Establishing an environmental DNA method to detect and estimate the biomass of Sakhalin taimen, a critically endangered Asian salmonid

Limnology ◽  
2017 ◽  
Vol 19 (2) ◽  
pp. 219-227 ◽  
Author(s):  
Hiroki Mizumoto ◽  
Hirokazu Urabe ◽  
Takashi Kanbe ◽  
Michio Fukushima ◽  
Hitoshi Araki
Keyword(s):  
Environmental Dna ◽  
Critically Endangered ◽  
Sakhalin Taimen

scholarly journals Environmental DNA sampling in a terrestrial environment: methods to detect a critically endangered frog and a global pathogen

2020 ◽  
Author(s):  
Thomas J. Burns ◽  
Nick Clemann ◽  
Anthony R. van Rooyen ◽  
Ben C. Scheele ◽  
Andrew R. Weeks ◽  
...  
Keyword(s):  
Field Experiments ◽  
Survey Methods ◽  
Environmental Dna ◽  
Wash Water ◽  
Critically Endangered ◽  
Chytrid Fungus ◽  
Amphibian Skin ◽  
Natural Habitats ◽  
Amphibian Species ◽  
Terrestrial Environment

AbstractEnvironmental DNA techniques have become established as a useful tool for biological monitoring and are used extensively to determine species presence in aquatic systems. However, their application in terrestrial systems has been more limited, likely in part due to difficulties in choosing where to sample and ensuring that collected DNA reflects current species presence. We developed methods to sample eDNA in the terrestrial environment and trialled them under controlled and field conditions. We targeted three species, an elusive critically endangered frog, an abundant non-threatened frog, and the globally distributed amphibian skin pathogen chytrid fungus, which has been implicated in the decline of over 500 amphibian species. We used a sandpaper-sampling surface to ‘trap’ DNA. After sampling, we washed the surface and filtered the wash water to gather material for DNA extraction and subsequent qPCR. Our controlled condition experiments demonstrated that frog and chytrid fungus DNA was detectable after as few as five contacts between a frog and the sampling surface. Furthermore, this DNA remained detectable after two weeks in cool, shaded, outdoor conditions. Our field experiments demonstrated that these techniques were transferable to natural habitats, where we detected both the common and rare amphibian target species, as well as chytrid fungus. Field sampling eDNA results were broadly consistent with those derived from conventional survey methods. Our methods have potential application in non-invasive sampling of amphibians and other species in terrestrial systems, broadening the applicability of eDNA techniques for species detection and monitoring.

scholarly journals Comparing conservation monitoring approaches: traditional and environmental DNA tools for a critically endangered mammal

2017 ◽  
Author(s):  
Chanjuan Qu ◽  
Kathryn A Stewart
Keyword(s):  
Data Collection ◽  
Environmental Dna ◽  
Critically Endangered ◽  
Conventional Pcr ◽  
Aquatic Mammal ◽  
Real Time Quantitative Pcr ◽  
Trade Offs ◽  
Sampling Protocols ◽  
Species Specific ◽  
The Cost

While conservation management has made tremendous strides in the last few decades, the decision of knowing where and how to invest (often) small surveying budgets for biodiversity data collection remains a central hurdle for impactful conservation decision making. New analytical tools, such as environmental DNA (eDNA), are now facilitating broader biodiversity monitoring to take place at unprecedented scales, in part due to its time-efficient, and presumably cost-efficient, premise. eDNA approaches vary from conventional PCR (detecting presence/absence of species), metabarcoding (community structure), to qPCR (relative DNA abundance), and knowing when to employ these techniques over traditional sampling protocols could enable conservation practitioners to make informed trade-offs between cost, accuracy, and speed of data collection. Using 12 species-specific primers designed for conventional PCR use in eDNA analysis of the Yangtze Finless Porpoise (Neophocaena asiaeorientalis asiaeorientalis), a critically endangered aquatic mammal within the Yangtze River, we validated and optimized these same primers for use in real-time Quantitative PCR (qPCR). We tested the repeatability and sensitivity of primer each to detect YFP eDNA and subsequently compared the cost of traditional visual sampling to both conventional PCR and qPCR eDNA tools. Our results suggest qPCR to be substantially more sensitive than conventional PCR eDNA analysis, although the later remains the least-expensive sampling option. Still, due to a lack of sensitivity causing an increased probability of false negatives, conventional PCR may not be the most robust sampling method for this taxa and should only be employed as a supplementary tool or when large populations are expected to be present. Alternatively, utilizing qPCR for eDNA protocols is still less-expensive than visual surveying and represents a highly repeatable and sensitive method for this behaviorally elusive species. Presenting a cost assessment of eDNA to traditional surveying practices has scarcely been discussed, while contrasting deliverables to the cost of different eDNA methods has, to date, been ignored. Yet given budgetary constraints, particularly for developing countries where low-governance and high endemism are present, we encourage managers to carefully consider the trade-offs among data accuracy, cost, coverage and speed for biodiversity collections.

