Marine Biodiversity of Raja Ampat Islands: the ARMS, Morphology, and Genetic Approaches for Inventorying and Monitoring Patterns of Marine Biodiversity

PEER Science Annual Report 1st June 2012- 30th April 2013

Marine Biodiversity of Raja Ampat Islands: the ARMS, Morphology, and Genetic approaches for inventorying and monitoring patterns of marine biodiversity

Project Title:

Marine Biodiversity of Raja Ampat Islands: the ARMS, Morphology, and Genetic approaches for inventorying and monitoring patterns of marine biodiversity

Principal Investigator(s): Institution(s): Abdul Hamid Toha State University of Papua

Reporting Period: June 2012-April 2013

Summary of Activities: Overview: Outcomes from this project include establishing the Genetics Laboratory of UNIPA as a site for a field station, the digitization of voucher specimens, a project web, and for databases of marine biodiversity. Other outcomes from this research also include a manuscript of Conservation Genetics and a newsletter. During the first period, research and laboratory equipment have been prepared and some field activities have been conducted. In Educational activities, we already held four workshops or training from June 1, 2012 through April 30, 2013 include the following: 1) Biodiversity, Molecular Ecology and Genetic Conservation, 2) Inventorying Marine Invertebrates and Microbes of Raja Ampat Islands, 3) Molecular Genetic Basics, and 4) Conservation Genetics. These courses had a total 129 participants from some institutions in Manokwari. We also support student’s field work practice in Raja Ampat along two months. In Research, we already collected invertebrate specimens included water sample in order to collect bacteria samples. In total, there are 33 species invertebrate that identified in this period. Among them, two species has already analyzed and in preparation of writing article for publication. The researches affair had a total 23 participants from State University of Papua and Brawijaya University. Data base of these specimens have already prepared and will be published in our website. Research related to the one species of invertebrate which was T. gratilla from Raja Ampat has been done by graduate student in Brawjaya University. We also got a new research grant from State Ministry of Research and Technology of the Republic of Indonesia. Beside that we are part of a consortium who won new NSF PIRE award to continue our collaborative biodiversity research in whole Indonesia. In Publications, we have already published 11 monthly Newsletters “Konservasi Biodiversitas Raja4” or “Raja Ampat Biodiversity Conservation” from June 2012 through April 2013. We also have a website in www.ibcraja4.org to socialize this project and other things related by conservations, biodiversity, Raja Ampat, laboratory and field methods. Book manuscript of “Diversity and Conservation of Sea Urchin” was in press for publication. Two articles have published in national journal. Beside that we were also preparing two articles else to published. We also socialized PEER sciences to all lecturers in UNIPA. The publications affair had a total 17 participants from State University of Papua and Brawijaya University. 2

Events: We held four workshops or training from June 1, 2012 through April 30, 2013. They are 1) training about Biodiversity, Molecular Ecology and Genetic Conservation on September, 2012 taught by Prof. Sutiman B. Sumitro, Luchman Hakim, Ph.D and Hamid Toha, 2) workshop the Field Work Practice for Inventorying Marine Invertebrates and Microbes of Raja Ampat Islands on December, 2012 taught by Hamid Toha and M. Dailami, 3) training Molecular Genetic Basics (DNA technology for Conservation) taught by Hamid Toha and Kuncoro, and 4) general lectures of Conservation Genetics on April, 2013 taught by Hamid Toha. These courses had a total 129 participants from different institutions in and outside UNIPA. We also support undergraduate student’s field work practice in Raja Ampat along two months. This field work had a total 10 participants from UNIPA. As a way of research building capacity for young faculty and students, our project had facilitated the faculty and students to join in research at Raja Ampat. Six participants are now conducting research with focus on invertebrates of Raja Ampat. In addition, we support undergraduate, master and doctoral students in research for their thesis and dissertation. These events had a total 7 participants from UNIPA and UB. Below is the detail of the workshops.

Number of Number of Number of exchange workshops conferences visits with U.S. partners 4 0 0

Date of Location of Title of workshop or Number of Number of workshop, workshop, conference or name of female male conference, or conference, visitor participants participants visit or visit April 11-12, UNIPA, Training of Molecular 9 8 2013 Manokwari Genetic Basics UNIPA, General Lecture of April 11, 2013 28 31 Manokwari Conservation Genetics UNIPA and March- July Support in research for Brawijaya 3 4 2013 thesis and dissertation University Dec, 2012-Peb Raja Ampat Field Work Practice 8 2 2013 Call for proposal Dec 2012- UNIPA (Capacity building in 5 1 March 2013 research) Inventory of Raja Ampat’s December 19- UNIPA, Invertebrates Biodiversity; 9 13 20, 2012 Manokwari Work Field Practice Workshop Biodiversity, Molecular September 10- UNIPA, Ecology and Genetic 15 16 12, 2012 Manokwari Conservation Workshop 3

Educational Impacts:

Researchers, students, and faculty from different backgrounds and institutions in and outside UNIPA get benefit from our project through three kinds of the activities (training and teaching, research, and publication). Educational curricula have been developed especially for Genetic subject in Fishery Department. We also add a practicum in existing subject course in Molecular Biology and Genetics for multi faculties in UNIPA. Formal educational activities included 4 new courses. We also had facilitated the faculty and student to join research as a way of research building capacity for young faculty and students in UNIPA and UB. Our project also supported undergraduate, master and doctoral students in research for their thesis and dissertation.

