The value of quantitative environmental DNA analyses for the management of invasive and endangered native fish

Rojahn, Jack; Pearce, Luke; Gleeson, Dianne; Duncan, Richard P.; Gilligan, Dean M.; Bylemans, Jonas

doi:10.1111/fwb.13779

Cited by 10 publications

(19 citation statements)

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“…We propose that there is a useful distinction to be made between within -species and across -species abundance information (Figures 1, 2). Within-species abundance information can be enough to improve the inference of species interactions, the modelling of population dynamics and species distributions, the biomonitoring of environmental state and change, and the inference of false positives and negatives (Carraro et al 2020, 2021; Abrego et al 2021; Rojahn et al 2021, and Figure 2). We thus recommend that future quantitative eDNA studies should make clear which abundance measure is being estimated.…”

Section: Discussionmentioning

confidence: 99%

“…The accurate extraction of species-abundance information from DNA-based data could contribute usefully to the reconstruction of diets and quantitative food webs, the inference of species interactions, the modelling of population dynamics and species distributions, the biomonitoring of environmental state and change, and more prosaically, the inference of false positives and negatives (Thomas et al 2016; Deagle et al 2019; Peel et al 2019; Carraro et al 2020, 2021; Abrego et al 2021; Rojahn et al 2021). Here we use the term abundance to mean any estimate of biomass or count of individuals .…”

Section: Introductionmentioning

confidence: 99%

“…Even without correcting for species biases, removal of pipeline noise (and capture noise) allows the detection of a negative correlation in abundances (inset). Example adapted from Rojahn et al (2021) who combined a similar result with external information to infer the competitive exclusion of a native fish species by an invasive species. Note that due to species biases, it is not possible to infer from these within-species abundance gradients which species is more abundant than the other (nor is it correct to infer that the two species are of similar abundance).…”

Section: Introductionmentioning

confidence: 99%

“…As we review and demonstrate below, some approaches remove pipeline noise, some remove species biases, and some remove both . Our take-home message is that removing only pipeline noise to achieve within-species quantification can be enough to improve the inference of species interactions, the modelling of population dynamics and species distributions, the biomonitoring of environmental state and change, and the inference of false positives and negatives (Carraro et al 2020, 2021; Abrego et al 2021; Rojahn et al 2021, and Figure 2).…”

Section: Introductionmentioning

confidence: 99%

“…The two species are seen to be negatively correlated over the gradient, even though absolute abundance information is unavailable. Example adapted from Rojahn et al (2021) who combined a similar result with additional information to infer the competitive exclusion of a native fish species by an invasive species. F .…”

Section: Introductionmentioning

confidence: 99%

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Extracting abundance information from DNA-based data

Luo

2022

Preprint

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The accurate extraction of species-abundance information from DNA-based data (metabarcoding, metagenomics) could contribute usefully to diet reconstruction and quantitative food webs, the inference of species interactions, the modelling of population dynamics and species distributions, the biomonitoring of environmental state and change, and the inference of false positives and negatives. However, capture bias, capture noise, species pipeline biases, and pipeline noise all combine to inject error into DNA-based datasets. We focus on methods for correcting the latter two error sources, as the first two are addressed extensively in the ecological literature. To extract abundance information, it is useful to distinguish two concepts. (1) Across-species quantification describes relative species abundances within one sample. (2) In contrast, within-species quantification describes how the abundance of each individual species varies from sample to sample, as in a time series, an environmental gradient, or different experimental treatments. Firstly, we review methods to remove species pipeline biases and pipeline noise. Secondly, we demonstrate experimentally (with a detailed protocol) how to use a 'DNA spike-in' to remove pipeline noise and recover within-species abundance information. We also introduce a statistical estimator that can partially remove pipeline noise from datasets that lack a physical DNA spike-in.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Extracting abundance information from DNA-based data

