1
|
Yang S, Jin Y, Li S, Liu Z. Integrated approaches for comprehensive cetacean research and conservation in the East China Sea. MARINE POLLUTION BULLETIN 2024; 206:116789. [PMID: 39094284 DOI: 10.1016/j.marpolbul.2024.116789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 04/30/2024] [Accepted: 07/27/2024] [Indexed: 08/04/2024]
Abstract
This study thoroughly examines three cetacean monitoring methods and assessing their advantages and limitations, establishing a foundational basis for comprehensive information on composition, distribution, and behavior. While real-time and non-invasive, visual surveys favor surface-active cetaceans and are weather-dependent. Local ecological knowledge supplements insights into group behavior. Environmental DNA (eDNA) analysis efficiently detects species like the narrow-ridged finless porpoise (Neophocaena asiaeorientalis) and common bottlenose dolphin (Tursiops truncatus), offering non-invasive, and spatially adept monitoring. Furthermore, eDNA provides prey species information, revealing the narrow-ridged finless porpoise's winter migration to deeper waters due to prey distribution. The study identifies prevalent prey species, like the Japanese Anchovy (Engraulis japonicus) and Osbeck's grenadier anchovy (Coilia mystus), offering insights into the porpoise's feeding ecology and adaptation to changing prey availability in winter. This study systematically compares diverse methodologies employed in cetacean surveys, thereby yielding a comprehensive understanding of cetacean distribution, behavior, and feeding ecology.
Collapse
Affiliation(s)
- Shaobo Yang
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China; College of Marine Sciences of Shanghai Ocean University, Shanghai 201306, China
| | - Yan Jin
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China; Key Laboratory of East China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 200090, China
| | - Shengfa Li
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China; Key Laboratory of East China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 200090, China
| | - Zunlei Liu
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China; Key Laboratory of East China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 200090, China.
| |
Collapse
|
2
|
Newton JP, Nevill P, Bateman PW, Campbell MA, Allentoft ME. Spider webs capture environmental DNA from terrestrial vertebrates. iScience 2024; 27:108904. [PMID: 38533454 PMCID: PMC10964257 DOI: 10.1016/j.isci.2024.108904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/22/2023] [Accepted: 01/10/2024] [Indexed: 03/28/2024] Open
Abstract
Environmental DNA holds significant promise as a non-invasive tool for tracking terrestrial biodiversity. However, in non-homogenous terrestrial environments, the continual exploration of new substrates is crucial. Here we test the hypothesis that spider webs can act as passive biofilters, capturing eDNA from vertebrates present in the local environment. Using a metabarcoding approach, we detected vertebrate eDNA from all analyzed spider webs (N = 49). Spider webs obtained from an Australian woodland locality yielded vertebrate eDNA from 32 different species, including native mammals and birds. In contrast, webs from Perth Zoo, less than 50 km away, yielded eDNA from 61 different vertebrates and produced a highly distinct species composition, largely reflecting exotic species hosted in the zoo. We show that higher animal biomass and proximity to animal enclosures increased eDNA detection probability in the zoo. Our results indicate a tremendous potential for using spider webs as a cost-effective means to monitor terrestrial vertebrates.
Collapse
Affiliation(s)
- Joshua P. Newton
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
- Minesite Biodiversity Monitoring with eDNA (MBioMe) research group, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - Paul Nevill
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
- Minesite Biodiversity Monitoring with eDNA (MBioMe) research group, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - Philip W. Bateman
- Minesite Biodiversity Monitoring with eDNA (MBioMe) research group, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
- Behavioural Ecology Lab, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - Matthew A. Campbell
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - Morten E. Allentoft
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| |
Collapse
|
3
|
Dyson K, Nicolau AP, Tenneson K, Francesconi W, Daniels A, Andrich G, Caldas B, Castaño S, de Campos N, Dilger J, Guidotti V, Jaques I, McCullough IM, McDevitt AD, Molina L, Nekorchuk DM, Newberry T, Pereira CL, Perez J, Richards-Dimitrie T, Rivera O, Rodriguez B, Sales N, Tello J, Wespestad C, Zutta B, Saah D. Coupling remote sensing and eDNA to monitor environmental impact: A pilot to quantify the environmental benefits of sustainable agriculture in the Brazilian Amazon. PLoS One 2024; 19:e0289437. [PMID: 38354171 PMCID: PMC10866516 DOI: 10.1371/journal.pone.0289437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/01/2023] [Indexed: 02/16/2024] Open
Abstract
