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All Journal Biodiversitas Journal of Biological Diversity
MUHAMMAD DAILAMI
Department of Aquaculture, Faculty of Fisheries and Marine Science, Universitas Brawijaya. Jl. Veteran, Malang 65145, East Java, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology

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Mitochondrial phylogeny and genetic diversity of Hampala barb (Hampala macrolepidota) from the Brantas River, Indonesia ELOK AMALIA; IFA SUFAICHUSAN; MUHAMMAD DAILAMI; ABD RAHEM FAQIH; MAHENO SRI WIDODO; DEWA GEDE RAKA WIADNYA; WAHYU ENDRA KUSUMA
Biodiversitas Journal of Biological Diversity Vol. 26 No. 11 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d261128

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Abstract. Amalia E, Sufaichusan I, Dailami M, Faqih AR, Widodo MS, Wiadnya DGR, Kusuma WE. 2025. Mitochondrial phylogeny and genetic diversity of Hampala barb (Hampala macrolepidota) from the Brantas River, Indonesia. Biodiversitas 26: 5694-5702. Hampala barb (Hampala macrolepidota), a native freshwater fish species in the Brantas River, East Java, is currently under severe threat due to intense fishing and environmental perturbations. The urgency of this situation necessitates the immediate implementation of effective genetic management and conservation programs, which rely on basic scientific information such as genetic characterization. This study aimed to assess the phylogenetic relationships, genetic diversity, population structure, and demographic history of H. macrolepidota using a 1,095 bp sequence of the mitochondrial DNA cytochrome b from 23 individuals collected across four sampling locations. Phylogenetic analysis showed that H. macrolepidota from the Brantas River clustered together and formed a single group with very shallow genetic divergence. Population structure analyses (both ?st and AMOVA) showed high gene flow and an absence of significant genetic clustering, suggesting the sampled area constitutes a single, interconnected population unit. The combination of high haplotype diversity (hd: 0.714-1.000) but low nucleotide diversity (?: 0.00156-0.00728), along with the negative Tajima’s D and Fu’s Fs values, suggested that the species has likely experienced a bottleneck effect followed by a rapid expansion in the past. This decline of genetic diversity points to a reduced long-term adaptive potential, causing the species to be highly vulnerable to future environmental changes, despite its current abundance. The results highlight the urgent need for effective genetic management and conservation programs for the species to focus on maintaining genetic connectivity and minimizing anthropogenic pressures to preserve the genetic integrity and long-term viability of the population. Future studies incorporating nuclear or genome-wide markers would provide finer resolution of population structure and complement the mitochondrial data presented here.
DNA barcoding of 19 Lutjanus species to support fisheries management in the Bird’s Head Seascape, Papua, Indonesia ABDUL HAMID A. TOHA; EMMANUEL MANANGKALANGI; BAYU PRANATA; MUHAMMAD DAILAMI; ANTAJALA R. MAULANA; DESTIA F. ARIYANI; MARTHIN D. T. GRATIA; RAKHMAD N. PRATAMA; SHINTA E. NURCAHYANI; SINDI MILANSAR; JENI JENI; RADWA F. H. PUTRI; ZETH PARINDING; ESIE M. WANGI; ANDI FAJERIANI WYRASTI; CORAZON E. M. P. MAYOR
Biodiversitas Journal of Biological Diversity Vol. 26 No. 10 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d261042

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Abstract. Toha AHA, Manangkalangi E, Pranata B, Dailami M, Maulana AR, Ariyani DF, Gratia MDT, Pratama RN, Nurcahyani SE, Milansari S, Jeni, Putri RFH, Parinding Z, Wangi EM, Wyrasti AF, Mayor CEMP. 2025. DNA barcoding of 19 Lutjanus species to support fisheries management in the Bird’s Head Seascape, Papua, Indonesia. Biodiversitas 26: 5287-5302. Red snapper species (family Lutjanidae) are economically important reef fishes traded at local, national, and international levels. However, species-level taxonomic resolution and conservation assessments remain limited in the Bird’s Head Seascape (BHS) region of West Papua, Indonesia. This study applied DNA barcoding of the mitochondrial cytochrome C Oxidase subunit I (COI) gene to assess Lutjanus species diversity and distribution within the Kaimana and Fakfak Marine Protected Areas (MPAs). A total of 77 specimens were successfully sequenced, resulting in a barcoding success rate of 100%. Nineteen species were identified: Lutjanus argentimaculatus, L. bengalensis, L. biguttatus, L. bohar, L. decussatus, L. ehrenbergii, L. erythropterus, L. fulviflamma, L. fulvus, L. gibbus, L. quinquelineatus, L. lemniscatus, L. malabaricus, L. monostigma, L. rufolineatus, L. russellii, L. sebae, L. timoriensis, and L. vitta. Thirteen species were recorded in Fakfak and twelve in Kaimana, with several species unique to each MPA. No genetic differences were observed among individuals within the same species. In contrast, the genetic distance between different species ranged from 2.8% to 19.3%. A total of nineteen monophyletic groups were recovered in the NJ phylogenetic trees, which were supported by high bootstrap values (91-100%). Lutjanus decussatus formed two subgroups in the phylogenetic trees. All identified species are currently listed as Least Concern (LC) by the IUCN, though population trends for most remain unknown, and some are declining. These findings demonstrate the utility of DNA barcoding for accurate species identification in data-poor tropical regions and provide a genetic baseline for future monitoring efforts. The confirmed presence of commercially exploited and potentially declining species underscores the need for site-specific fishery assessments and adaptive management strategies. Integrating molecular tools into routine monitoring can enhance enforcement of species-based catch limits and support sustainable fisheries management within Indonesia’s MPAs.
Co-Authors ABD RAHEM FAQIH ABDUL HAMID A. TOHA ANDI FAJERIANI WYRASTI ANTAJALA R. MAULANA BAYU PRANATA CORAZON E. M. P. MAYOR DESTIA F. ARIYANI DEWA GEDE RAKA WIADNYA ELOK AMALIA EMMANUEL MANANGKALANGI ESIE M. WANGI IFA SUFAICHUSAN JENI JENI MAHENO SRI WIDODO MARTHIN D. T. GRATIA RADWA F. H. PUTRI RAKHMAD N. PRATAMA SHINTA E. NURCAHYANI SINDI MILANSAR WAHYU ENDRA KUSUMA ZETH PARINDING