Publications
Our mission is to conserve the marine environment through research, education, and collaboration. We do this through both direct conservation efforts and contributing to global marine research through scientific publications. In collaboration with NGOs, marine biologists, and universities around the world, our research contributes to the scientific community with the aim of helping to inform marine policymakers.
Research Gate
ResearchGate is a social networking site and online platform used by academics and researchers to share publications, connect with peers, and collaborate on research project.
Explore our Featured Publications and Reports
Internal Publications
Research led or co-led by the Indo Ocean Foundation, reflecting our in-house scientific work and primary research initiatives.
Global Contributions
Publications arising from international collaborations where the Indo Ocean Foundation contributed data, expertise, or analysis.
Associate Publications
Scientific papers authored by marine biologists affiliated with the Indo Ocean Project, but not produced directly in-house.
Internal Publications
Our Internal Publications highlight research produced through Indo Ocean’s field programs and local scientific partnerships. This work is grounded in long-term ecological monitoring, including BRUVs, benthic surveys, and roving visual censuses, which generate standardized datasets on fish communities, habitat condition, and key ecological indicators.
These data underpin annual site reports, internal technical publications, and provide baseline information for independent research and management decision-making. This section also features research led by Indo Ocean Marine Research Fellows, who undertake independent thesis projects in collaboration with our scientific team, building on long-term datasets while contributing new analyses and perspectives.
State of the Marine Ecosystem in Nusa Penida 2021-2023
Publication Date: December, 2025
ISBN:978-969-9895-76-0
Authors: Rinaldi Gotama, Selene Gaiani, Pascal Sebastian, Ahmad Ilham Rabbani Erawan, Serena Stean, Lauren D Sparks, Michaela Dudasova, Mette Rosenberg Carlsen, I Nengah Swarya, Aliviannisha Winda Zachrany, Rahmadi Prasetijo
Institutions:
- Indo Ocean Foundation
- Universitas Dhyana Pura
- Indonesian Marine Education & Research Organization
Highlights
- Long term ecological monitoring conducted across the Nusa Penida Marine Protected Area between 2021 and 2023 using standardized, repeatable survey methodologies
- Integration of multiple monitoring approaches including roving visual surveys, benthic reef assessments, and Baited Remote Underwater Video surveys (BRUVs)
- Assessment of reef habitat condition, reef fish assemblages, and the occurrence of key megafauna species across multiple sites within the MPA
- Evaluation of spatial variability and temporal patterns to identify areas of ecological stability, change, and potential management concern
- Contribution to baseline datasets supporting long term monitoring, adaptive management, and evidence based conservation planning
- Data generated through ongoing field programs designed to support collaboration with managers, researchers, and conservation practitioners

ORCA: Object Recognition and Comprehension for Archiving Marine Species
Publication Date: December, 2025
Conference: The IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), 2026
Authors: Yuk-Kwan Wong, Haixin Liang, Zeyu Ma, Yiwei Chen, Ziqiang Zheng, Rinaldi Gotama, Pascal Sebastian, Lauren D. Sparks, Sai-Kit Yeung
Institutions:
- Hong Kong University of Science and Technology
- University of Electronic Science and Technology of China
- Indo Ocean Foundation
Highlights
-
ORCA introduces a large-scale, multimodal benchmark designed specifically for marine visual understanding and biological archiving.
-
The dataset comprises 14,647 images spanning 478 marine species, with 42,217 bounding box annotations and over 22,000 expert-verified instance-level captions
-
Instance captions capture fine-grained morphological, behavioral, and habitat-related traits, enabling biologically meaningful vision–language tasks.
-
Benchmark evaluations across object detection, instance captioning, and visual grounding reveal substantial challenges posed by species diversity and morphological overlap.
-
Results demonstrate that domain-specific annotations significantly improve model performance and highlight the need for tailored datasets in marine AI applications.