Monitoring is essential to ensure that environmental goals are being achieved, including those of sustainable agriculture. Growing interest in environmental monitoring provides an opportunity to improve monitoring practices. Approaches that directly monitor land cover change and biodiversity annually by coupling the wall-to-wall coverage from remote sensing and the site-specific community composition from environmental DNA (eDNA) can provide timely, relevant results for parties interested in the success of sustainable agricultural practices. To ensure that the measured impacts are due to the environmental projects and not exogenous factors, sites where projects have been implemented should be benchmarked against counterfactuals (no project) and control (natural habitat) sites. Results can then be used to calculate diverse sets of indicators customized to monitor different projects. Here, we report on our experience developing and applying one such approach to assess the impact of shaded cocoa projects implemented by the Instituto de Manejo e Certificação Florestal e Agrícola (IMAFLORA) near São Félix do Xingu, in Pará, Brazil. We used the Continuous Degradation Detection (CODED) and LandTrendr algorithms to create a remote sensing-based assessment of forest disturbance and regeneration, estimate carbon sequestration, and changes in essential habitats. We coupled these remote sensing methods with eDNA analyses using arthropod-targeted primers by collecting soil samples from intervention and counterfactual pasture field sites and a control secondary forest. We used a custom set of indicators from the pilot application of a coupled monitoring framework called TerraBio. Our results suggest that, due to IMAFLORA's shaded cocoa projects, over 400 acres were restored in the intervention area and the community composition of arthropods in shaded cocoa is closer to second-growth forests than that of pastures. In reviewing the coupled approach, we found multiple aspects worked well, and we conclude by presenting multiple lessons learned.
Collapse
Affiliation(s)
- Karen Dyson
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | - Andréa P. Nicolau
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | - Karis Tenneson
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | - Wendy Francesconi
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Kasarani, Nairobi
| | - Amy Daniels
- United States Agency for International Development (USAID), Washington, DC, United States of America
| | - Giulia Andrich
- Instituto de Manejo e Certificação Florestal e Agrícola (IMAFLORA), Piracicaba, Brazil
| | - Bernardo Caldas
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Kasarani, Nairobi
| | - Silvia Castaño
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Kasarani, Nairobi
| | - Nathanael de Campos
- Instituto de Manejo e Certificação Florestal e Agrícola (IMAFLORA), Piracicaba, Brazil
| | - John Dilger
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | - Vinicius Guidotti
- Instituto de Manejo e Certificação Florestal e Agrícola (IMAFLORA), Piracicaba, Brazil
| | - Iara Jaques
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | - Ian M. McCullough
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | | | - Luis Molina
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Kasarani, Nairobi
| | - Dawn M. Nekorchuk
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | - Tom Newberry
- University of Salford, Salford, Manchester, United Kingdom
| | | | - Jorge Perez
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Kasarani, Nairobi
| | | | - Ovidio Rivera
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Kasarani, Nairobi
| | - Beatriz Rodriguez
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Kasarani, Nairobi
| | - Naiara Sales
- University of Salford, Salford, Manchester, United Kingdom
| | - Jhon Tello
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Kasarani, Nairobi
| | - Crystal Wespestad
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | - Brian Zutta
- Spatial Informatics Group, LLC, Pleasanton, California, United States of America
| | - David Saah
- University of San Francisco, San Francisco, California, United States of America
| |
Collapse
|
4
|
Cheng R, Luo Y, Zhang Y, Li Q, Li Y, Shen Y. eDNA metabarcoding reveals differences in fish diversity and community structure in heterogeneous habitat areas shaped by cascade hydropower. Ecol Evol 2023; 13:e10275. [PMID: 37424941 PMCID: PMC10326610 DOI: 10.1002/ece3.10275] [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: 11/16/2022] [Revised: 06/14/2023] [Accepted: 06/25/2023] [Indexed: 07/11/2023] Open
Abstract
Freshwater ecosystems are under great threat from humans, among which habitat heterogeneity is the most obvious, being one of the important reasons for the decline of fish diversity. This phenomenon is particularly prominent in the Wujiang River, where the continuous rapids of the mainstream have been divided into 12 mutually isolated sections by 11 cascade hydropower reservoirs. Based on the fact that conventional survey methods are more harmful to the ecological environment, the efficient and noninvasive environmental DNA metabarcoding (eDNA) approach was used in this study to conduct an aquatic ecological survey of the 12 river sections of the mainstream of the Wujiang River. A total of 2299 operational taxonomic units (OTUs) were obtained, corresponding to 97 species, including four nationally protected fish species and 12 alien species. The results indicate that the fish community structure of the Wujiang River mainstream, which was originally dominated by rheophilic fish species, has been changed. And there are differences in fish species diversity and species composition among the reservoir areas of the mainstream of the Wujiang River. The fish species in the area have gradually declined under the influence of anthropogenic factors such as terraced hydropower and overfishing. The fish populations consequently have demonstrated a tendency to be species miniaturized, and the indigenous fish are severely threatened. In addition, the fish composition monitored by the eDNA approach was found to be close to the fish composition of historical information on the Wujiang River, indicating that eDNA approach may be used as a complementary tool to conventional methods in this basin.
