OPTIMASI AMPLIFIKASI DNA MENGGUNAKAN METODE PCR (Polymerase Chain Reaction) PADA IKAN KARANG ANGGOTA FAMILI Pseudochromidae (DOTTYBACK) UNTUK IDENTIFIKASI SPESIES SECARA MOLEKULAR

Polymerase Chain Reaction (PCR) merupakan salah satu metode yang digunakan dalam identifikasi suatu organisme. Identifikasi secara molekular menggunakan metode berbasis PCR perlu dilakukan pada ikan karang Famili Pseudochromidae karena ikan ini mempunyai variasi morfologi warna yang sangat tinggi dan menyulitkan identifikasi morfologi. Metode amplifikasi DNA untuk seluruh spesies ikan anggota famili ini belum banyak dilakukan. Penelitian ini bertujuan untuk mengetahui kondisi optimal untuk amplifikasi DNA menggunakan metode PCR (Polymerase Chain Reaction) pada 25 spesies ikan karang anggota famili Pseudochromidae, yang sebelumnya telah diidentifikasi secara morfologi. Amplifikasi dilakukan pada tiga loki DNA mitokondria, yaitu 16S rRNA, control region dan cytochrome oxidase I (COI). Hasil penelitian menunjukkan kondisi optimum amplifikasi tidak berhubungan dengan perbedaan spesies. Modifikasi amplifikasi dapat dilakukan dengan penambahan volume template DNA dan BSA 1X serta penggantian temperatur annealing; sedangkan pergantian reagen tidak memberikan pengaruh yang signifikan. Penggunaan primer depan CRK untuk amplifikasi lokus control region juga memberikan hasil yang lebih baik

Molecular Identification of Wedgefishes Stingrays (Rynchobatus sp.) at PPI Rigaih, Aceh Jaya Regency by using COI Gene

Indonesia is one of the largest shark and ray producing countries in the world. Based on FAO (Food and Agriculture Organization) data, Indonesia is the top country which produce plenty of sharks and rays every year. One of the stingray shark caught by the fishermen called ikan pari kekeh (kekeh stingray), data from the IUCN( International Union for Conservation of Nature and Natural Resources)  this ray is included in Red List and categorized in Appendix II CITES (Convention on international trade of endangered species) due to excessive fishing. In most cases, the identification of kekeh ray is not easy because the information and conservation data are very limited. This study was conducted to identify the species of kekeh stingray landed at Rigaih Fish Landing Port, Aceh Jaya Regency using the COI gene (Cytochrome c oxidase subunit I) molecular analysis.  Sampling was carried out in June 2021 and then analysed at Indonesian Biodiversity Foundation (BIONESIA) laboratory. The analysis results were adjusted to GenBank data via BLAST (Basic Local Alignment Search Tools). The results of the analysis found per value. The ident of 10 samples ranged around 99-100% each and the query qover value each sample is 100%. The farthest genetic distance value is 0.34. The phylogenetic tree managed to classify species from each sample and form a cluster together with the data obtained from the NCBI genban

Redefining Dispersal Boundaries of Siganus fuscescens In The Coral Triangle Area

The increasing demand of fish in the Coral Triangle Area has led to overexploitation of some species of fishes. One of the commercial fishes, which is also known to be the source of food and income for local communities, is the Mottled Spinefoot (Siganus fuscescens). Population studies on this species are important in order to manage sustainable stock populations. Genetic variation of the mitochondrial DNA was analyzed to examine the population structure of Siganus fuscescens in Indonesia, as part of the Coral Triangle Area. In total, 789 basepairs of control region mtDNA sequences were determined from 133 specimens collected from six localities, including Seribu Islands (n=27), Karimunjawa (n=19), Komodo (n=39), Selayar (n=20), Lembeh (n=19) and Luwuk (n=9). From the data, 27 variable sites and 24 haplotypes were detected, with most of the haplotypes unique to each location. Haplotype data show that one haplotype was shared among all populations, three haplotypes were shared between two populations (Komodo & Selayar; Lembeh & Seribu; Komodo & Karimunjawa), and 20 were unique to a single population. Haplotype diversity (h=0.444) and nucleotide diversity (π=0.00165) were low. The diversity result, i.e. the ΦST value (0.0658, P < 0.0001) revealed genetic structure in S. fuscescens populations in Indonesia. A non-dispersal strategy led to restricted gene flow and genetic structuring in S. fuscescens. However, both the neutrality test and the mismatch distribution indicated that S. fuscescens might have been in populations at demographic equilibrium, with restriction to the population expansion. Although indicating unexpected minor population structure pattern, the overall result still suggest the management of this species population as a single unit across Indonesia

