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opencc-zeroOct 2020View details →

Data from: Allometric scaling of eDNA production in stream-dwelling brook trout (Salvelinus fontinalis) inferred from population size structure

Environmental DNA (eDNA) concentration exhibits a positive correlation with organism abundance in nature, but modelling this relationship could be substantially improved by incorporating the biology of eDNA production. A recent model (Yates et al. 2020) extended models of physiological allometric scaling to eDNA production, hypothesizing that brook trout eDNA production scales non-linearly with mass as a power-function with scaling coefficients < 1 in lakes. To validate this hypothesis, we re-analysed data from Wilcox et al. (2016) that examined the correlation between eDNA concentration and brook trout abundance in streams. We found that allometrically scaled mass (ASM) (e.g. ∑(individual mass0.36) best described patterns of eDNA concentration across streams (r2 = 0.43). ASM exhibited substantially improved model fit relative to biomass (r2 = 0.31, ∆AIC = 5.19), indicating that eDNA production did not scale linearly with biomass. However, the explanatory power of ASM was comparable to density (r2 = 0.40, ∆AIC = 1.25). Additionally, the optimal scaling coefficient estimated from the data (0.36) was substantially lower than that found in Yates et al. (2020) (0.72). Discrepancies between datasets could be attributable to ecological differences between study habitats (streams vs lakes) or due to the exclusion of juveniles (i.e. individuals < 75 mm) that can be abundant in stream environments. Nevertheless, this study adds to the growing body of literature demonstrating that individual eDNA production does not scale linearly with biomass.

opencc-zeroDec 2012View details →

Data from: Factors influencing detection of eDNA from a stream-dwelling amphibian

Environmental DNA (eDNA) methods for detecting and estimating abundance of aquatic species are emerging rapidly, but little is known about how processes such as secretion rate, environmental degradation, and time since colonization or extirpation from a given site affect eDNA measurements. Using stream-dwelling salamanders and quantitative PCR (qPCR) analysis, we conducted three experiments to assess eDNA: (1) production rate, (2) persistence time under different temperature and light conditions, and (3) detectability and concentration through time following experimental introduction and removal of salamanders into previously unoccupied streams. We found that 44–50 g individuals held in aquaria produced 77 ng eDNA/hr for two hours, after which production either slowed considerably or began to equilibrate with degradation. eDNA in both full-sun and shaded treatments degraded exponentially to <1% of the original concentration after 3 days. eDNA was no longer detectable in full-sun samples after 8 days, whereas eDNA was detected in 20% of shaded samples after 11 days and 100% of refrigerated control samples after 18 days. When translocated into unoccupied streams, salamanders were detectable after 6 hours, but only when densities were relatively high (0.2481 individuals/m2) and when samples were collected within 5 m of the animals. Concentrations of eDNA detected were very low and increased steadily from 6–24 hours after introduction, reaching 0.0022 ng/L. Within 1 hour of removing salamanders from the stream, eDNA was no longer detectable. These results suggest that eDNA detectability and concentration depend on production rates of individuals, environmental conditions, density of animals, and their residence time.

opencc-zeroAug 2022View details →

Relationship between eDNA concentration from metabarcoding method and stream fish density under field conditions

Estimating abundance or biomass using eDNA metabarcoding is a powerful emerging tool that may provide an alternative to conventional laborious methods for biological monitoring. However, inferring aquatic macroorganism abundance or biomass using eDNA concentrations remains challenging, especially in lotic environments, because of several potential confounding factors. In this study, we tested whether quantitative eDNA metabarcoding that uses internal standard DNA can be used to estimate the abundance of four fish species. We collected eDNA samples and concurrently estimated fish densities using the conventional removal method in small tributaries in four seasons during a year. The effects of potential confounding factors, including the body mass of the individuals, water temperature, and discharge volume, were assessed using an allometric scaling model. We found an increasing trend of eDNA concentration against the increase in abundance across all species. In the most abundant species, a significant increase in the precision of predicted abundance was achieved by considering confounding factors, such as season and discharge. Although this study successfully determined the relationships between eDNA concentration and fish abundance under lotic field conditions, it also identified several limitations of quantitative eDNA metabarcoding. The relationship between eDNA concentration and fish abundance in rare species showed significant variances in the regression. More sequencing depth may be necessary to detect rare species sufficiently. The eDNA concentration estimation error effect was significant, particularly among the samples that showed the same abundance figures by direct capture estimation. The utilization of quantitative eDNA metabarcoding may be suitable for organisms that are expected to have a substantial variation in their population density. More comparative studies with various conventional methods would be informative, especially in lotic field environments, to overcome these limitations and achieve wider applications of eDNA metabarcoding in future research and monitoring.

