Characterizing spatial patterns among freshwater fishes and shrimps of the Poso River (Sulawesi, Indonesia) using DNA barcoding

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Poso River in Sulawesi, Indonesia presents a complex scenario where changes in fish biodiversity can be influenced by habitat alteration, the introduction of non-native fish species and overfishing. In this study, we assessed fish biodiversity in Poso River to gain a better understanding of the challenges to its aquatic biodiversity. This knowledge is critical for enhancing fisheries management and conservation programs, and is essential for improving the fishway system integrated into hydropower dams. The biodiversity study utilized a comprehensive methodology that encompassed both traditional taxonomic approaches and DNA barcoding, specifically targeting the mitochondrial Cytochrome C Oxidase Subunit-1 (COI) gene for accurately identify species and validate their boundaries. It was conducted in upstream, environmental flows of hydropower dams, and downstream areas of the river. We found 27 species of fish in the Poso River, including both native and non-native species. Two endangered species were also observed. DNA barcoding was performed to examine species boundaries and identity. The fish population in the Poso River is dominated by non-native species, accounting for 85.70% of the total population. The upstream area had the highest fish abundance and diversity, while the downstream area had the lowest. There was no significant difference in species richness and diversity across different locations and seasons. The dominance of non-native species in the Poso River necessitates the improvement of existing fish passages equipped in hydropower dams through the development of selective fish passages that can block the distribution of these invasive species. This research highlights the critical issue of non-native species proliferation and its potential threat they pose to native fish populations, providing valuable insights for conservation and management efforts in Indonesia and similar ecosystems worldwide. Aquatic biodiversity non-native species fishway hydropower conservation Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Introduction Freshwater resources and their biodiversity rank among the world's most imperiled ecosystems (McGregor Reid 2013 ; Yousefi et al. 2020 ), with a faster declining rate than terrestrial or marine ecosystems (McRae et al. 2017 ). One of the main reason is that freshwater biodiversity is jointly facing the direct impacts from human activities and climate change (Gozlan et al. 2019 ; Grafton et al. 2012 ). Within riverine ecosystems, the most significant threats to freshwater biodiversity include the introduction and proliferation of non-native species, water pollution, habitat fragmentation, overexploitation by local fisheries and climate change (Arthington et al. 2016 ; Xing et al. 2016 )). Most of these threats are currently being observed in the Poso River, Central Sulawesi, Indonesia. Connecting the ancient lake Poso of central Sulawesi, the main island of the Wallacea biodiversity hotspot (Myers et al. 2000 ), the area hosts a wealth of endemic species for multiple freshwater organisms such as fish, mollusks and crustaceans (Kottelat et al. 1993 ; von Rintelen et al. 2007 ). However, the Poso River is a productive river systems used for hydroelectric resource supplying electricity in the region, a source of animal protein and community livelihood (Krismono and Kartamihardja 2012; Watupongoh and Krismono 2015 ). The Poso river presents a complex scenario where alterations in fish biodiversity are not solely attributed to the presence of dams, the shifts in river hydrology, environmentally detrimental fishing practices, but although noticeable changes in biodiversity within the connected Poso Lake play a pivotal role in shaping fish population dynamics (Serdiati et al. 2023 ). This intricate interconnection arises from the fact that a significant portion of the water inflow of the Poso River originates from the Lake Poso. A comprehensive assessment of the freshwater biodiversity of the Poso River is urgently required to better understand ongoing biodiversity challenges and guiding conservation plans. A concerning factor jeopardizing fish biodiversity within Lake Poso is the widely spread of non-native fish species, which have asserted their dominance throughout the lake, extending to the lake’s outlet region, which feeds into the river. This invasive presence poses a significant threat to the ecological balance of Lake Poso ecosystems (Herder et al. 2022 ). A substantial number of non-native species have successfully established and grow large populations, and they are now negatively impacting the native endemic species of the lake (Gaygusuz et al. 2013 ; Shelton et al. 2014 ). The introduction of non-native fish species can detrimentally impact native fish through resource competition, predation, hybridization and pathogens transmission (Britton 2023 ; Jiang et al. 2021 ). These negative effects have emerged in many regions where non-native fish have been introduced (Okwiri et al. 2019 ; Spikmans et al. 2020 ). The alteration of the biodiversity of Lake Poso poses a serious challenges to the Poso River, which aquatic organisms are already heavily perturbed by the presence of dams and alterations in the river’s hydrological patterns. The construction of dams leads to fragmentation, resulting in various changes to the physical, chemical, and hydrological characteristics of both upstream and downstream ecosystems. These modifications include adjustments to the normal flow of the river, the occurrence of hydropeaking, and the blocking of sediment and some organisms such as fish and invertebrates (Capra et al. 2017 ; Silva et al. 2018 ). In an ecosystem where fish fauna plays a crucial role in ecosystem functioning, it is essential to restore connections in order to facilitate the completion of each species’ life cycle (Benitez et al. 2015 ; Lucas et al. 2001 ) and/or accessing habitats for feeding and development (feeding migration) and seeking refuge when severe environmental conditions occurs (refuge migration) (Lucas et al. 2001 ). Such movements may occur frequently during an individual’s lifespan, may involve a substantial proportion of a species’ population, and may occur at various stages of life (Lucas et al. 2001 ). Because of these barriers, it becomes impossible for organisms to move freely within the river, which jeopardize population average fitness (Birnie-Gauvin et al. 2020 ; Ovidio et al. 2020 ). One potential approach to addressing the issue of impeded connectivity is the implementation of a fish passage structure, commonly referred to as a fishway. This solution should be designed to accommodate multiple species and enable both diadromous ( i.e. species migrating between freshwater and the ocean) and potamodromous ( i.e. species migrating with freshwater system) species to bypass the obstacle in question (Benitez et al. 2015 ; Ovidio et al. 2020 ). Fishways are successful if they entail the removal or reduction of negative impacts of obstructions to movement and achieve the conservation of native species and nutrient fluxes between lacustrine, riverine, and marine ecosystems (Hall et al. 2012 ). Hydropower dams on the Poso River have been equipped with fishways designed to facilitate fish migration, with the aim of mitigating the impact of damming on fish biodiversity (Baumgartner and Wibowo 2018 ). However, the effectiveness of this passage has not yet been examined. To achieve this, it is essential to conduct an assessment of how habitat fragmentation influences the spatial and temporal distribution of fish both before and after the fishway dams are in place. The next challenge revolves around overfishing, a consequence of ecologically harmful fishing practices. This problem exacerbates the obstruction of eel migration in the upper section of the Poso River, stemming from the prolonged overfishing of eel broodstock through unsustainable fishing practice, habitat and environmental conditions (Triyanto et al. 2021 ). One of the effective fishing gears is sogili fences to block downstream migration of adult eels (Lukman et al. 2021 ). These ancestral sogili fences, which use if common in the Poso River have the potential to disrupt fish biodiversity, resulting in a reduction of eel populations – a key predator – and the uncontrolled proliferation of lower-level predators that can dominate river habitats. Additionally, near the estuary of the Poso River, unregulated capture of the glass eel and other amphidromous fish fry poses a significant threat to fish biodiversity, further destabilizing the ecosystem of the Poso River (Haryani 2022 ; Krismono and Putri 2012). Given the intricate nature of the challenges in the Poso River, we undertook a comprehensive study to assess fish and crustacean biodiversity and its spatial and temporal distribution. Our research encompassed direct fishing activities in the upstream, environmental flow, and downstream regions, with the Poso hydropower plant serving as our reference point. In addition, we investigated both adult fish biodiversity and larval distribution, employing a DNA barcoding approach for characterize species and identify specimens. DNA barcoding offers the capability to distinguish and identify morphologically similar species effectively. By sequencing the COI gene region in multiple individuals and populations across their range, coupled with species delimitation guided by mitochondrial sequences, we can clarify species boundaries and distribution. Materials and Methods Study Area The Poso River is located in the Poso Regency of Central Sulawesi Province, Indonesia, approximately 50 km south of Poso City (Fig. 1 ). The river primarily draws its water from the Lake Poso, positioned upstream. Lake Poso is a tectonic lake situated at an elevation of 485 meters above sea level (Lehmusluoto and Machbub 1997 ). At a minimum, 13 rivers contribute to Lake Poso, while the Poso River acts as an exit that spans 52 km and discharges into the Tomini Bay (Pangesti et al. 1995 ). The river traverses the middle section of Sulawesi Island, which is characterized by a tropical rainforest climate, with the mean annual precipitation is 2715 mm. The highest average temperature is 23 o C in October, while January is the coldest month with 20 o C (Peel et al. 2007 ). Two dams in the Poso River are harnessed for power generation, supplying electricity to the Sulawesi region. Additionally, two fishways have been installed within the dams to facilitate fish migration. Seven sites were determined to evaluate fish biodiversity status including two sites upstream, three areas in environmental flows and two sites located downstream of the Poso Energy dam (Fig. 1 ). Environmental flow refers to the release of water into the river once the majority of it has been utilized for hydropower generation. Experimental fishing Specimens were collected using multi-panel gillnets, collapsible bait traps, and cast nets. To ensure a broad coverage of fish and shrimps diversity in our sampling, including pelagic and bottom-dwelling species, we used a combination of active and passive methods including gillnets with six different mesh sizes (ranging from 19.05 to 101.6 mm), bait traps measuring 400 × 220 × 220 mm (length × width × height) with a 60 mm entry diameter, and 2 m diameter cast nets with 19.05 mm mesh size. The sampling effort was standardized to allow comparisons among sites with gillnets and bait traps set up for two hours and cast nets cast 15 times with 1-minute intervals between casts. We used 100g chicken intestine, fresh shrimp, and artificial feed purchased from a local market as bait in all experiments. We conducted experimental fishing from 8:00 a.m. to 2:00 p.m. during both dry season (March and June 2023) and wet season (September 2023) to cover potential seasonal variations in fish populations. All fish specimens underwent anesthesia using a solution of 2-phenoxyethanol at a dosage of 0.5 mL per liter of water. We documented all fish by photographing, measuring (total length, to 1 mm using rulers and millimeter graph paper), and weighing (to 0.1 g using digital scale) collected individuals. Individual fish were identified to the species level using the field guide from Kottelat et al. ( 1993 ) and names were updated according to the Fishbase website ( www.fishbase.org ). Amplifying and sequencing A total of 20 milligrams (mg) of fin tissue or whole larvae were dissected and subsequently collected for the purpose of DNA extraction. Tissue sample was taken and preserved in 1,5 ml tubes with absolute ethanol. Preserved tissues were stored in individual tubes, which were further in cryosafe boxes. DNA extraction was conducted with the Tissue Genomic DNA Mini Kit GT050 (Geneaid, Taiwan) following the recommandations from the manufacturer. The mitochondrial gene of the Cytochrome C Oxidase Subunit-1 gene (COI) was amplified using the universal primers Fish-COI-F (5’- TCA ACC AAC CAC AAA GAC ATT GGCAC-3’) and Fish-COI-R (5’-TAG ACT TCT GGG TGG CCA AAG AATCA-3’) from Ward et al. ( 2009 ). PCR reactions were performed in 30.0 µL including 15.0 µL of 1x DreamTag Green Master Mix, 2.0 µL of Primer CO1 Forward 1 (F1), 2.0 µL of Primer CO1 Reverse 1 (R1), 9.0 µL of deionized water (nuclease free), and 2 µL of DNA template. A negative controls were used and PCR cycling conditions included one cycle at 95°C for 3 min; 95°C for 30 s; 35 cycles at 56°C for 30 s, 72°C for 1 min; and 10 minutes final extension at 72°C for 10 min. PCR products were loaded into 5 µL per well (already stained) on a 2% agarose gel containing 0.01% gel stain (SafeDNA). Electrophoresis was performed with 100 bp Plus marker (Vivantis) in 3 µL wells at 100 volts for 25 minutes on 1x TBE (Tris borate EDTA) media using PowerPac Basic (Bio-Rad). Amplification results were visualized using the UVITEC Gel Documentation System. Samples were further sequenced in both direction on a Applied Biosystems™ 3500xL Genetic Analyzer, (Thermo Fisher Scientific, USA) at the Central Laboratory for Sequencing of the National Research and Innovation Agency (Indonesia). all sequences were deposited in the