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Larsen L. Why citizen scientists are gathering DNA from hundreds of lakes - on the same day. Nature 2024; 626:934-935. [PMID: 38383651 DOI: 10.1038/d41586-024-00520-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
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Fracasso I, Zaccone C, Oskolkov N, Da Ros L, Dinella A, Belelli Marchesini L, Buzzini P, Sannino C, Turchetti B, Cesco S, Le Roux G, Tonon G, Vernesi C, Mimmo T, Ventura M, Borruso L. Exploring different methodological approaches to unlock paleobiodiversity in peat profiles using ancient DNA. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168159. [PMID: 37923262 DOI: 10.1016/j.scitotenv.2023.168159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/28/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023]
Abstract
Natural and human-induced environmental changes deeply affected terrestrial ecosystems throughout the Holocene. Paleoenvironmental reconstructions provide information about the past and allow us to predict/model future scenarios. Among potential records, peat bogs are widely used because they present a precise stratigraphy and act as natural archives of highly diverse organic remains. Over the decades, several techniques have been developed to identify debris occurring in peat, including their morphological description. However, this is strongly constrained by the researcher's ability to distinguish residues at the species level, which typically requires many years of experience. In addition, potential contamination hampers using these techniques to obtain information from organisms such as fungi or bacteria. Environmental DNA metabarcoding and shotgun metagenome sequencing could represent a solution to detect specific groups of organisms without any a priori knowledge of their characteristics and/or to identify organisms that have rarely been considered in previous investigations. Moreover, shotgun metagenomics may allow the identification of bacteria and fungi (including both yeast and filamentous life forms), ensuring discrimination between ancient and modern organisms through the study of deamination/damage patterns. In the present review, we aim to i) present the state-of-the-art methodologies in paleoecological and paleoclimatic studies focusing on peat core analyses, proposing alternative approaches to the classical morphological identification of plant residues, and ii) suggest biomolecular approaches that will allow the use of proxies such as invertebrates, fungi, and bacteria, which are rarely employed in paleoenvironmental reconstructions.
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Affiliation(s)
- Ilaria Fracasso
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy.
| | - Claudio Zaccone
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Nikolay Oskolkov
- Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, 221 00 Lund, Sweden
| | - Luca Da Ros
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Anna Dinella
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Luca Belelli Marchesini
- Forest Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, 38098 San Michele all'Adige, Italy
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Science, University of Perugia, 06123 Perugia, Italy
| | - Ciro Sannino
- Department of Agricultural, Food and Environmental Science, University of Perugia, 06123 Perugia, Italy
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Science, University of Perugia, 06123 Perugia, Italy
| | - Stefano Cesco
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Gael Le Roux
- Laboratoire Ecologie Fonctionnelle et Environnement (UMR5245 CNRS/UPS/INPT), Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Giustino Tonon
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Cristiano Vernesi
- Forest Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, 38098 San Michele all'Adige, Italy
| | - Tanja Mimmo
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Maurizio Ventura
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Luigimaria Borruso
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy.
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Métris KL, Métris J. Aircraft surveys for air eDNA: probing biodiversity in the sky. PeerJ 2023; 11:e15171. [PMID: 37077310 PMCID: PMC10108859 DOI: 10.7717/peerj.15171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/13/2023] [Indexed: 04/21/2023] Open
Abstract
Air is a medium for dispersal of environmental DNA (eDNA) carried in bioaerosols, yet the atmosphere is mostly unexplored as a source of genetic material encompassing all domains of life. In this study, we designed and deployed a robust, sterilizable hardware system for airborne nucleic acid capture featuring active filtration of a quantifiable, controllable volume of air and a high-integrity chamber to protect the sample from loss or contamination. We used our hardware system on an aircraft across multiple height transects over major aerosolization sources to collect air eDNA, coupled with high-throughput amplicon sequencing using multiple DNA metabarcoding markers targeting bacteria, plants, and vertebrates to test the hypothesis of large-scale genetic presence of these bioaerosols throughout the planetary boundary layer in the lower troposphere. Here, we demonstrate that the multi-taxa DNA assemblages inventoried up to 2,500 m using our airplane-mounted hardware system are reflective of major aerosolization sources in the survey area and show previously unreported airborne species detections (i.e., Allium sativum L). We also pioneer an aerial survey flight grid standardized for atmospheric sampling of genetic material and aeroallergens using a light aircraft and limited resources. Our results show that air eDNA from terrestrial bacteria, plants, and vertebrates is detectable up to high altitude using our airborne air sampler and demonstrate the usefulness of light aircraft in monitoring campaigns. However, our work also underscores the need for improved marker choices and reference databases for species in the air column, particularly eukaryotes. Taken together, our findings reveal strong connectivity or mixing of terrestrial-associated eDNA from ground level aerosolization sources and the atmosphere, and we recommend that parameters and indices considering lifting action, atmospheric instability, and potential for convection be incorporated in future surveys for air eDNA. Overall, this work establishes a foundation for light aircraft campaigns to comprehensively and economically inventory bioaerosol emissions and impacts at scale, enabling transformative future opportunities in airborne DNA technology.
