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Partnerships for enhanced engagement in research (PEER) SCIENCE
Cycle 1 (2011 Deadline)

Marine biodiversity of Raja Ampat Islands: The ARMS, morphology, and genetic approaches for inventorying and monitoring patterns of marine biodiversity 

PI: Abdul-Hamid Toha, State University of Papua 
U.S. Partner:  Kent Carpenter, Old Dominion University
Project Dates: June 2012 - May 2015

Project Overview

1-208 Training on fish and coral reef
Training session on identification and survey methods of fish and coral reefs, November 2013 (Photo courtesy of Dr. Toha)

Raja Ampat, a remote archipelago of small islands and cays off New Guinea, has gained international scientific attention due to its high marine biodiversity and the discovery of multiple new species of corals and fish. The high levels of marine biodiversity in this region are an important part of Indonesia's natural heritage and global biodiversity. However, our understanding the processes responsible for shaping biodiversity patterns in this region are still lacking. The goals of this project are to describe the richness, study the status, and explain the spatial and temporal patterns in the biodiversity of Raja Ampat. Interest in these goals has gained momentum due to escalating anthropogenic impacts and the need to conserve resources in important hotspots of endemic species. This study employs a novel tool, Automated Reef Monitoring Structures (ARMS), to monitor marine biodiversity gradients across the Raja Ampat Islands in a standardized, highly efficient, and statistically robust way. Analyses based on DNA barcoding and metagenomics will show (1) whether visual surveys of conspicuous groups like fish and corals (the subjects of traditional surveys) can reliably capture biodiversity patterns for inconspicuous groups (smaller invertebrates, algae, and microbes) that actually comprise the vast majority of marine biodiversity, and (2) whether marine biodiversity varies predictably as a function of conservation management strategy (e.g., Marine Protected Areas).
The results of the project should dramatically improve our understanding of the contemporary processes shaping the distribution of marine biodiversity in the Raja Ampat, providing a scientific foundation to support the sustainability goals of the Papua and Indonesia in general. To reach these goals, the study builds on strong partnerships with UCLA developed as part of a previous NSF PIRE award. This project will also build linkages with Brawijaya University, the Indonesian Biodiversity Research Center, the Indonesian Institute of Science, and conservation organizations to provide the intellectual and physical resources to achieve the research aims as well as ensure that these results support conservation planning and the sustainability goals of the Coral Triangle Initiative.
Summary of Recent Activities
Dr.Toha and his team continued their research efforts during the last quarter of 2013. Some marine invertebrates collected from Raja Ampat and Cenderawasih Bay were identified using molecular techniques at the State University of Papua (UNIPA) Genetic Lab, and the other six ARMS were deployed in the Cenderawasih Bay. Publication and research results dissemination efforts have been ongoing. Dr. Toha continues publication of his group’s monthly newsletter “Raja Ampat Biodiversity Conservation” ( The team’s research article, “Spatial Distribution of Tripneustes gratilla on Ambon Island,” was published in the Journal of Tropical Life Science, and four other fast track articles have been identified for Bulletin of Marine Science in collaboration with U.S. partner Paul H. Barber. During this period, the team received a new grant funded by the National Geographic in collaboration with the Smithsonian Institution of Panama; Laboratorium of Marine Biotechnology, Institute of Bioscience, University Putra Malaysia, Marine Science Institute, University of the Phillippines; and University of Guam for a proposal titled “Phylogeographic Discontinuities between Indian Ocean and Western Pacific Population of Marine Invertebrates.  
In October 2013, the team hosted an open lab for junior and senior high school students, and four additional UNIPA undergraduates were hired for field work in Raja Ampat and lab work in Manokwari. Dr. Toha’s research team conducted several training sessions during the past quarter as well. During October 18-19, 2013, a training session on proposal writing on genetic methods and approaches was held in collaboration with the Students’ Executive Unit of UNIPA and was attended by junior and senior high school students and teachers. During November 15-16, 2013, the research team held a training session on identification and survey methods of fish and coral reefs. The event, which was organized in collaboration with DKP, MB-RAI, and the Students' Group of UNIPA, was attended by staff of the Marine and Fishery Ministry as well as UNIPA students. November 18-23, 2013, another training session on phylogenetic trees was organized in collaboration with the Indonesian Biodiversity Research Center Bali and MB-RAI of UNIPA and was attended by students and faculty of various departments in UNIPA. A bio reef monitoring event was organized on December 19, 2013. This follow-up event built on the ongoing work on artificial reefs that had been deployed in the Lemon area a couple of weeks prior and was attended by student groups from UNIPA departments of Fisheries, Marine Sciences, and Economy. During the next six months, the research team is planning to conduct more field work in Raja Ampat. A seminar on their research results will be presented in late February or early March 2014, followed by a general lecture on biodiversity research and its results. The laboratory work is expected to continue during the upcoming months as well.  

  Indonesia Photo 1

  Indonesia Photo 2

Coral rehabilitation in Lemon Island, September 2013 (Photo courtesy of Dr.Toha).Reed media being readied for deployment at Lemon Island, September 2013
(Photo courtesy of Dr.Toha).
1-205 Toha Deployment ARMSARMS at Cenderawasih Bay
Deployment of ARMS at the bottom of the sea (Photo courtesy of Dr. Toha) ARMS at Cenderawasih (Photo courtesy of Dr. Toha)