@book{dasmann1972environmental1, author = "Dasmann, R. F", title = "Environmental Conservation [3rd ed.]", year = "1972", publisher = "New York, Wiley, 473 p", note = "talkorigins\_source = {true}; raw\_reference = {Dasmann, R. F., 1972, Environmental Conservation [3rd ed.]: New York, Wiley, 473 p.}" } @article{doi1023071885257, author = "Fisher, Anthony C. and Krutilla, John V.", title = "Resource Conservation, Environmental Preservation, and the Rate of Discount", year = "1975", journal = "The Quarterly Journal of Economics", abstract = "I. Discounting and conservation, 359. — II. A model for natural environmental resource allocation: the concept of effective discount rates, 362. — III. Concluding remarks, 370.", url = "https://doi.org/10.2307/1885257", doi = "10.2307/1885257", openalex = "W2068341906" } @article{doi102307633494, author = "Grove, A. T. and Morgan, R. P. C.", title = "Soil Erosion and Conservation", year = "1988", journal = "Geographical Journal", abstract = "This is a review of worldwide land degradation problems. Four themes are emphasized: delineating and estimating the magnitude of soil erosion, quantifying erosion and sedimentation impacts on land productivity, establishing quantitative values for erosion-causing parameters, and implementing global and regional soil and water conservation programs. Papers deal with both developing and developed countries and illustrate how erosion control techniques used in developed countries can or cannot be applied in developing countries.", url = "https://doi.org/10.2307/633494", doi = "10.2307/633494", openalex = "W2122802215", references = "doi1010079789400956827, doi101016s0065211308604009, doi101093biomet371230, doi102307622211" } @book{openalexw2123629586, author = "Young, Anthony", title = "Agroforestry for Soil Conservation", year = "1989", booktitle = "OpenGrey (Institut de l'Information Scientifique et Technique)", openalex = "W2123629586", references = "doi101016s0065211308603971" } @book{doi101017cbo9780511735394, author = "Pimentel, David", title = "World Soil Erosion and Conservation", year = "1993", booktitle = "Cambridge University Press eBooks", abstract = "Land degradation from soil erosion has been considered by many to be a problem of significant proportion, affecting some 30–50\% of the earth's land surface. At the time of the first publication of this book in 1993, estimates indicated that 10–15 million hectares of land were being lost each year through erosion and salinisation from irrigation and that at such a rate of loss, topsoil reserves on most sloping lands would be depleted within two hundred years. Since humankind's dependency on the land for food is almost total, soil erosion represents a real threat to the security of our food supply. The need for the immediate conservation of the world's soil resources is therefore clear. As part of the response to this need, the International Union for the Conservation of Nature's Commission on Ecology convened a special working group to consider the problem of world soil erosion and to propose practical solutions for soil conservation. This important book presents the outcome of their work.", url = "https://doi.org/10.1017/cbo9780511735394", doi = "10.1017/cbo9780511735394", openalex = "W1509812492" } @article{doi101126science26752011117, author = "Pimentel, David and Harvey, Célia A. and Resosudarmo, Ida Aju Pradnja and Sinclair, K.B. and Kurz, Daniel and McNair, Michael and Crist, Scott D. and Shpritz, L. and Fitton, L. and Saffouri, R. and Blair, Ryan", title = "Environmental and Economic Costs of Soil Erosion and Conservation Benefits", year = "1995", journal = "Science", abstract = "Soil erosion is a major environmental threat to the sustainability and productive capacity of agriculture. During the last 40 years, nearly one-third of the world's arable land has been lost by erosion and continues to be lost at a rate of more than 10 million hectares per year. With the addition of a quarter of a million people each day, the world population's food demand is increasing at a time when per capita food productivity is beginning to decline.", url = "https://doi.org/10.1126/science.267.5201.1117", doi = "10.1126/science.267.5201.1117", openalex = "W2050154560", references = "doi101017cbo9780511735394, doi101071sr9910745, doi101111j136523891984tb00278x, doi1012019781351072519, doi102307215130, doi1023073451509, doi102307633494, doi105860choice451769, openalexw2123629586, openalexw3141838726" } @book{openalexw1546506088, author = "Ghimire, Krishna B. and Pimbert, Michel", title = "Social change and conservation: environmental politics and impacts of national parks and protected areas.", year = "1997", booktitle = "Earthscan Publications Ltd eBooks", abstract = "List of Contributors Acknowledgements and a Caveat to the Reader List of Figures List of Tables I. Social Change and Conservation: an Overview of Issues and Concepts Krishna B. Ghimire and Michel P. Pimbert II. Biodiversity and Human Welfare Piers Blaikie and Sally Jeanrenaud III. National Parks and Protected Area Management in Costa Rica and Germany: a Comparative Analysis Jens Briiggemann IV. Salvaging Nature: Indigenous Peoples and Protected Areas Marcus Colchester V. Women, Forest Products and Protected Areas: a Case Study of Jaldapara Wildlife Sanctuary, West Bengal, India Chandana Dey VI. Local Development and Parks in France Andrea Finger-Stich and Krishna B. Ghimire VII. Conservation and Social Development: an Assessment of Wolong and other Panda Reserves in China Krishna B. Ghirnire VIII. Ecotourism and Rural Reconstruction in South Africa: Reality or Rhetoric? Eddie Koch IX. Management of Wildlife, Tourism and Local Communities in Zimbabwe Chris Mayor X. Protected Areas, Conservationists and Aboriginal Interests in Canada James Morrison XI. Parks, People and Professionals: Putting 'Participation' into Protected Area Management Michel P. Pimbert and Jules N. Pretty List of Abbreviations and Acronyms Land and Weight Measurements Currency Conversion", url = "https://openalex.org/W1546506088", openalex = "W1546506088" } @article{doi101017s0376892901000169, author = "Walpole, Matthew J. and Goodwin, Harold", title = "Local attitudes towards conservation and tourism around Komodo National Park, Indonesia", year = "2001", journal = "Environmental Conservation", abstract = "Ensuring local support for protected areas is increasingly viewed as an important element of biodiversity conservation. This is often predicated on the provision of benefits from protected areas, and a common means of providing such benefits is tourism development. However, the relationship between receipt of tourism benefits and support for conservation has not been explored. This study examined local attitudes towards protected area tourism and the effects of tourism benefits on local support for Komodo National Park, Indonesia. Komodo National Park is a flagship for tourism in a region where protected areas are becoming increasingly visited and where local support for conservation has not been investigated. Results of a questionnaire survey revealed positive attitudes towards tourism and high support for conservation (93.7\%), as well as a recognition that tourism is dependent upon the existence of the park. Positive attitudes towards tourism were positively related to the receipt of economic benefits, and to support for conservation. However, a positive relationship between receipt of tourism benefits and support for conservation was not identified, suggesting that benefits from protected area conservation make no difference to local support for conservation. Local people recognized distributional inequalities in tourism benefits, and the most common complaints were of local inflation and tourist dress code. To fully identify the impacts of protected area tourism, long-term studies of local attitudes alongside traditional economic and ecological assessments are recommended.", url = "https://doi.org/10.1017/s0376892901000169", doi = "10.1017/s0376892901000169", openalex = "W2089900098", references = "doi101007bf00051774, doi101016000632079390507w, doi1010160160738387900454, doi101016016073839090029q, doi101016s0160738399000882, doi101017s037689290001064x, doi101017s037689299800040x, doi1023071444685, openalexw1546506088, openalexw1756902206, vitt1982the" } @article{doi101080089419202317174011, author = "Brechin, Steven R. and Wilshusen, Peter R. and Fortwangler, Crystal and West, Patrick C.", title = "Beyond the Square Wheel: Toward a More Comprehensive Understanding of Biodiversity Conservation as Social and Political Process", year = "2002", journal = "Society \& Natural Resources", abstract = "Metadata only record", url = "https://doi.org/10.1080/089419202317174011", doi = "10.1080/089419202317174011", openalex = "W2092666883", references = "doi105860choice330904, openalexw1546506088" } @article{doi101126science1067728, author = "Roberts, Callum M. and McClean, Colin J. and Veron, J. E. N. and Hawkins, Julie P. and Allen, Gerald R. and McAllister, Don E. and Mittermeier, Cristina G. and Schueler, Frederick W and Spalding, Mark and Wells, Fred E. and Vynne, Carly and Werner, Timothy B.", title = "Marine Biodiversity Hotspots and Conservation Priorities for Tropical Reefs", year = "2002", journal = "Science", abstract = "Coral reefs are the most biologically diverse of shallow water marine ecosystems but are being degraded worldwide by human activities and climate warming. Analyses of the geographic ranges of 3235 species of reef fish, corals, snails, and lobsters revealed that between 7.2\% and 53.6\% of each taxon have highly restricted ranges, rendering them vulnerable to extinction. Restricted-range species are clustered into centers of endemism, like those described for terrestrial taxa. The 10 richest centers of endemism cover 15.8\% of the world's coral reefs (0.012\% of the oceans) but include between 44.8 and 54.2\% of the restricted-range species. Many occur in regions where reefs are being severely affected by people, potentially leading to numerous extinctions. Threatened centers of endemism are major biodiversity hotspots, and conservation efforts targeted toward them could help avert the loss of tropical reef biodiversity.", url = "https://doi.org/10.1126/science.1067728", doi = "10.1126/science.1067728", openalex = "W2149529243", references = "doi101126science26752011117" } @misc{openalexw915666225, author = "Landell-Mills, Natasha and Porras, I.", title = "Silver bullet or fools' gold? A global review of markets for forest environmental services and their impact on the poor.", year = "2002", booktitle = "VTechWorks (Virginia Tech)", abstract = "Metadata only record", openalex = "W915666225" } @article{doi101017s0030605303000395, author = "Hutton, Jon and Leader‐Williams, Nigel", title = "Sustainable use and incentive-driven conservation: realigning human and conservation interests", year = "2003", journal = "Oryx", abstract = "Discussions of sustainable use have become polarized. Welfarists oppose all use that involves killing animals. Among conservationists polarization arises in part from failure to distinguish between different ideas nestled under the umbrella term of ‘sustainable use’. These include direct use as an imperative or choice, the ideal of keeping any use within biologically sustainable limits, and use as a possible conservation strategy that can create positive incentives, which are key where land could otherwise be converted to biodiversity-unfriendly practices. People will continue to use wild living resources, which increasing human populations could further deplete. In response the conservation community can follow one of two approaches. On the one hand, it can try to stop use through the establishment of strictly protected areas and by enforcing legislation, although many would question the ethical position of imposing such an approach. On the other hand, it can work to introduce the wider management systems needed to deliver sustainable use and, if possible, incentive-driven conservation. Because most rural populations will continue using wild living resources in human-dominated landscapes, sustainable use and incentive-driven conservation should both be at the centre of the conservation agenda this century. Both species- and ecosystem-based management are likely to have a role in sustainable use. However, current enthusiasm for the ecosystem approach may throw up unexpected consequences, making the search for sustainability even more polarized. Nevertheless, direct use of species cannot provide sufficient incentives to ensure the continued delivery of ecosystem services, which need to be fully incorporated in the global accounting system.", url = "https://doi.org/10.1017/s0030605303000395", doi = "10.1017/s0030605303000395", openalex = "W2150470222", references = "openalexw1546506088" } @article{doi101111j13652664200300868x, author = "Kleijn, David and Sutherland, William J.", title = "How effective are European agri‐environment schemes in conserving and promoting biodiversity?", year = "2003", journal = "Journal of Applied Ecology", abstract = "Summary Increasing concern over the environmental impact of agriculture in Europe has led to the introduction of agri‐environment schemes. These schemes compensate farmers financially for any loss of income associated with measures that aim to benefit the environment or biodiversity. There are currently agri‐environment schemes in 26 out of 44 European countries. Agri‐environment schemes vary markedly between countries even within the European Union. The main objectives include reducing nutrient and pesticide emissions, protecting biodiversity, restoring landscapes and preventing rural depopulation. In virtually all countries the uptake of schemes is highest in areas of extensive agriculture where biodiversity is still relatively high and lowest in intensively farmed areas where biodiversity is low. Approximately €24·3 billion has been spent on agri‐environment schemes in the European Union (EU) since 1994, an unknown proportion of it on schemes with biodiversity conservation aims. We carried out a comprehensive search for studies that test the effectiveness of agri‐environment schemes in published papers or reports. Only 62 evaluation studies were found originating from just five EU countries and Switzerland (5). Indeed 76\% of the studies were from the Netherlands and the United Kingdom, where until now only c. 6\% of the EU agri‐environmental budget has been spent. Other studies were from Germany (6), Ireland (3) and Portugal (1). In the majority of studies, the research design was inadequate to assess reliably the effectiveness of the schemes. Thirty‐one percent did not contain a statistical analysis. Where an experimental approach was used, designs were usually weak and biased towards giving a favourable result. The commonest experimental design (37\% of the studies) was a comparison of biodiversity in agri‐environment schemes and control areas. However, there is a risk of bias if either farmers or scheme co‐ordinators select the sites for agri‐environment schemes. In such cases the sites are likely to have a higher biodiversity at the outset compared to the controls. This problem may be addressed by collecting baseline data (34\% of studies), comparing trends (32\%) or changes (26\%) in biodiversity between areas with and without schemes or by pairing scheme and control sites that experience similar environmental conditions (16\%). Overall, 54\% of the examined species (groups) demonstrated increases and 6\% decreases in species richness or abundance compared with controls. Seventeen percent showed increases for some species and decreases for other species, while 23\% showed no change at all in response to agri‐environment schemes. The response varied between taxa. Of 19 studies examining the response of birds that included a statistical analysis, four showed significant increases in species richness or abundance, two showed decreases and nine showed both increases and decreases. Comparative figures for 20 arthropod studies yielded 11 studies that showed an increase in species richness or abundance, no study showed a decrease and three showed both increases and decreases. Fourteen plant studies yielded six studies that showed increases in species richness or abundance, two showed decreases and no study showed both increases and decreases. Synthesis and applications. The lack of robust evaluation studies does not allow a general judgement of the effectiveness of European agri‐environment schemes. We suggest that in the future, ecological evaluations must become an integral part of any scheme, including the collection of baseline data, the random placement of scheme and control sites in areas with similar initial conditions, and sufficient replication. Results of these studies should be collected and disseminated more widely, in order to identify the approaches and prescriptions that best deliver biodiversity enhancement and value for money from community support.", url = "https://doi.org/10.1111/j.1365-2664.2003.00868.x", doi = "10.1111/j.1365-2664.2003.00868.x", openalex = "W2119442719", references = "openalexw2112482114" } @book{openalexw1497677346, author = "Anderson, David G. and Berglund, Eeva", title = "Ethnographies of conservation: environmentalism and the distribution of privilege", year = "2003", abstract = "This is an excellent collection of articles...All are clearly written and any of them could be used in undergraduate teaching. Moreover, the range of case studies is impressively global...The articles all exhibit a good capacity to provoke...The result is an enjoyable book that is likely to be useful to teachers, students and practitioners of environmentalism. - Anthropological Forum Anthropologists know that conservation often disempowers already under-privileged groups, and that it also fails to protect environments. Through a series of ethnographic studies, this book argues that the real problem is not the disappearance of pristine nature or even the land-use practices of uneducated people. Rather, what we know about culturally determined patterns of consumption, production and unequal distribution, suggests that critical attention would be better turned on discourses of primitiveness and pristine nature so prevalent within conservation ideology, and on the historically formed power and exchange relationships that they help perpetuate. David G. Anderson is Senior Lecturer in the Department of Anthropology at the University of Aberdeen. Eeva Berglund was Lecturer in Anthropology at Goldsmiths College from 1998 to 2002 and has written on the anthropology and history of environmental politics.", url = "https://openalex.org/W1497677346", openalex = "W1497677346" } @article{doi101016jenvsci200402004, author = "Colchester, Marcus", title = "Conservation policy and indigenous peoples", year = "2004", journal = "Environmental Science \& Policy", url = "https://doi.org/10.1016/j.envsci.2004.02.004", doi = "10.1016/j.envsci.2004.02.004", openalex = "W2040897528", references = "openalexw1546506088" } @article{doi101016jtree200403018, author = "Sutherland, William J. and Pullin, Andrew S. and Dolman, Paul M. and Knight, Teri", title = "The need for evidence-based conservation", year = "2004", journal = "Trends in Ecology \& Evolution", url = "https://doi.org/10.1016/j.tree.2004.03.018", doi = "10.1016/j.tree.2004.03.018", openalex = "W2096369236" } @article{doi101111j15231739200400077x, author = "Berkes, Fikret", title = "Rethinking Community‐Based Conservation", year = "2004", journal = "Conservation Biology", abstract = "Abstract: Community‐based conservation (CBC) is based on the idea that if conservation and development could be simultaneously achieved, then the interests of both could be served. It has been controversial because community development objectives are not necessarily consistent with conservation objectives in a given case. I examined CBC from two angles. First, CBC can be seen in the context of paradigm shifts in ecology and applied ecology. I identified three conceptual shifts—toward a systems view, toward the inclusion of humans in the ecosystem, and toward participatory approaches to ecosystem management—that are interrelated and pertain to an understanding of ecosystems as complex adaptive systems in which humans are an integral part. Second, I investigated the feasibility of CBC, as informed by a number of emerging interdisciplinary fields that have been pursuing various aspects of coupled systems of humans and nature. These fields—common property, traditional ecological knowledge, environmental ethics, political ecology, and environmental history—provide insights for CBC. They may contribute to the development of an interdisciplinary conservation science with a more sophisticated understanding of social‐ecological interactions. The lessons from these fields include the importance of cross‐scale conservation, adaptive comanagement, the question of incentives and multiple stakeholders, the use of traditional ecological knowledge, and development of a cross‐cultural conservation ethic.", url = "https://doi.org/10.1111/j.1523-1739.2004.00077.x", doi = "10.1111/j.1523-1739.2004.00077.x", openalex = "W2101873753", references = "doi101007s1002100101015, openalexw2010189956" } @article{doi101126science1093857, author = "Venter, J. Craig and Remington, Karin and Heidelberg, John F. and Halpern, Aaron L. and Rusch, Doug and Eisen, Jonathan A. and Wu, Dongying and Paulsen, Ian T. and Nelson, Karen E. and Nelson, William and Fouts, Derrick E. and Lévy, Samuel and Knap, Anthony H. and Lomas, Michael W. and Nealson, K. and White, Owen and Peterson, Jeremy and Hoffman, Jeff and Parsons, Rachel and Baden-Tillson, Holly and Pfannkoch, Cynthia and Rogers, Yu-Hui and Smith, Hamilton O.", title = "Environmental Genome Shotgun Sequencing of the Sargasso Sea", year = "2004", journal = "Science", abstract = {We have applied "whole-genome shotgun sequencing" to microbial populations collected en masse on tangential flow and impact filters from seawater samples collected from the Sargasso Sea near Bermuda. A total of 1.045 billion base pairs of nonredundant sequence was generated, annotated, and analyzed to elucidate the gene content, diversity, and relative abundance of the organisms within these environmental samples. These data are estimated to derive from at least 1800 genomic species based on sequence relatedness, including 148 previously unknown bacterial phylotypes. We have identified over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity.