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Osathanunkul M, Suwannapoom C. An eDNA-based assessment of Garra cambodgiensis (stonelapping minnow) distribution on a megadiverse river, the Mekong. Ecol Evol 2024; 14:e10898. [PMID: 38333100 PMCID: PMC10850809 DOI: 10.1002/ece3.10898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/18/2023] [Accepted: 01/04/2024] [Indexed: 02/10/2024] Open
Abstract
Garra cambodgiensis (stonelapping minnow) has experienced significant population declines, prompting intensive research and management, although its distribution in river systems such as the Mekong remains obscure. Effective conservation and management necessitate accurate monitoring and survey data on the distribution of freshwater species. Traditional surveying techniques for fish may be challenging and generate insufficient data on species distribution. This study developed an eDNA-based method for detecting G. cambodgiensis to address this void. Twenty-one locations were surveyed. Water samples were collected in triplicate from the river's surface at each site and processed within 48 h in a dedicated laboratory. Primers and probes for G. cambodgiensis were meticulously designed and species-specificity tested to ensure accurate detection without interference from co-occurring species in the same geographic range. Each water sample was analysed by qPCR using six technical replicates. The results of qPCR were reported as positive with quantifiable eDNA concentration (copies/mL), below the limit of quantification, or non-detectable. G. cambodgiensis eDNA was detected in water samples collected from 10 out of 21 sampling sites, with concentrations ranging from 8.5 to 2990.0 copies/mL. Importantly, G. cambodgiensis eDNA was consistently detected in all three replicate water samples at each site where the qPCR experiment yielded positive results. The findings of this study demonstrate the feasibility and effectiveness of incorporating eDNA-based monitoring or surveys for G. cambodgiensis in the ecologically diverse Mekong River. Monitoring based on eDNA can aid in targeting and informing conservation and management of G. cambodgiensis in its natural habitat. Comprehensive and robust information on species distribution can be obtained via an eDNA-based survey, which could contribute to more efficient and informed decision-making processes in fisheries management and conservation efforts.
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Affiliation(s)
- Maslin Osathanunkul
- Department of Biology, Faculty of ScienceChiang Mai UniversityChiang MaiThailand
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2
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Gold Z, Koch MQ, Schooler NK, Emery KA, Dugan JE, Miller RJ, Page HM, Schroeder DM, Hubbard DM, Madden JR, Whitaker SG, Barber PH. A comparison of biomonitoring methodologies for surf zone fish communities. PLoS One 2023; 18:e0260903. [PMID: 37314989 DOI: 10.1371/journal.pone.0260903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 04/25/2023] [Indexed: 06/16/2023] Open
Abstract
Surf zones are highly dynamic marine ecosystems that are subject to increasing anthropogenic and climatic pressures, posing multiple challenges for biomonitoring. Traditional methods such as seines and hook and line surveys are often labor intensive, taxonomically biased, and can be physically hazardous. Emerging techniques, such as baited remote underwater video (BRUV) and environmental DNA (eDNA) are promising nondestructive tools for assessing marine biodiversity in surf zones of sandy beaches. Here we compare the relative performance of beach seines, BRUV, and eDNA in characterizing community composition of bony (teleost) and cartilaginous (elasmobranch) fishes of surf zones at 18 open coast sandy beaches in southern California. Seine and BRUV surveys captured overlapping, but distinct fish communities with 50% (18/36) of detected species shared. BRUV surveys more frequently detected larger species (e.g. sharks and rays) while seines more frequently detected one of the most abundant species, barred surfperch (Amphistichus argenteus). In contrast, eDNA metabarcoding captured 88.9% (32/36) of all fishes observed in seine and BRUV surveys plus 57 additional species, including 15 that frequent surf zone habitats. On average, eDNA detected over 5 times more species than BRUVs and 8 times more species than seine surveys at a given site. eDNA approaches also showed significantly higher sensitivity than seine and BRUV methods and more consistently detected 31 of the 32 (96.9%) jointly observed species across beaches. The four species detected by BRUV/seines, but not eDNA were only resolved at higher taxonomic ranks (e.g. Embiotocidae surfperches and Sygnathidae pipefishes). In frequent co-detection of species between methods limited comparisons of richness and abundance estimates, highlighting the challenge of comparing biomonitoring approaches. Despite potential for improvement, results overall demonstrate that eDNA can provide a cost-effective tool for long-term surf zone monitoring that complements data from seine and BRUV surveys, allowing more comprehensive surveys of vertebrate diversity in surf zone habitats.
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Affiliation(s)
- Zachary Gold
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - McKenzie Q Koch
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Nicholas K Schooler
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Kyle A Emery
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Jenifer E Dugan
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Robert J Miller
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Henry M Page
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Donna M Schroeder
- Bureau of Ocean Energy Management, Camarillo, CA, United States of America
| | - David M Hubbard
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Jessica R Madden
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Stephen G Whitaker
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
- Channel Islands National Park, Ventura, CA, United States of America
| | - Paul H Barber
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
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Merten Cruz M, Sauvage T, Chariton A, de Freitas TRO. The challenge of implementing environmental DNA metabarcoding to detect elasmobranchs in a resource-limited marine protected area. JOURNAL OF FISH BIOLOGY 2023. [PMID: 37060349 DOI: 10.1111/jfb.15406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/13/2023] [Indexed: 05/06/2023]
Abstract
Elasmobranchs are threatened and eDNA metabarcoding is a powerful tool that can help efforts to better understand and conserve them. Nevertheless, the inter-calibration between optimal methodological practices and its implementation in resource-limited situations is still an issue. Based on promising results from recent studies, the authors applied a cost-effective protocol with parameters that could be easily replicated by any conservationist. Nonetheless, the results with fewer elasmobranchs detected than expected reveal that endorsed primers and sampling strategies still require further optimization, especially for applications in resource-limited conservation programmes.
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Affiliation(s)
- Marcelo Merten Cruz
- Programa de Pós-graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Thomas Sauvage
- Programa de Pós-graduação em Ecologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Anthony Chariton
- School of Life Sciences, Macquarie University, Sydney, Australia
| | - Thales Renato Ochotorena de Freitas
- Programa de Pós-graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Detection of the Endangered Siamese Bat Catfish ( Oreoglanis siamensis Smith, 1933) in Doi Inthanon National Park Using Environmental DNA. Animals (Basel) 2023; 13:ani13030538. [PMID: 36766427 PMCID: PMC9913137 DOI: 10.3390/ani13030538] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/04/2023] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Siamese bat catfish (Oreoglanis siamensis Smith, 1993) has been listed as an endangered species, and its abundance has been severely declining due to habitat degradation and overfishing. To establish an appropriate management strategy, it is crucial to gain information about the distribution of this endangered species. As O. siamensis live under rocks in streams, detecting their presence is difficult. Recently, environmental DNA (eDNA)-based detection has been demonstrated to be a valid tool for monitoring rare species, such as O. siamensis. Therefore, this study developed an eDNA assay targeting a 160 bp fragment of the COI region to detect the presence of this species in its natural habitat. An amount of 300 mL of water samples (0.7 μm filtered) were collected from 15 sites in the Mae Klang sub-basin, where this fish species was visually detected at two locations. O. siamensis eDNA was detected at 12 of the 15 sites sampled with varying concentrations (0.71-20.27 copies/mL), including at the sites where this species was visually detected previously. The developed O. siamensis eDNA assay was shown to be effective for detecting the presence of this endangered species in the Klang Phat and Klang Rivers within the Doi Inthanon National Park.
