scholarly journals Seasonal and diel signature of eastern hellbender environmental DNA

2017 ◽  
Vol 82 (1) ◽  
pp. 217-225 ◽  
Author(s):  
Mizuki K. Takahashi ◽  
Mark J. Meyer ◽  
Carolyn Mcphee ◽  
Jordan R. Gaston ◽  
Matthew D. Venesky ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Eastern Hellbender

Using environmental DNA and occupancy modelling to identify drivers of eastern hellbender (Cryptobranchus alleganiensis alleganiensis) extirpation

2018 ◽  
Vol 64 (1) ◽  
pp. 208-221 ◽  
Author(s):  
Sean M. Wineland ◽  
Shane M. Welch ◽  
Thomas K. Pauley ◽  
Joseph J. Apodaca ◽  
Max Olszack ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Occupancy Modelling ◽  
Cryptobranchus Alleganiensis ◽  
Eastern Hellbender

An eDNA approach to detect eastern hellbenders (Cryptobranchus a. alleganiensis) using samples of water

2012 ◽  
Vol 39 (7) ◽  
pp. 629 ◽  
Author(s):  
Zachary H. Olson ◽  
Jeffrey T. Briggler ◽  
Rod N. Williams
Keyword(s):  
Water Samples ◽  
Effective Means ◽  
Environmental Dna ◽  
Cost Effective ◽  
Negative Control ◽  
Specificity And Sensitivity ◽  
Genetic Sampling ◽  
Conservation Concern ◽  
Species Specific ◽  
Eastern Hellbender

Context Environmental DNA, or eDNA, methods are a novel application of non-invasive genetic sampling in which DNA from organisms is detected via sampling of water or soil, typically for the purposes of determining the presence or absence of an organism. eDNA methods have the potential to revolutionise the study of rare or endangered taxa. Aims We evaluated the efficacy of eDNA sampling to detect populations of an amphibian of conservation concern, the eastern hellbender (Cryptobranchus a. alleganiensis), indirectly from their aquatic environments. Methods We developed species-specific primers, validated their specificity and sensitivity, and assessed the utility of our methods in silico and in laboratory trials. In the field, we collected water samples from three sites with known densities of hellbenders, and from one site where hellbenders do not occur. We filtered water samples, extracted DNA from filters, and assayed the extraction products for hellbender DNA by using polymerase chain reaction (PCR) and gel electrophoresis. Key results Our methods detected hellbenders at densities approaching the lowest of reported natural densities. The low-density site (0.16 hellbenders per 100 m2) yielded two positive amplifications, the medium-density site (0.38 hellbenders per 100 m2) yielded eight positive amplifications, and the high-density site (0.88 hellbenders per 100 m2) yielded 10 positive amplifications. The apparent relationship between density and detection was obfuscated when river discharge was considered. There was no amplification in any negative control. Conclusion eDNA methods may represent a cost-effective means by which to establish broad-scale patterns of occupancy for hellbenders. Implications eDNA can be considered a valuable tool for detecting many species that are otherwise difficult to study.

scholarly journals Noninvasive Method for a Statewide Survey of Eastern HellbendersCryptobranchus alleganiensisUsing Environmental DNA

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Amy J. Santas ◽  
Tyler Persaud ◽  
Barbara A. Wolfe ◽  
Jenise M. Bauman
Keyword(s):  
Population Density ◽  
Survey Methods ◽  
Aquatic Organisms ◽  
Environmental Dna ◽  
Specific Primers ◽  
Filtration Time ◽  
Sampling Protocols ◽  
Welfare Implications ◽  
Historical Accounts ◽  
Eastern Hellbender

Traditional survey methods of aquatic organisms may be difficult, lengthy, and destructive to the habitat. Some methods are invasive and can be harmful to the target species. The use of environmental DNA (eDNA) has proven to be effective at detecting low population density aquatic macroorganisms. This study refined the technique to support statewide surveys. Hellbender presence was identified by using hellbender specific primers (cytochrome b gene) to detect eDNA in water samples collected at rivers, streams and creeks in Ohio and Kentucky with historical accounts of the imperiled eastern hellbender (Cryptobranchus a. alleganiensis). Two sampling protocols are described; both significantly reduced the amount of water required for collection from the previously described 6 L collection. Two-liter samples were adequate to detect hellbender presence in natural waterways where hellbenders have been previously surveyed in both Ohio and Kentucky—1 L samples were not reliable. DNA extracted from 3 L of water collected onto multiple filters (1 L/filter) could be combined and concentrated through ethanol precipitation, supporting amplification of hellbender DNA and dramatically reducing the filtration time. This method improves the efficiency and welfare implications of sampling methods for reclusive aquatic species of low population density for statewide surveys that involve collecting from multiple watersheds.

scholarly journals Environmental DNA improves Eastern Hellbender ( Cryptobranchus alleganiensis alleganiensis ) detection over conventional sampling methods

2019 ◽  
Vol 1 (1) ◽  
pp. 86-96 ◽  
Author(s):  
Sean M. Wineland ◽  
Rachel F. Arrick ◽  
Shane M. Welch ◽  
Thomas K. Pauley ◽  
Jennifer J. Mosher ◽  
...  
Keyword(s):  
Sampling Methods ◽  
Environmental Dna ◽  
Cryptobranchus Alleganiensis ◽  
Eastern Hellbender

COMPARATIVE STUDY BETWEEN FISH COLLECTION BY NATIONAL CENSUS ON RIVER ENVIRONMENT AND ENVIRONMENTAL DNA METABARCODING

2018 ◽  
Vol 74 (5) ◽  
pp. I_415-I_420 ◽  
Author(s):  
Yoshihisa AKAMATSU ◽  
Takayoshi TSUZUKI ◽  
Ryota YOKOYAMA ◽  
Yayoi FUNAHASHI ◽  
Munehiro OHTA ◽  
...  
Keyword(s):  
Comparative Study ◽  
Environmental Dna ◽  
Dna Metabarcoding ◽  
Fish Collection

Environmental DNA for functional diversity

2018 ◽  
Author(s):  
Pierre Taberlet ◽  
Aurélie Bonin ◽  
Lucie Zinger ◽  
Eric Coissac
Keyword(s):  
Functional Groups ◽  
Functional Diversity ◽  
Environmental Dna ◽  
Soil Organisms ◽  
Meaningful Information ◽  
Dna Metabarcoding ◽  
Pros And Cons ◽  
Target Community

Chapter 10 “Environmental DNA for functional diversity” discusses the potential of environmental DNA to assess functional diversity. It first focuses on DNA metabarcoding and discusses the extent to which this approach can be used and/or optimized to retrieve meaningful information on the functions of the target community. This knowledge usually involves coarsely defined functional groups (e.g., woody, leguminous, graminoid plants; shredders or decomposer soil organisms; pathogenicity or decomposition role of certain microorganisms). Chapter 10 then introduces metagenomics and metatranscriptomics approaches, their advantages, but also the challenges and solutions to appropriately sampling, sequencing these complex DNA/RNA populations. Chapter 10 finally presents several strategies and software to analyze metagenomes/metatranscriptomes, and discusses their pros and cons.

Environmental DNA

2018 ◽  
Author(s):  
Pierre Taberlet ◽  
Aurélie Bonin ◽  
Lucie Zinger ◽  
Eric Coissac
Keyword(s):  
Graduate Students ◽  
Feeding Habits ◽  
Environmental Dna ◽  
Research Field ◽  
Background Information ◽  
Ecological Processes ◽  
Biodiversity Research ◽  
Dna Metabarcoding ◽  
Standard Information

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.

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