Educational Status Number of Number of Females Males Undergraduate (BS) 5 10 Masters Student (MS or M Phil) 0 1 Doctoral Student (PhD) 1 0 Postdoctoral scholars 0 0 Other junior collaborators 5 1 Laboratory Technicians 2 3 Other participant involved in our project was detailed in Supplementary information.

Infrastructure Development:

In this period, we got a new research grant from State Ministry of Research and Technology of the Republic of Indonesia. The title of research is ”Seleksi dan Domestikasi Kandidat Indukan Udang Galah Macrobrachium rosenbergii (de Man, 1879) asal Papua berdasarkan Marka Genetik untuk Pengembangan Indukan Baru”. This research began on January to December 2013. The team of this research is Robi Binur (Head, UNIPA), Adi Pancoro (Researcher, Bandung Institute of Technology) and Abdul Hamid Toha (Researcher, UNIPA). Beside that we are part of a consortium who won new NSF PIRE award to continue our collaborative biodiversity research in whole Indonesia. The proposal “PIRE: Assembly of Marine Biodiversity Along Geographic and Anthropogenic Stress Gradients” was funded by the U.S. National Science Foundation. The grant funding period will commence on January 1, 2013. Duration program is five years from 2013-2015. In this period we have already bought a camera for documentation, laptop for server database and website. We also purchased new micropipettes for training and teaching. We used these equipments when the training was running. The equipments also used in research of student and faculty who wants to finishing their study and conduct individual research.

Below is a list the number of new grants received as a result of PEER Science funding.

International Local (in PI’s country) Number of research grants 1 1 received Number of patent 0 0 applications submitted

We have not yet a patent applications until now. However, we are publishing our book manuscript that will get a copyright. The manuscript was not fully funded by PEER but PEER have already made this happen as soon as possible.

Publications:

We already published a monthly newsletter. Until now, we have published eleven editions of newsletters from June 2012-April 2013. For socializing of our project with the program, we also launched a website at www.ibcraja4.org (look at Supplementary Information). We are also preparing manuscript three books and three articles that related to our project but not include in our proposal before. Books 1. Toha, A.H.A. Molecular Genetics (Revision Edition). For submission to AlfaBeta Publisher, Bandung. (in Bahasa) 2. Toha, A.H.A., Sumitro, S.B., Hakim, L., Widodo. “Diversity and Conservation of Sea Urchin”. For submission to publisher. (in review) 3. Toha, A.H.A., Mahardika, A.P.W. “Sea Urchin Tripneustes gratilla”. For submission to publisher. (in Bahasa) Articles 4. Toha, A.H.A, Sumitro, S.B., Hakim, L., Widodo. Genetic connectivity of sea urchin Tripneustes gratilla in Cenderawasih Bay, Papua-Indonesia. For submission to International journal (in review). 5. Toha, A.H.A., Sumitro, S.B. L. Hakim., Widodo. 2012. Kondisi habitat bulu babi Tripneustes gratilla (Linnaeus, 1758). Berk. Penel. Hayati 17 (2): 139-145. 6. Toha, A.H.A., Permana, A., Sumitro, S.B. L. Hakim., Widodo. 2012. Penentuan jenis kelamin bulu babi Tripneustes gratilla secara morfologi. Berk. Penel. Hayati 17 (2): 211-215.

Local Number of joint Type of Technical International publications publications Publication Publications (in PEER PI’s with U.S. PEER country only) partner Journal articles 1 2 Proceedings 1 Technical reports Books 3 Book chapters Book editor

We are also preparing one paper about spiny lobster Panulirus versicolor for national journal entitled: Genetic structure of Lobster Panulirus versicolor in Raja Ampat waters.

Technical Research Presentations:

We attended four conferences and seminars of national or international in June to September 2012. First, we attended a national seminar (4th Biodiversity National Seminar) in Airlangga University at Surabaya, East Java on September 15, 2012. We presented a paper “Genetic diversity of Sea Urchin Tripneustes gratilla (Linnaeus 1758) in Papua”. Second, we presented a paper “Genetic diversity pattern of Tripneustes gratilla in Indonesia”. The paper was presented at Indonesian Biodiversity Research Center Synthesis Meetng in Udayana University at Denpasar on Augusts 7, 2012. Third, we presented Marine protected areas network, a mtDNA studies for conservation planning: A case study of Tripneustes gratilla. This paper was presented at the 3rd International conference on global resources conservation in Brawijaya University at Malang on July 7, 2012. Lastly, we present Comparative genetic diversity pattern of Tripneustes gratilla in the Indonesian Archipelago and Indo-Pacific at Coral Triangle Partnerships for International Research and Education synthesis meeting in Manila (Philippines) on June 16, 2012. I also presented a paper “Education and Research for Biodiversity in Raja Ampat and Indonesia”. Short Review: PEER, PIRE, IBRC, NESCent, etc. in State University of Papua on April 12, 2013. This seminar was done for monitoring and evaluation our project for full year.

