The ecology of environmental DNA and implications for conservation genetics
Reads0
Chats0
TLDR
This work outlines a framework for understanding the ecology of eDNA, including the origin, state, transport, and fate of extraorganismal genetic material, and identifies frontiers of conservation-focused eDNA application where it sees the most potential for growth.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.read more
Citations
More filters
Journal ArticleDOI
Environmental DNA metabarcoding: transforming how we survey animal and plant communities
Kristy Deiner,Holly M. Bik,Elvira Mächler,Elvira Mächler,Mathew Seymour,Anaïs Lacoursière-Roussel,Florian Altermatt,Florian Altermatt,Simon Creer,Iliana Bista,Iliana Bista,David M. Lodge,Natasha de Vere,Michael E. Pfrender,Louis Bernatchez +14 more
TL;DR: The use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance are reviewed, which distill what is known about the ability of different eDNA sample types to approximate richness in space and across time.
Journal ArticleDOI
Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA
TL;DR: In this paper, 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.
Journal ArticleDOI
Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment
Michael Stat,Megan J. Huggett,Rachele Bernasconi,Joseph D. DiBattista,Tina E. Berry,Stephen J. Newman,Stephen J. Newman,Euan S. Harvey,Michael Bunce +8 more
TL;DR: The potential of eDNA to inform on the breadth of biodiversity present in a tropical marine environment is investigated, and the sensitivity and low cost of e DNA metabarcoding are advocated, urging this approach to be rapidly integrated into biomonitoring programs.
Journal ArticleDOI
Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea
Satoshi Yamamoto,Reiji Masuda,Yukuto Sato,Tetsuya Sado,Hitoshi Araki,Michio Kondoh,Toshifumi Minamoto,Masaki Miya +7 more
TL;DR: The ability of eDNA metabarcoding to reveal fish community structures in species-rich coastal waters by using high-performance fish-universal primers and systematic spatial water sampling at 47 stations covering ~11 km2 revealed the fish community structure at a species resolution.
Journal ArticleDOI
Invasion Science: A Horizon Scan of Emerging Challenges and Opportunities
Anthony Ricciardi,Tim M. Blackburn,Tim M. Blackburn,James T. Carlton,Jaimie T. A. Dick,Philip E. Hulme,Josephine C. Iacarella,Jonathan M. Jeschke,Jonathan M. Jeschke,Andrew M. Liebhold,Julie L. Lockwood,Hugh J. MacIsaac,Petr Pyšek,Petr Pyšek,David M. Richardson,Gregory M. Ruiz,Daniel Simberloff,William J. Sutherland,David A. Wardle,David A. Wardle,David C. Aldridge +20 more
TL;DR: Diverse issues suggest an expanding interdisciplinary role for invasion science in biosecurity and ecosystem management, burgeoning applications of biotechnology in alien species detection and control, and new frontiers in the microbial ecology of invasions.
References
More filters
Journal ArticleDOI
Instability and decay of the primary structure of DNA
TL;DR: The spontaneous decay of DNA is likely to be a major factor in mutagenesis, carcinogenesis and ageing, and also sets limits for the recovery of DNA fragments from fossils.
Journal ArticleDOI
Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies
TL;DR: Improved quality-filtering pipeline was applied to several benchmarking studies and observed that even with the stringent data curation pipeline, biases in the data generation pipeline and batch effects were observed that could potentially confound the interpretation of microbial community data.
Journal ArticleDOI
Environmental DNA - An emerging tool in conservation for monitoring past and present biodiversity
TL;DR: The achievements gained through analyses of eDNA from macro-organisms in a conservation context are reviewed, its potential advantages and limitations are discussed, and it is expected 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.
Journal ArticleDOI
Species detection using environmental DNA from water samples.
TL;DR: A novel approach, based on the limited persistence of DNA in the environment, to detect the presence of a species in fresh water, using specific primers that amplify short mitochondrial DNA sequences to track the existence of a frog in controlled environments and natural wetlands.