NCBI Genbank database (Accession numbers PP595925-PP595976, PP556235-PP556294 and PP598893). Validating species boundaries and identities In order to obtain a comprehensive understanding of fish biodiversity at the research site, we conducted an iterative assessment of species identification involving DNA barcoding in conjunction with the examination of morphological characters in adult specimens. Larvae were subsequently identified by comparisons with COI sequences of adult specimens. We followed the procedure of species delimitation recommended by Ross et al. ( 2008 ). We combined phylogenetic reconstructions with estimates of genetic distances to guide species delimitation and detect potential conflict with the initial set of identifications performed in the field. Genetic distances were used to detect clades representing levels of genetic divergence beyond the expected threshold within species, and representing cryptic lineages. We used a 0.02 mean genetic distance as a criterion, which is a commonly used threshold (Hubert and Hanner 2015 ). The sequences obtained were aligned with ClustalW algorithm, and their quality was evaluated using the Geneious 10 software (Kearse et al. 2012 ). A phylogenetic tree was constructed with a Bayesian approach as implemented in MrBayes (Huelsenbeck and Ronquist 2001 ). Analyzing spatio-temporal patterns of species abundance Population abundance index is highly valuable to examine population dynamics. Abundance indices often utilize the catch per unit of effort (CPUE) value as a reliable measure of abundance (Francis 2011 ). The CPUE is calculated differently for each fishing gear, such as cast nets, traps, and gillnets. In cast nets, CPUE is calculated by measuring the width of the net opening, and expressing the number of fish per square meter of net opening. For traps and gillnets, CPUE estimates are based on the number of individuals caught per hour of operation. Both estimates of abundance were used here. Standard Length (SL) and weight was recorded for all the individuals captured. Indices of abundance, species richness, and species diversity were used to analyze patterns of fish community through time (dry and wet seasons) and space (upstream and downstream of the dam project). All analyses were conducted using Primer v7 (Clarke and Gorley 2015 ). Permutational analysis of variance (PERMANOVA) was used to examine if significant differences in the fish community were observed between different seasons (dry and wet) and locations (upstream and downstream) across 10 sampling sites. The fish catch counts were transformed using a log (X + 1) function and Bray-Curtis similarities were computed. Two factors (location and season) were integrated into the model and the significance of the values was assessed using 9999 raw data permutations without restrictions. Multidimensional scaling (MDS) was employed to illustrate disparities in fish community composition across different locations and seasons. We explored the distribution the SL in fish populations between upstream and downstream regions to determine if there were any noteworthy variations in length distribution between upstream and downstream stretches. The Kolmogorov-Smirnov (KS) test was employed to test the significance of any observed differences. Only species with at least 25 individuals in both upstream and downstream locations were included. Results Sampling and species delimitation During the study, 27 fish species belong to 17 families were delimited in the field. These species have various migratory behaviours, including diadromous (3 species), amphidromous (7 species), and potamodromous (17 species) (Table 1 ). The fish composition comprised both native and non-native species with varying conservation status, ranging from unknown to endangered. Notably, Adrianichthys poptae and Mugilogobius sarasinorum were identified as endangered species within the river following IUCN red list. Table 1 Fish diversity, migratory behavior, geographical origin and conservation status. No Family Species Name Migratory behaviour Geographic origin IUCN Conservation Status A Fish 1 Anguillidae Anguilla marmorata Diadromous Native LC 2 Anguillidae Anguilla bicolor Diadromous Native LC 3 Anguillidae Anguilla celebesensis Diadromous Native DD 4 Gobiidae Awaous melanocephalus Amphidromous Native LC 5 Gobiidae Awaous sp. Amphidromous Native Unknown 6 Gobiidae Mugilogobius sarasinorum Amphidromous Native EN 7 Gobiidae Sicyopterus sp. Amphidromous Native DD 8 Gobiidae Schismatogobius sp Amphidromous Native DD 9 Eleotridae Mogurnda mogurnda Amphidromous Native LC 10 Rhyacichthyidae Rhyacichthys aspro Amphidromous Native DD 11 Adrianichthyidae Adrianichthys poptae Potamodromous Native EN 12 Adrianichthyidae Adrianichthys oophorus Potamodromous Native LC 13 Adrianichthyidae Oryzias sp. Potamodromous Native Unknown 14 Adrianichthyidae Oryzias nebulosus Potamodromous Native NT 15 Adrianichthyidae Oryzias nigrimas Potamodromous Native NT 16 Cyprinidae Barbodes binotatus Potamodromous Non-Native LC 17 Chanidae Channa striata Potamodromous Non-Native LC 18 Cichlidae Cichlasoma trimaculatum Potamodromous Non-Native LC 19 Poecillidae Poecilia reticulata Potamodromous Non-Native LC 20 Kuhliidae Kuhlia marginata Potamodromous Native LC 21 Cichlidae Melanochromis auratus Potamodromous Non-Native LC 22 Cyprinidae Osteochilus vittatus Potamodromous Non-Native LC 23 Cichlidae Oreochromis niloticus Potamodromous Non-Native LC 24 Osphronemidae Trichogaster trichopterus Potamodromous Native LC B Crustacea 1 Atydae Caridina endehensis Potamodromous Native LC 2 Palaeomonidae Macrobrachium sp. Amphidromous Native LC 3 Parathelphusidae Parthelphusa sp. Potamodromous Native LC Among the 24 fish and 3 shrimp species sampled, 12 were selected which required an examination of their DNA barcode to confirm their boundaries and identity. For these species, a total of 113 sequences were generated during the present study and 11 additional sequences were mined from Genbank to compare with species names assigned in previous studies. In total, 124 sequences were analyzed. Sequences varied in lengths, ranging from 590 bp to 601 bp, with a range of 1 to 27 specimens per species. Species names assigned to the sequences mined from Genbank were matching those from our current study. A phylogenetic trees was generated for these 124 sequences (Fig. 2 ). Of the 12 species examined here with DNA barcodes, nine were effectively distinguished by their distinct set of tightly cluster sequences (Fig. 2 ). The combination of single-locus species delimitation statistics provides support for the distinctiveness of all proposed species (Table S2). However, greater values of intraspecific tree distances (as denoted by “intra” in the table S2) detected for three lineages, which cannot be identified to the species level, and displayed high levels of genetic divergence to other congeneric lineages with genetic distances ranging from 0.038 to 0.650. These correspond to exotic species (ex. Oreochromis niloticus , Poecilia reticulata ). By contrast, endemic species represented by sequences originating from a single site or region, such as Oryzias species, display lower intraspecific genetic distances. Greater values of interspecific tree distances (refer to “inter-closest” in the table S2) show that some species groups display high congeneric genetic distances. The mean values of P ID (liberal) were determined using the BI trees, indicating that all species had a probability equal to or greater than 0.95, except for Akihito sp. (0.88). The likelihood that a clade exhibits the observed level of uniqueness as a result of random coalescent processes, denoted as “P (randomly distinct)” in the tables, is represented by values ranging from 0.05 to 1. This range encompasses the majority of the values seen in putative species. The probability values indicating the reciprocal monophyly of species under the null model of random coalescence are all equal to or less than 0.05. This observation provides support for the hypothesis that these putative species can be considered different species. Fish abundance, species richness and diversity Based on the calculation of CPUE for the three fishing gears used during the study, the trap nets had a higher CPUE of 106.71 g/h compared to other fishing gears, namely gillnet and net, at 44.97 g/h and 2.76 g/h, respectively (Table S1 ). The lowest CPUE value was obtained in the gillnet gear at all research locations. Abundance data revealed contrasted patterns between upstream and downstream areas with upstream sites contributing the highest proportion of catches with 67%, while the environmental flow and downstream regions accounted for 27% and 6% of the total catches, respectively (Fig. 3 a, Fig. 5 ). Non-native species dominates in the sampling with Melanochromis auratus (25.93%), Oreochromis niloticus (19.41%), Cichlasoma trimaculatum (18.01%), Barbodes binotatus (13.03%), Osteochilus vittatus (6%), Poecilia reticulata (2.55%), Trichogaster trichopterus (0,64%) and Channa striata (0.13%) (Fig. 3 b). Native fishes only accounts for 15.07% of the total catches with Oryzias nigrimas (1.92%), Oryzias sp (1.4%), and Awaous melanocephalus (1.15%) constituting the majority of the native fish population, while the remainder is comprised of the other 15 native fish species and three genera of shrimps. Examining dominant fish species across sampling sites reveals that M. auratus (33.12 ± 22.17%) prevails upstream, while O. niloticus (42.77 ± 15.68%) dominates in the environmental flow area, and crustaceans, particularly Caridina endehensis (24.24 ± 22.88%) dominate downstream (Fig. 4 ). Table 2 Ecological index values of fish in the Poso River Abundance Diversity (Shannon-Wiener) Richness (Evenness) Location Upstream 91 1.48 7 Hydropower Area 63 0.96 5 Downstream 9 0.82 3 Season Dry 54 1.00 4.86 Wet 57 1.10 5.14 Upstream sites exhibit the highest diversity index with 1.48, followed by the hydropower area with 0.96 and the downstream area with 0.82 (Table 2 ). The diversity index value in the dry season was 1.0, while during the wet season was 1.10. In terms of species richness, upstream sites reached a score of 7, while the hydropower area scored 5, and downstream sites reach only 3 (Table 2 ). The results of the PERMANOVA analysis revealed a substantial difference in species abundance among study sites, although there was no discernible seasonal variation (Table 3). According to the analysis of species richness and diversity, no significant difference across sites and season was detected (Tables 4 and 5). In terms of temporal trends, M. auratus stands out as the predominant fish species captured in March and September, whereas O. niloticus dominated in June (Table S1 ). Spatially, these species hold dominance in both the upstream and environmental flow of hydropower areas. Estimates of biomass largely fluctuated across the three research areas. Upstream area displayed the highest biomass with 54766.93 g, whereas the hydropower and downstream areas reported significantly lower values of 8527.95 g and 383.76 g, respectively (Table S1 ). The higher biomass observed in upstream and downstream areas can be attributed to the substantial catch of large fish individuals, including eels Anguilla bicolor , Anguilla celebesensis , and Anguilla marmorata . These particular species were exclusively captured in the upstream and hydropower areas. Additionally, the study also identified three other fish species which mostly contributed to the biomass estimates namely B. binotatus , C. trimaculatum , and M. auratus . Discussion This research presents updated insights into the fish biodiversity of the Poso River including an updated species list and appraisal of fish abundance and biomass in the area. We successfully combined morphological identification and DNA barcoding to produce robust schemes of species delimitation, and validated species identifications from fish larvae and adult. By combining the examination of genetic divergence (Hebert et al. 2004 ; Ward et al. 2005 ) and the examination of physical characteristics (Ahnelt et al. 2019 ), we were able to determine if genetic variations form discrete clusters which align with species-level taxa (Atminarso et al. 2018 ). The increasing accessibility of DNA barcodes proved to facilitate the resolution of conflicting taxonomic cases (Dahruddin et al. 2021 ; Hubert et al. 2019 ; Wibowo et al. 2023 ; Wibowo et al. 2024 ). The absence of reference sequences is currently the main limit in the application of DNA barcoding for automated identification of unknown (Wibowo et al. 2016 ; Wibowo et al. 2022 ). The integration of DNA barcoding with conventional taxonomic workflow using morphological characters offers a robust procedure to delimitate species and identify specimens, resulting in taxonomic revisions and holding promise for future advancements as its adoption becomes more prevalent. Poso River is anticipated to undergo changes in fish community structure due to various factors, including the invasion of the system by exotic fish species, alterations in river hydrology, and unsustainable fishing practices both upstream and downstream of the current dam project. Fish biodiversity of fish in the Poso River is intricately linked to the lake Poso ecosystem and its biodiversity, which serves as the primary water source supplying the river. The introduction of exotic species and their invasion has been studied in Lake Poso, revealing the presence of 17 non-native fish species introduced since the last century for various purposes but mostly for increasing fish biomas by releasing pet fish from aquariums (Herder et al. 2012 ). During this study, a total of 27 fish and shrimps species were documented. Notably, eight non-native species, constituting 87.50% of the observed fish, have established dominance within the Poso River. The remaining 12.5% correspond to native fish species of Poso River. The five dominant non-native species include Melanochromis auratus (25.93%) from Lake Malawi, Oreochromis niloticus (19.41%) from Africa, Cichlasoma trimaculatum (18.01%) from Mexico and Central America, Barbodes binotatus (13.03%) from Sundaland (Java, Sumatra, Borneo), and Osteochilus vittatus (6%) from Sundaland. This situation is particularly