http://hdl.handle.net/20.500.12066/658 These papers were contributed by IFRDMD staff to various national and international journals 2026-04-07T18:27:53Z http://hdl.handle.net/20.500.12066/7404 Disentangling the taxonomy of the subfamily Rasborinae (Cypriniformes, Danionidae) in Sundaland using DNA barcodes Sholihah, Arni; Delrieu-Trottin, Erwan; Sukmono, Tedjo; Dahruddin, Hadi; Risdawati, Renny; Elvyra, Roza; Wibowo, Arif; Kustiati, Kustiati; Busson, Frederic; Sauri, Sopian; Nurhaman, Ujang; Dounias, Edmond; Zein, Muhamad Syamsul Arifin; Fitriana, Yuli; Utama, Ilham Vemandra; Muchlisin, Zainal Abidin; Agnese, Jean-Francois; Hanner, Robert; Wowor, Daisy; Steinke, Dirk; Keith, Philippe; Ruber, Lukas; Hubert, Nicolas Sundaland constitutes one of the largest and most threatened biodiversity hotspots; however, our understanding of its biodiversity is afflicted by knowledge gaps in taxonomy and distribution patterns. The subfamily Rasborinae is the most diversified group of freshwater fishes in Sundaland. Uncertainties in their taxonomy and systematics have constrained its use as a model in evolutionary studies. Here, we established a DNA barcode reference library of the Rasborinae in Sundaland to examine species boundaries and range distributions through DNA-based species delimitation methods. A checklist of the Rasborinae of Sundaland was compiled based on online catalogs and used to estimate the taxonomic coverage of the present study. We generated a total of 991 DNA barcodes from 189 sampling sites in Sundaland. Together with 106 previously published sequences, we subsequently assembled a reference library of 1097 sequences that covers 65 taxa, including 61 of the 79 known Rasborinae species of Sundaland. Our library indicates that Rasborinae species are defined by distinct molecular lineages that are captured by species delimitation methods. A large overlap between intraspecific and interspecific genetic distance is observed that can be explained by the large amounts of cryptic diversity as evidenced by the 166 Operational Taxonomic Units detected. Implications for the evolutionary dynamics of species diversification are discussed. 2020-01-01T00:00:00Z http://hdl.handle.net/20.500.12066/7335 Assessing the ecosystem approach to fisheries management in Indonesian inland fisheries Ditya, Yoga Candra; Muthmainnah, Dina; Wiadnyana, Ngurah Nyoman; Makmur, Safran; Kaban, Siswanta; Makmur, Hukmanan Rais; Hidayah, Taufiq; Anggraeni, Dian Pamularsih; Antoni, Rezki; Dwirastina, Mirna; Koeshendrajana, Sonny Inland waters provide huge fish resources and are exploited as food security by local people. The method used in this study was intended to evaluate the performance of the management in terms of the Ecosystem Approach to Fisheries Management (EAFM). The study was conducted in five districts in Indonesia, namely Cilacap, Sukabumi, Kampar, Kapuas, and South Barito, from February to August 2019. The primary data were gathered through observation and interviews with fishers, local government, indigenous community, NGO, and other stakeholders. The secondary data were collected from previous studies. The EAFM domains are presented in a questionnaire that refers to the technical guidelines for assessing fisheries management indicators with an ecosystem approach. The indicators are grouped into seven domains in rating the current management of inland fisheries. The Likert score is used to measure respondents’ attitudes to a particular question or statement. The score criteria used in examining fishery management by EAFM tools-based ordinal 1,2,3, designed to measure opinion or perception from the questionnaires. The results showed that the economy and stakeholder domain were poor categories, indicated by a red flag. Nevertheless, the management conditions, especially for the managed fish resources domain, were classified as good. 2021-12-01T00:00:00Z http://hdl.handle.net/20.500.12066/7336 Assessing temporal patterns and species composition of glass eel (Anguila spp.) cohorts in Sumatra and Java using DNA barcodes Wibowo, Arif; Hubert, Nicolas; Dahruddin, Hadi; Steinke, Dirk; Suhaimi, Rezki Antoni; Samuel; Atminarso, Dwi; Anggraeni, Dian Pamularsih; Trismawanti, Ike; Baumgartner, Lee; Ning, Nathan Anguillid eels are widely acknowledged for their ecological and socio-economic value in many countries. Yet, knowledge regarding their biodiversity, distribution and abundance remains superficial—particularly in tropical countries such as Indonesia, where demand for anguillid eels is steadily increasing along with the threat imposed by river infrastructure developments. We investigated the diversity of anguillid eels on the western Indonesian islands of Sumatra and Java using automated molecular classification and genetic species delimitation methods to explore temporal patterns of glass eel cohorts entering inland waters. A total of 278 glass eels were collected from monthly samplings along the west coast of Sumatra and the south coast of Java between March 2017 and February 2018. An automated, DNA-based glass eel identification was performed using a DNA barcode reference library consisting of 64 newly generated DNA barcodes and 117 DNA barcodes retrieved from BOLD for all nine Anguilla species known to occur in Indonesia. Species delimitation methods converged in delineating eight Molecular Operational Taxonomic Units (MOTUs), with A. nebolusa and A. bengalensis being undistinguishable by DNA barcodes. A total of four MOTUs were detected within the glass eel samples, corresponding to Anguilla bicolor, A. interioris, A. marmorata, and A. nebulosa/A. bengalensis. Monthly captures indicated that glass eel recruitment peaks in June, during the onset of the dry season, and that A. bicolor is the most prevalent species. Comparing indices of mitochondrial genetic diversity between yellow/silver eels, originating from several sites across the species range distribution, and glass eels, collected in West Sumatra and Java, indicated a marked difference. Glass eels displayed a much lower diversity than yellow/silver eels. Implications for the management of glass eel fisheries and species conservation are discussed. 2021-04-29T00:00:00Z http://hdl.handle.net/20.500.12066/7165 Challenges balancing fisheries resource management and river development in Indonesia Utomo, Agus Djoko; Wibowo, Arif; Suhaimi, Rezki Antoni; Atminarso, Dwi; Baumgartner, Lee Indonesia’s increasing human population will require more food and potable water into the future. Constructing more reservoirs has been deemed a national priority to help meet these basic needs. The number of reservoirs in Indonesia has increased gradually over time, but this may have affected fisheries resources. Of the 100 reservoirs already built, 80% are on the island of Java. The direct effects of reservoir on fisheries resources include sedimentation, reduced water flows, eutrophication and disturbance to the fish life cycle, and indirect effects may include overfishing. Reservoirs can also alter habitat, which can change fisheries productivity. Fisheries resources management, in a reservoir, has a high possibility of success if clear boundaries are set and expectations are managed. Fishermen need to participate in management and targets must be set to establish a complete ecosystem for a growing fish population. Other interventions, such as floating cage aquaculture and fish restocking, are suitable tools for management. However, at present there is no Indonesian framework to guide such management tools. With many more reservoirs planned into the future, there is a pressing need to develop a systematic and robust management system to ensure fisheries and river development can coexist. 2019-07-18T00:00:00Z