Open Access
Issue |
Knowl. Manag. Aquat. Ecosyst.
Number 426, 2025
Riparian ecology and management
|
|
---|---|---|
Article Number | 17 | |
Number of page(s) | 16 | |
DOI | https://doi.org/10.1051/kmae/2025009 | |
Published online | 05 June 2025 |
- Aditya T. et al. 2020. Aquatic invasions in Indonesia: current knowledge and management. J Environ Manag. [Google Scholar]
- Aida SN, Utomo AD, Anggraeni DP, Ditya YC, Wulandari TNM, Ali M, Caipiang CMA, Suharman I. 2022. Distribution of fish species in relation to water quality condition in Bengawan Solo river, Central Java, Indonesia. Polish J Environ Stud 31: 5549–5561. [CrossRef] [Google Scholar]
- Alshari NFMAH, Adnan MHI, Zainal Abidin DH. et al. 2024. Tracking the tropical aquatic dragon: environmental DNA (eDNA) detection for monitoring the endangered Asian arowana, Scleropages formosus (Müller and Schlegel, 1840). Hydrobiologia. https://doi.org/10.1007/s10750-024-05776-z [Google Scholar]
- Anadón JD, Giménez A, Ballestar R, Pérez I. 2009. Evaluation of local ecological knowledge as a method for collecting extensive data on animal abundance. Conserv Biol 23: 617–625. [CrossRef] [PubMed] [Google Scholar]
- Arlinghaus R, Lorenzen K, Johnson BM, Cooke SJ, Cowx IG. 2015. Management of freshwater fisheries: addressing habitat, people and fishes. Freshw Fish Ecol: 557–579. [Google Scholar]
- Astuti SS, Hariati AM, Kusuma WE, Yuniarti A, Kurniawan NIA, Wiadnya DGR. 2023. Anthropogenic introduction of the Spotted Barb, Barbodes binotatus, across the Wallace Line in western Sulawesi, Indonesia. Biodiversitas J Biolog Divers 24: 1916–1925. [Google Scholar]
- Austin KG, Schwantes A, Gu Y, Kasibhatla PS. 2019. What causes deforestation in Indonesia?. Environ Res Lett 14: 024007. [CrossRef] [Google Scholar]
- Aziz A, Shodikin A, Rana M. 2019. Java coastal community empowerment model. SSRN (3333949), 1–14. [Google Scholar]
- Barbarossa V, Bosmans J, Wanders N, King H, Marc FP, Bienkens Huijbergs MAJ, Schipper AM. 2021. Threats of global warming to the world's freshwater fishes. Nat Commun 12: 1702. [CrossRef] [PubMed] [Google Scholar]
- Bergman PS, Schumer G, Blankenship S, Campbell E. 2016. Detection of adult green sturgeon using environmental DNA analysis. PLoS One 11: e0153500. [CrossRef] [Google Scholar]
- Bernard HR. 2017. Research Methods in Anthropology: Qualitative and Quantitative Approaches (6th ed.). Rowman & Littlefield. [Google Scholar]
- Barnes MA, Turner CR. 2016. The ecology of environmental DNA and implications for conservation genetics. Heredity 117: 214–223. [Google Scholar]
- Bessesen BL, González-Suárez M. 2021. The value and limitations of local ecological knowledge: Longitudinal and retrospective assessment of flagship species in Golfo Dulce, Costa Rica. People Nat 3: 627–638. [CrossRef] [Google Scholar]
- Bohmann K, Evans A, Gilbert MT, Carvalho GR, Creer S, Knapp M, Yu DW, de Bruyn M. 2014. Environmental DNA for wildlife biology and biodiversity monitoring. Trends Ecol Evol 29: 358–367. [CrossRef] [PubMed] [Google Scholar]
- Britton JR. 2023. Contemporary perspectives on the ecological impacts of invasive freshwater fishes. J Fish Biol 103: 752–764. [CrossRef] [PubMed] [Google Scholar]