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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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DiBattista JD, Fowler AM, Riley IJ, Reader S, Hay A, Parkinson K, Hobbs JPA. The use of environmental DNA to monitor impacted coastal estuaries. MARINE POLLUTION BULLETIN 2022; 181:113860. [PMID: 35779383 DOI: 10.1016/j.marpolbul.2022.113860] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Environmental DNA (eDNA) metabarcoding is increasingly being used to assess community composition in coastal ecosystems. In this study, we chose to examine temporal and spatial changes in the aquatic community of Manly Lagoon - one of the most heavily developed and polluted estuaries in eastern Australia. Based on metabarcoding of the 16S mitochondrial gene (for fish) and the 18S nuclear gene (for macroinvertebrates), we identified seasonal differences in fish and macroinvertebrate community composition as well as species richness, which correlated, in some cases, with the environmental parameters of sea surface temperature and freshwater input. Moreover, given the greater taxonomic resolution of fish versus macroinvertebrate assignments, we identified several known migratory fish species of management importance that contributed significantly to the overall patterns observed. Overall, our data support the use of eDNA metabarcoding to track fish assemblages shifting in response to environmental drivers in polluted estuaries with increased sampling and consultation with historical data.
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Affiliation(s)
- Joseph D DiBattista
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia.
| | - Ashley M Fowler
- New South Wales Department of Primary Industries, Sydney Institute of Marine Science, Mosman, NSW 2088, Australia
| | - Indiana J Riley
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia; Sydney Institute of Marine Science, Mosman, NSW 2088, Australia
| | - Sally Reader
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia
| | - Amanda Hay
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia
| | - Kerryn Parkinson
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia
| | - Jean-Paul A Hobbs
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4069, Australia
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Jeunen GJ, Lipinskaya T, Gajduchenko H, Golovenchik V, Moroz M, Rizevsky V, Semenchenko V, Gemmell NJ. Environmental DNA (eDNA) metabarcoding surveys show evidence of non-indigenous freshwater species invasion to new parts of Eastern Europe. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.e68575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Active environmental DNA (eDNA) surveillance through species-specific amplification has shown increased sensitivity in the detection of non-indigenous species (NIS) compared to traditional approaches. When many NIS are of interest, however, active surveillance decreases in cost- and time-efficiency. Passive surveillance through eDNA metabarcoding takes advantage of the complex DNA signal in environmental samples and facilitates the simultaneous detection of multiple species. While passive eDNA surveillance has previously detected NIS, comparative studies are essential to determine the ability of eDNA metabarcoding to accurately describe the range of invasion for multiple NIS versus alternative approaches. Here, we surveyed twelve sites, covering nine rivers across Belarus for NIS with three different techniques, i.e. an ichthyological, hydrobiological and eDNA survey, whereby DNA was extracted from 500 ml surface water samples and amplified with two 16S rDNA primer assays targeting the fish and macroinvertebrate biodiversity. Nine non-indigenous fish and ten non-indigenous benthic macroinvertebrates were detected by traditional surveys, while seven NISeDNA signals were picked up, including four fish, one aquatic and two benthic macroinvertebrates. Passive eDNA surveillance extended the range of invasion further north for two invasive fish and identified a new NIS for Belarus, the freshwater jellyfish Craspedacusta sowerbii. False-negative detections for the eDNA survey might be attributed to: (i) preferential amplification of aquatic over benthic macroinvertebrates from surface water samples and (ii) an incomplete reference database. The evidence provided in this study recommends the implementation of both molecular-based and traditional approaches to maximise the probability of early detection of non-native organisms.
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Lim KC, Then AY. Environmental DNA approach complements social media reports to detect an endangered freshwater stingray species in the wild. ENDANGER SPECIES RES 2022. [DOI: 10.3354/esr01187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Fish Diversity Monitored by Environmental DNA in the Yangtze River Mainstream. FISHES 2021. [DOI: 10.3390/fishes7010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Surveys and assessments based on environmental DNA are not only efficient and time-saving, but also cause less harm to monitoring targets. Environmental DNA has become a common tool for the assessment and monitoring of aquatic organisms. In this study, we investigated fish resources in the Yangtze River mainstream using environmental DNA, and the variations in fish during two seasons (spring and autumn) were compared. The results showed that 13 species were identified in spring, and nine species of fish were identified in autumn. The fish with higher eDNA detection were Sinibotia superciliaris, Tachysurus fulvidraco, Cyprinus carpio, Ctenopharyngodon Idella, Monopterus albus, Acanthogobius hasta, Saurogobio dabryi, Oncorhynchus mykiss, Mugil cephalus, Odontamblyopus rubicundus. Seasonal variation between spring and autumn was not significant, and the environmental factors had different effects on fish assemblages during the two seasons. Our study used the eDNA technique to monitor the composition of fish in the spring and autumn in the Yangtze River mainstream, providing a new technology for the long-term management and protection of fishery resources in the region. Of course, problems such as pollution and insufficient databases are the current shortcomings of environmental DNA, which will be the focus of our future research and study.
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Banerjee P, Dey G, Antognazza CM, Sharma RK, Maity JP, Chan MWY, Huang YH, Lin PY, Chao HC, Lu CM, Chen CY. Reinforcement of Environmental DNA Based Methods ( Sensu Stricto) in Biodiversity Monitoring and Conservation: A Review. BIOLOGY 2021; 10:biology10121223. [PMID: 34943137 PMCID: PMC8698464 DOI: 10.3390/biology10121223] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 12/02/2022]
Abstract
Simple Summary Worldwide biodiversity loss points to a necessity of upgrading to a fast and effective monitoring method that can provide quick conservation action. Newly developed environmental DNA (eDNA) based method found to be more cost-effective, non-invasive, quick, and accurate than traditional monitoring (spot identification, camera trapping). Although the eDNA based methods are proliferating rapidly, as a newly developed branch, it needs more standardization and practitioner adaptation. The present study aims to evaluate the eDNA based methods, and their potential achievements in biodiversity monitoring, and conservation for quick practitioners’ adaption. The investigation shows that the eDNA technique is applicable largely in (i) early detection of invasive species, (ii) species detection for conservation, (iii) community-level biodiversity monitoring, (iv) ecosystem health monitoring, (v) study on trophic interactions, etc. Thus, the eDNA technique shows a great promise with its high accuracy and authenticity, and will be applicable alone or alongside other methods in the near future. Abstract Recently developed non-invasive environmental DNA-based (eDNA) techniques have enlightened modern conservation biology, propelling the monitoring/management of natural populations to a more effective and efficient approach, compared to traditional surveys. However, due to rapid-expansion of eDNA, confusion in terminology and collection/analytical pipelines can potentially jeopardize research progression, methodological standardization, and practitioner adoption in several ways. Present investigation reflects the developmental progress of eDNA (sensu stricto) including highlighting the successful case studies in conservation management. The eDNA technique is successfully relevant in several areas of conservation research (invasive/conserve species detection) with a high accuracy and authentication, which gradually upgrading modern conservation approaches. The eDNA technique related bioinformatics (e.g., taxon-specific-primers MiFish, MiBird, etc.), sample-dependent methodology, and advancement of sequencing technology (e.g., oxford-nanopore-sequencing) are helping in research progress. The investigation shows that the eDNA technique is applicable largely in (i) early detection of invasive species, (ii) species detection for conservation, (iii) community level biodiversity monitoring, (iv) ecosystem health monitoring, (v) study on trophic interactions, etc. Thus, the eDNA technique with a high accuracy and authentication can be applicable alone or coupled with traditional surveys in conservation biology. However, a comprehensive eDNA-based monitoring program (ecosystem modeling and function) is essential on a global scale for future management decisions.