Revealing Hidden Diversity in Menjangan Besar Island, Karimunjawa: Reef-Associated Decapods as a Proxy of Biodiversity Estimation (Mengungkap Keanekaragaman Tersembunyi di Pulau Menjangan Besar, Karimunjawa: Estimasi Biodiversitas Menggunakan Dekapoda..)

Kepulauan Indonesiamemiliki sejumlahArea Perlindungan Laut dan Taman Nasional yang merupakan tempat tinggal bagi organisme laut dengan tingkat keanekaragaman yang tinggi. Karimunjawa sebagai salah satu Taman Nasional, dikenal mempunyai keanekaragaman terumbu karang yang tinggi dan merupakan salah satu kawasan yang digunakan sebagai area studi keanekaragaman laut. Penelitian ini bertujuan untuk mengestimasi keanekaragaman organisme pada habitat terumbu karang yang terdapat di kawasan pesisir Karimunjawa. Metode sampling semi-kuantitatif digunakan untuk mengestimasi keanekaragaman terumbu karang, dengan menggunakan anggota kelompok dekapoda sebagai perwakilan. Enam belas terumbu karang mati (dead coral head) dari anggota Pocillopora, di koleksi dengan ukuran yang sama pada kedalaman 10 meter di kawasan Pulau Menjangan Besar, Karimunjawa. Seluruh dekapoda yang dikumpulkan, diidentifikasi sampai tingkat famili dan menunjukkan terdapat 11 famili dari total 203 individu. Nilai statistik dari kekayaan spesies (Chao1 and ACE) menunjukkan hanya 11 famili dekapoda yang dapat ditemukan di kawasan tersebut. Hasil kurva rarefaksi menunjukkan nilai yang mencapai titik kesetimbangan setelah karang mati ke-empat belas, yang mengindikasikan bahwa penambahan koleksi sampel tidak akan mengubah estimasi keanekaragaman yang ditemukan. Index keanekaragaman Shanon-Wiener juga menunjukkan nilai keanekaragaman yang rendah dengan nilai 1.9. Hasil penelitian ini dapat digunakan sebagai dasar pemahaman bagi keseluruhan keanekaragaman terumbu karang yang terdapat pada suatu kawasan dan sebagai dasar pengetahuan untuk tujuan pengamatan ekosistem terumbu karang bagi perlindungan dan konservasi. Kata kunci: keanekaragaman, terumbu karang, dekapoda, Indonesia, Karimunjawa. The Indonesian archipelago, with its higher number of Marine Protected Areas (MPA) and National Parks, is a home to a high diversity of marine organisms. Karimunjawa is an Indonesian National Park that is well known for its diverse coral reefs and therefore is an important place to study marine biodiversity. In the present study, the biodiversity of reef organisms was estimated in the coastal marine habitat of Karimunjawa. A semi-quantitative sampling method was used to estimate reef biodiversity using decapod group as a representative. Sixteen similar sized dead coral heads of Pocillopora were sampled from 10 m depth at Menjangan Besar Island, Karimunjawa. All decapods were sorted and identified to the family level, yielding 11 families from total 203-collected individuals. Species richness statistics (Chao1 and ACE) suggest that only 11 families of decapods can be found in this area. Rarefaction curves approached an asymptote after sampling fourteen heads, indicated that sample addition will not alter the estimate diversity found in this location with Shanon-Wiener diversity index of 1.9 indicated low diversity. Our findings may provide a basic understanding of the overall biodiversity of a reef area and a basic knowledge in monitoring coral reefs ecosystems for protection and conservation. Keywords: biodiversity, coral reefs, decapod, Indonesia, Karimunjaw