International Journal of Aquaculture, 2025, Vol.15, No.5, 240-247 http://www.aquapublisher.com/index.php/ija 243 monophyletic clades correspond to geographic origin, which is in accordance with the role of geographic isolation in lineage divergence. Figure 2 UPGMA dendrogram of the different populations of tilapia species constructed using Nei’s genetic distance (Adopted from Kwikiriza et al., 2025) Image caption: support is given by bootstrap values. Red: Cages, Blue: Hatcheries, Green: Wild and Black: Ponds (Adopted from Kwikiriza et al., 2025) 4.3 Identification of hybrids and cryptic species and their evolutionary implications Mitochondrial analyses will frequently disclose cryptic lineages and supposed hybridization events. However, mito-nuclear discordance where mtDNA and nuclear DNA suggest different evolutionary histories is widespread. Discordance is caused by ancient introgression, incomplete lineage sorting, or recent hybridization and complicates recovery of true cryptic species. Integrative approaches that use both mtDNA and nuclear markers are recommended for accurate delimitation of species and inference of evolutionary processes (Abreu et al., 2020). 4.4 Monophyletic/paraphyletic status of key populations and taxonomic interpretations Phylogenetic analyses reveal the general trend of finding that not all populations or species are monophyletic for mtDNA and some are paraphyletic due to hybridization or incomplete lineage sorting. While mtDNA can resolve much of the relationships, nuclear markers can reveal more in the way of complexity, such as admixture or no well-defined species boundaries. These findings suggest the prudence with which taxonomic inference based on mtDNA alone should be conducted and their support for the use of integrative taxonomic methods (Abreu et al., 2020). 5 Mitochondrial Genetic Mechanisms of Adaptive Evolution in Tilapias 5.1 Selective pressures from ecological factors on mitochondrial evolution rates Environmental and climatic factors can impose selective pressures on mitochondrial genomes, possibly regulating their evolution rates. Accounts in other groups indicate mitochondrial genes are subjected to strong purifying selection with varied intensity between species and genes depending on the metabolic requirements and environmental stress. For example, energy production genes like ND1, ND2, ND6, COIII, and ATP8 may be under higher purifying selection in harsher environments of some species, and such mechanisms may dominate in tilapias taking on varied aquatic environments (Ghosh et al., 2024). 5.2 Functional evolution of mitochondrial genes related to energy metabolism and reproductive adaptation Mitochondrial genes play a central role in energy metabolism, particularly through oxidative phosphorylation (OXPHOS). Adaptive evolution in such genes can affect ATP and reactive oxygen species (ROS) production, which can impact organismal performance, life-history characteristics, and adaptation to new thermal or ecological environments. Furthermore, mitochondrial genetic variation can influence reproductive traits, with evidence that mtDNA variants have a role in sperm performance and can be the target of sex-specific selection, which may find applicability for tilapia reproductive adaptation (Koch et al., 2021).
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