}, url = "https://doi.org/10.1126/science.1093857", doi = "10.1126/science.1093857", openalex = "W2113601822", references = "doi101038nature01947, doi101073pnas142680199, doi101093nargkg039, doi101093nargkg095, doi101126science28754612196, doi101126science28954861902, doi101128aem335122512281977, doi101128aem666254125472000, doi1023073875, openalexw1558982506" } @article{doi101126science1097920, author = "Adams, William M. and Aveling, Ros and Brockington, Dan and Dickson, Barney and Elliott, J and Hutton, Jon and Roe, Dilys and Vira, Bhaskar and Wolmer, William", title = "Biodiversity Conservation and the Eradication of Poverty", year = "2004", journal = "Science", abstract = "It is widely accepted that biodiversity loss and poverty are linked problems and that conservation and poverty reduction should be tackled together. However, success with integrated strategies is elusive. There is sharp debate about the social impacts of conservation programs and the success of community-based approaches to conservation. Clear conceptual frameworks are needed if policies in these two areas are to be combined. We review the links between poverty alleviation and biodiversity conservation and present a conceptual typology of these relationships.", url = "https://doi.org/10.1126/science.1097920", doi = "10.1126/science.1097920", openalex = "W2073321019" } @article{doi1016410006356820040541110kbaasc20co2, author = "Eken, Güven and Bennun, Leon and Brooks, Thomas M. and Darwall, Will and Fishpool, Lincoln and Foster, Matt and Knox, David and Langhammer, Penny F. and Matiku, Paul and Radford, Elizabeth A. and Salaman, Paul and Sechrest, Wes and Smith, Michael L. and Spector, Sacha and Tordoff, Andrew W.", title = "Key Biodiversity Areas as Site Conservation Targets", year = "2004", journal = "BioScience", abstract = "Site conservation is among the most effective means to reduce global biodiversity loss. Therefore, it is critical to identify those sites where unique biodiversity must be conserved immediately. To this end, the concept of key biodiversity areas (KBAs) has been developed, seeking to identify and, ultimately, ensure that networks of globally important sites are safeguarded. This methodology builds up from the identification of species conservation targets (through the IUCN Red List) and nests within larger-scale conservation approaches. Sites are selected using standardized, globally applicable, threshold-based criteria, driven by the distribution and population of species that require site-level conservation. The criteria address the two key issues for setting site conservation priorities: vulnerability and irreplaceability. We also propose quantitative thresholds for the identification of KBAs meeting each criterion, based on a review of existing approaches and ecological theory to date. However, these thresholds require extensive testing, especially in aquatic systems.", url = "https://doi.org/10.1641/0006-3568(2004)054[1110:kbaasc]2.0.co;2", doi = "10.1641/0006-3568(2004)054[1110:kbaasc]2.0.co;2", openalex = "W2154735712" } @article{doi101017s1464793105006950, author = "Dudgeon, David and Arthington, Angela H. and Gessner, Mark O. and Kawabata, Zen’ichiro and Knowler, Duncan and Lévêque, Christian and Naiman, Robert J. and Prieur‐Richard, Anne‐Hélène and Soto, Doris and Stiassny, Melanie L. J. and Sullivan, Caroline A", title = "Freshwater biodiversity: importance, threats, status and conservation challenges", year = "2005", journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society", abstract = "Freshwater biodiversity is the over-riding conservation priority during the International Decade for Action - 'Water for Life' - 2005 to 2015. Fresh water makes up only 0.01\% of the World's water and approximately 0.8\% of the Earth's surface, yet this tiny fraction of global water supports at least 100000 species out of approximately 1.8 million - almost 6\% of all described species. Inland waters and freshwater biodiversity constitute a valuable natural resource, in economic, cultural, aesthetic, scientific and educational terms. Their conservation and management are critical to the interests of all humans, nations and governments. Yet this precious heritage is in crisis. Fresh waters are experiencing declines in biodiversity far greater than those in the most affected terrestrial ecosystems, and if trends in human demands for water remain unaltered and species losses continue at current rates, the opportunity to conserve much of the remaining biodiversity in fresh water will vanish before the 'Water for Life' decade ends in 2015. Why is this so, and what is being done about it? This article explores the special features of freshwater habitats and the biodiversity they support that makes them especially vulnerable to human activities. We document threats to global freshwater biodiversity under five headings: overexploitation; water pollution; flow modification; destruction or degradation of habitat; and invasion by exotic species. Their combined and interacting influences have resulted in population declines and range reduction of freshwater biodiversity worldwide. Conservation of biodiversity is complicated by the landscape position of rivers and wetlands as 'receivers' of land-use effluents, and the problems posed by endemism and thus non-substitutability. In addition, in many parts of the world, fresh water is subject to severe competition among multiple human stakeholders. Protection of freshwater biodiversity is perhaps the ultimate conservation challenge because it is influenced by the upstream drainage network, the surrounding land, the riparian zone, and - in the case of migrating aquatic fauna - downstream reaches. Such prerequisites are hardly ever met. Immediate action is needed where opportunities exist to set aside intact lake and river ecosystems within large protected areas. For most of the global land surface, trade-offs between conservation of freshwater biodiversity and human use of ecosystem goods and services are necessary. We advocate continuing attempts to check species loss but, in many situations, urge adoption of a compromise position of management for biodiversity conservation, ecosystem functioning and resilience, and human livelihoods in order to provide a viable long-term basis for freshwater conservation. Recognition of this need will require adoption of a new paradigm for biodiversity protection and freshwater ecosystem management - one that has been appropriately termed 'reconciliation ecology'.", url = "https://doi.org/10.1017/s1464793105006950", doi = "10.1017/s1464793105006950", openalex = "W2107140090", references = "doi1010079789400958517, doi101007s1053300403700, doi10103835002501, doi101038387253a0, doi101065espr200212142, doi101093acprofoso97801985208630010001, doi101126science1064088, doi101126science1103538, doi101126science27753331808, doi101126science28754591770, doi101126science2895477284, doi1016410006356820010510933teotwa20co2, doi101890040922, doi1023071313099, doi1023072257385, doi105860choice496872" } @article{doi1010800803941020059666319, author = "Hutton, Jon and Adams, William M. and Murombedzi, James", title = "Back to the Barriers? Changing Narratives in Biodiversity Conservation", year = "2005", journal = "Forum for Development Studies", abstract = "Abstract The dominant approach to conservation in the 20th century was the establishment of protected areas from which people were excluded. However, in the 1980s, decentralised, community-based approaches to biodiversity conservation and natural resource management began to spread rapidly, especially in southern Africa. From the early 1990s, there has been a growing divide between proponents of community-based approaches to conservation (particularly community-based natural resource management, CBNRM) and those advocating a return to more traditional preservationist approaches to biodiversity conservation. Here we examine the growth of the community narrative and the subsequent revival of what we call the ‘back to the barriers’ movement. We discuss the importance of various actors and sets of policy ideas to this revival in Africa. Changes in narratives have had profound impacts upon conservation and natural resource management, livelihood strategies and political processes. We suggest that policy debate needs to become less formulaic if outcomes are to be positive.", url = "https://doi.org/10.1080/08039410.2005.9666319", doi = "10.1080/08039410.2005.9666319", openalex = "W2039275157", references = "doi105860choice330904, openalexw1546506088" } @book{doi1017528cifor001760, author = "Wunder, Sven", title = "Payments for environmental services: some nuts and bolts", year = "2005", booktitle = "Center for International Forestry Research (CIFOR) eBooks", abstract = "Payments for environmental services (PES) are part of a new and more direct conservation paradigm, explicitly recognizing the need to bridge the interests of landowners and outsiders. Eloquent theoretical assessments have praised the absolute advantages of PES over traditional conservation approaches. Some pilot PES exist in the tropics, but many field practitioners and prospective service buyers and sellers remain skeptical about the concept. This paper aims to help demystify PES for non-economists, starting with a simple and coherent definition of the term. It then provides practical ‘how-to' hints for PES design. It considers the likely niche for PES in the portfolio of conservation approaches. This assessment is based on a literature review, combined with field observations from research in Latin America and Asia. It concludes that service users will continue to drive PES, but their willingness to pay will only rise if schemes can demonstrate clear additionality vis-à-vis carefully established baselines, if trust-building processes with service providers are sustained, and PES recipients' livelihood dynamics is better understood. PES best suits intermediate and/or projected threat scenarios, often in marginal lands with moderate conservation opportunity costs. People facing credible but medium-sized environmental degradation are more likely to become PES recipients than those living in relative harmony with Nature. The choice between PES cash and in-kind payments is highly context-dependent. Poor PES recipients are likely to gain from participation, though their access might be constrained and non-participating landless poor could lose out. PES is a highly promising conservation approach that can benefit buyers, sellers and improve the resource base, but it is unlikely to completely outstrip other conservation instruments.", url = "https://doi.org/10.17528/cifor/001760", doi = "10.17528/cifor/001760", openalex = "W1836765585" } @article{doi101016jtree200611004, author = "Bickford, David and Lohman, David J. and Sodhi, Navjot S. and Ng, Peter K. L. and Meier, Rudolf and Winker, Kevin and Ingram, Krista K. and Das, Indraneil", title = "Cryptic species as a window on diversity and conservation", year = "2006", journal = "Trends in Ecology \& Evolution", url = "https://doi.org/10.1016/j.tree.2006.11.004", doi = "10.1016/j.tree.2006.11.004", openalex = "W2116226846", references = "doi1010079781461523819, doi101016jtree200501003, doi10103835059215, doi101073pnas0406166101, doi101098rspb20022218, doi101146annurevecolsys34012103144032, doi101146annureves24110193001201, doi101146annureves25110194002555, doi104159harvard9780674865327, doi107312steb94536" } @article{doi1010800803941020069666337, author = "Sullivan, Sian", title = "Elephant in the Room? Problematising ‘New’ (Neoliberal) Biodiversity Conservation", year = "2006", journal = "Forum for Development Studies", abstract = "Abstract As argued recently in Forum for Development Studies, a ‘back to the barriers’ approach to biodiversity conservation is again prevalent, after some two decades of emphasis on ‘community-based’ initiatives. This involves the establishment and expansion of national parks from which people are variously excluded. In this article, however, I suggest that community-based approaches such as Community-Based Natural Resources Management (CBNRM) remain important, and in many ways simply constitute the other side of the same coin of modem conservation practice under the political and economic, and cultural, value-frame of neoliberalism. My aim is to highlight some shared conceptualizations and rationalisations regarding perceptions of ‘the environment’ and of people-environment relationships that inform both of these two broad-brush policy and practical orientations towards ‘biodiversity conservation’. The article thus draws on a Foucaultian analytics to ‘problematise’ the contemporaly and globalising neoliberal episteme within which both these approaches are produced; and to open a space where orientations (towards ‘the environment’) that are ‘othered’ and thereby silenced by this frame might be articulated.", url = "https://doi.org/10.1080/08039410.2006.9666337", doi = "10.1080/08039410.2006.9666337", openalex = "W2028878025", references = "openalexw1497677346" } @article{doi101111j15231739200600485x, author = "Pullin, Andrew S. and Stewart, Gavin", title = "Guidelines for Systematic Review in Conservation and Environmental Management", year = "2006", journal = "Conservation Biology", abstract = "An increasing number of applied disciplines are utilizing evidence-based frameworks to review and disseminate the effectiveness of management and policy interventions. The rationale is that increased accessibility of the best available evidence will provide a more efficient and less biased platform for decision making. We argue that there are significant benefits for conservation in using such a framework, but the scientific community needs to undertake and disseminate more systematic reviews before the full benefit can be realized. We devised a set of guidelines for undertaking formalized systematic review, based on a health services model. The guideline stages include planning and conducting a review, including protocol formation, search strategy, data inclusion, data extraction, and analysis. Review dissemination is addressed in terms of current developments and future plans for a Web-based open-access library. By the use of case studies we highlight critical modifications to guidelines for protocol formulation, data-quality assessment, data extraction, and data synthesis for conservation and environmental management. Ecological data presented significant but soluble challenges for the systematic review process, particularly in terms of the quantity, accessibility, and diverse quality of available data. In the field of conservation and environmental management there needs to be further engagement of scientists and practitioners to develop and take ownership of an evidence-based framework.", url = "https://doi.org/10.1111/j.1523-1739.2006.00485.x", doi = "10.1111/j.1523-1739.2006.00485.x", openalex = "W2027094073", references = "doi101001jama199503520290060030, doi101001jama2735408, doi101001jama282111054, doi1010029781119536604, doi101016019724569400031w, doi101016jtree200403018, doi101177001316446002000104, doi1023071164691, doi1023072533295, openalexw612372977" } @article{doi101111j15231739200600559x, author = "Wunder, Sven", title = "The Efficiency of Payments for Environmental Services in Tropical Conservation", year = "2006", journal = "Conservation Biology", abstract = {Payments for environmental services (PES) represent a new, more direct way to promote conservation. They explicitly recognize the need to address difficult trade-offs by bridging the interests of landowners and external actors through compensations. Theoretical assessments praise the advantages of PES over indirect approaches, but in the tropics PES application has remained incipient. Here I aim to demystify PES and clarify its scope for application as a tool for tropical conservation. I focus on the supply side of PES (i.e., how to convert PES funding into effective conservation on the ground), which until now has been widely neglected. I reviewed the PES literature for developing countries and combined these findings with observations from my own field studies in Latin America and Asia. A PES scheme, simply stated, is a voluntary, conditional agreement between at least one "seller" and one "buyer" over a well-defined environmental service--or a land use presumed to produce that service. Major obstacles to effective PES include demand-side limitations and a lack of supply-side know-how regarding implementation. The design of PES programs can be improved by explicitly outlining baselines, calculating conservation opportunity costs, customizing payment modalities, and targeting agents with credible land claims and threats to conservation. Expansion of PES can occur if schemes can demonstrate clear additionality (i.e., incremental conservation effects vis-à-vis predefined baselines), if PES recipients' livelihood dynamics are better understood, and if efficiency goals are balanced with considerations of fairness. PES are arguably best suited to scenarios of moderate conservation opportunity costs on marginal lands and in settings with emerging, not-yet realized threats. Actors who represent credible threats to the environment will more likely receive PES than those already living in harmony with nature. A PES scheme can thus benefit both buyers and sellers while improving the resource base, but it is unlikely to fully replace other conservation instruments.}, url = "https://doi.org/10.1111/j.1523-1739.2006.00559.x", doi = "10.1111/j.1523-1739.2006.00559.x", openalex = "W2082252945", references = "doi101016jagee200401015, doi101037003329091256627, doi101111j09567976200400757x, doi101111j15231739200400077x, doi101126science1078104, doi101126science1097920, doi101126science2915501125, doi101371journalpbio0040105, doi1017528cifor001760, openalexw915666225" } @article{doi101371journalpbio0040105, author = "Ferraro, Paul J. and Pattanayak, Subhrendu K.", title = "Money for Nothing? A Call for Empirical Evaluation of Biodiversity Conservation Investments", year = "2006", journal = "PLoS Biology", abstract = "The field of conservation policy must adopt state-of-the-art program evaluation methods to determine what works, and when, if we are to stem the global decline of biodiversity and improve the effectiveness of conservation investments.", url = "https://doi.org/10.1371/journal.pbio.0040105", doi = "10.1371/journal.pbio.0040105", openalex = "W2027133828" } @book{doi10478869781888569797, author = "U.S Geological Survey 12201 Sunrise Park Drive, MS-301 Reston, Virginia 20192 and Kolar, Cindy S. and Chapman, Duane and Courtenay, Walter R. and Housel, Christine M. and Williams, James D. and Jennings, Dawn P. and Fish, U.S. and Wildlife Service North Florida Field Office 6620 Southpoint Drive South, Suite 310 Jacksonville, Florida 32216-0958", title = "Bigheaded Carps: A Biological Synopsis and Environmental Risk Assessment", year = "2007", booktitle = "American Fisheries Society eBooks", url = "https://doi.org/10.47886/9781888569797", doi = "10.47886/9781888569797", openalex = "W64675103" } @article{openalexw2117551548, author = "Adams, William M. and Hutton, Jon", title = "People, Parks and Poverty: Political Ecology and Biodiversity Conservation", year = "2007", journal = "Digital Library Of The Commons Repository (Indiana University)", abstract = {"Action to conserve biodiversity, particularly through the creation of protected areas (PAs), is inherently political. Political ecology is a field of study that embraces the interactions between the way nature is understood and the politics and impacts of environmental action. This paper explores the political ecology of conservation, particularly the establishment of PAs. It discusses the implications of the idea of pristine nature, the social impacts of and the politics of PA establishment and the way the benefits and costs of PAs are allocated. It considers three key political issues in contemporary international conservation policy: the rights of indigenous people, the relationship between biodiversity conservation and the reduction of poverty, and the arguments of those advocating a return to conventional PAs that exclude people."}, openalex = "W2117551548", references = "doi101111j13669516200500143x, doi105860choice330904, openalexw1546506088" } @article{doi101073pnas0707823105, author = "Naidoo, Robin and Balmford, Andrew and Costanza, Robert and Fisher, Brendan and Green, R. E. and Lehner, Bernhard and Malcolm, Trent R. and Ricketts, Taylor H.", title = "Global mapping of ecosystem services and conservation priorities", year = "2008", journal = "Proceedings of the National Academy of Sciences", abstract = {Global efforts to conserve biodiversity have the potential to deliver economic benefits to people (i.e., "ecosystem services"). However, regions for which conservation benefits both biodiversity and ecosystem services cannot be identified unless ecosystem services can be quantified and valued and their areas of production mapped. Here we review the theory, data, and analyses needed to produce such maps and find that data availability allows us to quantify imperfect global proxies for only four ecosystem services. Using this incomplete set as an illustration, we compare ecosystem service maps with the global distributions of conventional targets for biodiversity conservation. Our preliminary results show that regions selected to maximize biodiversity provide no more ecosystem services than regions chosen randomly. Furthermore, spatial concordance among different services, and between ecosystem services and established conservation priorities, varies widely. Despite this lack of general concordance, "win-win" areas-regions important for both ecosystem services and biodiversity-can be usefully identified, both among ecoregions and at finer scales within them. An ambitious interdisciplinary research effort is needed to move beyond these preliminary and illustrative analyses to fully assess synergies and trade-offs in conserving biodiversity and ecosystem services.