- Buchner D, Sinclair JS, Ayasse M, Beermann AJ, Buse J, Dziock F, Leese F. 2024. Upscaling biodiversity monitoring: metabarcoding estimates 31,846 insect species from Malaise traps across Germany. Mol Ecol Resour 25: e14023. [Google Scholar]
- Burian A, Mauvisseau Q, Bulling M, Domisch S, Qian S, Sweet M. 2021. Improving the reliability of eDNA data interpretation. Mol Ecol Resour 21: 1422–1433. [CrossRef] [PubMed] [Google Scholar]
- Carraro L, Hartikainen H, Jokela J, Bertuzzo E, Rinaldo A. 2018. Estimating species distribution and abundance in river networks using environmental DNA. Proc Natl Acad Sci 115: 11724–11729. [CrossRef] [PubMed] [Google Scholar]
- Castagnino F, Estévez RA, Caillaux M, Velez-Zuazo X, Gelcich S. 2023. Local ecological knowledge (LEK) suggests overfishing and sequential depletion of Peruvian coastal groundfish. Mar Coast Fish: Dyn Manag Ecosyst Sci 15: e10272. [Google Scholar]
- Civade R, Dejean T, Valentini A, Roset N, Raymond JC, Bonin A, Taberlet P, Pont D. 2016. Spatial representativeness of environmental DNA metabarcoding signal for fish biodiversity assessment in a natural freshwater system. PLoS ONE 11: e0157366. [CrossRef] [PubMed] [Google Scholar]
- Collins RA, Bakker J, Wangensteen OS, Soto AZ, Corrigan L, Sims DW, Genner MJ, Mariani S. 2019. Non‐specific amplification compromises environmental DNA metabarcoding with COI. Methods Ecol Evol 10: 1985–2001. [CrossRef] [Google Scholar]
- Cooke SJ, Nyboer E, Bennett A, Lynch AJ, Infante DM, Cowx IG, Beard TD, Bartley D, Paukert CP, Reid AJ, Funge-Smith S, Gondwe E, Kaunda E, Koehn JD, Souter NJ, Stokes GL, Castello L, Leonard NJ, Skov C, Berg S, Taylor WW. 2021. The ten steps to responsible Inland fisheries in practice: reflections from diverse regional case studies around the globe. Rev Fish Biol Fisher 31: 843–877. [CrossRef] [Google Scholar]
- Coutant O, et al. 2021. Assessing the efficiency of environmental DNA sampling for rare fish detection in large rivers. Environ DNA 3: 157–169. [Google Scholar]
- Dahruddin H, Hutama A, Busson F, Sauri S, Hanner R, Keith P, Hadiaty R, Hubert N. 2017. Revisiting the ichthyodiversity of Java and Bali through DNA barcodes: taxonomic coverage, identification accuracy, cryptic diversity and identification of exotic species. Mol Ecol Resour 17: 288–299. [CrossRef] [PubMed] [Google Scholar]
- Deiner K, et al. 2015. Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA. Biol Conserv 183: 53–63. [CrossRef] [Google Scholar]
- Dewantoro GW, Rachmatika I. 2016. The introduction and Invasive fishes in Indonesia. LIPI PRESS, Jakarta [In Indonesian]. [Google Scholar]
- Djuangsih N. 1993. Understanding the state of river basin management from an environmental toxicology perspective: an example from water pollution at Citarum river basin, West Java, Indonesia. Sci Total Environ 134: 283–292. [CrossRef] [Google Scholar]
- Dlamini V, Samson M, Curtis C, O'Brien G. 2022. Co-opting small-scale fishers' knowledge with scientific data to improve understanding of fish community structures in the Lower Komati River, South Africa. Mar Freshw Res 74: 111–124. [CrossRef] [Google Scholar]
