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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 -  December 2014

Project Overview 

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

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

Dr. Mahardika reports that he and his group have completed all planned research, workshops, and training events as of the end date of their project on December 31, 2014. He singles out as a paramount milestone the publication of their shark research results in an international publication, Fisheries Research Volume 164, April 2015, pages 130–134, doi:10.1016/j.fishres.2014.11.003. The publication is extremely important for shark conservation strategies in Indonesia, bringing insight into what species are still targeted by fishermen and what provinces are the major areas for shark fisheries, as well as their conservation status. Along with the results reported in the teams other publications produced on this project (one international and four in local journals), this information should help government officials to design strategies and define areas needing more attention in terms of conservation efforts. Another major achievement is the success the team has had in building long-lasting collaboration with major institutions working in tuna conservation, including LOKA TUNA Indonesia (LTI) and Yayasan Masyarakat dan Perikanan Tuna Indonesia (YMDPI). LTI has agreed to extend an existing memorandum of understanding with Dr. Mahardika’s center for another two years to focus more on studying population genetics of Southern Pacific Bluefin Tuna.

On the capacity building side, this group also successfully organized summer courses at Karimunjawa National Park, Jepara, Central Java. The courses focused on studying marine decapod biodiversity by exposing the participants to dead coral head methods, a rapid and reliable means of sample collection. Following fieldwork, the students also took part in an intensive one-week molecular ecology class completed with lab work experience. One contributing factor hampering the development of marine education and research in Indonesia is the limited opportunities for students to do field work or experience intensive marine ecosystems courses. Through this PEER program, Dr. Mahardika and his team enlightened teachers, faculty members, and students with real life examples of marine animals and showed them the uniqueness of each habitat. The workshops also provided a set of research methods that could provide quick estimate of unseen biodiversity in coral reef ecosystem. The project has also been successful in promoting phylogenetic science to wider research networks in Indonesia. During the span of this two-year project, the center has successfully arranged seven phylogenetic workshops. Despite still being limited in number, the workshops have been successful in laying the groundwork of basic phylogenetic science in Indonesia while also promoting the importance of the method for marine science and biodiversity studies. Facilitated by this project, the center has also successfully assisted more than a dozen undergraduate students to complete internships in various research projects and provided advanced training opportunities (including in the United States) for three Master’s students.
IBRC interns and staff_C1-102

C1-102 UNSYIAH students

1-102 Local school visit group picture

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)

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

With regard to the policy relevance of the project, USAID Indonesia through its IMACS program has supported various species conservation program in Indonesia, including protecting sharks and manta rays from unsustainable and sporadic fishing. The PEER team’s newest international publication provides important information on the status of shark fisheries in Indonesia; hence, IMACS could adjust and find the best way to improve its current and conservation strategy in Indonesia. This research has also been disseminated to USAID Indonesia’s marine specialist, and Dr. Mahardika expects that other conservation partners could also adapt and use this information for future conservation planning. Through its Ministry of Marine and Fisheries (MMF), the Indonesian Government has also devoted a significant amount of effort to protecting sharks from unsustainable fisheries and over exploitation. The team’s research results could provide better understanding on where to concentrate conservation efforts in Indonesia. Dr. Mahardika and his colleagues have developed initial communications with the ministry to use their results as policy input.

During its final months with PEER support, the center successfully secured a $250,000 grant from the Alice Tyler Perpetual Trust. This funding represents a continuation of the first grant secured in March 2014 and is designated to build a marine research station in Pemuteran, Western Bali, which will be used to develop and facilitate interest in marine science research and education. 

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