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Summary: Millions of native fish are entrained into irrigation pumps in Australian rivers every year. It is often assumed these fish are wild, but stocked fish may also be affected. During fish entrainment surveys at two pump intakes on the Macquarie River, New South Wales, a noticeable increase of entrained juvenile Murray Cod (Maccullochella peelii) was observed. DNA parentage analysis confirmed that a large proportion of these fish were linked to nearby fish restocking events. At both pump intakes, genetic analysis confirmed that at least 70% and 17% of the individuals sampled were stocked fish. This equated to up to 3% of the fish that were stocked – most of which were entrained less than 24 h after their release. Given the large number of unscreened irrigation pumps in this reach of river, and more broadly throughout the Murray–Darling Basin, fish losses at pump intakes have the potential to remove large numbers of stocked fish from the river where they are released to support native fish recovery and boost recreational fishing opportunities. The use of fish‐protection screens at pump intakes may be a suitable solution to reduce the number of fish entrained and thus increase the survival of recently stocked fish in the rivers. [ABSTRACT FROM AUTHOR]

The analysis of environmental DNA (eDNA) is a powerful and non-invasive method for monitoring the presence of species in ecosystems. However, ecologists and laboratory staff can find it challenging to use eDNA analysis software effectively due to the unfamiliar command-line interfaces used by many of these packages. Therefore, we developed the eDNA-container app, a free and open-source software package that provides a simple user-friendly interface for eDNA analysis. The application is based on the popular QIIME2 library and is distributed as a Docker image. The use of Docker makes it compatible with a wide range of operating systems and facilitates the reproducible analysis of data across different laboratories. The application includes a point-and-click user interface for selecting sequencing files, configuring parameters, and accessing the results. Key pipeline outputs, such as sequence quality plots, denoising, and ASV generation statistics, are automatically included in a PDF report. This open-source and freely available analysis package should be a valuable tool for scientists using eDNA in biodiversity and biosecurity applications. [ABSTRACT FROM AUTHOR]

Context: Rapid human population growth has increased demand for water supply, food security, electricity, and flood mitigation worldwide. To address these challenges, governments have invested heavily in the expansion of water infrastructure. However, there is substantial evidence that globally, this infrastructure impacts aquatic ecosystems and can have a significant impact on the persistence of fish species. Despite being well understood globally, the impacts of dams on fish have been given scant attention in Indonesia. Thus, considerations for fish are rarely included in river development planning frameworks. Methods: To document the impact of riverine barriers on Indonesian freshwater fish, we surveyed multiple sites, using three different kinds of gear (gillnets, castnets, and bait traps), upstream and downstream of Perjaya Dam in the Komering River. Key results: The study revealed 13 of 36 species were found only downstream of the dam and five of 36 species were found only above the dam. There were significant differences in fish community composition between upstream and downstream regions using either fish abundance (Pseudo- F = 4.495, d.f. = 1, P < 0.05), species richness (Pseudo- F = 15.837, d.f. = 1, P < 0.05) or species diversity as the response metrics (Pseudo- F = 8.3256, d.f. = 1, P < 0.05). Conclusions: The local extirpation of many species from upstream areas suggests that the Perjaya Dam hinders fish migration. Implications: Despite containing a fishway, the results indicate that fish are not successfully recolonising upstream reaches. Dams are known to impact fish community structure, however, the impacts of dams on the fish community in Indonesia is understudied. We sampled the fish community upstream and downstream of a dam fitted with a fishway, identifying significant differences in fish community structure. This highlights the need for further research into the operation of the dam, and fishway, to improve fish passage success. [ABSTRACT FROM AUTHOR]

