International Journal of Aquaculture, 2025, Vol.15, No.5, 240-247 http://www.aquapublisher.com/index.php/ija 241 Mitochondrial DNA (mtDNA) has been a useful marker in phylogenetic and evolutionary studies due to its maternal inheritance, relatively high mutation rate, and absence of recombination. In tilapias, mtDNA markers including cytochrome oxidase I (COI), cytochrome b (CYTB), and the D-loop region have been extensively used for elucidating species relationships, genetic divergences, and detecting hybridization events. Recent studies have demonstrated that mtDNA data can easily resolve problematic phylogenetic relationships, particularly in cryptic or closely related species, founded on morphology characters alone. Additionally, mtDNA has been important in revealing the origin and evolutionary history of domestic strains. The objectives of this study are to compare mitochondrial DNA sequences of representative Oreochromis species for resolving their phylogenetic relationships, estimating intra- and interspecific genetic diversity, and providing molecular evidence for guiding taxonomy, conservation, and breeding programs. In doing this, the current study expects to improve our understanding of tilapia evolutionary biology and aid in sustainable management of their genetic resources. 2 Genetic Basis and Phylogenetic Differentiation of Tilapias 2.1 Species composition and phylogenetic relationships within the genus Oreochromis The genus Oreochromis comprises morphologically disparate group of tilapia species with a complex evolutionary history that is the product of ancient and contemporary hybridization events, as revealed by recent genome-scale phylogenies. These broader-level systematics are complemented by molecular phylogenies at fine taxonomic scales using mitochondrial and nuclear markers, which have revealed repeated adaptation to environmental extremes (e.g., temperature and salinity) within the genus. Of specific interest is the subgenus Alcolapia, now embedded in Oreochromis, as taxonomic updates unfold. Mitochondrial and nuclear DNA trees generally fall in disagreement, perhaps due to incomplete lineage sorting and introgression, with the consequence of obscuring species limits and evolutionary history (Ford et al., 2019; Mojekwu et al., 2020; Ciezarek et al., 2024). 2.2 Genetic diversity and geographic differentiation among tilapia populations Tilapia are characterized by great genetic diversity and geographically related differentiation due to natural biogeographic and man-imposed factors such as translocations and aquaculture introductions (Popoola, 2024; Tibihika et al., 2024; Kwikiriza et al., 2025). Mitochondrial and nuclear markers have described certain genetic clusters within and across regions with some of the populations (e.g., Ethiopian and Ugandan) being highly differentiated and with surfacing genetic resources (Tibihika et al., 2024; Kwikiriza et al., 2025). Genetic diversity is usually lost in farmed or stocked populations, however, by bottlenecks, founder effects, and inbreeding. Introduction of foreign strains and hybridization incidents have also reshaped the genetic landscape, sometimes leading to admixture and loss of local genetic purity (Tibihika et al., 2019; Tesfaye et al., 2021; Nyaku, et al., 2023) (Figure 1). Figure 1 Principal Coordinate Analysis (PCoA) plots illustrating genetic similarity of Nile tilapia populations in Ethiopia considering all populations. The first axis explains 26.2%, second axis 10% and third axis 7.2% of the variation, accumulating to 43.3% (Adopted from Tesfaye et al., 2021)
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