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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

 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

As of May 2014, most of the samples required for the project have been collected and are currently undergoing advanced data and lab analysis at UCLA. Restriction-site associated DNA (RAD) data have been acquired from Next Generation sequencing technologies for Yellow Fin Tuna and Big Eye Tuna and are being analyzed. Dr. Mahardika and his group of researchers and students expect to finish data analysis and submit their results for publication by the late fall of 2014. Partial support for their successful data acquisition was also provided by a separate ongoing award supported directly by USAID. A paper entitled “DNA Barcoding reveals targeted fisheries for endangered sharks in Indonesia” has already been submitted to the journal Nature as a way to familiarizing international readers with the Indonesian shark fisheries situation. Co-authors of the publication include IBRC researchers, Paul Barber and colleagues from UCLA, and researchers from Bogor Agricultural University. On the outreach side, Dr. Mahardika and his team continue their visits to schools and education centers around Bali. More than 100 students attended a February 2014 workshop conducted by young IBRC instructors for students, teachers, and members of the public.

Two members of the PEER project team, Ni Kadek Dita Cahyani and Aji Wahyu Anggoro, visited the United States in the spring of 2014. In late April they began a short internship at National Evolutionary Synthesis Center at Duke University in North Carolina, during which they gained a substantial amount of knowledge that will allow them to arrange and prepare courses on phylogenetics in their home country. Following this two-week internship, they traveled to UCLA in early May to receive additional training at UCLA to finish their current 2B-Rad data analysis. After Aji returned home from UCLA, Dita completed a two-week metagenomics course at San Diego State University before finishing her visit.
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)
















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