International Journal of Aquaculture, 2025, Vol.15, No.5, 240-247 http://www.aquapublisher.com/index.php/ija 245 7.2 Challenges in sample coverage and data representativeness Representative and broad sampling coverage are still an issue in mtDNA studies. Limited geographic or taxonomic sampling may give rise to skewed results and mask actual genetic diversity and population structure patterns. Partial or skewed sampling may further hinder the detection of rare haplotypes or cryptic lineages, reducing the power of phylogenetic analysis and conservation assessment. Improved sampling designs and use of high-quality, large reference alignments can enable the resolution of such issues as well as enhance the solidity of mtDNA-informed studies. 7.3 Lack of experimental validation and ecological correlation for functional mtDNA variants While mtDNA variation is often associated with phenotypic and ecological character, experimental evidence for functional effect is rare. The majority of reports are based on correlative data, and the ecological relevance of specific mtDNA variants has been inadequately examined. The requirement exists for integrative systems synthesizing genetic, functional, and ecological data to prove the adaptive worth of mtDNA variants and determine their functions in organismal fitness and adaptation (Kopinski et al., 2021; Wang and Wang, 2024). 7.4 Establishing a multi-marker and multi-scale framework for phylogenetic and adaptive studies of tilapias Subsequent work should involve the development of multi-marker and multi-scale models integrating mtDNA, nuclear DNA, and additional genomic data. Throughputs in high-throughput sequencing and improvements in bioinformatics now make it possible to simultaneously analyze thousands of nuclear and mitochondrial loci simultaneously, increasing phylogenetic resolution and the detection of mito-nuclear discordance. All such integrative approaches are critical for robust species delimitation, understanding adaptive evolution, and informing conservation and management in tilapias and other groups (Lareau et al., 2023). 8 Concluding Remarks Phylogenies of large molecular datasets, integrating both mitochondrial and nuclear markers, have clarified the evolutionary relationships among Oreochromis species. Multi-marker phylogenies have pervasive mito-nuclear discordance, which is often due to incomplete lineage sorting or introgression, but nuclear phylogenies reproduce major clades regularly and confirm the nesting of Alcolapia in Oreochromis. The findings have instigated taxonomic revision and improved understanding of the adaptation and diversification of Oreochromis, especially in stressful environments such as soda lakes. Ancient and recent hybridization has played a role in the evolutionary history of Oreochromis, producing genetic variation and, in certain cases, hybrid speciation. However, ongoing hybridization-typically by aquaculture introductions-is compromising the genetic integrity of native populations. Geographical isolation and ecological adaptation, including to stressful environments, have independently resulted in lineage divergence and repeated evolution of major adaptive traits within the genus. Molecular markers, particularly mtDNA and nuclear markers, are excellent tools for correct species identification, taxonomic delimitation, and hybrid detection. These methods are the foundation for conservation efforts through the facilitation of the revelation of genetic structure, establishing distinctive lineages, and tracking introgression. Molecular data are used to guide breeding programs, for genetic diversity assurance, and market regulation through accurate species identification even in processed products, aquaculture, and resource management. Acknowledgments Thanks to the animal research team for their support and help in data collection and data collection. Conflict of Interest Disclosure The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.
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