Number of technical research presentations made 5

Linkages and Potential Development Impacts:

We attended a PEER Financial Workshop that held by USAID in Jakarta on November 20-21, 2012. In this workshop, we shared our activities and financial management with other institutions that invited by USAID. We also get important things from this workshop in financial management. When we held the training in UNIPA, we have any linkages developed with different backgrounds and institutions outside UNIPA. They are from government agencies in our country (Center of Research and Development of Agricultural Papua Barat, Center of Research and Development of Forestry Province Papua Barat, National Park of Teluk Cenderawasih agency, and Ministry of Marine and Fishery Province Papua Barat), from private companies (STKIP Muhammadiyah, local private university in Manokwari), and Community groups or nongovernmental organizations (Conservation International-Indonesia). We intend to expand this work in the future especially in working of biodiversity etc. Our project was visited by IBTC team (International Business and Technical Consultant Inc.) for monitoring and evaluating the Indonesian Biodiversity Research Center (IBRC) on November 2-3, 2012. Besides that team of Directorate of Bilateral Foreign Funding, National Development Planning Agency (BAPPENAS) of Republic of Indonesia was also visit us on December 10, 2012. Although they weren’t coming solely for PEER project, however, they also got information about PEER project from us. These important for us and the project to anticipate what will happen in the future. 6

This project was also result in significant benefits for national co-operation and collaboration with Brawijaya University, as an state institution poised to be a resource for scientific collaboration in Indonesia. This partnership creates a strong platform for research and a direct mechanism into actionable conservation. We also have started to work together with Warren Wilson College, US, in partnership on educational and research at Raja Ampat.

Organization Yes No USAID Yes Government agencies in your country Yes Community groups or nongovernmental organizations Yes Private companies Yes

Problems Encountered:

We ordered ARMS equipments from US then ARMS shipped from Jakarta to Sorong (West Papua) since 2012. However, the ARMS deployment in Raja Ampat waters is not yet running until now. The ARMS will be deployed at the Raja Ampat waters adjust with US our partner’s schedule on summer. Because of ARMS will keep in a full year in bottom of the sea, we think to get the results of ARMS will need more time. This condition will make any problems we may have encountered in making progress on our project objectives. To resolve the problem, we have to deploy the ARMS in this summer with or without our U.S. partners. We also tried to conduct research with other method (without ARMS). By this method we have already collected many specimens from Raja Ampat. I think we have to run the same ways again in the next period. Although ARMS results will be taken, the data of this method will still function and could be compared with ARMS products. We also have difficulties related by processing ISSN for our monthly newsletter. Until now, our monthly newsletters have no ISSN. We also have difficulties related by publishing our books. Recently, UNIPA press (UNIPA publisher) did not work again and we could not get a support letter for publishing ISSN and ISBN. Therefore, we interest to set up a publisher for supporting our publications. The publisher will function and keep on both in the short term and in the long term.

Plans for Activities During the Coming Year:

We intend to deploy ARMS at Raja Ampat waters adjust with our US partner’s schedule on this summer. We also intend to conduct lab researches with selected young researcher from our invitation in call for proposal. In addition, we will publish activities and some of the result from field work practice in posters form, and we will upload in website and newsletter. We also planned to publish our two books and three articles. We want to make a copy of our published book and available free for all on our website. We intend to held field work with the US students and faculty in Raja Ampat on May, 2013. We will work together with lecturers of Brawijaya University, professor from 7

Warren Wilson College who will run a field trip in Raja Ampat. Our team will conduct research about conservation and will collect specimen of invertebrate. Some travel will run in the second year of this project. The project is now preparing the second year molecular genetics course, there are 35 participants from different institutions in and outside UNIPA anticipated to join 2013. Furthermore, in the second year of the project we increasing both the number of courses taught and the number of students involved. We also will expand our research projects by partnering with various local and international institutions and project personnel that have submit their proposal through the national and international competitions.

Additional Comments:

We intend to revise our budgeting to maximize our project workings. This is including revise in other direct costs, for instance, publication costs, workshops and conferences, and digitizing collection. We have no allocate budget for these item before. The fund will be taken from equipment’s fund that not fully used.

Supplementary Information: Below is supplementary information of our project.

TRAINING AND TEACHING 1. Training Workshop: Biodiversity, Molecular Ecology and Genetic Conservation Agenda Day 1 Time Activities Presenter Moderator 09:00 – 09:10 Welcome Ketua panitia Committee 09:10 – 09:30 Review of MB-RAI A.Hamid Toha Committee 09:30 – 09:45 Speech Rektor Committee 09:45 – 10:00 Break 10:00 – 11:15 Molecular Ecology 1 Prof. Sutiman B. Sumitro, SU, Hamid D.Sc (UB) 11:15 – 12:30 Biodiversity 1 Luchman Hakim, M.AgrSc, Ema Ph.D (UB) 12:30 – 13:15 Break 13:15 – 14:00 Extraction Method of DNA Hamid Toha 14:00 – 15:00 Amplification Method (PCR) Hamid Toha 15:00 – 15:15 Break 15:15 – 16:00 GenBank Hamid Toha Day 2 Time Activities Presenter Moderator 09:00 – 09:30 MB-RAI website Jeni, M.Si/M. Dailami Panitia 09:30 – 09:45 Review of ctPIRE A.Hamid Toha Panitia 09:45 – 10:00 Break Panitia 10:00 – 11:15 Biodiversity 2 Luchman Hakim, M.AgrSc, Ema Ph.D (UB) 11:15 – 12:30 Molecular Ecology 2 Prof. Sutiman B. Sumitro, SU, Sabarita D.Sc (UB) 12:30 – 13:15 Break 13:15 – 14:00 Agarose Electrophoresis Hamid Toha Method 14:00 – 15:00 Clean up amplification Hamid Toha product method 15:00 – 15:15 Break 15:15 – 16:00 Cycle sequencing Hamid Toha Day 3 Time Activities Presenter Moderator 09:00 – 09:45 Aricle writing techniques Luchman Hakim, M.AgrSc, Committee Ph.D (UB) 09:45 – 10:00 Break Committee 10:00 – 11:00 Conservation Genetics Widodo, M.Si, Jeni Ph.D.Med.Sc/A. Hamid Toha 11:00 – 12:00 Genetic analysis Widodo, M.Si, Sabarita Ph.D.Med.Sc./A. Hamid Toha 12:00 – 13:15 Break 13:15 – 14:00 Mega5 Hamid Toha 14:00 – 15:00 DNAsp 5.10 Hamid Toha 15:00 – 15:15 Break 15:15 – 16:00 Arlequin Hamid Toha 9