}, url = "https://doi.org/10.1073/pnas.0707823105", doi = "10.1073/pnas.0707823105", openalex = "W2027370059", references = "doi101111j15231739200600559x" } @article{doi101086586910, author = "Goldstein, Noah J. and Cialdini, Robert B. and Griskevicius, Vladas", title = "A Room with a Viewpoint: Using Social Norms to Motivate Environmental Conservation in Hotels", year = "2008", journal = "Journal of Consumer Research", abstract = "Abstract Two field experiments examined the effectiveness of signs requesting hotel guests' participation in an environmental conservation program. Appeals employing descriptive norms (e.g., “the majority of guests reuse their towels”) proved superior to a traditional appeal widely used by hotels that focused solely on environmental protection. Moreover, normative appeals were most effective when describing group behavior that occurred in the setting that most closely matched individuals' immediate situational circumstances (e.g., “the majority of guests in this room reuse their towels”), which we refer to as provincial norms. Theoretical and practical implications for managing proenvironmental efforts are discussed.", url = "https://doi.org/10.1086/586910", doi = "10.1086/586910", openalex = "W2130950828", references = "doi101016s0065260108603305, doi101086208911, doi101086209186, doi101086266996, doi101111j14679280200701917x, doi101146annurevpsych55090902142015, doi101177001872675400700202, doi1011770146167296228002, doi1023072089062, openalexw1871433632" } @article{doi101098rsbl20080118, author = "Ficetola, Gentile Francesco and Miaud, Claude and Pompanon, François and Taberlet, Pierre", title = "Species detection using environmental DNA from water samples", year = "2008", journal = "Biology Letters", abstract = "The assessment of species distribution is a first critical phase of biodiversity studies and is necessary to many disciplines such as biogeography, conservation biology and ecology. However, several species are difficult to detect, especially during particular time periods or developmental stages, potentially biasing study outcomes. Here we present a novel approach, based on the limited persistence of DNA in the environment, to detect the presence of a species in fresh water. We used specific primers that amplify short mitochondrial DNA sequences to track the presence of a frog (Rana catesbeiana) in controlled environments and natural wetlands. A multi-sampling approach allowed for species detection in all environments where it was present, even at low densities. The reliability of the results was demonstrated by the identification of amplified DNA fragments, using traditional sequencing and parallel pyrosequencing techniques. As the environment can retain the molecular imprint of inhabiting species, our approach allows the reliable detection of secretive organisms in wetlands without direct observation. Combined with massive sequencing and the development of DNA barcodes that enable species identification, this approach opens new perspectives for the assessment of current biodiversity from environmental samples.", url = "https://doi.org/10.1098/rsbl.2008.0118", doi = "10.1098/rsbl.2008.0118", openalex = "W2131545754", references = "doi101038nature03959, doi101046j14610248200100230x, doi101093nar24163189, doi101093nargkl938, doi101111j13652664200601227x, doi101126science1084114, doi101126science1093857, doi101126science28954821139b, doi105860choice421547, openalexw1513215516" } @article{doi101111j15231739200800937x, author = "Salafsky, Nick and Salzer, Daniel W. and Stattersfield, Alison J. and Hilton‐Taylor, Craig and Neugarten, Rachel and Butchart, Stuart H. M. and Collen, Ben and Cox, Neil A. and Master, Lawrence L. and O’Connor, Sheila and Wilkie, David", title = "A Standard Lexicon for Biodiversity Conservation: Unified Classifications of Threats and Actions", year = "2008", journal = "Conservation Biology", abstract = "An essential foundation of any science is a standard lexicon. Any given conservation project can be described in terms of the biodiversity targets, direct threats, contributing factors at the project site, and the conservation actions that the project team is employing to change the situation. These common elements can be linked in a causal chain, which represents a theory of change about how the conservation actions are intended to bring about desired project outcomes. If project teams want to describe and share their work and learn from one another, they need a standard and precise lexicon to specifically describe each node along this chain. To date, there have been several independent efforts to develop standard classifications for the direct threats that affect biodiversity and the conservation actions required to counteract these threats. Recognizing that it is far more effective to have only one accepted global scheme, we merged these separate efforts into unified classifications of threats and actions, which we present here. Each classification is a hierarchical listing of terms and associated definitions. The classifications are comprehensive and exclusive at the upper levels of the hierarchy, expandable at the lower levels, and simple, consistent, and scalable at all levels. We tested these classifications by applying them post hoc to 1191 threatened bird species and 737 conservation projects. Almost all threats and actions could be assigned to the new classification systems, save for some cases lacking detailed information. Furthermore, the new classification systems provided an improved way of analyzing and comparing information across projects when compared with earlier systems. We believe that widespread adoption of these classifications will help practitioners more systematically identify threats and appropriate actions, managers to more efficiently set priorities and allocate resources, and most important, facilitate cross-project learning and the development of a systematic science of conservation.", url = "https://doi.org/10.1111/j.1523-1739.2008.00937.x", doi = "10.1111/j.1523-1739.2008.00937.x", openalex = "W2068031289", references = "doi101111j15231739200600485x" } @article{doi101016jbiocon200902021, author = "Ribeiro, Milton Cézar and Metzger, Jean Paul and Martensen, Alexandre Camargo and Ponzoni, Flávio Jorge and Hirota, Márcia Makiko", title = "The Brazilian Atlantic Forest: How much is left, and how is the remaining forest distributed? Implications for conservation", year = "2009", journal = "Biological Conservation", url = "https://doi.org/10.1016/j.biocon.2009.02.021", doi = "10.1016/j.biocon.2009.02.021", openalex = "W2104462056", references = "doi101016jbiocon200602019, doi101111j14610248200701114x" } @article{doi101016jecolecon200911006, author = "Muradian, Roldán and Corbera, Esteve and Pascual, Unai and Kosoy, Nicolás and May, Peter H.", title = "Reconciling theory and practice: An alternative conceptual framework for understanding payments for environmental services", year = "2009", journal = "Ecological Economics", url = "https://doi.org/10.1016/j.ecolecon.2009.11.006", doi = "10.1016/j.ecolecon.2009.11.006", openalex = "W2117386630", references = "doi101111j15231739200600559x" } @article{doi101007s1066101015825, author = "Conrad, Cathy and Hilchey, Krista G.", title = "A review of citizen science and community-based environmental monitoring: issues and opportunities", year = "2010", journal = "Environmental Monitoring and Assessment", url = "https://doi.org/10.1007/s10661-010-1582-5", doi = "10.1007/s10661-010-1582-5", openalex = "W2152608856" } @article{doi101037a0017346, author = "Griskevicius, Vladas and Tybur, Joshua M. and den Bergh, Bram Van", title = "Going green to be seen: Status, reputation, and conspicuous conservation.", year = "2010", journal = "Journal of Personality and Social Psychology", abstract = {Why do people purchase proenvironmental "green" products? We argue that buying such products can be construed as altruistic, since green products often cost more and are of lower quality than their conventional counterparts, but green goods benefit the environment for everyone. Because biologists have observed that altruism might function as a "costly signal" associated with status, we examined in 3 experiments how status motives influenced desire for green products. Activating status motives led people to choose green products over more luxurious nongreen products. Supporting the notion that altruism signals one's willingness and ability to incur costs for others' benefit, status motives increased desire for green products when shopping in public (but not private) and when green products cost more (but not less) than nongreen products. Findings suggest that status competition can be used to promote proenvironmental behavior.}, url = "https://doi.org/10.1037/a0017346", doi = "10.1037/a0017346", openalex = "W2157399030", references = "doi101086586910, doi101111j154045601994tb02420x" } @article{doi101093reepreq006, author = "Pattanayak, Subhrendu K. and Wunder, Sven and Ferraro, Paul J.", title = "Show Me the Money: Do Payments Supply Environmental Services in Developing Countries?", year = "2010", journal = "Review of Environmental Economics and Policy", abstract = "Many of the services supplied by nature are externalities. Economic theory suggests that some form of subsidy or contracting between the beneficiaries and the providers could result in an optimal supply of environmental services. Moreover, if the poor own resources that give them a comparative advantage in the supply of environmental services, then payments for environmental services (PES) can improve environmental and poverty outcomes. While the theory is relatively straightforward, the practice is not, particularly in developing countries where institutions are weak. This article reviews the empirical literature on PES additionality by asking, “Do payments deliver environmental services, everything else being equal, or, at least, the land-use changes believed to generate environmental services?” We examine both qualitative case studies and rigorous econometric quasi-experimental analyses. We find that government-coordinated PES have caused modest or no reversal of deforestation. Case studies of smaller-scale, user-financed PES schemes claim more substantial impacts, but few of these studies eliminate rival explanations for the positive effects. We conclude by discussing how the dearth of evidence about PES impacts, and unanswered questions about institutional preconditions and motivational “crowding out,” limit the prospects for using international carbon payments to reduce emissions from deforestation and degradation.", url = "https://doi.org/10.1093/reep/req006", doi = "10.1093/reep/req006", openalex = "W2157805396", references = "doi101111j15231739200600559x" } @article{doi101126science1194442, author = "Hoffmann, Michael and Hilton‐Taylor, Craig and Angulo, Ariadne and Böhm, Monika and Brooks, Thomas M. and Butchart, Stuart H. M. and Carpenter, Kent E. and Chanson, Janice and Collen, Ben and Cox, Neil A. and Darwall, William and Dulvy, Nicholas K. and Harrison, Lucy R. and Katariya, Vineet and Pollock, Caroline M. and Quader, Suhel and Richman, Nadia I. and Rodrigues, Ana S. L. and Tognelli, Marcelo F. and Vié, Jean-Christophe and Aguiar, John M. and Allen, David J. and Allen, Gerald R. and Amori, Giovanni and Ananjeva, Natalia B. and Andreone, Franco and Andrew, Paul and Ortiz, Aida Luz Aquino and Baillie, Jonathan and Baldi, Ricardo and Bell, Ben D. and Biju, S. D. and Bird, Jeremy P. and Black‐Décima, Patricia and Blanc, Julian and Bolaños, Federico and Bolívar-G, Wilmar and Burfield, Ian J. and Burton, James and Capper, David R. and Castro‐Herrera, Fernando and Catullo, Gianluca and Cavanagh, Rachel D. and Channing, Alan and Chao, Ning Labbish and Chenery, Anna M. and Chiozza, Federica and Clausnitzer, Viola and Collar, Nigel and Collett, Leah and Collette, Bruce B. and Fernández, Claudia Fabiola Cortez and Craig, Matthew T. and Crosby, Michael J. and Cumberlidge, Neil and Cuttelod, Annabelle and Derocher, Andrew E. and Diesmos, Arvin C. and Donaldson, John S. and Duckworth, J. W. and Dutson, Guy and Dutta, Sushil Kumar and Emslie, R.H. and Farjon, Aljos and Fowler, Sarah and Freyhof, Jörg and Garshelis, David L. and Gerlach, Justin and Gower, David J. and Grant, Tandora D. and Hammerson, Geoffrey A. and Harris, Richard B. and Heaney, Lawrence R. and Hedges, S. Blair and Hero, Jean‐Marc and Hughes, Baz and Hussain, Syed Ainul and M., Javier Icochea and Inger, Robert F. and Ishii, Nobuo and Iskandar, Djoko T. and Jenkins, Richard K. B. and Kaneko, Yoshio and Kottelat, Maurice and Kovacs, Kit M. and Kuzmin, Sergius L. and Marca, Enrique La and Lamoreux, John F. and Lau, Michael and Lavilla, Esteban O. and Leus, Kristin and Lewison, Rebecca L. and Lichtenstein, Gabriela and Livingstone, Suzanne R. and Lukoschek, Vimoksalehi and Mallon, David and McGowan, Philip J.K. and McIvor, Anna and Moehlman, Patricia D. and Molur, Sanjay", title = "The Impact of Conservation on the Status of the World’s Vertebrates", year = "2010", journal = "Science", abstract = "Using data for 25,780 species categorized on the International Union for Conservation of Nature Red List, we present an assessment of the status of the world's vertebrates. One-fifth of species are classified as Threatened, and we show that this figure is increasing: On average, 52 species of mammals, birds, and amphibians move one category closer to extinction each year. However, this overall pattern conceals the impact of conservation successes, and we show that the rate of deterioration would have been at least one-fifth again as much in the absence of these. Nonetheless, current conservation efforts remain insufficient to offset the main drivers of biodiversity loss in these groups: agricultural expansion, logging, overexploitation, and invasive alien species.", url = "https://doi.org/10.1126/science.1194442", doi = "10.1126/science.1194442", openalex = "W2111760270", references = "doi101098rsbl20070292, doi101111j15231739200801044x, doi1023071223169" } @article{doi101111j1365294x201105418x, author = "Thomsen, Philip Francis and Kielgast, Jos and Iversen, Lars and Wiuf, Carsten and Rasmussen, Morten and Gilbert, M. Thomas P. and Orlando, Ludovic and Willerslev, Eske", title = "Monitoring endangered freshwater biodiversity using environmental DNA", year = "2011", journal = "Molecular Ecology", abstract = "Freshwater ecosystems are among the most endangered habitats on Earth, with thousands of animal species known to be threatened or already extinct. Reliable monitoring of threatened organisms is crucial for data-driven conservation actions but remains a challenge owing to nonstandardized methods that depend on practical and taxonomic expertise, which is rapidly declining. Here, we show that a diversity of rare and threatened freshwater animals--representing amphibians, fish, mammals, insects and crustaceans--can be detected and quantified based on DNA obtained directly from small water samples of lakes, ponds and streams. We successfully validate our findings in a controlled mesocosm experiment and show that DNA becomes undetectable within 2 weeks after removal of animals, indicating that DNA traces are near contemporary with presence of the species. We further demonstrate that entire faunas of amphibians and fish can be detected by high-throughput sequencing of DNA extracted from pond water. Our findings underpin the ubiquitous nature of DNA traces in the environment and establish environmental DNA as a tool for monitoring rare and threatened species across a wide range of taxonomic groups.", url = "https://doi.org/10.1111/j.1365-294x.2011.05418.x", doi = "10.1111/j.1365-294x.2011.05418.x", openalex = "W2163290397", references = "doi101017s1464793105006950, doi101038362709a0, doi101038nature09678, doi101038nrg2626, doi101098rsbl20080118, doi101111j1755263x201000158x, doi101126science2695222347, doi101126science28754591770, doi101186147121051238, doi105860choice496872" } @article{doi101111j1755263x201000158x, author = "Jerde, Christopher L. and Mahon, Andrew R. and Chadderton, W. Lindsay and Lodge, David M.", title = "“Sight‐unseen” detection of rare aquatic species using environmental DNA", year = "2011", journal = "Conservation Letters", abstract = "Abstract Effective management of rare species, including endangered native species and recently introduced nonindigenous species, requires the detection of populations at low density. For endangered species, detecting the localized distribution makes it possible to identify and protect critical habitat to enhance survival or reproductive success. Similarly, early detection of an incipient invasion by a harmful species increases the feasibility of rapid responses to eradicate the species or contain its spread. Here we demonstrate the efficacy of environmental DNA (eDNA) as a detection tool in freshwater environments. Specifically, we delimit the invasion fronts of two species of Asian carps in Chicago, Illinois, USA area canals and waterways. Quantitative comparisons with traditional fisheries surveillance tools illustrate the greater sensitivity of eDNA and reveal that the risk of invasion to the Laurentian Great Lakes is imminent.", url = "https://doi.org/10.1111/j.1755-263x.2010.00158.x", doi = "10.1111/j.1755-263x.2010.00158.x", openalex = "W1552342091", references = "doi101007s1053000481226, doi101016jtree200502004, doi101016s0006320703001903, doi101093bibbbn017, doi101098rsbl20080118, doi101098rspb20022179, doi101111j17550998200902699x, doi1018901051076120060162035birfup20co2, doi10478869781888569797, openalexw2946440777" } @article{doi101002job1820, author = "Robertson, Jennifer L. and Barling, Julian", title = "Greening organizations through leaders' influence on employees' pro‐environmental behaviors", year = "2012", journal = "Journal of Organizational Behavior", url = "https://doi.org/10.1002/job.1820", doi = "10.1002/job.1820", openalex = "W2162310951", references = "doi101016jjenvp200612002, doi10108013504620220145401, doi101086586910" } @article{doi101080104557522012674149, author = "Büscher, Bram and Sullivan, Sian and Neves, Katja and Igoe, Jim and Brockington, Dan", title = "Towards a Synthesized Critique of Neoliberal Biodiversity Conservation", year = "2012", journal = "Capitalism Nature Socialism", abstract = "Duffy (", url = "https://doi.org/10.1080/10455752.2012.674149", doi = "10.1080/10455752.2012.674149", openalex = "W2095184253", references = "doi101016s0016718502000891, openalexw1497677346" } @article{doi101371journalpone0035868, author = "Takahara, Teruhiko and Minamoto, Toshifumi and Yamanaka, Hiroki and Doi, Hideyuki and Kawabata, Zen’ichiro", title = "Estimation of Fish Biomass Using Environmental DNA", year = "2012", journal = "PLoS ONE", abstract = "Environmental DNA (eDNA) from aquatic vertebrates has recently been used to estimate the presence of a species. We hypothesized that fish release DNA into the water at a rate commensurate with their biomass. Thus, the concentration of eDNA of a target species may be used to estimate the species biomass. We developed an eDNA method to estimate the biomass of common carp (Cyprinus carpio L.) using laboratory and field experiments. In the aquarium, the concentration of eDNA changed initially, but reached an equilibrium after 6 days. Temperature had no effect on eDNA concentrations in aquaria. The concentration of eDNA was positively correlated with carp biomass in both aquaria and experimental ponds. We used this method to estimate the biomass and distribution of carp in a natural freshwater lagoon. We demonstrated that the distribution of carp eDNA concentration was explained by water temperature. Our results suggest that biomass data estimated from eDNA concentration reflects the potential distribution of common carp in the natural environment. Measuring eDNA concentration offers a non-invasive, simple, and rapid method for estimating biomass. This method could inform management plans for the conservation of ecosystems.", url = "https://doi.org/10.1371/journal.pone.0035868", doi = "10.1371/journal.pone.0035868", openalex = "W2063726689", references = "doi101111j13652427200601592x" } @article{doi101371journalpone0041732, author = "Thomsen, Philip Francis and Kielgast, Jos and Iversen, Lars and Møller, Peter Rask and Rasmussen, Morten and Willerslev, Eske", title = "Detection of a Diverse Marine Fish Fauna Using Environmental DNA from Seawater Samples", year = "2012", journal = "PLoS ONE", abstract = "Marine ecosystems worldwide are under threat with many fish species and populations suffering from human over-exploitation. This is greatly impacting global biodiversity, economy and human health. Intriguingly, marine fish are largely surveyed using selective and invasive methods, which are mostly limited to commercial species, and restricted to particular areas with favourable conditions. Furthermore, misidentification of species represents a major problem. Here, we investigate the potential of using metabarcoding of environmental DNA (eDNA) obtained directly from seawater samples to account for marine fish biodiversity. This eDNA approach has recently been used successfully in freshwater environments, but never in marine settings. We isolate eDNA from ½-litre seawater samples collected in a temperate marine ecosystem in Denmark. Using next-generation DNA sequencing of PCR amplicons, we obtain eDNA from 15 different fish species, including both important consumption species, as well as species rarely or never recorded by conventional monitoring. We also detect eDNA from a rare vagrant species in the area; European pilchard (Sardina pilchardus). Additionally, we detect four bird species. Records in national databases confirmed the