biodiversity
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Lacoursière-Roussel, Anaïs, Howland, Kimberly, Normandeau, Eric, Grey, Erin K, Archambault, Philippe, Deiner, Kristy, Lodge, David M, Hernandez, Cecilia, Leduc, Noémie, Bernatchez, Louis, Lacoursière-Roussel, Anaïs, Howland, Kimberly, Normandeau, Eric, Grey, Erin K, Archambault, Philippe, Deiner, Kristy, Lodge, David M, Hernandez, Cecilia, Leduc, Noémie, and Bernatchez, Louis
- 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) meta-barcoding 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 data-bases. 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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- 2018
36. The future of biodiversity monitoring and conservation utilizing environmental DNA.
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Deiner, Kristy, Yamanaka, Hiroki, and Bernatchez, Louis
- Published
- 2021
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37. Fish community assessment with eDNA metabarcoding: effects of sampling design and bioinformatic filtering
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Evans, Nathan T., Li, Yiyuan, Renshaw, Mark A., Olds, Brett P., Deiner, Kristy, Turner, Cameron R., Jerde, Christopher L., Lodge, David M., Lamberti, Gary A., and Pfrender, Michael E.
- Abstract
Species richness is a metric of biodiversity that represents the number of species present in a community. Traditional fisheries assessments that rely on capture of organisms often underestimate true species richness. Environmental DNA (eDNA) metabarcoding is an alternative tool that infers species richness by collecting and sequencing DNA present in the ecosystem. Our objective was to determine how spatial distribution of samples and “bioinformatic stringency” affected eDNA-metabarcoding estimates of species richness compared with capture-based estimates in a 2.2 ha reservoir. When bioinformatic criteria required species to be detected only in a single sample, eDNA metabarcoding detected all species captured with traditional methods plus an additional 11 noncaptured species. However, when we required species to be detected with multiple markers and in multiple samples, eDNA metabarcoding detected only seven of the captured species. Our analysis of the spatial patterns of species detection indicated that eDNA was distributed relatively homogeneously throughout the reservoir, except near the inflowing stream. We suggest that interpretation of eDNA metabarcoding data must consider the potential effects of water body type, spatial resolution, and bioinformatic stringency., La richesse spécifique est une mesure de la biodiversité qui représente le nombre d’espèces présentes dans une communauté. Les évaluations traditionnelles des ressources halieutiques qui reposent sur la capture d’organismes sous-estiment souvent la richesse spécifique réelle. Les méta-codes à barres d’ADN environnemental) (ADNe) constituent un autre outil qui permet d’inférer la richesse spécifique en recueillant et en séquençant l’ADN présent dans l’écosystème. Notre objectif consistait à déterminer comment la répartition spatiale des échantillons et la « rigueur bioinformatique » influent sur les estimations de la richesse spécifique reposant sur les méta-codes à barres d’ADNe par rapport aux estimations reposant sur la capture, dans un réservoir de 2,2 ha. Quand les critères bioinformatiques exigeaient la détection d’une espèce dans un seul échantillon, la méthode des méta-codes à barres d’ADNe a détecté toutes les espèces capturées par les méthodes traditionnelles en plus de 11 autres espèces non capturées. Toutefois, quand il fallait que les espèces soient détectées sur la base de plus d’un marqueur et dans plus d’un échantillon, les méta-codes à barres d’ADNe n’ont détecté que sept des espèces capturées. Notre analyse de la répartition spatiale de la détection d’espèces indique que l’ADNe était réparti de manière assez uniforme dans tout le réservoir, sauf près de l’embouchure du cours d’eau qui l’alimente. Nous proposons que l’interprétation des données obtenues par la méthode des méta-codes à barres d’ADNe doit tenir compte des effets potentiels du type de plan d’eau, de la résolution spatiale et de la rigueur bioinformatique. [Traduit par la Rédaction], Canadian Journal of Fisheries and Aquatic Sciences, 74 (9), ISSN:0706-652X, ISSN:1205-7533
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- 2017
38. Species richness and biogeography of Lake Tanganyika estimated from environmental DNA metabarcoding
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Deiner, Kristy, Hamann, Ellen, Li, Yiyuan, Lodge, David, Lopez, Jacqueline, Mcintyre, Peter, Pfrender, Michael, and Wagner, Catherine
- Subjects
Lake Tanganyika -- Natural history ,Biogeography -- Research ,Freshwater animals -- Distribution -- Genetic aspects -- Environmental aspects ,Zoological research ,DNA barcoding -- Methods ,Company distribution practices ,Biological sciences - Abstract
Background: Lake Tanganyika is one of only a handful of ancient lakes greater than 1 million years old and is home to an astonishing 600 endemic freshwater species. About one [...]
