Environmental DNA for the enumeration and management of Pacific salmon

Levi, Taal; Allen, Jennifer M.; Bell, Donovan A.; Joyce, John; Russell, Joshua R.; Tallmon, David A.; Vulstek, Scott C.; Yang, Chunyan; Yu, Douglas W.

doi:10.1101/394445

Cited by 40 publications

(79 citation statements)

References 27 publications

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“…eDNA concentrations varied substantially from near zero to a high of 328,000 copies/μl during the peak of the run in 2017. The product of streamflow and eDNA concentration, which we refer to as "flow-corrected eDNA rate" (Figure 3, see also Levi et al, 2019), was highly predictive of the eulachon population estimate generated through the mark-recapture method. The natural log of the eDNA peak was significantly related to, and explained 84.…”

Section: Environmental Dnamentioning

confidence: 99%

“…While the environmental DNA shed from an organism is now widely used for species detection in a wide variety of contexts (Barnes & Turner, 2016;Jerde, Mahon, Chadderton, & Lodge, 2011;Laramie, Pilliod, & Goldberg, 2015;Mächler, Deiner, Steinmann, & Altermatt, 2014;Rees, Maddison, Middleditch, Patmore, & Gough, 2014;Takahara, Minamoto, Yamanaka, Doi, & Kawabata, 2012), mobilizing environmental DNA for management requires estimation of population size and trends in addition to assessing presence or absence. Recent research suggests that eDNA quantified with real-time quantitative polymerase chain reaction (PCR) or digital-droplet PCR can provide a proxy for actual abundance in controlled experiments (Rees et al, 2014), in ponds (Lacoursière-Roussel, Côté, Leclerc, & Bernatchez, 2016;Takahara et al, 2012) in streams (Doi et al, 2015;Levi et al, 2019;Lodge et al, 2012;Tillotson et al, 2018;Wilcox et al, 2016) and in marine bays (Plough et al, 2018). However, the efficacy of environmental DNA based indices of abundance in natural settings have produced mixed results (Yates, Fraser, & Derry, 2019) and have not yet been assessed in a management context for long-term population monitoring.…”

Section: Introductionmentioning

confidence: 99%

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Environmental DNA facilitates accurate, inexpensive, and multiyear population estimates of millions of anadromous fish

Pochardt

Allen

Hart³

et al. 2019

Molecular Ecology Resources

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Although environmental DNA shed from an organism is now widely used for species detection in a wide variety of contexts, mobilizing environmental DNA for management requires estimation of population size and trends in addition to assessing presence or absence. However, the efficacy of environmental‐DNA‐based indices of abundance for long‐term population monitoring have not yet been assessed. Here we report on the relationship between six years of mark‐recapture population estimates for eulachon (Thaleichthys pacificus) and “eDNA rates” which are calculated from the product of stream flow and DNA concentration. Eulachon are a culturally and biologically important anadromous fish that have significantly declined in the southern part of their range but were historically rendered into oil and traded. Both the peak eDNA rate and the area under the curve of the daily eDNA rate were highly predictive of the mark‐recapture population estimate, explaining 84.96% and 92.53% of the deviance, respectively. Even in the absence of flow correction, the peak of the daily eDNA concentration explained an astonishing 89.53% while the area under the curve explained 90.74% of the deviance. These results support the use of eDNA to monitor eulachon population trends and represent a >80% cost savings over mark‐recapture, which could be further increased with automated water sampling, reduced replication, and focused temporal sampling. Due to its logistical ease and affordability, eDNA sampling can facilitate monitoring a larger number of rivers and in remote locations where mark‐recapture is infeasible.

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Section: Environmental Dnamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Environmental DNA facilitates accurate, inexpensive, and multiyear population estimates of millions of anadromous fish

Pochardt

Allen

Hart³

et al. 2019

Molecular Ecology Resources

Self Cite

View full text Add to dashboard Cite

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“…Additionally, some previous studies have not found read depth for species biodiversity to correlate with individuals, biomass, or density [59,[100][101][102]. However, a more recent study indicates strong evidence that flow-corrected eDNA abundance reflects salmon count abundance in two species across two years and life stages [103]. Relating allelic abundance to eDNA genetic variation is necessary to understand allelic frequency differences between and within populations.…”

Section: Challenges Facing Environmental Dna Population Geneticsmentioning

confidence: 99%

“…Other ways to get at quantification of allelic copy number include a correction factor depending on cell type, size, life-history stage and species, which could be integrated into single-cell methodology [104]. Lastly, the more that is understood about the ecology of eDNA in a field setting, the better we can understand and model eDNA abundance [103,141].…”

Section: Further Developments and Future Technologiesmentioning

confidence: 99%

Beyond Biodiversity: Can Environmental DNA (eDNA) Cut it as a Population Genetics Tool?