Training Workshop: Biodiversity, Molecular Ecology and Genetic Conservation

2. Debriefing Field Work Practice for Inventorying Marine Invertebrates and Microbes of in Raja Ampat Islands. Agenda

Time Activities Titles Presenter

Wednesday, Desember 19, 2012 09.00 – Head of Fishery Opening 09.30 Departmen, FPPK Teknik Pengambilan Sampel 09.30 - 10.30 Iinvertebrata dan Mikroba untuk Data A.Hamid A. Toha Morfologi dan Genetik Debriefing and Simon P.O. 10.30 – Introducing Panduan Penulisan Laporan PKL dan Leatemia, S.Pi, 11.30 research Kriteria Penilaian PKL M.Si program Nurhani Dinamika Sosial Masyarakat Pesisir 11.30 - 12.30 Widiastuti, S.Pi, dan Etika Penelitian di Masyarakat M.Si Tuesday, Desember 20, 2012 1. Inventarisasi dan Pemanfaatan Sampari Suruan Jenis-Jenis Mangrove oleh Masyarakat Lokal di Kabupaten Raja Ampat Presentation 09.00 – 2. Komposisi Jenis dan Kerapatan Harry Silalahi of Mangrove 10.00 Mangrove di Kampung Amdui Selat group Sagawin Kabupaten Raja Ampat 3. Inventarisasi jenis-jenis mangrove di Pulau Kaki Distrik Manokwari Maryo B. Utara Kabupaten Manokwari Mandacan 1. Inventarisasi Makrozoobenthos di Putri Ngilawane Presentation Ekosistem Mangrove pada of Kampung Amdui Distrik Selat 10.00 – Makrozoobent Sagawin Kabupaten Raja Ampat 11.00 os & Mollusca 2. Asosiasi moluska pada ekosistem Deasy Yamco at Mangrove Mangrove di Kampung Amdui Selat groups Sagawin Kabupaten Raja Ampat 3. Asosiasi Gastropoda pada 10

Ekosistem Mangrove di Kampung David Lomban Sawinggrai Distrik Meosmanswar Kabupaten Raja Ampat 4. Kelimpahan jenis Bia Kodok (Polimesoda spp) di Kampung Steven Ayomi Amdui Distrik Selat Sagawin Kabupaten Raja Ampat 1. Inventarisasi Jenis-Jenis Teripang Hasil Tangkapan dan Pemanfaatan oleh Nelayan Bayu Pranata 2. Kelimpahan Jenis Teripang di Kampung Sawinggrai Distrik Meosmanswar Kabupaten Raja Ronald Presentation Ampat Hambuako of groups of 11.00 – 3. Kelimpahan Jenis Kima sea cucumber, 12.00 (Tridacnidae) di Kampung Amdui Kima and Selat Sagawin Kabupaten Raja Absalom Wakum Sepuncula Ampat 4. Sebaran dan Pemanfaatan Filum Sipuncula di Kampung Amdui Distrik Selat Sagawin Kabupaten Rico R. Mailissa Raja Ampat

12.00 – Break 13.00 1. Analisis Hasil Pendapatan usaha Siti Mariyam budidaya ikan lele dumbo dengan

system kolam di Distrik Masni dan Presentation Distrik Prafi of Group of Erick Wanggai 2. Sasi di Kofiau Kabupaten Raja 13.00 – Social Ampat 14.00 economy, 3. Budidaya kerang mutiara (Pinctada aquaculture Hugo Rumbewas sp) di Kampung Amdui Distrik Selat and fisihing Sagawin Kabupaten Raja Ampat

4. Konstruksi Alat Tangkap Jaring Wanny Kambu Payang di Kabupaten Manokwari 1. Inventarisasi Jenis-jenis Makroalga di Kabupaten Raja Ampat Marlon Iwanggin Presentation 2. Komposisi dan Kelimpahan Jenis 14.00 – of group of Lamun di Kabupaten Raja Ampat Yerri Mundoni 15.00 seaweed and 3. Inventarisasi jenis-jenis lamun di Macroalgae Pulau Kaki Distrik Manokwari Utara Lidia Kandipi Kabupaten Manokwari

1. Asosiasi dan Komposisi Ikan pada Jefri Arizona Ekosistem Lamun di Distrik Amdui Presentation Kabupaten Raja Ampat of groups of 2. Kelimpahan Jenis-Jenis M. Fajar Marsaoly 15.00 – Mollusc and Gastropoda Dan Bivalvia (Molusca) 16.00 fish at pada Ekosistem Lamun di . seaweed Kampung Amdui Distrik Selat Sagawin Kabupaten Raja Ampat 3. Kelimpahan jenis Gastropoda dan Yulius Tata 11

Bivalvia (Moluska) pada ekosistem Lamun di Kampung Kapisawar Distrik Meosmanswar Kabupaten Raja Ampat 4. Komposisi jenis ikan yang Verbelina berasosiasi pada hamparan Lamun Baransano di Pulau Mansinam

Closing

Debriefing Practice Field Work for Inventorying Marine Invertebrates and Microbes of in Raja Ampat Islands.

