International Journal of Aquaculture, 2025, Vol.15, No.5, 240-247 http://www.aquapublisher.com/index.php/ija 240 Research Insight Open Access Mitochondrial DNA Analysis for Resolving the Phylogenetic Relationships of Tilapia Species XianLi 1, Xiaoli Chen1, RudiMai 2 1 Tropical Animal Resources Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China 2 Tropical Marine Fisheries Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China Corresponding author: rudi.mai@hitar.org International Journal of Aquaculture, 2025, Vol.15, No.5 doi: 10.5376/ija.2025.15.0023 Received: 15 Aug., 2025 Accepted: 27 Sep., 2025 Published: 09 Oct., 2025 Copyright © 2025 Li et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Li X., Chen X.L., and Mai R.D., 2025, Mitochondrial DNA analysis for resolving the phylogenetic relationships of tilapia species, International Journal of Aquaculture, 15(5): 240-247 (doi: 10.5376/ija.2025.15.0023) Abstract Oreochromis spp. (Tilapias) are commercially important fishes with extensive distribution in Africa and other tropical and subtropical regions. Due to morphological similarity, high incidence of hybridization, and complex domestication history, the phylogenetic relationships and taxonomic limits of tilapia species are disputed. In this study, mitochondrial DNA (mtDNA) sequences-COI, CYTB, and D-loop gene fragments-were resolved for some representative Oreochromis species and geographical populations. Phylogenetic trees were reconstructed using Neighbor-Joining (NJ), Maximum Likelihood (ML), and Bayesian Inference (BI) methods to infer evolutionary relationships. The analyses revealed clear genetic differentiation among tilapia species, while some local strains and hybrid populations contained admixed lineages or overlapping taxonomic signals. Genetic distances among populations generally corresponded to geographic separation, suggesting the combined effects of natural selection and human activity on genetic structure. Functional analysis of the variants of mitochondrial genes identified key loci with a putative association with energy metabolism and reproductive adaptation, suggesting their roles in ecological adaptation and phenotypic evolution. The study explains phylogenetic structure among Oreochromis species, verifies the feasibility of mtDNA in species identification, germplasm conservation, and molecular breeding, and provides basic data and theoretical basis for further study on tilapia molecular evolution and environmental adaptation. Keywords Oreochromis; Mitochondrial DNA; Phylogeny; Genetic diversity; Molecular marker 1 Introduction The genus Oreochromis of the family Cichlidae is a complex and ecologically variable group of African and Middle Eastern freshwater fish. The genus comprises more than 30 validly described species, as well as a variety of locally distinct populations or subspecies. The tilapias occupy a very wide range of aquatic habitats, from rivers and lakes to reservoirs and brackish water. Their adaptability to different ecological conditions has fostered their widespread introduction throughout the world, particularly for aquaculture and aquatic vegetation control. As a result, Oreochromis species are now established in Asia, Latin America, and certain Pacific Islands. However, rampant hybridization, phenotypic similarity, and rapid evolutionary radiation within the genus have imposed great difficulty on taxonomy and species classification, leading to long-standing disputes in their systematic classification (Kinaro et al., 2016; Geletu and Zhao, 2022). Tilapias, especially Oreochromis niloticus, O. mossambicus, and O. aureus, are the most important aquaculture species globally due to their high growth rate, high fertility, tolerance to low water quality, and diversification to different types of farming systems. They play a crucial role in food security and rural livelihood in developing countries, particularly low- and middle-income countries. Tilapia aquaculture contributes significantly to global freshwater aquaculture production, as per FAO reports. Over the past few years, advancements have been made in aquaculture technology like Recirculating Aquaculture Systems (RAS), Biofloc Technology (BFT), and Integrated Multi-Trophic Aquaculture (IMTA) further optimizing production efficiency and profitability. Tilapia is also being produced on commercial scale, as in smallholder systems for the development of local economies as well as food security. However, large breeding and translocation have increased the risk of genetic homogenization and introgression, raising alarm for conservation of indigenous germplasm (Ford et al., 2019; Fatsi et al., 2020).
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