Adams

Knapp

Gemmell

et al. 2019

Preprint

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Population genetic data underpin many studies of behavioral, ecological, and evolutionary processes in wild populations and contribute to effective conservation management. However, collecting genetic samples can be challenging when working with endangered, invasive, or cryptic species. Environmental DNA (eDNA) offers a way to sample genetic material non-invasively without requiring visual observation. While eDNA has been trialed extensively as a biodiversity and biosecurity monitoring tool with a strong taxonomic focus, it has yet to be fully explored as a means for obtaining population genetic information. Here, we review current research that employs eDNA approaches for the study of populations. We outline challenges facing eDNA-based population genetic methodologies, and suggest avenues of research for future developments. We advocate that with further optimizations, this emergent field holds great potential as part of the population genetics toolkit.

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“…quantity of eDNA may be related not only to species presence, but also to abundance 16,21,[28][29][30][31][32] . Although promising as a method for shark detection, more research in well-studied ecosystems is necessary to understand whether eDNA monitoring can also be used to track population dynamics over time.…”

mentioning

confidence: 99%

Environmental DNA detection tracks established seasonal occurrence of blacktip sharks (Carcharhinus limbatus) in a semi-enclosed subtropical bay

Postaire

Bakker

Gardiner

et al. 2020

Sci Rep

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the integration of eDnA analysis into the population assessment and monitoring of sharks could greatly improve temporal and spatial data used for management purposes. this study aimed to compare eDnA detection against well-established seasonal changes in blacktip shark (Carcharhinus limbatus) abundance in Terra Ceia Bay (FL, USA). We used a species-specific real-time PCR approach to detect C. limbatus eDNA in the bay on a near monthly basis from spring through mid-fall in 2018 and 2019. Previous studies have shown that C. limbatus give birth in the bay in early summer and immature sharks occur there until late fall, when decreasing water temperatures cause them to move offshore and southwards. Water samples (2 L) were collected (4-6 per month) and filtered in the field, with each then being subjected to real-time PCR. Carcharhinus limbatus 'positive' filters were significantly more commonly collected during the April-July sampling period than during the August-October sampling period. While following the predicted pattern, eDNA concentration was generally too low for accurate quantification. Our results show that C. limbatus eDnA detection follows known seasonal residency patterns consistently over 2 years of monitoring. Species-specific eDNA analysis using real-time PCR could therefore represent a cost-effective, scalable sampling tool to facilitate improved shark population monitoring in semi-enclosed marine habitats. Many shark populations have been heavily impacted by overexploitation and environmental disturbances 1-6. Effective assessment, monitoring and management of these predators will rely on accurate knowledge of species spatiotemporal distribution and abundance trends, which are often incomplete or absent 7. Commonly employed methods to obtain these data, such as sampling with gillnets or longlines, are invasive and resource intensive, which often leads to a strong dependence on non-standard data from fisheries 8-10. Cost-effective and scalable alternatives are needed to improve our understanding of shark distributions and population dynamics. The application of environmental DNA (eDNA) analysis has emerged as a new approach to detect macroorganisms from trace DNA in water samples 11-13. eDNA approaches are based on the isolation, amplification and sequencing of DNA traces from skin cells, egestion, and metabolic waste left behind in the environment 14,15. They offer a promising avenue for non-invasive, cost-effective, and scalable monitoring studies of aquatic organisms that can achieve very high replication independent of fisheries 16,17. Shark eDNA represents a naturally rare target for sampling given their positions as upper level predators (naturally lower densities compared to species occupying lower trophic levels), coupled with low abundances due to overexploitation in many areas 18 , suggesting a high probability of negative results 17,19. Nevertheless, eDNA analysis has recently been applied for the detection of sharks and their relatives and has proven to have potential for presence/absence...

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Environmental DNA for the enumeration and management of Pacific salmon

Abstract: Pacific salmon are a keystone resource in Alaska, with an economic impact of well over

Cited by 40 publications

References 27 publications

Environmental DNA facilitates accurate, inexpensive, and multiyear population estimates of millions of anadromous fish

Environmental DNA facilitates accurate, inexpensive, and multiyear population estimates of millions of anadromous fish

Beyond Biodiversity: Can Environmental DNA (eDNA) Cut it as a Population Genetics Tool?

Environmental DNA detection tracks established seasonal occurrence of blacktip sharks (Carcharhinus limbatus) in a semi-enclosed subtropical bay

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