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- 2017
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39. eDNA metabarcoding as a new surveillance approach for coastal Arctic biodiversity
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Lacoursière‐Roussel, Anaïs, primary, Howland, Kimberly, additional, Normandeau, Eric, additional, Grey, Erin K., additional, Archambault, Philippe, additional, Deiner, Kristy, additional, Lodge, David M., additional, Hernandez, Cecilia, additional, Leduc, Noémie, additional, and Bernatchez, Louis, additional
- Published
- 2018
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40. Estimating fish alpha- and beta-diversity along a small stream with environmental DNA metabarcoding
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Li, Yiyuan, primary, Evans, Nathan T., additional, Renshaw, Mark A., additional, Jerde, Christopher L., additional, Olds, Brett P., additional, Shogren, Arial J., additional, Deiner, Kristy, additional, Lodge, David M., additional, Lamberti, Gary A., additional, and Pfrender, Michael E., additional
- Published
- 2018
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41. Scale and scope matter when explaining varying patterns ofcommunity diversity in riverine metacommunities
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Seymour, Mathew, Deiner, Kristy, Altermatt, Florian, University of Zurich, and Seymour, Mathew
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10127 Institute of Evolutionary Biology and Environmental Studies ,Phylogenetic ,1105 Ecology, Evolution, Behavior and Systematics ,Freshwater ,Macroinvertebrates ,Functional ,570 Life sciences ,biology ,590 Animals (Zoology) ,Variance partitioning ,Metacommunity phylogenetics - Published
- 2016
42. Long‐range PCR allows sequencing of mitochondrial genomes from environmental DNA
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Deiner, Kristy, primary, Renshaw, Mark A., additional, Li, Yiyuan, additional, Olds, Brett P., additional, Lodge, David M., additional, and Pfrender, Michael E., additional
- Published
- 2017
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43. DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe
- Author
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Leese, Florian, primary, Altermatt, Florian, additional, Bouchez, Agnès, additional, Ekrem, Torbjørn, additional, Hering, Daniel, additional, Meissner, Kristian, additional, Mergen, Patricia, additional, Pawlowski, Jan, additional, Piggott, Jeremy, additional, Rimet, Frédéric, additional, Steinke, Dirk, additional, Taberlet, Pierre, additional, Weigand, Alexander, additional, Abarenkov, Kessy, additional, Beja, Pedro, additional, Bervoets, Lieven, additional, Björnsdóttir, Snaedís, additional, Boets, Pieter, additional, Boggero, Angela, additional, Bones, Atle, additional, Borja, Ángel, additional, Bruce, Kat, additional, Bursić, Vojislava, additional, Carlsson, Jens, additional, Čiampor, Fedor, additional, Čiamporová-Zatovičová, Zuzana, additional, Coissac, Eric, additional, Costa, Filipe, additional, Costache, Marieta, additional, Creer, Simon, additional, Csabai, Zoltán, additional, Deiner, Kristy, additional, DelValls, Ángel, additional, Drakare, Stina, additional, Duarte, Sofia, additional, Eleršek, Tina, additional, Fazi, Stefano, additional, Fišer, Cene, additional, Flot, Jean-François, additional, Fonseca, Vera, additional, Fontaneto, Diego, additional, Grabowski, Michael, additional, Graf, Wolfram, additional, Guðbrandsson, Jóhannes, additional, Hellström, Micaela, additional, Hershkovitz, Yaron, additional, Hollingsworth, Peter, additional, Japoshvili, Bella, additional, Jones, John, additional, Kahlert, Maria, additional, Kalamujic