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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 2016

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 of 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
In the final quarter of 2014, Dr. Toha and the project team attended two international conferences in Bogor, IPB and Denpasar, Bali. The first conference was held by Enhancing Marine Biodiversity Research in Indonesia (EMBRIO) on November 19, 2014 at the IPB International Convention Center. The team presented their paper “Close Genetic Relatedness of Whale Shark Rhincodon Typus between Cenderawasih Bay, Indonesia and Indo-Pacific Populations Revealed by Mitochondrial Cytochrom Oxidase C (subunit 1) DNA: Implications for Conservation”. The second conference was held by Science and Technology Applications in Climate Change (STACLIM) on November 17-19, 2014 at Inna Grand Bali Beach Sanur Hotel. Dr. Toha presented a paper entitled “DNA Barcoding Reveals Genetic Diversity of Giant Clams (Family Tridacnide).”

In addition to the conferences, MB-RAI held a serial training to build working groups and collaboration among scientists from multiple institutions in Indonesia. Many Indonesian scientists are interested in genetic approaches pertaining to their dissertation research, but have limited experience and basic knowledge in the use of genetic data especially the methods to analyze genetic data. To address this limitation, the team offered to train and teach participants the fundamentals of genetic data analysis with the goal of transferring knowledge to PhD students so that they can analyze their genetic data and publish articles to peer-reviewed journals.

In the coming months, the team will continue to hold training related activities that focus on the analyses of genetic data. The training will start in January and continue until participants are able to independently analyze and write about genetic data. The team also plans to finish their book manuscript and publish it on both their website and through a national publisher. This book will be written by a working group of MB-RAI. Finally the team intends to hold a national seminar at Brawijaya University in May 2015.

The project's monthly newsletter can be found at


  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)