International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.2, 54-62 http://ecoevopublisher.com/index.php/ijmec 60 formation. Genome-wide association analysis also detected SNPs and candidate genes for economically important traits such as growth, muscle, and bone development, thus leaving a molecular legacy of adaptation and trait evolution in Siniperca. Together with high-quality genome assemblies, phylogenetic analysis, and functional genomics, they provide new insights into Siniperca breeding and conservation. Genomic resources facilitate accurate species identification, genetic diversity inference, and marker-assisted selection breeding in aquaculture. Population history and adaptive evolution guide conservation management, and adaptive evolution genes involved in growth and adaptation aid precision breeding and environmental adaptability. These improvements collectively enhance the Siniperca species' ecological adaptation and sustainable use research. 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. References Bafna V., Zhou D., Stobdan T., Iranmehr A., Kryazhimskiy S., Haddad G., and Zhao H., 2021, Multiple mechanisms drive genomic adaptation to extreme O₂ levels in Drosophila melanogaster, Nature Communications, 12: 997. https://doi.org/10.1038/s41467-021-21281-6 Bao L., Peng J., Tuo Y., Fang H., and Chu W., 2024, Research progress on nutritional requirements and formulated feeds for Siniperca: a comprehensive review, Fishes, 9(12): 487. https://doi.org/10.3390/fishes9120487 Chen J., Lin L., Han L., Li G., Liu X., Huang C., Zhang Z., Bi S., Liang J., Li H., Zhang Y., Liu S., Yi H., Sun J., Wei X., and Chen Q., 2024, Morphological characteristics, genetic diversity, and microsatellite analysis of the progenies (F1, F2, and backcross descendant) of Siniperca chuatsi and Siniperca scherzeri, Aquaculture Research, 2024(1): 6672569. https://doi.org/10.1155/2024/6672569 Chen X., Zhang Z., Yin Z., Li J., He S., Tang S., Xu J., Lv L., Dou Y., Li L., Liang X., Cai W., Zhang Y., Kuhl H., Wuertz S., and Tao Y., 2020, Mandarin fish (Sinipercidae) genomes provide insights into innate predatory feeding, Communications Biology, 3: 361. https://doi.org/10.1038/s42003-020-1094-y Csilléry K., Rodríguez-Verdugo A., Guillaume F., and Rellstab C., 2018, Detecting the genomic signal of polygenic adaptation and the role of epistasis in evolution, Molecular Ecology, 27: 606-612. https://doi.org/10.1111/mec.14499 DeGiorgio M., Santos A., Arnab S., and Fumagalli M., 2025, Efficient detection and characterization of targets of natural selection using transfer learning, Molecular Biology and Evolution, 42(5): msaf094. https://doi.org/10.1093/molbev/msaf094 Dissanayake A., 2020, Applied aspects of methods to infer phylogenetic relationships amongst fungi, Mycosphere, 11: 2652-2676. https://doi.org/10.5943/mycosphere/11/1/18 Ellegren H., 2008, Comparative genomics and the study of evolution by natural selection, Molecular Ecology, 17(21): 4586-4596. https://doi.org/10.1111/j.1365-294X.2008.03954.x Guo C., Zhang T., Li Z., Beauchamp D., Li W., Hicks B., Liu J., and Lin M., 2018, Impacts of hatchery-reared mandarin fish Siniperca chuatsi stocking on wild fish community and water quality in a shallow Yangtze lake, Scientific Reports, 8: 11481. https://doi.org/10.1038/s41598-018-29758-z Han Y.P., 2024, Population genomics of primates: diversity, structure, and evolutionary dynamics, International Journal of Molecular Evolution and Biodiversity, 14(3): 108-119. https://doi.org/10.5376/ijmeb.2024.14.0014 Horiike T., 2016, An introduction to molecular phylogenetic analysis, Robotics and Autonomous Systems, 4: 36-45. https://doi.org/10.7831/RAS.4.36-45 Huang Y., 2020, Dissecting genomic determinants of positive selection with an evolution-guided regression model, Molecular Biology and Evolution, 39(1): msab291. https://doi.org/10.1093/molbev/msab291 Jiang J., Zhao J., Lu L., and Li C., 2023, Comparative genomics revealed drastic gene difference in two small Chinese perches, Siniperca undulata and S. obscura, G3: Genes|Genomes|Genetics, 13(7): jkad101. https://doi.org/10.1093/g3journal/jkad101
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