Project 1-205 Indonesia

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 Indonesian 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. Dr. Toha and his fellow researchers on this project aimed 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 employed 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. Researched undertook analyses based on DNA barcoding and metagenomics to show whether visual surveys of conspicuous groups like fish and corals (the subjects of traditional surveys) can reliably capture biodiversity patterns for the inconspicuous groups (smaller invertebrates, algae, and microbes) that actually comprise the vast majority of marine biodiversity. They also sought to understand whether marine biodiversity varies predictably as a function of conservation management strategy (e.g., Marine Protected Areas).

The goal of the project was to 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 Papua and Indonesia in general. The study built on strong partnerships with UCLA developed as part of a previous National Science Foundation (NSF) Partnerships for International Research and Education (PIRE) award.

Final Summary of Project Activities

Researchers deployed 48 ARMS, collecting more than 200 individuals of 63 invertebrate species and published data on these specimens on their website. The PEER team presented their work at national and international conferences, published regular newsletters to share results, and have published more than 20 academic papers and a book, Diversity and Conservation of Sea Urchin.

The PI 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, provided training in proposal writing for high school students to apply to the Indonesian Institute of Sciences, and shared their results with all lecturers within the University of Papua.

The PEER project supported students’ thesis research and the PI’s lab hosted undergraduates and fishery students to study laboratory work practices and genetic approaches. Indonesia’s State Ministry of Research and Technology awarded the PEER team an additional research grant to continue their work. The researchers are also part of a consortium that won a new NSF PIRE award to continue collaborative biodiversity research across Indonesia.

The project's monthly newsletter can be found at www.ibcraja4.org.


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).

Deployment of ARMS at the bottom of the sea (Photo courtesy of Dr. Toha)	ARMS at Cenderawasih (Photo courtesy of Dr. Toha)

Publications

A.H.A. Toha, N. Widodo, B. Subhan, R. Himawan, C. Tania, B.A. Noor, B.S. Stewart, and H.H. Madduppa. 2016. Close genetic relatedness of whale sharks, Rhincodon typhus, in the Indo-Pacific region. AACL Bioflux 9(3): 458-564. http://www.bioflux.com.ro/docs/2016.458-465.pdf

D. Saleky, I. Setyobudiandi, A.H.A. Toha, M. Takdir, and H. Madduppa. 2016. Length-weight relationship and population genetic of two marine gastropods species (Turbinidae: Turbo sparverius and Turbo bruneus) in the Bird Head’s Seascape Papua, Indonesia. Biodiversitas 17(1): 208-217. https://doi.org/10.13057/biodiv/d170130

C.J. Starger, M.V. Erdmann, A.H.A. Toha, A.C. Baker, and P.H. Barber. 2015. Strong genetic structure among coral populations within a conservation priority region, the Bird’s Head Seascape (Papua, Indonesia). Frontiers of Biogeography 7(3): 91-106. https://doi.org/10.21425/F5FBG22326

A.H.A. Toha, B. Sutiman, Sumitro, Widodo, and L. Hakim. 2015. Color diversity and distribution of Sea Urchin Tripneustes gratilla in Cenderawasih Bay ecoregion of Papua, Indonesia. The Egyptian Journal of Aquatic Research 41(3): 273-278. https://doi.org/10.1016/j.ejar.2015.05.001

D.A. Willette, A.R. Iñiguez, E.K. Kupriyanova, C.J. Starger, T. Varman, A.H. Toha, B.A. Maralit, and P.H. Barber. 2015. Christmas tree worms of Indo-Pacific coral reefs: untangling the Spirobranchus corniculatus (Grube, 1862) complex. Coral Reefs 34(3): 899-904. https://ui.adsabs.harvard.edu/link_gateway/2015CorRe..34..899W/doi:10.1007/s00338-015-1294-y

A.H.A. Toha, R. Binur, Suhaemi, Lutfi, L. Hakin, N. Widodo, and S.B. Sumitro. 2014. Genetic aspects of the commercially used sea urchin Tripneustes gratilla. Journal of Biological Researches 20(2): 12-17.