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Affiliation(s)
- Pritam Banerjee
- Department of Biomedical Science, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (P.B.); (G.D.); (M.W.Y.C.)
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (R.K.S.); (J.P.M.); (Y.-H.H.); (H.-C.C.)
| | - Gobinda Dey
- Department of Biomedical Science, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (P.B.); (G.D.); (M.W.Y.C.)
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (R.K.S.); (J.P.M.); (Y.-H.H.); (H.-C.C.)
| | - Caterina M. Antognazza
- Department of Theoretical and Applied Science, University of Insubria, Via J.H. Dunant, 3, 21100 Varese, Italy;
| | - Raju Kumar Sharma
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (R.K.S.); (J.P.M.); (Y.-H.H.); (H.-C.C.)
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan;
| | - Jyoti Prakash Maity
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (R.K.S.); (J.P.M.); (Y.-H.H.); (H.-C.C.)
- Department of Chemistry, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar 751024, India
| | - Michael W. Y. Chan
- Department of Biomedical Science, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (P.B.); (G.D.); (M.W.Y.C.)
| | - Yi-Hsun Huang
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (R.K.S.); (J.P.M.); (Y.-H.H.); (H.-C.C.)
| | - Pin-Yun Lin
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan;
| | - Hung-Chun Chao
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (R.K.S.); (J.P.M.); (Y.-H.H.); (H.-C.C.)
| | - Chung-Ming Lu
- Department of Chemical Engineering, National Chung Cheng University, 168 University Road, Ming-Shung, Chiayi County, Jiayi 62102, Taiwan;
| | - Chien-Yen Chen
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (R.K.S.); (J.P.M.); (Y.-H.H.); (H.-C.C.)
- Correspondence: or ; Tel.: +886-5-2720411 (ext. 66220); Fax: +886-5-2720807
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López-Angarita J, Cubillos-M JC, Villate-Moreno M, Del Cid A, Díaz JM, Cooke R, Cagua EF, Tilley A. Bright spots for research and conservation of the largetooth sawfish Pristis pristis in Colombia and Panamá. ENDANGER SPECIES RES 2021. [DOI: 10.3354/esr01150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Sawfishes are considered one of the most endangered families of fishes globally. Their diadromous ecology and vulnerability to fishing nets have brought most populations to the brink of collapse. Conservation of surviving populations is hindered by limited knowledge of historic and contemporary distribution. Colombia and Panamá are 2 of 22 countries considered as high priority for the development of species-specific national legal protection of the Critically Endangered largetooth sawfish Pristis pristis. To construct a baseline for the temporal and spatial distribution of the largetooth sawfish in Colombia and Panamá, we collected historical records from museum databases and literature over the past century, analysed available small-scale fisheries landings databases, and conducted interviews with fishers in 38 locations. We found 248 records of sawfish occurrences across both countries between 1896 and 2015, with 69% of the records from before 2000. The declining frequency of observations was corroborated by fishers, who reported fewer sawfish sightings and catches over the last 20 yr. Results from a regression model of total length and observed date suggest that the maximum size of observed sawfish individuals has also declined over time. We use location data from sawfish records to identify potential ‘bright spots’ that may foster remaining populations of sawfish. The locations of sawfish records were broadly characterised as remote areas with high mangrove forest cover. Given the length and cultural diversity of the Pacific coastlines of Colombia and Panamá, our findings provide important guidance to implement rapid conservation and fisheries interventions in these priority areas and highlight geographical gaps in knowledge for further work.
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Affiliation(s)
| | - JC Cubillos-M
- Fundación Talking Oceans, KR 16-127 61, Bogotá 110121, Colombia
- Ecological Genomics Group, Institute of Biology and Environmental Sciences, University of Oldenburg, 26129 Oldenburg, Germany
| | - M Villate-Moreno
- Fundación Talking Oceans, KR 16-127 61, Bogotá 110121, Colombia
- Biology II, Aquatic Ecology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - A Del Cid
- Fundación MarViva, Clayton, Ciudad del Saber, Calle Gustavo Lara Casa 145-5, Ciudad de Panamá, Panamá
| | - JM Díaz
- Fundación MarViva, KR 45A-93 71, Bogotá 111211, Colombia
| | - R Cooke
- Smithsonian Tropical Research Institute, PO Box 0843-03092, Panamá City, Panamá
- Sistema Nacional de Investigadores, Edificio 205 Ciudad del Saber, Calle Luis Bonilla, Ciudad de Panamá, Panamá
| | - EF Cagua
- WorldFish, Batu Maung, 11960 Bayan Lepas, Pulau Pinang, Malaysia
| | - A Tilley
- Fundación Talking Oceans, KR 16-127 61, Bogotá 110121, Colombia
- WorldFish, Batu Maung, 11960 Bayan Lepas, Pulau Pinang, Malaysia
- Department of Chemical, Pharmaceutical and Agricultural Sciences (DOCPAS), University of Ferrara, Via Luigi Borsari, 44121 Ferrara, Italy
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Veilleux HD, Misutka MD, Glover CN. Environmental DNA and environmental RNA: Current and prospective applications for biological monitoring. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 782:146891. [PMID: 33848866 DOI: 10.1016/j.scitotenv.2021.146891] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/22/2021] [Accepted: 03/28/2021] [Indexed: 06/12/2023]
Abstract
Traditional environmental biomonitoring approaches have limitations in terms of species detectability and their capacity to account for spatial and temporal variation. Furthermore, as invasive techniques they can be harmful to individual organisms, populations and habitats. The application of non-invasive sampling methods that extract, isolate and identify nucleic acid sequences (i.e. DNA, RNA) from environmental matrices have significant potential for complementing, or even ultimately replacing, current methods of biological environmental assessment. These environmental DNA (eDNA) and environmental RNA (eRNA) techniques increase spatial and temporal acuity of monitoring, and in the case of the latter, may provide functional information regarding the health of individuals, and thus ecosystems. However, these assessments require robust analysis of factors such as the detectability and specificity of the developed assays. The presented work highlights the current and future uses of nucleic acid-based biomonitoring regimes, with a focus on fish and aquatic invertebrates and their utility for water quality, biodiversity and species-specific monitoring. These techniques are compared to traditional approaches, with a particular emphasis on the potential insights that could be provided by eRNA analysis, including the benefits of microRNAs as assay targets.
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Affiliation(s)
- Heather D Veilleux
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
| | - Melissa D Misutka
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada; Faculty of Science and Technology and Athabasca River Basin Research Institute, Athabasca University, Athabasca, Alberta, Canada
| | - Chris N Glover
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada; Faculty of Science and Technology and Athabasca River Basin Research Institute, Athabasca University, Athabasca, Alberta, Canada
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Dunton KJ, Sparta K, Frisk MG, Martinez CM, Shipley ON. First Observation of Movement Rates and Repeated Migration in a Western Atlantic Torpedo (Tetronarce occidentalis) in the Northwest Atlantic Ocean. Northeast Nat (Steuben) 2021. [DOI: 10.1656/045.028.0210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Keith J. Dunton
- Department of Biology, Monmouth University, 400 Cedar Avenue, West Long Branch, NJ 07764
| | - Kelsey Sparta
- Department of Biology, Monmouth University, 400 Cedar Avenue, West Long Branch, NJ 07764
| | - Michael G. Frisk
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794
| | | | - Oliver N. Shipley
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794
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15
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Progress on Research Regarding Ecology and Biodiversity of Coastal Fisheries and Nektonic Species and Their Habitats within Coastal Landscapes. DIVERSITY 2021. [DOI: 10.3390/d13040168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This paper aims to highlight the new research and significant advances in our understanding of links between coastal habitat quality/quantity/diversity and the diversity of fisheries species and other mobile aquatic species (hereafter nekton) that use them within coastal landscapes. This topic is quite diverse owing to the myriad of habitat types found in coastal marine waters and the variety of life history strategies fisheries species and nekton use in these environments. Thus, we focus our review on five selective but relevant topics, habitat templates, essential fish habitat, habitat mosaics/habitat connectivity, transitory/ephemeral habitat, and the emerging/maturing approaches to the study of fish-habitat systems as a roadmap to its development. We have highlighted selected important contributions in the progress made on each topic to better identify and quantify landscape scale interactions between living biota and structured habitats set within a dynamic landscape.