occurrence of all detected species. To investigate the efficiency of the eDNA approach, we compared its performance with 9 methods conventionally used in marine fish surveys. Promisingly, eDNA covered the fish diversity better than or equal to any of the applied conventional methods. Our study demonstrates that even small samples of seawater contain eDNA from a wide range of local fish species. Finally, in order to examine the potential dispersal of eDNA in oceans, we performed an experiment addressing eDNA degradation in seawater, which shows that even small (100-bp) eDNA fragments degrades beyond detectability within days. Although further studies are needed to validate the eDNA approach in varying environmental conditions, our findings provide a strong proof-of-concept with great perspectives for future monitoring of marine biodiversity and resources.", url = "https://doi.org/10.1371/journal.pone.0041732", doi = "10.1371/journal.pone.0041732", openalex = "W2039133821", references = "doi101111j1365294x201105418x, doi101111j1755263x201000158x, doi105860choice501469" } @article{doi101016jgloenvcha201305014, author = "Klöckner, Christian A.", title = "A comprehensive model of the psychology of environmental behaviour—A meta-analysis", year = "2013", journal = "Global Environmental Change", url = "https://doi.org/10.1016/j.gloenvcha.2013.05.014", doi = "10.1016/j.gloenvcha.2013.05.014", openalex = "W2056753197", references = "doi101016jjenvp200612002, doi101086586910, doi1011110022453700175, doi101111j154045601994tb02420x" } @article{doi101139cjfas20130047, author = "Pilliod, David S. and Goldberg, Caren S. and Arkle, Robert S. and Waits, Lisette P.", title = "Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples", year = "2013", journal = "Canadian Journal of Fisheries and Aquatic Sciences", abstract = "Environmental DNA (eDNA) methods for detecting aquatic species are advancing rapidly, but with little evaluation of field protocols or precision of resulting estimates. We compared sampling results from traditional field methods with eDNA methods for two amphibians in 13 streams in central Idaho, USA. We also evaluated three water collection protocols and the influence of sampling location, time of day, and distance from animals on eDNA concentration in the water. We found no difference in detection or amount of eDNA among water collection protocols. eDNA methods had slightly higher detection rates than traditional field methods, particularly when species occurred at low densities. eDNA concentration was positively related to field-measured density, biomass, and proportion of transects occupied. Precision of eDNA-based abundance estimates increased with the amount of eDNA in the water and the number of replicate subsamples collected. eDNA concentration did not vary significantly with sample location in the stream, time of day, or distance downstream from animals. Our results further advance the implementation of eDNA methods for monitoring aquatic vertebrates in stream habitats.", url = "https://doi.org/10.1139/cjfas-2013-0047", doi = "10.1139/cjfas-2013-0047", openalex = "W2000256327", references = "doi101016jbiocon201411019, doi101016jbiocon201411038, doi101021es404734p, doi101098rsbl20080118, doi1011111365266412306, doi101111j1365294x201105418x, doi101111j1755263x201000158x, doi101371journalpone0035868, openalexw2054580376" } @article{doi102458v20i121748, author = "Vaccaro, Ismael and Beltrán, Oriol and Paquet, Pierre", title = "Political ecology and conservation policies: some theoretical genealogies", year = "2013", journal = "Journal of Political Ecology", abstract = "This article explicitly connects a growing body of specific literature, the political ecology of conservation, to some of the often overlooked, main conceptual components emerging from political anthropology and geography (sources of legitimacy, governmentality, territoriality, or state making), political economy (commoditization, market integration, niche markets, or gentrification), and cultural studies of the environment (cultural transformations of nature, cultural heritage and landscapes, taste, and identity politics). All these concepts and literary fields are at the basis of the contemporary social analysis of conservation policies and their consequences. The article also provides an updated large bibliography on the concepts potentially relevant to a political ecology of conservation.", url = "https://doi.org/10.2458/v20i1.21748", doi = "10.2458/v20i1.21748", openalex = "W2781593193", references = "openalexw1497677346" } @article{doi101016jbiocon201411019, author = "Thomsen, Philip Francis and Willerslev, Eske", title = "Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity", year = "2014", journal = "Biological Conservation", abstract = "The continuous decline in Earth’s biodiversity represents a major crisis and challenge for the 21st century, and there is international political agreement to slow down or halt this decline. The challenge is in large part impeded by the lack of knowledge on the state and distribution of biodiversity – especially since the majority of species on Earth are un-described by science. All conservation efforts to save biodiversity essentially depend on the monitoring of species and populations to obtain reliable distribution patterns and population size estimates. Such monitoring has traditionally relied on physical identification of species by visual surveys and counting of individuals. However, traditional monitoring techniques remain problematic due to difficulties associated with correct identification of cryptic species or juvenile life stages, a continuous decline in taxonomic expertise, non-standardized sampling, and the invasive nature of some survey techniques. Hence, there is urgent need for alternative and efficient techniques for large-scale biodiversity monitoring. Environmental DNA (eDNA) – defined here as: genetic material obtained directly from environmental samples (soil, sediment, water, etc.) without any obvious signs of biological source material – is an efficient, non-invasive and easy-to-standardize sampling approach. Coupled with sensitive, cost-efficient and ever-advancing DNA sequencing technology, it may be an appropriate candidate for the challenge of biodiversity monitoring. Environmental DNA has been obtained from ancient as well as modern samples and encompasses single species detection to analyses of ecosystems. The research on eDNA initiated in microbiology, recognizing that culture-based methods grossly misrepresent the microbial diversity in nature. Subsequently, as a method to assess the diversity of macro-organismal communities, eDNA was first analyzed in sediments, revealing DNA from extinct and extant animals and plants, but has since been obtained from various terrestrial and aquatic environmental samples. Results from eDNA approaches have provided valuable insights to the study of ancient environments and proven useful for monitoring contemporary biodiversity in terrestrial and aquatic ecosystems. In the future, we expect the eDNA-based approaches to move from single-marker analyses of species or communities to meta-genomic surveys of entire ecosystems to predict spatial and temporal biodiversity patterns. Such advances have applications for a range of biological, geological and environmental sciences. Here we review the achievements gained through analyses of eDNA from macro-organisms in a conservation context, and discuss its potential advantages and limitations for biodiversity monitoring.", url = "https://doi.org/10.1016/j.biocon.2014.11.019", doi = "10.1016/j.biocon.2014.11.019", openalex = "W2063580733", references = "doi101038nature09678, doi101038nature10574, doi101038nature12921, doi101038nmethf303, doi101073pnas0507535103, doi101073pnas0605127103, doi101073pnas1117018109, doi101098rsbl20080118, doi101098rspb20022218, doi101111j1365294x201105418x, doi101111j1365294x201205537x, doi101111j1755263x201000158x, doi101126science1093857, doi101126science1187512, doi101126science1251817, doi101139cjfas20130047, doi101371journalpone0059520, doi101373clinchem2008112797" } @article{doi101016jtree201404003, author = "Bohmann, Kristine and Evans, Alice and Gilbert, M. Thomas P. and Carvalho, Gary R. and Creer, Simon and Knapp, Michael and Yu, Douglas W. and de Bruyn, Mark", title = "Environmental DNA for wildlife biology and biodiversity monitoring", year = "2014", journal = "Trends in Ecology \& Evolution", url = "https://doi.org/10.1016/j.tree.2014.04.003", doi = "10.1016/j.tree.2014.04.003", openalex = "W1979060637", references = "doi101016jtree200809011, doi101038362709a0, doi101038nature12921, doi101038nrmicro2832, doi101098rsbl20030025, doi101098rsbl20080118, doi101111j1365294x201105403x, doi101111j1365294x201105418x, doi101111j1365294x201205470x, doi101111j1365294x201205537x, doi101111j1755263x201000158x, doi101371journalpone0059520" } @article{doi101021es404734p, author = "Barnes, Matthew A. and Turner, Cameron R. and Jerde, Christopher L. and Renshaw, Mark A. and Chadderton, W. Lindsay and Lodge, David M.", title = "Environmental Conditions Influence eDNA Persistence in Aquatic Systems", year = "2014", journal = "Environmental Science \& Technology", abstract = "Environmental DNA (eDNA) surveillance holds great promise for improving species conservation and management. However, few studies have investigated eDNA dynamics under natural conditions, and interpretations of eDNA surveillance results are clouded by uncertainties about eDNA degradation. We conducted a literature review to assess current understanding of eDNA degradation in aquatic systems and an experiment exploring how environmental conditions can influence eDNA degradation. Previous studies have reported macrobial eDNA persistence ranging from less than 1 day to over 2 weeks, with no attempts to quantify factors affecting degradation. Using a SYBR Green quantitative PCR assay to observe Common Carp (Cyprinus carpio) eDNA degradation in laboratory mesocosms, our rate of Common Carp eDNA detection decreased over time. Common Carp eDNA concentration followed a pattern of exponential decay, and observed decay rates exceeded previously published values for aquatic macrobial eDNA. Contrary to our expectations, eDNA degradation rate declined as biochemical oxygen demand, chlorophyll, and total eDNA (i.e., from any organism) concentration increased. Our results help explain the widely divergent, previously published estimates for eDNA degradation. Measurements of local environmental conditions, consideration of environmental influence on eDNA detection, and quantification of local eDNA degradation rates will help interpret future eDNA surveillance results.", url = "https://doi.org/10.1021/es404734p", doi = "10.1021/es404734p", openalex = "W2329540589", references = "doi101139cjfas20130047" } @article{doi1011111365266412306, author = "Rees, Helen C. and Maddison, Ben C. and Middleditch, David J. and Patmore, James R. M. and Gough, Kevin C.", title = "REVIEW: The detection of aquatic animal species using environmental DNA – a review of eDNA as a survey tool in ecology", year = "2014", journal = "Journal of Applied Ecology", abstract = "Summary Knowledge of species distribution is critical to ecological management and conservation biology. Effective management requires the detection of populations, which can sometimes be at low densities and is usually based on visual detection and counting. Recently, there has been considerable interest in the detection of short species‐specific environmental DNA (e DNA) fragments to allow aquatic species monitoring within different environments due to the potential of greater sensitivity over traditional survey methods which can be time‐consuming and costly. Environmental DNA analysis is increasingly being used in the detection of rare or invasive species and has also been applied to e DNA persistence studies and estimations of species biomass and distribution. When combined with next‐generation sequencing methods, it has been demonstrated that entire faunas can be identified. Different environments require different sampling methodologies, but there remain areas where laboratory methodologies could be standardized to allow results to be compared across studies. Synthesis and applications. We review recently published studies that use e DNA to monitor aquatic populations, discuss the methodologies used and the application of e DNA analysis as a survey tool in ecology. We include innovative ideas for how e DNA can be used for conservation and management citing test cases, for instance, the potential for on‐site analyses, including the application of e DNA analysis to carbon nanotube platforms or laser transmission spectroscopy to facilitate rapid on‐site detections. The use of e DNA monitoring is already being adopted in the UK for ecological surveys.", url = "https://doi.org/10.1111/1365-2664.12306", doi = "10.1111/1365-2664.12306", openalex = "W2088695664", references = "doi101093nar24163189, doi101111j13652427200601592x, doi101111j1365294x201105418x, doi101111j1755263x201000158x, doi101139cjfas20130047, doi101371journalpone0059520" } @article{doi101371journalpone0088786, author = "Deiner, Kristy and Altermatt, Florian", title = "Transport Distance of Invertebrate Environmental DNA in a Natural River", year = "2014", journal = "PLoS ONE", abstract = "Environmental DNA (eDNA) monitoring is a novel molecular technique to detect species in natural habitats. Many eDNA studies in aquatic systems have focused on lake or ponds, and/or on large vertebrate species, but applications to invertebrates in river systems are emerging. A challenge in applying eDNA monitoring in flowing waters is that a species' DNA can be transported downstream. Whether and how far eDNA can be detected due to downstream transport remains largely unknown. In this study we tested for downstream detection of eDNA for two invertebrate species, Daphnia longispina and Unio tumidus, which are lake dwelling species in our study area. The goal was to determine how far away from the source population in a lake their eDNA could be detected in an outflowing river. We sampled water from eleven river sites in regular intervals up to 12.3 km downstream of the lake, developed new eDNA probes for both species, and used a standard PCR and Sanger sequencing detection method to confirm presence of each species' eDNA in the river. We detected D. longispina at all locations and across two time points (July and October); whereas with U. tumidus, we observed a decreased detection rate and did not detect its eDNA after 9.1 km. We also observed a difference in detection for this species at different times of year. The observed movement of eDNA from the source amounting to nearly 10 km for these species indicates that the resolution of an eDNA sample can be large in river systems. Our results indicate that there may be species' specific transport distances for eDNA and demonstrate for the first time that invertebrate eDNA can persist over relatively large distances in a natural river system.", url = "https://doi.org/10.1371/journal.pone.0088786", doi = "10.1371/journal.pone.0088786", openalex = "W2093478636", references = "doi101139cjfas20130047, doi101371journalpone0059520" } @article{doi107554elife00590, author = "Dulvy, Nicholas K. and Fowler, Sarah and Musick, John A. and Cavanagh, Rachel D. and Kyne, Peter M. and Harrison, Lucy R. and Carlson, John K. and Davidson, Lindsay N. K. and Fordham, Sonja V. and Francis, Malcolm P. and Pollock, Caroline M. and Simpfendorfer, Colin A. and Burgess, George H. and Carpenter, Kent E. and Compagno, Leonard J. V. and Ebert, David A. and Gibson, Claudine and Heupel, Michelle R. and Livingstone, Suzanne R. and Sanciangco, Jonnell C. and Stevens, John D. and Valenti, Sarah and White, William T.", title = "Extinction risk and conservation of the world’s sharks and rays", year = "2014", journal = "eLife", abstract = "The rapid expansion of human activities threatens ocean-wide biodiversity. Numerous marine animal populations have declined, yet it remains unclear whether these trends are symptomatic of a chronic accumulation of global marine extinction risk. We present the first systematic analysis of threat for a globally distributed lineage of 1,041 chondrichthyan fishes-sharks, rays, and chimaeras. We estimate that one-quarter are threatened according to IUCN Red List criteria due to overfishing (targeted and incidental). Large-bodied, shallow-water species are at greatest risk and five out of the seven most threatened families are rays. Overall chondrichthyan extinction risk is substantially higher than for most other vertebrates, and only one-third of species are considered safe. Population depletion has occurred throughout the world's ice-free waters, but is particularly prevalent in the Indo-Pacific Biodiversity Triangle and Mediterranean Sea. Improved management of fisheries and trade is urgently needed to avoid extinctions and promote population recovery. DOI: http://dx.doi.org/10.7554/eLife.00590.001.", url = "https://doi.org/10.7554/elife.00590", doi = "10.7554/elife.00590", openalex = "W2105316344", references = "doi101017s0376892909990191, doi101111j13652486200902128x, doi101111j15231739200801044x, doi101126science1103538, doi101126science1187512" } @article{doi101007s1059201507754, author = "Barnes, Matthew A. and Turner, Cameron R.", title = "The ecology of environmental DNA and implications for conservation genetics", year = "2015", journal = "Conservation Genetics", abstract = "Environmental DNA (eDNA) refers to the genetic material that can be extracted from bulk environmental samples such as soil, water, and even air. The rapidly expanding study of eDNA has generated unprecedented ability to detect species and conduct genetic analyses for conservation, management, and research, particularly in scenarios where collection of whole organisms is impractical or impossible. While the number of studies demonstrating successful eDNA detection has increased rapidly in recent years, less research has explored the ''ecology'' of eDNA-myriad interactions between extraorganismal genetic material and its environment-and its influence on eDNA detection, quantification, analysis, and application to conservation and research. Here, we outline a framework for understanding the ecology of eDNA, including the origin, state, transport, and fate of extraorganismal genetic material. Using this framework, we review and synthesize the findings of eDNA studies from diverse environments, taxa, and fields of study to highlight important concepts and knowledge gaps in eDNA study and application. Additionally, we identify frontiers of conservation-focused eDNA application where we see the most potential for growth, including the use of eDNA for estimating population size, population genetic and genomic analyses via eDNA, inclusion of other indicator biomolecules such as environmental RNA or proteins, automated sample collection and analysis, and consideration of an expanded array of creative environmental samples. We discuss how a more complete understanding of the ecology of eDNA is integral to advancing these frontiers and maximizing the potential of future eDNA applications in conservation and research.", url = "https://doi.org/10.1007/s10592-015-0775-4", doi = "10.1007/s10592-015-0775-4", openalex = "W1815195908", references = "doi101016jbiocon201411019, doi101016jtree201404003, doi101038362709a0, doi101093bioinformaticsbtv401, doi101098rsbl20080118, doi101111j1365294x201105418x, doi101111j1365294x201205505x, doi101111j1755263x201000158x, doi101139cjfas20130047, doi101146annurevanimal090414014900, doi101371journalpone0027310, doi101371journalpone0059520, doi10261816153922fe919c" } @article{doi101016jtree201511005, author = "Socolar, Jacob B. and Gilroy, James J. and Kunin, William E. and Edwards, David P.", title = "How Should Beta-Diversity Inform Biodiversity Conservation?", year = "2015", journal = "Trends in Ecology \& Evolution", url = "https://doi.org/10.1016/j.tree.2015.11.005", doi = "10.1016/j.tree.2015.11.005", openalex = "W2216692843", references = "doi101111j14610248201101628x, doi101126science1251817" } @article{doi101098rsos150088, author = "Miya, Masaki and Sato, Yukuto and Fukunaga, Tsukasa and Sado, Tetsuya and Poulsen, Jan Yde and Sato, Keiichi and Minamoto, Toshifumi and Yamamoto, Satoshi and Yamanaka, Hiroki and Araki, Hitoshi and Kondoh, Michio and Iwasaki, Wataru", title = "MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species", year = "2015", journal = "Royal Society Open Science", abstract = "We developed a set of universal PCR primers (MiFish-U/E) for metabarcoding environmental DNA (eDNA) from fishes. Primers were designed using aligned whole mitochondrial genome (mitogenome) sequences from 880 species, supplemented by partial mitogenome sequences from 160 elasmobranchs (sharks and rays). The primers target a hypervariable region of the 12S rRNA gene (163-185 bp), which contains sufficient information to identify fishes to taxonomic family, genus and species except for some closely related congeners. To test versatility of the primers across a diverse range of fishes, we sampled eDNA from four tanks in the Okinawa Churaumi Aquarium with known species compositions, prepared dual-indexed libraries and performed paired-end sequencing of the region using high-throughput next-generation sequencing technologies. Out of the 180 marine fish species contained in the four tanks with reference sequences in a custom database, we detected 168 species (93.3\%) distributed across 59 families and 123 genera. These fishes are not only taxonomically diverse, ranging from sharks and rays to higher teleosts, but are also greatly varied in their ecology, including both pelagic and benthic species living in shallow coastal to deep waters. We also sampled natural seawaters around coral reefs near the aquarium and detected 93 fish species using this approach. Of the 93 species, 64 were not detected in the four aquarium tanks, rendering the total number of species detected to 232 (from 70 families and 152 genera). The metabarcoding approach