Short Communication: Genetic structure of Longtail Tuna Thunnus tonggol (Bleeker, 1851) in Java Sea, Indonesia

Abstract

Abstract. Al Malik MD, Pertiwi NPD, Sembiring A, Yusmalinda NLA, Ningsing EY, Astarini IA. 2020. Short Communication: Genetic structure of Longtail Tuna Thunnus tonggol (Bleeker, 1851) in Java Sea, Indonesia. Biodiversitas 21: 3637-3643. Thunnus tonggol (Longtail Tuna) is an economically important fish found in Indonesia waters, however, the information regarding this fish is lacking. Known to be a neritic fish and found in shallow water, Java Sea is one of the ideal habitats for T. tonggol species. Due to high fishing rates activities in Java Sea, a better management plan to ensure the conservation and fisheries sustainability around this area is needed, especially to protect T. tonggol population. In order to complete the Indonesian tuna data, we aim to study the diversity and genetic structure of T. tonggol in Java Sea at three different locations; i.e. Semarang, Banjarmasin, and Jakarta. In this study, population genetic methods with the marker of mitochondrial DNA (mtDNA) control region were used in population structure analysis. A total of 115 specimens were collected from the fish market around the area of study locations and amplified using polymerase chain reaction (PCR) and sequenced using Sanger methods. The result showed genetic diversity (Hd) value of 0.99366, and nucleotide diversity (π) value of 0.01906. Both of these values indicated high genetic diversity. Population analyses using Analysis of Molecular Variance (AMOVA) showed nonsignificant differences between the three populations of study (mixing population), with the ΦST value of 0,00375 (p-value > 0.05). Based on this result, the fisheries management for T. tonggol in Java Sea needs to be managed as one single population management.

Characterization of Some Commercially Important Octopus (Mollusca: Cephalopoda) from Indonesian Waters using Mitochondrial DNA Cytochrome Oxidase Sub-Unit I (Mt-DNA COI)

“…The sequence was then aligned using MEGA X (Kumar et al, 2018). The species identity was determined by comparing sequences to GenBank database (www.ncbi.nlm.nih.gov) enforcing a homology threshold of >99 % (Malik et al, 2020;Pertiwi et al, 2020). Identification using phylogenetic tree was also reconstructed using Bayesian method with BEAST2 package program (Drummond et al, 2007;Bilderbeek and Etienne, 2018).…”

Analisis Filogenetik Ikan Tuna (Thunnus spp.) yang didaratkan di Pelabuhan Benoa, Bali

“…Walsh et al (1991) menyebutkan bahwa metode ini banyak digunakan karena praktis, lebih cepat, dan tidak melibatkan pelarut organik serta tidak memerlukan banyak transfer tube untuk prosesnya sehingga mendapatkan genome sampel yang menjadi tujuan penelitian dibandingkan metode lainnya. Metode chelex juga telah berhasil diterapkan pada sampel Tuna (Jackson et al, 2014;Iranawati et al, 2016;Pertiwi et al, 2017;Malik et al, 2020).. .…”

“…Proses amplifikasi DNA dilakukan pada mtDNA control region dan primer yang digunakan yaitu primer forward CRK 5'-AGC TCA GCG CCA GAG CGC CGG TCT TGT AAA-3', primer reverse CRE 5'-CCT GAA GTA GGA ACC AGA TG-3' (Lee et al, 1995). Primer ini digunakan secara universal terkait identifikasi genetik ataupun populasi Tuna (Pertiwi et al, 2017;Malik et al, 2020). Pengaturan tahapan PCR meliputi denaturasi awal pada suhu 80°C selama 10 detik, denaturasi pada suhu 94°C selama 30 detik, annealing pada suhu 50°C selama 30 detik, extension pada suhu 72°C selama 45 detik (Barber et al, 2006).…”

Population Analysis of Bali Sardinella (Sardinella lemuru, Bleeker 1853) Landed in PPI Kedonganan using Length-Weight Data and Digital Analysis (ImageJ)

“…Information of the population condition of fish species can be understand using fishery stock analysis (Rago, 2005), fish length-weight and growth data (Famoofo and Abdul, 2020;Indarjo et al, 2020;Olopade et al, 2020;Annisa et al, 2021), and genetic data (Pertiwi et al, 2017;Sartimbul et al, 2018;Malik et al, 2020). Length-weight data has been also widely used to understand the population dynamic of S. lemuru (Wujdi et al, 2012;Pertami et al, 2018;Annisa et al, 2021), especially within Bali Strait waters.…”