International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.2, 54-62 http://ecoevopublisher.com/index.php/ijmec 59 ability to assess and estimate adaptive genetic variation improves the possibility of predicting and estimating the environmental fitness of culture stocks, promoting the development of resilient aquaculture systems in the shadows of a changing environment. The use of genomic information within these fields mirrors larger trends in science research, where new technologies and new modes of analysis are propelling limits of innovation and utilitarian applications in industry and conservation alike (Konieczny, 2023; Shi, 2024). 7 Challenges and Strategic Recommendations 7.1 Limitations in genome data coverage and representativeness Current studies of Siniperca spp. are severely handicapped by inadequate coverage and representativeness of genome data. Most genomic studies sample only a small number of species or populations, whose scope in attempting to cover the complete scope of genetic diversity and adaptive variation necessary in order to make robust evolutionary and functional inference is limited. This lack of whole-genome resources also restrains finding key genes for important traits and adaptation and thereby reduces breeding and conservation program efficiency (Guo et al., 2018; Xiao et al., 2020; Zhong et al., 2022; Bao et al., 2024; Shao et al., 2025). 7.2 Constraints in phylogenetic and functional analysis models Phylogenetic and functional analysis platforms of Siniperca tend to be limited by reliance on a small number of genetic markers or a single-omics that are unable to produce good resolution to distinguish between genetically close species or to uncover complex evolutionary relationships. In addition, the incomplete reference databases and restricted experimental verification reduce gene function annotation and adaptive mechanisms understanding precision (Guo et al., 2018; Xiao et al., 2020; Zhong et al., 2022; Bao et al., 2024). 7.3 Necessity of multi-omics integration and fine-scale functional validation One of the emerging requirements is to utilize multi-omics approaches including genomics, transcriptomics, proteomics, and metabolomics to respond to Siniperca biology in an integrated manner. Multi-omics can be used in combination to reveal the molecular basis of attributes like growth, immunity, and environment adaptation at different levels of biology. However, sophisticated high-resolution functional verification such as gene editing and physiological assays is underdeveloped, while uses of omics information are limited to aquaculture and conservation (Guo et al., 2018; Xiao et al., 2020; Zhong et al., 2022; Bao et al., 2024; Shao et al., 2025). 7.4 Future research suggestions: integration of functional experiments, physiological validation, and ecological simulation Future research should expand the number of genome sequencing study objects to more Siniperca species and populations, thus ensuring broader data representativeness and coverage. Evolution and use of advanced phylogenetic and functional analysis models, supported by improved reference databases, will help in more accurate evolutionary and functional inference. Incorporation of multi-omics data with functional assays, physiological validation, and ecological modeling will provide an integrated picture of trait development and environmental acclimatization, eventually leading to precision breeding, sustainable aquaculture, and effective conservation planning for Siniperca spp. (Guo et al., 2018; Xiao et al., 2020; Bao et al., 2024; Zhong et al., 2022; Shao et al., 2025). 8 Concluding Remarks Recent advances in large-scale genomic sequencing and phylogenetic analysis have enabled Siniperca phylogeny to be reconstructed more confidently. High-throughput sequencing of thousands of nuclear coding sequences and comprehensive analyses have confirmed the monophyly of Sinipercidae, supporting classification into two genera, Siniperca and Coreoperca. Notably, Siniperca scherzeri was identified as the most basal taxon, and well-defined Siniperca clades were delineated, providing unequivocal support to the validity of several contentious species and clarifying relationships that had hitherto remained ambiguous due to limited morphological differentiation. Genomic analysis has revealed widespread signals of adaptive evolution in Siniperca, particularly in genes associated with predatory feeding, growth, and environmental adaptation. Positive selection scans revealed sudden evolution in feeding behavior, aggressiveness, and physiological traits such as euryhalinity and pyloric caeca
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