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Affiliation(s)
- Kimberly L. Métris
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, United States
- Airborne Science LLC, Clemson, SC, United States
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Environmental DNA (eDNA): Powerful Technique for Biodiversity Conservation. J Nat Conserv 2022. [DOI: 10.1016/j.jnc.2022.126325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Dubois B, Debode F, Hautier L, Hulin J, Martin GS, Delvaux A, Janssen E, Mingeot D. A detailed workflow to develop QIIME2-formatted reference databases for taxonomic analysis of DNA metabarcoding data. BMC Genom Data 2022; 23:53. [PMID: 35804326 PMCID: PMC9264521 DOI: 10.1186/s12863-022-01067-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 07/01/2022] [Indexed: 11/10/2022] Open
Abstract
Background The DNA metabarcoding approach has become one of the most used techniques to study the taxa composition of various sample types. To deal with the high amount of data generated by the high-throughput sequencing process, a bioinformatics workflow is required and the QIIME2 platform has emerged as one of the most reliable and commonly used. However, only some pre-formatted reference databases dedicated to a few barcode sequences are available to assign taxonomy. If users want to develop a new custom reference database, several bottlenecks still need to be addressed and a detailed procedure explaining how to develop and format such a database is currently missing. In consequence, this work is aimed at presenting a detailed workflow explaining from start to finish how to develop such a curated reference database for any barcode sequence. Results We developed DB4Q2, a detailed workflow that allowed development of plant reference databases dedicated to ITS2 and rbcL, two commonly used barcode sequences in plant metabarcoding studies. This workflow addresses several of the main bottlenecks connected with the development of a curated reference database. The detailed and commented structure of DB4Q2 offers the possibility of developing reference databases even without extensive bioinformatics skills, and avoids ‘black box’ systems that are sometimes encountered. Some filtering steps have been included to discard presumably fungal and misidentified sequences. The flexible character of DB4Q2 allows several key sequence processing steps to be included or not, and downloading issues can be avoided. Benchmarking the databases developed using DB4Q2 revealed that they performed well compared to previously published reference datasets. Conclusion This study presents DB4Q2, a detailed procedure to develop custom reference databases in order to carry out taxonomic analyses with QIIME2, but also with other bioinformatics platforms if desired. This work also provides ready-to-use plant ITS2 and rbcL databases for which the prediction accuracy has been assessed and compared to that of other published databases. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-022-01067-5.
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Garcés-Pastor S, Coissac E, Lavergne S, Schwörer C, Theurillat JP, Heintzman PD, Wangensteen OS, Tinner W, Rey F, Heer M, Rutzer A, Walsh K, Lammers Y, Brown AG, Goslar T, Rijal DP, Karger DN, Pellissier L, Heiri O, Alsos IG. High resolution ancient sedimentary DNA shows that alpine plant diversity is associated with human land use and climate change. Nat Commun 2022; 13:6559. [PMID: 36333301 PMCID: PMC9636257 DOI: 10.1038/s41467-022-34010-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
The European Alps are highly rich in species, but their future may be threatened by ongoing changes in human land use and climate. Here, we reconstructed vegetation, temperature, human impact and livestock over the past ~12,000 years from Lake Sulsseewli, based on sedimentary ancient plant and mammal DNA, pollen, spores, chironomids, and microcharcoal. We assembled a highly-complete local DNA reference library (PhyloAlps, 3923 plant taxa), and used this to obtain an exceptionally rich sedaDNA record of 366 plant taxa. Vegetation mainly responded to climate during the early Holocene, while human activity had an additional influence on vegetation from 6 ka onwards. Land-use shifted from episodic grazing during the Neolithic and Bronze Age to agropastoralism in the Middle Ages. Associated human deforestation allowed the coexistence of plant species typically found at different elevational belts, leading to levels of plant richness that characterise the current high diversity of this region. Our findings indicate a positive association between low intensity agropastoral activities and precipitation with the maintenance of the unique subalpine and alpine plant diversity of the European Alps.
