scholarly journals Generating and testing ecological hypotheses at the pondscape with environmental DNA metabarcoding: A case study on a threatened amphibian

2020 ◽  
Vol 2 (2) ◽  
pp. 184-199 ◽  
Author(s):  
Lynsey R. Harper ◽  
Lori Lawson Handley ◽  
Christoph Hahn ◽  
Neil Boonham ◽  
Helen C. Rees ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Dna Metabarcoding

scholarly journals Testing the performance of environmental DNA metabarcoding for surveying highly diverse tropical fish communities: A case study from Lake Tanganyika

2019 ◽  
Vol 2 (1) ◽  
pp. 24-41 ◽  
Author(s):  
Christopher J. Doble ◽  
Helen Hipperson ◽  
Walter Salzburger ◽  
Gavin J. Horsburgh ◽  
Chacha Mwita ◽  
...  
Keyword(s):  
Lake Tanganyika ◽  
Fish Communities ◽  
Environmental Dna ◽  
Tropical Fish ◽  
Dna Metabarcoding

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

Mammal Review ◽  
2020 ◽  
Vol 50 (3) ◽  
pp. 221-225 ◽  
Author(s):  
Naiara Guimarães Sales ◽  
Mariane da Cruz Kaizer ◽  
Ilaria Coscia ◽  
Joseph C. Perkins ◽  
Andrew Highlands ◽  
...  
Keyword(s):  
Atlantic Forest ◽  
Environmental Dna ◽  
Neotropical Mammals ◽  
Dna Metabarcoding

scholarly journals Environmental DNA metabarcoding as an effective and rapid tool for fish monitoring in canals:

2018 ◽  
Author(s):  
Allan D McDevitt ◽  
Naiara Guimaraes Sales ◽  
Samuel S Browett ◽  
Abbie Sparnenn ◽  
Stefano Mariani ◽  
...  
Keyword(s):  
Fish Assemblages ◽  
Fish Communities ◽  
Environmental Dna ◽  
Cost Effective ◽  
Aquatic Habitats ◽  
Dna Metabarcoding ◽  
Canal Systems ◽  
Rapid Tool ◽  
Fish Monitoring

Environmental DNA (eDNA) metabarcoding has revolutionized biomonitoring of aquatic habitats. Man-made canal systems are among the least-studied environments in terms of biodiversity in Britain. Here we focus on a case study along an English canal comparing eDNA metabarcoding with two types of electrofishing techniques (wade-and-reach and boom-boat). In addition to corroborating data obtained by electrofishing, eDNA provided a wider snapshot of fish assemblages. Given the semi-lotic nature of canals, we encourage the use of eDNA as a fast and cost-effective tool to detect and monitor whole fish communities.

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.

Environmental DNA metabarcoding as a useful tool for evaluating terrestrial mammal diversity in tropical forests

2021 ◽  
Author(s):  
José Luis Mena ◽  
Hiromi Yagui ◽  
Vania Tejeda ◽  
Emilio Bonifaz ◽  
Eva Bellemain ◽  
...  
Keyword(s):  
Tropical Forests ◽  
Environmental Dna ◽  
Terrestrial Mammal ◽  
Dna Metabarcoding ◽  
Mammal Diversity
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