of concern, particularly for predator fish that pose a potential threat to native fish. Numerous activities, such as aquaculture, restocking, biological control, and recreational fishing, have contributed to the introduction of exotic fish into Indonesia’s freshwater ecosystems (Andriyono and Fitrani 2021 ; Suryandari et al. 2021 ). The expansion of the invasive fish species could result in reduced abundance of native fish and species diversity, and lead to the extinction of native fish species (Gaye-Siessegger et al. 2022 ; Zhao et al. 2019 ). This phenomenon is exemplified by the unfortunate loss of native fish species such as Adrianichthys kruyti and Xenopoecilus poptae in Lake Poso, attributed to the introduction of Nile Tilapia (Yanuarita et al. 2020 ). Notably, the rapid reproductive rates of non-native fish have been observed to outcompete and displace native species (Escobar et al. 2018 ; Saba et al. 2021 ). The prevalence of non-native fish may compete for limited food and habitat resources. Furthermore, they could act as the host for various diseases previously absent in the ecosystem (Havel et al. 2015 ). Currently, the number of invasive fish is increasing, one of which is M. auratus (Herder et al. 2022 ). This cichlid fish was caught in both the upstream area and the hydropower area but was not found yet in the downstream area. The presence of barriers in the form of dams can prevent the spread of invasive fish downstream. However, negative impacts in the form of habitat fragmentation may occur. Habitat fragmentation can particularly affect migratory fishes and can alter fish populations and distribution (Arantes et al. 2019 ; Pavlov et al. 2020 ). The challenge of future development of fish passage is selective passage design to prioritize native migratory fish species without enabling the spread of invasive species (Cooper et al. 2021 ; Kerr et al. 2021 ). The fragmentation of river systems stands as a primary driver behind the decline in freshwater fish biodiversity (Franklin et al. 2022 ; Stendera et al. 2012 ). This study reveals noteworthy disparities in fish biodiversity between the upstream, environmental flow and downstream sections of the river. Specifically, the upstream area exhibits a notably higher fish abundance compared to both the environmental flow and downstream regions. Within the upstream zone of the Poso River, a diverse community comprising 15 fish species was observed, representing a substantial 69.35% of the overall fish population. In the environmental flow and downstream sections of the Poso River, the observed fish species numbered 14 and 7, respectively, accounting for 24% and 7% of the total fish population in these respective areas. A striking illustration of this impact can be observed in the case of the Djuanda Reservoir on the Citarum River, West Java. This reservoir, constructed in 1968 as the first major Indonesian hydropower dam, led to a significant transformation in the native freshwater fish community. Prior to dam construction, a rich diversity of 31 freshwater fish species was recorded, however, this diversity dwindled to just 18 species after four decades of dam operation (Kartamihardja 2008 ). River network connectivity, a fundamental concept in river ecology, encompasses the dynamic movement of matter, energy, and organisms along the longitudinal (upstream-downstream), lateral, and vertical axes of a river. This connectivity is pivotal for sustaining the functional integrity of the river ecosystem (Allan and Castillo 2007 ; Xia et al. 2012 ). Recognizing the intricate interplay between fish diversity and river network connectivity holds immense significance for the survival of species, the ecological health of river systems, and the well-being of human communities, as emphasized by Shao et al. ( 2019 ). Investigation of fish biomass revealed significantly higher values in the upstream area compared to other locations. Elevated fish biomass can serve as an indicator of the environment’s capacity to support fish growth (Hashim and Ismail 2015 ). Conversely, a decline in fish biomass may result from deteriorating habitat quality caused by factors such as pollution, sedimentation, and environmental degradation. Irresponsible fishing practices can also contribute to diminishing fish biomass in water bodies (Palomares et al. 2020 ). The lower fish biomass in the downstream area, in contrast to other regions, is believed to be linked to habitat fragmentation, as evidenced by the substantial difference in fish biomass between the upstream area and other locations. Habitat fragmentation has the potential to alter the composition of fish species and reduce their overall diversity. Several studies showed that habitat fragmentation can reduce the number of two types of native species, migratory fish species and rheophilic fish, that are no longer found due to barriers (Sun et al. 2023 ). The study also revealed the presence of several endemic fish species in the river Poso, notably from the Adrianichthyidae family, known as ricefish. Three species of the genus were observed, namely O. nebulosus, O. nigrimas , and Oryzias sp. which we considered as 3 sympatric endemic species from Lake Poso (Sutra et al. 2019 ). Additionally, three migratory species were identified, specifically the eels Anguilla bicolor , Anguilla celebesensis , and Anguilla marmorata . Oryzias species were observed in both the upstream and hydropower areas, where they were caught using the traps. Notably, these species were conspicuously absent in the downstream region. Previous research reported the presence of Oryzias fish species in Lake Poso and its inlet (Herjayanto et al. 2019 ). The discrepancy in the number of species captured can be attributed to the burgeoning population of invasive species, which are gradually displacing native fish. Invasive fish species have the potential to engage in competition with native fish for both food and habitat resources (Busst and Britton 2017 ; Sayer et al. 2020 ). Furthermore, a diverse diet of Melanochromis auratus , encompassing larvae and fish eggs, primarily preying on Oryzias fish, and also encountering the endemic fish species Mugilogobius sarasinorum as well (Herder et al. 2022 ). In addition to the invasive species issue, overfishing and various anthropogenic activities pose additional threats to the ecosystem (Arthington et al. 2016 ; Häder et al. 2020 ). The Poso River hosts numerous species with complex migratory habits, involving both adults and juveniles. The presence of catadromous and amphidromous species in this study underscores the critical need to maintain the connectivity of the Poso River. Hydropower dams on the river are equipped with fishways designed to facilitate fish migration, aiming to mitigate the impact of damming on fish biodiversity (Baumgartner and Wibowo 2018 ). The primary objectives of fish passage development are to support the migration of multiple species, both upstream and downstream, thereby contributing to the preservation of fish biodiversity (O’Connor et al. 2022 ). However, the dominance of non-native species in the Poso River necessitates the development of selective fish passages that can block the distribution of these invasive species. The creation of selective passages relies on interspecific variations in physical capabilities, body shape, sensory capacities, behavior, and movement patterns. Understanding these distinctions is crucial for designing effective selective passages (Rahel and McLaughlin 2018 ) (Rahel & McLaughlin, 2018 ). Conclusions This study highlights a comprehensive overview of aquatic biodiversity in Poso River, Indonesia identifying 27 species, including two endangered ones. The predominance of non-native species, which make up 85.70% of the population, underscores a significant ecological concern. The presence of non-native species proliferation poses a potential threat to native fish populations. The dominance of non-native species in the Poso River necessitates the improvement of existing fish passages equipped in hydropower dams through the development of selective fish passages that can block the distribution of these invasive species. This study offers valuable insights for conservation and management efforts in the Poso River and similar ecosystems worldwide, ensuring the preservation of biodiversity and the health of aquatic ecosystems. Declarations Acknowledgement The project funding of this study was fully supported by Australian Centre for International Agricultural Research (ACIAR) Project in Indonesia (FIS/2018/153 – Translating fish passage research outcomes into policy and legislation across South-East Asia); Educational Fund Management Institution (LPDP), Ministry of Finance; National Research and Innovation Agency (BRIN), Indonesia through the Research Funding Programme “ Research and Innovation for Advanced Indonesia” (82/II.7/HK/2022: Fish biodiversity and hydrology assessment for improvement of the effectivity and functional fishway development: Case study of Poso Dam 1, Poso Dam 2, and planned Poso Dam 3 of Poso energy), and PT. Poso Energy, Indonesia. Therefore, we appreciate ACIAR and PT. Poso Energy team for providing us with the great opportunity and collaboration. We also would like to thank the assistance and information provided by local fishermen, PT. Poso Energy staffs, the laboratory analyst of Genomic Building, BRIN, and local government staffs during the fieldwork and laboratory analysis. Author Contributions AW, LB, KK, VAP, and IS conceptualized the research. AW, LB, DA, KK, VAP, MZ, and ILS developed the methods. AW, MZ, KK, DA, BKAS, and AC performed the data analysis. BKAS, AC, SAA, and TD prepared the figures and tables. AW, NH, LB, KK, VAP, FR, RG, DI, IS, ANS, AA, and AC conducted the research, data interpretation, and manuscript writing. All authors reviewed the manuscript. Data Availability The data used in this manuscript are organized by the first author (Arif Wibowo). All sequences were deposited in the NCBI Genbank database www.ncbi.nlm.nih.gov/genbank (Accession numbers PP595925-PP595976, PP556235-PP556294 and PP598893). 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Water 11(6):1217 Additional Declarations No competing interests reported. Supplementary Files SuplementaryMaterialBiodiveristPoso.docx Cite Share Download PDF Status: Published Journal Publication published 15 Oct, 2024 Read the published version in Aquatic Sciences → Version 1 posted Editorial decision: Revision requested 01 Aug, 2024 Reviews received at journal 01 Aug, 2024 Reviews received at journal 03 Jul, 2024 Reviewers agreed at journal 13 Jun, 2024 Reviewers agreed at journal 12 Jun, 2024 Reviewers invited by journal 12 Jun, 2024 Editor assigned by journal 31 May, 2024 Submission checks completed at journal 30 May, 2024 First submitted to journal 29 May, 2024 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-4496842","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":312016745,"identity":"f337d4e3-04d4-4604-9828-5ed8c9437e5b","order_by":0,"name":"Arif Wibowo","email":"","orcid":"","institution":"National Research and Innovation Agency","correspondingAuthor":false,"prefix":"","firstName":"Arif","middleName":"","lastName":"Wibowo","suffix":""},{"id":312016749,"identity":"81f0f121-2e3b-4655-8c37-c819c704e9e7","order_by":1,"name":"Kurniawan Kurniawan","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA3ElEQVRIiWNgGAWjYBACCRCRACLYG8ACjA3Ea+E5QIoWCCuBSC2SM3KfPXhQc1jeXPLx4888DDayGw4wP5PAp0VaIt3cIOHYYcOds9PMpHkY0ow3HGAzw6tFTiKNTSKB7Tbjhts5bMw8DIcTNxxgIEbLv9v2G26eYQY67D9QC/s3Ag4Daklsu5244QYPA9BhB4BaePDbItnzDKil73/yhjNpZpJzDJKNZx7mKbbAp0XieBqb5I9vabYbjh9+/OFNhZ1s3/H2jTfwaUEDBkDMTIL6UTAKRsEoGAXYAQA5AUa44sZPqAAAAABJRU5ErkJggg==","orcid":"","institution":"National Research and Innovation Agency","correspondingAuthor":true,"prefix":"","firstName":"Kurniawan","middleName":"","lastName":"Kurniawan","suffix":""},{"id":312016753,"identity":"8f85a218-c10e-457b-b77b-9634678a31a3","order_by":2,"name":"Vitas Atmadi Prakoso","email":"","orcid":"","institution":"National Research and Innovation Agency","correspondingAuthor":false,"prefix":"","firstName":"Vitas","middleName":"Atmadi","lastName":"Prakoso","suffix":""},{"id":312016754,"identity":"ce79a94a-960e-44ba-84c6-955e379ae91b","order_by":3,"name":"Rendy Ginanjar","email":"","orcid":"","institution":"National Research and Innovation Agency","correspondingAuthor":false,"prefix":"","firstName":"Rendy","middleName":"","lastName":"Ginanjar","suffix":""},{"id":312016757,"identity":"77519a3f-36fa-4858-bf8e-1701b4c50000","order_by":4,"name":"Fathur Rochman","email":"","orcid":"","institution":"National Research and Innovation Agency","correspondingAuthor":false,"prefix":"","firstName":"Fathur","middleName":"","lastName":"Rochman","suffix":""},{"id":312016758,"identity":"e329b9c2-f49a-4b96-8556-3e2b6531a828","order_by":5,"name":"Mochammad Zamroni","email":"","orcid":"","institution":"National Research and Innovation Agency","correspondingAuthor":false,"prefix":"","firstName":"Mochammad","middleName":"","lastName":"Zamroni","suffix":""},{"id":312016760,"identity":"a57236cd-5bff-4755-a6a5-034683420f6d","order_by":6,"name":"Dwi Atminarso","email":"","orcid":"","institution":"National Research and Innovation Agency","correspondingAuthor":false,"prefix":"","firstName":"Dwi","middleName":"","lastName":"Atminarso","suffix":""},{"id":312016761,"identity":"3af37435-2ac0-4e58-98c5-5323d5bfd3ae","order_by":7,"name":"Bayu Kreshna Adhitya Sumarto","email":"","orcid":"","institution":"National Research and Innovation Agency","correspondingAuthor":false,"prefix":"","firstName":"Bayu","middleName":"Kreshna Adhitya","lastName":"Sumarto","suffix":""},{"id":312016762,"identity":"5100a335-0659-473d-b126-251abe1131b4","order_by":8,"name":"Andi Chadijah","email":"","orcid":"","institution":"National Research and Innovation Agency","correspondingAuthor":false,"prefix":"","firstName":"Andi","middleName":"","lastName":"Chadijah","suffix":""},{"id":312016763,"identity":"4e1f221c-1b11-4b9c-9f45-b0174f6c342e","order_by":9,"name":"Deni Irawan","email":"","orcid":"","institution":"National Research and Innovation Agency","correspondingAuthor":false,"prefix":"","firstName":"Deni","middleName":"","lastName":"Irawan","suffix":""},{"id":312016764,"identity":"c87eec06-0aff-4329-be83-cf56d1451518","order_by":10,"name":"Tri