Environmental DNA metabarcoding elucidates patterns of fish colonisation and co‐occurrences with amphibians in temperate wetlands created for biodiversity

Petersson, Erik; Arlt, Debora; Hellström, Micaela; Knape, Jonas; Spens, Johan; Żmihorski, Michał; Pärt, Tomas

doi:10.1111/fwb.13800

Cited by 19 publications

(13 citation statements)

References 89 publications

(146 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Some of these species (e.g., fish) are important predators of amphibians (Joseph et al, 2016), while others (e.g., waterfowl) are involved in dispersing parasites of amphibians to ponds (Wood et al, 2019). These additional detections therefore provide ecological information relevant to amphibian management and conservation (Kačergytė et al, 2021). For managers tasked with developing multi‐species monitoring programs, metabarcoding offers the opportunity to estimate broader biodiversity alongside the presence of focal species (Table 1).…”

Section: Discussionmentioning

confidence: 99%

Navigating the trade‐offs between environmental DNA and conventional field surveys for improved amphibian monitoring

et al. 2022

View full text Add to dashboard Cite

The need for efficient, accurate biodiversity monitoring is growing, especially for globally imperiled taxa, such as amphibians. Environmental DNA (eDNA) analysis holds enormous potential for enhancing monitoring programs, but as this tool is increasingly adopted, it is imperative for users to understand its potential benefits and shortcomings. We conducted a comparative study to evaluate the efficacy of two eDNA methodologies (quantitative (q)PCR and metabarcoding) and conventional field sampling approaches (seining, dipnetting, and visual encounter surveys) in a system of 20 ponds containing six different amphibian species. Using an occupancy modeling framework, we estimated differences in detection sensitivity across methods, with a focus on how eDNA survey design could be further optimized. Overall, both metabarcoding and qPCR were competitive with or improved upon conventional methods. Specifically, qPCR (species-specific approach) was the most effective technique for detecting two rare species, the California tiger salamander (Ambystoma californiense) and California red-legged frog (Rana draytonii), with a detection probability of >0.80 per survey. Metabarcoding (community approach) estimated amphibian diversity with comparable rates to field techniques on average, and detected an additional 41 vertebrate taxa. However, for two abundant species (western toads, Anaxyrus boreas, and Pacific chorus frogs, Pseudacris regilla), field techniques outperformed metabarcoding, especially as individuals metamorphosed. Our results indicate that eDNA approaches would be most effective when paired with visual encounter surveys to detect terrestrial life stages, and that more optimization, specifically primer choice and validation, is needed. By comparing methods across a diverse set of ponds and species, we provide guidance for future studies integrating eDNA approaches into amphibian monitoring.

show abstract

Section: Discussionmentioning

confidence: 99%

Navigating the trade‐offs between environmental DNA and conventional field surveys for improved amphibian monitoring

et al. 2022

View full text Add to dashboard Cite

show abstract

“…The direct sampling of fish can require more intensive techniques compared to amphibians, such as electrofishing or netting (Radinger et al., 2019). Emerging techniques such as environmental DNA metabarcoding can provide reliable information about the composition of fish communities, improving our understanding of how interspecific interaction shape temporal variation of communities, and providing better information for conservation (Kačergytė et al., 2021).…”