- Early-Capistrán MM, Solana-Arellano E, Abreu-Grobois FA, Narchi NE, Garibay-Melo G, Seminoff JA, .., Saenz-Arroyo A. 2020. Quantifying local ecological knowledge to model historical abundance of long-lived, heavily-exploited fauna. PeerJ 8: e9494. [CrossRef] [PubMed] [Google Scholar]
- Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460–2461. [CrossRef] [PubMed] [Google Scholar]
- Etikan I, Musa SA, Alkassim RS. 2016. Comparison of convenience sampling and purposive sampling. Am J Theor Appl Stat 5: 1–4. [CrossRef] [Google Scholar]
- Evans NT, Shirey PD, Wieringa JG, Mahon AR, Lamberti GA. 2017. Comparative cost and effort of fish distribution detection via environmental DNA analysis and electrofishing. Fisheries 42: 90–99. [CrossRef] [Google Scholar]
- Gehri RR, Larson WA, Gruenthal K, Sard NM, Shi Y. 2021. eDNA metabarcoding outperforms traditional fisheries sampling and reveals fine-scale heterogeneity in a temperate freshwater lake. Environ DNA 3: 912–929. [CrossRef] [Google Scholar]
- Gray TNE, Phommachak A, Vannachomchan K, Guegan F. 2017. Using local ecological knowledge to monitor threatened Mekong megafauna in Lao PDR. PLOS ONE 12: e0183247. [CrossRef] [PubMed] [Google Scholar]
- Gustiano R, Kurniawan K, Haryono H. 2021. Optimizing the utilization of genetic resources of indonesian native freshwater fish. Asian J Conserv Biol 10: 189–196. [CrossRef] [Google Scholar]
- Hadiaty RK. 2011. Diversity and fish species loss in ciliwung and cisadane rivers. Berita Biologi 10: 491–504. [Google Scholar]
- Herawati T, Sidik RAR, Sahidin A, Herawati H. 2020. Struktur Komunitas Ikan di Hilir Sungai Cimanuk Provinsi Jawa Barat pada Musim Penghujan. Jurnal Perikanan Universitas Gadjah Mada 22 (2): 113–122. [CrossRef] [Google Scholar]
- Herve A, Domaizon I, Baudoin JM, Dejean T, Gibert P, Jean P, Peroux T, Raymond JC, Valentini A, Vautier M, Logez, M. 2022. Spatio-temporal variability of eDNA signal and its implication for fish monitoring in lakes. PLoS One 17: e0272660. [CrossRef] [PubMed] [Google Scholar]
- He X, Jeffery NW, Stanley RRE, Hamilton LC, Rubidge EM, Abbott CL. 2023. eDNA metabarcoding enriches traditional trawl survey data for monitoring biodiversity in the marine environment, ICES J Mar Sci 80: 1529–1538. [CrossRef] [Google Scholar]
- Hind EJ. 2015. A review of the past, the present, and the future of fishers' knowledge research: a challenge to established fisheries science. ICES J Mar Sci 72: 341–358. [CrossRef] [Google Scholar]
- Hubert N, Kadarusman Wibowo A, Busson F, Caruso D, Sulandari S, Nafiqoh N, Pouyaud L, Rüber L, Avarre JC, Herder F, Hanner R, Keith P, Hadiaty RK. 2015. DNA Barcoding Indonesian freshwater fishes: challenges and prospects. DNA Barcodes. https://doi.org/10.1515/dna-2015-0018 [Google Scholar]
- Jerde CL. 2021. Can we manage fisheries with the inherent uncertainty from eDNA? J Fish Biol 98: 341–353. [CrossRef] [PubMed] [Google Scholar]
- Kartamihardja ES. 2019. Degradation of native fish diversity in Citarum River, West Java. WARTA IKTIOLOGI 3: 1–8. [Google Scholar]
- Kartamihardja ES. 2008. Change of fish community composition and the influencing important factors during fourty years of the Djuanda reservoir impounded. Journal Iktiologi Indonesia 8: 67–78. [Google Scholar]