Deniansen","email":"","orcid":"","institution":"National Research and Innovation Agency","correspondingAuthor":false,"prefix":"","firstName":"Tri","middleName":"","lastName":"Deniansen","suffix":""},{"id":312016765,"identity":"54206036-879e-4992-9b8f-ccf450a5a05f","order_by":11,"name":"Irma Suriani","email":"","orcid":"","institution":"PT. Poso Energy","correspondingAuthor":false,"prefix":"","firstName":"Irma","middleName":"","lastName":"Suriani","suffix":""},{"id":312016766,"identity":"faf88841-ba5e-4702-8def-a64ab2192cef","order_by":12,"name":"Agus Noor Syamsi","email":"","orcid":"","institution":"PT. Poso Energy","correspondingAuthor":false,"prefix":"","firstName":"Agus","middleName":"Noor","lastName":"Syamsi","suffix":""},{"id":312016768,"identity":"d74f4ead-86df-496f-9d51-54f04ef2346e","order_by":13,"name":"Andi Achmadi","email":"","orcid":"","institution":"PT. Poso Energy","correspondingAuthor":false,"prefix":"","firstName":"Andi","middleName":"","lastName":"Achmadi","suffix":""},{"id":312016770,"identity":"f3262265-ec6f-422d-9977-a285ae335a14","order_by":14,"name":"Indah Lestari Surbani","email":"","orcid":"","institution":"Diversitas Lestari Nusantara","correspondingAuthor":false,"prefix":"","firstName":"Indah","middleName":"Lestari","lastName":"Surbani","suffix":""},{"id":312016772,"identity":"ececc925-a9ad-4531-ad2e-aa3bb2134648","order_by":15,"name":"Sabda Alam Akbar","email":"","orcid":"","institution":"Diversitas Lestari Nusantara","correspondingAuthor":false,"prefix":"","firstName":"Sabda","middleName":"Alam","lastName":"Akbar","suffix":""},{"id":312016773,"identity":"60b8eb5b-1651-4ade-99b9-b7bc8fe80de6","order_by":16,"name":"Nicolas Hubert","email":"","orcid":"","institution":"Université Montpellier (UMR) 5554 Institut des sciences de l’évolution de Montpellier (ISEM) (IRD, UM, CNRS, Université de Montpellier","correspondingAuthor":false,"prefix":"","firstName":"Nicolas","middleName":"","lastName":"Hubert","suffix":""},{"id":312016774,"identity":"cb1b70ae-c5a6-4e2f-93dd-f7667a22680b","order_by":17,"name":"Lee Baumgartner","email":"","orcid":"","institution":"Charles Sturt University","correspondingAuthor":false,"prefix":"","firstName":"Lee","middleName":"","lastName":"Baumgartner","suffix":""}],"badges":[],"createdAt":"2024-05-29 11:51:14","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-4496842/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-4496842/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1007/s00027-024-01128-0","type":"published","date":"2024-10-15T15:57:20+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":58200755,"identity":"218507d1-a964-46bd-9927-d770496a0b4f","added_by":"auto","created_at":"2024-06-12 10:41:09","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":302432,"visible":true,"origin":"","legend":"\u003cp\u003eCollection sites of fish diversity investigation within the Poso River system in Sulawesi, Indonesia. Upstream 1 1°45’57.4”S 120°38’24.5”E. Upstream 2: 1°42’36.0”S 120°38’51.3”E. Environmental flow hydropower plant Poso 1 (Env. flow 1): 1°39’28.2”S 120°39’35.6”E. Environmental flow hydropower plant Poso 2.1 (Env. flow 2.1): 1°38’53.6”S 120°39’24.0”E. Environmental flow hydropower plant Poso 2.2 (Env. Flow 2.2) : 1°38’37.6”S 120°38’41.8”E. Downstream 1: 1°36’44.9”S 120°40’30.9”E and Downstream 2: 1°29’21.9”S 120°45’26.2”E.\u003c/p\u003e","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-4496842/v1/5d8533b25fcd304398d06e5c.png"},{"id":58201716,"identity":"c85cacca-de60-4c27-8b0a-e88726350192","added_by":"auto","created_at":"2024-06-12 10:57:09","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":1177614,"visible":true,"origin":"","legend":"\u003cp\u003eBayesian phylogenetic tree of COI sequences of freshwater fish in Poso River. Detailed posterior probabilities are given at branches of interest. The scale represents substitutions per site.\u003c/p\u003e","description":"","filename":"2.png","url":"https://assets-eu.researchsquare.com/files/rs-4496842/v1/65059db9e5a143508993f54d.png"},{"id":58201240,"identity":"d24e2be4-01ee-44c2-9127-964a8f768c04","added_by":"auto","created_at":"2024-06-12 10:49:09","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":81816,"visible":true,"origin":"","legend":"\u003cp\u003eSpecies distribution in upstream. environmental flow and downstream of the Poso River (a). Species proportion in all sites ranked by abundance (b) during three survey periods including March. June and September 2023.\u003c/p\u003e","description":"","filename":"3.png","url":"https://assets-eu.researchsquare.com/files/rs-4496842/v1/a5c3806aae64179979628c07.png"},{"id":58200756,"identity":"55ddf15f-af0a-4400-a91a-cd2eed74d619","added_by":"auto","created_at":"2024-06-12 10:41:09","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":73573,"visible":true,"origin":"","legend":"\u003cp\u003eRelative abundance of fish-based species identified in upstream. environmental flow of hydropower dams and downstream sampling sites. Experimental Fishing was conducted during 3 survey periods including March. June and September 2023 at Poso River. (UP1=Upstream 1. UP2=Upstream 2. EVP1=Environmental flow hydropower Poso 1. EVP2.1=Environmental flow hydropower Poso 2.1. EVP2.2=Environmental flow hydropower Poso 2.2. DS1=Downstream 1. DS2=Downstream 2).\u003c/p\u003e","description":"","filename":"4.png","url":"https://assets-eu.researchsquare.com/files/rs-4496842/v1/e556b549a5022bffc3250e68.png"},{"id":58200760,"identity":"a2403b1d-745a-4437-868e-055f4b74dfc0","added_by":"auto","created_at":"2024-06-12 10:41:09","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":149587,"visible":true,"origin":"","legend":"\u003cp\u003eHeat map showing the abundance for fish species at upstream. environmental flow of hydropower areas and downstream sites in the Poso River. (UPS: upstream. ENF: Environmental Flow. DOS: downstream followed by a number 03. 06 and 09 referring to month March. June and September 2023).\u003c/p\u003e","description":"","filename":"5.png","url":"https://assets-eu.researchsquare.com/files/rs-4496842/v1/e5b7d9b7a7f8683002aa7360.png"},{"id":67149160,"identity":"f504bb2b-fe17-462e-ba8e-23e0b270c262","added_by":"auto","created_at":"2024-10-21 16:12:32","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2547559,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4496842/v1/7e4c3b33-2212-454e-86af-cd73e25ee6fc.pdf"},{"id":58201715,"identity":"7edc723b-ca21-4738-ba22-edc2bc08d393","added_by":"auto","created_at":"2024-06-12 10:57:09","extension":"docx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":35399,"visible":true,"origin":"","legend":"","description":"","filename":"SuplementaryMaterialBiodiveristPoso.docx","url":"https://assets-eu.researchsquare.com/files/rs-4496842/v1/042c4c2bf4dad0aa0f98efe4.docx"}],"financialInterests":"No competing interests reported.","formattedTitle":"Characterizing spatial patterns among freshwater fishes and shrimps of the Poso River (Sulawesi, Indonesia) using DNA barcoding","fulltext":[{"header":"Introduction","content":"\u003cp\u003eFreshwater resources and their biodiversity rank among the world's most imperiled ecosystems (McGregor Reid \u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e2013\u003c/span\u003e; Yousefi et al. \u003cspan citationid=\"CR80\" class=\"CitationRef\"\u003e2020\u003c/span\u003e), with a faster declining rate than terrestrial or marine ecosystems (McRae et al. \u003cspan citationid=\"CR46\" class=\"CitationRef\"\u003e2017\u003c/span\u003e). One of the main reason is that freshwater biodiversity is jointly facing the direct impacts from human activities and climate change (Gozlan et al. \u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e2019\u003c/span\u003e; Grafton et al. \u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e2012\u003c/span\u003e). Within riverine ecosystems, the most significant threats to freshwater biodiversity include the introduction and proliferation of non-native species, water pollution, habitat fragmentation, overexploitation by local fisheries and climate change (Arthington et al. \u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e2016\u003c/span\u003e; Xing et al. \u003cspan citationid=\"CR78\" class=\"CitationRef\"\u003e2016\u003c/span\u003e)). Most of these threats are currently being observed in the Poso River, Central Sulawesi, Indonesia. Connecting the ancient lake Poso of central Sulawesi, the main island of the Wallacea biodiversity hotspot (Myers et al. \u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e2000\u003c/span\u003e), the area hosts a wealth of endemic species for multiple freshwater organisms such as fish, mollusks and crustaceans (Kottelat et al. \u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e1993\u003c/span\u003e; von Rintelen et al. \u003cspan citationid=\"CR69\" class=\"CitationRef\"\u003e2007\u003c/span\u003e). However, the Poso River is a productive river systems used for hydroelectric resource supplying electricity in the region, a source of animal protein and community livelihood (Krismono and Kartamihardja 2012; Watupongoh and Krismono \u003cspan citationid=\"CR72\" class=\"CitationRef\"\u003e2015\u003c/span\u003e). The Poso river presents a complex scenario where alterations in fish biodiversity are not solely attributed to the presence of dams, the shifts in river hydrology, environmentally detrimental fishing practices, but although noticeable changes in biodiversity within the connected Poso Lake play a pivotal role in shaping fish population dynamics (Serdiati et al. \u003cspan citationid=\"CR59\" class=\"CitationRef\"\u003e2023\u003c/span\u003e). This intricate interconnection arises from the fact that a significant portion of the water inflow of the Poso River originates from the Lake Poso. A comprehensive assessment of the freshwater biodiversity of the Poso River is urgently required to better understand ongoing biodiversity challenges and guiding conservation plans.\u003c/p\u003e \u003cp\u003eA concerning factor jeopardizing fish biodiversity within Lake Poso is the widely spread of non-native fish species, which have asserted their dominance throughout the lake, extending to the lake\u0026rsquo;s outlet region, which feeds into the river. This invasive presence poses a significant threat to the ecological balance of Lake Poso ecosystems (Herder et al. \u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). A substantial number of non-native species have successfully established and grow large populations, and they are now negatively impacting the native endemic species of the lake (Gaygusuz et al. \u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e2013\u003c/span\u003e; Shelton et al. \u003cspan citationid=\"CR61\" class=\"CitationRef\"\u003e2014\u003c/span\u003e). The introduction of non-native fish species can detrimentally impact native fish through resource competition, predation, hybridization and pathogens transmission (Britton \u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e2023\u003c/span\u003e; Jiang et al. \u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e2021\u003c/span\u003e). These negative effects have emerged in many regions where non-native fish have been introduced (Okwiri et al. \u003cspan citationid=\"CR49\" class=\"CitationRef\"\u003e2019\u003c/span\u003e; Spikmans et al. \u003cspan citationid=\"CR63\" class=\"CitationRef\"\u003e2020\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eThe alteration of the biodiversity of Lake Poso poses a serious challenges to the Poso River, which aquatic organisms are already heavily perturbed by the presence of dams and alterations in the river\u0026rsquo;s hydrological patterns. The construction of dams leads to fragmentation, resulting in various changes to the physical, chemical, and hydrological characteristics of both upstream and downstream ecosystems. These modifications include adjustments to the normal flow of the river, the occurrence of hydropeaking, and the blocking of sediment and some organisms such as fish and invertebrates (Capra et al. \u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e2017\u003c/span\u003e; Silva et al. \u003cspan citationid=\"CR62\" class=\"CitationRef\"\u003e2018\u003c/span\u003e). In an ecosystem where fish fauna plays a crucial role in ecosystem functioning, it is essential to restore connections in order to facilitate the completion of each species\u0026rsquo; life cycle (Benitez et al. \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e2015\u003c/span\u003e; Lucas et al. \u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e2001\u003c/span\u003e) and/or accessing habitats for feeding and development (feeding migration) and seeking refuge when severe environmental conditions occurs (refuge migration) (Lucas et al. \u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e2001\u003c/span\u003e). Such movements may occur frequently during an individual\u0026rsquo;s lifespan, may involve a substantial proportion of a species\u0026rsquo; population, and may occur at various stages of life (Lucas et al. \u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e2001\u003c/span\u003e). Because of these barriers, it becomes impossible for organisms to move freely within the river, which jeopardize population average fitness (Birnie-Gauvin et al. \u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e2020\u003c/span\u003e; Ovidio et al. \u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). One potential approach to addressing the issue of impeded connectivity is the implementation of a fish passage structure, commonly referred to as a fishway. This solution should be designed to accommodate multiple species and enable both diadromous (\u003cem\u003ei.e.\u003c/em\u003e species migrating between freshwater and the ocean) and potamodromous (\u003cem\u003ei.e.