DNA-based species detection capabilities using laser transmission spectroscopy

Summary1. 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. 2. Recently, there has been considerable interest in the detection of short species-specific environmental DNA (eDNA) 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. 3. Environmental DNA analysis is increasingly being used in the detection of rare or invasive species and has also been applied to eDNA 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. 4. Different environments require different sampling methodologies, but there remain areas where laboratory methodologies could be standardized to allow results to be compared across studies. 5. Synthesis and applications. We review recently published studies that use eDNA to monitor aquatic populations, discuss the methodologies used and the application of eDNA analysis as a survey tool in ecology. We include innovative ideas for how eDNA can be used for conservation and management citing test cases, for instance, the potential for on-site analyses, including the application of eDNA analysis to carbon nanotube platforms or laser transmission spectroscopy to facilitate rapid on-site detections. The use of eDNA monitoring is already being adopted in the UK for ecological surveys.

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“…) or laser transmission spectroscopy (Mahon et al . ) could also be used to provide rapid on‐site detections.…”

Section: Edna As a Survey Tool For Conservation And Managementmentioning

confidence: 99%

REVIEW: The detection of aquatic animal species using environmental DNA – a review of eDNA as a survey tool in ecology

Rees

Maddison

Middleditch

et al. 2014

Journal of Applied Ecology

829

826

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“…Much interest exists in the application of eDNA barcoding to surveillance of ballast water in ships, a substantial source of aquatic invasions, with novel tools being developed to enable rapid screening by nonspecialists (Mahon et al. ).…”

Section: The Initial Stages – Entrainment Risk and Transportmentioning

confidence: 99%

Biological invasions, climate change and genomics

Chown

Hodgins

Griffin

et al. 2014

Evolutionary Applications

223

218

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The rate of biological invasions is expected to increase as the effects of climate change on biological communities become widespread. Climate change enhances habitat disturbance which facilitates the establishment of invasive species, which in turn provides opportunities for hybridization and introgression. These effects influence local biodiversity that can be tracked through genetic and genomic approaches. Metabarcoding and metagenomic approaches provide a way of monitoring some types of communities under climate change for the appearance of invasives. Introgression and hybridization can be followed by the analysis of entire genomes so that rapidly changing areas of the genome are identified and instances of genetic pollution monitored. Genomic markers enable accurate tracking of invasive species’ geographic origin well beyond what was previously possible. New genomic tools are promoting fresh insights into classic questions about invading organisms under climate change, such as the role of genetic variation, local adaptation and climate pre-adaptation in successful invasions. These tools are providing managers with often more effective means to identify potential threats, improve surveillance and assess impacts on communities. We provide a framework for the application of genomic techniques within a management context and also indicate some important limitations in what can be achieved.

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“…For example, multiple studies have proposed the use of eDNA to detect invasive organisms within ballast waters of transoceanic ships (Li et al 2011;Mahon et al 2012;Egan et al 2013). Similar assays have successfully identified benthic invertebrates and their resting stages within ballast tank sediments (Darling and Tepolt 2008;Harvey et al 2009;Briski et al 2011).…”

Section: Introductionmentioning

confidence: 99%

The ecology of environmental DNA and implications for conservation genetics

2015

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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.

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DNA-based species detection capabilities using laser transmission spectroscopy

Cited by 21 publications

References 31 publications

REVIEW: The detection of aquatic animal species using environmental DNA – a review of eDNA as a survey tool in ecology

REVIEW: The detection of aquatic animal species using environmental DNA – a review of eDNA as a survey tool in ecology

Biological invasions, climate change and genomics

The ecology of environmental DNA and implications for conservation genetics

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