- Kurniawan K, Wibowo A, Prakoso VA, Rochman F, Irawan D, Atminarso D, Prasetyo AP, Deniansen T, Ginanjar R, Zamroni M, Iswantari A, Andriyono S, Surbani IL, Rosadi I, Jaya YYP, Sudarsono S, Nagai S, Rourke M, Hubert N, Stuart I, Baumgartner L. 2024. Integrating direct experimental fishing and environmental DNA metabarcoding to assess fish biodiversity in the Cibareno River, Indonesia, to support fishway design. Aquat Conserv: 34 e4250. [CrossRef] [Google Scholar]
- Kusuma WE, Ratmuangkhwang S, Kumazawa Y. 2016. Molecular phylogeny and historical biogeography of the Indonesian freshwater fish Rasbora lateristriata species complex (Actinopterygii: Cyprinidae): Cryptic species and west-to-east divergences. Molec Phylogen Evol 105: 212–223. [CrossRef] [Google Scholar]
- Leduc AOHC, De Carvalho FHD, Hussey NE, Reis-Filho JA, Longo GO, Lopes PFM. 2021. Local ecological knowledge to assist conservation status assessments in data poor contexts: a case study with the threatened sharks of the Brazilian Northeast. Biodivers Conserv 30: 819–845. [CrossRef] [Google Scholar]
- Li J, Lawson Handley LJ, Harper LR, Brys R, Watson HV, Di Muri C, Zhang X, Hänfling B. 2019. Limited dispersion and quick degradation of environmental DNA in fish ponds inferred by metabarcoding. Environmental DNA 1: 238–250 [CrossRef] [Google Scholar]
- Macher TH, Beermann AJ, Leese F. 2021. TaxonTableTools: a comprehensive, platform-independent graphical user interface software to explore and visualise DNA metabarcoding data. Mol Ecol Resour 21: 1705–1714. [CrossRef] [PubMed] [Google Scholar]
- Martinelli Marín D, Lasso CA, Caballero Gaitan SJ. 2024. eDNA metabarcoding: an effective tool for vertebrate diversity studies in the Colombian Amazon and Orinoco basins. Front Ecol Evol 12: 1409296. [CrossRef] [Google Scholar]
- Martins IM, Medeiros RP, Di Domenico M, Hanazaki N. 2018. What fishers' local ecological knowledge can reveal about the changes in exploited fish catches. Fish Res 198: 109–116. [CrossRef] [Google Scholar]
- McIntyre PB, Reidy Liermann CA, Revenga C. 2016. Linking freshwater fishery management to global food security and biodiversity conservation. Proc Natl Acad Sci USA 113: 12880–12885. [CrossRef] [PubMed] [Google Scholar]
- McRae L, Deinet S, Freeman R. 2017. The diversity-weighted living planet index: controlling for taxonomic bias in a global biodiversity indicator. PloS One: 12 e0169156. [CrossRef] [PubMed] [Google Scholar]
- Miya M, Sato Y, Fukunaga T, Sado T, Poulsen JY, Sato K, Minamoto T, Yamamoto S, Yamanaka H, Araki H, Kondoh M. 2015. MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. Royal Soc Open Sci 2: 150088. [CrossRef] [Google Scholar]
- Morris L, Beesley LS, Stevens ER, Gwinn DC, Hyde J, Thompson S, Douglas MM. 2024. Active eDNA is more cost-effective than fyke nets or passive eDNA collection when monitoring the invasion of an alien freshwater fish. Environ DNA 6: e70010. [CrossRef] [MathSciNet] [Google Scholar]
- Moyle PB, Leidy RA. 2023. Freshwater Fishes: Threatened Species and Threatened Waters on a Global Scale. In N. Maclean (Ed.), The Living Planet: The State of the World's Wildlife. Cambridge University Press, pp. 177–205. [Google Scholar]