\u003c/em\u003e species migrating with freshwater system) species to bypass the obstacle in question (Benitez et al. \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e2015\u003c/span\u003e; Ovidio et al. \u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). Fishways are successful if they entail the removal or reduction of negative impacts of obstructions to movement and achieve the conservation of native species and nutrient fluxes between lacustrine, riverine, and marine ecosystems (Hall et al. \u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e2012\u003c/span\u003e). Hydropower dams on the Poso River have been equipped with fishways designed to facilitate fish migration, with the aim of mitigating the impact of damming on fish biodiversity (Baumgartner and Wibowo \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e2018\u003c/span\u003e). However, the effectiveness of this passage has not yet been examined. To achieve this, it is essential to conduct an assessment of how habitat fragmentation influences the spatial and temporal distribution of fish both before and after the fishway dams are in place.\u003c/p\u003e \u003cp\u003eThe next challenge revolves around overfishing, a consequence of ecologically harmful fishing practices. This problem exacerbates the obstruction of eel migration in the upper section of the Poso River, stemming from the prolonged overfishing of eel broodstock through unsustainable fishing practice, habitat and environmental conditions (Triyanto et al. \u003cspan citationid=\"CR68\" class=\"CitationRef\"\u003e2021\u003c/span\u003e). One of the effective fishing gears is sogili fences to block downstream migration of adult eels (Lukman et al. \u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e2021\u003c/span\u003e). These ancestral sogili fences, which use if common in the Poso River have the potential to disrupt fish biodiversity, resulting in a reduction of eel populations \u0026ndash; a key predator \u0026ndash; and the uncontrolled proliferation of lower-level predators that can dominate river habitats. Additionally, near the estuary of the Poso River, unregulated capture of the glass eel and other amphidromous fish fry poses a significant threat to fish biodiversity, further destabilizing the ecosystem of the Poso River (Haryani \u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e2022\u003c/span\u003e; Krismono and Putri 2012).\u003c/p\u003e \u003cp\u003eGiven the intricate nature of the challenges in the Poso River, we undertook a comprehensive study to assess fish and crustacean biodiversity and its spatial and temporal distribution. Our research encompassed direct fishing activities in the upstream, environmental flow, and downstream regions, with the Poso hydropower plant serving as our reference point. In addition, we investigated both adult fish biodiversity and larval distribution, employing a DNA barcoding approach for characterize species and identify specimens. DNA barcoding offers the capability to distinguish and identify morphologically similar species effectively. By sequencing the COI gene region in multiple individuals and populations across their range, coupled with species delimitation guided by mitochondrial sequences, we can clarify species boundaries and distribution.\u003c/p\u003e"},{"header":"Materials and Methods","content":"\u003cdiv id=\"Sec3\"\u003e\n \u003ch2\u003eStudy Area\u003c/h2\u003e\n \u003cp\u003eThe Poso River is located in the Poso Regency of Central Sulawesi Province, Indonesia, approximately 50 km south of Poso City (Fig.\u0026nbsp;\u003cspan\u003e1\u003c/span\u003e). The river primarily draws its water from the Lake Poso, positioned upstream. Lake Poso is a tectonic lake situated at an elevation of 485 meters above sea level (Lehmusluoto and Machbub \u003cspan\u003e1997\u003c/span\u003e). At a minimum, 13 rivers contribute to Lake Poso, while the Poso River acts as an exit that spans 52 km and discharges into the Tomini Bay (Pangesti et al. \u003cspan\u003e1995\u003c/span\u003e). The river traverses the middle section of Sulawesi Island, which is characterized by a tropical rainforest climate, with the mean annual precipitation is 2715 mm. The highest average temperature is 23\u003csup\u003eo\u003c/sup\u003eC in October, while January is the coldest month with 20\u003csup\u003eo\u003c/sup\u003eC (Peel et al. \u003cspan\u003e2007\u003c/span\u003e). Two dams in the Poso River are harnessed for power generation, supplying electricity to the Sulawesi region. Additionally, two fishways have been installed within the dams to facilitate fish migration. Seven sites were determined to evaluate fish biodiversity status including two sites upstream, three areas in environmental flows and two sites located downstream of the Poso Energy dam (Fig.\u0026nbsp;\u003cspan\u003e1\u003c/span\u003e). Environmental flow refers to the release of water into the river once the majority of it has been utilized for hydropower generation.\u003c/p\u003e\n\u003c/div\u003e\n\u003cdiv id=\"Sec4\"\u003e\n \u003ch2\u003eExperimental fishing\u003c/h2\u003e\n \u003cp\u003eSpecimens were collected using multi-panel gillnets, collapsible bait traps, and cast nets. To ensure a broad coverage of fish and shrimps diversity in our sampling, including pelagic and bottom-dwelling species, we used a combination of active and passive methods including gillnets with six different mesh sizes (ranging from 19.05 to 101.6 mm), bait traps measuring 400 \u0026times; 220 \u0026times; 220 mm (length \u0026times; width \u0026times; height) with a 60 mm entry diameter, and 2 m diameter cast nets with 19.05 mm mesh size. The sampling effort was standardized to allow comparisons among sites with gillnets and bait traps set up for two hours and cast nets cast 15 times with 1-minute intervals between casts. We used 100g chicken intestine, fresh shrimp, and artificial feed purchased from a local market as bait in all experiments. We conducted experimental fishing from 8:00 a.m. to 2:00 p.m. during both dry season (March and June 2023) and wet season (September 2023) to cover potential seasonal variations in fish populations. All fish specimens underwent anesthesia using a solution of 2-phenoxyethanol at a dosage of 0.5 mL per liter of water. We documented all fish by photographing, measuring (total length, to 1 mm using rulers and millimeter graph paper), and weighing (to 0.1 g using digital scale) collected individuals. Individual fish were identified to the species level using the field guide from Kottelat et al. (\u003cspan\u003e1993\u003c/span\u003e) and names were updated according to the Fishbase website (\u003cspan\u003e\u003cspan\u003ewww.fishbase.org\u003c/span\u003e\u003c/span\u003e).\u003c/p\u003e\n\u003c/div\u003e\n\u003cdiv id=\"Sec5\"\u003e\n \u003ch2\u003eAmplifying and sequencing\u003c/h2\u003e\n \u003cp\u003eA total of 20 milligrams (mg) of fin tissue or whole larvae were dissected and subsequently collected for the purpose of DNA extraction. Tissue sample was taken and preserved in 1,5 ml tubes with absolute ethanol. Preserved tissues were stored in individual tubes, which were further in cryosafe boxes. DNA extraction was conducted with the Tissue Genomic DNA Mini Kit GT050 (Geneaid, Taiwan) following the recommandations from the manufacturer. The mitochondrial gene of the Cytochrome C Oxidase Subunit-1 gene (COI) was amplified using the universal primers Fish-COI-F (5\u0026rsquo;- TCA ACC AAC CAC AAA GAC ATT GGCAC-3\u0026rsquo;) and Fish-COI-R (5\u0026rsquo;-TAG ACT TCT GGG TGG CCA AAG AATCA-3\u0026rsquo;) from Ward et al. (\u003cspan\u003e2009\u003c/span\u003e).\u003c/p\u003e\n \u003cp\u003ePCR reactions were performed in 30.0 \u0026micro;L including 15.0 \u0026micro;L of 1x DreamTag Green Master Mix, 2.0 \u0026micro;L of Primer CO1 Forward 1 (F1), 2.0 \u0026micro;L of Primer CO1 Reverse 1 (R1), 9.0 \u0026micro;L of deionized water (nuclease free), and 2 \u0026micro;L of DNA template. A negative controls were used and PCR cycling conditions included one cycle at 95\u0026deg;C for 3 min; 95\u0026deg;C for 30 s; 35 cycles at 56\u0026deg;C for 30 s, 72\u0026deg;C for 1 min; and 10 minutes final extension at 72\u0026deg;C for 10 min. PCR products were loaded into 5 \u0026micro;L per well (already stained) on a 2% agarose gel containing 0.01% gel stain (SafeDNA). Electrophoresis was performed with 100 bp Plus marker (Vivantis) in 3 \u0026micro;L wells at 100 volts for 25 minutes on 1x TBE (Tris borate EDTA) media using PowerPac Basic (Bio-Rad). Amplification results were visualized using the UVITEC Gel Documentation System. Samples were further sequenced in both direction on a Applied Biosystems\u0026trade; 3500xL Genetic Analyzer, (Thermo Fisher Scientific, USA) at the Central Laboratory for Sequencing of the National Research and Innovation Agency (Indonesia). all sequences were deposited in the NCBI Genbank database (Accession numbers PP595925-PP595976, PP556235-PP556294 and PP598893).\u003c/p\u003e\n\u003c/div\u003e\n\u003cdiv id=\"Sec6\"\u003e\n \u003ch2\u003eValidating species boundaries and identities\u003c/h2\u003e\n \u003cp\u003eIn order to obtain a comprehensive understanding of fish biodiversity at the research site, we conducted an iterative assessment of species identification involving DNA barcoding in conjunction with the examination of morphological characters in adult specimens. Larvae were subsequently identified by comparisons with COI sequences of adult specimens. We followed the procedure of species delimitation recommended by Ross et al. (\u003cspan\u003e2008\u003c/span\u003e). We combined phylogenetic reconstructions with estimates of genetic distances to guide species delimitation and detect potential conflict with the initial set of identifications performed in the field. Genetic distances were used to detect clades representing levels of genetic divergence beyond the expected threshold within species, and representing cryptic lineages. We used a 0.02 mean genetic distance as a criterion, which is a commonly used threshold (Hubert and Hanner \u003cspan\u003e2015\u003c/span\u003e). The sequences obtained were aligned with ClustalW algorithm, and their quality was evaluated using the Geneious 10 software (Kearse et al. \u003cspan\u003e2012\u003c/span\u003e). A phylogenetic tree was constructed with a Bayesian approach as implemented in MrBayes (Huelsenbeck and Ronquist \u003cspan\u003e2001\u003c/span\u003e).\u003c/p\u003e\n\u003c/div\u003e\n\u003cdiv id=\"Sec7\"\u003e\n \u003ch2\u003eAnalyzing spatio-temporal patterns of species abundance\u003c/h2\u003e\n \u003cp\u003ePopulation abundance index is highly valuable to examine population dynamics. Abundance indices often utilize the catch per unit of effort (CPUE) value as a reliable measure of abundance (Francis \u003cspan\u003e2011\u003c/span\u003e). The CPUE is calculated differently for each fishing gear, such as cast nets, traps, and gillnets. In cast nets, CPUE is calculated by measuring the width of the net opening, and expressing the number of fish per square meter of net opening. For traps and gillnets, CPUE estimates are based on the number of individuals caught per hour of operation. Both estimates of abundance were used here. Standard Length (SL) and weight was recorded for all the individuals captured.\u003c/p\u003e\n \u003cp\u003eIndices of abundance, species richness, and species diversity were used to analyze patterns of fish community through time (dry and wet seasons) and space (upstream and downstream of the dam project). All analyses were conducted using Primer v7 (Clarke and Gorley \u003cspan\u003e2015\u003c/span\u003e). Permutational analysis of variance (PERMANOVA) was used to examine if significant differences in the fish community were observed between different seasons (dry and wet) and locations (upstream and downstream) across 10 sampling sites. The fish catch counts were transformed using a log (X\u0026thinsp;+\u0026thinsp;1) function and Bray-Curtis similarities were computed. Two factors (location and season) were integrated into the model and the significance of the values was assessed using 9999 raw data permutations without restrictions. Multidimensional scaling (MDS) was employed to illustrate disparities in fish community composition across different locations and seasons. We explored the distribution the SL in fish populations between upstream and downstream regions to determine if there were any noteworthy variations in length distribution between upstream and downstream stretches. The Kolmogorov-Smirnov (KS) test was employed to test the significance of any observed differences. Only species with at least 25 individuals in both upstream and downstream locations were included.\u003c/p\u003e\n\u003c/div\u003e"},{"header":"Results","content":"\u003cdiv id=\"Sec9\" class=\"Section2\"\u003e\n \u003ch2\u003eSampling and species delimitation\u003c/h2\u003e\n \u003cp\u003eDuring the study, 27 fish species belong to 17 families were delimited in the field. These species have various migratory behaviours, including diadromous (3 species), amphidromous (7 species), and potamodromous (17 species) (Table \u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003e). The fish composition comprised both native and non-native species with varying conservation status, ranging from unknown to endangered. Notably, \u003cem\u003eAdrianichthys poptae\u003c/em\u003e and \u003cem\u003eMugilogobius sarasinorum\u003c/em\u003e were identified as endangered species within the river following IUCN red list.\u0026nbsp;\u003c/p\u003e\u0026nbsp;\u003ctable id=\"Tab1\" border=\"1\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e\n \u003cdiv class=\"CaptionContent\"\u003e\n \u003cp\u003eFish diversity, migratory behavior, geographical origin and conservation status.