A Snapshot of the Ecological Contributions of an Active Coral Restoration Effort in an Indo-Pacific Reef
Publication Date: December, 2025
Journal: Thalassas: An International Journal of Marine Science (2025)
Authors: Henriikka Malkamäki, Rinaldi Gotama, Lauren D. Sparks, Serena J. Stean, Rahmadi Prasetijo, Florian Roth, Pascal Sebastian
Institutions:
- University of Helsinki
- The University of Queensland
- Indo Ocean Foundation
- Universitas Dhyana Pura
- Indonesian Marine Education & Research Organization
- Stockholm University
DOI: doi.org/10.48550/arXiv.2512.21150oi.org/10.1007/s41208-025-01018-8
Highlights
- Ecological outcomes of an active coral restoration site were compared with adjacent natural reef and degraded rubble habitats in the Nusa Penida Marine Protected Area, Indonesia.
- The restoration site showed intermediate live coral cover and structural complexity relative to natural reef and rubble areas, indicating partial habitat recovery.
- Fish abundance and diversity were higher at the restoration site than at degraded rubble habitat, with multiple trophic guilds represented.
- Benthic recruitment patterns were broadly similar across sites, suggesting that substrate condition and post-settlement processes may limit coral recovery.
- Results indicate that active restoration can enhance habitat structure and fish assemblages, while long-term monitoring remains essential to evaluate sustained ecological recovery.



State of the Marine Ecosystem in Tanjung Bira – 2023
Publication Date: October, 2025
ISBN:978-969-9292-91-0
Authors: Qinthan Azzahra Aulia, Pascal Sebastian, Ahmad Ilham Rabbani Erawan, Lauren Dawn Sparks, Michaela Dudasova, Benjamin Graves, Jessica Graves, Rinaldi Gotama, Serena Stean, Syafyudin Yusuf
Institutions:
- Indo Ocean Foundation
- Pusat Penelitian dan Pengembangan Laut, Pesisir, dan Pulau Kecil, Universitas Hasanuddin, Sulawesi Selatan, Indonesia
Highlights
-
Results from ecological monitoring at 13 dive sites across Bira, Liukang Loe, and Kambing Island
-
Roving surveys documenting reef fish, sharks, rays, and sea turtles
-
Benthic surveys measuring coral cover, algae, sponge, and reef substrate composition
-
Water quality data including pH, salinity, dissolved oxygen, and nutrient levels
-
Findings from marine debris monitoring underwater and on beaches, with plastics as the main threat
-
Records of charismatic species mortality from bycatch and entanglement
-
Insights from the Unite Bira citizen science initiative, including manta rays, dolphins, and seasonal mola sightings
-
Comparisons between 2022 and 2023 showing trends in fish, shark, ray, and turtle populations
-
Management and research recommendations to support the establishment of a Marine Protected Area in South Sulawes




Quantifying the influence of environmental factors on elasmobranch distribution and abundance in a high-use marine protected area
Publication Date: June, 2025
Journal: Marine Environmental Research (2024),
Authors: Pascal Sebastian, Serena Jane Stean, Ahmad Ilham Rabbani Erawan, Rinaldi Gotama, I Nengah Swarya, Lauren Dawn Sparks, Rahmadi Prasetijo, Andhika Prima Prasetyo
Institutions:
- Indo Ocean Foundation
- The University of Queensland
- Dhyana Pura Universtiy
- Indonesian Marine Education & Research Organisation
- National Research and Innovation Agency
Highlights
- BRUV surveys recorded 13 elasmobranch species across Nusa Penida MPA
- Ray SPUE was higher in southern no-take zonesl shark SPUE showed no differences
- Reef, demersal, and pelagic species showed distinct habitat associations
- Elasmobranch recoery remains limited under current management capacity
- Findings support inclusive spatial planning and targeted enforcement efforts


