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The Tonle Sap Lake in Cambodia is a crucial freshwater biodiversity hotspot and supports one of the world’s largest inland fisheries. Within the Tonle Sap basin, freshwater molluscs provide vital ecosystem services and are among the fauna targetted for commercial harvesting. Despite their importance, freshwater molluscs of the Tonle Sap basin remain poorly studied. The historical literature was reviewed and at least 153 species of freshwater molluscs have been previously recorded from throughout Cambodia, including 33 from the Tonle Sap basin. Surveys of the Tonle Sap Lake and surrounding watershed were also conducted and found 31 species, 15 bivalves (five families) and 16 gastropods (eight families), in the Tonle Sap basin, including three new records for Cambodia (Scaphula minuta, Novaculina siamensis, Wattebledia siamensis), the presence of globally invasive Pomacea maculata and potential pest species like Limnoperna fortunei. This study represents the most comprehensive documentation of freshwater molluscs of the Tonle Sap basin, and voucher specimens deposited at the Inland Fisheries Research and Development Institute, Cambodia, represent the first known reference collection of freshwater molluscs in the country. In order to combat the combined anthropogenic pressures, including invasive species, climate change and dams along the Mekong River, a multi-pronged approach is urgently required to study the biodiversity, ecology, ecosystem functioning of freshwater molluscs and other aquatic fauna in the Tonle Sap basin.

The Tonle Sap Lake in Cambodia supports several species of threatened megafish and contains one of the largest networks of freshwater fish reserves in the world. Despite these traits, this system remains understudied in terms of its utility for endangered fish conservation and restoration. This study was the first of a series of planned fish releases designed to test the effectiveness of conservation supplementation programs in the Tonle Sap Lake. In March 2022 (during the dry season), 1582 captive-reared fishes, including 1538 striped catfish Pangasianodon hypopthalmus, 42 giant barb Catlocarpio siamensis, and two Mekong giant catfish Pangasianodon gigas, were tagged and released into a 986-hectare fish reserve to assess post-release dispersal and survival. Brightly colored external tags with unique identification numbers were used to facilitate tag returns. A high-profile release event was held to raise awareness about the activity, bringing attention to the importance of fish reserves and endangered species conservation, and disseminating information about the research and tag return and reward program. This, in concert with other efforts, served to be an important education and outreach tool and increased tag return rates. We found that mortality from fishing was rapid and very high. Nineteen percent of released fishes were recaptured in the first 2 days after the fish release, and 46% were recaptured by day 83 after the release, indicating intense fishing pressure on the Tonle Sap Lake fisheries. Eighty percent of recaptured fishes were caught in stationary gill nets, most within 10 km of the release site. Fishing mortality rates were independent of fish size or source (pond-reared or cage-reared). Environmental DNA (eDNA) was found to be capable of detecting each of these species’ presence in the water at the release site and could prove to be a useful tool for endangered species monitoring and restoration. Future research should explore alternative release timing, release location, and other methods of increasing post-release survival. Ultimately, underlying sources of mortality, especially fishing, will need to be addressed for conservation supplementation programs to succeed in the Tonle Sap Lake. Conservation supplementation should not be viewed as a substitute for more fundamental conservation measures, such as maintenance of environmental flows, preservation of ecological connectivity, and science-based fisheries management.

Environmental DNA (eDNA) metabarcoding approaches to surveillance have great potential for advancing biodiversity monitoring and fisheries management. For eDNA metabarcoding, having a genetic reference sequence identified to fish species is vital to reduce detection errors. Detection errors will increase when there is no reference sequence for a species or when the reference sequence is the same between different species at the same sequenced region of DNA. These errors will be acute in high biodiversity systems like the Mekong River Basin, where many fish species have no reference sequences and many congeners have the same or very similar sequences. Recently developed tools allow for inspection of reference database coverage and the sequence similarity between species. These evaluation tools provide a useful pre-deployment approach to evaluate the breadth of fish species richness potentially detectable using eDNA metabarcoding. Here we combined established species lists for the Mekong River Basin, resulting in a list of 1345 fish species, evaluated the genetic library coverage across 23 peer-reviewed primer pairs, and measured the species specificity for one primer pair across four genera to demonstrate that coverage of genetic reference libraries is but one consideration before deploying an eDNA metabarcoding surveillance program. This analysis identifies many of the eDNA metabarcoding knowledge gaps with the aim of improving the reliability of eDNA metabarcoding applications in the Mekong River Basin. Genetic reference libraries perform best for common and commercially valuable Mekong fishes, while sequence coverage does not exist for many regional endemics, IUCN data deficient, and threatened fishes.

Mekong River Basin is one of the world’s fish biodiversity hotspots. Fisheries of the Cambodian Mekong are characterized by high diversity and productivity. However, few studies have focused on broad scale patterns and fish assemblage structure of this important system at a national level. Here, we describe spatial and seasonal variation in fish assemblages by analyzing one year of daily fish catch data sampled at 32 sites covering Cambodia’s main inland water bodies. We recorded 125 fish species. Four clusters were distinguished based on assemblage composition similarity, and 95 indicator species were identified to characterize each of the identified assemblage clusters. High diversity fish assemblages were associated with the upper Mekong system and Mekong/Bassac/Tonle Sap Rivers in Kandal Province and southern Tonle Sap Lake while lower diversity assemblages were observed in the Mekong River in Kratie and the northern area of the Tonle Sap Lake. We find significant variation in the assemblage composition between wet and dry seasons, indicating strong seasonal species turnover within clusters. Length–weight relationship analysis indicated a negative allometric growth among a majority of indicator species, reflecting suboptimal conditions for growth. Our study establishes contemporary structure and diversity patterns in the Lower Mekong River system of Cambodia, which can be used to map fish biodiversity hotspots and assess key indicative fish stocks’ statuses for conservation and management.

Megafishes are important to people and ecosystems worldwide. These fishes attain a maximum body weight of ≥30 kg. Global population declines highlight the need for more information about megafishes’ conservation status to inform management and conservation. The northern Cambodian Mekong River and its major tributaries are considered one of the last refugia for Mekong megafishes. We collected data on population abundance and body size trends for eight megafishes in this region to better understand their conservation statuses. Data were collected in June 2018 using a local ecological knowledge survey of 96 fishers in 12 villages. Fishers reported that, over 20 years, most megafishes changed from common to uncommon, rare, or locally extirpated. The most common and rarest species had mean last capture dates of 4.5 and 95 months before the survey, respectively. All species had declined greatly in body size. Maximum body weights reported by fishers ranged from 11–88% of their recorded maxima. Fishers identified 10 threats to megafishes, seven of which were types of illegal fishing. Electrofishing was the most prevalent. Results confirm that Mekong megafishes are severely endangered. Species Conservation Strategies should be developed and must address pervasive illegal fishing activities, alongside habitat degradation and blocked migrations, to recover declining populations.