\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003cthead\u003e\n \u003ctr\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eNo\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eFamily\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eSpecies Name\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eMigratory behaviour\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eGeographic origin\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eIUCN Conservation Status\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eA\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eFish\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAnguillidae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eAnguilla marmorata\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eDiadromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNative\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eLC\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAnguillidae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eAnguilla bicolor\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eDiadromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNative\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eLC\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e3\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAnguillidae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eAnguilla celebesensis\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eDiadromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNative\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eDD\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e4\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eGobiidae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eAwaous melanocephalus\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAmphidromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNative\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eLC\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e5\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eGobiidae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eAwaous\u003c/em\u003e sp.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAmphidromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNative\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eUnknown\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e6\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eGobiidae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eMugilogobius sarasinorum\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAmphidromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNative\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eEN\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e7\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eGobiidae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eSicyopterus\u003c/em\u003e sp.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAmphidromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNative\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eDD\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e8\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eGobiidae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eSchismatogobius\u003c/em\u003e sp\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAmphidromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNative\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eDD\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e9\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eEleotridae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eMogurnda mogurnda\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAmphidromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNative\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eLC\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e10\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eRhyacichthyidae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eRhyacichthys aspro\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAmphidromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNative\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eDD\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e11\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAdrianichthyidae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eAdrianichthys poptae\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePotamodromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNative\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eEN\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e12\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAdrianichthyidae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eAdrianichthys oophorus\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePotamodromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNative\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eLC\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e13\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAdrianichthyidae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eOryzias\u003c/em\u003e sp.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePotamodromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNative\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eUnknown\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e14\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAdrianichthyidae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eOryzias nebulosus\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePotamodromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNative\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNT\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e15\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAdrianichthyidae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eOryzias nigrimas\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePotamodromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNative\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNT\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e16\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eCyprinidae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eBarbodes binotatus\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePotamodromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNon-Native\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eLC\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e17\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eChanidae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eChanna striata\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePotamodromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNon-Native\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eLC\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e18\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eCichlidae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eCichlasoma trimaculatum\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePotamodromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNon-Native\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eLC\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e19\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePoecillidae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003ePoecilia reticulata\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePotamodromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNon-Native\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eLC\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e20\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eKuhliidae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eKuhlia marginata\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePotamodromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNative\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eLC\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e21\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eCichlidae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eMelanochromis auratus\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePotamodromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNon-Native\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eLC\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e22\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eCyprinidae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eOsteochilus vittatus\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePotamodromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNon-Native\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eLC\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e23\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eCichlidae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eOreochromis niloticus\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePotamodromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNon-Native\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eLC\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e24\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eOsphronemidae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eTrichogaster trichopterus\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePotamodromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNative\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eLC\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eB\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eCrustacea\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAtydae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eCaridina endehensis\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePotamodromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNative\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eLC\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePalaeomonidae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eMacrobrachium\u003c/em\u003e sp.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAmphidromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNative\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eLC\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e3\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eParathelphusidae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eParthelphusa\u003c/em\u003e sp.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePotamodromous\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNative\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eLC\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003c/table\u003e\n \u003cp\u003e\u003c/p\u003e\n \u003cp\u003eAmong the 24 fish and 3 shrimp species sampled, 12 were selected which required an examination of their DNA barcode to confirm their boundaries and identity. For these species, a total of 113 sequences were generated during the present study and 11 additional sequences were mined from Genbank to compare with species names assigned in previous studies. In total, 124 sequences were analyzed. Sequences varied in lengths, ranging from 590 bp to 601 bp, with a range of 1 to 27 specimens per species. Species names assigned to the sequences mined from Genbank were matching those from our current study. A phylogenetic trees was generated for these 124 sequences (Fig. \u003cspan class=\"InternalRef\"\u003e2\u003c/span\u003e). Of the 12 species examined here with DNA barcodes, nine were effectively distinguished by their distinct set of tightly cluster sequences (Fig. \u003cspan class=\"InternalRef\"\u003e2\u003c/span\u003e).\u003c/p\u003e\n \u003cp\u003eThe combination of single-locus species delimitation statistics provides support for the distinctiveness of all proposed species (Table S2). However, greater values of intraspecific tree distances (as denoted by \u0026ldquo;intra\u0026rdquo; in the table S2) detected for three lineages, which cannot be identified to the species level, and displayed high levels of genetic divergence to other congeneric lineages with genetic distances ranging from 0.038 to 0.650. These correspond to exotic species (ex. \u003cem\u003eOreochromis niloticus\u003c/em\u003e, \u003cem\u003ePoecilia reticulata\u003c/em\u003e). By contrast, endemic species represented by sequences originating from a single site or region, such as \u003cem\u003eOryzias\u003c/em\u003e species, display lower intraspecific genetic distances. Greater values of interspecific tree distances (refer to \u0026ldquo;inter-closest\u0026rdquo; in the table S2) show that some species groups display high congeneric genetic distances. The mean values of P ID (liberal) were determined using the BI trees, indicating that all species had a probability equal to or greater than 0.95, except for \u003cem\u003eAkihito\u003c/em\u003e sp. (0.88). The likelihood that a clade exhibits the observed level of uniqueness as a result of random coalescent processes, denoted as \u0026ldquo;P (randomly distinct)\u0026rdquo; in the tables, is represented by values ranging from 0.05 to 1. This range encompasses the majority of the values seen in putative species. The probability values indicating the reciprocal monophyly of species under the null model of random coalescence are all equal to or less than 0.05. This observation provides support for the hypothesis that these putative species can be considered different species.\u003c/p\u003e\n\u003c/div\u003e\n\u003cdiv id=\"Sec10\" class=\"Section2\"\u003e\n \u003ch2\u003eFish abundance, species richness and diversity\u003c/h2\u003e\n \u003cp\u003eBased on the calculation of CPUE for the three fishing gears used during the study, the trap nets had a higher CPUE of 106.71 g/h compared to other fishing gears, namely gillnet and net, at 44.97 g/h and 2.76 g/h, respectively (Table \u003cspan class=\"InternalRef\"\u003eS1\u003c/span\u003e). The lowest CPUE value was obtained in the gillnet gear at all research locations. Abundance data revealed contrasted patterns between upstream and downstream areas with upstream sites contributing the highest proportion of catches with 67%, while the environmental flow and downstream regions accounted for 27% and 6% of the total catches, respectively (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003ea, Fig. \u003cspan class=\"InternalRef\"\u003e5\u003c/span\u003e). Non-native species dominates in the sampling with \u003cem\u003eMelanochromis auratus\u003c/em\u003e (25.93%), \u003cem\u003eOreochromis niloticus\u003c/em\u003e (19.41%), \u003cem\u003eCichlasoma trimaculatum\u003c/em\u003e (18.01%), \u003cem\u003eBarbodes binotatus\u003c/em\u003e (13.03%), \u003cem\u003eOsteochilus vittatus\u003c/em\u003e (6%), \u003cem\u003ePoecilia reticulata\u003c/em\u003e (2.55%), \u003cem\u003eTrichogaster trichopterus\u003c/em\u003e (0,64%) and \u003cem\u003eChanna striata\u003c/em\u003e (0.13%) (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003eb). Native fishes only accounts for 15.07% of the total catches with \u003cem\u003eOryzias nigrimas\u003c/em\u003e (1.92%), \u003cem\u003eOryzias sp\u003c/em\u003e (1.4%), and \u003cem\u003eAwaous melanocephalus\u003c/em\u003e (1.15%) constituting the majority of the native fish population, while the remainder is comprised of the other 15 native fish species and three genera of shrimps. Examining dominant fish species across sampling sites reveals that \u003cem\u003eM. auratus\u003c/em\u003e (33.12\u0026thinsp;\u0026plusmn;\u0026thinsp;22.17%) prevails upstream, while \u003cem\u003eO. niloticus\u003c/em\u003e (42.77\u0026thinsp;\u0026plusmn;\u0026thinsp;15.68%) dominates in the environmental flow area, and crustaceans, particularly \u003cem\u003eCaridina endehensis\u003c/em\u003e (24.24\u0026thinsp;\u0026plusmn;\u0026thinsp;22.88%) dominate downstream (Fig. \u003cspan class=\"InternalRef\"\u003e4\u003c/span\u003e).