eDNA uncovers hidden fish diversity in the coral reef ecosystems of Karimunjawa National Park, Indonesia
Environmental DNA is transforming coral‑reef biodiversity assessment. In Indonesia’s Karimunjawa National Park, eDNA sampling across core, protection, tourism and open‑access zones revealed 147 fish species—60% detected only through eDNA. Diversity was highest in the tourism zone, though beta‑diversity patterns were similar across zones. eDNA also captured functional traits such as habitat preference, migratory behavior and nocturnality, outperforming visual census alone. These findings show how integrated eDNA–visual monitoring can fill major gaps in reef‑fish assessment and strengthen conservation planning in Marine Protected Areas like KNP.
Subject Tags
- Conservation Technology
- Life Sciences
- Wildlife
Abstract
Environmental DNA (eDNA) has emerged as a powerful tool for swiftly assessing coral reef ecosystems, particularly for detecting fish diversity. This study focused on employing eDNA to investigate fish biodiversity and its functional traits in the Karimunjawa National Park (KNP), Indonesia. The use of eDNA and then validating with visual census results to reveal fish diversity was implemented across four management zones within the park (i.e., the core zone at Taka Malang, the protection zone at Menjangan Kecil Island, the tourism zone at Cilik Island and an open access location at Genting Island). Sampling involved collecting one liter of seawater per site, filtering, and processing to target the 12S locus, and then sequencing using the MinION machine (Oxford nanopore). The eDNA results show higher species diversity in the tourism zone compared to the core, protection and open access zones. However, beta diversity analysis revealed no significant differences in community composition between the zones. Moreover, this research revealed 147 species belonging to 31 families, with 60% species and 30% families identified solely through eDNA, that were not covered by the visual census. This research also reveals that eDNA is an excellent approach to detecting functional trait diversity, including environment preference and migratory and nocturnal behavior. This research underscores the potential of eDNA for evaluating fish diversity in KNP, proposing a combined eDNA and visual census approach to fill existing gaps in biodiversity assessment. Such integration promises to bolster conservation efforts within Marine Protection Areas like KNP.
Citation
Al Malik, M. D., Ambariyanto, A., Hartati, R., Nursalim, N., Kholilah, N., Kurniasih, E. M., ... & Cahyani, N. K. D. (2025). eDNA uncovers hidden fish diversity in the coral reef ecosystems of Karimunjawa National Park, Indonesia. Regional Studies in Marine Science, 81, 103945. https://doi.org/10.1016/j.rsma.2024.103945
TNC Authors
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Aji Wahyu Anggoro
Blue Carbon Program Manager, Indonesia
The Nature Conservancy
Email: aji.anggoro@tnc.org