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Worldwide, freshwater vertebrate populations are declining with increasing pressure on rivers due to numerous environmental and climatic threats. Environmental DNA (eDNA) could potentially provide a more efficient and non‐invasive mechanism to monitor freshwater systems, either as a complement or in replacement to traditional methods to accurately assess species' distributions. Here, we utilize a hierarchical multispecies N‐mixture model to compare three fish sampling methods: traditional fyke netting and active and passive environmental DNA sampling along a 30 km stretch of the Canning River in Western Australia. We used the fitted model to compare capture probabilities among sampling methods and reveal the sampling effort required to describe the species assemblage. Results indicated that while all methods could detect fish, combined eDNA methodologies detected one more fish species than those caught by fyke netting. In addition, active eDNA sampling produced the highest capture probabilities and more consistently described the entire fish assemblage at any given site. Fyke netting and passive eDNA did not show significant differences in their average capture probabilities, and both methods had lower abilities to capture individual species than active eDNA. Active eDNA also required fewer replicate samples to detect the expected observed richness, and fyke netting required the most replicates. Additionally, a hierarchical multispecies abundance model showed that active environmental DNA (eDNA) sampling is the most effective method for monitoring freshwater fish populations. This study contributes to our understanding of eDNA in aquatic systems and demonstrates that, at least under current conditions, active sampling is still the preferred method in freshwater systems with low flow compared to both passive sampling and fyke netting. This study compared three fish sampling methods: traditional fyke netting, and active and passive environmental DNA sampling along a 30 km stretch of the Canning River in Western Australia. The effectiveness of the three different methods of detecting fish was tested with a hierarchical multispecies abundance model fit, with the model used to estimate both detection probability and replication effort required. This study contributes to our understanding of eDNA in aquatic systems and demonstrates that, at least under current conditions, active sampling is still the preferred method in freshwater systems with low flow compared to both passive sampling and fyke netting.

Site‐occupancy modelling is widely used in ecology for understanding species distribution, habitat‐use and community changes but its application is still limited in paleoecology, where incomplete detection is also routine. Here, we make extensive expansions to an earlier multispecies occupancy model used to estimate the dynamics of relative species abundance in fossil communities. These expansions include incorporating counts of individuals at sites, explicitly allowing for the inclusion of specimens assignable to genus – but not species‐level, a situation common in paleontology, and modelling regional presence/absence. We provide simulations to check the performance of this new model, as well as simulations to quantify the benefits of using individual count data versus subsample occupancy data, and model estimates versus face‐value (raw) estimates, respectively. We also provide an empirical case study using occupancy data from a community of marine benthic colonial animals preserved in the Pleistocene of New Zealand. We find that the new model performs well, especially when it comes to recovering relative abundance dynamics and that it is well worth the effort to both collect individual count data and to include individuals unidentified to species‐level in the site‐occupancy modelling framework. This extended model can be widely applied in paleoecological settings and is necessary when both the average and uncertainty values of relative abundance dynamics need to be robustly estimated.

While wetlands have been converted into farmlands, large amounts of farmlands are now being abandoned, and this novel habitat is expected to be inhabited by species which depend on wetlands. Here we examined the effects of habitat and landscape variables on the densities of wetland bird species in abandoned farmlands. We surveyed birds in abandoned farmlands with different patch area, habitat, and landscape variables in Kushiro district, eastern Hokkaido, northern Japan. We also surveyed birds in 15 ha of the remaining wetlands as a reference habitat. We used abundance-based hierarchical community models (HCMs) to estimate patch-level estimates of abundance of each species based on sampling plots data that only partially covered the studied patches. We observed 14 wetland species and analyzed them with HCMs. Abandoned farmland patch areas had significant positive effects on the densities of two species. Tree densities and shrub coverage exerted positive and negative effects on some species. Amounts of surrounding wetland/grassland had positive effects on many species. Ensemble of species-level models suggested that 24.7 and 10.6 ha of abandoned farmlands would be needed to harbor a comparable total abundance and species richness in 15-ha wetlands, respectively. These required amounts can be increased/decreased depending on the covariates. The use of HCMs allows us to predict species- and community-level responses under varied conditions based on incomplete sampling data. A quantity of 1.6 times larger areas of abandoned farmlands may be required to restore wetland bird communities in eastern Hokkaido.