3 & 4 Genetic Basics, General Course and Training Genetic Basic Agenda Time Activities Presenter Thursday, April 11, 2013 Head of Fishery 09.00 – 09.30 Opening Departmen, FPPK 09.30 – 11.30 General Course: Conservation Genetics Abdul Hamid Toha 11.30 –12.00 Discussion Moderator 13.00 – 14.00 Meeting Fishery Department 14.00 – 16.00 Genetic Basics Abdul Hamid Toha Friday, April 12, 2013 09.30 - 10.30 Socialization of PEER project Abdul Hamid Toha

14.00 – 16.00 Practicum: Extraction, PCR, Electrophoresis Andry Kuncoro 12

General Course

Training Genetic Basics 13

RESEARCH Field Work

No Species n Ekstraction PCR Seq Note 1 Acteon tornalitis 3 No No No No 2 Actinopyga palauensis 1 No No No No 3 Atilia ocelata 3 No No No No 4 Bohadsia marmorata 4 No No No No 5 Bolmaguttata millegranosa 1 No No No No 6 Casidula vespertillionis 4 No No No No 7 Chicoreus capucinus 3 No No No No 8 Euapta godeffroyi 5 No No No No 9 Fissilabia decollate 3 No No No No 10 Herpetopoma atrata 3 No No No No 11 Hippopus hippopus 3 No No No No 12 Holothuria fuscopuntata 1 No No No No 13 Littorina cocinea 5 No No No No 14 Littorina scabra 3 No No No No 15 Littorina sp 3 No No No No 16 Nerita costata 4 No No No No 17 Nerita undata 3 No No No No 18 Nerita planespira 3 No No No No 19 Opheodesoma sp 5 No No No No 20 Panulirus versicolor 42 Yes Yes Yes, 32 No 21 Polymesoda spp 4 No No No No 22 Sipunculus nudus 5 No No No No 23 Stichopus variegates 1 No No No No 24 Telebraria palustris 7 No No No No 25 Telescopion-telescopion 1 No No No No 26 Terebrallia sulcata 3 No No No No 27 Tripneutes gratilla 11 Yes Yes Yes, 11 No 28 Tridacna crocea 3 No No No No 29 Tridacna squamossa 3 No No No No 30 Tridacna maxima 3 No No No No 31 Tridacna gigas 3 No No No No 32 Turritella simplex 1 No No No No 33 Vitoida auqatilis 4 No No No No 151

Euapta godeffroyi E. godeffroyi distributed in Raja Ampat coastal. Habitat of E. godeffroyi is Intertidal pool, in sand, beneath stones. Ecology: benthic, continental shelf, detritus feeder, deposit feeder. This species inhabit in depth range 0-77 m. E. godeffroyi or paraer in local name at Raja Ampat was found in rocky or sandy mud in Waigeo Island, Raja Ampat

E. godeffroyi. Kingdom Animalia. Phylum Echinodermata. Class Holothuroidea. Order Apodida. Family Synaptidae. Genus Euapta. E. godeffroyi from Waigeo Island

Specimens in UNIPA Genetic Lab No ID Sampel Species Sites n Ext PCR Seq 1 UNP.000 E. godeffoyi P. Batanta Raja Ampat 5 No No No ID Sample No ID Sampel Collected Date Locality Exist in Containers 1 UNP.000.01 08-feb-13 P. Batanta LGU Box R4 2 UNP.000.02 08-feb-13 P. Batanta LGU Box R4 3 UNP.000.03 08-feb-13 P. Batanta LGU Box R4 4 UNP.000.02 08-feb-13 P. Batanta LGU Box R4 5 UNP.000.03 08-feb-13 P. Batanta LGU Box R4

Fissilabia decollata F. decollata distributed in Indonesia, including in Raja Ampat. These neatly spiraled snails sometimes seen, usually in large numbers on rocky shores and seawalls on our Southern shores. Elsewhere, they are called cluster winks for their habit of gathering in clusters. But disperse to feed at high tide. The size was about 2cm. The snails brood their young. Fertilization is internal and fertilized embryos are stored in a brood pouch behind the head of the female. They are then released into the sea as free-swimming larvae.

F. decollata found between rocks of Mangroves in Waigeo Island, Raja Ampat. F. decollata. Kingdom Animalia. Phylum Mollusca. Class Gastropoda. Order Neogastropoda. Family Planaxidae. Genus Fissilabia. 15

Specimens in UNIPA Genetic Lab No ID Sampel Species Sites n Ext PCR Seq 1 UNP.000 F. decollata P. Batanta Raja Ampat 3 No No No ID Sample No ID Sampel Collected Date Locality Exist in Containers 1 UNP.000.01 08-feb-13 P. Batanta LGU Box R4 2 UNP.000.02 08-feb-13 P. Batanta LGU Box R4 3 UNP.000.03 08-feb-13 P. Batanta LGU Box R4

Herpetopoma atrata H. atrata were distributed in Indonesia including in Raja Ampat water. It preferred intertidal rocky reefs as its habitat and have size 15–20mm.

H. atrata found in sandy mud (loam) and Mangrove, Batanta Island, Raja Ampat. H. atrata. Kingdom Animalia. Phylum Mollusca. Class Gastropoda. Order Archaegastropoda. Family Trochidae. Genus Herpetopoma.

