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All Journal ILMU KELAUTAN: Indonesian Journal of Marine Sciences Biotropika Current Biochemistry Journal of Innovation and Applied Technology Journal of Environmental Engineering and Sustainable Technology The Journal of Pure and Applied Chemistry Research Jurnal Kelautan Tropis Jurnal Sumberdaya Akuatik Indopasifik JFMR (Journal of Fisheries and Marine Research) Jurnal Biologi Tropis Indonesian Journal of Chemistry Jurnal Perikanan Universitas Gadjah Mada Jurnal Iktiologi Indonesia (Indonesian Journal of Ichthyology) Musamus Fisheries and Marine Journal PRIMA: Journal of Community Empowering and Services Jurnal Riset Biologi dan Aplikasinya Tomini Journal of Aquatic Science Bioscientist : Jurnal Ilmiah Biologi Nekton ACROPORA: Jurnal Ilmu Kelautan dan Perikanan Papua Jurnal Pijar MIPA STATISTIKA Jurnal Perikanan Berita Biologi Journal of Tropical Diversity
Muhammad Dailami, Muhammad
Aquaculture Study Program, Faculty Of Fisheries And Marine Science, Brawijaya University, Veteran Street, Malang 65145, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Control & Systems Engineering Decision Sciences, Operations Research & Management Earth & Planetary Sciences Economics, Econometrics & Finance Education Energy Engineering Environmental Science Immunology & microbiology Materials Science & Nanotechnology Mathematics Mechanical Engineering Medicine & Pharmacology Physics Social Sciences

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Identifikasi Genetik Ikan Nilem dengan Pendekatan DNA Barcoding Dailami, Muhammad; Yuniarti, Ating; Widodo, Maheno Sri; Pratama, Rakhmad Ndaru; Ariyani, Destia Fitri; Siahaan, Marthin Daniel Theo Gratia; Maulana, Antajala Rian; Ramadhan, Surya Dewa; Putri, Radwa Fathin H; Nurcahyani, Shinta Eka; Milansari, Sindi; Mayor, Corazon Ell Merilia Papuani
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):3

Abstract

Nilem fish (Osteochilus vittatus) is a species of freshwater fish from the Cyprinidae family which has ecological and economic importance in Indonesia, with its natural habitat in rivers, swamps and stagnant waters. Accurate species identification is very important in biological research and fisheries resource management, but morphological identification methods have several limitations. DNA barcoding is a revolutionary molecular technique that uses short DNA sequences to identify and differentiate species with high accuracy. The use of DNA barcoding in identifying freshwater fish in Indonesia has shown significant development, including in a comprehensive study documenting 1,172 native freshwater fish species. The research "Genetic Identification of Nilem Fish using the DNA Barcoding Approach" aims to characterize the genetics of nilem fish, compare the genetic profiles of various populations, and evaluate the effectiveness of DNA barcoding in distinguishing nilem fish from other Osteochilus species, with the hope of contributing to fish conservation and sustainable management efforts nilem in Indonesia. The DNA sequencing results obtained a sequence with a length of 619 base pairs with the composition of Nucleotides A (27.2%), G (17.6%), C (26.4%), T (28.8%). The BLAST results with the NCBI database showed a similarity of 99.84% with the O. vittatus sequence and 99.83% with O. hasseltii. Both species are synonyms with the official name O. vittatus. Phylogenetic analysis is also in line with the BLAST results which show that the sample sequence is in the same clade as the O. vittatus and O. hasseltii sequences. Identification with molecular markers of the COI gene was successfully used in determining the species of the Nilem fish (O. vittatus).
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.
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.
Addressing Autocorrelation in Aquaculture Data: A Canonical Correlation Analysis of Water Quality and Shrimp Growth Supriatin, Febriyani Eka; Rahmawati, Aulia; Dailami, Muhammad
Statistika Vol. 25 No. 2 (2025): Statistika
Publisher : Department of Statistics, Faculty of Mathematics and Natural Sciences, Universitas Islam Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29313/statistika.v25i2.8387