An initial fish and megafauna biomass assessment from Tanjung Bira, a remote unprotected marine area
Publication Date: February, 2024
Journal: Regional Studies in Marine Science, Vol 72, 103447.
Authors: Pascal Sebastian, Rinaldi Gotama, Qinthan A. Aulia, Serena J. Stean, Lauren D. Sparks, Syafyudin Yusuf
Institutions:
- Indo Ocean Project, Bali, Indonesia
- Pusat Penelitian dan Pengembangan Laut, Pesisir, dan Pulau Kecil, Universitas Hasanuddin, Sulawesi Selatan, Indonesia
Highlights
- Tanjung Bira in South Sulawesi is an unprotected marine area that possesses understudied marine biodiversity.
- Roving surveys and citizen science assessed fish biomass in Tanjung Bira surroundings, including key species and megafauna.
- The offshore sites in Kambing exhibited higher richness and biomass of elasmobranchs and pelagic fish.
- The diverse habitats of Bira and Liukang Loe supported sea turtles, benthic rays, and parrotfishes.
- Spatial assemblages were influenced by site topography and oceanic factors
- All regions face threats from human impacts that could be mitigated through the implementation of protective measures.



Connecting communities to coral reefs: a socio-ecological perspective on coral restoration programs in a remote marine protected area
Publication Date: February, 2024
Journal: Journal of Coastal Conservation, vol. 28,39 (2024)
Authors: Pascal Sebastian, Lauren D. Sparks, Prisilia Resolute, Rahmadi Prasetyo
Institutions:
- Indo Ocean Project, Bali, Indonesia
- Yayasan Terra Segara Indonesia, Bali, Indonesia
- Institute of Development Studies, University of Sussex, Brighton, UK
- Faculty of Health, Science and Technology, Universitas Dhyana Pura, Bali, Indonesia
- Indonesian Marine Education & Research Organization, Bali, Indonesia
Highlights
There has been a discernible rise in coral restoration initiatives over the past few years, with Indonesia emerging as a global leader. Due to advancements in accessible methodologies, favorable public opinion, and government-backed initiatives, local communities now have more opportunities to participate in coral restoration projects. The purpose of this study is to provide a fundamental assessment of a community’s level of knowledge concerning coral restoration activities in a remote marine protected area in Indonesia.


Citizen science approach of monitoring fish and megafauna assemblages in a remote marine protected area
Publication Date: June, 2023
Journal:Regional Studies in Marine Science, p.103058.
Authors: Rinaldi Gotama, Serena J. Stean, Lauren D. Sparks, Rahmadi Prasetyo, Pascal Sebastian
Institutions:
- Indo Ocean Project, Bali, Indonesia
- Faculty of Health Sciences, Science and Technology, Dhyana Pura University, Bali, Indonesia
- Indoneisan Marine Education & Research Organization, Bali, Indonesia
Highlights
Marine Protected Areas (MPA) safeguard threatened marine ecosystems by protecting fish populations, limiting anthropogenic stressors, and providing additional livelihood for local populations. However, many MPAs do not function effectively due to lack of funding and manpower, engendering the need to find long-lasting, sustainable solutions to monitor and maintain MPA performance. In this study, we utilized citizen science involvement to survey select fish families, key fish species, and megafauna in Nusa Penida MPA, Indonesia using the roving survey method.

Coral reef carnivorous fish biomass relates to oceanographic features depending on habitat and prey preference
Publication Date: December, 2021
Journal: Marine Environmental Research, p.105504.
Authors: Greta Sartori, Michelle L. Taylor, Pascal Sebastian, Rahmadi Prasetyo
Institutions:
- University of Essex, United Kingdom
- Indo Ocean Project, Indonesia
- Dhyana Pura University, Bali, Indonesia
Highlights
Southern Indonesia is characterised by vertical mixing phenomena, which drives the presence of marine megafauna. Large predatory fish can exploit ocean currents and patterns in primary production. The magnitude of the influence of oceanography on carnivorous fish depends on their living and feeding habits. Local oceanography must be considered when studying the movements of large motile species.


