Dna Barcoding Of The Family Scombridae In Malaysia And Phylogeography And Population Structure Of The Indian Mackerel, Rastrelliger Kanagurta For Sustainable Fisheries

This research was conducted to develop a molecular systematic identification of the commercially important family Scombridae as well as to understand the phylogeography and phylogenetics of a member species, the Indian mackerel, Rastrelliger kanagurta for sustainable fisheries in Malaysian waters. DNA barcoding based on the mitochondrial cytochrome oxidase subunit I gene, widely known as the barcoding gene successfully identified and delineated 14 species of the family Scombridae sampled in Malaysian waters. The phylogeography and population structure of the pelagic Indian mackerel, R. kanagurta was also investigated among 19 Malaysian populations and one population each from Thailand, Vietnam, Indonesia (Southeast Asian region) and an Iranian population (West Indian Ocean-WIO) using mitochondrial cytochrome b gene analysis. A parallel investigation was conducted on 11 Malaysian populations and an Iranian population based on eight newly developed microsatellite markers. In this study, the next generation sequencing platform, Ion Torrent PGMTM was used to generate a partial genome survey sequence (GSS) dataset to develop microsatellite markers from R. kanagurta genomic DNA. The data generated included a total of 399,794 sequence reads (81.29 Mbp) of which 16,209 sequence reads were successfully assembled, producing 327 contigs averaging 677 bp in length in addition to the single sequence repeats (SSR) markers

Genetic Population Structure of Yellowfin Tuna (Thunnus albacares) as Based Data of Fish Conservation in North Mallucas Sea

Tuna is a migratory species with high economic value. Utilization of tuna is increasing and growing every year. Fishing intensity of tuna in the Maluku Sea is high and can disrupt the population. The existence of the population will be threatened if not managed properly. The latest genetic information approach is necessary to prevent the population decline. The purpose of this research was to know the genetic structure of yellowfin tuna in North Maluku waters, Indonesi. Sampling was conducted in May-July 2016 in Morotai Island, Obi and Sanana, while secondary data was gathered in Ternate Island, Bacan and Ambon. A total of 72 samples were collected and analyzed. The result of the study found that the base length (bp) of the control region of mtDNA was found to be 512 bp (base pairs). the genetic distance in the nearest population is at Sanana and Obi (0.025). The results of genetic distance analysis between population found genetic similarity between Morotai-Sanana (0,021), Obi-Sanana (0,025), Obi-Morotai (0,026) and Ambon-Sanana (0,026), while the furthest genetic distance was found in Ternate-Bacan (0,040) and Ternate-Obi (0,042). The pairwise comparison test (Fst) shows a few genetic differentiation between yellowfin tuna populations. The value (Fst) of the yellowfin tuna population shows a strong gene flow between populations. The haplotype distribution shows a relationship between haplotypes in both yellowfin tuna, thus failing to show clade between different geographic locations. Unsustainable use can harm the population through genetic quality. Several approaches should be taken to support the life cycle of yellowfin tuna. The overall result shows that there has not been any change of genetic structure of yellowfin tuna in North Maluku Sea. Keywords : Haplotype, genetic distance, North Maluku, yellowfin tuna, pairwise comparison tes

Keragaman genetik ikan tuna sirip kuning (Thunnus albacares) dari dua populasi di Laut Maluku, Indonesia

Abstract. Yellowfin tuna (Thunnus albacores) is a large, pelagic, and migratory species of tuna that inhabits Moluccas Sea in Indonesia, and most sea environment worldwide. However, high fishing activities tend to happen in the Indonesia region and catch product appear to be decreasing. A better understanding of yellowfin tuna genetic diversity is required to plan better conservation strategy of tuna. The study was conducted to infer the genetic diversity of yellowfin tuna (T. albacores) in the Moluccas Sea. A total of 41 tissue samples of yellowfin tuna were collected from two regions in the Moluccas Sea (North Moluccas and Ambon) during an expedition in February 2013. The results showed that genetic diversity and nucleotide diversity of yellowfin tuna from North Moluccas population was 0.984 and 0.021, respectively; while in Ambon population, the genetic and nucleotide diversities were 1.00 and 0.018, respectively. The high genetic diversity (0.990) and nucleotide diversity (0.020) between two populations were observed. Based on phylogenetic analysis, no genetic differentiation between the two populations in Moluccas Sea was revealed .Keywords :  Population genetics; Haplotype diversity; Coral Triangle; Phylogenetics; Polymerase Chain Reactions (PCRs) Abstrak. Tuna sirip kuning (Thunnus albacores) adalah ikan komersial penting dan ditemukan di Laut Maluku, Indonesia. Tetapi, aktivitas penangkapan ikan tuna sirip kuning dapat menurunkan kualitas dan kuantitas stok ikan, sehingga perlu adanya pengkajian keragaman genetik ikan tuna sirip kuning. Pemahaman yang baik tentang keragaman genetika dibutuhkan untuk merencanakan strategi konservasi tuna yang lebih baik. Penelitian ini bertujuan untuk mengetahui keragaman genetik  ikan tuna sirip kuning dari dua populasi di Laut Maluku. Sebanyak 41 sampel jaringan dari tuna sirip kuning dikumpulkan dari dua populasi di Laut Maluku (Maluku Utara dan Ambon) selama ekspedisi pada bulan Februari 2013. Hasil penelitian menunjukkan bahwa keragaman genetik populasi tuna sirip kuning pada perairan Maluku Utara dan Ambon masing-masing sebesar 0,984 dan 1,00 sedangkan nilai keragaman nukleotida masing-masing bernilai 0,021 dan 0,018. Nilai keragaman genetik dan keragaman nukloetida yang tinggi didaptkan antar kedua populasi masing-masing sebesar 0,990 dan 0,020. Berdasarkan analisis filogenetik, dua populasi di Laut Maluku ini memiliki kedekatan secara genetik.Kata kunci : Genetika populasi; Keragaman haplotipe; Segitiga Terumbu Karang; Filogenetika; Polymerase Chain Reaction (PCR