Specimens in UNIPA Genetic Lab No ID Sampel Spesies Lokasi n Eks PCR Seq 1 UNP.0040 H. atrata Raja Ampat 3 No No No ID Sample No ID Sampel Collected Date Locality Exist in Containers 1 UNP.0040.01 08-feb-13 P. Batanta LGU Box R4 2 UNP.0040.02 08-feb-13 P. Batanta LGU Box R4 3 UNP.0040.03 08-feb-13 P. Batanta LGU Box R4

Holothuria fuscopunctata H. fuscopunctata was also found in Raja Ampat. This species is deep creases in the thick body wall and distinct fine spots easily distinguish this large holothurian from others. H. fuscopunctata is more common in water deeper than about 10 metres on sand or a mixture or rubble and sand. It occurs at the outer barrier reefs as well as other mid-shelf reefs.

H. fuscopunctata foun in rocky/sandy mud, Waigeo Island, Raja Ampat. H. fuscopunctata. Kingdom Animalia. Phylum Echinodermata. Class Holothuroidea. Order Aspidochirotida. Family Holothuriidae. Genus Holothuria. 16

Specimens in UNIPA Genetic Lab No ID Sampel Spesies Lokasi n Eks PCR Seq 1 UNP.0039 H. fuscopuntata P. Batanta Raja Ampat 3 No No No ID Sample No ID Sampel Collected Date Locality Exist in Containers 1 UNP.0039.01 08-feb-13 P. Batanta LGU Box R4 2 UNP.0039.02 08-feb-13 P. Batanta LGU Box R4 3 UNP.0039.03 08-feb-13 P. Batanta LGU Box R4

Hippopus hippopus Hippopus is a genus of large tropical saltwater clams, marine bivalve mollusks in the family Tridacnidae, the giant clam family. This species distributed in Raja Ampat coastal. The shell of this clam is very thick with prominent ribs, and has reddish blotches making it easy to differentiate from other clams. The mantle of these clams does not extend past the edge of the shell, and are brownish-green to gray in color with faint gold stripes. The large opening in the mantle, which is called the incurrent aperture, lacks the tentacles that are common with other clams within the Tridacnidae family.

Kima H. hippopus in rocky coral Batanta Island, Raja Ampat. H. hippopus. Kingdom Animalia. Phylum Mollusca. Class Bivalvia. Order Veneroida. Family Tridacnidae. Genus Hippopus.

Specimens in UNIPA Genetic Lab No ID Sampel Spesies Lokasi n Eks PCR Seq 1 UNP.0019 H. hippopus P. Batanta Raja Ampat 3 No No No

ID Sample No ID Sampel Collected Date Locality Exist in Containers 1 UNP.0019.01 08-feb-13 P. Batanta LGU Box R4 2 UNP.0019.02 08-feb-13 P. Batanta LGU Box R4 3 UNP.0019.03 08-feb-13 P. Batanta LGU Box R4

Tridacna sp Tridacna sp. features a deeply folded, almost zig-zag dorsal shell margin, reminiscent of the distantly related T. gigas. This character allows for an easy distinction from the two Red Sea congeners, the ﬂuted clam (T. squamosa Lamarck 1819) and Tridacna maxima Ro¨ding 1798. The latter two species show only weakly sinusoidal dorsal shell margins. The species occurs throughout the Indonesia area including in Raja Ampat. Live specimens were found exclusively in very shallow water 17

including reef flat, sea grass beds, sandy-rubble flats, on slight depressions in barren rocky flat, or under branching corals orcoral heads, shallower than 2 m.

(a) T. costata (b) T. maxima (c) T. squamosa Tridacna sp in rocky coral in Batanta Island, Raja Ampat. T. costata. Kingdom Animalia. Phylum Mollusca. Class Bivalvia. Order Veneroida. Family Tridacnidae. Genus Tridacna.

Specimens in UNIPA Genetic Lab No ID Sampel Species Sites n Ext PCR Seq 1 UNP.0021 T. crocea P. Batanta Raja Ampat 3 No No No No ID Sampel Species Sites n Ext PCR Seq 1 UNP.0017 T. squamosa P. Batanta Raja Ampat 3 No No No No ID Sampel Species Sites n Ext PCR Seq 1 UNP.0018 T. maxima P. Batanta Raja Ampat 3 No No No No ID Sampel Spesies Sites n Ext PCR Seq 1 UNP.0020 T. gigas P. Batanta Raja Ampat 3 No No No

ID Sample No ID Sampel Collected Date Locality Exist in Containers 1 UNP.0021.01 08-feb-13 P. Batanta LGU Box R4 2 UNP.0021.02 08-feb-13 P. Batanta LGU Box R4 3 UNP.0021.03 08-feb-13 P. Batanta LGU Box R4 No ID Sampel Collected Date Locality Exist in Containers 1 UNP.0017.01 08-feb-13 P. Batanta LGU Box R4 2 UNP.0017.02 08-feb-13 P. Batanta LGU Box R4 3 UNP.0017.03 08-feb-13 P. Batanta LGU Box R4 No ID Sampel Collected Date Locality Exist in Containers 1 UNP.0018.01 08-feb-13 P. Batanta LGU Box R4 2 UNP.0018.02 08-feb-13 P. Batanta LGU Box R4 3 UNP.0018.03 08-feb-13 P. Batanta LGU Box R4 No ID Sampel Collected Date Locality Exist in Containers 1 UNP.0020.01 08-feb-13 P. Batanta LGU Box R4 2 UNP.0020.02 08-feb-13 P. Batanta LGU Box R4 3 UNP.0020.03 08-feb-13 P. Batanta LGU Box R4

Panulirus versicolor P. versicolor (Latreille, 1804) is one of the six varieties of spiny lobster that found in the Indonesian Archipelago including in Raja Ampat waters. The other five being P. homarus, P. longipes, P. penicillatus, P. polyphagus and P. ornatus (Girsang et al 1995). P. versicolor grows up to 40 centimetres. Like all spiny lobster, this animal 18

has no claws, two spiny rostra over the eyes, and two pairs of large antennae. Both antennae are usually white with the first pair are double ended and the second hard and spiny. The carapace is white, pink and black, with horizontal bands and a reticulate.