Context: The ability to accurately assess biodiversity is a critical first step towards effective conservation and management. However, assessment of biodiversity using conventional monitoring programs is often constrained by high cost and a lack of taxonomic expertise. Environmental DNA (eDNA) metabarcoding may be a useful tool to efficiently catalogue biodiversity in areas that cannot be easily assessed using other methods. Aims: Here, we evaluated the potential of eDNA metabarcoding for assessing fish biodiversity and distribution in the Kumbe River, Papua Province, Indonesia. Methods: We selected four sampling locations and collected seven eDNA samples from each location. We used eDNA metabarcoding of the Cytochrome- b gene to characterise the fish community. Key results: A total of 23 species were detected, three of which comprised 92% of sequence reads detected: Melanotaenia goldiei (32%), Craterocephalus randi (31%), and the invasive tilapia Oreochromis niloticus (29%). Only five species that were previously detected using conventional methods were detected by metabarcoding: M. goldiei , Craterocephalus stercusmuscarum , O. niloticus , Neoarius graeffei , and Arius arius. We detected 18 species (70% native) that have never been recorded from the Kumbe River. Conclusions: This work has demonstrated that fish biodiversity is substantially underestimated in the Kumbe River. Environmental DNA metabarcoding is a promising rapid, non-invasive and cost-effective method for assessing fish biodiversity in Papua. Implications: The findings support future investment in eDNA metabarcoding to characterise the fish biodiversity in Papua. This will assist in allocating the limited resources for conservation and management to areas most at risk from anthropogenic impacts. Environmental DNA (eDNA) metabarcoding shows great promise as a novel tool for fish biomonitoring programs in tropical freshwater habitats. It is sensitive, non-invasive and cost-effective. However, our results highlight that eDNA metabarcoding cannot be routinely applied without further research into sampling design, marker choice, seasonal data, and an improved reference database to reduce false negative detections. Despite this, eDNA metabarcoding will play an important role in the future characterisation of the fish community in tropical river systems. [ABSTRACT FROM AUTHOR]

River regulation infrastructure has been implicated in worldwide aquatic biodiversity loss. In‐stream barriers such as weirs prevent fish migration and the impact can be particularly severe for diadromous species. Fishways are frequently installed on in‐stream barriers to reconnect migratory pathways and rehabilitate diadromous fish populations. Sequential fishways may be necessary in rivers where multiple barriers prevent migration. We monitored a coastal fish community's response to fish passage restoration at 10 predominantly low‐level weirs in the freshwater reaches of the Nepean River in southeastern Australia. Few studies have simultaneously assessed fish community passage at successive fishways within a river system. Prior to the installation of the fishways, there was a gradient of reduced species diversity in an upstream direction including the absence of many diadromous species, despite the regular inundation frequency of most weirs. Following the installation of the fishways, species diversity was still greater in the downstream monitoring sites; however, there was evidence of a positive change in fish community structure in middle and upstream sites. Most notably, three diadromous species rapidly expanded their distribution upstream and one amphidromous species expanded its downstream distribution. This study demonstrates appropriately designed successive fishways can successfully reconnect river systems for an entire fish community, encompassing species with a broad range of swimming abilities and diverse life histories. [ABSTRACT FROM AUTHOR]

ABSTRACT Genomic vulnerability is a measure of how much evolutionary change is required for a population to maintain optimal genotype‐environment associations under projected climates. Aquatic species, and in particular migratory ectotherms, are largely underrepresented in studies of genomic vulnerability. Such species might be well equipped for tracking suitable habitat and spreading diversity that could promote adaptation to future climates. We characterised range‐wide genomic diversity and genomic vulnerability in the migratory and fisheries‐important golden perch (Macquaria ambigua) from Australia's expansive Murray–Darling Basin (MDB). The MDB has a steep hydroclimatic gradient and is one of the world's most variable regions in terms of climate and streamflow. Golden perch are threatened by fragmentation and obstruction of waterways, alteration of flow regimes, and a progressively hotter and drying climate. We gathered a genomic dataset of 1049 individuals from 186 MDB localities. Despite high range‐wide gene flow, golden perch in the warmer, northern catchments had higher predicted vulnerability than those in the cooler, southern catchments. A new cross‐validation approach showed that these predictions were insensitive to the exclusion of individual catchments. The results raise concern for populations at warm range edges, which may already be close to their thermal limits. However, a population with functional variants beneficial for climate adaptation found in the most arid and hydrologically variable catchment was predicted to be less vulnerable. Native fish management plans, such as captive breeding and stocking, should consider spatial variation in genomic vulnerability to improve conservation outcomes under climate change, even for dispersive species with high connectivity. [ABSTRACT FROM AUTHOR]