A Conventional Multiplex PCR Assay for the Detection of Toxic Gemfish Species (Ruvettus pretiosus and Lepidocybium flavobrunneum): A Simple Method to Combat Health Frauds

The meat of Ruvettus pretiosus and Lepidocybium flavobrunneum (gemfishes) contains high amounts of indigestible wax esters that provoke gastrointestinal disorders. Although some countries have banned the sale of these species, mislabeling cases have been reported in sushi catering. This work developed a simple conventional multiplex PCR, which discriminates the two toxic gemfishes from other potentially replaced species, such as tunas, cod, and sablefish. A common degenerate forward primer and three species-specific reverse primers were designed to amplify cytochrome oxidase subunit I (COI) gene regions of different lengths (479, 403, and 291 bp) of gemfishes, tunas, and sablefish, respectively. A primer pair was designed to amplify a fragment (193 bp) of the cytb gene of cod species. Furthermore, a primer pair targeting the 16S rRNA gene was intended as common positive control (115 bp). The method developed in this study, by producing the expected amplicon for all of the DNA samples tested (reference and commercial), provides a rapid and reliable response in identifying the two toxic species to combat health frauds

Studi pendahuluan genetika populasi ikan tuna sirip kuning (thunnus albacares) dari dua populasi di laut Kepulauan Maluku, Indonesia

Abstract. Yellowfin tuna (Thunnus albacares) is a large pelagic fish that have high economic value and inhabits the Moluccas Sea, Indonesia. Tuna catches in the Moluccas sea was very high and might decrease the yellowfin tuna population in this region. The research on population genetic of yellowfin tuna is fundamental to answer the problem. This information can be used as baseline data for future management, utilization, and basis of genetic conservation. The objective of this research was to infer the genetic population structure of two populations (North Maluku and Ambon) in the Moluccas Sea, Indonesia. In total, 41 tissue samples from pectoral fins of yellowfin tuna were collected in this study (North Maluku 33 samples and Ambon 8 samples). The results showed that genetic distances were low between the two populations. Additionally, the comparison of genetic distance between the Moluccas population and Indian Ocean waters also showed no significant differences. The Fst analysis showed the high gene flow between these two populations. Furthermore, haplotype network analysis showed that these two populations were the panmixia population. The overall result showed that no refraction genetic in the yellowfin tuna population from two populations in the Moluccas Sea.Keywords: Haplotype, genetic distance, Moluccas Sea, index fixation analysis, yellowfin tuna, population genetic structure. Abstrak. Tuna sirip kuning (Thunnus albacares) merupakan jenis pelagis besar bernilai ekonomis tinggi yang hidup di perairan Laut Maluku, Indonesia. Tangkapan ikan tuna di Laut Maluku berstatus tinggi, sehingga dapat menurunkan jumlah populasi. Penelitian tentang genetika populasi ikan tuna sirip kuning penting dilakukan untuk menjawab permasalahan ini. Informasi ini dapat menjadi sumber data untuk pengelolaan, pemanfaatan dan pelestarian untuk konservasi genetik. Tujuan penelitian untuk mengetahui struktur populasi genetik pada dua populasi di Laut Maluku (Maluku Utara dan Ambon). Secara total, 41 sampel jaringan dari sirip pectoral Tuna sirip kuning dikumpulkan dalam penelitian ini (Maluku Utara 33 sampel dan Ambon 8 sampel). Hasil penelitian menemukan jarak genetik yang dekat antar kedua populasi. Perbandingan jarak genetik pada populasi Perairan Maluku dan Samudera Hindia tidak menunjukan perbedaan signifikan. Analisis fiksasi indeks (Fst) memperlihatkan aliran genetik kuat antar populasi. Analisis jaringan haplotipe menunjukan kedua populasi merupakan populasi panmiksia. Penelitian ini secara umum menunjukkan belum terjadi perubahan struktur genetik populasi ikan tuna sirip kuning pada dua populasi di Laut Maluku.Kata kunci: Haplotipe, jarak genetik, Laut Maluku, analisis fiksasi indeks, tuna sirip kuning, struktur populasi genetik.    