Abstract

Abstract. This study evaluates the multivariate relationship between shrimp pond water quality and vannamei shrimp growth using Canonical Correlation Analysis (CCA) with autocorrelation handling. Observational data was collected from 13 ponds (3 visits/pond; N = 39) in Banyuwangi (DOC 32–50; Nov 2022–Jan 2023), encompassing pH, temperature (Temp), dissolved oxygen (DO), Average Body Weight (ABW), and Specific Growth Rate (SGR). Diagnosis indicated residual autocorrelation, so CCA inference was made robust through cluster bootstrap per pond (B = 2000), partial CCA controlling for Visit, and within-approach (demeaning per pond), as well as being triangulated with mixed-effects models and GEE AR(1). The first canonical root was significant (ρ1 = 0.648; Wilks’ Λ = 0.541; p = 0.0015) and stable based on bootstrap (median ρ1 = 0.692; 95% CI 0.340–0.894). Canonical loading shows Temp as the main contributor on the water quality side (supporting pH, low DO), while SGR dominates on the growth side and is in the opposite direction to ABW. The redundancy index indicates a moderate level of cross-set explanation (Y from X = 13.7%; X from Y = 36.8%). These findings underscore the importance of daily temperature stability (supported by pH stability) and DO monitoring in shrimp farm management.
Morphological Distinction and Phenotypic Variance of Mystus (Mystus gulio, M. nigriceps, and M. singaringan) from Java Island, Indonesia: Morphological analysis of three Javanese Mystus (Mystus gulio, M. nigriceps, and M. singaringan) Larasati, Ni Putu Anggun; Amalia, Elok; Rhafsyanjani, Bintang; Dailami, Muhammad; Faqih, Abd Rahem; Yuniarti, Ating; Endra Kusuma, Wahyu
Jurnal Riset Biologi dan Aplikasinya Vol. 8 No. 1 (2026)
Publisher : Universitas Negeri Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.26740/jrba.v8n1.p1-17

Abstract

Genus Mystus is widely distributed across Indonesia with eleven currently valid species. Three species are confirmed to inhabit Java Island: Mystus gulio, M. nigriceps, and M. singaringan. Due to their similar morphological appearances and relatively subtle diagnostic features, species identification and discrimination between these three species is somewhat challenging. This study evaluates the morphological differentiation of M. gulio, M. nigriceps, and M. singaringan at both interspecific and intraspecific levels using samples collected across Java Island. Morphological data including thirty morphometric and five meristic characters from 143 individuals in sampling sites were analyzed using Principal Component Analysis (PCA) and UPGMA clustering. PCA (75.32% total variance) effectively discriminated the three species, identifying maxillary barbel length and adipose-fin base length as the primary diagnostic characters. Intraspecific analyses revealed high morphological homogeneity across geographic sampling sites; however, significant phenotypic variance was observed, primarily attributed to ontogenetic allometric growth in juveniles and localized environmental plasticity. Despite testing for novel morphometric and meristic markers, this study reinforces the reliability of traditional adipose and barbel proportions as the definitive tools for field identification. These results provide a critical morphological baseline essential for the conservation, germplasm verification, and potential domestication of these indigenous aquatic resources. Highlighted Finding 1. Maxillary barbels and adipose fins are key diagnostic traits for Javanese Mystus2. PCA results reveal a unique morphological divergence in the Bogor M. singaringan3. Findings prioritize M. singaringan for farming and M. nigriceps for conservation Graphical View
Kombinasi Media dan Pupuk untuk Produksi Padi dalam Sistem Budidaya Akuaponik di Bengkel Mimpi Malang Herlina, Cucun; Syaifullah, Syaifullah; Rahmawati, Aulia; Dailami, Muhammad; Fadjar, Mohamad; Sanoesi, Ellana; Suprastiyani, Heny; Rangkuti, Rizky Fadilla Agustin; Kusuma, Wahyu Endra; Faqih, Abd. Rahem
PRIMA: Journal of Community Empowering and Services Vol 10, No 1 (2026): June
Publisher : Universitas Sebelas Maret