Luo

2022

Preprint

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Using quantitative eDNA analyses to accurately estimate American bullfrog abundance and to evaluate management efficacy

et al. 2022

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Biological invasions contribute now more than ever to the global homogenization of fauna and flora. Large‐scale monitoring programs are, therefore, needed to detect incipient invasions and to evaluate management interventions. As conventional monitoring methods are constrained by large costs, environmental DNA (eDNA)‐based methods are increasingly recognized as valuable monitoring tools. However, accurately estimating species abundance from eDNA concentrations in natural systems remains challenging and consequently hinders their integration in management applications. Here, we used droplet digital PCR (ddPCR) in eDNA surveys to estimate the abundance of invasive American bullfrogs (Lithobates catesbeianus). We first introduced bullfrog tadpoles in natural ponds to assess the relationship between abundances and eDNA concentrations under field conditions. Next, we combined eDNA sampling with fyke netting in naturally colonized ponds to investigate whether bullfrog eDNA concentrations can estimate bullfrog capture success and conventional abundance measures obtained via depletion sampling. Finally, we evaluated eradication measures by comparing bullfrog eDNA concentrations before and after fyke netting. We found a strong linear relationship between the numbers of introduced tadpoles and eDNA concentrations (r2 = 0.988). Bullfrog eDNA concentrations were not only linearly related to the catch‐per‐unit‐effort (r2 = 0.739), but also to conventional abundance estimates (r2 = 0.716), particularly when eDNA concentrations were standardized for pond area (r2 = 0.834) and volume (r2 = 0.888). Bullfrog tadpoles were only captured when eDNA concentrations exceeded 1.5 copies µl−1, indicating that quantitative eDNA analyses enable the localization of breeding ponds. We found a significant reduction in eDNA concentrations after fyke netting proportional to the number of captured bullfrogs. These results demonstrate that eDNA quantification is a reliable tool that accurately estimates bullfrog abundance in natural lentic systems. We show that quantitative eDNA analyses can complement the toolbox of natural resource managers and facilitate the coordination of eradication campaigns targeting alien invasive species.

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Including environmental covariates clarifies the relationship between endangered Atlantic salmon (Salmo salar) abundance and environmental DNA

et al. 2023

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Collecting environmental DNA (eDNA) as a nonlethal sampling approach has been valuable in detecting the presence/absence of many imperiled taxa; however, its application to indicate species abundance poses many challenges. A deeper understanding of eDNA dynamics in aquatic systems is required to better interpret the substantial variability often associated with eDNA samples. Our sampling design took advantage of natural variation in juvenile Atlantic salmon (Salmo salar) distribution and abundance along 9 km of a single river in the Province of New Brunswick (Canada), covering different spatial and temporal scales to address the unknown seasonal impacts of environmental variables on the quantitative relationship between eDNA concentration and species abundance. First, we asked whether accounting for environmental variables strengthened the relationship between eDNA and salmon abundance by sampling eDNA during their spring seaward migration. Second, we asked how environmental variables affected eDNA dynamics during the summer as the parr abundance remained relatively constant. Spring eDNA samples were collected over a 6‐week period (12 times) near a rotary screw trap that captured approximately 18.6% of migrating smolts, whereas summer sampling occurred (i) at three distinct salmon habitats (9 times) and (ii) along the full 9 km (3 times). We modeled eDNA concentration as a product of fish abundance and environmental variables, demonstrating that (1) with inclusion of abundance and environmental covariates, eDNA was highly correlated with spring smolt abundance and (2) the relationships among environmental covariates and eDNA were affected by seasonal variation with relatively constant parr abundance in summer. Our findings underscore that with appropriate study design that accounts for seasonal environmental variation and life history phenology, eDNA salmon population assessments may have the potential to evaluate abundance fluctuations in spring and summer.

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The value of quantitative environmental DNA analyses for the management of invasive and endangered native fish

Cited by 10 publications

References 50 publications

Extracting abundance information from DNA-based data

Extracting abundance information from DNA-based data

Using quantitative eDNA analyses to accurately estimate American bullfrog abundance and to evaluate management efficacy

Including environmental covariates clarifies the relationship between endangered Atlantic salmon (Salmo salar) abundance and environmental DNA

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