Stroil, Belma, additional, Kasapidis, Panagiotis, additional, Kelly, Martyn, additional, Kelly-Quinn, Mary, additional, Keskin, Emre, additional, Kõljalg, Urmas, additional, Ljubešić, Zrinka, additional, Maček, Irena, additional, Mächler, Elvira, additional, Mahon, Andrew, additional, Marečková, Marketa, additional, Mejdandzic, Maja, additional, Mircheva, Georgina, additional, Montagna, Matteo, additional, Moritz, Christian, additional, Mulk, Vallo, additional, Naumoski, Andreja, additional, Navodaru, Ion, additional, Padisák, Judit, additional, Pálsson, Snæbjörn, additional, Panksep, Kristel, additional, Penev, Lyubomir, additional, Petrusek, Adam, additional, Pfannkuchen, Martin, additional, Primmer, Craig, additional, Rinkevich, Baruch, additional, Rotter, Ana, additional, Schmidt-Kloiber, Astrid, additional, Segurado, Pedro, additional, Speksnijder, Arjen, additional, Stoev, Pavel, additional, Strand, Malin, additional, Šulčius, Sigitas, additional, Sundberg, Per, additional, Traugott, Michael, additional, Tsigenopoulos, Costas, additional, Turon, Xavier, additional, Valentini, Alice, additional, van der Hoorn, Berry, additional, Várbíró, Gábor, additional, Vasquez Hadjilyra, Marlen, additional, Viguri, Javier, additional, Vitonytė, Irma, additional, Vogler, Alfried, additional, Vrålstad, Trude, additional, Wägele, Wolfgang, additional, Wenne, Roman, additional, Winding, Anne, additional, Woodward, Guy, additional, Zegura, Bojana, additional, and Zimmermann, Jonas, additional
- Published
- 2016
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44. Critical considerations for the application of environmental DNA methods to detect aquatic species
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Goldberg, Caren S., Turner, Cameron R., Deiner, Kristy, Klymus, Katy E., Thomsen, Philip Francis, Murphy, Melanie A., Spear, Stephen F., McKee, Anna, Oyler-McCance, Sara J., Cornman, Robert Scott, Laramie, Matthew B., Mahon, Andrew R., Lance, Richard F., Pilliod, David S., Strickler, Katherine M., Waits, Lisette P., Fremier, Alexander K., Takahara, Teruhiko, Herder, Jelger E., Taberlet, Pierre, Goldberg, Caren S., Turner, Cameron R., Deiner, Kristy, Klymus, Katy E., Thomsen, Philip Francis, Murphy, Melanie A., Spear, Stephen F., McKee, Anna, Oyler-McCance, Sara J., Cornman, Robert Scott, Laramie, Matthew B., Mahon, Andrew R., Lance, Richard F., Pilliod, David S., Strickler, Katherine M., Waits, Lisette P., Fremier, Alexander K., Takahara, Teruhiko, Herder, Jelger E., and Taberlet, Pierre
- Published
- 2016
45. DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe
- Author
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European Commission, Leese, Florian, Altermatt, Florian, Bouchez, Agnès, Ekrem, Torbjørn, Hering, Daniel, Meissner, Kristian, Mergen, Patricia, Pawlowski, Jan, Piggott, Jeremy Jay, Rimet, Frédéric, Steinke, Dirk, Taberlet, Pierre, Weigand, Alexander M., Abarenkov, Kessy, Beja, Pedro, Bervoets, Lieven, Björnsdóttir, Snaedís, Boets, Pieter, Boggero, Angela, Bones, Atle Magnar, Borja, Ángel, Bruce, Kat, Bursić, Vojislava, Carlsson, Jens, Čiampor, Fedor, Čiamporová-Zatovičová, Zuzana, Coissac, Eric, Costa, Filipe, Costache, Marieta, Creer, Simon, Csabai, Zoltán, Deiner, Kristy, DelValls, Ángel, Drakare, Stina, Duarte, Sofia, Eleršek, Tina, Fazi, Stefano, Fišer, Cene, Flot, Jean-François, Fonseca, Vera, Fontaneto, Diego, Grabowski, Michael, Graf, Wolfram, Guðbrandsson, Jóhannes, Hershkovitz, Yaron, Hollingsworth, Peter, Japoshvili, Bella, Jones, John I., Kahlert, Maria, Kalamujic Stroil, Belma, Kasapidis, Panagiotis, Kelly, Martyn G., Kelly-Quinn, Mary, Keskin, Emre, Kõljalg, Urmas, Ljubešić, Zrinka, Maček, Irena, Mächler, Elvira, Mahon, Andrew, Marečková, Marketa, Mejdandzic, Maja, Mircheva, Georgina, Montagna, Matteo, Moritz, Christian, Mulk, Vallo, Naumoski, Andreja, Navodaru, Ion, Padisák, Judit, Pálsson, Snæbjörn, Panksep, Kristel, Penev, Lyubomir, Petrusek, Adam, Pfannkuchen, Martin