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Juhel J, Marques V, Polanco Fernández A, Borrero‐Pérez GH, Mutis Martinezguerra M, Valentini A, Dejean T, Manel S, Loiseau N, Velez L, Hocdé R, Letessier TB, Richards E, Hadjadj F, Bessudo S, Ladino F, Albouy C, Mouillot D, Pellissier L. Detection of the elusive Dwarf sperm whale ( Kogia sima) using environmental DNA at Malpelo island (Eastern Pacific, Colombia). Ecol Evol 2021; 11:2956-2962. [PMID: 33841757 PMCID: PMC8019034 DOI: 10.1002/ece3.7057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/05/2020] [Accepted: 10/20/2020] [Indexed: 11/09/2022] Open
Abstract
Monitoring large marine mammals is challenging due to their low abundances in general, an ability to move over large distances and wide geographical range sizes.The distribution of the pygmy (Kogia breviceps) and dwarf (Kogia sima) sperm whales is informed by relatively rare sightings, which does not permit accurate estimates of their distribution ranges. Hence, their conservation status has long remained Data Deficient (DD) in the Red list of the International Union for Conservation of Nature (IUCN), which prevent appropriate conservation measures.Environmental DNA (eDNA) metabarcoding uses DNA traces left by organisms in their environments to detect the presence of targeted taxon, and is here proved to be useful to increase our knowledge on the distribution of rare but emblematic megafauna.Retrieving eDNA from filtered surface water provides the first detection of the Dwarf sperm whale (Kogia sima) around the remote Malpelo island (Colombia).Environmental DNA collected during oceanic missions can generate better knowledge on rare but emblematic animals even in regions that are generally well sampled for other taxa.
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Affiliation(s)
| | - Virginie Marques
- MARBECUniversity of MontpellierCNRS, Ifremer, IRDMontpellierFrance
- CEFEUniversity of MontpellierCNRSEPHE‐PSL UniversityIRDUniv Paul Valéry Montpellier 3MontpellierFrance
| | - Andrea Polanco Fernández
- Instituto de Investigaciones Marinas y Costeras‐INVEMARMuseo de Historia Natural Marina de Colombia (MHNMC)Santa MartaColombia
| | - Giomar H. Borrero‐Pérez
- Instituto de Investigaciones Marinas y Costeras‐INVEMARMuseo de Historia Natural Marina de Colombia (MHNMC)Santa MartaColombia
| | - Maria Mutis Martinezguerra
- Instituto de Investigaciones Marinas y Costeras‐INVEMARMuseo de Historia Natural Marina de Colombia (MHNMC)Santa MartaColombia
| | | | | | - Stéphanie Manel
- CEFEUniversity of MontpellierCNRSEPHE‐PSL UniversityIRDUniv Paul Valéry Montpellier 3MontpellierFrance
| | - Nicolas Loiseau
- MARBECUniversity of MontpellierCNRS, Ifremer, IRDMontpellierFrance
| | - Laure Velez
- MARBECUniversity of MontpellierCNRS, Ifremer, IRDMontpellierFrance
| | - Régis Hocdé
- MARBECUniversity of MontpellierCNRS, Ifremer, IRDMontpellierFrance
| | | | - Eilísh Richards
- Department of Environmental Systems ScienceLandscape EcologyInstitute of Terrestrial EcosystemsETHUniversitӓt ZürichZürichSwitzerland
| | - Florine Hadjadj
- MARBECUniversity of MontpellierCNRS, Ifremer, IRDMontpellierFrance
| | | | | | - Camille Albouy
- IFREMERUnité Ecologie et Modèles pour l'HalieutiqueEMHNantesFrance
| | - David Mouillot
- MARBECUniversity of MontpellierCNRS, Ifremer, IRDMontpellierFrance
| | - Loïc Pellissier
- Department of Environmental Systems ScienceLandscape EcologyInstitute of Terrestrial EcosystemsETHUniversitӓt ZürichZürichSwitzerland
- Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
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17
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Ellis JR, Barker J, McCully Phillips SR, Meyers EKM, Heupel M. Angel sharks (Squatinidae): A review of biological knowledge and exploitation. JOURNAL OF FISH BIOLOGY 2021; 98:592-621. [PMID: 33174197 DOI: 10.1111/jfb.14613] [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: 09/02/2020] [Revised: 11/02/2020] [Accepted: 11/09/2020] [Indexed: 06/11/2023]
Abstract
Angel sharks (Squatina spp.) are distributed in warm temperate to tropical waters around the world. Many species occur in shelf seas and exhibit seasonal inshore-offshore migrations, moving inshore to give birth. Consequently, there can be high spatial overlap of angel shark populations with fisheries and other human activities. Their dorso-ventrally flattened body shape, large size (most species attain >100 cm total length, LT ) and demersal nature means that they may be taken in a variety of demersal fishing gears from birth. Available data indicate that angel sharks typically have a biennial reproductive cycle, with litter sizes generally <20 and the young born at c. 20-30 cm. The biological characteristics of angel sharks render them susceptible to overexploitation, as exemplified by the decline of Squatina squatina from many parts of its former range in the north-east Atlantic and Mediterranean Sea. Currently, half of the 22 recognized extant species of angel shark are classed as Threatened on the International Union for Conservation of Nature (IUCN) Red List (with a further three classified as Data Deficient). Given the biological vulnerability of angel sharks, and that many species are data-limited, the current paper provides a review of available biological information and fisheries data pertaining to this family.
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Affiliation(s)
- Jim R Ellis
- Centre for Environment, Fisheries and Aquaculture Science, Suffolk, UK
| | | | | | - Eva K M Meyers
- Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Michelle Heupel
- Australian Institute of Marine Science, Townsville, Queensland, Australia
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18
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Jerde CL. Can we manage fisheries with the inherent uncertainty from eDNA? JOURNAL OF FISH BIOLOGY 2021; 98:341-353. [PMID: 31769024 DOI: 10.1111/jfb.14218] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 11/25/2019] [Indexed: 06/10/2023]
Abstract
Environmental (e)DNA, as a general approach in aquatic systems, seeks to connect the presence of species' genetic material in the water and hence to infer the species' physical presence. However, fisheries managers face making decisions with risk and uncertainty when eDNA indicates a fish is present but traditional methods fail to capture the fish. In comparison with traditional methods such as nets, electrofishing and piscicides, eDNA approaches have more sources of underlying error that could give rise to false positives. This has resulted in some managers to question whether eDNA can be used to make management decisions because there is no fish in hand. As a relatively new approach, the methods and techniques have quickly evolved to improve confidence in eDNA. By evaluating an eDNA based research programmes through the pattern of the eDNA signal, assay design, experimental design, quality assurance and quality control checks, data analyses and concurrent search for fish using traditional gears, the evidence for fish presence can be evaluated to build confidence in the eDNA approach. The benefits for fisheries management from adopting an eDNA approach are numerous but include cost effectiveness, broader geographic coverage of habitat occupancy, early detection of invasive species, non-lethal stock assessments, exploration of previously inaccessible aquatic environments and discovery of new species hidden beneath the water's surface. At a time when global freshwater and marine fisheries are facing growing threats from over-harvest, pollution and climate change, we anticipate that growing confidence in eDNA will overcome the inherent uncertainty of not having a fish in hand and will empower the informed management actions necessary to protect and restore our fisheries.