Collapse
Affiliation(s)
- Ruli Cheng
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
| | - Yang Luo
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
| | - Yufeng Zhang
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
| | - Qinghua Li
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
| | - Yingwen Li
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
| | - Yanjun Shen
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
| |
Collapse
|
5
|
Croose E, Hanniffy R, Harrington A, Põdra M, Gómez A, Bolton PL, Lavin JV, Browett SS, Pinedo J, Lacanal D, Galdos I, Ugarte J, Torre A, Wright P, MacPherson J, McDevitt AD, Carter SP, Harrington LA. Mink on the brink: comparing survey methods for detecting a critically endangered carnivore, the European mink Mustela lutreola. EUR J WILDLIFE RES 2023. [DOI: 10.1007/s10344-023-01657-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
AbstractMonitoring rare and elusive species is critical in guiding appropriate conservation management measures. Mammalian carnivores are challenging to monitor directly, due to their generally nocturnal and solitary lifestyle, and relatively large home ranges. The European mink Mustela lutreola is a critically endangered, small, semi-aquatic carnivore and is one of the most threatened mammal species in Europe. In northern Spain, the European mink population is monitored regionally using different methods and approaches, making assessment of national population status difficult. There is an urgent need to 1) assess the efficacy of survey methods and 2) identify a standard monitoring methodology that can be deployed rapidly and inexpensively over large areas of the mink’s range. We deployed four methods—camera trapping, hair tubes, live trapping, and environmental DNA (eDNA) from water samples—to compare the probability of detecting European mink when present at 25 sampling sites within five 10 × 10 km2, and the economic cost and time required for each method. All four methods successfully detected European mink but the probability of detection varied by method. Camera trapping and hair tubes had the highest probability of detection; however, eDNA and live trapping detected mink in one 10 × 10 km2 where the latter two methods did not. For future European mink monitoring programs, we recommend a combination of at least two methods and suggest that camera traps or hair tubes are combined with live trapping or eDNA (depending on the scale and aims of the study), to gather critical information on distribution, occupancy and conservation status.
Collapse
|
6
|
Mendoza E, Camargo-Sanabria AA, Godínez-Gómez O. Is camera trapping helping us to fill knowledge gaps related to the conservation of wild mammals? J Nat Conserv 2022. [DOI: 10.1016/j.jnc.2022.126282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
7
|
van der Heyde M, Bunce M, Nevill P. Key factors to consider in the use of environmental DNA metabarcoding to monitor terrestrial ecological restoration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157617. [PMID: 35901901 DOI: 10.1016/j.scitotenv.2022.157617] [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: 03/21/2022] [Revised: 05/30/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Ecological restoration of terrestrial environments is a globally important process to combat the loss of biodiversity and ecosystem services. Holistic monitoring of restored biota and active management of restoration is necessary to improve restoration processes and outcomes, and provide evidence to stakeholders that targets are being achieved. Increasingly, environmental DNA (eDNA) metabarcoding is used as a restoration monitoring tool because it is able to generate biodiversity data rapidly, accurately, non-destructively, and reliably, on a wide breadth of organisms from soil microbes to mammals. The overall objective of this review is to discuss the key factors to consider in the use of environmental DNA for monitoring of restored terrestrial ecosystems, hopefully improving monitoring, and ultimately, restoration outcomes. We identified that the majority of eDNA based studies of ecosystem restoration are currently conducted in Europe, North America, and Australia, and that almost half of total studies were published in 2021-22. Soil was the most popular sample substrate, soil microbial communities the most targeted taxa, and forests the most studied ecosystem. We suggest there is no 'one size fits all' approach to restoration monitoring using eDNA, and discuss survey design. Factors to consider include substrate selection, sample collection and storage, assay selection, and data interpretation, all of which require careful planning to obtain reliable, and accurate information that can be used for restoration monitoring and decision making. We explore future directions for research and argue that eDNA metabarcoding can be a useful tool in the restoration monitoring 'toolkit', but requires informed application and greater accessibility to data by a wide spectrum of stakeholders.
