Sri Riska Rahayu, Abdul Rahman Siregar, Mutia Ramadhaniaty, Nanda Muhammad Razi, Syamsul Rizal, Nur Fadli, Luvi Syafrida Handayani, Martin Wilkes, Mohd Nor Siti-Azizah, Su-Fang Niu, Zainal Abidin Muchlisin
There are over 113 species of Lutjanidae, commonly known as snapper worldwide, with 58 species found in the marine waters of Indonesia. This study aimed to examine the genetic characteristics of Rusty jobfish Aphareus rutilans using DNA barcodes from selected locations across the globe, with highlight of new sequences from the waters of South Aceh, Indonesia. A total of 26 DNA barcodes of mitochondrial COI sequences (639 bp) were analysed. The Indonesian subset included new barcodes from South Aceh (n = 3) and BOLD records from Maluku (n = 4) and West Java (n = 2); the remaining 17 sequences were GenBank records from Mozambique (n = 2), South Africa (n = 3), Japan (n = 4), Mauritius (n = 2), China (n = 2), and the Philippines (n = 4). Haplotype network, pairwise genetic distances, and ML phylogeny consistently revealed a western Indo-Pacific cluster (Indonesia, Philippines, Mozambique, South Africa, Mauritius) sharing a dominant haplotype and appearing highly connected. The second clade is made up of Japan which exhibited several closely related local variants while China formed another distinct lineage from the rest. AMOVA corroborated these patterns, indicating significant differentiation within Indonesia (Fst = 0.373; P = 0.033) and very strong structure across the Indo-Pacific (FST = 0.911; P < 0.001). The genetic analysis of samples from Indonesia revealed a moderate diversity value (Hd = 0.833 ± 0.01; π = 0.028 ± 0.01), from a total of five haplotypes. The reconstruction of the phylogenetic tree using maximum likelihood indicated two main clades: Clade 1 consisted of subpopulations from Maluku and West Java, while Clade 2 represented the subpopulation from South Aceh. Interclade genetic distances ranged from 13.2% to 13.5%, supporting a clear genetic divergence of populations from different clades. This study provides valuable genetic data for the Rusty jobfish and supports the conservation and sustainable management of snapper species worldwide especially in Indonesia. © The Author(s), under exclusive licence to Springer Nature Switzerland AG 2025.
Graduate School of Mathematics and Applied Sciences, Universitas Syiah Kuala, Banda Aceh, 23111, Indonesia; Department of Aquaculture, Faculty of Marine and Fisheries, Universitas Syiah Kuala, Banda Aceh, 23111, Indonesia; School of Life Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom; Institute of Climate Adaptation and Marine Biotechnology, University Malaysia Terengganu, Kuala Terengganu, Malaysia; College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China
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