- Nakao R, Inui R, Akamatsu Y, Goto M, Doi H, Matsuoka S. 2021. Illumina iSeq 100 and MiSeq exhibit similar performance in freshwater fish environmental DNA metabarcoding. Sci Rep 11: 15763. [CrossRef] [PubMed] [Google Scholar]
- Newing H. 2011. Conducting Research in Conservation: Social Science Methods and Practice (1st ed.) Routledge. https://doi.org/10.4324/9780203846452 [Google Scholar]
- Osathanunkul M, Madesis P. 2022. Environmental DNA detection of giant snakehead in Thailand's major rivers for wild stock assessment. PLoS ONE 17: e0267667. [CrossRef] [PubMed] [Google Scholar]
- Petriki O, Kouletsos A, Ntislidou C, Bobori DC. 2024. Local ecological knowledge (LEK) can guide decision-making in Inland fisheries management. Appl Sci 14: 8819. [CrossRef] [Google Scholar]
- Pravitasari AE, Indraprahasta GS, Rustiadi E, Rosandi VB, Stanny YA, Wulandari S, Priatama RA, Murtadho A. 2024. Dynamics and predictions of urban expansion in Java, Indonesia: continuity and change in mega-urbanization. ISPRS Int J Geo-Inform 13: 102. [CrossRef] [Google Scholar]
- Reid A, Carlson A, Creed I, Eliason E. 2019. Emerging threats and persistent conservation challenges for freshwater biodiversity. Biol Rev Camb Philos Soc 94: 849–873. [CrossRef] [PubMed] [Google Scholar]
- Robin Valen F, Nomleni A, Turnip G, Luhulima M, Insani L. 2023. Presence of non-native freshwater fish in Indonesia: a review − risk and ecological impacts. Aquac Aquar Conserv Legisl Bioflux 16: 66–79. [Google Scholar]
- Runde A, Hallwass G, Silvano RAM. 2020. Fishers' knowledge indicates extensive socioecological impacts downstream of proposed Dams in a Tropical River. One Earth 2: 255–268. [CrossRef] [Google Scholar]
- Ruppert KM, Kline RJ, Rahman MS. 2019. Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA. Glob Ecol Conserv 17. [Google Scholar]
- Sahu A, Kumar N, Pal Singh C, Singh M. 2023. Environmental DNA (eDNA): Powerful technique for biodiversity conservation. J Nat Conserv 71: 126325. [CrossRef] [Google Scholar]
- Sani LMI, Benyamin A, Husna AK, Arafat D, Subhan B, Sunuddin A, Cakasana N, Lestari DF, Madduppa H. 2021. A contrast pattern of reef fish species diversity and distribution using environmental DNA (eDNA) metabarcoding in longitudinal distance from Jakarta Bay. Jurnal Ilmu dan Teknologi Kelautan Tropis 13: 467–482. [Google Scholar]
- Sato Y, Miya M, Fukunaga T, Sado T, Iwasaki W. 2018. MitoFish and MiFish pipeline: a mitochondrial genome database of fish with an analysis pipeline for environmental DNA metabarcoding. Mol Biol Evol 35: 1553–1555. [CrossRef] [PubMed] [Google Scholar]
- Schoenle A, Scepanski D, Floss A, Buchel P, Koblitz AK, Scherwass A, Arndt H, Waldvogel AM. 2024. The dilemma of underestimating freshwater biodiversity: morphological and molecular approaches. BMC Ecol Evol 24: 69. [CrossRef] [PubMed] [Google Scholar]
- Shahi N, Singh B, Mohamad A, Mallik SK. 2024. Environmental DNA and Its Application in Microbial Biodiversity Assessment. In Handbook of Aquatic Microbiology (pp. 239–250). CRC Press [CrossRef] [Google Scholar]