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Affiliation(s)
- Sandra Garcés-Pastor
- grid.10919.300000000122595234The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Eric Coissac
- grid.462909.00000 0004 0609 8934Université Grenoble-Alpes, Université Savoie Mont Blanc, CNRS, LECA, 38000 Grenoble, Rhône-Alpes France
| | - Sébastien Lavergne
- grid.462909.00000 0004 0609 8934Université Grenoble-Alpes, Université Savoie Mont Blanc, CNRS, LECA, 38000 Grenoble, Rhône-Alpes France
| | - Christoph Schwörer
- grid.5734.50000 0001 0726 5157Palaeoecology, Institute of Plant Sciences & Oeschger Centre for Climate Change Research, University of Bern, 3013 Bern, Switzerland
| | - Jean-Paul Theurillat
- grid.8591.50000 0001 2322 4988Fondation Aubert, 1938 Champex-Lac, Switzerland, Department of Plant Sciences, University of Geneva, 1292 Chambésy, Switzerland
| | - Peter D. Heintzman
- grid.10919.300000000122595234The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Owen S. Wangensteen
- grid.10919.300000000122595234Norwegian College of Fishery Science, UiT - The Arctic University of Norway, Tromsø, Norway ,grid.5841.80000 0004 1937 0247Department of Evolutionary Biology, Ecology and Environmental Sciences and Biodiversity Research Institute (IRBIO), University of Barcelona, Barcelona, Catalonia Spain
| | - Willy Tinner
- grid.5734.50000 0001 0726 5157Palaeoecology, Institute of Plant Sciences & Oeschger Centre for Climate Change Research, University of Bern, 3013 Bern, Switzerland
| | - Fabian Rey
- grid.6612.30000 0004 1937 0642Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Martina Heer
- grid.6612.30000 0004 1937 0642Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Astrid Rutzer
- grid.6612.30000 0004 1937 0642Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Kevin Walsh
- grid.5685.e0000 0004 1936 9668Department of Archaeology, University of York, York, 11 YO1 7EP UK
| | - Youri Lammers
- grid.10919.300000000122595234The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Antony G. Brown
- grid.10919.300000000122595234The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Tomasz Goslar
- grid.5633.30000 0001 2097 3545Faculty of Geographical and Geological Sciences, Adam Mickiewicz University, 61-680 Poznań, Poland
| | - Dilli P. Rijal
- grid.10919.300000000122595234The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Dirk N. Karger
- grid.419754.a0000 0001 2259 5533Swiss Federal Research Institute for Forest, Snow, and Landscape Research (WSL), Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Loïc Pellissier
- grid.5801.c0000 0001 2156 2780Department of Environmental System Science, Institute of Terrestrial Ecosystems, ETH Zurich, Zürich, Switzerland ,grid.419754.a0000 0001 2259 5533Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | | | - Oliver Heiri
- grid.6612.30000 0004 1937 0642Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Inger Greve Alsos
- grid.10919.300000000122595234The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
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A Critical Assessment of the Congruency between Environmental DNA and Palaeoecology for the Biodiversity Monitoring and Palaeoenvironmental Reconstruction. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19159445. [PMID: 35954801 PMCID: PMC9368151 DOI: 10.3390/ijerph19159445] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 02/01/2023]
Abstract
The present study suggests that standardized methodology, careful site selection, and stratigraphy are essential for investigating ancient ecosystems in order to evaluate biodiversity and DNA-based time series. Based on specific keywords, this investigation reviewed 146 publications using the SCOPUS, Web of Science (WoS), PUBMED, and Google Scholar databases. Results indicate that environmental deoxyribose nucleic acid (eDNA) can be pivotal for assessing and conserving ecosystems. Our review revealed that in the last 12 years (January 2008–July 2021), 63% of the studies based on eDNA have been reported from aquatic ecosystems, 25% from marine habitats, and 12% from terrestrial environments. Out of studies conducted in aquatic systems using the environmental DNA (eDNA) technique, 63% of the investigations have been reported from freshwater ecosystems, with an utmost focus on fish diversity (40%). Further analysis of the literature reveals that during the same period, 24% of the investigations using the environmental DNA technique were carried out on invertebrates, 8% on mammals, 7% on plants, 6% on reptiles, and 5% on birds. The results obtained clearly indicate that the environmental DNA technique has a clear-cut edge over other biodiversity monitoring methods. Furthermore, we also found that eDNA, in conjunction with different dating techniques, can provide better insight into deciphering eco-evolutionary feedback. Therefore, an attempt has been made to offer extensive information on the application of dating methods for different taxa present in diverse ecosystems. Last, we provide suggestions and elucidations on how to overcome the caveats and delineate some of the research avenues that will likely shape this field in the near future. This paper aims to identify the gaps in environmental DNA (eDNA) investigations to help researchers, ecologists, and decision-makers to develop a holistic understanding of environmental DNA (eDNA) and its utility as a palaeoenvironmental contrivance.