Collapse
Affiliation(s)
- Mieke van der Heyde
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Bentley, GPP Box U1987, Perth, Western Australia 6102, Australia; Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPO Box U1987, Perth, Western Australia 6102, Australia.
| | - Michael Bunce
- Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPO Box U1987, Perth, Western Australia 6102, Australia; Institute of Environmental Science and Research (ESR), Kenepuru, Porirua 5022, New Zealand
| | - Paul Nevill
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Bentley, GPP Box U1987, Perth, Western Australia 6102, Australia; Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPO Box U1987, Perth, Western Australia 6102, Australia
| |
Collapse
|
8
|
Snapshot of the Atlantic Forest canopy: surveying arboreal mammals in a biodiversity hotspot. ORYX 2022. [DOI: 10.1017/s0030605321001563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Abstract
The Atlantic Forest of South America supports a rich terrestrial biodiversity but has been reduced to only a small extent of its original forest cover. It hosts a large number of endemic mammalian species but our knowledge of arboreal mammal ecology and conservation has been limited because of the challenges of observing arboreal species from ground level. Camera trapping has proven to be an effective tool in terrestrial mammal monitoring but the technique has rarely been used for arboreal species. For the first time in the Atlantic Forest, we obtained data on the arboreal mammal community using arboreal camera trapping, focusing on Caparaó National Park, Brazil. We placed 24 infrared camera traps in the forest canopy in seven areas within the Park, operating them continuously during January 2017–June 2019. During this period the camera traps accumulated 4,736 camera-days of footage and generated a total of 2,256 photographs and 30-s videos of vertebrates. The arboreal camera traps were able to detect arboreal mammals of a range of body sizes. The mammal assemblage comprised 15 identifiable species, including the Critically Endangered northern muriqui Brachyteles hypoxanthus and buffy-headed marmoset Callithrix flaviceps as well as other rare, nocturnal and inconspicuous species. We confirmed for the first time the occurrence of the thin-spined porcupine Chaetomys subspinosus in the Park. Species richness varied across survey areas and forest types. Our findings demonstrate the potential of arboreal camera trapping to inform conservation strategies.
Collapse
|
9
|
Seeber PA, Epp LS. Environmental
DNA
and metagenomics of terrestrial mammals as keystone taxa of recent and past ecosystems. Mamm Rev 2022. [DOI: 10.1111/mam.12302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Peter A. Seeber
- Limnological Institute University of Konstanz Konstanz Germany
| | - Laura S. Epp
- Limnological Institute University of Konstanz Konstanz Germany
| |
Collapse
|
10
|
Broadhurst HA, Gregory LM, Bleakley EK, Perkins JC, Lavin JV, Bolton P, Browett SS, Howe CV, Singleton N, Tansley D, Sales NG, McDevitt AD. Mapping differences in mammalian distributions and diversity using environmental DNA from rivers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 801:149724. [PMID: 34467903 DOI: 10.1016/j.scitotenv.2021.149724] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
Finding more efficient ways to monitor and estimate the diversity of mammalian communities is a major step towards their management and conservation. Environmental DNA (eDNA) from river water has recently been shown to be a viable method for biomonitoring mammalian communities. Most of the studies to date have focused on the potential for eDNA to detect individual species, with little focus on describing patterns of community diversity and structure. Here, we first focus on the sampling effort required to reliably map the diversity and distribution of semi-aquatic and terrestrial mammals and allow inferences of community structure surrounding two rivers in southeastern England. Community diversity and composition was then assessed based on species richness and β-diversity, with differences between communities partitioned into nestedness and turnover, and the sampling effort required to rapidly detect semi-aquatic and terrestrial species was evaluated based on species accumulation curves and occupancy modelling. eDNA metabarcoding detected 25 wild mammal species from five orders, representing the vast majority (82%) of the species expected in the area. The required sampling effort varied between orders, with common species (generally rodents, deer and lagomorphs) more readily detected, with carnivores detected less frequently. Measures of species richness differed between rivers (both overall and within each mammalian order) and patterns of β-diversity revealed the importance of species replacement in sites within each river, against a pattern of species loss between the two rivers. eDNA metabarcoding demonstrated its capability to rapidly detect mammal species, allowing inferences of community composition that will better inform future sampling strategies for this Class. Importantly, this study highlights the potential use of eDNA data for investigating mammalian community dynamics over different spatial scales.
