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Partnerships for enhanced engagement in research (PEER)
Cycle 4 (2015 Deadline)

One Fits All: developing decapods biodiversity research for education, conservation and research benefits

PI: Ambariyanto (,, Indonesian Biodiversity Research Center and Diponegoro University
U.S. Partner: Christopher Meyer, Smithsonian National Museum of Natural History
Project Dates: January 2016 - December 2018

Project Overview

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Photos courtesy of Andrianus Sembiring

Biodiversity is defined as the variety of organisms within a given area. The Convention on Biological Diversity indicates that the richer the diversity of life, the greater the opportunity for economic growth. However, despite having the highest marine biodiversity in the world, Indonesia frequently faces significant economic challenges and poor development due to unsustainable exploitation of their natural resources. Efforts to quantify biodiversity have traditionally relied on easily observed parameters like coral cover and fish biomass, while smaller invertebrates that significantly contribute to reef diversity are often ignored due to difficulties in identification, potentially resulting in inaccurate assessment of biodiversity and reef health. Although Indonesia is home to seas featuring more than half of all known marine species, not all taxa of these species have been assessed and quantified, and local expertise to support biodiversity research is small in relation to Indonesia’s size and biodiversity. This project focuses on quantifying the biodiversity of decapods (an order of crustaceans that includes crayfish, crabs, lobsters, prawns, and shrimp) across the Indonesia while also nurturing international collaboration and improving local taxonomic expertise. The research team will implement an integrated research and education program using autonomous reef monitoring structure (ARMS) and dead coral heads (DCH) as artificial and natural collection platforms for reef-associated decapods. Decapod diversity will then be assessed using both traditional taxonomy and cutting-edge genetic approaches. The results of this project will provide the the first insights into the magnitude of marine biodiversity in one of the most diverse groups of marine metazoans in Indonesia, while also assessing how this diversity is distributed throughout the archipelago. Results will help inform local researchers and managers regarding health of reef ecosystems across Indonesia, facilitating the development of conservation strategies based on current biodiversity assessments.

The data collected will be helpful in designing management strategies to preserve biodiversity hotspots within Indonesia and in focusing conservation efforts on particularly threatened areas. Trainings and workshops organized through this project will increase local capacity to develop high quality biodiversity research and nurture the growth of local taxonomists. In addition, smartphone applications ( and online database produced through this project will, for the first time, make biodiversity research accessible to people beyond the scientific community, which is critical for mobilizing grassroots support for marine conservation. Through joint research and educational programs with the Smithsonian Institution, the team will train dozens of Indonesian students and researchers through experiential learning in research-intensive courses. By using research as a platform for education, the project will simultaneously improve understanding of Indonesian marine biodiversity and develop the next generation of biodiversity scientists.

Summary of Recent Activities

During the third quarter of 2017, this PEER team was busy with several activities in the field and back in the lab. They conducted dead coral head sampling and genetic training at Bunaken National Park, Manado, North Sulawesi, July 13-15. The 21 student participants from the Department of Marine and Fisheries at Samratulangi University (UNSRAT) successfully collected almost 300 samples from three different locations within the national park. Along with the field work, the team also presented their methods, recent findings, and future project plans to National Park staff and rangers, allowing local stakeholders to contribute and support the project. A similar training program was conducted July 19-21 at Bontang East, Kalimantan, in collaboration with Faculty of Marine and Fisheries Sciences at Mulawarman University and the Kutai Timur Fisheries College. This workshop involved 17 students and 5 faculty staff, with all being highly involved in the activities, including diving, species morphosorting and identification, and sample vouchering for DNA analysis. The Departemen Kelautan Perikanan Bontang, the local government regulator for fisheries activities, also supported the research effort by providing facilities and supplies during the field work. The high sedimentation resulting from intense local oil industry activities and the shipping business have affected coral reef ecosystems in this area, including the decapods collected during the expedition, but many of them are unique and rarely found in other areas in Indonesia. The remoteness of the area also added extra challenges to the sample collection. August 28-30, the PEER team led a workshop on data analysis using R and the use of Next Generation Sequencing as a powerful genetic technique. Held at Diponegoro University in Semarang, the workshop involved 15 students and 2 faculty staff and was taught by Aji Wahyu Anggoro and Ni Kadek Dita Cahyani, two Indonesian PhD students currently based at the Department of Ecology and Evolutionary Biology at UCLA. Although R language is widely used in many other countries, its use is relatively rare in Indonesian universities, primarily due to lack of computational expertise and dependency on available and readily used statistical software. This workshop opened new perspectives for the students and faculty staff on a fast and powerful way of analyzing research data. Besides R, the participants were also introduced to the concept of Next Generation Sequencing, a new high throughput sequencing method used and developed in the United States and many other countries.

As a part of the PEER collaboration, Eka Maya Kurniasih started her short-term residency at the Smithsonian Institution in July 2017 as an intern under the supervision of U.S. partner Dr. Christopher Meyer. Eka’s main task was to finish up the laboratory part of DNA analysis of samples the team had collected and learn how to do DNA data analysis. Eka successfully completed her visit and returned home on October 16. Now that she is back home, she is in a good position to be able to share her new knowledge and skills with other researchers and students. Besides sending Eka as an intern for training abroad, the project also involves opportunities for other Indonesian students to serve as interns to learn new lab and data analysis skills. During this past quarter, two student interns at Diponegoro University had the chance to be involved in both the daily lab activities and field sampling expeditions.

In the coming months, the team will focus on analyzing the data Eka brought back from her visit to the Smithsonian. They also plan to conduct a training workshop at Trunojoyo University in Madura, East Timur.

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