Global Contributions
This section highlights research outputs from international projects where Indo Ocean plays a supporting or collaborative role. While these studies may extend beyond the direct scope of Indo Ocean’s field programs, core members of the Indo Ocean Foundation contribute as co-authors through their scientific expertise, data analysis, methodological input, or long-term research partnerships.
These collaborations reflect ongoing engagement with the wider research community and participation in larger, multi-institutional projects addressing marine ecology, conservation technology, and applied environmental science. Global Contributions demonstrate how Indo Ocean’s scientific team contributes to broader discussions and advancements in marine research while remaining grounded in field-based experience from Indonesia.
Coral reef conservation gaps under a socioeconomic perspective
Publication Date: March, 2025
Journal: Coral Reefs (2025)
Lead Authors: Nathalie Hilmi, Aurélien Calas, Emanuela Fanelli, Zaira Da Ros, Ulysse Flandrin, Eva Maire, Amal Al-Gergawi, Maryam Al-Memari, Pascal Sebastian & Massimo Ponti
ICRS
Widespread diversity deficits of coral reef sharks and rays
Publication Date: June, 2023
Journal: Science
Lead Author: Colin A. Simpfendorfer, et. al.
Global FinPrint Project
Directed conservation of the world's reef sharks and rays
Publication Date: May, 2024
Journal: Nature Ecology & Evolution
Lead Author: Jordan S. Goetze, et al.
Global FinPrint Project
Global status and conservation potential of reef sharks
Publication Date: July, 2020
Journal: Nature
Lead Author: M. Aaron MacNeil, et al.
Global FinPrint Project
Associate Publications
Associate Publications feature research outputs led by affiliated or associate researchers whose work aligns with Indo Ocean’s areas of expertise. In these studies, Indo Ocean may be consulted, acknowledged, referenced, or included through individual contributions, data context, or methodological input, rather than direct project leadership.
These publications highlight the broader research network connected to Indo Ocean and reflect the influence of shared field experience, scientific exchange, and professional collaboration across the marine research community.
*Please note that affiliated authors are underlined
MSC: A Marine Wildlife Dataset for Video Understanding with Grounded Segmentation and Clip-Level Captions
Publication Date: October, 2025
Conference: MM ’25: Proceedings of the 33rd ACM International Conference on Multimedia
Authors: Quang-Trung Truong, Yuk-Kwan Wong, Vo Hoang Kim Tuyen Dang, Rinaldi Gotama, Duc Thanh Nguyen, Sai-Kit Yeung
Prolonged instability in blast-fished rubble beds impedes coral recovery
Publication Date: August, 2025
Journal: Marine Environmental Research
Authors: Satrio Hani Samudra, Tania M. Kenyon, Cut Aja Gita Alisa, Rindah Talitha Vida, Dietriech G. Bengen, Tries B. Razak
Coral Bleaching and Recovery on Urban Reefs off Jakarta, Indonesia, During the 2023–2024 Thermal Stress Event
Publication Date: August, 2025
Journal: Diversity
Authors: Tries B. Razak, Muhammad Irhas, Laura Nikita, Rindah Talitha Vida, Sera Maserati, Cut Aja Gita Alise
Benthic communities on restored coral reefs confer equivalent aesthetic value to healthy reefs
Publication Date: July, 2025
Journal: Nature – Scientific Reports
Authors: Cut Aja GitaAlisa, Tries B. Razak, Nicolas Mouquet, Nicholas A. J.Graham, Christopher R. Hemingson, David Mouillot, Mars Coral Restoration Project monitoring team*, Beginer Subhan, Neviaty P. Zamani, Rindah TalithaVida & Timothy A. C. Lamont
Mars Coral Restoration Project
How a coastal megacity affects marine biodiversity and ecosystem function: Impacts of reduced water quality and other anthropogenic stressors
Publication Date: February, 2024
Journal: Ecological Indicators
Lead Author: Rinaldi Gotama, David M. Baker, Isis Guibert, Shelby E. McIlroy, Bayden D. Russell
University of Hong Kong




