Collapse
Affiliation(s)
- Holly A Broadhurst
- School of Science, Engineering and Environment, University of Salford, UK
| | - Luke M Gregory
- School of Science, Engineering and Environment, University of Salford, UK
| | - Emma K Bleakley
- School of Science, Engineering and Environment, University of Salford, UK
| | - Joseph C Perkins
- School of Science, Engineering and Environment, University of Salford, UK
| | - Jenna V Lavin
- School of Science, Engineering and Environment, University of Salford, UK
| | - Polly Bolton
- School of Science, Engineering and Environment, University of Salford, UK
| | - Samuel S Browett
- School of Science, Engineering and Environment, University of Salford, UK; School of Science and Computing, Waterford Institute of Technology, Waterford, Ireland
| | - Claire V Howe
- Natural England, Horizon House, Deanery Road, Bristol, UK
| | - Natalie Singleton
- Essex Wildlife Trust, Abbotts Hall Farm, Great Wigborough, Colchester, UK
| | - Darren Tansley
- Essex Wildlife Trust, Abbotts Hall Farm, Great Wigborough, Colchester, UK
| | | | - Allan D McDevitt
- School of Science, Engineering and Environment, University of Salford, UK.
| |
Collapse
|
11
|
Polanco F. A, Mutis Martinezguerra M, Marques V, Villa‐Navarro F, Borrero Pérez GH, Cheutin M, Dejean T, Hocdé R, Juhel J, Maire E, Manel S, Spescha M, Valentini A, Mouillot D, Albouy C, Pellissier L. Detecting aquatic and terrestrial biodiversity in a tropical estuary using environmental DNA. Biotropica 2021. [DOI: 10.1111/btp.13009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Andrea Polanco F.
- Instituto de Investigaciones Marinas y Costeras‐INVEMAR, Santa Marta, Colombia, Programa de Biodiversidad y Ecosistemas MarinosMuseo de Historia Natural Marina de Colombia (MHNMC Santa Marta Colombia)
| | - Maria Mutis Martinezguerra
- Instituto de Investigaciones Marinas y Costeras‐INVEMAR, Santa Marta, Colombia, Programa de Biodiversidad y Ecosistemas MarinosMuseo de Historia Natural Marina de Colombia (MHNMC Santa Marta Colombia)
| | - Virginie Marques
- MARBEC CNRS Ifremer IRD Univ. Montpellier Montpellier France
- CEFE Univ. Montpellier CNRS EPHE‐PSL University IRD Univ. Paul Valéry Montpellier Montpellier France
| | - Francisco Villa‐Navarro
- Grupo de Investigación en Zoología Facultad de Ciencias Universidad del Tolima Ibagué Colombia
| | - Giomar Helena Borrero Pérez
- Instituto de Investigaciones Marinas y Costeras‐INVEMAR, Santa Marta, Colombia, Programa de Biodiversidad y Ecosistemas MarinosMuseo de Historia Natural Marina de Colombia (MHNMC Santa Marta Colombia)
| | - Marie‐Charlotte Cheutin
- CEFE Univ. Montpellier CNRS EPHE‐PSL University IRD Univ. Paul Valéry Montpellier Montpellier France
| | | | - Régis Hocdé
- MARBEC CNRS Ifremer IRD Univ. Montpellier Montpellier France
| | | | - Eva Maire
- MARBEC CNRS Ifremer IRD Univ. Montpellier Montpellier France
- Lancaster Environment Centre Lancaster University Lancaster UK
| | - Stéphanie Manel
- MARBEC CNRS Ifremer IRD Univ. Montpellier Montpellier France
- CEFE Univ. Montpellier CNRS EPHE‐PSL University IRD Univ. Paul Valéry Montpellier Montpellier France
| | - Manuel Spescha
- Landscape Ecology Department of Environmental Systems Science Institute of Terrestrial Ecosystems ETH Zürich Zürich Switzerland
| | | | - David Mouillot
- MARBEC CNRS Ifremer IRD Univ. Montpellier Montpellier France
| | - Camille Albouy
- IFREMER Unité Écologie et Modèles pour l’Halieutique Nantes cedex 3 France
| | - Loïc Pellissier
- Landscape Ecology Department of Environmental Systems Science Institute of Terrestrial Ecosystems ETH Zürich Zürich Switzerland
- Unit of Land Change Science Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland
| |
Collapse
|
12
|
eDNA sampled from stream networks correlates with camera trap detection rates of terrestrial mammals. Sci Rep 2021; 11:11362. [PMID: 34131168 PMCID: PMC8206079 DOI: 10.1038/s41598-021-90598-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/13/2021] [Indexed: 11/14/2022] Open
Abstract
Biodiversity monitoring delivers vital information to those making conservation decisions. Comprehensively measuring terrestrial biodiversity usually requires costly methods that can rarely be deployed at large spatial scales over multiple time periods, limiting conservation efficiency. Here we investigated the capacity of environmental DNA (eDNA) from stream water samples to survey terrestrial mammal diversity at multiple spatial scales within a large catchment. We compared biodiversity information recovered using an eDNA metabarcoding approach with data from a dense camera trap survey, as well as the sampling costs of both methods. Via the sampling of large volumes of water from the two largest streams that drained the study area, eDNA metabarcoding provided information on the presence and detection probabilities of 35 mammal taxa, 25% more than camera traps and for half the cost. While eDNA metabarcoding had limited capacity to detect felid species and provide individual-level demographic information, it is a cost-efficient method for large-scale monitoring of terrestrial mammals that can offer sufficient information to solve many conservation problems.