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Johnson MD, Fokar M, Cox RD, Barnes MA. Airborne environmental DNA metabarcoding detects more diversity, with less sampling effort, than a traditional plant community survey. BMC Ecol Evol 2021; 21:218. [PMID: 34872490 PMCID: PMC8647488 DOI: 10.1186/s12862-021-01947-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/24/2021] [Indexed: 01/04/2023] Open
Abstract
Background Airborne environmental DNA (eDNA) research is an emerging field that focuses on the detection of species from their genetic remnants in the air. The majority of studies into airborne eDNA of plants has until now either focused on single species detection, specifically only pollen, or human health impacts, with no previous studies surveying an entire plant community through metabarcoding. We therefore conducted an airborne eDNA metabarcoding survey and compared the results to a traditional plant community survey. Results Over the course of a year, we conducted two traditional transect-based visual plant surveys alongside an airborne eDNA sampling campaign on a short-grass rangeland. We found that airborne eDNA detected more species than the traditional surveying method, although the types of species detected varied based on the method used. Airborne eDNA detected more grasses and forbs with less showy flowers, while the traditional method detected fewer grasses but also detected rarer forbs with large showy flowers. Additionally, we found the airborne eDNA metabarcoding survey required less sampling effort in terms of the time needed to conduct a survey and was able to detect more invasive species than the traditional method. Conclusions Overall, we have demonstrated that airborne eDNA can act as a sensitive and efficient plant community surveying method. Airborne eDNA surveillance has the potential to revolutionize the way plant communities are monitored in general, track changes in plant communities due to climate change and disturbances, and assist with the monitoring of invasive and endangered species. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01947-x.
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Affiliation(s)
- Mark D Johnson
- Department of Natural Resources Management, Texas Tech University, Lubbock, TX, 79409, USA.
| | - Mohamed Fokar
- Center for Biotechnology & Genomics, Texas Tech University, Lubbock, TX, 79409, USA
| | - Robert D Cox
- Department of Natural Resources Management, Texas Tech University, Lubbock, TX, 79409, USA
| | - Matthew A Barnes
- Department of Natural Resources Management, Texas Tech University, Lubbock, TX, 79409, USA
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Massey AL, Bronzoni RVDM, da Silva DJF, Allen JM, de Lázari PR, Dos Santos-Filho M, Canale GR, Bernardo CSS, Peres CA, Levi T. Invertebrates for vertebrate biodiversity monitoring: Comparisons using three insect taxa as iDNA samplers. Mol Ecol Resour 2021; 22:962-977. [PMID: 34601818 DOI: 10.1111/1755-0998.13525] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 09/17/2021] [Accepted: 09/29/2021] [Indexed: 11/30/2022]
Abstract
Metabarcoding of environmental DNA (eDNA) is now widely used to build diversity profiles from DNA that has been shed by species into the environment. There is substantial interest in the expansion of eDNA approaches for improved detection of terrestrial vertebrates using invertebrate-derived DNA (iDNA) in which hematophagous, sarcophagous, and coprophagous invertebrates sample vertebrate blood, carrion, or faeces. Here, we used metabarcoding and multiple iDNA samplers (carrion flies, sandflies, and mosquitos) collected from 39 forested sites in the southern Amazon to profile gamma and alpha diversity. Our main objectives were to (1) compare diversity found with iDNA to camera trapping, which is the conventional method of vertebrate diversity surveillance; and (2) compare each of the iDNA samplers to assess the effectiveness, efficiency, and potential biases associated with each sampler. In total, we collected and analysed 1759 carrion flies, 48,686 sandflies, and 4776 mosquitos. Carrion flies revealed the greatest total vertebrate species richness at the landscape level, despite the least amount of sampling effort and the fewest number of individuals captured for metabarcoding, followed by sandflies. Camera traps had the highest median species richness at the site-level but showed strong bias towards carnivore and ungulate species and missed much of the diversity described by iDNA methods. Mosquitos showed a strong feeding preference for humans as did sandflies for armadillos, thus presenting potential utility to further study related to host-vector interactions.
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Affiliation(s)
- Aimee L Massey
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | | | | | - Jennifer M Allen
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Patrick Ricardo de Lázari
- Centro de Estudos de Limnologia e Biodiversidade e Etnobiologia do Pantanal, Universidade do Estado de Mato Grosso, Cáceres, Brazil
| | - Manoel Dos Santos-Filho
- Centro de Estudos de Limnologia e Biodiversidade e Etnobiologia do Pantanal, Universidade do Estado de Mato Grosso, Cáceres, Brazil
| | - Gustavo Rodrigues Canale
- Instituto de Ciências Naturais, Humanas e Sociais, Universidade Federal de Mato Grosso, Sinop, Brazil
| | | | - Carlos Augusto Peres
- School of Environmental Sciences, University of East Anglia, Norwich, UK.,Instituto Juruá, Manaus, Brazil
| | - Taal Levi
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
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