\u0026nbsp;\u003c/p\u003e\u0026nbsp;\u003ctable id=\"Tab2\" border=\"1\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv class=\"CaptionNumber\"\u003eTable 2\u003c/div\u003e\n \u003cdiv class=\"CaptionContent\"\u003e\n \u003cp\u003eEcological index values of fish in the Poso River\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003cthead\u003e\n \u003ctr\u003e\n \u003cth align=\"left\"\u003e\u0026nbsp;\u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eAbundance\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eDiversity\u003c/p\u003e\n \u003cp\u003e(Shannon-Wiener)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eRichness\u003c/p\u003e\n \u003cp\u003e(Evenness)\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003eLocation\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eUpstream\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e91\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1.48\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e7\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eHydropower Area\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e63\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.96\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e5\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eDownstream\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e9\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.82\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e3\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003eSeason\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eDry\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e54\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1.00\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e4.86\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWet\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e57\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1.10\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e5.14\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003c/table\u003e\n \u003cp\u003e\u003c/p\u003e\n \u003cp\u003eUpstream sites exhibit the highest diversity index with 1.48, followed by the hydropower area with 0.96 and the downstream area with 0.82 (Table \u003cspan class=\"InternalRef\"\u003e2\u003c/span\u003e). The diversity index value in the dry season was 1.0, while during the wet season was 1.10. In terms of species richness, upstream sites reached a score of 7, while the hydropower area scored 5, and downstream sites reach only 3 (Table \u003cspan class=\"InternalRef\"\u003e2\u003c/span\u003e). The results of the PERMANOVA analysis revealed a substantial difference in species abundance among study sites, although there was no discernible seasonal variation (Table 3). According to the analysis of species richness and diversity, no significant difference across sites and season was detected (Tables 4 and 5). In terms of temporal trends, \u003cem\u003eM. auratus\u003c/em\u003e stands out as the predominant fish species captured in March and September, whereas \u003cem\u003eO. niloticus\u003c/em\u003e dominated in June (Table \u003cspan class=\"InternalRef\"\u003eS1\u003c/span\u003e). Spatially, these species hold dominance in both the upstream and environmental flow of hydropower areas.\u003c/p\u003e\n \u003cp\u003e\u003cbr\u003e\u003c/p\u003e\n \u003cp\u003e\u003cimg src=\"https://myfiles.space/user_files/122228_c8a1650c59388082/122228_custom_files/img171818836456.png\"\u003e\u003c/p\u003e\n \u003cp\u003e\u003cimg src=\"https://myfiles.space/user_files/122228_c8a1650c59388082/122228_custom_files/img1718188364.png\"\u003e\u003cbr\u003e\u003c/p\u003e\n \u003cp\u003e\u003cimg src=\"https://myfiles.space/user_files/122228_c8a1650c59388082/122228_custom_files/img1718188363.png\"\u003e\u003cbr\u003e\u003c/p\u003e\n \u003cp\u003eEstimates of biomass largely fluctuated across the three research areas. Upstream area displayed the highest biomass with 54766.93 g, whereas the hydropower and downstream areas reported significantly lower values of 8527.95 g and 383.76 g, respectively (Table \u003cspan class=\"InternalRef\"\u003eS1\u003c/span\u003e). The higher biomass observed in upstream and downstream areas can be attributed to the substantial catch of large fish individuals, including eels \u003cem\u003eAnguilla bicolor\u003c/em\u003e, \u003cem\u003eAnguilla celebesensis\u003c/em\u003e, and \u003cem\u003eAnguilla marmorata\u003c/em\u003e. These particular species were exclusively captured in the upstream and hydropower areas. Additionally, the study also identified three other fish species which mostly contributed to the biomass estimates namely \u003cem\u003eB. binotatus\u003c/em\u003e, \u003cem\u003eC. trimaculatum\u003c/em\u003e, and \u003cem\u003eM. auratus\u003c/em\u003e.\u003c/p\u003e\n\u003c/div\u003e"},{"header":"Discussion","content":"\u003cp\u003eThis research presents updated insights into the fish biodiversity of the Poso River including an updated species list and appraisal of fish abundance and biomass in the area. We successfully combined morphological identification and DNA barcoding to produce robust schemes of species delimitation, and validated species identifications from fish larvae and adult. By combining the examination of genetic divergence (Hebert et al. \u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e2004\u003c/span\u003e; Ward et al. \u003cspan citationid=\"CR71\" class=\"CitationRef\"\u003e2005\u003c/span\u003e) and the examination of physical characteristics (Ahnelt et al. \u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e2019\u003c/span\u003e), we were able to determine if genetic variations form discrete clusters which align with species-level taxa (Atminarso et al. \u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e2018\u003c/span\u003e). The increasing accessibility of DNA barcodes proved to facilitate the resolution of conflicting taxonomic cases (Dahruddin et al. \u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e2021\u003c/span\u003e; Hubert et al. \u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e2019\u003c/span\u003e; Wibowo et al. \u003cspan citationid=\"CR74\" class=\"CitationRef\"\u003e2023\u003c/span\u003e; Wibowo et al. \u003cspan citationid=\"CR75\" class=\"CitationRef\"\u003e2024\u003c/span\u003e). The absence of reference sequences is currently the main limit in the application of DNA barcoding for automated identification of unknown (Wibowo et al. \u003cspan citationid=\"CR73\" class=\"CitationRef\"\u003e2016\u003c/span\u003e; Wibowo et al. \u003cspan citationid=\"CR76\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). The integration of DNA barcoding with conventional taxonomic workflow using morphological characters offers a robust procedure to delimitate species and identify specimens, resulting in taxonomic revisions and holding promise for future advancements as its adoption becomes more prevalent.\u003c/p\u003e \u003cp\u003ePoso River is anticipated to undergo changes in fish community structure due to various factors, including the invasion of the system by exotic fish species, alterations in river hydrology, and unsustainable fishing practices both upstream and downstream of the current dam project. Fish biodiversity of fish in the Poso River is intricately linked to the lake Poso ecosystem and its biodiversity, which serves as the primary water source supplying the river. The introduction of exotic species and their invasion has been studied in Lake Poso, revealing the presence of 17 non-native fish species introduced since the last century for various purposes but mostly for increasing fish biomas by releasing pet fish from aquariums (Herder et al. \u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e2012\u003c/span\u003e). During this study, a total of 27 fish and shrimps species were documented. Notably, eight non-native species, constituting 87.50% of the observed fish, have established dominance within the Poso River. The remaining 12.5% correspond to native fish species of Poso River. The five dominant non-native species include \u003cem\u003eMelanochromis auratus\u003c/em\u003e (25.93%) from Lake Malawi, \u003cem\u003eOreochromis niloticus\u003c/em\u003e (19.41%) from Africa, \u003cem\u003eCichlasoma trimaculatum\u003c/em\u003e (18.01%) from Mexico and Central America, \u003cem\u003eBarbodes binotatus\u003c/em\u003e (13.03%) from Sundaland (Java, Sumatra, Borneo), and \u003cem\u003eOsteochilus vittatus\u003c/em\u003e (6%) from Sundaland. This situation is particularly of concern, particularly for predator fish that pose a potential threat to native fish. Numerous activities, such as aquaculture, restocking, biological control, and recreational fishing, have contributed to the introduction of exotic fish into Indonesia\u0026rsquo;s freshwater ecosystems (Andriyono and Fitrani \u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e2021\u003c/span\u003e; Suryandari et al. \u003cspan citationid=\"CR66\" class=\"CitationRef\"\u003e2021\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eThe expansion of the invasive fish species could result in reduced abundance of native fish and species diversity, and lead to the extinction of native fish species (Gaye-Siessegger et al. \u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e2022\u003c/span\u003e; Zhao et al. \u003cspan citationid=\"CR81\" class=\"CitationRef\"\u003e2019\u003c/span\u003e). This phenomenon is exemplified by the unfortunate loss of native fish species such as \u003cem\u003eAdrianichthys kruyti\u003c/em\u003e and \u003cem\u003eXenopoecilus poptae\u003c/em\u003e in Lake Poso, attributed to the introduction of Nile Tilapia (Yanuarita et al. \u003cspan citationid=\"CR79\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). Notably, the rapid reproductive rates of non-native fish have been observed to outcompete and displace native species (Escobar et al. \u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e2018\u003c/span\u003e; Saba et al. \u003cspan citationid=\"CR57\" class=\"CitationRef\"\u003e2021\u003c/span\u003e). The prevalence of non-native fish may compete for limited food and habitat resources. Furthermore, they could act as the host for various diseases previously absent in the ecosystem (Havel et al. \u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e2015\u003c/span\u003e). Currently, the number of invasive fish is increasing, one of which is \u003cem\u003eM. auratus\u003c/em\u003e (Herder et al. \u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). This cichlid fish was caught in both the upstream area and the hydropower area but was not found yet in the downstream area. The presence of barriers in the form of dams can prevent the spread of invasive fish downstream. However, negative impacts in the form of habitat fragmentation may occur. Habitat fragmentation can particularly affect migratory fishes and can alter fish populations and distribution (Arantes et al. \u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e2019\u003c/span\u003e; Pavlov et al. \u003cspan citationid=\"CR53\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). The challenge of future development of fish passage is selective passage design to prioritize native migratory fish species without enabling the spread of invasive species (Cooper et al. \u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e2021\u003c/span\u003e; Kerr et al. \u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e2021\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eThe fragmentation of river systems stands as a primary driver behind the decline in freshwater fish biodiversity (Franklin et al. \u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e2022\u003c/span\u003e; Stendera et al. \u003cspan citationid=\"CR64\" class=\"CitationRef\"\u003e2012\u003c/span\u003e). This study reveals noteworthy disparities in fish biodiversity between the upstream, environmental flow and downstream sections of the river. Specifically, the upstream area exhibits a notably higher fish abundance compared to both the environmental flow and downstream regions. Within the upstream zone of the Poso River, a diverse community comprising 15 fish species was observed, representing a substantial 69.35% of the overall fish population. In the environmental flow and downstream sections of the Poso River, the observed fish species numbered 14 and 7, respectively, accounting for 24% and 7% of the total fish population in these respective areas. A striking illustration of this impact can be observed in the case of the Djuanda Reservoir on the Citarum River, West Java. This reservoir, constructed in 1968 as the first major Indonesian hydropower dam, led to a significant transformation in the native freshwater fish community. Prior to dam construction, a rich diversity of 31 freshwater fish species was recorded, however, this diversity dwindled to just 18 species after four decades of dam operation (Kartamihardja \u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e2008\u003c/span\u003e). River network connectivity, a fundamental concept in river ecology, encompasses the dynamic movement of matter, energy, and organisms along the longitudinal (upstream-downstream), lateral, and vertical axes of a river. This connectivity is pivotal for sustaining the functional integrity of the river ecosystem (Allan and Castillo \u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2007\u003c/span\u003e; Xia et al. \u003cspan citationid=\"CR77\" class=\"CitationRef\"\u003e2012\u003c/span\u003e). Recognizing the intricate