Collapse
|
13
|
Snow Leopard (Panthera uncia) Genetics: The Knowledge Gaps, Needs, and Implications for Conservation. J Indian Inst Sci 2021. [DOI: 10.1007/s41745-021-00236-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
14
|
Fediajevaite J, Priestley V, Arnold R, Savolainen V. Meta-analysis shows that environmental DNA outperforms traditional surveys, but warrants better reporting standards. Ecol Evol 2021; 11:4803-4815. [PMID: 33976849 PMCID: PMC8093654 DOI: 10.1002/ece3.7382] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/01/2021] [Accepted: 02/12/2021] [Indexed: 01/05/2023] Open
Abstract
Decades of environmental DNA (eDNA) method application, spanning a wide variety of taxa and habitats, has advanced our understanding of eDNA and underlined its value as a tool for conservation practitioners. The general consensus is that eDNA methods are more accurate and cost-effective than traditional survey methods. However, they are formally approved for just a few species globally (e.g., Bighead Carp, Silver Carp, Great Crested Newt). We conducted a meta-analysis of studies that directly compare eDNA with traditional surveys to evaluate the assertion that eDNA methods are consistently "better."Environmental DNA publications for multiple species or single macro-organism detection were identified using the Web of Science, by searching "eDNA" and "environmental DNA" across papers published between 1970 and 2020. The methods used, focal taxa, habitats surveyed, and quantitative and categorical results were collated and analyzed to determine whether and under what circumstances eDNA outperforms traditional surveys.Results show that eDNA methods are cheaper, more sensitive, and detect more species than traditional methods. This is, however, taxa-dependent, with amphibians having the highest potential for detection by eDNA survey. Perhaps most strikingly, of the 535 papers reviewed just 49 quantified the probability of detection for both eDNA and traditional survey methods and studies were three times more likely to give qualitative statements of performance. Synthesis and applications: The results of this meta-analysis demonstrate that where there is a direct comparison, eDNA surveys of macro-organisms are more accurate and efficient than traditional surveys. This conclusion, however, is based on just a fraction of available eDNA papers as most do not offer this granularity. We recommend that conclusions are substantiated with comparable and quantitative data. Where a direct comparison has not been made, we caution against the use of qualitative statements about relative performance. This consistency and rigor will simplify how the eDNA research community tracks methods-based advances and will also provide greater clarity for conservation practitioners. To this end suggest reporting standards for eDNA studies.
Collapse
Affiliation(s)
| | | | - Richard Arnold
- Thomson Environmental Consultants Compass House Surrey Research Park Guildford UK
| | | |
Collapse
|
15
|
Coutant O, Richard-Hansen C, de Thoisy B, Decotte JB, Valentini A, Dejean T, Vigouroux R, Murienne J, Brosse S. Amazonian mammal monitoring using aquatic environmental DNA. Mol Ecol Resour 2021; 21:1875-1888. [PMID: 33787010 DOI: 10.1111/1755-0998.13393] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/14/2021] [Accepted: 03/22/2021] [Indexed: 11/26/2022]
Abstract
Environmental DNA (eDNA) metabarcoding has emerged as one of the most efficient methods to assess aquatic species presence. While the method can in theory be used to investigate nonaquatic fauna, its development for inventorying semi-aquatic and terrestrial fauna is still at an early stage. Here we investigated the potential of aquatic eDNA metabarcoding for inventorying mammals in Neotropical environments, be they aquatic, semi-aquatic or terrestrial. We collected aquatic eDNA in 96 sites distributed along three Guianese watersheds and compared our inventories to expected species distributions and field observations derived from line transects located throughout French Guiana. Species occurrences and emblematic mammalian fauna richness patterns were consistent with the expected distribution of fauna and our results revealed that aquatic eDNA metabarcoding brings additional data to line transect samples for diurnal nonaquatic (terrestrial and arboreal) species. Aquatic eDNA also provided data on species not detectable in line transect surveys such as semi-aquatic, aquatic and nocturnal terrestrial and arboreal species. Although the application of eDNA to inventory mammals still needs some developments to optimize sampling efficiency, it can now be used as a complement to traditional surveys.