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Affiliation(s)
- Christopher L Jerde
- Marine Science Institute, University of California, Santa Barbara, California, USA
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19
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West K, Travers MJ, Stat M, Harvey ES, Richards ZT, DiBattista JD, Newman SJ, Harry A, Skepper CL, Heydenrych M, Bunce M. Large‐scale eDNA metabarcoding survey reveals marine biogeographic break and transitions over tropical north‐western Australia. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13228] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Katrina West
- Trace and Environmental DNA (TrEnD) Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
| | - Michael J. Travers
- Western Australian Fisheries and Marine Research Laboratories Department of Primary Industries and Regional Development Government of Western AustraliaNorth Beach WA Australia
| | - Michael Stat
- School of Environmental and Life Sciences The University of Newcastle Callaghan NSW Australia
| | - Euan S. Harvey
- Trace and Environmental DNA (TrEnD) Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
| | - Zoe T. Richards
- Trace and Environmental DNA (TrEnD) Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
| | - Joseph D. DiBattista
- Trace and Environmental DNA (TrEnD) Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
- Australian Museum Australian Museum Research Institute Sydney NSW Australia
| | - Stephen J. Newman
- Western Australian Fisheries and Marine Research Laboratories Department of Primary Industries and Regional Development Government of Western AustraliaNorth Beach WA Australia
| | - Alastair Harry
- Western Australian Fisheries and Marine Research Laboratories Department of Primary Industries and Regional Development Government of Western AustraliaNorth Beach WA Australia
| | - Craig L. Skepper
- Western Australian Fisheries and Marine Research Laboratories Department of Primary Industries and Regional Development Government of Western AustraliaNorth Beach WA Australia
| | - Matthew Heydenrych
- Trace and Environmental DNA (TrEnD) Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
- Environmental Protection Authority Wellington New Zealand
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20
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Ladin ZS, Ferrell B, Dums JT, Moore RM, Levia DF, Shriver WG, D'Amico V, Trammell TLE, Setubal JC, Wommack KE. Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems. Sci Rep 2021; 11:1629. [PMID: 33452291 PMCID: PMC7811025 DOI: 10.1038/s41598-020-80602-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/11/2020] [Indexed: 01/29/2023] Open
Abstract
We investigated the nascent application and efficacy of sampling and sequencing environmental DNA (eDNA) in terrestrial environments using rainwater that filters through the forest canopy and understory vegetation (i.e., throughfall). We demonstrate the utility and potential of this method for measuring microbial communities and forest biodiversity. We collected pure rainwater (open sky) and throughfall, successfully extracted DNA, and generated over 5000 unique amplicon sequence variants. We found that several taxa including Mycoplasma sp., Spirosoma sp., Roseomonas sp., and Lactococcus sp. were present only in throughfall samples. Spiroplasma sp., Methylobacterium sp., Massilia sp., Pantoea sp., and Sphingomonas sp. were found in both types of samples, but more abundantly in throughfall than in rainwater. Throughfall samples contained Gammaproteobacteria that have been previously found to be plant-associated, and may contribute to important functional roles. We illustrate how this novel method can be used for measuring microbial biodiversity in forest ecosystems, foreshadowing the utility for quantifying both prokaryotic and eukaryotic lifeforms. Leveraging these methods will enhance our ability to detect extant species, describe new species, and improve our overall understanding of ecological community dynamics in forest ecosystems.
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Affiliation(s)
- Zachary S Ladin
- Department of Plant and Soil Sciences, University of Delaware, 264 Townsend Hall, Newark, DE, 19716, USA.
| | - Barbra Ferrell
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19716, USA
| | - Jacob T Dums
- Biotechnology Program, North Carolina State University, Raleigh, NC, 27695, USA
| | - Ryan M Moore
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19716, USA
| | - Delphis F Levia
- Department of Entomology and Wildlife Ecology, University of Delaware, 250 Townsend Hall, Newark, DE, 19716, USA
| | - W Gregory Shriver
- Departments of Geography and Spatial Sciences and Plant and Soil Sciences, University of Delaware, 216C Pearson Hall, Newark, DE, 19716, USA
| | - Vincent D'Amico
- US Forest Service, Northern Research Station, Newark, DE, USA
| | - Tara L E Trammell
- Department of Plant and Soil Sciences, University of Delaware, 264 Townsend Hall, Newark, DE, 19716, USA
| | - João Carlos Setubal
- Instituto de Química, University of Sao Paulo, São Paulo, SP, 05508-000, Brazil
| | - K Eric Wommack
- Department of Plant and Soil Sciences, University of Delaware, 264 Townsend Hall, Newark, DE, 19716, USA
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21
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Postaire BD, Bakker J, Gardiner J, Wiley TR, Chapman DD. Environmental DNA detection tracks established seasonal occurrence of blacktip sharks (Carcharhinus limbatus) in a semi-enclosed subtropical bay. Sci Rep 2020; 10:11847. [PMID: 32678294 PMCID: PMC7367289 DOI: 10.1038/s41598-020-68843-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 06/29/2020] [Indexed: 11/27/2022] Open
Abstract
The integration of eDNA analysis into the population assessment and monitoring of sharks could greatly improve temporal and spatial data used for management purposes. This study aimed to compare eDNA detection against well-established seasonal changes in blacktip shark (Carcharhinus limbatus) abundance in Terra Ceia Bay (FL, USA). We used a species-specific real-time PCR approach to detect C. limbatus eDNA in the bay on a near monthly basis from spring through mid-fall in 2018 and 2019. Previous studies have shown that C. limbatus give birth in the bay in early summer and immature sharks occur there until late fall, when decreasing water temperatures cause them to move offshore and southwards. Water samples (2 L) were collected (4–6 per month) and filtered in the field, with each then being subjected to real-time PCR. Carcharhinus limbatus ‘positive’ filters were significantly more commonly collected during the April-July sampling period than during the August-October sampling period. While following the predicted pattern, eDNA concentration was generally too low for accurate quantification. Our results show that C. limbatus eDNA detection follows known seasonal residency patterns consistently over 2 years of monitoring. Species-specific eDNA analysis using real-time PCR could therefore represent a cost-effective, scalable sampling tool to facilitate improved shark population monitoring in semi-enclosed marine habitats.
