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1. Environmental DNA detects Spawning Habitat of an ephemeral migrant fish (Anadromous Rainbow Smelt: Osmerus mordax)

   https://doi.org/10.1186/s12862-022-02073-y  

   Holmes, Vaughn; Aman, Jacob; York, Geneva; Kinnison, Michael T. (December 2022, BMC Ecology and Evolution)

   Abstract Background Anadromous rainbow smelt ( Osmerus mordax ) have experienced a large range reduction in recent decades and the status of remnant spawning populations is poorly known in Maine, where these fish have significant ecological, cultural, and commercial relevance. Defining the remnant range of anadromous smelt is more difficult than for many declining fish species because adults are only ephemerally present while spawning in small coastal streams at night during spring runoff periods when traditional assessments can be unreliable or even hazardous. We hypothesized that eDNA might facilitate improved survey efforts to define smelt spawning habitat, but that detection could also face challenges from adult eDNA quickly flushing out of these small stream systems. We combined daytime eDNA sampling with nighttime fyke netting to ascertain a potential window of eDNA detection before conducting eDNA surveys in four streams of varying abundance. Hierarchical occupancy modeling was in turn employed to estimate eDNA encounter probabilities relative to numbers of sampling events (date), samples within events, and qPCR replicates within samples. Results Results from the combined eDNA and fyke net study indicated eDNA was detectable over an extended period, culminating approximately 8–13 days following peak spawning, suggesting developing smelt larvae might be the primary source of eDNA. Subsequently, smelt eDNA was readily detected in eDNA surveys of four streams, particularly following remediation of PCR inhibitors. Hierarchical occupancy modeling confirmed our surveys had high empirical detection for most sites, and that future surveys employing at least three sampling events, three samples per event, and six qPCR replicates can afford greater than 90% combined detection capability in low abundance systems. Conclusions These results demonstrate that relatively modest eDNA sampling effort has high capacity to detect this ephemerally present species of concern at low to moderate abundances. As such, smelt eDNA detection could improve range mapping by providing longer survey windows, safer sampling conditions, and lower field effort in low density systems, than afforded by existing visual and netting approaches. 

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2. Needles in an ocean haystack: using environmental DNA to study marine mammals in the North Atlantic

   https://doi.org/10.7557/3.6482  

   Székely, Dóra; Cammen, Kristina M.; Tange Olsen, Morten (May 2021, NAMMCO Scientific Publications)

   Marine mammals in the North Atlantic have experienced severe depletions due to overexploitation. While some species and populations have now recovered, there are numerous other anthropogenic activities impacting their North Atlantic ecosystem. Studying marine mammals is often associated with logistical challenges, and many species have an elusive nature, resulting in substantial knowledge gaps on the distribution, abundance and diversity of marine mammals in the North Atlantic. Environmental DNA (eDNA) is an emerging tool in biodiversity monitoring and has successfully been demonstrated to complement traditional monitoring methods for a wide range of marine taxonomic groups. The promising potential of seawater eDNA is owe to advances within an array of molecular methods used to extract, detect and/or sequence the genetic material of marine organisms from a single seawater sample.  We present a literature review of eDNA studies of marine mammals and discuss the potential applications and practical challenges of eDNA in marine mammal research, management and conservation.  Environmental DNA has already been introduced to a wide range of applications within marine mammal science, from detection of endangered species to population genetic assessments. Furthermore, eDNA has the power to capture other biologically important species in the marine ecosystem and food web, which could facilitate insight into the spatiotemporal variation of different marine communities in a changing environment. With methodological and technological standardization, eDNA based approaches have a promising potential to be integrated into regular monitoring practices and management strategies. 

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3. Spatial Heterogeneity of eDNA Transport Improves Stream Assessment of Threatened Salmon Presence, Abundance, and Location

   https://doi.org/10.3389/fevo.2021.650717  

   Wood, Zachary T.; Lacoursière-Roussel, Anaïs; LeBlanc, Francis; Trudel, Marc; Kinnison, Michael T.; Garry McBrine, Colton; Pavey, Scott A.; Gagné, Nellie (April 2021, Frontiers in Ecology and Evolution)