P. versicolor. Kingdom animalia, Phylum arthropoda, subphylum Crustacea, Class Malacostraca, Ordo Decapoda, Family Palinuridae, Genus Panulirus.

Telescopium telecospium T. telescopium is commonly seen in Indonesia mangroves including in Raja Ampat, on mud, sometimes in the hundreds covering a large area. This large snail has a tall, conical shell strongly reminiscent of an ice cream cone. Features of T. telecospium are 8-15cm. The Operculum of Telescopium is small and circular. The animal is velvety black with a highly extendible proboscis. There is a third eye on its mantle margin, in addition to a pair of eyes at the tentacles. It can stay out of water for long periods of time. Telescopium feeds on detritus and algae from the mud surface at low tide by sucking using its proboscis (Reid et al., 2008).

T. telescopium found in Mangrove and Mud, Batanta Island, Raja Ampat. T. telescopium. Kingdom Animalia. Phylum Mollusca. Class Gastropoda. Order Sorbeoconcha. Family Potamididae. Genus Telescopium.

Tripneutes gratilla T. gratilla, a sea urchin widely distribution throughout the Indo-Pacific including in Raja Ampat. This species is ecologically important, especially in sea grass habitats and is a food source with good potential for aquaculture. Habitat of T. gratilla are sheltered and moderatley exposed reef. They can reach 10 to 15 centimetres (4 to 6 in) in size. They are dark in colour, usually bluish-purple with white spines. The pedicles are also white, with a dark or black base. The spines of some specimens are wholly orange, while those of others are only orange-tipped or completely white. This colour disappears when the individual dies or is taken out of the ocean, and is difficult to preserve.

T. gratilla. Kingdom Animalia. Phylum Echinodermata. Class Echinodea. Order Temnopleuroida. Family Toxopneustidae. Genus Tripneutes.

Vitoida auqatilis

V. auqatilis, found on Mangrove leaves and muddy loam in Batanta Island, Raja Ampat. V. auqatilis. Genus Vitoida.

Littorina sp Height commonly exceeding 5 mm, and in some species slightly exceeding 1.5 cm; operculum horny ; periostracum not uniformly tan or brown (Almagorda subrotundata is brown, but usually has spiral banding ) (mostly at higher tide levels on rocly shores, or on rocks, concrete and wood in bays , sometimes in salt marshes). The periwinkles are found on the seashore in the littoral zone and sub littoral zone in all parts of the Raja Ampat. Littoraria scabra, common name: the mangrove periwinkle, is a species of sea snail, a marine gastropod mollusk in the family Littorinidae, the winkles or periwinkles. The size of an adult shell varies between 15 mm and 40 mm. This species is distributed in Indonesia including in Raja Ampat. Littoraria coccinea is a species of sea snail, a marine gastropod mollusk in the family Littorinidae, the winkles or periwinkles.

Littorina sp, found on Mangrove leaves and muddy loam in Batanta Island, Raja Ampat

Lab Work

PCR Products

Sequencing Results

Data Analyses

Presentation

PUBLICATIONS 1. Website: http://www.ibcraja4.org/

2. Monthly Newsletters: http://ibcraja4.org/page/read/newsletters

June 2012 July 2012 August 2012

September 2012 October 2012 November 2012

December 2012 January 2012 Pebruary 2013 25

March 2012 April 2013

3. Article 1: http://berkalahayati.org/index.php/bph/article/view/642

Article 2: http://berkalahayati.org/index.php/bph/article/view/658

4. Cover of Book Manuscript (in Press) Abdul Hamid A. Toha Sutiman B. Sumitro Luchman Hakim Widodo

KEANEKARAGAMAN DAN KONSERVASI BULU BABI

Information on the numbers and types of students and other junior collaborators involved in the project.

Name Department No Title (Gender) (Faculties), Goal Undergraduate (Field Trip) Fishery (Faculty of Asosiasi dan Komposisi Ikan pada Jefri Arizona Husbandry, Fishery 1 Ekosistem Lamun di Distrik Amdui (Male) and Marine Sciences- Kabupaten Raja Ampat FPPK) Field Work Komposisi Jenis Gastropoda pada David Lomban Ekosistem Mangrove di Kampung Fishery (FPPK), Field 2 (M) Sawinggrai Distrik Meosmanswar Work Kabupaten Raja Ampat Sebaran dan Pemanfaatan Filum Rico Ricardo Fishery (FPPK), Field 3 Sipuncula di Kampung Amdui Distrik Selat Mailisa (M) Work Sagawin Kabupaten Raja Ampat Budidaya kerang mutiara (Pinctada sp) di Hugo Fishery (FPPK), Field 4 Kampung Amdui Distrik Selat Sagawin Rumbewas (M) Work Kabupaten Raja Ampat Inventarisasi Makrozoobenthos di Putri P. Ekosistem Mangrove pada Kampung Fishery (FPPK), Field 5 Ngilawane Amdui Distrik Selat Sagawin Kabupaten Work (Female) Raja Ampat Asosiasi gastropoda pada ekosistem Deasy Yamco Fishery (FPPK), Field 6 Mangrove di Kampung Amdui Selat (F) Work Sagawin Kabupaten Raja Ampat Kelimpahan Jenis Kima (Tridacnidae) di Absalom Fishery (FPPK), Field 7 Kampung Amdui Selat Sagawin Kabupaten Wakum (M) Work Raja Ampat Kelimpahan Jenis Teripang di Kampung Ronald Fishery (FPPK), Field 8 Sawinggrai Distrik Meosmanswar Hambuako (M) Work Kabupaten Raja Ampat Kelimpahan jenis Bia Kodok (Polimesoda Steven Ayomi Fishery (FPPK), Field 9 spp) di Kampung Amdui Distrik Selat (M) Work Sagawin Kabupaten Raja Ampat Kelimpahan jenis Gastropoda dan Bivalvia (Moluska) pada ekosistem lamun di Fishery (FPPK), Field 10 Yulius Tata (M) Kampung Kapisawar Distrik Meosmanswar Work Kabupaten Raja Ampat Other junior collaborators-Capacity Building in Research