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Affiliation(s)
- Bautisse D Postaire
- Department of Biological Sciences, Florida International University, 3000 NE 151st Street, North Miami, FL, 33181, USA.
| | - Judith Bakker
- Department of Biological Sciences, Florida International University, 3000 NE 151st Street, North Miami, FL, 33181, USA
| | - Jayne Gardiner
- Division of Natural Sciences, New College of Florida, 5800 Bayshore Rd, Sarasota, FL, 34243, USA
| | - Tonya R Wiley
- Havenworth Coastal Conservation, 5120 Beacon Road, Palmetto, FL, 34221, USA
| | - Demian D Chapman
- Department of Biological Sciences, Florida International University, 3000 NE 151st Street, North Miami, FL, 33181, USA
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22
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An environmental DNA tool for monitoring the status of the Critically Endangered Smalltooth Sawfish, Pristis pectinata, in the western Atlantic. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01149-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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23
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Huerlimann R, Cooper MK, Edmunds RC, Villacorta‐Rath C, Le Port A, Robson HLA, Strugnell JM, Burrows D, Jerry DR. Enhancing tropical conservation and ecology research with aquatic environmental DNA methods: an introduction for non‐environmental DNA specialists. Anim Conserv 2020. [DOI: 10.1111/acv.12583] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- R. Huerlimann
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
- Centre for Tropical Bioinformatics and Molecular Biology James Cook University Townsville QLD Australia
| | - M. K. Cooper
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
- Centre for Tropical Bioinformatics and Molecular Biology James Cook University Townsville QLD Australia
| | - R. C. Edmunds
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER) James Cook University Townsville QLD Australia
| | - C. Villacorta‐Rath
- Centre for Tropical Bioinformatics and Molecular Biology James Cook University Townsville QLD Australia
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER) James Cook University Townsville QLD Australia
| | - A. Le Port
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
| | - H. L. A. Robson
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
| | - J. M. Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
- Centre for Tropical Bioinformatics and Molecular Biology James Cook University Townsville QLD Australia
| | - D. Burrows
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER) James Cook University Townsville QLD Australia
| | - D. R. Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
- Tropical Futures Institute James Cook University Singapore Singapore
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Eble JA, Daly-Engel TS, DiBattista JD, Koziol A, Gaither MR. Marine environmental DNA: Approaches, applications, and opportunities. ADVANCES IN MARINE BIOLOGY 2020; 86:141-169. [PMID: 32600544 DOI: 10.1016/bs.amb.2020.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Environmental DNA (eDNA) is increasingly being used to document species distributions and habitat use in marine systems, with much of the recent effort focused on leveraging advances in next-generation DNA sequencing to assess and track biodiversity across taxonomic groups. Environmental DNA offers a number of important advantages over traditional survey techniques, including non-invasive sampling, sampling where traditional approaches are impractical or inefficient (e.g. deep oceans), reduced cost, and increased detection sensitivity. However, eDNA applications are currently limited because of an insufficient understanding of the influence of sample source, analytical approach, and marker type on eDNA detections. Because approaches vary considerably among eDNA studies, we present a summary of the current state of the field and emerging best practices. The impact of observed variation in rates of eDNA production, persistence, and transport are also discussed and future research needs are highlighted with the goal of expanding eDNA applications, including the development of statistical models to improve the predictability of eDNA detection and quantification.
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Affiliation(s)
- Jeff A Eble
- Ocean Engineering and Marine Sciences, Florida Institute of Technology, Melbourne, FL, United States.
| | - Toby S Daly-Engel
- Ocean Engineering and Marine Sciences, Florida Institute of Technology, Melbourne, FL, United States
| | - Joseph D DiBattista
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia; School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Adam Koziol
- Evolutionary Genomics, GLOBE institute, University of Copenhagen, Copenhagen, Denmark
| | - Michelle R Gaither
- Genomics and Bioinformatics Cluster, Department of Biology, University of Central Florida, Orlando, FL, United States
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25
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26
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Valerio-Vargas JA, Espinoza M. A beacon of hope: distribution and current status of the largetooth sawfish in Costa Rica. ENDANGER SPECIES RES 2019. [DOI: 10.3354/esr00992] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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27
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Poulakis GR, Grubbs RD. Biology and ecology of sawfishes: global status of research and future outlook. ENDANGER SPECIES RES 2019. [DOI: 10.3354/esr00955] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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28
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Lyons K, Bigman JS, Kacev D, Mull CG, Carlisle AB, Imhoff JL, Anderson JM, Weng KC, Galloway AS, Cave E, Gunn TR, Lowe CG, Brill RW, Bedore CN. Bridging disciplines to advance elasmobranch conservation: applications of physiological ecology. CONSERVATION PHYSIOLOGY 2019; 7:coz011. [PMID: 31110763 PMCID: PMC6519003 DOI: 10.1093/conphys/coz011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 02/02/2019] [Accepted: 03/19/2019] [Indexed: 06/09/2023]
Abstract
A strength of physiological ecology is its incorporation of aspects of both species' ecology and physiology; this holistic approach is needed to address current and future anthropogenic stressors affecting elasmobranch fishes that range from overexploitation to the effects of climate change. For example, physiology is one of several key determinants of an organism's ecological niche (along with evolutionary constraints and ecological interactions). The fundamental role of physiology in niche determination led to the development of the field of physiological ecology. This approach considers physiological mechanisms in the context of the environment to understand mechanistic variations that beget ecological trends. Physiological ecology, as an integrative discipline, has recently experienced a resurgence with respect to conservation applications, largely in conjunction with technological advances that extended physiological work from the lab into the natural world. This is of critical importance for species such as elasmobranchs (sharks, skates and rays), which are an especially understudied and threatened group of vertebrates. In 2017, at the American Elasmobranch Society meeting in Austin, Texas, the symposium entitled `Applications of Physiological Ecology in Elasmobranch Research' provided a platform for researchers to showcase work in which ecological questions were examined through a physiological lens. Here, we highlight the research presented at this symposium, which emphasized the strength of linking physiological tools with ecological questions. We also demonstrate the applicability of using physiological ecology research as a method to approach conservation issues, and advocate for a more available framework whereby results are more easily accessible for their implementation into management practices.
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Affiliation(s)
- K Lyons
- Georgia Aquarium, Atlanta, GA, USA
| | - J S Bigman
- Simon Fraser University, Burnaby, Canada
| | - D Kacev
- Southwest Fisheries Science Center, La Jolla, CA, USA
| | - C G Mull
- Simon Fraser University, Burnaby, Canada
| | | | - J L Imhoff
- Florida State University Coastal and Marine Laboratory, St. Teresa, FL, USA
| | - J M Anderson
- University of Hawai`i at Mānoa, Honolulu, HI, USA
| | - K C Weng
- Virginia Institute of Marine Science, Gloucester Point, VA, USA
| | - A S Galloway
- South Carolina Department of Natural Resources, SC, USA
| | - E Cave
- Florida Atlantic University, Boca Raton, FL, USA
| | - T R Gunn
- Georgia Southern University, Statesboro, GA USA
| | - C G Lowe
- California State University Long Beach, Long Beach, CA, USA
| | - R W Brill
- Virginia Institute of Marine Science, Gloucester Point, VA, USA
| | - C N Bedore
- Georgia Southern University, Statesboro, GA USA
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Awruch CA, Somoza GM, Baldock C. Chondrichthyan research in South America: Endocrinology overview and research trends over 50 years (1967-2016) compared to the rest of the world. Gen Comp Endocrinol 2019; 273:118-133. [PMID: 29913167 DOI: 10.1016/j.ygcen.2018.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/22/2018] [Accepted: 06/15/2018] [Indexed: 12/17/2022]
Abstract
The endocrine system plays a crucial role in regulating the activity of cells and organs among vertebrates, including the class Chondrichthyes. Accordingly, Chondrichthyan endocrinology publications have been steadily increasing in the global literature. However, while interest in South American Chondrichthyan research has been growing over the last 50 years, the field of endocrinology related to Chondrichthyans has been limited. Understanding the trajectory of a scientific discipline assists researchers and stakeholders in making decisions regarding which research areas require further attention. Further, visualisation techniques based on bibliometric analysis of scientific publications assist in understanding fluctuations in the trends of specific research fields over time. In this study, Chondrichthyan research publications over time were analysed by creating visualisation maps using VOSviewer bibliometric software. Trends in South America Chondrichthyan research with an emphasis on endocrinology were explored over a 50-year period (1967-2016). These trends were compared with Chondrichthyans research worldwide for the more recent 15-year period (2002-2016). The number of South America Chondrichthyan scientific publications increased from six during the 1967-1981 period to 112 in 2016. However, only eight papers were found published in the area of Chondrichthyan endocrinology research. Fisheries, reproduction and taxonomy were the dominate research areas in South America over the 50 years. For the more recent 15 years, South American publications comprised 11% of the total literature published globally. While South America research outputs fluctuated closely with global research trends, differences appeared when comparing areas of growth. This study describes the trends in Chondrichthyan research literature globally and more specifically in South America. Although South American countries may never contribute to the same scale as the wider international scientific community, the future of Chondrichthyans would strongly benefit from the contributions of the many diverse research groups around the world.