Collapse
Affiliation(s)
- Opale Coutant
- Laboratoire Evolution et Diversité Biologique, CNRS, IRD, UPS, (UMR5174) - Université de Toulouse, Toulouse, France
| | | | | | | | | | - Tony Dejean
- VIGILIFE, Le Bourget-du-Lac, France.,SPYGEN, Le Bourget-du-Lac, France
| | - Régis Vigouroux
- Laboratoire Environnement de Petit Saut, HYDRECO, Kourou Cedex, French Guiana
| | - Jérôme Murienne
- Laboratoire Evolution et Diversité Biologique, CNRS, IRD, UPS, (UMR5174) - Université de Toulouse, Toulouse, France
| | - Sébastien Brosse
- Laboratoire Evolution et Diversité Biologique, CNRS, IRD, UPS, (UMR5174) - Université de Toulouse, Toulouse, France
| |
Collapse
|
16
|
Sales NG, Wangensteen OS, Carvalho DC, Deiner K, Præbel K, Coscia I, McDevitt AD, Mariani S. Space-time dynamics in monitoring neotropical fish communities using eDNA metabarcoding. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142096. [PMID: 32898783 DOI: 10.1016/j.scitotenv.2020.142096] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/24/2020] [Accepted: 08/29/2020] [Indexed: 06/11/2023]
Abstract
The biodiverse Neotropical ecoregion remains insufficiently assessed, poorly managed, and threatened by unregulated human activities. Novel, rapid and cost-effective DNA-based approaches are valuable to improve understanding of the biological communities and for biomonitoring in remote areas. Here, we evaluate the potential of environmental DNA (eDNA) metabarcoding for assessing the structure and distribution of fish communities by analysing water and sediment from 11 locations along the Jequitinhonha River catchment (Brazil). Each site was sampled twice, before and after a major rain event in a five-week period and fish diversity was estimated using high-throughput sequencing of 12S rRNA amplicons. In total, 252 Molecular Operational Taxonomic Units (MOTUs) and 34 fish species were recovered, including endemic, introduced, and previously unrecorded species for this basin. Spatio-temporal variation of eDNA from fish assemblages was observed and species richness was nearly twice as high before the major rain event compared to afterwards. Yet, peaks of diversity were primarily associated with only four of the locations. No correlation between β-diversity and longitudinal distance or presence of dams was detected, but low species richness observed at sites located near dams might that these anthropogenic barriers may have an impact on local fish diversity. Unexpectedly high α-diversity levels recorded at the river mouth suggest that these sections should be further evaluated as putative "eDNA reservoirs" for rapid monitoring. By uncovering spatio-temporal changes, unrecorded biodiversity components, and putative anthropogenic impacts on fish assemblages, we further strengthen the potential of eDNA metabarcoding as a biomonitoring tool, especially in regions often neglected or difficult to access.
Collapse
Affiliation(s)
- Naiara Guimarães Sales
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, UK; CESAM - Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal.
| | - Owen Simon Wangensteen
- Norwegian College of Fishery Science, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Daniel Cardoso Carvalho
- Programa de Pós-graduação em Biologia de Vertebrados, Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, Brazil
| | | | - Kim Præbel
- Norwegian College of Fishery Science, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Ilaria Coscia
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, UK
| | - Allan D McDevitt
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, UK
| | - Stefano Mariani
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, UK; School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK
| |
Collapse
|
17
|
Milan DT, Mendes IS, Damasceno JS, Teixeira DF, Sales NG, Carvalho DC. New 12S metabarcoding primers for enhanced Neotropical freshwater fish biodiversity assessment. Sci Rep 2020; 10:17966. [PMID: 33087755 PMCID: PMC7578065 DOI: 10.1038/s41598-020-74902-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/18/2020] [Indexed: 11/23/2022] Open
Abstract
The megadiverse Neotropical fish fauna lacks a comprehensive and reliable DNA reference database, which hampers precise species identification and DNA based biodiversity assessment in the region. Here, we developed a mitochondrial 12S ribosomal DNA reference database for 67 fish species, representing 54 genera, 25 families, and six major Neotropical orders. We aimed to develop mini-barcode markers (i.e. amplicons with less than 200 bp) suitable for DNA metabarcoding by evaluating the taxonomic resolution of full-length and mini-barcodes and to determine a threshold value for fish species delimitation using 12S. Evaluation of the target amplicons demonstrated that both full-length library (565 bp) and mini-barcodes (193 bp) contain enough taxonomic resolution to differentiate all 67 fish species. For species delimitation, interspecific genetic distance threshold values of 0.4% and 0.55% were defined using full-length and mini-barcodes, respectively. A custom reference database and specific mini-barcode markers are important assets for ecoregion scale DNA based biodiversity assessments (such as environmental DNA) that can help with the complex task of conserving the megadiverse Neotropical ichthyofauna.