   The integration of environmental DNA (eDNA) within management strategies for lotic organisms requires translating eDNA detection and quantification data into inferences of the locations and abundances of target species. Understanding how eDNA is distributed in space and time within the complex environments of rivers and streams is a major factor in achieving this translation. Here we study bidimensional eDNA signals in streams to predict the position and abundance of Atlantic salmon ( Salmo salar ) juveniles. We use data from sentinel cages with a range of abundances (3–63 juveniles) that were deployed in three coastal streams in New Brunswick, Canada. We evaluate the spatial patterns of eDNA dispersal and determine the effect of discharge on the dilution rate of eDNA. Our results show that eDNA exhibits predictable plume dynamics downstream from sources, with eDNA being initially concentrated and transported in the midstream, but eventually accumulating in stream margins with time and distance. From these findings we developed a fish detection and distribution prediction model based on the eDNA ratio in midstream versus bankside sites for a variety of fish distribution scenarios. Finally, we advise that sampling midstream at every 400 m is sufficient to detect a single fish at low velocity, but sampling efforts need to be increased at higher water velocity (every 100 m in the systems surveyed in this study). Studying salmon eDNA spatio-temporal patterns in lotic environments is essential to developing strong quantitative population assessment models that successfully leverage eDNA as a tool to protect salmon populations. 

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4. Pushing the Boundaries: Investigating Physiological Limits of Invasive Species and Edna Detection Methods

   Lancaster, E (August 2024, University of Maine Electronic Theses and Dissertations)

   Invasive species are organisms moved from one region to another by humans. Although they are not always harmful to the recipient community, their lack of evolutionary history with their new community can set the stage for destruction. In a world of increasing interconnectivity and warming waters, we expect invasive species will continue to be introduced and that their ranges will expand as more areas become suitable habitats. At this critical point in our planet’s natural history, the need to understand where invasive species can survive and how to detect them are important. Here, I begin with a review of invasive species physiology measurements using species identified as invasive through the Marine Invader Monitoring and Information Collaborative. These data points highlight inconsistencies in measurement technique as well as the importance that acclimation temperature and life stage play on thermal thresholds. Based on the noise in the data, I recommend laboratory experiments to understand the absolute maximum and minimum survivable temperatures for each species, followed by field observations of temperatures needed to grow and reproduce. Then, using a newer invader to Maine Hemigrapsus sanguineus, I measured thermal thresholds for summer and winter-acclimated crabs and found shifts in thermal thresholds as well as evidence that winter temperatures are stressful for these crabs. Lastly, to effectively detect invasive species early, I tested and designed assays for environmental DNA (eDNA) detection of 9 invasive or nuisance species in the Gulf of Maine. Using laboratory experiments and a two-year time series in a local tide pool, I found that not all of the studied invertebrate species can be detected equally. Some organisms with soft, exposed tissues shed eDNA consistently with their abundance, while organisms with exoskeletons or shells do not. This trend does not hold true for all of the studied taxa, but this premise alongside an understanding of natural history and morphology helps clarify the observed trends. Thus, eDNA techniques should not be applied equally across all taxa for management purposes without a clear understanding of the message of the signal. Overall, I made recommendations to better predict suitable habitats for invasive species, characterized thresholds for an understudied invasive species in New England, and continued building upon the challenges of detecting invertebrates with eDNA. 

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5. Environmental DNA reveals the fine-grained and hierarchical spatial structure of kelp forest fish communities

   https://doi.org/10.1038/s41598-021-93859-5  

   Lamy, Thomas; Pitz, Kathleen J.; Chavez, Francisco P.; Yorke, Christie E.; Miller, Robert J. (July 2021, Scientific Reports)

   Abstract Biodiversity is changing at an accelerating rate at both local and regional scales. Beta diversity, which quantifies species turnover between these two scales, is emerging as a key driver of ecosystem function that can inform spatial conservation. Yet measuring biodiversity remains a major challenge, especially in aquatic ecosystems. Decoding environmental DNA (eDNA) left behind by organisms offers the possibility of detecting species sans direct observation, a Rosetta Stone for biodiversity. While eDNA has proven useful to illuminate diversity in aquatic ecosystems, its utility for measuring beta diversity over spatial scales small enough to be relevant to conservation purposes is poorly known. Here we tested how eDNA performs relative to underwater visual census (UVC) to evaluate beta diversity of marine communities. We paired UVC with 12S eDNA metabarcoding and used a spatially structured hierarchical sampling design to assess key spatial metrics of fish communities on temperate rocky reefs in southern California. eDNA provided a more-detailed picture of the main sources of spatial variation in both taxonomic richness and community turnover, which primarily arose due to strong species filtering within and among rocky reefs. As expected, eDNA detected more taxa at the regional scale (69 vs. 38) which accumulated quickly with space and plateaued at only ~ 11 samples. Conversely, the discovery rate of new taxa was slower with no sign of saturation for UVC. Based on historical records in the region (2000–2018) we found that 6.9 times more UVC samples would be required to detect 50 taxa compared to eDNA. Our results show that eDNA metabarcoding can outperform diver counts to capture the spatial patterns in biodiversity at fine scales with less field effort and more power than traditional methods, supporting the notion that eDNA is a critical scientific tool for detecting biodiversity changes in aquatic ecosystems. 

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