A simple,rapid method for detecting seven common invasive fish species in Europe from environmental DNA

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Improving the detection of rare native fish species in environmental DNA metabarcoding surveys

1. The presence of threatened or endangered species often strongly influences management and conservation decisions. Within the Murray–Darling Basin (MDB), Australia, the presence of threatened native fish affects the management and allocation of water resources. In New South Wales, these decisions are currently based on traditional fisheries data and a predictive MaxEnt model. However, it is important to verify the model's predictive power given the implication it may have, but this requires methods with a high detection sensitivity for rare species.
2. Although the use of environmental DNA (eDNA) monitoring, in particular eDNA metabarcoding, achieves a higher detection sensitivity compared with traditional methods, earlier surveys in the MDB have shown that the highly abundant and invasive common carp (Cyprinus carpio) can reduce detection probabilities for rare species. Consequently, a polymerase chain reaction (PCR) blocking primer designed to block the amplification of carp eDNA could increase the detection probabilities for rare native species while simultaneously reducing the required sampling effort and survey costs. Although PCR blocking primers are often used in ancient DNA and dietary studies, no aquatic eDNA metabarcoding study to date has evaluated the potential benefits of using PCR blocking primers.
3. A laboratory and field-based pilot study was used to address this knowledge gap and assess the impact of a blocking primer, targeting cyprinid fishes (including carp), on the detection probabilities of native species and the minimum sampling effort required.
4. Results showed that the inclusion of the blocking primer increased the detection probabilities for native species by 10–20% and reduced the minimum required sampling effort by 25–50%. These findings provide important insights into possible methods for optimizing eDNA metabarcoding surveys for the detection of rare aquatic species.

     

Occupancy dynamics of rare cyprinids after invasive fish eradication

1. The eradication of invasive species is a management strategy implemented to eliminate adverse impacts of invaders on native species communities. After eradications, follow‐up studies are done to confirm eradication of the invasive species and the short‐term recovery of the native species, but long‐term monitoring to confirm full population recovery and stability is often not completed.
2. In this study, long‐term monitoring of native fishes was carried out over 5 years after the eradication of an invasive fish from the Rondegat River, South Africa. Forty‐six sites distributed along four river sections were sampled for presence/absence using underwater cameras and snorkel surveys. Density data were collected by snorkel surveys.
3. Using multi‐season occupancy models, the annual probability of colonization and local extinction of the native fishes and annual rate of change in occupancy along the river were estimated. Changes in native fish densities across time and across the control and treatment sections were analysed using Kruskal–Wallis analysis, followed by Dunn's post‐hoc test.
4. Probability of colonization and local extinction differed for each native fish species and may have been affected by extrinsic factors, such as rainfall, and intrinsic density‐dependent factors, hypothesized from the density data. The occupancy rates of change revealed that the two Near Threatened fish species have reached an occupancy dynamic equilibrium but the Endangered fish has not, suggesting that other conservation efforts may be needed.
5. Long‐term monitoring of native fishes after an eradication programme has confirmed the successful removal of the invader and the recovery and stability of the community. However, successful eradication was not sufficient for full recovery of all species; additional conservation management strategies are needed to secure the population stability and persistence of endangered fishes. We recommend that eradication programmes, regardless of locality, should employ long‐term monitoring to ensure full recovery of a native fish community.

     

Dead or alive — Old empty shells do not prompt false-positive results in environmental DNA surveys targeting the freshwater pearl mussel (Margaritifera margaritifera L.)

1. Environmental DNA (eDNA) from water samples is increasingly used to detect the presence and distribution of species in aquatic ecosystems. However, before implementing eDNA in monitoring programmes, various species-specific sampling or analytical issues remain to be resolved in order to minimize frequencies of false-positive and -negative results. For example, empty shells from freshwater pearl mussels (Margaritifera margaritifera) contain extractable DNA (chemical extraction from ground-up shells) suggesting a risk of false-positive samples at stream sites with extinct populations but with empty shell material remaining.
2. The aim of this study was to investigate whether empty and naturally degrading shells from M. margaritifera can cause false-positive eDNA signals in water samples.
3. Water samples were collected from outdoor stream channels (in Lemming, Denmark) with living freshwater pearl mussels or empty shell material (density ~10 individuals m⁻²) during a 3-week experimental period. Living freshwater pearl mussels were collected from Hemgravs stream in Sweden and transported to Denmark according to permissions granted by the Swedish and Danish authorities.
4. All water samples from stream channels containing empty shells were negative for eDNA indicating that eDNA traces in stream water are most likely to originate from living individuals located upstream of the sampling site. Water samples collected from stream channels containing living individuals of M. margaritifera were consistently positive for eDNA except for one sample (interpreted as a false negative).
5. The study shows that positive eDNA signals for freshwater pearl mussels most likely reflect the presence of living individuals. Consequently, we suggest that eDNA should be used to locate remaining population fragments of M. margaritifera in deep and turbulent streams, providing a platform for faster and more efficient decision making when launching investigative and mitigation initiatives.