Collapse
Affiliation(s)
- David T Milan
- Conservation Genetics Lab, Postgraduate Program in Vertebrate Biology, Pontifical Catholic University of Minas Gerais, PUC Minas, Belo Horizonte, Brazil
| | - Izabela S Mendes
- Conservation Genetics Lab, Postgraduate Program in Vertebrate Biology, Pontifical Catholic University of Minas Gerais, PUC Minas, Belo Horizonte, Brazil.,Postgraduate Program in Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Júnio S Damasceno
- Conservation Genetics Lab, Postgraduate Program in Vertebrate Biology, Pontifical Catholic University of Minas Gerais, PUC Minas, Belo Horizonte, Brazil
| | - Daniel F Teixeira
- Conservation Genetics Lab, Postgraduate Program in Vertebrate Biology, Pontifical Catholic University of Minas Gerais, PUC Minas, Belo Horizonte, Brazil.,Postgraduate Program in Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Naiara G Sales
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, UK.,CESAM - Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Daniel C Carvalho
- Conservation Genetics Lab, Postgraduate Program in Vertebrate Biology, Pontifical Catholic University of Minas Gerais, PUC Minas, Belo Horizonte, Brazil. .,Postgraduate Program in Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil.
| |
Collapse
|
18
|
Browett SS, O'Meara DB, McDevitt AD. Genetic tools in the management of invasive mammals: recent trends and future perspectives. Mamm Rev 2020. [DOI: 10.1111/mam.12189] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Samuel S. Browett
- Ecosystems and Environment Research Centre School of Science, Engineering and Environment University of Salford Salford M5 4WTUK
| | - Denise B. O'Meara
- Molecular Ecology Research Group Eco‐Innovation Research Centre School of Science and Computing Waterford Institute of Technology Waterford Ireland
| | - Allan D. McDevitt
- Ecosystems and Environment Research Centre School of Science, Engineering and Environment University of Salford Salford M5 4WTUK
| |
Collapse
|
19
|
Sales NG, McKenzie MB, Drake J, Harper LR, Browett SS, Coscia I, Wangensteen OS, Baillie C, Bryce E, Dawson DA, Ochu E, Hänfling B, Lawson Handley L, Mariani S, Lambin X, Sutherland C, McDevitt AD. Fishing for mammals: Landscape‐level monitoring of terrestrial and semi‐aquatic communities using eDNA from riverine systems. J Appl Ecol 2020. [DOI: 10.1111/1365-2664.13592] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Naiara Guimarães Sales
- Environment and Ecosystem Research Centre School of Science, Engineering and Environment University of Salford Salford UK
| | - Maisie B. McKenzie
- Environment and Ecosystem Research Centre School of Science, Engineering and Environment University of Salford Salford UK
| | - Joseph Drake
- Department of Environmental Conservation University of Massachusetts‐Amherst Amherst USA
| | - Lynsey R. Harper
- Department of Biological and Marine Sciences University of Hull Kingston upon Hull UK
| | - Samuel S. Browett
- Environment and Ecosystem Research Centre School of Science, Engineering and Environment University of Salford Salford UK
| | - Ilaria Coscia
- Environment and Ecosystem Research Centre School of Science, Engineering and Environment University of Salford Salford UK
| | | | - Charles Baillie
- Environment and Ecosystem Research Centre School of Science, Engineering and Environment University of Salford Salford UK
| | - Emma Bryce
- School of Biological Sciences University of Aberdeen Aberdeen UK
| | - Deborah A. Dawson
- Department of Animal and Plant Sciences University of Sheffield Sheffield UK
| | - Erinma Ochu
- Environment and Ecosystem Research Centre School of Science, Engineering and Environment University of Salford Salford UK
| | - Bernd Hänfling
- Department of Biological and Marine Sciences University of Hull Kingston upon Hull UK
| | - Lori Lawson Handley
- Department of Biological and Marine Sciences University of Hull Kingston upon Hull UK
| | - Stefano Mariani
- Environment and Ecosystem Research Centre School of Science, Engineering and Environment University of Salford Salford UK
- School of Natural Sciences and Psychology Liverpool John Moores University Liverpool UK
| | - Xavier Lambin
- School of Biological Sciences University of Aberdeen Aberdeen UK
| | - Christopher Sutherland
- Department of Environmental Conservation University of Massachusetts‐Amherst Amherst USA
- Centre for Research into Ecological and Environmental Modelling University of St Andrews St Andrews UK
| | - Allan D. McDevitt
- Environment and Ecosystem Research Centre School of Science, Engineering and Environment University of Salford Salford UK
| |
Collapse
|