Andreas, Primmer, Craig R., Rinkevich, Baruch, Rotter, Ana, Schmidt-Kloiber, Astrid, Segurado, Pedro, Speksnijder, Arjen, Stoev, Pavel, Strand, Malin, Šulčius, Sigitas, Traugott, Michael, Tsigenopoulos, Costas S., Turon, Xavier, Valentini, Alice, van der Hoorn, Berry, Várbíró, Gábor, Vasquez Hadjilyra, Marlen Ines, Viguri, Javier, Vitonytė, Irma, Vogler, Alfried P., Vrålstad, Trude, Wägele, Wolfgang, Wenne, Roman, Winding, Anne, Woodward, Guy, Zegura, Bojana, Zimmermann, Jonas, European Commission, Leese, Florian, Altermatt, Florian, Bouchez, Agnès, Ekrem, Torbjørn, Hering, Daniel, Meissner, Kristian, Mergen, Patricia, Pawlowski, Jan, Piggott, Jeremy Jay, Rimet, Frédéric, Steinke, Dirk, Taberlet, Pierre, Weigand, Alexander M., Abarenkov, Kessy, Beja, Pedro, Bervoets, Lieven, Björnsdóttir, Snaedís, Boets, Pieter, Boggero, Angela, Bones, Atle Magnar, Borja, Ángel, Bruce, Kat, Bursić, Vojislava, Carlsson, Jens, Čiampor, Fedor, Čiamporová-Zatovičová, Zuzana, Coissac, Eric, Costa, Filipe, Costache, Marieta, Creer, Simon, Csabai, Zoltán, Deiner, Kristy, DelValls, Ángel, Drakare, Stina, Duarte, Sofia, Eleršek, Tina, Fazi, Stefano, Fišer, Cene, Flot, Jean-François, Fonseca, Vera, Fontaneto, Diego, Grabowski, Michael, Graf, Wolfram, Guðbrandsson, Jóhannes, Hershkovitz, Yaron, Hollingsworth, Peter, Japoshvili, Bella, Jones, John I., Kahlert, Maria, Kalamujic Stroil, Belma, Kasapidis, Panagiotis, Kelly, Martyn G., Kelly-Quinn, Mary, Keskin, Emre, Kõljalg, Urmas, Ljubešić, Zrinka, Maček, Irena, Mächler, Elvira, Mahon, Andrew, Marečková, Marketa, Mejdandzic, Maja, Mircheva, Georgina, Montagna, Matteo, Moritz, Christian, Mulk, Vallo, Naumoski, Andreja, Navodaru, Ion, Padisák, Judit, Pálsson, Snæbjörn, Panksep, Kristel, Penev, Lyubomir, Petrusek, Adam, Pfannkuchen, Martin Andreas, Primmer, Craig R., Rinkevich, Baruch, Rotter, Ana, Schmidt-Kloiber, Astrid, Segurado, Pedro, Speksnijder, Arjen, Stoev, Pavel, Strand, Malin, Šulčius, Sigitas, Traugott, Michael, Tsigenopoulos, Costas S., Turon, Xavier, Valentini, Alice, van der Hoorn, Berry, Várbíró, Gábor, Vasquez Hadjilyra, Marlen Ines, Viguri, Javier, Vitonytė, Irma, Vogler, Alfried P., Vrålstad, Trude, Wägele, Wolfgang, Wenne, Roman, Winding, Anne, Woodward, Guy, Zegura, Bojana, and Zimmermann, Jonas
- Abstract
The protection, preservation and restoration of aquatic ecosystems and their functions are of global importance. For European states it became legally binding mainly through the EUWater Framework Directive (WFD). In order to assess the ecological status of a given water body, aquatic biodiversity data are obtained and compared to a reference water body. The quantified mismatch obtained determines the extent of potential management actions. The current approach to biodiversity assessment is based on morpho-taxonomy. This approach has many drawbacks such as being time consuming, limited in temporal and spatial resolution, and error-prone due to the varying individual taxonomic expertise of the analysts. Novel genomic tools can overcome many of the aforementioned problems and could complement or even replace traditional bioassessment. Yet, a plethora of approaches are independently developed in different institutions, thereby hampering any concerted routine application. The goal of this Action is to nucleate a group of researchers across disciplines with the task to identify gold-standard genomic tools and novel ecogenomic indices for routine application in biodiversity assessments of European fresh- and marine water bodies. Furthermore, DNAqua-Net will provide a platform for training of the next generation of European researchers preparing them for the new technologies. Jointly with water managers, politicians, and other stakeholders, the group will develop a conceptual framework for the standard application of eco-genomic tools as part of legally binding assessments.
