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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
Dr. Toha reports that two UNIPA undergraduate students involved in his PEER project graduated in July 2015. Other students on the team are still working in Dr. Toha’s laboratory to study Raja Ampat invertebrates using molecular approaches. In September 2015, he and his colleagues published a book entitled (in Bahasa) Hiu Paus di Taman Nasional Teluk Cenderawasih (Whale Shark in Cenderawasih Bay National Park). They have also drafted three other books on their research results and course materials entitled (1) Diversity and Conservation of Sea Urchin Tripneustes gratilla: Ecotype, Phenotype, and Genotype in Cenderawasih Bay Ecoregion, Papua-Indonesia; (2) Keragaman Genetik dan Pengelolaan Berkelanjutan Tripneustes gratilla di Ekoregion Teluk Cenderawasih; and (3) Bahasa Genetik (Genetic Language, in Bahasa). They will be submitting the first book as part of an application for a competitive grant under the NEF Publication Programme. In addition, they have published a review article entitled “Genetic aspects of the commercially used sea urchin Tripneustes gratilla” in the Journal of Biological Researches ( In May 2015, Dr. Toha and his group organized a national seminar celebrating the 20th anniversary of this journal. Another of the team’s research articles, entitled “Color diversity and distribution of sea urchin Tripneustes gratilla in Cenderawasih Bay ecoregion of Papua, Indonesia,” was accepted for publication in the Egyptian Journal of Aquatic Research (;

In early August 2015, Dr. Toha visited Jakarta to take part in a PEER Indonesian Principal Investigators’ Roundtable at the USAID Mission. As for future activities, he and his colleagues are planning a training workshop on genetics and bioinformatics analysis to be held at Brawijaya University in October. The participants will include lecturers from various Indonesian universities who are involved in the Research Group for Marine Resource Exploration and Management. As the project moves into its final phase, Dr. Toha and his team intend to publish two more research articles in international journals, with the book manuscripts to appear within the next year. On the research side, they hope to host a visiting PhD student from the University of California, San Diego, and Dr. Toha plans to attend a meeting with his U.S. colleagues at UCLA in February 2016 to discuss ARMS recovery efforts for the next year.

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)