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Affiliation(s)
- Cynthia A Awruch
- School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia; CESIMAR (Centro Para el Estudio de Sistemas Marinos) - CENPAT - CONICET, Puerto Madryn, Chubut U9120ACD, Argentina.
| | - Gustavo M Somoza
- IIB-INTECH (CONICET-UNSAM), Chascomús, Provincia de Buenos Aires B7130IWA. Argentina
| | - Clive Baldock
- Research Division, University of Tasmania, Hobart, TAS 7004, Australia
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Cuevas JM, García M, Hozbor N, Faria VV, Paesch L. Tracing the occurrence of the Critically Endangered smalltooth sawfish Pristis pectinata at its southernmost distribution in the Southwest Atlantic Ocean. ENDANGER SPECIES RES 2019. [DOI: 10.3354/esr00932] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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31
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Green ME, D’Anastasi BR, Hobbs JPA, Feldheim K, McAuley R, Peverell S, Stapley J, Johnson G, Appleyard SA, White WT, Simpfendorfer CA, van Herwerden L. Mixed-marker approach suggests maternal philopatry and sex-biased behaviours of narrow sawfish Anoxypristis cuspidata. ENDANGER SPECIES RES 2018. [DOI: 10.3354/esr00912] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Bonfil R, Ricaño-Soriano M, Mendoza-Vargas OU, Méndez-Loeza I, Pérez-Jiménez JC, Bolaño-Martínez N, Palacios-Barreto P. Tapping into local ecological knowledge to assess the former importance and current status of sawfishes in Mexico. ENDANGER SPECIES RES 2018. [DOI: 10.3354/esr00899] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Cilleros K, Valentini A, Allard L, Dejean T, Etienne R, Grenouillet G, Iribar A, Taberlet P, Vigouroux R, Brosse S. Unlocking biodiversity and conservation studies in high‐diversity environments using environmental DNA (eDNA): A test with Guianese freshwater fishes. Mol Ecol Resour 2018; 19:27-46. [DOI: 10.1111/1755-0998.12900] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 03/29/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Kévin Cilleros
- Laboratoire Évolution & Diversité Biologique (EDB UMR5174) Université de Toulouse, CNRS, IRD, UPS Toulouse Cedex France
| | | | - Luc Allard
- Laboratoire Environnement de Petit Saut HYDRECO Kourou Cedex French Guiana
| | - Tony Dejean
- SPYGEN, Savoie Technolac Le Bourget‐du‐Lac France
| | - Roselyne Etienne
- Laboratoire Évolution & Diversité Biologique (EDB UMR5174) Université de Toulouse, CNRS, IRD, UPS Toulouse Cedex France
| | - Gaël Grenouillet
- Laboratoire Évolution & Diversité Biologique (EDB UMR5174) Université de Toulouse, CNRS, IRD, UPS Toulouse Cedex France
| | - Amaia Iribar
- Laboratoire Évolution & Diversité Biologique (EDB UMR5174) Université de Toulouse, CNRS, IRD, UPS Toulouse Cedex France
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine (LECA UMR5553) CNRS Université Joseph Fourier Grenoble France
| | - Régis Vigouroux
- Laboratoire Environnement de Petit Saut HYDRECO Kourou Cedex French Guiana
| | - Sébastien Brosse
- Laboratoire Évolution & Diversité Biologique (EDB UMR5174) Université de Toulouse, CNRS, IRD, UPS Toulouse Cedex France
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Feldheim KA, Fields AT, Chapman DD, Scharer RM, Poulakis GR. Insights into reproduction and behavior of the smalltooth sawfish Pristis pectinata. ENDANGER SPECIES RES 2017. [DOI: 10.3354/esr00868] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Bakker J, Wangensteen OS, Chapman DD, Boussarie G, Buddo D, Guttridge TL, Hertler H, Mouillot D, Vigliola L, Mariani S. Environmental DNA reveals tropical shark diversity in contrasting levels of anthropogenic impact. Sci Rep 2017; 7:16886. [PMID: 29203793 PMCID: PMC5715122 DOI: 10.1038/s41598-017-17150-2] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 11/19/2017] [Indexed: 01/27/2023] Open
Abstract
Sharks are charismatic predators that play a key role in most marine food webs. Their demonstrated vulnerability to exploitation has recently turned them into flagship species in ocean conservation. Yet, the assessment and monitoring of the distribution and abundance of such mobile species in marine environments remain challenging, often invasive and resource-intensive. Here we pilot a novel, rapid and non-invasive environmental DNA (eDNA) metabarcoding approach specifically targeted to infer shark presence, diversity and eDNA read abundance in tropical habitats. We identified at least 21 shark species, from both Caribbean and Pacific Coral Sea water samples, whose geographical patterns of diversity and read abundance coincide with geographical differences in levels of anthropogenic pressure and conservation effort. We demonstrate that eDNA metabarcoding can be effectively employed to study shark diversity. Further developments in this field have the potential to drastically enhance our ability to assess and monitor elusive oceanic predators, and lead to improved conservation strategies.
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Affiliation(s)
- Judith Bakker
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences, University of Salford, Salford, M5 4WT, UK
| | - Owen S Wangensteen
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences, University of Salford, Salford, M5 4WT, UK
| | - Demian D Chapman
- Department of Biological Sciences, Florida International University, 11200 S.W., 8th Street, Miami, Florida, 33199, USA
| | - Germain Boussarie
- MARBEC, UMR IRD-CNRS-UM-IFREMER 9190, Université Montpellier, Languedoc-Roussillon, 34095, Montpellier Cedex, France
- IRD (Institut de Recherche pour le Développement), Laboratoire d'Excellence Labex Corail, UMR IRD-UR-CNRS ENTROPIE, Centre IRD de Noumea, BP A5, 98800, Noumea Cedex, New Caledonia, France
| | - Dayne Buddo
- University of the West Indies, Discovery Bay Marine Laboratory and Field Station, P.O. Box 35, Discovery Bay, St. Ann, Jamaica
| | | | - Heidi Hertler
- The SFS Centre for Marine Resource Studies, Turks and Caicos Islands, UK
| | - David Mouillot
- MARBEC, UMR IRD-CNRS-UM-IFREMER 9190, Université Montpellier, Languedoc-Roussillon, 34095, Montpellier Cedex, France
| | - Laurent Vigliola
- IRD (Institut de Recherche pour le Développement), Laboratoire d'Excellence Labex Corail, UMR IRD-UR-CNRS ENTROPIE, Centre IRD de Noumea, BP A5, 98800, Noumea Cedex, New Caledonia, France
| | - Stefano Mariani
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences, University of Salford, Salford, M5 4WT, UK.
