Skip to Main Content
Development, Security, and Cooperation (DSC) Development, Security, and Cooperation
The National Academies
The National Academies
Home About DSC Events
Quick Links

FREE Reports     

Download free PDFs of
ALL Academy Reports

All reports available on the National Academies Press (NAP) website are now offered free of charge to web visitors.

Contact us

The National Academies
500 5th St NW - KWS 502
Washington, DC 20001

Tel: (202) 334-2800
Fax: (202) 334-2139


Partnerships for enhanced engagement in research (PEER) SCIENCE
Cycle 1 (2011 Deadline)

Building Indonesian research capacity through genetic assessment of commercial fish species 

PI: I Gusti Ngurah Kade Mahardika (Universitas Udayana, Indonesian Biodiversity Research Center--IBRC)
U.S. Partner:  Kent Carpenter (Old Dominion University)
Project Dates: June 2012 - May 2014

 Indonesia Partnership Picture A
Andrianus, the course instructor, helped participants in reading outputs from software calculations.

Project Overview 

The Coral Triangle is a region of Southeast Asia defined by the presence of 500 or more coral species. This region is the global epicenter of marine biodiversity, and its importance as an economic and natural resource for the six Coral Triangle countries resulted in the 2009 Coral Triangle Initiative, which is aimed at responding to the increasing natural stresses and overexploitation of marine environments in the region. Of particular concern is the intensifying pressure on two key Indonesian fisheries, namely tuna and shark.
Realizing the importance of subsistence tuna fishing in Indonesia and the high value of tuna exports, the Indonesian government initiated conservation efforts in 2000 in cooperation with various worldwide tuna commissions, which presently regulate tuna as single fishery stock. However, recent genetic data suggests that there are multiple tuna stocks within the Indian Ocean alone. Managing tuna as a single stock fishery when there are multiple distinct subpopulations could result in inappropriate conservation planning, resulting in ineffective management actions that could result in depleted tuna stocks in the future. In addition to tuna, Indonesia has also been an area of intense shark fishing, which is driven by high demand for shark fins in markets of Hong Kong and China. To date, there are no Indonesian wide management policies to promote shark conservation, and one major obstacle is the lack of reliable data on the current status of Indonesian shark fisheries. Obtaining these data is especially challenging because most body parts by which species identification can be made have been removed at the time of landing. However, DNA barcoding can identify samples to species based only on a tissue sample, offering an alternative way to identify sharks. 
This project aims to study genetic differentiation in Big Eye Tuna (Thunnus obesus) populations across Indonesia to test whether there are different stocks requiring separate management plans. The results of this research will lead to scientific papers that could have a significant influence on how tuna resources are managed by different tuna commissions. In addition, the researchers will collect and DNA barcode shark fins from multiple areas across Indonesia, providing critical information on Indonesian shark catch data. The project will sample sharks fin from fishmongers and determine species identity via barcoding, providing detailed shark catch data across Indonesia to aid in framing of management plans for shark fisheries. In addition, the overall aim of the project is to build Indonesian research capacity in performing genetics research.
Summary of Recent Activities
During October-December 2013, Dr. Mahardika and his group continued their training activities. A shark and tuna sample collection activity was conducted November 4-8, 2013. Facilitated by University Diponegoro, the research team collaborated with Perum Perikanan Indonesia, a government-owned company that manages port and harbor for tuna landing, to gain full access for collection of fresh tuna samples in Muara Baru, Jakarta. In collaboration with Flora Fauna International, Dr. Mahardika’s group also collected tuna samples in Padang West Sumatra. As part of the shark conservation awareness program designed to facilitate direct elementary school student involvement, the team visited local schools in Bali and gave a talk and conducted interactive activities on coral reef environment and the declining shark population. NGOs and the embassy have been involved in efforts trying to raise shark conservation awareness to a wider audience using smart, interactive mechanisms. The Indonesian Biodiversity Research Center (IBRC) supported these activities by presenting their most recent findings in shark barcoding research at the @america campaign workshop, which was organized on November 19, 2013 and was attended by school teachers, senior high school students, and the general public. During November 17-21, 2013, Universitas Negeri Papua (UNIPA) held a Phylogenetic Workshop, which introduced the participants to basic methods of DNA sequence data analysis and the latest software in phylogenetic science. The one-week long workshop opened with a lecture by fellow PEER Science PI Dr. Hamid Toha, which was followed by theory classes and hands-on software practice sessions. This workshop helped UNIPA, Universitas Udayana, and IBRC develop future collaboration for strengthening the ongoing capacity-building efforts. During December 14-18, 2013, a course on Molecular Ecology and Evolution was held at Universitas Syiah Kuala, (UNSYIAH) Banda Aceh. The research team is anticipating that this training will open up more opportunities for local students to study genetics and develop further collaboration with IBRC and Universitas Udayana. In the next few months the team is planning to complete shark and tuna sample collection, finalize drafting the paper on shark barcoding, and start preparing a draft paper on tuna.
IBRC interns and staff_C1-102

C1-102 UNSYIAH students

IBRC interns and staff identifying tuna for DNA sampling
(Photo courtesy I Gusti Mahardika)

UNSYIAH students learning how to load gel into electrophoresis chamber for DNA visualization
(Photo courtesy I Gusti Mahardika)















1-102 Local school visit group picture

Local school visit: students mimicking shark fins (Photo courtesy I Gusti Mahardika)
















Back to PEER Cycle 1 Grant Recipients