- Sheppard DJ, Stark DJ, Muturi SW, Munene PH. 2024. Benefits of traditional and local ecological knowledge for species recovery when scientific inference is limited. Front Conserv Sci 5: 1383611. [CrossRef] [Google Scholar]
- Syafei DS, Wirjoatmodjo S, Rahardjo MF, Susilo SB. 2001. Fish fauna of Cimanuk River, West Java. Journal Iktiologi Indonesia 1: 1–6. [Google Scholar]
- Tsuji S, Yamanaka H, Minamoto T. 2017. Effects of water pH and proteinase K treatment on the yield of environmental DNA from water samples. Limnology 18: 1–7. [CrossRef] [Google Scholar]
- von Ammon U, Casanovas P, Pochon X, Zirngibl M, Leonard K, Smith A, Chetham J, Milner D, Zaiko A. 2023. Harnessing environmental DNA to reveal biogeographical patterns of non-indigenous species for improved co-governance of the marine environment in Aotearoa New Zealand. Sci Rep 13: 17061. [CrossRef] [PubMed] [Google Scholar]
- Wang B, Jiao L, Ni L, Wang M You P. 2024. Bridging the gap: the integration of eDNA techniques and traditional sampling in fish diversity analysis. Front Mar Sci 11: 1289589. [CrossRef] [Google Scholar]
- Wang S, Yan Z, Hanfling B, Zheng X, Wang P, Fan J, Li J. 2021. Methodology of fish eDNA and its applications in ecology and environment. Sci Total Environ 755: 142622. [CrossRef] [PubMed] [Google Scholar]
- Wang X, Wang J, Lin L, Huang L, Liu K, Dai G, Cai Q, Li J, Feng S, Wang G, Hui Y, Qiu L, Ji F. 2024. Comparison of environmental DNA metabarcoding and a traditional survey method for assessing fish diversity and distribution along salinity gradient in an Urban Brackish Reservoir, China. Biology 13: 930. [CrossRef] [PubMed] [Google Scholar]
- Wibowo A, Atminarso D, Baumgartner L, Vasemagi A. 2020. High prevalence of non-native fish species in a remote region of the Mamberamo River, Indonesia. Pacific Conserv Biol 26: 293–300. [CrossRef] [Google Scholar]
- Wibowo A, Haryono H, Kurniawan K, Prakoso VA, Dahruddin H, Surbani IL, Muslimin B, Jaya YYP, Sudarsono S, Stuart IG, Ahnelt H, Funge-Smith S, Vasemägi A, Hubert N. 2024. Genetic and morphological evidence of a single species of bronze featherback (Notopterus notopterus) in Sundaland. Glob Ecol Conserv 49. https://doi.org/10.1016/j.gecco.2023.e02786 [Google Scholar]
- Wibowo A, Kurniawan K, Atminarso D, Prihadi TH, Baumgartner LJ, Rourke ML, Nagai S, Hubert N, Vasemagi A. 2022. Assessing freshwater fish biodiversity of Kumbe River, Papua (Indonesia) through environmental DNA metabarcoding. Pacific Conserv Biol 29: 340–350. [CrossRef] [Google Scholar]
- Yuen KW, Park E, Hazrina M, Taufik M, Santikayasa P, Latrubesse E, Le JSH. 2023. A comprehensive database of Indonesian dams and its spatial distribution. Remote Sens 15. https://doi.org/10.3390/genes1030413 [Google Scholar]
- Zaiko A, Pochon X, Garcia-Vazquez E, Olenin S, Wood SA. 2018. Advantages and limitations of environmental DNA/RNA tools for marine biosecurity: management and surveillance of non-indigenous species. Front Mar Sci 5. [Google Scholar]
- Zou K, Chen J, Ruan H, Li Z. 2020. eDNA metabarcoding as a promising conservation tool for monitoring fish diversity in a coastal wetland of the Pearl River Estuary compared to bottom trawling. Sci Total Environ 702: 134704. [CrossRef] [PubMed] [Google Scholar]
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