presented here is non-invasive, more efficient, more cost-effective and more sensitive than the traditional survey methods. It has the potential to serve as an alternative (or complementary) tool for biodiversity monitoring that revolutionizes natural resource management and ecological studies of fish communities on larger spatial and temporal scales.", url = "https://doi.org/10.1098/rsos.150088", doi = "10.1098/rsos.150088", openalex = "W2254267781", references = "doi101016jbiocon201411019, doi101093bibbbn013, doi101093bioinformaticsbtq461, doi101093bioinformaticsbtr507, doi101093nargkm234, doi101093nargkp1137, doi101098rsbl20080118, doi101098rspb20042813, doi101111j1365294x201105418x, doi101111j1365294x201205470x, doi101111j1755263x201000158x, doi1011861471210510421, doi1011861471210511485, doi101371journalpone0059520" } @article{doi101111cobi12536, author = "Batáry, Péter and Dicks, Lynn V. and Kleijn, David and Sutherland, William J.", title = "The role of agri‐environment schemes in conservation and environmental management", year = "2015", journal = "Conservation Biology", abstract = "Over half of the European landscape is under agricultural management and has been for millennia. Many species and ecosystems of conservation concern in Europe depend on agricultural management and are showing ongoing declines. Agri-environment schemes (AES) are designed partly to address this. They are a major source of nature conservation funding within the European Union (EU) and the highest conservation expenditure in Europe. We reviewed the structure of current AES across Europe. Since a 2003 review questioned the overall effectiveness of AES for biodiversity, there has been a plethora of case studies and meta-analyses examining their effectiveness. Most syntheses demonstrate general increases in farmland biodiversity in response to AES, with the size of the effect depending on the structure and management of the surrounding landscape. This is important in the light of successive EU enlargement and ongoing reforms of AES. We examined the change in effect size over time by merging the data sets of 3 recent meta-analyses and found that schemes implemented after revision of the EU's agri-environmental programs in 2007 were not more effective than schemes implemented before revision. Furthermore, schemes aimed at areas out of production (such as field margins and hedgerows) are more effective at enhancing species richness than those aimed at productive areas (such as arable crops or grasslands). Outstanding research questions include whether AES enhance ecosystem services, whether they are more effective in agriculturally marginal areas than in intensively farmed areas, whether they are more or less cost-effective for farmland biodiversity than protected areas, and how much their effectiveness is influenced by farmer training and advice? The general lesson from the European experience is that AES can be effective for conserving wildlife on farmland, but they are expensive and need to be carefully designed and targeted.", url = "https://doi.org/10.1111/cobi.12536", doi = "10.1111/cobi.12536", openalex = "W1594129108", references = "doi101016jjenvman200907005, doi101038nature10452, doi101046j13652664200200695x, doi101098rstb20100143, doi101111j13652664200300868x, doi101111j13652664200501005x, doi101111j14610248200801255x, doi1018637jssv036i03, doi1023071164953, doi1023072531069" } @article{doi101111mec13428, author = "Valentini, Alice and Taberlet, Pierre and Miaud, Claude and Civade, Raphaël and Herder, Jelger and Thomsen, Philip Francis and Bellemain, Eva and Besnard, Aurélien and Coissac, Éric and Boyer, Frédéric and Gaboriaud, Coline and Jean, Pauline and Poulet, Nicolas and Roset, Nicolas and Copp, Gordon H. and Géniez, Philippe and Pont, Didier and Argillier, Christine and Baudoin, Jean‐Marc and Peroux, Tiphaine and Crivellì, Alain J. and Olivier, Anthony and Acqueberge, Manon and Brun, Matthieu Le and Møller, Peter Rask and Willerslev, Eske and Déjean, Tony", title = "Next‐generation monitoring of aquatic biodiversity using environmental DNA metabarcoding", year = "2015", journal = "Molecular Ecology", abstract = "Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for rare and secretive species, are important for efficient and timely management. Recent advances in DNA sequencing have provided a new tool for species detection from DNA present in the environment. In this study, we tested whether an environmental DNA (eDNA) metabarcoding approach, using water samples, can be used for addressing significant questions in ecology and conservation. Two key aquatic vertebrate groups were targeted: amphibians and bony fish. The reliability of this method was cautiously validated in silico, in vitro and in situ. When compared with traditional surveys or historical data, eDNA metabarcoding showed a much better detection probability overall. For amphibians, the detection probability with eDNA metabarcoding was 0.97 (CI = 0.90-0.99) vs. 0.58 (CI = 0.50-0.63) for traditional surveys. For fish, in 89\% of the studied sites, the number of taxa detected using the eDNA metabarcoding approach was higher or identical to the number detected using traditional methods. We argue that the proposed DNA-based approach has the potential to become the next-generation tool for ecological studies and standardized biodiversity monitoring in a wide range of aquatic ecosystems.", url = "https://doi.org/10.1111/mec.13428", doi = "10.1111/mec.13428", openalex = "W2171100005", references = "doi101016jbiocon201411019, doi101038nature09678, doi101073pnas77116715, doi101098rsos150088, doi101111j1365294x201105418x, doi101126science1103538, doi101126science1246752, doi1011770049124104268644, doi1018637jssv043i10, doi1018900012965820020832248esorwd20co2" } @article{doi101111mec13481, author = "Port, Jesse A. and O’Donnell, James L. and Romero‐Maraccini, Ofelia C. and Leary, Paul and Litvin, Steven Y. and Nickols, Kerry J. and Yamahara, Kevan M. and Kelly, Ryan P.", title = "Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA", year = "2015", journal = "Molecular Ecology", abstract = "Abstract Preserving biodiversity is a global challenge requiring data on species’ distribution and abundance over large geographic and temporal scales. However, traditional methods to survey mobile species’ distribution and abundance in marine environments are often inefficient, environmentally destructive, or resource‐intensive. Metabarcoding of environmental DNA (eDNA) offers a new means to assess biodiversity and on much larger scales, but adoption of this approach for surveying whole animal communities in large, dynamic aquatic systems has been slowed by significant unknowns surrounding error rates of detection and relevant spatial resolution of eDNA surveys. Here, we report the results of a 2.5 km eDNA transect surveying the vertebrate fauna present along a gradation of diverse marine habitats associated with a kelp forest ecosystem. Using PCR primers that target the mitochondrial 12S rRNA gene of marine fishes and mammals, we generated eDNA sequence data and compared it to simultaneous visual dive surveys. We find spatial concordance between individual species’ eDNA and visual survey trends, and that eDNA is able to distinguish vertebrate community assemblages from habitats separated by as little as \textasciitilde 60 m. eDNA reliably detected vertebrates with low false‐negative error rates (1/12 taxa) when compared to the surveys, and revealed cryptic species known to occupy the habitats but overlooked by visual methods. This study also presents an explicit accounting of false negatives and positives in metabarcoding data, which illustrate the influence of gene marker selection, replication, contamination, biases impacting eDNA count data and ecology of target species on eDNA detection rates in an open ecosystem.", url = "https://doi.org/10.1111/mec.13481", doi = "10.1111/mec.13481", openalex = "W2248984422", references = "doi101098rsos150088" } @article{doi101038ncomms12544, author = "Deiner, Kristy and Fronhofer, Emanuel A. and Mächler, Elvira and Walser, Jean‐Claude and Altermatt, Florian", title = "Environmental DNA reveals that rivers are conveyer belts of biodiversity information", year = "2016", journal = "Nature Communications", abstract = "DNA sampled from the environment (eDNA) is a useful way to uncover biodiversity patterns. By combining a conceptual model and empirical data, we test whether eDNA transported in river networks can be used as an integrative way to assess eukaryotic biodiversity for broad spatial scales and across the land-water interface. Using an eDNA metabarcode approach, we detect 296 families of eukaryotes, spanning 19 phyla across the catchment of a river. We show for a subset of these families that eDNA samples overcome spatial autocorrelation biases associated with the classical community assessments by integrating biodiversity information over space. In addition, we demonstrate that many terrestrial species are detected; thus suggesting eDNA in river water also incorporates biodiversity information across terrestrial and aquatic biomes. Environmental DNA transported in river networks offers a novel and spatially integrated way to assess the total biodiversity for whole landscapes and will transform biodiversity data acquisition in ecology.", url = "https://doi.org/10.1038/ncomms12544", doi = "10.1038/ncomms12544", openalex = "W2951985551", references = "doi101016jtree201404003" } @article{doi1011112041210x12595, author = "Goldberg, Caren S. and Turner, Cameron R. and Deiner, Kristy and Klymus, Katy E. and Thomsen, Philip Francis and Murphy, Melanie A. and Spear, Stephen F. and McKee, Anna M. and Oyler‐McCance, Sara J. and Cornman, Robert S. and Laramie, Matthew B. and Mahon, Andrew R. and Lance, Richard F. and Pilliod, David S. and Strickler, Katherine M. and Waits, Lisette P. and Fremier, Alexander K. and Takahara, Teruhiko and Herder, Jelger and Taberlet, Pierre", title = "Critical considerations for the application of environmental DNA methods to detect aquatic species", year = "2016", journal = "Methods in Ecology and Evolution", abstract = "Summary Species detection using environmental DNA (eDNA) has tremendous potential for contributing to the understanding of the ecology and conservation of aquatic species. Detecting species using eDNA methods, rather than directly sampling the organisms, can reduce impacts on sensitive species and increase the power of field surveys for rare and elusive species. The sensitivity of eDNA methods, however, requires a heightened awareness and attention to quality assurance and quality control protocols. Additionally, the interpretation of eDNA data demands careful consideration of multiple factors. As eDNA methods have grown in application, diverse approaches have been implemented to address these issues. With interest in eDNA continuing to expand, supportive guidelines for undertaking eDNA studies are greatly needed. Environmental DNA researchers from around the world have collaborated to produce this set of guidelines and considerations for implementing eDNA methods to detect aquatic macroorganisms. Critical considerations for study design include preventing contamination in the field and the laboratory, choosing appropriate sample analysis methods, validating assays, testing for sample inhibition and following minimum reporting guidelines. Critical considerations for inference include temporal and spatial processes, limits of correlation of eDNA with abundance, uncertainty of positive and negative results, and potential sources of allochthonous DNA. We present a synthesis of knowledge at this stage for application of this new and powerful detection method.", url = "https://doi.org/10.1111/2041-210x.12595", doi = "10.1111/2041-210x.12595", openalex = "W2398092094", references = "doi101111j1755263x201000158x, doi101111mec13428, doi101139cjfas20130047, doi101371journalpone0059520, doi101373clinchem2008112797" } @article{doi101111mec13660, author = "Hänfling, Bernd and Handley, Lori Lawson and Read, Daniel S. and Hahn, Christoph and Li, Jianlong and Nichols, Paul and Blackman, Rosetta C. and Oliver, Anna and Winfield, Ian J.", title = "Environmental DNA metabarcoding of lake fish communities reflects long‐term data from established survey methods", year = "2016", journal = "Molecular Ecology", abstract = "Organisms continuously release DNA into their environments via shed cells, excreta, gametes and decaying material. Analysis of this 'environmental DNA' (eDNA) is revolutionizing biodiversity monitoring. eDNA outperforms many established survey methods for targeted detection of single species, but few studies have investigated how well eDNA reflects whole communities of organisms in natural environments. We investigated whether eDNA can recover accurate qualitative and quantitative information about fish communities in large lakes, by comparison to the most comprehensive long-term gill-net data set available in the UK. Seventy-eight 2L water samples were collected along depth profile transects, gill-net sites and from the shoreline in three large, deep lakes (Windermere, Bassenthwaite Lake and Derwent Water) in the English Lake District. Water samples were assayed by eDNA metabarcoding of the mitochondrial 12S and cytochrome b regions. Fourteen of the 16 species historically recorded in Windermere were detected using eDNA, compared to four species in the most recent gill-net survey, demonstrating eDNA is extremely sensitive for detecting species. A key question for biodiversity monitoring is whether eDNA can accurately estimate abundance. To test this, we used the number of sequence reads per species and the proportion of sampling sites in which a species was detected with eDNA (i.e. site occupancy) as proxies for abundance. eDNA abundance data consistently correlated with rank abundance estimates from established surveys. These results demonstrate that eDNA metabarcoding can describe fish communities in large lakes, both qualitatively and quantitatively, and has great potential as a complementary tool to established monitoring methods.", url = "https://doi.org/10.1111/mec.13660", doi = "10.1111/mec.13660", openalex = "W2337259322", references = "doi101016jtree201404003, doi101098rsos150088, doi101111mec13428" } @article{doi101038srep40368, author = "Yamamoto, Satoshi and Masuda, Reiji and Sato, Yukuto and Sado, Tetsuya and Araki, Hitoshi and Kondoh, Michio and Minamoto, Toshifumi and Miya, Masaki", title = "Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea", year = "2017", journal = "Scientific Reports", abstract = "revealed the fish community structure at a species resolution. The eDNA metabarcoding based on a 6-h collection of water samples detected 128 fish species, of which 62.5\% (40 species) were also observed by underwater visual censuses conducted over a 14-year period. This method also detected other local fishes (≥23 species) that were not observed by the visual censuses. These eDNA metabarcoding features will enhance marine ecosystem-related research, and the method will potentially become a standard tool for surveying fish communities.", url = "https://doi.org/10.1038/srep40368", doi = "10.1038/srep40368", openalex = "W2576417104", references = "doi101007s1059201507754, doi101016jbiocon201411019, doi101016jtree201404003, doi101038nature01610, doi101038nmeth1184, doi101093bioinformaticsbtr381, doi101093bioinformaticsbtr507, doi101098rsbl20080118, doi101098rsos150088, doi101111mec13428, doi1011861471210510421, openalexw1558982506" } @article{doi1011112041210x12849, author = "Alberdi, Antton and Aizpurua, Ostaizka and Gilbert, M. Thomas P. and Bohmann, Kristine", title = "Scrutinizing key steps for reliable metabarcoding of environmental samples", year = "2017", journal = "Methods in Ecology and Evolution", abstract = "Abstract Metabarcoding of environmental samples has many challenges and limitations that require carefully considered laboratory and analysis workflows to ensure reliable results. We explore how decisions regarding study design, laboratory set‐up, and bioinformatic processing affect the final results, and provide guidelines for reliable study of environmental samples. We evaluate the performance of four primer sets targeting COI and 16S regions characterizing arthropod diversity in bat faecal samples, and investigate how metabarcoding results are affected by parameters including: (1) number of PCR replicates per sample, (2) sequencing depth, (3) PCR replicate processing strategy (i.e. either additively, by combining the sequences obtained from the PCR replicates, or restrictively, by only retaining sequences that occur in multiple PCR replicates for each sample), (4) minimum copy number for sequences to be retained, (5) chimera removal, and (6) similarity thresholds for Operational Taxonomic Unit (OTU) clustering. Lastly, we measure within‐ and between‐taxa dissimilarities when using sequences from public databases to determine the most appropriate thresholds for OTU clustering and taxonomy assignment. Our results show that the use of multiple primer sets reduces taxonomic biases and increases taxonomic coverage. Taxonomic profiles resulting from each primer set are principally affected by how many PCR replicates are carried out per sample and how sequences are filtered across them, the sequence copy number threshold and the OTU clustering threshold. We also report considerable diversity differences between PCR replicates from each sample. Sequencing depth increases the dissimilarity between PCR replicates unless the bioinformatic strategies to remove allegedly artefactual sequences are adjusted according to the number of analysed sequences. Finally, we show that the appropriate identity thresholds for OTU clustering and taxonomy assignment differ between markers. Metabarcoding of complex environmental samples ideally requires (1) investigation of whether more than one primer sets targeting the same taxonomic group is needed to offset primer biases, (2) more than one PCR replicate per sample, (3) bioinformatic processing of sequences that balance diversity detection with removal of artefactual sequences, and (4) empirical selection of OTU clustering and taxonomy assignment thresholds tailored to each marker and the obtained taxa.", url = "https://doi.org/10.1111/2041-210x.12849", doi = "10.1111/2041-210x.12849", openalex = "W2724989966", references = "doi101016jtree201404003, doi101111j1365294x201205537x" } @article{doi101111mec14350, author = "Deiner, Kristy and Bik, Holly M. and Mächler, Elvira and Seymour, Mathew and Lacoursière‐Roussel, Anaïs and Altermatt, Florian and Creer, Simon and Bista, Iliana and Lodge, David M. and de Vere, Natasha and Pfrender, Michael E. and Bernatchez, Louis", title = "Environmental DNA metabarcoding: Transforming how we survey animal and plant communities", year = "2017", journal = "Molecular Ecology", abstract = {The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing ("HTS") platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed "environmental DNA" or "eDNA"). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called "eDNA metabarcoding" and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education.