- Published
- 2016
46. DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe
- Author
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Leese, Florian, Altermatt, Florian, Bouchez, Agnès, Ekrem, Tobjorn, Hering, Daniel, Meissner, Kristian, Mergen, Patricia, Pawlowski, Jan, Piggott, Jeremy Jay, Rimet, Frédéric, Steinke, Dirk, Taberlet, Pierre, Weigand, M.A., Abarenkov, Kessy, Beja, Pedro, Bervoets, Lieven, Björnsdóttir, Snaedis, Boets, Pieter, Boggero, Angela, Magnar Bones, Atle, Borja, Angel, Bruce, Kat, Bursic, Vojislava, Carlsson, J., Ciampor, Fedor, Ciamporová-Zatovicová, Zuzana, Coissac, Eric, Costa, Filipe, Costache, Marieta, Creer, Simon, Csabai, Zoltán, Deiner, Kristy, DelValls, Angel, Drakare, Stina, Duarte, Sofia, Elersek, Tina, Fazi, Stefano, Fišer, Cene, Flot, Jean-François, Fonseca, Vera, Fontaneto, Diego, Grabowski, Michael, Graf, Wolfram, Guobrandsson, Jóhannes, Hellström, Micaela, Hershkovitz, Yaron, Hollingsworth, Peter, Japoshvili, Bella, Jones, John, Kahlert, Maria, Kalamujic Stroil, Belma, Kasapidis, Panagiotis, Kelly, Martyn G., Kelly-Quinn, Mary, Keskin, Emre, Koljalg, Urmas, Ljubesic, Zrinka, Macek, Irena, Mächler, Elvira, Mahon, Andrew, Marecková, Marketa, Mejdandzic, Maja, Mircheva, Georgina, Montagna, Matteo, Moritz, Christian, Mulk, Vallo, Naumoski, Andreja, Navodaru, Ion, Padisák, Judit, Pálsson, Snæbjörn, Panksep, Kristel, Penev, L., Petrusek, Adam, Pfannkuchen, Martin Andreas, Primmer, Craig R., Rinkevich, Baruch, Rotter, Ana, Schmidt-Kloiber, Astrid, Segurado, Pedro, Speksnijder, Arjen Gerard Cornelis Lambertus, Stoev, Pavel, Strand, Malin, Sulcius, Sigitas, Sundberg, Per, Traugott, Michael, Tsigenopoulos, Costas, Turon, Xavier, Valentini, Alice, Van der Hoorn, Berry, Várbiró, Gábor, Vasquez Hadjilyra, Marlen Ines, Viguri, Javier, Vitonyte, Irma, Vogler, Alfried, Vralstad, Trud, Wägele, Wolfgang, Wenne, Roman, Winding, Anne, Woodward, Guy, Zegura, Bojana, Zimmermann, Jonas, Leese, Florian, Altermatt, Florian, Bouchez, Agnès, Ekrem, Tobjorn, Hering, Daniel, Meissner, Kristian, Mergen, Patricia, Pawlowski, Jan, Piggott, Jeremy Jay, Rimet, Frédéric, Steinke, Dirk, Taberlet, Pierre, Weigand, M.A., Abarenkov, Kessy, Beja, Pedro, Bervoets, Lieven, Björnsdóttir, Snaedis, Boets, Pieter, Boggero, Angela, Magnar Bones, Atle, Borja, Angel, Bruce, Kat, Bursic, Vojislava, Carlsson, J., Ciampor, Fedor, Ciamporová-Zatovicová, Zuzana, Coissac, Eric, Costa, Filipe, Costache, Marieta, Creer, Simon, Csabai, Zoltán, Deiner, Kristy, DelValls, Angel, Drakare, Stina, Duarte, Sofia, Elersek, Tina, Fazi, Stefano, Fišer, Cene, Flot, Jean-François, Fonseca, Vera, Fontaneto, Diego, Grabowski, Michael, Graf, Wolfram, Guobrandsson, Jóhannes, Hellström, Micaela, Hershkovitz, Yaron, Hollingsworth, Peter, Japoshvili, Bella, Jones, John, Kahlert, Maria, Kalamujic Stroil, Belma, Kasapidis, Panagiotis, Kelly, Martyn G., Kelly-Quinn, Mary, Keskin, Emre, Koljalg, Urmas, Ljubesic, Zrinka, Macek, Irena, Mächler, Elvira, Mahon, Andrew, Marecková, Marketa, Mejdandzic, Maja, Mircheva, Georgina, Montagna, Matteo, Moritz, Christian, Mulk, Vallo, Naumoski, Andreja, Navodaru, Ion, Padisák, Judit, Pálsson, Snæbjörn, Panksep, Kristel, Penev, L., Petrusek, Adam, Pfannkuchen, Martin Andreas, Primmer, Craig R., Rinkevich, Baruch, Rotter, Ana, Schmidt-Kloiber, Astrid, Segurado, Pedro, Speksnijder, Arjen Gerard Cornelis Lambertus, Stoev, Pavel, Strand, Malin, Sulcius, Sigitas, Sundberg, Per, Traugott, Michael, Tsigenopoulos, Costas, Turon, Xavier, Valentini, Alice, Van der Hoorn, Berry, Várbiró, Gábor, Vasquez Hadjilyra, Marlen Ines, Viguri, Javier, Vitonyte, Irma, Vogler, Alfried, Vralstad, Trud, Wägele, Wolfgang, Wenne, Roman, Winding, Anne, Woodward, Guy, Zegura, Bojana, and Zimmermann, Jonas
- Abstract