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20961/prima.v10i1.109840

Abstract

Combination of Growing Media and Fertilizers for Rice Production in the Aquaponic Farming System at Bengkel Mimpi Malang. Dependence on chemical fertilizers and limited home-garden space drive the search for efficient food production models. The aquaponic rice–catfish system is proposed as a solution to address land constraints, climate variability, and reliance on chemical fertilizers. This initiative aims to implement a smart farming model based on aquaponic principles to maintain household food security, enhance water-use efficiency, and reduce chemical input usage. The program will be conducted from May to September 2025 at Bengkel Mimpi (Kepanjen, Malang) through outreach, training, system installation, and mentoring. The system utilizes PVC pipes (plant spacing 25×25 cm) with wick-fed net pots placed above a tarpaulin-lined pond containing 3,000–5,000 catfish fingerlings. Two media formulations are tested: rice husk:manure (1:1) and rice husk charcoal:organic powder (1:3). The IR64 rice variety is harvested 80–90 days after planting, with 10–12 tillers per clump and 150–200 grains per panicle. One installation unit (2×12 m) yields approximately 30 kg of dry harvested paddy (≈20 kg of organic rice), with seven units producing approximately 210 kg/cycle, and a potential of 840 kg/year (four cycle). In the fish compartment, survival rates of 85-90% from an initial stocking of 5,000 fish yield approximately 500 kg of catfish/cycle, resulting in a net profit of about IDR 4.3 million/cycle. Media with higher organic proportions tend to increase tiller count and grain set. These findings confirm that the aquaponic system, when integrated, is a viable solution for household food security and income diversification, with measurable performance, making it suitable for widespread adoption in limited land environments.
Co-Authors Abdul Hamid A. Toha Abdul Hamid A. Toha Abdul Rahem Faqih Afnan, Naufal Izzudin Agoes Soeprijanto Agus Mohammad Hikam Aji Wahyu Anggoro Amalia, Elok Ambariyanto Ambariyanto Andrianus Sembiring Aradea Bujana Kusuma Ariyani, Destia Fitri Asus Maizar Suryanto H Ating Yuniarti Ating Yuniarti Aulia Rahmawati, Aulia Bayu Pranata, Bayu Buana Insan Kamil Christopher P. Meyer Condro Puspo Nugroho Dandi Saleky Dandi Saleky Dandi Saleky Dandi Saleky Dandi Saleky Dandi Saleky Darma Santi Dean Rama Prayoga Delvira Riska Ananta Denanta, I Made Kresna Dewa Gede Raka Wiadnya Dewa Gede Raka Wiadnya Diah Permata Wijayanti Dodi Safari Dyah Kinasih Wuragil EDY H.P. MELMAMBESSY Eka Maya Kurniasih Elsa Syafi’ul Umma Emmanuel Manangkalangi Endra Kusuma, Wahyu Febriyana Novita Damayanti Febriyani Eka Supriatin Febriyani Eka Supriyatin Firda, Wahyuma Fitri Nur Azizah Harahap, Muhammad Alfiandi Rachmad Hardoko Hardoko Hardoko Hardoko Hariati, Anik Martinah Heder Djamaludin Hendrikus R Siga Herlina, Cucun Hermawaty Abubakar I MADE ARTIKA Indria Graha Hayuningtyas Isma Isma Jeni, Jeni Kholil, Kiki Nur Azzam Kusuma, Wahyu Endra Lalu Panji Imam Agamawan Larasati, Ni Putu Anggun Maftuch Maftuch Mahariawan, I Made Dedi Maheno Sri Widodo, Maheno Sri Manan, Jemmy Manumpil, Abraham Welliam Marius Agustinus Welliken Maulana, Antajala Rian Mayor, Corazon E.M.P. Mayor, Corazon Ell Merilia Papuani Mega Fatimah Rosana Milansari, Sindi Mirza Dikari Kusrini MOHAMAD FADJAR Mohammad Sholeh Uluwwi Mudjirahayu Mudjirahayu Muhammad Fakhri Muhammad Musa Murtihapsari . Nasrullah Bai Arifin Ni Kadek Dita Cahyani Ni Putu Dian Pertiwi Novaldo Yuri Muhammad Nugroho, Nurul Nurcahyani, Shinta Eka Nurul Jadid Mubarokati Paricahya, Akhsan Fikrillah Permatasari, Felyta Dian Pratama, Rakhmad Ndaru Putri Nur Azizah Putri, Ajeng Ayu Restuaning Putri, Radwa Fathin H Rahardjo, Seto Sugianto Prabowo Ramadhan, Surya Dewa Rangkuti, Rizky Fadilla Agustin Reny Sianturi Renyaan, Alberth W. Rhafsyanjani, Bintang Roni Bawole Rosa D. Pangaribuan RR. Ella Evrita Hestiandari Saleky, Dandi Salsabila, Sivana Yesica Ayu Sanoesi, Ellana Satria, Ibnu Darma Siahaan, Marthin Daniel Theo Gratia Simon P.O Leatemia Sri Andayani Suciati, Lusia Dyah Sufaichusan, Ifa Suprastiyani, Heny Supriatin, Febriyani Eka Surya Dewa Ramadhan Syaifullah Syaifullah Thomas Frans Pattiasina Tresia Tururaja Tristany Brighton Jorghi Vivi Nurhadianty Vivi Nurhadianty, Vivi Widyawati, Yuni Yenny Risjani Yuni Widyawati Yuni Widyawati Yusup A Jentewo Zeth Parinding