     

Taxonomic and geographical representation of freshwater environmental DNA research in aquatic conservation

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Novel tools for early detection of a global aquatic invasive,the zebra mussel Dreissena polymorpha

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Multiple survey methods reveal greater abundance of endangered pupfish in restored habitats

1. Freshwater organisms inhabiting arid ecosystems are imperilled by human alterations to water-limited landscapes. This is especially true among desert-dwelling cyprinodontid fishes, 90% of which are imperilled by habitat destruction within limited or shrinking ranges. Constructing habitats that mimic natural habitat form and function may provide a tool for species conservation, especially within freshwater protected areas. However, pupfish population assessments within degraded compared with restored habitats are infrequent, and few comparisons among survey methods exist.
2. Density estimates were developed for Endangered Comanche Springs pupfish Cyprinodon elegans throughout altered and restored habitats in a freshwater protected area by using mark–recapture and N-mixture models fitted to data collected using minnow trap and visual count survey methods. This allowed comparison of habitats, survey methods, and statistical methods commonly used to generate population size estimates for imperilled pupfish.
3. Population estimates varied across major habitat types and were largest among habitats constructed to mimic naturally occurring ciénegas. Estimates using visual counts were higher than estimates from minnow traps where water was deeper and where macroalgae cover was highest. N-mixture models generally estimated higher abundances than mark–recapture and were not limited by recapture ability.
4. The results provide strong evidence that restored habitats house greater abundances of pupfish, but survey and statistical methods commonly used to detect these differences have trade-offs in performance according to the habitats surveyed. This work benefits the field of conservation biology by providing guidance for existing and emerging monitoring programmes assessing abundance-based fish responses to habitat improvements.

     

Vulnerability of Cape Fold Ecoregion freshwater fishes to climate change and other human impacts

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Monitoring a loss: Detection of the semi‐aquatic crocodile lizard (Shinisaurus crocodilurus) in inaccessible habitats via environmental DNA

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Heads you win,tails you lose: Life‐history traits predict invasion and extinction risk of the world's freshwater fishes

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Introduction of exotic fish species and decline of native species in the lower Po basin,north‐eastern Italy

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Native and introduced fish community structure in a freshwater swamp forest: Implications for conservation and management

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Niche‐based species distribution models and conservation planning for endangered freshwater crayfish in south‐western Germany

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Exploring uncertainty in population viability analysis and its implications for the conservation of a freshwater fish

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Replacement of fish meal by potato protein concentrate in diets for rainbow trout, Oncorhynchus mykiss (Walbaum): growth, feed utilization and body composition

Five experimental diets (PPC1, PPC2, PPC3, PPC4 and PPC5) containing about 465 g kg⁻¹ crude protein were formulated to contain graded levels of potato protein concentrate (PPC) (a by-product of potato starch manufacturing) by replacement of fish meal protein. The contents of PPC were 0, 94, 200, 304 and 510 g kg⁻¹ respectively. The diets were prepared isonitrogenously and isocalorically. A 6-week growth trial was conducted with rainbow trout, Oncorhynchus mykiss (Walbaum), at about 14°C to evaluate the potential use of the potato protein concentrate in trout diets.
The results showed that fish fed diets containing PPC showed decreased growth, feed utilization and condition factor, and increased mortality when PPC constituted the sole protein source. Incorporation of PPC in the diets resulted in decreased dry matter, protein and fat and increased ash contents of the fish body. In conclusion, the type of potato protein concentrate used, especially at high levels, was not suitable as an ingredient in trout feed.     

Contrasting changes in freshwater fish assemblages and food webs follow modification of tropical waterways

Fresh waters are increasingly threatened by flow modification. Knowledge about the impacts of flow modification is incomplete, especially in the tropics where ecological studies are only starting to emerge in recent years. Using presence/absence data dated approximately four decades apart (~1966 to ~2010) from 10 tropical rivers, we assessed the changes in freshwater fish assemblage and food web after flow modification. The sites were surveyed with methods best suited to habitat conditions (e.g., tray/push netting for low‐order forest streams, visual surveys for canalised rivers and net casting for impounded rivers). With the presence/absence data, we derived and compared six measures of fish assemblage and food web structure: species richness, proportion of native species, overall functional diversity, native functional diversity, food web complexity and maximum trophic level. We found that changes in community assemblage and food web structure were not generalisable across modification regimes. In canalised sites, species richness and maximum trophic levels were lower in the second time period while the opposite was true for impounded sites. However, proportion of native species was consistently lower in the second time period across modification regimes. Changes in fish assemblages and food webs appear to be driven by species turnover. We recorded 79 cases of site‐specific extirpation and 117 cases of site‐specific establishment. Our data further suggest that turnover in assemblage is again contingent on flow‐modification regime. While the process was stochastic in canalised rivers, benthopelagic species were more likely to be extirpated from impounded rivers where species lost were replaced by predominantly alien fish taxa.     

Predicting non‐native fish dispersal under conditions of climate change: case study in England of dispersal and establishment of pumpkinseed Lepomis gibbosus in a floodplain pond

Predictions of future climate change include shifts in patterns of precipitation, evapotranspiration and water run‐off, resulting in increased periods of drought as well as variability and intensity of rainfall events. In the United Kingdom, the non‐native North American sunfish, pumpkinseed Lepomis gibbosus (L.), is expected to benefit from these changes. We examine how hydrological variability induced by predicted changes in climate will affect the dispersal and spread of pumpkinseed in England by: (i) determining the relationship between discharge regime and pumpkinseed propagule pressure; (ii) examining a newly‐established pumpkinseed population following a flood event in 2007; and (iii) comparing the growth and life‐history traits of this new population with fish collected from the source population to demonstrate how the pumpkinseed's life‐history plasticity contributes to its success as a coloniser. Using Bayesian modelling, we determined that the number of pumpkinseed escapees is likely to increase with increasing discharge. The newly‐established pumpkinseed population showed fast juvenile growth, early age at maturity and small size at maturity. These traits differed significantly from the source population, specifically total length (TL) means at ages 1 and 2 were significantly greater in the new population, whereas TL at age 4 was significantly greater in the source population, and a significantly higher proportion of mature females were found at smaller size classes in the newly established pumpkinseed population. This study demonstrates the potential link between hydrological variability (current and future) and the dispersal of non‐native pumpkinseed, leading to the establishment of new populations.     

Integrating fishing and conservation in a risk framework: A stochastic population model to guide the proactive management of a threatened freshwater crayfish

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