Nurhani Partisipasi masyarakat local dalam Fishery (FPPK, 1 Widiastuti,S.Pi, pengelolaan ekowisata di Kampung X Raja UNIPA), Capacity M.Si (F) Ampat building in research

Fanny Partisipasi masyarakat local dalam Fishery (FPPK, 2 Simatauw, S.Pi, pengelolaan ekowisata di Kampung X Raja UNIPA), Capacity M.Si (F) Ampat building in research 29

Juliana Fishery (FPPK, Ekologi Molekuler Ketam Kenari (Birgus 3 Leiwakabessy, UNIPA), Capacity Latro L.) di Raja Ampat dan Manokwari S.Pi, M.Si (F) building in research

Fishery (FPPK, Ida Lapadi, Ekologi Molekuler Ketam Kenari (Birgus 4 UNIPA), Capacity S.Pi, M.Si (F) Latro L.) di Raja Ampat dan Manokwari building in research Identifikasi Kima (Tridacna) Dengan Tresia Menggunakan Pendekatan Metode DNA Fishery (FPPK, 5 Tururaja,. S.Ik, Barcoding dan Variasi Genetik di Perairan UNIPA), Capacity M.Si (F) Raja Ampat Papua Barat building in research

Seleksi dan domestikasi kandidat indukan Biology (Faculty of udang galah Macrobachium rosenbergii (de Robi Binur, Sciences, UNIPA), 6 Man, 1879) asal Papua berdasarkan marka S.Si, M.Si (M) Capacity building in genetik untuk pengembangan indukan research baru. Undergraduate (Research)

Identifikasi spesies laut menggunakan Marine Sciences, 1 Kuncoro (M) pendekatan DNA barcoding Thesis

Variasi Warna Menunjukkan Keragaman Nur Aisyah Genetik Teripang (Holothuridea) Di Biology (Faculty of 2 Hasniar (F) Perairan Raja Ampat Sciences), Thesis

Bayu Pranata Bioekologi dan filogeni ketam kenari Raja Fishery (FPPK), 3 (M) Ampat Thesis

Identifikasi kima (Tridacna) dengan menggunakan DNA barcoding dan variasi Marine Sciences, 4 Masriana (F) genetik di Perairan Raja Ampat, Teluk Thesis Doreri dan Teluk Wondama Kajian kearifan local dalam bentuk Herimiel Fishery Sciences, 5 penerapan sasi hasil laut di Distrik Kofiau, Ambrauw (M) Thesis Kabupaten Raja Ampat

Master Students

Distribusi spasial dan keragaman genetik Biology (Faculty of Veince Silahooy 6 bulu babi (Tripneustes gratilla) di Pulau Sciences, Brawijaya (M) Ambon dan Raja Ampat University), Thesis

Doctoral Students Social Economy (Agriculture Faculty of Jumiati Mustiah Eksistensi sosial-lingkungan dalam 7 UNIPA-Brawijaya (F) ekowisata di Kepulauan Raja Ampat University), Dissertation

Laboratory Technicians, Newsletter contributors, Website operators

1 Jehan Haryati, S.Si, M.Si (F) Admin staff Biology Graduated student, UB

2 Q. Mohammed (M) IT staff Biology Graduated student, UB

Chemistry Graduated (Faculty of 3 M. Dailami, S.Si (M) Admin/technician Sciences, UNIPA), Capacity building in research Marine Sciences Graduated, 4 Andyka AriWibowo, S.Ik (M) Technician Thesis Nurhani Widiastuti, S.Pi, M.Si 5 Admin staff Faculty of UNIPA (F) Prof. Sutiman B. Sumitro, Consultant, 6 Faculty of Brawijaya University D.Sc Trainer Newsletter 7 M. Takdir Faculty of UNIPA contributor Researcher, 8 Widodo, Ph.D Faculty of Brawijaya University Coauthor Researcher, 9 L. Hakim, Ph.D Faculty of Brawijaya University Trainer 10 Jeni, S.Pd, M.Si Researcher Faculty of UNIPA

11 Hamid Toha PI, Trainer Faculty of UNIPA Contributor in 12 Robi Binur Faculty of UNIPA newsletter Contributor in 13 Yuliana L, S.Pi, M.Si Faculty of UNIPA newsletter Contributor in 14 Irma A., S.Ik, M.Si LIPI staff newsletter Contributor in 15 Hermawaty A., S.Si, M.Si Faculty of UNIPA newsletter Contributor in 16 Lutfi Faculty of UNIPA newsletter 17 Kuncoro Technician UNIPA student