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Partnerships for enhanced engagement in research (PEER) SCIENCE
Cycle 2 (2012 Deadline)

Connecting science and management through biodiversity research and collaboration

PI: Made Pharmawati (Universitas Udayana)
U.S. Partners: Forest Rohwer (San Diego State University) and Paul H. Barber (University of California, Los Angeles)
Project Dates: September 2013 to August 2015

Indonesian Picture A
Eka Fibayani Imaniar, a fourth-year undergraduate student, harvests seagrasses at Sindhu Beach, Bali under the supervision of I Made Pharmawati, left (Photo courtesy Dr. Pharmawati).

Indonesia has almost 80,000 km of coastline surrounded by human development; almost 50 percent of Indonesia’s 240 million inhabitants rely heavily on coastal areas for their livelihood and as source of protein. More than 60 percent of the population’s protein intake is derived from fish and other ocean-related products. Despite an increasing conservation focus throughout Indonesia, coastal environmental degradation is still growing exponentially and fisheries are still not properly managed. Addressing degradation of key coastal habitats and achieving proper fisheries management are essential in reducing pressures on marine ecosystems and threats to coral reef fish. This project has two primary focus areas. The first is coastal sea grass, a coastal ecosystem that receives little attention but is a critical nursery ground for economically important coastal fisheries. The second is humphead wrasse fisheries, the habitats of an extremely valuable reef fish that is being rapidly depleted throughout Indonesia and the Coral Triangle.
Using genetic methods, the researchers will describe sea grass genetic diversity throughout Indonesia and identify those regions of the country most susceptible to environmental threats, including climate change. The result will be useful in helping marine managers determine which areas need to be prioritized for conservation efforts. The scientists will also investigate humphead wrasse fisheries in western Indonesia, supplementing fisheries data with information on habitat community connectivity and parentage analysis that could aid the Indonesian government in effectively managing these fisheries. This information is particularly important in assuring that the fisheries activities sustainable while at the same time assuring a reliable basis for livelihoods in this area. While many universities and research institutions have started using genetics techniques, Indonesian research capacity in genetics is still relatively small. A key goal of this project is to promote genetic methods, which will provide significant training opportunities to the broader Indonesian scientific community by involving more than 10 universities across the country. By increasing their technical capabilities, Indonesian scientists will be able to increase their involvement in the global scientific community. Thus, this project should help to advance the Indonesian science community while producing scientifically reliable data that will promote the better management of marine environments by conservationists. 
Summary of Recent Activities
PI Dr. Made Pharmawati and colleagues from the Indonesian Biodiversity Research Center (IBRC), Bogor Agricultural University, and the Indonesian Research Institute collected seagrass samples at Pramuka Island and Panggang Island, Jakarta, January 18-20, 2014. Students collected additional samples from the Tunda Islands (West Java Province), Papua, Ambon, Malang (East Java Province), Kupang, Komodo Island, and Sumbawa. The DNA analyses for species barcoding of seagrass collected from Sanur and Sindhu Beach, Bali, have been completed, and analyses of the other samples are ongoing.
The project team organized a two-part workshop on Seagrass Genetic Diversity February 3-15, 2014. Fieldwork was conducted on Lembongan Island for the first four days and lab activities were carried out at IBRC, Udayana University, for the balance of the workshop. The workshop included seagrass sampling techniques, introduction of genetic laboratory work, and analysis. Comprehensive lectures about molecular techniques and ecology, seagrass bio-ecology, and phylogenetic analysis were given by Dr. Pharmawati and six colleagues: Dr. Deny Suhernawan Yusup (Udayana University), Prof. Dr. IGNK Mahardika (IBRC), Dr. Hawis Madduppa (Bogor Agricultural University), Dr. Wawan Kiswara (Indonesian Institute of Science), Ni Kadek Dita Cahyani (IBRC), and Aji Wahyu Anggoro (IBRC).

Indonesian Picture B
Dr. I Made Pharmawati, center, supervises the sampling of seagrasses at Pramuka Island (Photo courtesy Dr. Pharmawati).

Indonesian Picture C
Students during their workshop activities in Bali (Photo courtesy Dr. Pharmawati).

Future plans include seagrass sampling in Sulawesi, Sumatra, and Central Java. Genetic diversity analyses of those samples using both microsatellite DNA markers and sequencing of DNA regions are to be done in the lab. Manuscripts on Enhalus acoroides diversites from Lesser Sunda and on the DNA barcoding of seagrass species from Bali will be ready in the coming six months.
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