interplay between fish diversity and river network connectivity holds immense significance for the survival of species, the ecological health of river systems, and the well-being of human communities, as emphasized by Shao et al. (\u003cspan citationid=\"CR60\" class=\"CitationRef\"\u003e2019\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eInvestigation of fish biomass revealed significantly higher values in the upstream area compared to other locations. Elevated fish biomass can serve as an indicator of the environment\u0026rsquo;s capacity to support fish growth (Hashim and Ismail \u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e2015\u003c/span\u003e). Conversely, a decline in fish biomass may result from deteriorating habitat quality caused by factors such as pollution, sedimentation, and environmental degradation. Irresponsible fishing practices can also contribute to diminishing fish biomass in water bodies (Palomares et al. \u003cspan citationid=\"CR51\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). The lower fish biomass in the downstream area, in contrast to other regions, is believed to be linked to habitat fragmentation, as evidenced by the substantial difference in fish biomass between the upstream area and other locations. Habitat fragmentation has the potential to alter the composition of fish species and reduce their overall diversity. Several studies showed that habitat fragmentation can reduce the number of two types of native species, migratory fish species and rheophilic fish, that are no longer found due to barriers (Sun et al. \u003cspan citationid=\"CR65\" class=\"CitationRef\"\u003e2023\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eThe study also revealed the presence of several endemic fish species in the river Poso, notably from the Adrianichthyidae family, known as ricefish. Three species of the genus were observed, namely \u003cem\u003eO. nebulosus, O. nigrimas\u003c/em\u003e, and \u003cem\u003eOryzias\u003c/em\u003e sp. which we considered as 3 sympatric endemic species from Lake Poso (Sutra et al. \u003cspan citationid=\"CR67\" class=\"CitationRef\"\u003e2019\u003c/span\u003e). Additionally, three migratory species were identified, specifically the eels \u003cem\u003eAnguilla bicolor\u003c/em\u003e, \u003cem\u003eAnguilla celebesensis\u003c/em\u003e, and \u003cem\u003eAnguilla marmorata\u003c/em\u003e. \u003cem\u003eOryzias\u003c/em\u003e species were observed in both the upstream and hydropower areas, where they were caught using the traps. Notably, these species were conspicuously absent in the downstream region. Previous research reported the presence of \u003cem\u003eOryzias\u003c/em\u003e fish species in Lake Poso and its inlet (Herjayanto et al. \u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e2019\u003c/span\u003e). The discrepancy in the number of species captured can be attributed to the burgeoning population of invasive species, which are gradually displacing native fish. Invasive fish species have the potential to engage in competition with native fish for both food and habitat resources (Busst and Britton \u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e2017\u003c/span\u003e; Sayer et al. \u003cspan citationid=\"CR58\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). Furthermore, a diverse diet of \u003cem\u003eMelanochromis auratus\u003c/em\u003e, encompassing larvae and fish eggs, primarily preying on \u003cem\u003eOryzias\u003c/em\u003e fish, and also encountering the endemic fish species \u003cem\u003eMugilogobius sarasinorum\u003c/em\u003e as well (Herder et al. \u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). In addition to the invasive species issue, overfishing and various anthropogenic activities pose additional threats to the ecosystem (Arthington et al. \u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e2016\u003c/span\u003e; H\u0026auml;der et al. \u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e2020\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eThe Poso River hosts numerous species with complex migratory habits, involving both adults and juveniles. The presence of catadromous and amphidromous species in this study underscores the critical need to maintain the connectivity of the Poso River. Hydropower dams on the river are equipped with fishways designed to facilitate fish migration, aiming to mitigate the impact of damming on fish biodiversity (Baumgartner and Wibowo \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e2018\u003c/span\u003e). The primary objectives of fish passage development are to support the migration of multiple species, both upstream and downstream, thereby contributing to the preservation of fish biodiversity (O\u0026rsquo;Connor et al. \u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). However, the dominance of non-native species in the Poso River necessitates the development of selective fish passages that can block the distribution of these invasive species. The creation of selective passages relies on interspecific variations in physical capabilities, body shape, sensory capacities, behavior, and movement patterns. Understanding these distinctions is crucial for designing effective selective passages (Rahel and McLaughlin \u003cspan citationid=\"CR55\" class=\"CitationRef\"\u003e2018\u003c/span\u003e) (Rahel \u0026amp; McLaughlin, \u003cspan citationid=\"CR55\" class=\"CitationRef\"\u003e2018\u003c/span\u003e).\u003c/p\u003e"},{"header":"Conclusions","content":"\u003cp\u003eThis study highlights a comprehensive overview of aquatic biodiversity in Poso River, Indonesia identifying 27 species, including two endangered ones. The predominance of non-native species, which make up 85.70% of the population, underscores a significant ecological concern. The presence of non-native species proliferation poses a potential threat to native fish populations. The dominance of non-native species in the Poso River necessitates the improvement of existing fish passages equipped in hydropower dams through the development of selective fish passages that can block the distribution of these invasive species. This study offers valuable insights for conservation and management efforts in the Poso River and similar ecosystems worldwide, ensuring the preservation of biodiversity and the health of aquatic ecosystems.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAcknowledgement\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe project funding of this study was fully supported by Australian Centre for International Agricultural Research (ACIAR) Project in Indonesia (FIS/2018/153 \u0026ndash; Translating fish passage research outcomes into policy and legislation across South-East Asia); Educational Fund Management Institution (LPDP), Ministry of Finance; National Research and Innovation Agency (BRIN), Indonesia through the Research Funding Programme \u003cspan dir=\"RTL\"\u003e\u0026ldquo;\u003c/span\u003eResearch and Innovation for Advanced Indonesia\u0026rdquo; (82/II.7/HK/2022: Fish biodiversity and hydrology assessment for improvement of the effectivity and functional fishway development: Case study of Poso Dam 1, Poso Dam 2, and planned Poso Dam 3 of Poso energy), and PT. Poso Energy, Indonesia. Therefore, we appreciate ACIAR and PT. Poso Energy team for providing us with the great opportunity and collaboration. We also would like to thank the assistance and information provided by local fishermen, PT. Poso Energy staffs, the laboratory analyst of Genomic Building, BRIN, and local government staffs during the fieldwork and laboratory analysis.\u003cstrong\u003e\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthor Contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eAW, LB, KK, VAP, and IS conceptualized the research. AW, LB, DA, KK, VAP, MZ, and ILS developed the methods. AW, MZ, KK, DA, BKAS, and AC performed the data analysis. BKAS, AC, SAA, and TD prepared the figures and tables. AW, NH, LB, KK, VAP, FR, RG, DI, IS, ANS, AA, and AC conducted the research, data interpretation, and manuscript writing. All authors reviewed the manuscript. \u003cstrong\u003e\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eData Availability\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe data used in this manuscript are organized by the first author (Arif Wibowo). All sequences were deposited in the NCBI Genbank database www.ncbi.nlm.nih.gov/genbank (Accession numbers PP595925-PP595976, PP556235-PP556294 and PP598893).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConflict of Interest Statement\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors declare that they do not have any conflicts of interest\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eEthics Approval Statement\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eAll procedures pertaining to the capture and handling of fish were carried out in accordance with the ARRIVE guidelines and approved by Animal Care and Ethic Research Integrity Unit, Charles Sturt University (Protocol No. A20253, Name of project: Translating fish passage research outcomes into policy and legislation across South-East Asia).\u0026nbsp;\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eAhnelt H, Wibowo A, Prianto E (2019) A new species of Pectenocypris (Teleostei: Cyprinidae) from peat swamps in Sumatra. 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Water 11(6):1217\u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"aquatic-sciences","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"aqsc","sideBox":"Learn more about [Aquatic Sciences](http://link.springer.com/journal/27)","snPcode":"27","submissionUrl":"https://submission.nature.com/new-submission/27/3","title":"Aquatic Sciences","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"Aquatic biodiversity, non-native species, fishway, hydropower, conservation","lastPublishedDoi":"10.21203/rs.3.rs-4496842/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-4496842/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eFish biodiversity assessments play a crucial role in identifying potential threats, and the overall health of aquatic ecosystems. Poso River in Sulawesi, Indonesia presents a complex scenario where changes in fish biodiversity can be influenced by habitat alteration, the introduction of non-native fish species and overfishing. In this study, we assessed fish biodiversity in Poso River to gain a better understanding of the challenges to its aquatic biodiversity. This knowledge is critical for enhancing fisheries management and conservation programs, and is essential for improving the fishway system integrated into hydropower dams. The biodiversity study utilized a comprehensive methodology that encompassed both traditional taxonomic approaches and DNA barcoding, specifically targeting the mitochondrial Cytochrome C Oxidase Subunit-1 (COI) gene for accurately identify species and validate their boundaries. It was conducted in upstream, environmental flows of hydropower dams, and downstream areas of the river. We found 27 species of fish in the Poso River, including both native and non-native species. Two endangered species were also observed. DNA barcoding was performed to examine species boundaries and identity. The fish population in the Poso River is dominated by non-native species, accounting for 85.70% of the total population. The upstream area had the highest fish abundance and diversity, while the downstream area had the lowest. There was no significant difference in species richness and diversity across different locations and seasons. The dominance of non-native species in the Poso River necessitates the improvement of existing fish passages equipped in hydropower dams through the development of selective fish passages that can block the distribution of these invasive species. This research highlights the critical issue of non-native species proliferation and its potential threat they pose to native fish populations, providing valuable insights for conservation and management efforts in Indonesia and similar ecosystems worldwide.\u003c/p\u003e","manuscriptTitle":"Characterizing spatial patterns among freshwater fishes and shrimps of the Poso River (Sulawesi, Indonesia) using DNA barcoding","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-06-12 10:41:05","doi":"10.21203/rs.3.rs-4496842/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2024-08-01T08:49:19+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2024-08-01T08:15:42+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2024-07-03T11:24:54+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"7944430504831645337984205737822808866","date":"2024-06-13T04:20:33+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"227172209452731557328880136583386593984","date":"2024-06-13T02:57:02+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2024-06-12T12:57:11+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2024-05-31T07:12:17+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2024-05-30T09:52:23+00:00","index":"","fulltext":""},{"type":"submitted","content":"Aquatic Sciences","date":"2024-05-29T11:47:44+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"aquatic-sciences","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"aqsc","sideBox":"Learn more about [Aquatic Sciences](http://link.springer.com/journal/27)","snPcode":"27","submissionUrl":"https://submission.nature.com/new-submission/27/3","title":"Aquatic Sciences","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"d95bf4a8-a44e-401e-b716-4c31dda4ca0f","owner":[],"postedDate":"June 12th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2024-10-21T16:06:54+00:00","versionOfRecord":{"articleIdentity":"rs-4496842","link":"https://doi.org/10.1007/s00027-024-01128-0","journal":{"identity":"aquatic-sciences","isVorOnly":false,"title":"Aquatic Sciences"},"publishedOn":"2024-10-15 15:57:20","publishedOnDateReadable":"October 15th, 2024"},"versionCreatedAt":"2024-06-12 10:41:05","video":"","vorDoi":"10.1007/s00027-024-01128-0","vorDoiUrl":"https://doi.org/10.1007/s00027-024-01128-0","workflowStages":[]},"version":"v1","identity":"rs-4496842","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-4496842","identity":"rs-4496842","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}