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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

In the last quarter of 2017, the PI and his group continued their efforts on data analysis, focusing in particular on data generated as a result of graduate student Eka Maya Kurniasih’s three-month internship at the Smithsonian National Museum of Natural History. Specific analytical work has included sequence editing and alignment, database cross-referencing, and phylogenetic tree assembly. Due to the massive amount of data generated, more time is still needed to complete the overall process of analysis, but as of January 2018 the team had completed as many as five datasets from five sampling locations, accounting for 25% of the total data they have.

Meanwhile, the project also involves training and capacity building components. As part of their ongoing effort to train young researchers, the group continuously hosts students and researchers from other universities to work, learn, and contribute to their ongoing PEER-supported research. In the past three months, as many as five students have helped with ongoing activities like sample extraction, thermocycling sample preparation, and DNA sequence data editing. Some of the students are also using the data as a part of their mini-thesis projects required to complete their undergraduate degrees. In another recent training activity, at the request of Trunojoyo University, the PEER team provided basic genetic training to 20 students at that institution, covering various aspects such as sample maintenance, thermocycler machine operation, and data analysis. The university is located in Madura, East Java Province, and it is moving rapidly to develop its genetic expertise and lab infrastructures. In addition, one student from the university has also successfully completed a bachelor’s degree using the data generated from the project.

The plan for the first few months of 2018 includes analyzing unfinished data, as well as inviting more students to work and contribute to the project through various training programs. The team is also planning to conduct an awareness program for high school students in central Java, working in collaboration with the NGO Yayasan Taka Indonesia.

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