Cycle 1 (2011 Deadline)
Building Indonesian research capacity through genetic assessment of commercial fish species
PI: I Gusti Ngurah Kade Mahardika (Universitas Udayana)
US Partner: Kent Carpenter (Old Dominion University)
Project Dates: June 2012 - May 2014
Andrianus, the course instructor, helped participants in reading outputs resulted 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
At the beginning of this past quarter, two of Dr. Mahardika’s researchers, Aji Wahyu Anggoro and Ni Kadek Dita Cahyani, arrived at the lab of U.S. co-partner Dr. Paul Barber at UCLA. During their visits, the two received intensive training on new methods for analyzing DNA samples, including a novel technique called 2b-RAD (Restriction Site-Associated Genomic DNA). Their visit began on January 15, 2013, with Aji staying for one month and Dita for seven weeks. While they were away, Dr. Mahardika and other students and members of his research group continued their efforts to collect shark and tuna samples. In early 2013 their activities took them to North Maluku, Ambon, and West Kalimantan. By the end of the quarter, including samples gathered in 2012, the team had amassed 635 tuna samples and 572 shark samples from 20 different areas across Indonesia. About 80 percent of the samples have been analyzed, either in Dr. Mahardika’s lab or in the lab of Dr. Barber during Dita and Aji’s visits.
Beginning on April 1, 2013, Dr. Mahardika and instructors from his research group held a week-long workshop at Gadjah Mada University (GMU). Nearly 40 graduate students and faculty members from GMU and Sebelas Maret and Diponegoro universities took part. After general lectures during the opening day, activities on the remaining four days involved instruction on theory during the morning sessions and hands-on software practice in the afternoon. Later in April they are planning to visit Diponegoro University, and a summer course will be held from June through August 2013. Their fish sampling and analytical work will also proceed in the coming months.
Aji Wahyu Anggoro is finalizing the 2B-RAD sequencing method.
Though there were no major difficulties in collecting these samples,
sometimes collecting shark samples requires a personal and delicate
approach due to the sensitivities of fisherman and traders.
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