publicOct 2020View details →

Data from: Allometric scaling of eDNA production in stream-dwelling brook trout (Salvelinus fontinalis) inferred from population size structure

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publicAug 2013View details →

Data from: Factors influencing detection of eDNA from a stream-dwelling amphibian

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publicAug 2022View details →

eDNA sampled from stream networks correlates with camera trap detection rates of terrestrial mammals

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publicAug 2022View details →

Relationship between eDNA concentration from metabarcoding method and stream fish density under field conditions

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Multi-species models reveal that eDNA metabarcoding is more sensitive than backpack electrofishing for conducting fish surveys in freshwater streams

Environmental DNA (eDNA) sampling can provide accurate, cost-effective, landscape-level data on species distributions. Previous studies have compared the sensitivity of eDNA sampling to traditional sampling methods for single species, but similar comparative studies on multi-species eDNA metabarcoding are rare. Using hierarchical species occupancy-detection models, we examined whether key choices associated with eDNA metabarcoding (primer selection, low-abundance read filtering, and the number of positive water samples used to classify a species as present at a site) affect the sensitivity of metabarcoding, relative to backpack electrofishing for fish in freshwater streams. Under all scenarios (teleostei and vertebrate primers; 0%, 0.1% and 1% read filtering thresholds; 1 or 2 positive samples required to classify species as present), we found that eDNA metabarcoding is, on average, more sensitive than electrofishing. Combining vertebrate and teleostei markers resulted in higher detection probabilities relative to the use of either marker in isolation. Increasing the threshold used to filter low abundance reads decreased species detection probabilities but did not change our overall finding that eDNA metabarcoding was more sensitive than electrofishing. Using a threshold of two positive water samples (out of 5) to classify a species as present typically had negligible effects on detection probabilities compared to using one positive water sample. Our findings demonstrate that eDNA metabarcoding is generally more sensitive than electrofishing for conducting fish surveys in freshwater streams, and that this outcome is not sensitive to methodological decisions associated with metabarcoding.

opencc-zeroAug 2020View details →

Supplementary material 3 from: Macher T-H, Schütz R, Arle J, Beermann AJ, Koschorreck J, Leese F (2021) Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species. Metabarcoding and Metagenomics 5: e66557. https://doi.org/10.3897/mbmg.5.66557

Table S3. Filtered taXon table

Supplementary material 2 from: Macher T-H, Schütz R, Arle J, Beermann AJ, Koschorreck J, Leese F (2021) Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species. Metabarcoding and Metagenomics 5: e66557. https://doi.org/10.3897/mbmg.5.66557

Table S2. Raw taXon table as created with TaxonTableTools

Supplementary material 1 from: Macher T-H, Schütz R, Arle J, Beermann AJ, Koschorreck J, Leese F (2021) Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species. Metabarcoding and Metagenomics 5: e66557. https://doi.org/10.3897/mbmg.5.66557

Table S1. BLAST taxonomy table

Supplementary material 5 from: Macher T-H, Schütz R, Arle J, Beermann AJ, Koschorreck J, Leese F (2021) Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species. Metabarcoding and Metagenomics 5: e66557. https://doi.org/10.3897/mbmg.5.66557

Figure S2

Supplementary material 4 from: Macher T-H, Schütz R, Arle J, Beermann AJ, Koschorreck J, Leese F (2021) Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species. Metabarcoding and Metagenomics 5: e66557. https://doi.org/10.3897/mbmg.5.66557

Figure S1