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All Journal HAYATI Journal of Biosciences Jurnal Ilmu-Ilmu Perairan dan Perikanan Indonesia Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences Jurnal Biologi Udayana ILMU KELAUTAN: Indonesian Journal of Marine Sciences Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati Jurnal Kelautan : Indonesian Journal of Marine Science and Technology Biotropika JURNAL ENGGANO Jurnal Biologi Tropis Musamus Fisheries and Marine Journal Cassowary Igya ser hanjop: Jurnal Pembangunan Berkelanjutan Bioscientist : Jurnal Ilmiah Biologi Berkala Penelitian Hayati ACROPORA: Jurnal Ilmu Kelautan dan Perikanan Papua Journal of Tropical Diversity
Abdul Hamid A. Toha
Program Studi Manajemen Sumberdaya Perairan, Jurusan Perikanan Fakultas Perikanan Dan Ilmu Kelautan, Universitas Papua Jln.Gunung Salju Amban, Manokwari. Papua Barat, 9831
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Earth & Planetary Sciences Education Environmental Science Immunology & microbiology Materials Science & Nanotechnology Medicine & Pharmacology Social Sciences Other

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Identifikasi Genetik Ikan Gabus Asal Merauke dengan Menggunakan Fragmen Gen Sitokrom Oksidase Sub Unit I Dailami, Muhammad; Yuniarti, Ating; Saleky, Dandi; Toha, Abdul Hamid A.
Bioscientist : Jurnal Ilmiah Biologi Vol. 12 No. 1 (2024): June
Publisher : Department of Biology Education, FSTT, Mandalika University of Education, Indonesia.

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33394/bioscientist.v12i1.11446

Abstract

Efforts to cultivate snakehead fish (Chanidae) still experience many problems, especially the availability of high-quality fry. To improve the quality of fry, improving the quality of broodstock is important. Genetic factors play an important role in the selection and breeding of snakehead fish parents. Therefore, it is necessary to explore sources of superior parents with good genetic characteristics. To achieve this goal requires studies from various fields such as ecology, biology, and genetics. Genetic studies can be started by examining the identity and relationships of snakehead fish from Merauke, as a first step in finding a source of germplasm that has high diversity. The aim of this research is to analyze the cytochrome oxidase subunit 1 (COI) gene fragment of snakehead fish from Merauke, Papua. DNA isolation was carried out using the Promega kit with standard protocols, amplification of the COI gene with primers F2 and R2 with the Go Taq Green amplification kit. A total of 653 base pairs of the COI gene fragment were obtained from the sequencing process, with a nucleotide composition of T (29.9%), C (28.8%), A (24.0%), G (17.3%). BLAST results on the NCBI database show that this sequence has 100% similarity to the Channa striata sequence from Papua with sequence ID OQ405388.1. This shows that the identification results of the snakehead fish from Merauke are Channa striata. Phylogenetic tree analysis also showed consistent results, namely the formation of a clade that was the same as the Channa striata fish group derived from GenBank data.
Analisis Identitas Genetik Ikan Gabus Sentani (Oxyeleotris heterodon) berdasarkan Marka Gen Sitokrom Oksidase 1 Dailami, Muhammad; Maulana, Antajala Rian; Siahaan, Marthin Daniel Theo Gratia; Kusuma, Wahyu Endra; Agamawan, Lalu Panji Imam; Toha, Abdul Hamid A.; Yuniarti, Ating
Journal of Tropical Diversity Vol 1 No 1 (2025): Februari
Publisher : Penerbit Brainy Bee

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.64283/jotdiverse.2025.1(1):4

Abstract

The Sentani snakehead fish (Oxyeleotris heterodon) is an endemic fish species that inhabits Lake Sentani and several other lakes in Papua Province, Indonesia. This species has important ecological and economic value, but is vulnerable to environmental change and overexploitation. Genetic identification, especially using the Cytochrome Oxidase 1 (COI) gene, is very important for conservation efforts and understanding the genetic diversity of Sentani Snakehead Fish. DNA barcoding techniques with the COI gene have become the standard method in molecular identification of species, allowing rapid and accurate identification. Unfortunately, the Sentani Snakehead Fish faces various threats such as habitat degradation, pollution, overfishing and the introduction of invasive foreign species. Therefore, genetic research is becoming increasingly important to support conservation efforts, providing in-depth understanding of the population status and adaptive potential of species. The results of DNA amplification and sequencing of COI gene fragments showed a DNA sequence with a length of 619 base pairs with the composition A (23.9%), G (18.1%), C (29.1%), T (28.9%). The results of identification by homology analysis in the NCBI and BOLD databases showed the highest similarity at 97.58% and 97.84% with the O. lineolate sequence. This is because there is no O. heterodon sequence from the COI gene fragment found in Genbank or the BOLD system. Phylogenetic tree analysis with several sequences that have close similarities shows a difference in clade between the O. heterodon sequence from this study with the O. lineolate sequence and other species.
Hubungan antara Kelimpahan Mikroplastik dan Keanekaragaman Jenis Plankton Astricyah, Iis; Leuwakabessy, Juliana; Toha, Abdul Hamid A.
Journal of Tropical Diversity Vol 1 No 1 (2025): Februari
Publisher : Penerbit Brainy Bee

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.64283/jotdiverse.2025.1(1):6