KAJIAN FILOGENETIK IKAN TUNA (Thunnus spp) SEBAGAI DATA PENGELOLAAN DI PERAIRAN SEKITAR KEPULAUAN MALUKU, INDONESIA

Ikan tuna (Thunnus Spp) adalah ikan pelagis yang memilili kemampuan migrasi dan nilai komersial. Kondisi oseanografie Maluku Utara dan Ambon mendukung kelimpahan stok populasi sumberdaya. Pengetahuan filogenetik dapat membantu menunjukan hubungan evolusioner dari suatu organisme yang disimpulkan dari data morfologi dan molekuler. Tujuan penelitian untuk mengetahui filogenetik ikan tuna di perairan Maluku Utara dan Ambon. Penelitian ini menggunakan metode PCR-Sequencing. Analisis molekuler menggunakan Polymerase Chain Reaction (PCR) dengan primer CRK-CRE, elektroforesis. Rekonstruksi pohon filogenetik menggunakan metode Neighbor joining dan model evolusi Kimura 2-parameter dilakukan dengan aplikasi MEGA5. Hasil penelitian filogenetik menemukan terdapat empat empat clade spesies ikan tuna yang saling berbeda (tuna mata besar ; tuna sirip kuing ; tuna alalunga ; cakalang ). Jarak genetik tuna mata besar (T.obesus)  dengan tuna sirip kuning (T.albacares)  adalah 0.09, tuna mata besar (T.obesus)  dengan tuna alalunga (T.albacore) adalah 0.19, tuna sirip kuning (T.albacares)  dengan tuna alalunga (T.albacore),  sebesar 0.21,  tuna mata besar (T.obesus)  dengan tuna alalunga (T.albacore)  cakalang (K.pelamis) adalah 0.34, cakalang (K.pelamis) dengan tuna alalunga (T.albacore) adalah  0.39 dan tuna sirip kuning (T.albacares)  dengan Cakalang (K.pelamis) adalah 0.34. Semua hasil menunjukan perbedaan genetik yang signifikan, genetik spesies tuna berasal dari satu kelompok dan filogeografi memiliki batas distribusi yang nyata antar satu dengan yang lain.Kata Kunci :     Thunnus, Polymerase Chain Reaction (PCR), Pohon Filogenetik, primer CRK-CRE, , Neighbor joining, Kimura 2-parameter, jarak genetik, MEGA5, filogeografi.  ABSTRACTTuna (Thunnus Spp) is a pelagic fish that has migration capabilities and commercial value. The condition of North Maluku and Ambon oceanographies supports the abundance of resource population stocks. Phylogenetic knowledge can help show the evolutionary relationship of an organism inferred from morphological and molecular data. The aim of the study was to determine phylogenetic of tuna in the waters of North Maluku and Ambon. This study used the PCR-Sequencing method. Molecular analysis uses a polymerase chain reaction (PCR) with CRK-CRE primer, electrophoresis. Reconstruction of the phylogenetic tree using the Neighbor joining method and the Kimura 2-parameter evolution model was carried out with the MEGA5 application. The results of phylogenetic research found that there were four four different clades of tuna species (bigeye tuna; kuing fin tuna; alalunga tuna; cakalang). The genetic distance of big eye tuna (T.obesus) with yellow fin tuna (T.albacares) is 0.09, bigeye tuna (T.obesus) with tuna alalunga (T.albacore) is 0.19, yellow fin tuna (T.albacares) with tuna alalunga (T.albacore), for 0.21, big eye tuna (T.obesus) with alalunga tuna (T.albacore) cakalang (K.pelamis) is 0.34, cakalang (K.pelamis) with alalunga tuna (T.albacore) is 0.39 and yellow fin tuna (T.albacares) with Cakalang (K. pelamis) are 0.34. All results show significant genetic differences, genetic tuna species come from one group and filogeography has a real distribution boundary between one another.Keywords: Thunnus, Polymerase Chain Reaction (PCR), Phylogenetic Tree, CRK-CRE primer, Neighbor joining, Kimura 2-parameter, genetic distance, MEGA5, filogeography

一塩基置換に基づいたPCR増幅法による新規マグロ種鑑別法の開発

東京海洋大学修士学位論文 平成23年度(2011) 食機能保全科学 第1278号指導教員: 石崎松一郎全文公表年月日: 2013-09-05東京海洋大学201

World Trade Agreement and Indian Fisheries Paradigms:A Policy Outlook

International trade is duly called as the “engine of growth” and is inextricably linked with economic development. Nevertheless, trade is also vulnerable to economic slowdown as in the current global environment. Many of the developing countries are getting exposed to declining demand for exports and increased protectionism. Even in times of strong economic growth, trade and its benefits had not been evenly distributed across the developing world and the growth had been asymmetric. The World Trade Organization (WTO) which officially commenced on January 1st, 1995 under the Marrakesh Agreement, replacing the General Agreement on Tariffs and Trade (GATT), intends to supervise and liberalize international trade through negotiations aiming at expansion of rules–based trade and thereby gearing trade policies to support development. When the developing countries were liberalizing their economies, they felt the need for better export opportunities. The establishment of WTO is an important landmark in the history of international trade as it provides opportunities for countries to grow and realize their export potentials, with appropriate domestic policies in place