}, url = "https://doi.org/10.1111/mec.14350", doi = "10.1111/mec.14350", openalex = "W2754769271", references = "doi101007s1059201507754, doi101016jbiocon201411019, doi101038nature03959, doi101038nature12921, doi101038nmethf303, doi101038srep40368, doi101073pnas0905845106, doi101073pnas1000080107, doi101093bioinformaticsbtq461, doi101093bioinformaticsbtr381, doi101093nargks1219, doi101098rsbl20080118, doi101098rsos150088, doi101111j1365294x201105418x, doi101111j1755263x201000158x, doi101111mec13428, doi101126science1187512, doi101126science1256688, doi101128aem0006207, doi101128aem0154109, doi101139cjfas20130047, doi1011861471210510421, doi107717peerj2584" } @article{doi101007s1075001837505, author = "Harper, Lynsey R. and Buxton, Andrew S. and Rees, Helen C. and Bruce, Kat and Brys, Rein and Halfmaerten, David and Read, Daniel S. and Watson, Hayley V. and Sayer, Carl D. and Jones, Eleanor P. and Priestley, Victoria and Mächler, Elvira and Múrria, Cesc and Garcés‐Pastor, Sandra and Medupin, Cecilia and Burgess, Katherine B. and Benson, G. B. G. and Boonham, Neil and Griffiths, Richard A. and Handley, Lori Lawson and Hänfling, Bernd", title = "Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds", year = "2018", journal = "Hydrobiologia", abstract = "Environmental DNA (eDNA) analysis is a rapid, non-invasive, cost-efficient biodiversity monitoring tool with enormous potential to inform aquatic conservation and management. Development is ongoing, with strong commercial interest, and new uses are continually being discovered. General applications of eDNA and guidelines for best practice in freshwater systems have been established, but habitat-specific assessments are lacking. Ponds are highly diverse, yet understudied systems that could benefit from eDNA monitoring. However, eDNA applications in ponds and methodological constraints specific to these environments remain unaddressed. Following a stakeholder workshop in 2017, researchers combined knowledge and expertise to review these applications and challenges that must be addressed for the future and consistency of eDNA monitoring in ponds. The greatest challenges for pond eDNA surveys are representative sampling, eDNA capture, and potential PCR inhibition. We provide recommendations for sampling, eDNA capture, inhibition testing, and laboratory practice, which should aid new and ongoing eDNA projects in ponds. If implemented, these recommendations will contribute towards an eventual broad standardisation of eDNA research and practice, with room to tailor workflows for optimal analysis and different applications. Such standardisation will provide more robust, comparable, and ecologically meaningful data to enable effective conservation and management of pond biodiversity.", url = "https://doi.org/10.1007/s10750-018-3750-5", doi = "10.1007/s10750-018-3750-5", openalex = "W2889134269", references = "doi101016jwatres201803003" } @article{doi101016jgeoforum201805010, author = "Schnegg, Michael and Kiaka, Richard Dimba", title = "Subsidized elephants: Community-based resource governance and environmental (in)justice in Namibia", year = "2018", journal = "Geoforum", abstract = "After independence, and in accordance with global environmental policies, the government of Namibia partly transferred the responsibility for managing wildlife and water to local communities. In this article, we use the concept of environmental justice as a theoretical guide to explore the combined effects that these new policies have had for pastoralists in arid, rural Namibia. We find, firstly, that partly due to conservation efforts, the elephant population has increased significantly. While a healthy elephant population supports exclusive, international tourism, the elephants are causing ever-increasing destruction at communal water points thus leading to increasing local financial costs. Only a small fraction of the revenues from community-based tourism, however, remains in the communities, and relatively few people profit from these revenues directly. Secondly, as new community- level sharing institutions for water emerge, pastoralists who are economically marginalized are subsidizing the financial costs of water for both their wealthy neighbours and the tourism industry. Looking at the combined effects of CBNRM policies for water and wildlife management, these policies are likely to lead to better resource management but greater economic inequality. To interpret these findings, we consider how CBNRM transforms landscapes and wildlife into global commodities. This process pulls communities into new common property regimes as well as towards privatization at the same time and helps to explain the social- ecological changes we observe.", url = "https://doi.org/10.1016/j.geoforum.2018.05.010", doi = "10.1016/j.geoforum.2018.05.010", openalex = "W2803787839", references = "openalexw1497677346" } @article{doi101038s41598018284248, author = "Pont, Didier and Rocle, Mathieu and Valentini, Alice and Civade, Raphaël and Jean, Pauline and Maire, Anthony and Roset, Nicolas and Schabuss, Michael and Zornig, Horst and Déjean, Tony", title = "Environmental DNA reveals quantitative patterns of fish biodiversity in large rivers despite its downstream transportation", year = "2018", journal = "Scientific Reports", abstract = "Despite the ecological and societal importance of large rivers, fish sampling remains costly and limited to specific habitats (e.g., river banks). Using an eDNA metabarcoding approach, we regularly sampled 500 km of a large river (Rhône River). Comparisons with long-term electrofishing surveys demonstrated the ability of eDNA metabarcoding to qualitatively and quantitatively reveal fish assemblage structures (relative species abundance) but eDNA integrated a larger space than the classical sampling location. Combination of a literature review and field data showed that eDNA behaves in the water column like fine particulate organic matter. Its detection distance varied from a few km in a small stream to more than 100 km in a large river. To our knowledge, our results are the first demonstration of the capacity of eDNA metabarcoding to describe longitudinal fish assemblage patterns in a large river, and metabarcoding appears to be a reliable, cost-effective method for future monitoring.", url = "https://doi.org/10.1038/s41598-018-28424-8", doi = "10.1038/s41598-018-28424-8", openalex = "W2809994961", references = "doi101038srep40368, doi101111mec14350" } @article{doi101038s4200301801926, author = "Collins, Rupert A. and Wangensteen, Owen S. and O’Gorman, Eoin J. and Mariani, Stefano and Sims, David and Genner, Martin J.", title = "Persistence of environmental DNA in marine systems", year = "2018", journal = "Communications Biology", abstract = "As environmental DNA (eDNA) becomes an increasingly valuable resource for marine ecosystem monitoring, understanding variation in its persistence across contrasting environments is critical. Here, we quantify the breakdown of macrobial eDNA over a spatio-temporal axis of locally extreme conditions, varying from ocean-influenced offshore to urban-inshore, and between winter and summer. We report that eDNA degrades 1.6 times faster in the inshore environment than the offshore environment, but contrary to expectation we find no difference over season. Analysis of environmental covariables show a spatial gradient of salinity and a temporal gradient of pH, with salinity-or the biotic correlates thereof-most important. Based on our estimated inshore eDNA half-life and naturally occurring eDNA concentrations, we estimate that eDNA may be detected for around 48 h, offering potential to collect ecological community data of high local fidelity. We conclude by placing these results in the context of previously published eDNA decay rates.", url = "https://doi.org/10.1038/s42003-018-0192-6", doi = "10.1038/s42003-018-0192-6", openalex = "W2899195544", references = "doi1010079780387874586, doi101007s1059201507754, doi101016jbiocon201411019, doi101016jtree201404003, doi101038srep40368, doi101093nargks596, doi101098rstb20051716, doi1011111365266412306, doi101111mec14350, doi1013851592591922365, openalexw3086315876" } @book{doi101093oso97801987672200010001, author = "Taberlet, Pierre and Bonin, Aurélie and Zinger, Lucie and Coissac, Éric", title = "Environmental DNA", year = "2018", abstract = "Abstract Environmental DNA (eDNA), i.e. DNA released in the environment by any living form, represents a formidable opportunity to gather high-throughput and standard information on the distribution or feeding habits of species. It has therefore great potential for applications in ecology and biodiversity management. However, this research field is fast-moving, involves different areas of expertise and currently lacks standard approaches, which calls for an up-to-date and comprehensive synthesis. Environmental DNA for biodiversity research and monitoring covers current methods based on eDNA, with a particular focus on “eDNA metabarcoding”. Intended for scientists and managers, it provides the background information to allow the design of sound experiments. It revisits all steps necessary to produce high-quality metabarcoding data such as sampling, metabarcode design, optimization of PCR and sequencing protocols, as well as analysis of large sequencing datasets. All these different steps are presented by discussing the potential and current challenges of eDNA-based approaches to infer parameters on biodiversity or ecological processes. The last chapters of this book review how DNA metabarcoding has been used so far to unravel novel patterns of diversity in space and time, to detect particular species, and to answer new ecological questions in various ecosystems and for various organisms. Environmental DNA for biodiversity research and monitoring constitutes an essential reading for all graduate students, researchers and practitioners who do not have a strong background in molecular genetics and who are willing to use eDNA approaches in ecology and biomonitoring.", url = "https://doi.org/10.1093/oso/9780198767220.001.0001", doi = "10.1093/oso/9780198767220.001.0001", openalex = "W4250963355", references = "doi101007s1059201507754, doi101016b9780123721808500421, doi101016jtree200504005, doi101016jtree201404003, doi101038nmeth3869, doi101038nmethf303, doi101038srep40368, doi101073pnas74125463, doi101093nar25173389, doi101093nargks1219, doi101098rsos150088, doi101111j1365294x201105418x, doi101111j1365294x201205537x, doi101111j175348871981tb06752x, doi101111j1755263x201000158x, doi101126science2448875, doi101126scienceaac9323, doi101126scienceaam9695, doi101128aem0006207, doi101128aem0154109, doi101139cjfas20130047, doi101146annurevgenet37110801143214, doi101371journalpone0059520, doi1018901119521" } @article{doi1011111755099812982, author = "Jeunen, Gert‐Jan and Knapp, Michael and Spencer, Hamish G. and Lamare, Miles D. and Taylor, Helen R. and Stat, Michael and Bunce, Michael and Gemmell, Neil J.", title = "Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement", year = "2018", journal = "Molecular Ecology Resources", abstract = "While in recent years environmental DNA (eDNA) metabarcoding surveys have shown great promise as an alternative monitoring method, the integration into existing marine monitoring programs may be confounded by the dispersal of the eDNA signal. Currents and tidal influences could transport eDNA over great distances, inducing false-positive species detection, leading to inaccurate biodiversity assessments and, ultimately, mismanagement of marine environments. In this study, we determined the ability of eDNA metabarcoding surveys to distinguish localized signals obtained from four marine habitats within a small spatial scale (<5 km) subject to significant tidal and along-shore water flow. Our eDNA metabarcoding survey detected 86 genera, within 77 families and across 11 phyla using three established metabarcoding assays targeting fish (16S rRNA gene), crustacean (16S rRNA gene) and eukaryotic (cytochrome oxidase subunit 1) diversity. Ordination and cluster analyses for both taxonomic and OTU data sets show distinct eDNA signals between the sampled habitats, suggesting dispersal of eDNA among habitats was limited. Individual taxa with strong habitat preferences displayed localized eDNA signals in accordance with their respective habitat, whereas taxa known to be less habitat-specific generated more ubiquitous signals. Our data add to evidence that eDNA metabarcoding surveys in marine environments detect a broad range of taxa that are spatially discrete. Our work also highlights that refinement of assay choice is essential to realize the full potential of eDNA metabarcoding surveys in marine biodiversity monitoring programs.", url = "https://doi.org/10.1111/1755-0998.12982", doi = "10.1111/1755-0998.12982", openalex = "W2906482497", references = "doi101038s41598017125015" } @article{doi101126sciadvaap9661, author = "Boussarie, Germain and Bakker, Judith and Wangensteen, Owen S. and Mariani, Stefano and Bonnin, Lucas and Juhel, Jean‐Baptiste and Kiszka, Jérémy J. and Kulbicki, Michel and Manel, Stéphanie and Robbins, William D. and Vigliola, Laurent and Mouillot, David", title = "Environmental DNA illuminates the dark diversity of sharks", year = "2018", journal = "Science Advances", abstract = {In the era of "Anthropocene defaunation," large species are often no longer detected in habitats where they formerly occurred. However, it is unclear whether this apparent missing, or "dark," diversity of megafauna results from local species extirpations or from failure to detect elusive remaining individuals. We find that despite two orders of magnitude less sampling effort, environmental DNA (eDNA) detects 44\% more shark species than traditional underwater visual censuses and baited videos across the New Caledonian archipelago (south-western Pacific). Furthermore, eDNA analysis reveals the presence of previously unobserved shark species in human-impacted areas. Overall, our results highlight a greater prevalence of sharks than described by traditional survey methods in both impacted and wilderness areas. This indicates an urgent need for large-scale eDNA assessments to improve monitoring of threatened and elusive megafauna. Finally, our findings emphasize the need for conservation efforts specifically geared toward the protection of elusive, residual populations.}, url = "https://doi.org/10.1126/sciadv.aap9661", doi = "10.1126/sciadv.aap9661", openalex = "W2802297949", references = "doi101038s41598017125015" } @article{doi101186s1375001801217, author = "Haddaway, Neal and Macura, Biljana and Whaley, Paul and Pullin, Andrew S.", title = "ROSES RepOrting standards for Systematic Evidence Syntheses: pro forma, flow-diagram and descriptive summary of the plan and conduct of environmental systematic reviews and systematic maps", year = "2018", journal = "Environmental Evidence", abstract = "Reliable synthesis of the various rapidly expanding bodies of evidence is vital for the process of evidence-informed decision-making in environmental policy, practice and research. With the rise of evidence-base medicine and increasing numbers of published systematic reviews, criteria for assessing the quality of reporting have been developed. First QUOROM (Lancet 354:1896–1900, 1999) and then PRISMA (Ann Intern Med 151:264, 2009) were developed as reporting guidelines and standards to ensure medical meta-analyses and systematic reviews are reported to a high level of detail. PRISMA is now widely used by a range of journals as a pre-submission checklist. However, due to its development for systematic reviews in healthcare, PRISMA has limited applicability for reviews in conservation and environmental management. We highlight 12 key problems with the application of PRISMA to this field, including an overemphasis on meta-analysis and no consideration for other synthesis methods. We introduce ROSES (RepOrting standards for Systematic Evidence Syntheses), a pro forma and flow diagram designed specifically for systematic reviews and systematic maps in the field of conservation and environmental management. We describe how ROSES solves the problems with PRISMA. We outline the key benefits of our approach to designing ROSES, in particular the level of detail and inclusion of rich guidance statements. We also introduce the extraction of meta-data that describe key aspects of the conduct of the review. Collated together, this summary record can help to facilitate rapid review and appraisal of the conduct of a systematic review or map, potentially speeding up the peer-review process. We present the results of initial road testing of ROSES with systematic review experts, and propose a plan for future development of ROSES.", url = "https://doi.org/10.1186/s13750-018-0121-7", doi = "10.1186/s13750-018-0121-7", openalex = "W2795357522", references = "doi101111j15231739200600485x" } @article{doi101002pan321, author = "Graß, Ingo and Loos, Jacqueline and Baensch, Svenja and Batáry, Péter and Librán‐Embid, Felipe and Ficiciyan, Anoush and Klaus, Felix and Riechers, Maraja and Rosa, Julia and Tiede, Julia and Udy, Kristy and Westphal, Catrin and Wurz, Annemarie and Tscharntke, Teja", title = "Land‐sharing/‐sparing connectivity landscapes for ecosystem services and biodiversity conservation", year = "2019", journal = "People and Nature", abstract = "Abstract The land‐sharing versus land‐sparing debate recently stagnated, lacking an integrating perspective in agricultural landscapes as well as consideration of ecosystem services. Here, we argue that land‐sharing (i.e. wildlife‐friendly farming systems) and land‐sparing (i.e. separation of high‐yielding agriculture and natural habitats) are not mutually exclusive, as both are needed to balance management needs for the multifunctionality of agricultural landscapes. Land‐sharing promotes ecosystem services in agricultural settings, thereby allowing for environmentally friendly production. Land set aside in protected areas by land‐sparing is crucial for conservation of those species that are incompatible with agriculture. Importantly, as species move throughout the landscape and exploit different habitats, increased connectivity between environmentally friendly managed and protected areas is needed to (a) promote spillover of ecosystem service providers from land‐sharing/‐sparing measures to agricultural production and rescue service‐providing species from extinction in hostile areas, (b) to facilitate immigration and counteract possible extinctions in spared habitats and (c) to conserve response diversity of species communities for ensuring resilience of ecosystem services in changing environments. In conclusion, the successful management of multifunctional landscapes requires the combination of context‐specific land‐sharing and land‐sparing measures within spatially well‐connected landscape mosaics, resulting in land‐sharing/‐sparing connectivity landscapes. A plain language summary is available for this article.", url = "https://doi.org/10.1002/pan3.21", doi = "10.1002/pan3.21", openalex = "W2942710351", references = "doi101038nature24457, doi101111cobi12536" } @article{doi101016jbiocon2019108224, author = "Ardoin, Nicole M. and Bowers, Alison W. and Gaillard, Estelle", title = "Environmental education outcomes for conservation: A systematic review", year = "2019", journal = "Biological Conservation", abstract = "Effective environmental education represents more than a unidirectional transfer of information: rather, this suite of tools develops and enhances environmental attitudes, values, and knowledge, as well as builds skills that prepare individuals and communities to collaboratively undertake positive environmental action. Environmental education also facilitates connections between actionable research findings and on-the-ground practices, creating synergistic spaces where stakeholders collaborate to address dynamic environmental issues over time. Because of this commitment to application and iteration, environmental education can result in direct benefits to the environment and address conservation issues concretely. Yet, the path to achieving those tangible impacts can be winding, with robust data documenting changes challenging to produce. To better understand the research-implementation spaces where those environmental education outcomes occur, are measured, and are reported, we undertook a systematic review of research on environmental education's contributions to conservation and environmental quality outcomes. Given the variation in research designs and data, we used a mixed-methods approach to the review; analysis of the 105 resulting studies documented strongly positive environmental education outcomes overall and highlighted productive research-implementation spaces. Chi-square analyses revealed that programs reporting direct outcomes, compared with those reporting indirect outcomes, differed on primary topic addressed. A narrative analysis indicated that environmental education programs documenting direct impacts included: a focus on localized issues or locally relevant dimensions of broader issues; collaboration with scientists, resource managers, and/or community organizations; integrated action elements; and intentional measurement/reporting structures. Those themes suggest program development and documentation ideas as well as further opportunities for productive research-implementation spaces.", url = "https://doi.org/10.1016/j.biocon.2019.108224", doi = "10.1016/j.biocon.2019.108224", openalex = "W2984404402", references = "doi101111j15231739200600485x" } @article{doi101016jgecco2019e00547, author = "Ruppert, Krista M. and Kline, Richard J. and Rahman, Md Saydur", title = "Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA", year = "2019", journal = "Global Ecology and Conservation", abstract = "Environmental DNA (eDNA) metabarcoding is a novel method of assessing biodiversity wherein samples are taken from the environment via water, sediment or air from which DNA is extracted, and then amplified using general or universal primers in polymerase chain reaction and sequenced using next-generation sequencing to generate thousands to millions of reads. From this data, species presence can be determined, and overall biodiversity assessed. It is an interdisciplinary method that brings together traditional fieldbased ecology with in-depth molecular methods and advanced computational tools. As an emerging monitoring method, there are many pitfalls and roadblocks to be considered and avoided, but the method may still have the ability to revolutionize modern biodiversity surveys for the molecular era. In this paper, we review the basic methodology, benefits, and concerns of eDNA metabarcoding, and systematically cover the applications of the method in global ecology thus far, including biodiversity monitoring across all habitats and taxonomic groups, ancient ecosystem reconstruction, plant-pollinator interactions, diet analysis, invasive species detection, pollution responses, and air quality monitoring. We also discuss the future applications of the method as well as expected technological advances and how they may impact the way that eDNA metabarcoding may used in the future. eDNA metabarcoding is a unique method still in development and will likely remain in flux for some time as technology advances and procedures become standardized. However, as metabarcoding is optimized and its use becomes more widespread, it is likely to become an essential tool for ecological monitoring and global conservation study.", url = "https://doi.org/10.1016/j.gecco.2019.e00547", doi = "10.1016/j.gecco.2019.e00547", openalex = "W2912959159", references = "doi101007s1059201507754, doi101016jbiocon201411019, doi101016jtree201404003, doi101016jwatres201803003, doi101038nature12921, doi101038s41598017125015, doi101038srep40368, doi101098rsbl20080118, doi101098rsos150088, doi1011112041210x12595, doi101111j1365294x201205470x, doi101111j1365294x201205537x, doi101111mec13428, doi101111mec14350, doi101139cjfas20130047, doi101371journalpone0041732" } @article{doi101038s4159801948546x, author = "Kelly, Ryan P. and Shelton, Andrew O. and Gallego, Ramón", title = "Understanding PCR Processes to Draw Meaningful Conclusions from Environmental DNA Studies", year = "2019", journal = "Scientific Reports", abstract = "Abstract As environmental DNA (eDNA) studies have grown in popularity for use in ecological applications, it has become clear that their results differ in significant ways from those of traditional, non-PCR-based surveys. In general, eDNA studies that rely on amplicon sequencing may detect hundreds of species present in a sampled environment, but the resulting species composition can be idiosyncratic, reflecting species’ true biomass abundances poorly or not at all. Here, we use a set of simulations to develop a mechanistic understanding of the processes leading to the kinds of results common in mixed-template PCR-based (metabarcoding) studies. In particular, we focus