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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 - November 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
On October 15, 2015, Dr. Toha and his colleagues presented a workshop entitled Genetic Analysis and Bioinformatics for the research group on marine resource exploration and management of fisheries and marine sciences of Brawijaya University. They also held several training sessions on genetic data analysis for PhD students from Brawijaya and the State University of Malang in November 2015. On November 7, the team attended a national seminar entitled “Perspectives on the Newest Biological Research at Brawijaya University,” during which made a presentation on the genetic diversity and distribution of sea urchin Tripnesutes gratilla in the Cenderawasih Bay Ecoregion. They took part in a discussion on “Indonesia, the hotspot of marine biodiversity in the Coral Triangle Area” at @america in Jakarta on November 17, 2015, organized by the U.S Embassy and USAID/Indonesia.

In recent months the researchers have published two papers related to their project. The first, entitled “Strong genetic structure among coral populations within a conservation priority region, the Bird’s Head Seascape (Papua, Indonesia),” was published by Frontiers of Biogeography, Vol. 7, No. 3 (October 2015) ( item/6ds1g7bt). The second research article, entitled “Length-weight relationship and population genetics of two marine gastropod species (Turbinidae: Turbo sparverius and Turbo bruneus) in the Bird’s Head Seascape, Papua, Indonesia,” appeared in the April 1, 2016, edition of Biodiversitas Journal (

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)