Section: Discussionmentioning

confidence: 99%

Explaining declines of newt abundance in northern Italy

et al. 2022

View full text Add to dashboard Cite

Amphibians are an exemplary case of the current biodiversity crisis, being among the vertebrates suffering the fastest decline. Population dynamics of amphibians can result from processes acting at different scales. Both the local characteristics of breeding wetlands and the features of the surrounding landscape can strongly affect the temporal dynamics of amphibian populations. European newts are particularly threatened by land‐use change and invasive alien species. While it is known that newts are declining across Europe, few studies have performed broad‐scale assessments of their decline, either because abundance dynamics are more complex to analyse than presence/absence data or because they require a high sampling effort and long‐term monitoring. In this study, we show that long‐term distribution data can be combined with demographic models to quantify the decline in abundance of newt species at the regional scale, and to assess the importance of multiple factors in determining abundance dynamics. We performed multiple surveys between 1996 and 2020 and used N‐mixture models in a Bayesian framework. We then calculated abundance changes between the first and the last sampling season, which were performed with an average timespan of 13 years across all wetlands. Both Italian crested newts and smooth newts showed large declines, with an average estimated abundance loss between the first and last sampling season of 57% and 63%, respectively. Local characteristics of the wetlands were the main determinants of abundance dynamics: the abundance of both species showed a positive relationship with the area and the permanence of the wetland and a negative relationship with the presence of fish. Additionally, the abundance of Italian crested newts was negatively related to the presence of invasive crayfish. No relationship was detected between abundance and terrestrial habitat availability or connectivity measures. Despite uncertainties in the absolute values of estimated abundance, the striking regional‐scale decline of newts is evident. Among the major determinants of population dynamics, fish and crayfish presence increased their prevalence in the study area, while other factors remained more stable. Management actions aimed at eradicating or controlling invasive fish and crayfish might halt abundance loss and even revert this declining trend. The application of N‐mixture models to long‐term data from representative sites permits the analysis of temporal trends of species at the regional scale even when data come from complex monitoring schemes. We found large declines in abundance of two newt species, suggesting that European newts may be more threatened than previously thought.

show abstract

“…This can be difficult to obtain for species with sedentary lifestyles and whose catchability in passive gears, such as gillnets and traps, is restricted (Villegas-Ríos et al 2014). Environmental DNA (eDNA) has been suggested as a possible tool for fish stock monitoring in general, and monitoring of species with low catchability in particular (Kačergytė et al 2021). While eDNA can be successfully used in biodiversity monitoring based on presence/absence data (Dejean et al 2011, Thomsen et al 2012, Takahara et al 2013, Dunker et al 2016, Hernandez et al 2020), it’s potential use for biomass estimation is still under development.…”

Section: Introductionmentioning

confidence: 99%

Temperature moderates eDNA-biomass relationships in northern pike

Ogonowski

Karlsson

Vasemägi

et al. 2022

Preprint

View full text Add to dashboard Cite

Support for eDNA as a quantitative monitoring tool is growing worldwide. Despite advances there are still uncertainties regarding the representability of the eDNA signal over varying spatiotemporal scales, influence of abiotic forcing and phenological changes affecting behavior of the study organism, particularly in open environments. To assess the spatiotemporal variability and predictive power of quantitative eDNA analysis, we applied species-specific real-time quantitative PCR on water filtrates during two visits to 22 coastal bays in the Baltic Sea. Within bays, we collected water along four transects across each bay and compared the pooled eDNA concentration to temporally matched catches from standardized angling targeting the northern pike (Esox lucius), a species for which reliable monitoring data is lacking. We found the variability in eDNA concentrations between transects to be moderate (21%) but still considerably lower than across bays and visits (52%), suggesting small scale spatial differences are of less importance during spring when pike spawn. Standardized angling catches, bay area, and water temperature together explained 48% of the variance in eDNA concentrations. DNA concentrations decreased with increasing bay area, likely indicating a dilution effect. Notably, the relationship between eDNA and standardized catches was positive but varied with temperature and the eDNA-abundance relationship was only significant at higher temperatures, which also coincided with a higher proportion of spawning/spent fish. We conclude that temperature is a key moderating factor driving changes in pike behaviour and spring DNA-dynamics. We recommend that future surveys focus on larger spatiotemporal scales during times when the influence of changing temperatures is minimized.

show abstract

Environmental DNA metabarcoding elucidates patterns of fish colonisation and co‐occurrences with amphibians in temperate wetlands created for biodiversity

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 19 publications

References 89 publications

Navigating the trade‐offs between environmental DNA and conventional field surveys for improved amphibian monitoring

Navigating the trade‐offs between environmental DNA and conventional field surveys for improved amphibian monitoring

Explaining declines of newt abundance in northern Italy

Temperature moderates eDNA-biomass relationships in northern pike

Contact Info

Product

Resources

About