on the effects of PCR cycle number and primer amplification efficiency on the results of diversity metrics in sequencing studies. We then show that proportional indices of amplicon reads capture trends in taxon biomass with high accuracy, particularly where amplification efficiency is high (median correlation up to 0.97). Our results explain much of the observed behavior of PCR-based studies, and lead to recommendations for best practices in the field.", url = "https://doi.org/10.1038/s41598-019-48546-x", doi = "10.1038/s41598-019-48546-x", openalex = "W2969600503", references = "doi101038s41598017125015, doi101073pnas0404300101" } @article{doi1011111755099813055, author = "Wood, Susanna A. and Pochon, Xavier and Laroche, Olivier and von Ammon, Ulla and Adamson, Janet and Zaiko, Anastasija", title = "A comparison of droplet digital polymerase chain reaction (PCR), quantitative PCR and metabarcoding for species‐specific detection in environmental DNA", year = "2019", journal = "Molecular Ecology Resources", abstract = "= 0.68, p <.001); however, qPCR copy numbers were on average 125-fold lower than those measured using ddPCR. Using metabarcoding there was higher detection in water samples when targeting the COI (40\%) compared to 18S rRNA (5.4\%). The difference was less pronounced in biofouling samples (25\% COI, 29\% 18S rRNA). Occupancy modelling showed that although the occupancy estimate was higher for biofouling samples (ψ = 1.0), higher probabilities of detection were derived for water samples. Detection probabilities of ddPCR (1.0) and qPCR (0.93) were nearly double metabarcoding (0.57 to 0.27 marker dependent). Studies that aim to detect specific invasive or rare species in environmental samples should consider using targeted approaches until a detailed understanding of how community and matrix complexity, and primer biases affect metabarcoding data.", url = "https://doi.org/10.1111/1755-0998.13055", doi = "10.1111/1755-0998.13055", openalex = "W2959499736", references = "doi101111mec15060" } @article{doi1011112041210x13276, author = "Collins, Rupert A. and Bakker, Judith and Wangensteen, Owen S. and Soto, Ana Z. and Corrigan, Laura and Sims, David and Genner, Martin J. and Mariani, Stefano", title = "Non‐specific amplification compromises environmental DNA metabarcoding with COI", year = "2019", journal = "Methods in Ecology and Evolution", abstract = "Abstract Metabarcoding extra‐organismal DNA from environmental samples is now a key technique in aquatic biomonitoring and ecosystem health assessment. Of critical consideration when designing experiments, and especially so when developing community standards and legislative frameworks, is the choice of genetic marker and primer set. Mitochondrial cytochrome c oxidase subunit I (COI), the standard DNA barcode marker for animals, with its extensive reference library, taxonomic discriminatory power and predictable sequence variation, is the natural choice for many metabarcoding applications. However, for targeting specific taxonomic groups in environmental samples, the utility of COI has yet to be fully scrutinized. Here, by using a case study of marine and freshwater fishes from the British Isles, we quantify the in silico performance of twelve primer pairs from four mitochondrial loci – COI, cytochrome b, 12S and 16S – in terms of reference library coverage, taxonomic discriminatory power and primer universality. We subsequently test in vitro four primer pairs – three COI and one 12S – for their specificity, reproducibility, and congruence with independent datasets derived from traditional survey methods at five estuarine and coastal sites around the English Channel and North Sea. Our results show that for aqueous extra‐organismal DNA at low template concentrations, both metazoan‐targeted and fish‐targeted COI primers perform poorly in comparison to 12S, exhibiting low levels of reproducibility due to non‐specific amplification of prokaryotic and non‐target eukaryotic DNAs. An ideal metabarcode would have an extensive reference library upon which custom primers could be designed, either for broad assessments of biodiversity, or taxon specific surveys. Such a database is available for COI, but low primer specificity hinders practical application, while conversely, 12S primers offer high specificity, but lack adequate references. The latter, however, can be mitigated by expanding the concept of DNA barcodes to include whole mitochondrial genomes generated by genome‐skimming existing tissue collections.", url = "https://doi.org/10.1111/2041-210x.13276", doi = "10.1111/2041-210x.13276", openalex = "W2965120276", references = "doi101016jwatres201803003, doi101038s41598017125015, doi101038s4200301801926, doi101093oso97801987672200010001" } @article{doi103390genes10030192, author = "Adams, Clare I. M. and Knapp, Michael and Gemmell, Neil J. and Jeunen, Gert‐Jan and Bunce, Michael and Lamare, Miles D. and Taylor, Helen R.", title = "Beyond Biodiversity: Can Environmental DNA (eDNA) Cut It as a Population Genetics Tool?", year = "2019", journal = "Genes", abstract = "Population genetic data underpin many studies of behavioral, ecological, and evolutionary processes in wild populations and contribute to effective conservation management. However, collecting genetic samples can be challenging when working with endangered, invasive, or cryptic species. Environmental DNA (eDNA) offers a way to sample genetic material non-invasively without requiring visual observation. While eDNA has been trialed extensively as a biodiversity and biosecurity monitoring tool with a strong taxonomic focus, it has yet to be fully explored as a means for obtaining population genetic information. Here, we review current research that employs eDNA approaches for the study of populations. We outline challenges facing eDNA-based population genetic methodologies, and suggest avenues of research for future developments. We advocate that with further optimizations, this emergent field holds great potential as part of the population genetics toolkit.", url = "https://doi.org/10.3390/genes10030192", doi = "10.3390/genes10030192", openalex = "W2913725860", references = "doi101038s4200301801926" } @article{doi101002edn3121, author = "Minamoto, Toshifumi and Miya, Masaki and Sado, Tetsuya and SEINO, Satoquo and Doi, Hideyuki and Kondoh, Michio and Nakamura, Keigo and Takahara, Teruhiko and Yamamoto, Satoshi and Yamanaka, Hiroki and Araki, Hitoshi and Iwasaki, Wataru and Kasai, Akihide and Masuda, Reiji and Uchii, Kimiko", title = "An illustrated manual for environmental DNA research: Water sampling guidelines and experimental protocols", year = "2020", journal = "Environmental DNA", abstract = "Abstract Environmental DNA (eDNA)‐based assessments of macro‐organisms have now become an essential approach for biomonitoring. eDNA survey methods have a number of advantages over conventional survey methods. However, the value of the data that will accumulate would be greatly enhanced by standardizing the analysis methods, which would allow us to compare data from multiple monitoring sites at different points in time. The eDNA Society (http://ednasociety.org/en/about), whose founding members consist of Japanese researchers conducting eDNA studies on macro‐organisms, was established in 2018, with the aim of expanding eDNA technology and science. Here, we introduce our key publication, “Environmental DNA Sampling and Experiment Manual” (http://ednasociety.org/en/manual), which was published under the initiative of the eDNA Society. Detailed methods for the surveys and experiments are described in the manual, including the selection of sampling sites, sampling methods, filtration methods, DNA extraction, species‐specific detection by real‐time polymerase chain reaction, and fish eDNA metabarcoding. The manual assists users in conducting standardized surveys and quality experiments, and provides a basis for collecting comparable data. Given that the efficacy of methods can be context dependent and variable, and that procedures may sometimes conflict with standardization, it is difficult to ensure that all processes are equally effective. However, even in such cases, it is important to maintain sufficiently high data quality by setting the minimum standards to be followed. Implementation of such standardized methodologies will enable the systematic and frequent collection of flawless, comparable eDNA data from around the world; this will provide important fundamental information for biodiversity conservation, as well as the sustainable use of fisheries resources.", url = "https://doi.org/10.1002/edn3.121", doi = "10.1002/edn3.121", openalex = "W3048869260", references = "doi101016jgecco2019e00547" } @article{doi101002edn3141, author = "Allan, Elizabeth Andruszkiewicz and Zhang, Weifeng G. and Lavery, Andone C. and Govindarajan, Annette F.", title = "Environmental DNA shedding and decay rates from diverse animal forms and thermal regimes", year = "2020", journal = "Environmental DNA", abstract = "Abstract Environmental DNA (eDNA) analysis from water samples is a promising new method to identify both targeted species and whole communities of aquatic organisms. However, the current literature regarding eDNA shedding rates primarily focuses on fish and most decay rate constants are reported for warm sunlit waters. Here, we conducted experiments to investigate how eDNA shedding differs between animal forms and how long eDNA can persist in waters of varying temperature and light conditions. We designed quantitative PCR assays for one fish (mummichog, Fundulus heteroclitus), one crustacean (grass shrimp, Palaemon spp.), and two scyphomedusae (moon jelly, Aurelia aurita and nettle, Chrysaora spp.) to estimate eDNA shedding and decay rates. We found that shedding rates were highly variable for all organisms, but grass shrimp had the lowest shedding rate. We quantified eDNA decay rate constants at 6, 15, and 23°C and found that decay rate constants of mummichog and grass shrimp were larger at higher temperatures, while those of scyphomedusae did not show clear temperature dependence. We also found that higher‐order decay models with tails fit the data better than first‐order log‐linear models, suggesting temporal variability in eDNA decay rates. Results indicate that different animal forms shed different types of eDNA, impacting both shedding and decay rates. These findings fill critical knowledge gaps regarding variation in eDNA shedding and decay across animal forms under a range of realistic marine temperature conditions. These data will be useful for interpreting field studies that utilize eDNA to investigate ocean habitats that are otherwise difficult to access.", url = "https://doi.org/10.1002/edn3.141", doi = "10.1002/edn3.141", openalex = "W3090119047", references = "doi101016jgecco2019e00547, doi101038s4200301801926" } @article{doi101007s10531020019800, author = "Beng, Kingsly C. and Corlett, Richard T.", title = "Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects", year = "2020", journal = "Biodiversity and Conservation", url = "https://doi.org/10.1007/s10531-020-01980-0", doi = "10.1007/s10531-020-01980-0", openalex = "W3016113032", references = "doi101007s1059201507754, doi101016jbiocon201411019, doi101016jwatres201803003, doi101038362709a0, doi101038s415980160028x, doi101038s41598018371862, doi101038s4200301801926, doi101038srep40368, doi101093bioinformaticsbtr381, doi101098rsbl20080118, doi101098rspb20191409, doi101111j13652672201205384x, doi101111j1365294x201205537x, doi101111j14718286200701678x, doi101111mec13428, doi101111mec14350, doi101186174299941034, doi101371journalpone0059520" } @article{doi101007s1256202001461x, author = "Miya, Masaki and Gotoh, Ryo O. and Sado, Tetsuya", title = "MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples", year = "2020", journal = "Fisheries Science", abstract = "Abstract We reviewed the current methodology and practices of the DNA metabarcoding approach using a universal PCR primer pair MiFish, which co-amplifies a short fragment of fish DNA (approx. 170 bp from the mitochondrial 12S rRNA gene) across a wide variety of taxa. This method has mostly been applied to biodiversity monitoring using environmental DNA (eDNA) shed from fish and, coupled with next-generation sequencing technologies, has enabled massively parallel sequencing of several hundred eDNA samples simultaneously. Since the publication of its technical outline in 2015, this method has been widely used in various aquatic environments in and around the six continents, and MiFish primers have demonstrably outperformed other competing primers. Here, we outline the technical progress in this method over the last 5 years and highlight some case studies on marine, freshwater, and estuarine fish communities. Additionally, we discuss various applications of MiFish metabarcoding to non-fish organisms, single-species detection systems, quantitative biodiversity monitoring, and bulk DNA samples other than eDNA. By recognizing the MiFish eDNA metabarcoding strengths and limitations, we argue that this method is useful for ecosystem conservation strategies and the sustainable use of fishery resources in “ecosystem-based fishery management” through continuous biodiversity monitoring at multiple sites.", url = "https://doi.org/10.1007/s12562-020-01461-x", doi = "10.1007/s12562-020-01461-x", openalex = "W3085313947", references = "doi1010029781119174844, doi101007s10531020019800, doi101093oso97801987672200010001, doi101098rspb20191409" } @article{doi101038s415860202773z, author = "Maxwell, Sean and Cazalis, Victor and Dudley, Nigel and Hoffmann, Michael and Rodrigues, Ana S. L. and Stolton, Sue and Visconti, Piero and Woodley, Stephen and Kingston, Naomi and Lewis, Edward and Maron, Martine and Strassburg, Bernardo B. N. and Wenger, Amelia and Jonas, Harry D. and Venter, Oscar and Watson, James", title = "Area-based conservation in the twenty-first century", year = "2020", journal = "Nature", abstract = "Humanity will soon define a new era for nature-one that seeks to transform decades of underwhelming responses to the global biodiversity crisis. Area-based conservation efforts, which include both protected areas and other effective area-based conservation measures, are likely to extend and diversify. However, persistent shortfalls in ecological representation and management effectiveness diminish the potential role of area-based conservation in stemming biodiversity loss. Here we show how the expansion of protected areas by national governments since 2010 has had limited success in increasing the coverage across different elements of biodiversity (ecoregions, 12,056 threatened species, 'Key Biodiversity Areas' and wilderness areas) and ecosystem services (productive fisheries, and carbon services on land and sea). To be more successful after 2020, area-based conservation must contribute more effectively to meeting global biodiversity goals-ranging from preventing extinctions to retaining the most-intact ecosystems-and must better collaborate with the many Indigenous peoples, community groups and private initiatives that are central to the successful conservation of biodiversity. The long-term success of area-based conservation requires parties to the Convention on Biological Diversity to secure adequate financing, plan for climate change and make biodiversity conservation a far stronger part of land, water and sea management policies.", url = "https://doi.org/10.1038/s41586-020-2773-z", doi = "10.1038/s41586-020-2773-z", openalex = "W3091919204", references = "doi101002joc1276, doi101016jbiocon201609004, doi101038nature13947, doi101038nature21707, doi101038nclimate1958, doi101073pnas1710465114, doi101093bioscibix014, doi101126science1244693, doi101126scienceaax3100, doi101641b570707, doi102305iucnch2008paps2en, doi103389fmars201700158" } @article{doi101111mec15472, author = "Cordier, Tristan and Alonso‐Sáez, Laura and Apothéloz‐Perret‐Gentil, Laure and Aylagas, Eva and Bohan, David A. and Bouchez, Agnès and Chariton, Anthony A. and Creer, Simon and Frühe, Larissa and Keck, François and Keeley, Nigel and Laroche, Olivier and Leese, Florian and Pochon, Xavier and Stoeck, Thorsten and Pawłowski, Jan and Lanzén, Anders", title = "Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap", year = "2020", journal = "Molecular Ecology", abstract = {A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or "in development", hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.}, url = "https://doi.org/10.1111/mec.15472", doi = "10.1111/mec.15472", openalex = "W3002699777", references = "doi101016jgecco2019e00547, doi101016jwatres201803003, doi101038nature11148, doi101038nbt2676, doi101038nrmicro2832, doi101038s41598017125015, doi101038s4200301801926, doi101093nargks1219, doi101093nargky1022, doi101093oso97801987672200010001, doi1011111365243512425, doi101111brv12252, doi101111j14718286200701678x, doi101111mec15060, doi101111mec15472, doi101126science1187512, doi101146annurevecolsys33010802150448, doi1018900012961519970670345saaist20co2, doi101890040922" } @article{doi101111mec15643, author = "Pawłowski, Jan and Apothéloz‐Perret‐Gentil, Laure and Altermatt, Florian", title = "Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring", year = "2020", journal = "Molecular Ecology", abstract = {The last decade brought a spectacular development of so-called environmental (e)DNA studies. In general, "environmental DNA" is defined as DNA isolated from environmental samples, in contrast to genomic DNA that is extracted directly from specimens. However, the variety of different sources of eDNA and the range of taxonomic groups that are targeted by eDNA studies is large, which has led to some discussion about the breadth of the eDNA concept. In particular, there is a recent trend to restrict the use of the term "eDNA" to the DNA of macro-organisms, which are not physically present in environmental samples. In this paper, we argue that such a distinction may not be ideal, because the eDNA signal can come from organisms across the whole tree of life. Consequently, we advocate that the term "eDNA" should be used in its generic sense, as originally defined, encompassing the DNA of all organisms present in environmental samples, including microbial, meiofaunal and macrobial taxa. We first suggest specifying the environmental origin of the DNA sample, such as water eDNA, sediment eDNA or soil eDNA. A second specification would then define the taxonomic group targeted through polymerase chain reaction amplification, such as fish eDNA, invertebrate eDNA and bacterial eDNA. This terminology does also not require assumptions about the specific state of the DNA sampled (intracellular or extracellular). We hope that such terminology will help better define the scope of eDNA studies, especially for environmental managers, who use them as reference in routine biomonitoring and bioassessment.