The protection, preservation and restoration of aquatic ecosystems and their functions are of global importance. For European states it became legally binding mainly through the EU-Water Framework Directive (WFD). In order to assess the ecological status of a given water body, aquatic biodiversity data are obtained and compared to a reference water body. The quantified mismatch obtained determines the extent of potential management actions. The current approach to biodiversity assessment is based on morpho-taxonomy. This approach has many drawbacks such as being time consuming, limited in temporal and spatial resolution, and error-prone due to the varying individual taxonomic expertise of the analysts. Novel genomic tools can overcome many of the aforementioned problems and could complement or even replace traditional bioassessment. Yet, a plethora of approaches are independently developed in different institutions, thereby hampering any concerted routine application. The goal of this Action is to nucleate a group of researchers across disciplines with the task to identify gold-standard genomic tools and novel eco-genomic indices for routine application in biodiversity assessments of European fresh- and marine water bodies. Furthermore, DNAqua-Net will provide a platform for training of the next generation of European researchers preparing them for the new technologies. Jointly with water managers, politicians, and other stakeholders, the group will develop a conceptual framework for the standard application of eco-genomic tools as part of legally binding assessments., info:eu-repo/semantics/published
- Published
- 2016
47. Environmental DNA reveals that rivers are conveyer belts of biodiversity information
- Author
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Deiner, Kristy, Fronhofer, Emanuel A, Mächler, Elvira, Walser, Jean-Claude, Altermatt, Florian, Deiner, Kristy, Fronhofer, Emanuel A, Mächler, Elvira, Walser, Jean-Claude, and Altermatt, Florian
- 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.
- Published
- 2016
48. Environmental DNA reveals that rivers are conveyer belts of biodiversity information
- Author
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Deiner, Kristy, primary, Fronhofer, Emanuel A., additional, Mächler, Elvira, additional, Walser, Jean-Claude, additional, and Altermatt, Florian, additional
- Published
- 2016
- Full Text
- View/download PDF
49. Critical considerations for the application of environmental DNA methods to detect aquatic species
- Author
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Goldberg, Caren S., primary, Turner, Cameron R., additional, Deiner, Kristy, additional, Klymus, Katy E., additional, Thomsen, Philip Francis, additional, Murphy, Melanie A., additional, Spear, Stephen F., additional, McKee, Anna, additional, Oyler‐McCance, Sara J., additional, Cornman, Robert Scott, additional, Laramie, Matthew B., additional, Mahon, Andrew R., additional, Lance, Richard F., additional, Pilliod, David S., additional, Strickler, Katherine M., additional, Waits, Lisette P., additional, Fremier, Alexander K., additional, Takahara, Teruhiko, additional, Herder, Jelger E., additional, and Taberlet, Pierre, additional
- Published
- 2016
- Full Text
- View/download PDF
50. Estimating species richness using environmental DNA
- Author
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Olds, Brett P., primary, Jerde, Christopher L., additional, Renshaw, Mark A., additional, Li, Yiyuan, additional, Evans, Nathan T., additional, Turner, Cameron R., additional, Deiner, Kristy, additional, Mahon, Andrew R., additional, Brueseke, Michael A., additional, Shirey, Patrick D., additional, Pfrender, Michael E., additional, Lodge, David M., additional, and Lamberti, Gary A., additional
- Published
- 2016
- Full Text
- View/download PDF
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