Abstract

This paper aims to evaluate the relationship between microplastic abundance and plankton species diversity. Microplastics, as a new and increasingly disturbing pollutant, can affect the quality of aquatic ecosystems, including plankton communities. Water samples were taken from several points in Kwatisore waters to measure microplastic concentrations, as well as to identify and count the types of plankton present. The results of the analysis will later show that there is a negative relationship between the abundance of microplastics and the diversity of plankton types. An increase in microplastic concentrations is associated with a decrease in the amount and diversity of plankton, which can impact the stability of aquatic ecosystems. These findings underscore the importance of managing and mitigating plastic pollution to maintain healthy aquatic ecosystems. Further research is needed to understand the impact mechanisms of microplastics in more depth and to develop effective conservation strategies.
Keragaman Genetik Antar Individu Bulu Babi (Tripneustes gratilla) di Pantai Rendani Kabupaten Manokwari Firda, Wahyuma; Toha, Abdul Hamid A.; Mudjirahayu, Mudjirahayu; Dailami, Muhammad
Journal of Tropical Diversity Vol 1 No 1 (2025): Februari
Publisher : Penerbit Brainy Bee

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.64283/jotdiverse.2025.1(1):7

Abstract

Understanding the genetic diversity of sea urchins is essential for studying species diversity and the genetic relationships among species and individuals. The primary objective of the research was to determine the genetic diversity of sea urchins from Rendani Waters, Manokwari Regency. Specifically, the study aimed to identify the species of sea urchins, assess their nucleotide diversity and composition, measure genetic distances, and explore the kinship relationships between individual sea urchins. The research used a descriptive method and was conducted from November to December 2022. The species identification, based on genetic analysis, revealed that all samples belonged to T. gratilla, with a 99.20-100.00% similarity to the reference species. Genetic diversity among individual samples was found to be relatively low. The nucleotide composition showed an average GC content of 39.34-40.34%, which was lower than the AT content (53.87-60.66%). The genetic distance between the samples ranged from 0.00 to 0.07. A phylogenetic tree, constructed from the data, grouped all samples into two clusters with bootstrap values of 62/54.
DNA Barcoding of Snapper Fish (Lutjanus spp.) from Kaimana and Fakfak, West Papua Ariyani, Destia Fitri; Kusuma, Wahyu Endra; Pranata, Bayu; Manangkalangi, Emmanuel; Jeni, Jeni; Toha, Abdul Hamid A.; Dailami, Muhammad
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 31, No 1 (2026): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/ik.ijms.31.1.26-36

Abstract

Kaimana and Fakfak are two regions in West Papua which have high biodiversity. The total fish production in Kaimana and Fakfak are 10,039 tons.y-1 and 17,806 tons.y-1, respectively. The snapper fish (Lutjanus spp.) is one of the important economic commodities in Kaimana and Fakfak regions. There has been a decrease in the number of exports of snapper fish in 2018 to 2019 from 4,742 tons to 4,290 tons due to overfishing and environmental pollution. This study employed DNA barcoding technology to identify the species of snapper fish collected from Kaimana and Fakfak. The DNA isolation was conducted by using genomic DNA mini kit (tissue) and the amplification of COI gene with Go Taq green master mix. Agarose gel electrophoresis was used to visualize the PCR product.  A total of 16 sequences with length 654 base pairs of COI gene were identified as five species of Lutjanidae, which were Lutjanus decussatus, L. gibbus, L. quinquelineatus, L. malabaricus, and L. johnii. Homology analysis with BLAST NCBI and BOLD System showed that all samples have similarity of 99.08-100% and query cover of 93-100%. Relationship analysis using phylogenetic tree and genetic distances showed results of intraspecific close relatives (0.001-0.016) and interspecific distant relatives (>0.1000). The phylogenetic tree illustrated that all species of Lutjanidae are separated into monophyletic clades. DNA barcoding technology successfully identified the snapper fish collected from Kaimana and Fakfak. 
Co-Authors Agus Mohammad Hikam Agustina L.N. Aminin Alfarani Bawole, Christover Ambariyanto Ambariyanto Aradea Bujana Kusuma, Aradea Bujana Ariyani, Destia Fitri Astricyah, Iis Ating Yuniarti Bawole, Christover Alfarani Bayu Pranata Bayu Pranata, Bayu Duaiht Kolibongso Emmanuel Manangkalangi Fanny Fransina Carolina Simatauw Firda, Wahyuma Fitriyah I.E Saleh Jamhari Jamhari Jeni, Jeni Jenly Haurissa Kusuma, Wahyu Endra Lalu Panji Imam Agamawan Leuwakabessy, Juliana Luchman Hakim Lutfi Lutfi Lutfi Lutfi Maharani, Andi Nacisa Malfin Savina Manuhutu, Jafry Ferdinan Maulana, Antajala Rian Mayor, Corazon E.M.P. Milansari, Sindi Mokodongan, Daniel Frikli Mudjirahayu Mudjirahayu Mudjirahayu Mudjirahayu Muhammad Dailami, Muhammad Musyeri, Philipus Nashi Widodo Nifaan, Welmincie Milana Nurul Jadid Mubarokati Pattiasina, Selfinus Paulus Boli Purba, Gandi YS Purbani, Debora Christin Renyaan, Alberth W. Ricardo Ferdinand Tapilatu Ridwan Sala Robi Binur Roni Bawole RR. Ella Evrita Hestiandari Saleky, Dandi Sembel, Luky Siahaan, Marthin Daniel Theo Gratia Suhaemi Sultary, Ayu Sutiman B. Sumitro Sutiman B. Sumitro Tasya M.R. Sihabudin Tebaiy, Selvi Thomas Frans Pattiasina Tutik Handayani Veince Benyamin Silahooy, Veince Benyamin Vera Sabariah Widodo Widodo Yemima Kaliele, Mariance Yohanes Aibesa Yonavin Maryon Titaley Yuli E. Demana Yuni Widyawati