Publications
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Toward a national eDNA strategy for the United States (Kelly et al. 2023)
Environmental DNA (eDNA) data make it possible to measure and monitor biodiversity at unprecedented resolution and scale. As use-cases multiply and scientific consensus grows regarding the value of eDNA analysis, public agencies have an opportunity to decide how and where eDNA data fit into their mandates. Within the United States, many federal and state agencies are individually using eDNA data in various appli- cations and developing relevant scientific expertise. A national strategy for eDNA implementation would capitalize on recent scientific developments, providing a com- mon set of next-generation tools for natural resource management and public health protection. Such a strategy would avoid patchwork and possibly inconsistent guide- lines in different agencies, smoothing the way for efficient uptake of eDNA data in management. Because eDNA analysis is already in widespread use in both ocean and freshwater settings, we focus here on applications in these environments. However, we foresee the broad adoption of eDNA analysis to meet many resource management issues across the nation because the same tools have immediate terrestrial and aerial applications.
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Quantifying impacts of an environmental intervention using environmental DNA (Allan et al. 2023)
Environmental laws around the world require some version of an environmental-impact assessment surrounding construction projects and other discrete instances of human development. Information requirements for these assessments vary by jurisdiction, but nearly all require an analysis of the biological elements of ecosystems. Amplicon-sequencing—also called metabarcoding—of environmental DNA (eDNA) has made it possible to sample and amplify the genetic material of many species present in those environments, providing a tractable, powerful, and increasingly common way of doing environmental-impact analysis for development projects. Here, we analyze an 18-month time series of water samples taken before, during, and after two culvert removals in a salmonid-bearing freshwater stream. We also sampled multiple control streams to develop a robust background expectation against which to evaluate the impact of this discrete environmental intervention in the treatment stream. We generate calibrated, quantitative metabarcoding data from amplifying the 12s MiFish mtDNA locus and complementary species-specific quantitative PCR data to yield multispecies estimates of absolute eDNA concentrations across time, creeks, and sampling stations. We then use a linear mixed effects model to reveal patterns of eDNA concentrations over time, and to estimate the effects of the culvert removal on salmonids in the treatment creek. We focus our analysis on four common salmonid species: cutthroat trout (Oncorhynchus clarkii), coho salmon (Oncorhynchus kisutch), rainbow trout (Oncorhynchus mykiss), and sockeye salmon (Oncorhynchus nerka). We find that one culvert in the treatment creek seemed to have no impact while the second culvert had a large impact on fish passage. The construction itself seemed to have only transient effects on salmonid species during the two construction events. In the context of billions of dollars of court-mandated road culvert replacements taking place in Washington State, USA, our results suggest that culvert replacement can be conducted with only minimal impact of construction to key species of management concern. Furthermore, eDNA methods can be an effective and efficient approach for monitoring hundreds of culverts to prioritize culverts that are required to be replaced. More broadly, we demonstrate a rigorous, quantitative method for environmental-impact reporting using eDNA that is widely applicable in environments worldwide.
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Adoption of environmental DNA in public agency practice (Lee et al, 2023)
Environmental DNA (eDNA) analysis has matured to the point that it is ready for deployment in many applications, particularly in aquatic environments. But public agencies have yet to adopt eDNA methods into their environmental decision making routines at scale, even when eDNA offers clear advantages to those now in use. This article provides a perspective on this gap by considering adoption of a new technology as a path-dependent, social process in which some paths lead to outcomes that provide far greater benefits than others. We use the diffusion of innovations to investigate eDNA adoption by government agencies, in an effort to (1) identify likely paths toward institutionalized uptake, and (2) suggest ways of avoiding societally inefficient adoption outcomes. Because—as in any scientific endeavor—the best eDNA practices will continue to change, public agencies must remain open to improvements while building a useful and validated array of methods for routine eDNA application. Here we suggest one mechanism for doing so, which we call collaborative governance.
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Critical considerations for communicating environmental DNA science (Stein et al, 2023)
The economic and methodological efficiencies of environmental DNA (eDNA) based survey approaches provide an unprecedented opportunity to assess and monitor aquatic environments. However, instances of inadequate communication from the sci-entific community about confidence levels, knowledge gaps, reliability, and appropri-ate parameters of eDNA- based methods have hindered their uptake in environmental monitoring programs and, in some cases, has created misperceptions or doubts in the management community. To help remedy this situation, scientists convened a session at the Second National Marine eDNA Workshop to discuss strategies for improving communications with managers. These include articulating the readiness of different eDNA applications, highlighting the strengths and limitations of eDNA tools for vari-ous applications or use cases, communicating uncertainties associated with specified uses transparently, and avoiding the exaggeration of exploratory and preliminary find-ings. Several key messages regarding implementation, limitations, and relationship to existing methods were prioritized. To be inclusive of the diverse managers, practi-tioners, and researchers, we and the other workshop participants propose the de-velopment of communication workflow plans, using RACI (Responsible, Accountable, Consulted, Informed) charts to clarify the roles of all pertinent individuals and parties and to minimize the chance for miscommunications. We also propose developing de-cision support tools such as Structured Decision-Making (SDM) to help balance the benefits of eDNA sampling with the inherent uncertainty, and developing an eDNA readiness scale to articulate the technological readiness of eDNA approaches for spe-cific applications. These strategies will increase clarity and consistency regarding our understanding of the utility of eDNA-based methods, improve transparency, foster a common vision for confidently applying eDNA approaches, and enhance their benefit to the monitoring and assessment community.
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Environmental DNA provides quantitative estimates of Pacific hake abundance and distribution in the open ocean (Shelton et al. 2022)
We sampled eDNA in parallel with a traditional acoustic-trawl survey to assess the value of eDNA surveys at a scale relevant to fisheries management. Despite local differences, the two methods yield comparable information about the broad-scale spatial distribution and abundance. Furthermore, we find depth and spatial patterns of eDNA closely correspond to acoustic-trawl estimates for hake. We demonstrate the power and efficacy of eDNA sampling for estimating abundance and distribution and move the analysis of eDNA data beyond sample-to-sample comparisons to management relevant scales. We posit that eDNA methods are capable of providing general quantitative applications that will prove especially valuable in data-or resource-limited contexts.
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Tracking an invasion front with environmental DNA (Keller et al. 2022)
We jointly modeled eDNA via qPCR and traditional trap data to estimate the density of invasive European green crab (Carcinus maenas), a species for which, historically, baited traps have been used for both detection and control. Our analytical framework simultaneously quantifies uncertainty in both detection methods and provides a robust way of integrating different data streams into management processes. Moreover, the joint model makes clear the marginal information benefit of adding eDNA data to an existing monitoring program, offering a path to optimizing sampling efforts for species of management interest. Here, we document green crab eDNA beyond the previously known invasion front and find that the value of eDNA dramatically increases with low population densities and low traditional sampling effort, as is often the case at leading-edge locations.
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Toward quantitative metabarcoding (Shelton et al. in press)
At present, eDNA metabarcoding studies struggle to link genetic observations to underlying biology in a quantitative way, in large part due to biases during the PCR amplification process. Here we link previously disparate sets of techniques for making such data quantitative, showing that the underlying PCR mechanism explains observed patterns of amplicon data in a general way. By modeling the process through which amplicon-sequence data arises, rather than transforming the data post-hoc, we can estimate the starting proportions of DNA for many taxa simultaneously. This model can be calibrated with a variety of methods, including mock communities and variable-PCR-cycle sequencing runs, which we illustrate using simulations and in a series of empirical examples. Our approach opens the door to a wide range of applications in ecology, public health, and related fields.