Environmental DNA evidence of the Critically Endangered smalltooth sawfish, Pristis pectinata , in historically occupied US waters

2021 ◽  
Author(s):  
Ryan N. Lehman ◽  
Gregg R. Poulakis ◽  
Rachel M. Scharer ◽  
Jill M. Hendon ◽  
Alia G. Court ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Critically Endangered ◽  
Dna Evidence ◽  
Pristis Pectinata

scholarly journals Assessing the potential of environmental DNA metabarcoding for monitoring Neotropical mammals: a case study in the Amazon and Atlantic Forest, Brazil

2019 ◽  
Author(s):  
Naiara Guimarães Sales ◽  
Mariane da Cruz Kaizer ◽  
Ilaria Coscia ◽  
Joseph C. Perkins ◽  
Andrew Highlands ◽  
...  
Keyword(s):  
Atlantic Forest ◽  
Mammalian Species ◽  
Environmental Dna ◽  
Camera Trapping ◽  
Critically Endangered ◽  
Neotropical Mammals ◽  
Dna Metabarcoding ◽  
Biomonitoring Tool

AbstractThe application of environmental DNA (eDNA) metabarcoding as a biomonitoring tool has greatly increased in the last decade. However, most studies have focused on aquatic macro-organisms in temperate areas (e.g., fishes). We apply eDNA metabarcoding to detect the mammalian community in two high-biodiversity regions of Brazil, the Amazon and Atlantic Forest. We identified critically endangered and endangered mammalian species in the Atlantic Forest and Amazon respectively and found congruence with species identified via camera trapping in the Atlantic Forest. In light of our results, we highlight the potential and challenges of eDNA monitoring for mammals in these high biodiverse areas.

scholarly journals Trails of river monsters: Detecting critically endangered Mekong giant catfish Pangasianodon gigas using environmental DNA

2016 ◽  
Vol 7 ◽  
pp. 148-156 ◽  
Author(s):  
Bellemain Eva ◽  
Patricio Harmony ◽  
Gray Thomas ◽  
Guegan Francois ◽  
Valentini Alice ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Critically Endangered ◽  
Pangasianodon Gigas ◽  
Giant Catfish ◽  
Mekong Giant Catfish

Eco-geographic units, population hierarchy, and a two-level conservation strategy with reference to a critically endangered salmonid, Sakhalin taimen Parahucho perryi

2014 ◽  
Vol 16 (2) ◽  
pp. 431-441 ◽  
Author(s):  
Lev A. Zhivotovsky ◽  
Andrey A. Yurchenko ◽  
Vitaly D. Nikitin ◽  
Sergei N. Safronov ◽  
Marina V. Shitova ◽  
...  
Keyword(s):  
Critically Endangered ◽  
Conservation Strategy ◽  
Sakhalin Taimen

scholarly journals First detection of critically endangered scalloped hammerhead sharks (Sphyrna lewini) in Guam, Micronesia, in five decades using environmental DNA

2021 ◽  
Vol 127 ◽  
pp. 107649
Author(s):  
Alyssa M. Budd ◽  
Madalyn K. Cooper ◽  
Agnès Le Port ◽  
Tom Schils ◽  
Matthew S. Mills ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Critically Endangered ◽  
Sphyrna Lewini ◽  
Scalloped Hammerhead ◽  
Hammerhead Sharks
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