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Larson SE, Daly-Engel TS, Phillips NM. Review of Current Conservation Genetic Analyses of Northeast Pacific Sharks. ADVANCES IN MARINE BIOLOGY 2017; 77:79-110. [PMID: 28882215 DOI: 10.1016/bs.amb.2017.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Conservation genetics is an applied science that utilizes molecular tools to help solve problems in species conservation and management. It is an interdisciplinary specialty in which scientists apply the study of genetics in conjunction with traditional ecological fieldwork and other techniques to explore molecular variation, population boundaries, and evolutionary relationships with the goal of enabling resource managers to better protect biodiversity and identify unique populations. Several shark species in the northeast Pacific (NEP) have been studied using conservation genetics techniques, which are discussed here. The primary methods employed to study population genetics of sharks have historically been nuclear microsatellites and mitochondrial (mt) DNA. These markers have been used to assess genetic diversity, mating systems, parentage, relatedness, and genetically distinct populations to inform management decisions. Novel approaches in conservation genetics, including next-generation DNA and RNA sequencing, environmental DNA (eDNA), and epigenetics are just beginning to be applied to elasmobranch evolution, physiology, and ecology. Here, we review the methods and results of past studies, explore future directions for shark conservation genetics, and discuss the implications of molecular research and techniques for the long-term management of shark populations in the NEP.
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Affiliation(s)
| | | | - Nicole M Phillips
- The University of Southern Mississippi, Hattiesburg, MS, United States
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Moore ABM. Are guitarfishes the next sawfishes? Extinction risk and an urgent call for conservation action. ENDANGER SPECIES RES 2017. [DOI: 10.3354/esr00830] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Weltz K, Lyle JM, Ovenden J, Morgan JAT, Moreno DA, Semmens JM. Application of environmental DNA to detect an endangered marine skate species in the wild. PLoS One 2017; 12:e0178124. [PMID: 28591215 PMCID: PMC5462358 DOI: 10.1371/journal.pone.0178124] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 05/07/2017] [Indexed: 11/18/2022] Open
Abstract
Environmental DNA (eDNA) techniques have only recently been applied in the marine environment to detect the presence of marine species. Species-specific primers and probes were designed to detect the eDNA of the endangered Maugean skate (Zearaja maugeana) from as little as 1 L of water collected at depth (10–15 m) in Macquarie Harbour (MH), Tasmania. The identity of the eDNA was confirmed as Z. maugeana by sequencing the qPCR products and aligning these with the target sequence for a 100% match. This result has validated the use of this eDNA technique for detecting a rare species, Z. maugeana, in the wild. Being able to investigate the presence, and possibly the abundance, of Z. maugeana in MH and Bathurst harbour (BH), would be addressing a conservation imperative for the endangered Z. maugeana. For future application of this technique in the field, the rate of decay was determined for Z. maugeana eDNA under ambient dissolved oxygen (DO) levels (55% saturation) and lower DO (20% saturation) levels, revealing that the eDNA can be detected for 4 and 16 hours respectively, after which eDNA concentration drops below the detection threshold of the assay. With the rate of decay being influenced by starting eDNA concentrations, it is recommended that samples be filtered as soon as possible after collection to minimize further loss of eDNA prior to and during sample processing.
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Affiliation(s)
- Kay Weltz
- Fisheries and Aquaculture Centre, Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
- * E-mail:
| | - Jeremy M. Lyle
- Fisheries and Aquaculture Centre, Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Jennifer Ovenden
- Molecular Fisheries Laboratory, School of Biomedical Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Jessica A. T. Morgan
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
| | - David A. Moreno
- Fisheries and Aquaculture Centre, Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Jayson M. Semmens
- Fisheries and Aquaculture Centre, Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
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Jabado RW, Al Baharna RA, Al Ali SR, Al Suwaidi KO, Al Blooshi AY, Al Dhaheri SS. Is this the last stand of the Critically Endangered green sawfish Pristis zijsron in the Arabian Gulf? ENDANGER SPECIES RES 2017. [DOI: 10.3354/esr00805] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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40
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Cariani A, Messinetti S, Ferrari A, Arculeo M, Bonello JJ, Bonnici L, Cannas R, Carbonara P, Cau A, Charilaou C, El Ouamari N, Fiorentino F, Follesa MC, Garofalo G, Golani D, Guarniero I, Hanner R, Hemida F, Kada O, Lo Brutto S, Mancusi C, Morey G, Schembri PJ, Serena F, Sion L, Stagioni M, Tursi A, Vrgoc N, Steinke D, Tinti F. Improving the Conservation of Mediterranean Chondrichthyans: The ELASMOMED DNA Barcode Reference Library. PLoS One 2017; 12:e0170244. [PMID: 28107413 PMCID: PMC5249125 DOI: 10.1371/journal.pone.0170244] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/30/2016] [Indexed: 11/18/2022] Open
Abstract
Cartilaginous fish are particularly vulnerable to anthropogenic stressors and environmental change because of their K-selected reproductive strategy. Accurate data from scientific surveys and landings are essential to assess conservation status and to develop robust protection and management plans. Currently available data are often incomplete or incorrect as a result of inaccurate species identifications, due to a high level of morphological stasis, especially among closely related taxa. Moreover, several diagnostic characters clearly visible in adult specimens are less evident in juveniles. Here we present results generated by the ELASMOMED Consortium, a regional network aiming to sample and DNA-barcode the Mediterranean Chondrichthyans with the ultimate goal to provide a comprehensive DNA barcode reference library. This library will support and improve the molecular taxonomy of this group and the effectiveness of management and conservation measures. We successfully barcoded 882 individuals belonging to 42 species (17 sharks, 24 batoids and one chimaera), including four endemic and several threatened ones. Morphological misidentifications were found across most orders, further confirming the need for a comprehensive DNA barcoding library as a valuable tool for the reliable identification of specimens in support of taxonomist who are reviewing current identification keys. Despite low intraspecific variation among their barcode sequences and reduced samples size, five species showed preliminary evidence of phylogeographic structure. Overall, the ELASMOMED initiative further emphasizes the key role accurate DNA barcoding libraries play in establishing reliable diagnostic species specific features in otherwise taxonomically problematic groups for biodiversity management and conservation actions.
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Affiliation(s)
- Alessia Cariani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Silvia Messinetti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Alice Ferrari
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Marco Arculeo
- Department STEBICEF, University of Palermo, Palermo, Italy
| | | | | | - Rita Cannas
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | | | - Alessandro Cau
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Charis Charilaou
- Department of Fisheries and Marine Research, Ministry of Agriculture, Rural Development and Environment, Nicosia, Republic of Cyprus
| | - Najib El Ouamari
- Centre Régional de Institut National Recherche Halieutique, Nador, Morocco
| | - Fabio Fiorentino
- Institute for Coastal Marine Environment (IAMC) National Research Council (CNR), Mazara del Vallo, Italy
| | | | - Germana Garofalo
- Institute for Coastal Marine Environment (IAMC) National Research Council (CNR), Mazara del Vallo, Italy
| | - Daniel Golani
- Department of Evolution, Systematics and Ecology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ilaria Guarniero
- Department DIMEVET, University of Bologna, Ozzano dell'Emilia, Italy
| | - Robert Hanner
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Farid Hemida
- Ecole Nationale Superieure des Sciences de la Mer et d'Amenagement du Littoral, Campus Universitaire de Dely Ibrahim, Alger, Algeria
| | - Omar Kada
- Centre Régional de Institut National Recherche Halieutique, Nador, Morocco
| | | | - Cecilia Mancusi
- Regional Agency for Environmental Protection-Toscana (ARPAT), Livorno, Italy
| | | | | | - Fabrizio Serena
- Regional Agency for Environmental Protection-Toscana (ARPAT), Livorno, Italy
| | - Letizia Sion
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
| | - Marco Stagioni
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Angelo Tursi
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
| | - Nedo Vrgoc
- Institute of Oceanography and Fisheries, Split, Croatia
| | - Dirk Steinke
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Fausto Tinti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
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