}, url = "https://doi.org/10.1111/mec.15643", doi = "10.1111/mec.15643", openalex = "W3088144981", references = "doi101038s41598017125015, doi101093oso97801987672200010001, doi101111j1365294x201205505x" } @article{doi101002ece37382, author = "Fediajevaite, Julija and Priestley, Victoria and Arnold, Richard and Savolainen, Vincent", title = "Meta‐analysis shows that environmental DNA outperforms traditional surveys, but warrants better reporting standards", year = "2021", journal = "Ecology and Evolution", abstract = ": 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.", url = "https://doi.org/10.1002/ece3.7382", doi = "10.1002/ece3.7382", openalex = "W3137998749", references = "doi101007s10531020019800, doi101016jwatres201803003" } @article{doi101002edn3185, author = "Rourke, Meaghan L. and Fowler, Ashley M. and Hughes, Julian M. and Broadhurst, Matt K. and DiBattista, Joseph D. and Fielder, D. Stewart and Walburn, Jackson Wilkes and Furlan, Elise M.", title = "Environmental DNA (eDNA) as a tool for assessing fish biomass: A review of approaches and future considerations for resource surveys", year = "2021", journal = "Environmental DNA", abstract = "Abstract Environmental DNA (eDNA) has revolutionized our ability to identify the presence and distributions of terrestrial and aquatic organisms. Recent evidence suggests the concentration of eDNA could also provide a rapid, cost‐effective indicator of abundance and/or biomass for fisheries stock assessments. Globally, fisheries resources are under immense pressure, and their sustainable harvest requires accurate information on the sizes of fished stocks. However, in many cases the required information remains elusive because of a reliance on imprecise or costly fishery‐dependent and independent data. Here, we review the literature describing relationships between eDNA concentrations and fish abundance and/or biomass, as well as key influencing factors, as a precursor to determining the broader utility of eDNA for monitoring fish populations. We reviewed 63 studies published between 2012 and 2020 and found 90\% identified positive relationships between eDNA concentrations and the abundance and/or biomass of focal species. Key influencing biotic factors included the taxon examined as well as their body size, distribution, reproduction, and migration. Key abiotic factors mostly comprised hydrological processes affecting the dispersal and persistence of eDNA, especially water flow and temperature, although eDNA collection methods were also influential. The cumulative influence of these different factors likely explains the substantial variability observed in eDNA concentrations, both within and among studies. Nevertheless, there is considerable evidence to support using eDNA as an ancillary tool for assessing fish population abundance and/or biomass across discrete spatio‐temporal scales, following preliminary investigations to determine species‐ and context‐specific factors influencing the eDNA abundance/biomass relationship. Advantages of eDNA monitoring relative to other approaches include reduced costs, increased efficiencies, and nonlethal sampling.", url = "https://doi.org/10.1002/edn3.185", doi = "10.1002/edn3.185", openalex = "W3133743945", references = "doi101016jtree200409004, doi101038s4200301801926, doi101038srep40368, doi101098rspb20191409, doi101111mec14350" } @article{doi101016jscitotenv2021146891, author = "Veilleux, Heather D. and Misutka, Melissa D. and Glover, Chris N.", title = "Environmental DNA and environmental RNA: Current and prospective applications for biological monitoring", year = "2021", journal = "The Science of The Total Environment", url = "https://doi.org/10.1016/j.scitotenv.2021.146891", doi = "10.1016/j.scitotenv.2021.146891", openalex = "W3145480541", references = "doi101007s10531020019800" } @article{doi101038s41598021822054, author = "Marshall, Nathaniel T. and Vanderploeg, Henry A. and Chaganti, Subba Rao", title = "Environmental (e)RNA advances the reliability of eDNA by predicting its age", year = "2021", journal = "Scientific Reports", abstract = "Environmental DNA (eDNA) analysis has advanced conservation biology and biodiversity management. However, accurate estimation of age and origin of eDNA is complicated by particle transport and the presence of legacy genetic material, which can obscure accurate interpretation of eDNA detection and quantification. To understand the state of genomic material within the environment, we investigated the degradation relationships between (a) size of fragments (long vs short), (b) genomic origins (mitochondrial vs nuclear), (c) nucleic acids (eDNA vs eRNA), and (d) RNA types (messenger (m)RNA vs ribosomal (r)RNA) from non-indigenous Dreissena mussels. Initial concentrations of eRNA followed expected transcriptional trends, with rRNAs found at > 1000 × that of eDNA, and a mitosis-associated mRNA falling below detection limits within 24 h. Furthermore, the ratio of eRNA:eDNA significantly decreased throughout degradation, potentially providing an estimate for the age of genomic material. Thus, eRNA quantification can increase detection due to the high concentrations of rRNAs. Furthermore, it may improve interpretation of positive detections through the eRNA:eDNA ratio and/or by detecting low abundant mitosis-associated mRNAs that degrade within \textasciitilde\ 24 h.", url = "https://doi.org/10.1038/s41598-021-82205-4", doi = "10.1038/s41598-021-82205-4", openalex = "W3126207216", references = "doi101007s10531020019800" } @article{doi101093bioscibiab073, author = "Lahoz‐Monfort, José J. and Magrath, Michael J. L.", title = "A Comprehensive Overview of Technologies for Species and Habitat Monitoring and Conservation", year = "2021", journal = "BioScience", abstract = "The range of technologies currently used in biodiversity conservation is staggering, with innovative uses often adopted from other disciplines and being trialed in the field. We provide the first comprehensive overview of the current (2020) landscape of conservation technology, encompassing technologies for monitoring wildlife and habitats, as well as for on-the-ground conservation management (e.g., fighting illegal activities). We cover both established technologies (routinely deployed in conservation, backed by substantial field experience and scientific literature) and novel technologies or technology applications (typically at trial stage, only recently used in conservation), providing examples of conservation applications for both types. We describe technologies that deploy sensors that are fixed or portable, attached to vehicles (terrestrial, aquatic, or airborne) or to animals (biologging), complemented with a section on wildlife tracking. The last two sections cover actuators and computing (including web platforms, algorithms, and artificial intelligence).", url = "https://doi.org/10.1093/biosci/biab073", doi = "10.1093/biosci/biab073", openalex = "W3185673854", references = "doi101007s10531020019800, doi1011112041210x13256" } @article{doi101146annurevenviron020420042100, author = "Polasky, Stephen and Dampha, Nfamara K.", title = "Discounting and Global Environmental Change", year = "2021", journal = "Annual Review of Environment and Resources", abstract = "Discounting plays a central role in decisions about global environmental change that affect the well-being of future generations. Discounting the future more heavily tilts decisions toward the present, making it less likely that society will undertake actions to mitigate climate change or other global environmental change. This article reviews the standard economics approach to discounting that emerges from solving for optimal savings and investment through time. Discounting depends on the pure rate of time preference and differences in consumption levels across time, giving rise to different marginal utilities of consumption. Discounting for problems like climate change that impact future generations involves an ethical dimension. This article includes discussions of ethical dimensions of discounting related to intragenerational and intergenerational equity and also covers behavioral economics, ecological economics, and mainstream economics approaches to discounting. The article closes with a review of the debates over discounting in climate change policy.", url = "https://doi.org/10.1146/annurev-environ-020420-042100", doi = "10.1146/annurev-environ-020420-042100", openalex = "W3157594988", references = "doi1023071885257" } @article{doi101146annurevmarine041421082251, author = "Miya, Masaki", title = "Environmental DNA Metabarcoding: A Novel Method for Biodiversity Monitoring of Marine Fish Communities", year = "2021", journal = "Annual Review of Marine Science", abstract = "Environmental DNA (eDNA) is genetic material that has been shed from macroorganisms. It has received increased attention as an indirect marker for biodiversity monitoring. This article reviews the current status of eDNA metabarcoding (simultaneous detection of multiple species) as a noninvasive and cost-effective approach for monitoring marine fish communities and discusses the prospects for this growing field. eDNA metabarcoding coamplifies short fragments of fish eDNA across a wide variety of taxa and, coupled with high-throughput sequencing technologies, allows massively parallel sequencing to be performed simultaneously for dozens to hundreds of samples. It can predict species richness in a given area, detect habitat segregation and biogeographic patterns from small to large spatial scales, and monitor the spatiotemporal dynamics of fish communities. In addition, it can detect an anthropogenic impact on fish communities through evaluation of their functional diversity. Recognizing the strengths and limitations of eDNA metabarcoding will help ensure that continuous biodiversity monitoring at multiple sites will be useful for ecosystem conservation and sustainable use of fishery resources, possibly contributing to achieving the targets of the United Nations' Sustainable Development Goal 14 for 2030.", url = "https://doi.org/10.1146/annurev-marine-041421-082251", doi = "10.1146/annurev-marine-041421-082251", openalex = "W3187258794", references = "doi1010029781119174844, doi101007s10531020019800, doi101016jcub201704060, doi101016jgecco2019e00547, doi101038s41598017125015, doi101093oso97801987672200010001, doi101098rspb20191409" } @article{doi101016jcub202112014, author = "Lynggaard, Christina and Bertelsen, Mads F. and Jensen, Casper Vindahl and Johnson, Matthew S. and Frøslev, Tobias Guldberg and Olsen, Morten Tange and Bohmann, Kristine", title = "Airborne environmental DNA for terrestrial vertebrate community monitoring", year = "2022", journal = "Current Biology", url = "https://doi.org/10.1016/j.cub.2021.12.014", doi = "10.1016/j.cub.2021.12.014", openalex = "W4225722231", references = "doi101038s4146701701312x" } @article{doi101021acsest1c07638, author = "Mauvisseau, Quentin and Harper, Lynsey R. and Sander, Michael and Hanner, Robert and Kleyer, Hannah and Deiner, Kristy", title = "The Multiple States of Environmental DNA and What Is Known about Their Persistence in Aquatic Environments", year = "2022", journal = "Environmental Science \& Technology", abstract = "Increased use of environmental DNA (eDNA) analysis for indirect species detection has spurred the need to understand eDNA persistence in the environment. Understanding the persistence of eDNA is complex because it exists in a mixture of different states (e.g., dissolved, particle adsorbed, intracellular, and intraorganellar), and each state is expected to have a specific decay rate that depends on environmental parameters. Thus, improving knowledge about eDNA conversion rates between states and the reactions that degrade eDNA in different states is needed. Here, we focus on eukaryotic extraorganismal eDNA, outline how water chemistry and suspended mineral particles likely affect conversion among each eDNA state, and indicate how environmental parameters affect persistence of states in the water column. On the basis of deducing these controlling parameters, we synthesized the eDNA literature to assess whether we could already derive a general understanding of eDNA states persisting in the environment. However, we found that these parameters are often not being measured or reported when measured, and in many cases very few experimental data exist from which to draw conclusions. Therefore, further study of how environmental parameters affect eDNA state conversion and eDNA decay in aquatic environments is needed. We recommend analytic controls that can be used during the processing of water to assess potential losses of different eDNA states if all were present in a water sample, and we outline future experimental work that would help determine the dominant eDNA states in water.", url = "https://doi.org/10.1021/acs.est.1c07638", doi = "10.1021/acs.est.1c07638", openalex = "W4225391021", references = "doi101098rspb20191409, doi101111mec15060" } @article{doi101038s43586022001444, author = "Fraisl, Dilek and Hager, Gerid and Bedessem, Baptiste and Gold, Margaret M. and Hsing, Pen‐Yuan and Danielsen, Finn and Hitchcock, Colleen and Hulbert, Joseph M. and Piera, Jaume and Spiers, Helen and Thiel, Martín and Haklay, Muki", title = "Citizen science in environmental and ecological sciences", year = "2022", journal = "Nature Reviews Methods Primers", abstract = "Citizen science is an increasingly acknowledged approach applied in many scientific domains, and particularly within the environmental and ecological sciences, in which non-professional participants contribute to data collection to advance scientific research. We present contributory citizen science as a valuable method to scientists and practitioners within the environmental and ecological sciences, focusing on the full life cycle of citizen science practice, from design to implementation, evaluation and data management. We highlight key issues in citizen science and how to address them, such as participant engagement and retention, data quality assurance and bias correction, as well as ethical considerations regarding data sharing. We also provide a range of examples to illustrate the diversity of applications, from biodiversity research and land cover assessment to forest health monitoring and marine pollution. The aspects of reproducibility and data sharing are considered, placing citizen science within an encompassing open science perspective. Finally, we discuss its limitations and challenges and present an outlook for the application of citizen science in multiple science domains. Contributory citizen science is a method in which non-professional participants contribute to data collection in whole or in part to advance scientific research. This Primer outlines the use of citizen science in the environmental and ecological sciences, discussing participant engagement, data quality assurance and bias correction.", url = "https://doi.org/10.1038/s43586-022-00144-4", doi = "10.1038/s43586-022-00144-4", openalex = "W4293231014", references = "doi101016jbiocon201609004" } @book{doi101093oso97801988565660010001, author = "Allendorf, Fred W. and Funk, W. Chris and Aitken, Sally N. and Byrne, Margaret and Luikart, Gordon and Antunes, Agostinho", title = "Conservation and the Genomics of Populations", year = "2022", abstract = "Abstract Loss of biodiversity is among the greatest problems facing the world today. Conservation and the Genomics of Populations gives a comprehensive overview of the essential background, concepts, and tools needed to understand how genetic information can be used to conserve species threatened with extinction, and to manage species of ecological or commercial importance. New molecular techniques, statistical methods, and computer programs, genetic principles, and methods are becoming increasingly useful in the conservation of biological diversity. Using a balance of data and theory, coupled with basic and applied research examples, this book examines genetic and phenotypic variation in natural populations, the principles and mechanisms of evolutionary change, the interpretation of genetic data from natural populations, and how these can be applied to conservation. The book includes examples from plants, animals, and microbes in wild and captive populations. This third edition has been thoroughly revised to include advances in genomics and contains new chapters on population genomics, genetic monitoring, and conservation genetics in practice, as well as new sections on climate change, emerging diseases, metagenomics, and more. More than one-third of the references in this edition were published after the previous edition. Each of the 24 chapters and the Appendix end with a Guest Box written by an expert who provides an example of the principles presented in the chapter from their own work. This book is essential for advanced undergraduate and graduate students of conservation genetics, natural resource management, and conservation biology, as well as professional conservation biologists and policy-makers working for wildlife and habitat management agencies. Much of the book will also interest nonprofessionals who are curious about the role of genetics in conservation and management of wild and captive populations.", url = "https://doi.org/10.1093/oso/9780198856566.001.0001", doi = "10.1093/oso/9780198856566.001.0001", openalex = "W4224274233", references = "doi101002evl3189, doi101007s10531020019800, doi101016jppees201002002, doi101046j14209101200100339x, doi101093czzow088, doi101093genetics902349, doi101111gcb13976" } @article{doi101111mec16659, author = "Yao, Meng and Zhang, Shan and Lu, Qi and Chen, Xiaoyu and Zhang, Si‐Yu and Kong, Yueqiao and Zhao, Jindong", title = "Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward", year = "2022", journal = "Molecular Ecology", abstract = "Vast global declines of freshwater and marine fish diversity and population abundance pose serious threats to both ecosystem sustainability and human livelihoods. Environmental DNA (eDNA)-based biomonitoring provides robust, efficient, and cost-effective assessment of species occurrences and population trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks to facilitate fish conservation and fisheries management. However, the many technical considerations and rapid developments underway in the eDNA arena can overwhelm researchers and practitioners new to the field. Here, we systematically analysed 416 fish eDNA studies to summarize research trends in terms of investigated targets, research aims, and study systems, and reviewed the applications, rationales, methodological considerations, and limitations of eDNA methods with an emphasis on fish and fisheries research. We highlighted how eDNA technology may advance our knowledge of fish behaviour, species distributions, population genetics, community structures, and ecological interactions. We also synthesized the current knowledge of several important methodological concerns, including the qualitative and quantitative power eDNA has to recover fish biodiversity and abundance, and the spatial and temporal representations of eDNA with respect to its sources. To facilitate ecological applications implementing fish eDNA techniques, recent literature was summarized to generate guidelines for effective sampling in lentic, lotic, and marine habitats. Finally, we identified current gaps and limitations, and pointed out newly emerging research avenues for fish eDNA. As methodological optimization and standardization improve, eDNA technology should revolutionize fish monitoring and promote biodiversity conservation and fisheries management that transcends geographic and temporal boundaries.", url = "https://doi.org/10.1111/mec.16659", doi = "10.1111/mec.16659", openalex = "W4291963967", references = "doi101002edn3232, doi101038s4146702121655w, doi101098rspb20191409, doi101111mec15472" } @article{doi101016jscitotenv2023162322, author = "Takahashi, Miwa and Saccò, Mattia and Kestel, Joshua H. and Nester, Georgia and Campbell, Matthew A. and van der Heyde, Mieke and Heydenrych, Matthew J. and Juszkiewicz, David J. and Nevill, Paul and Dawkins, Kathryn L. and Bessey, Cindy and Fernandes, Kristen and Miller, Haylea C. and Power, Matthew and Mousavi‐Derazmahalleh, Mahsa and Newton, Joshua P. and White, Nicole E. and Richards, Zoe T. and Allentoft, Morten E.", title = "Aquatic environmental DNA: A review of the macro-organismal biomonitoring revolution", year = "2023", journal = "The Science of The Total Environment", abstract = "Environmental DNA (eDNA) is the fastest growing biomonitoring tool fuelled by two key features: time efficiency and sensitivity. Technological advancements allow rapid biodiversity detection at both species and community levels with increasing accuracy. Concurrently, there has been a global demand to standardise eDNA methods, but this is only possible with an in-depth overview of the technological advancements and a discussion of the pros and cons of available methods. We therefore conducted a systematic literature review of 407 peer-reviewed papers on aquatic eDNA published between 2012 and 2021. We observed a gradual increase in the annual number of publications from four (2012) to 28 (2018), followed by a rapid growth to 124 publications in 2021. This was mirrored by a tremendous diversification of methods in all aspects of the eDNA workflow. For example, in 2012 only freezing was applied to preserve filter samples, whereas we recorded 12 different preservation methods in the 2021 literature. Despite an ongoing standardisation debate in the eDNA community, the field is seemingly moving fast in the opposite direction and we discuss the reasons and implications. Moreover, by compiling the largest PCR-primer database to date, we provide information on 522 and 141 published species-specific and metabarcoding primers targeting a wide range of aquatic organisms. This works as a user-friendly 'distillation' of primer information that was hitherto scattered across hundreds of papers, but the list also reflects which taxa are commonly studied with eDNA technology in aquatic environments such as fish and amphibians, and reveals that groups such as corals, plankton and algae are under-studied. Efforts to improve sampling and extraction methods, primer specificity and reference databases are crucial to capture these ecologically important taxa in future eDNA biomonitoring surveys. In a rapidly diversifying field, this review synthetises aquatic eDNA procedures and can guide eDNA users towards best practice.", url = "https://doi.org/10.1016/j.scitotenv.2023.162322", doi = "10.1016/j.scitotenv.2023.162322", openalex = "W4321253950", references = "doi101002edn3232, doi101007s10531020019800, doi101111j1365294x201205505x" } @article{doi101016jtig202301005, author = "Theißinger, Kathrin and Fernandes, Carlos and Formenti, Giulio and Bista, Iliana and Berg, Paul R. and Bleidorn, Christoph and Bombarely, Aureliano and Crottini, Angelica and Gallo, Guido Roberto and Godoy, José A. and Jentoft, Sissel and Malukiewicz, Joanna and Mouton, Alice and Oomen, Rebekah A. and Paez, Sadye and Palsbøll, Per J. and Pampoulie, Christophe and Ruiz‐López, María José and Secomandi, Simona and Svardal, Hannes and Theofanopoulou, Constantina and de Vries, Jan and Waldvogel, Ann‐Marie and Zhang, Guojie and Jarvis, Erich D. and Bálint, Miklós and Ciofi, Claúdio and Waterhouse, Robert M. and Mazzoni, Camila J. and Höglund, ‎Jacob and Aghayan, Sargis A. and Alioto, Tyler and Almudí, Isabel and Álvarez, Nadir and Alves, Paulo C. and Amorim, Isabel R. and Antunes, Agostinho and Arribas, Paula and Baldrián, Petr and Bertorelle, Giorgio and Böhne, Astrid and Bonisoli‐Alquati, Andrea and Boštjančić, Ljudevit Luka and Boussau, Bastien and Breton, Catherine and Bužan, Elena and Campos, Paula F. and Carreras, Carlos and Castro, L. Filipe C. and Chueca, Luis J. and Čiampor, Fedor and Conti, Elena and Cook‐Deegan, Robert and Croll, Daniel and Cunha, Mónica V. and Delsuc, Frédéric and Dennis, Alice B. and Dimitrov, Dimitar and Faria, Rui and Favre, Adrien and Fédrigo, Olivier and Fernández, Rosa and Ficetola, Gentile Francesco and Flot, Jean‐François and Gabaldón, Toni and Agius, D. and Giani, Alice Maria and Gilbert, M. Thomas P. and Grebenc, Tine and Guschanski, Katerina and Guyot, Romain and Hausdorf, Bernhard and Hawlitschek, Oliver and Heintzman, Peter D. and Heinze, Berthold and Hiller, Michael and Husemann, Martin and Iannucci, Alessio and Irisarri, Iker and Jakobsen, Kjetill S. and Klinga, Peter and Kloch, Agnieszka and Kratochwil, Claudius F. and Kusche, Henrik and Layton, Kara K S and Leonard, Jennifer A. and Lerat, Emmanuelle and Liti, Gianni and Manousaki, Tereza and Marquès‐Bonet, Tomàs and Matos‐Maraví, Pável and Matschiner, Michael and Maumus, Florian and Cartney, Ann M. Mc and Meiri, Shai and Melo‐Ferreira, José and Mengual, Ximo and Monaghan, Michael T. and Montagna, Matteo and Mysłajek, Robert W.", title = "How genomics can help biodiversity conservation", year = "2023", journal = "Trends in Genetics", abstract = "The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.", url = "https://doi.org/10.1016/j.tig.2023.01.005", doi = "10.1016/j.tig.2023.01.005", openalex = "W4321019193", references = "doi101016jgecco2019e00547, doi101038s415590180717x, doi101111mec14350, doi101111mec14726" }