P.H. Barber, M.C.A. Ablan-Lagman, Ambariyanto, R.G.S. Berlinck, D. Dahyani, E.D. Crandall, R. Ravago-Gotanco, M.A. Juinio-Meñez, I.G.N. Mahardika, K. Shanker, C.J. Starger, A.H.A. Toha, A.W. Anggoro, and D.A. Willette. 2014. Advancing biodiversity research in developing countries: the need for changing paradigms. Bulletin of Marine Science 90(1): 187– 210. https://doi.org/10.5343/bms.2012.1108

A.M. Jackson, Ambariyanto, M.V. Erdmann, A.H.A. Toha, L.A. Stevens, and P.H. Barber. 2014. Phylogeography of commercial tuna and mackerel in the Indonesian Archipelago. Bulletin of Marine Science 90(1): 471–492.
http://dx.doi.org/10.5343/bms.2012.1097

T.S. DeBoer, M.R.A. Naguit, M.V. Erdmann, M.C. Ablan-Lagman, Ambariyanto, K.E. Carpenter, A.H.A. Toha, and P.H. Barber. 2014. Concordant phylogenetic patterns inferred from mitochondrial and microsatellite DNA in the giant clam, Tridacna crocea. Bulletin of Marine Science 90(1):301–329. https://doi.org/10.5343/bms.2013.1002

T.S. DeBoer, M.R.A. Naguit, M.V. Erdmann, M.C. Ablan-Lagman, Ambariyanto, K.E. Carpenter, A.H.A. Toha, and P.H. Barber. 2014. Concordance between phylogeographic and biogeographic boundaries in the Coral Triangle: conservation implications based on comparative analyses of multiple giant clam species. Bulletin of Marine Science 90(1):277–300. https://doi.org/10.5343/bms.2013.1003

N. Sahriyani, Widodo, and A.H.A. Toha. 2014. Amplifikasi Gen Coi (Cytochrome C Oxidase Subunit I) pada Holothuroidea yang dikoleksi dari Kepulauan Raja Ampat. Jurnal Biotropika 2 (4): 232-234. https://biotropika.ub.ac.id/index.php/biotropika/article/view/297

R.D. Kurniasari, A. Soewondo, and A.H. Toha. 2014. Identifikasi Synaptula (Echinodermata: Holothuroidea) Raja Ampat berdasarkan gen COI. Jurnal Biotropika 2 (5): 265-268. https://biotropika.ub.ac.id/index.php/biotropika/article/view/312

F.E. Aprilia, A. Soewondo, Widodo, and A.H.A. Toha. 2014. Amplifikasi Gen COI dan 16s rRNA dari Invertebrata Laut Plakobranchus ocellatus. Jurnal Biotropika 2 (5):276-278. https://biotropika.ub.ac.id/index.php/biotropika/article/view/301

Abdul Hamid A. Toha, Sutiman B. Sumitro, and Luchman Hakim. 2013. Keanekaragaman dan Konservasi Bulu Babi [Diversity and Conservation of Sea Urchin]. ISBN 978-602-7611-08-5. Available for download at https://ibcraja4.org/page/read/book_of_seaurchin/

V.B. Silahooy, A.H. Toha, L. Hakim, and N. Widodo. 2013. Spatial distribution of Tripneustes gratilla on Ambon Island. The Journal of Tropical Life Science 3(3): 177-181. https://jtrolis.ub.ac.id/index.php/jtrolis/article/download/122/148

A.H.A. Toha, S.B. Sumitro, L. Hakim, and Widodo. 2012. Kondisi habitat bulu babi Tripneustes gratilla (Linnaeus, 1758). Berkala Penelitian Hayati 17(2): 139-145. https://doi.org/10.23869/205

A.H.A. Toha, A. Permana, S.B. Sumitro, L. Hakim, and Widodo. 2012. Penentuan jenis kelamin bulu babi Tripneustes gratilla secara morfologi. Berkala Penelitian Hayati 17(2): 211-215. https://doi.org/10.23869/224

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