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
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
Training activities were a key focus of the fifth quarter of this project (July – September 2013). In collaboration with trainers from the Smithsonian, Dr. Mahardika and his group organized a two-week Biodiversity Inventory Training course beginning July 1, 2013. This course was aimed at introducing participants to various marine biodiversity sampling methods, including a technique for coral head biodiversity sampling. This technique allows participants to collect a huge amount of marine animals (mostly decapods and crustaceans) relatively quickly and simply. A head of dead Pocillopora verrucosa coral approximately the size of a five-gallon bucket was broken apart to expel animals living inside it. The animals were then identified to the nearest known taxonomic level, photographed, and subsampled for genetic analysis. All participants (including 9 Indonesians and 14 Americans) were exposed to and trained on all steps of this process as part of their course activities. Besides the hands-on lab work during the day, nightly lectures were presented to expose students to the current state of knowledge in marine biodiversity science. Also this past summer, IBRC researcher Ni Kadek Dita Cahyani attended a 10-day training course on Molecular Evolution at the Marine Biological Laboratory at Woods Hole July 21-31. On her way home, Ms. Cahyani stopped off in Washington, DC, to present a seminar on the PEER Science project at USAID headquarters. The final training event of the summer was a two-week phylogenetic analysis course held at IBRC August 19-30. This intensive course covered phylogenetic systematics and phylogenetic tree construction methods. The 17 participants were taught basic technique for analyzing sequence data and exposed to a variety of underlying theories. Students tried a variety of software packages and built phylogenetic trees from their own independent research during the first week and received additional training during the second week.
On the research side of the project, members of Dr. Mahardika’s team continued collecting shark and tuna samples for DNA analysis. A first publication on the shark portion of the research has been submitted to the journal Nature and is expected to appear in print near the end of 2013. Two more publications are to be submitted in early 2014. Meanwhile, project participants are organizing workshops involving the easternmost (Universitas Negeri Papua) and westernmost universities (Universitas Syiah Kuala, Banda Aceh) in Indonesia. The workshops, which will feature an introduction to molecular ecology and to phylogenetic analysis, are planned for mid-November and early December.
Smithsonian postdoc Fransesca Leasi explains how to preserve
marine animals. (Photo courtesy I Gusti Mahardika).
Students in the project gather specimens
from dead coral head. (Photo courtesy I Gusti Mahardika).
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