International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.2, 54-62 http://ecoevopublisher.com/index.php/ijmec 57 4.3 Candidate genes related to environmental adaptation and their biological functions Most of the candidate genes uncovered by positive selection analysis or gene family evolution analysis in Siniperca are involved in key functions of environmental adaptation, including immune regulation, sensory perception (especially olfaction and vision), reproduction, and stress response. These functions are critical for Siniperca species to adapt to freshwater systems with fluctuating thermal, oxygen, and feeding regimes. Functional enrichment and annotation analysis also connect these genes to important adaptive characters such as disease resistance, prey specialization, and environmental stress tolerance and shed light on their ecological functions in evolutionary divergence (Ellegren, 2008; Csilléry et al., 2018; Salazar-Tortosa et al., 2023). 4.4 Convergent evolution at the genomic level and inter-species ecological comparisons Comparative genomic analysis between Siniperca and other freshwater fish have found examples of convergent evolution—where unrelated lineages develop the same characters or gene changes independently under the same environmental pressures. For example, conserved signatures of selection have been detected across species in genes that are associated with visual receptors, mucosal immunity, and metabolism. Comparisons of gene regulatory networks and adaptive loci among taxa may uncover convergent adaptive strategies and the level of regulatory and functional convergence (Figure 2). Such studies improve our understanding of Siniperca species and other species adapting to similar hydrology and temperature environments, and reveals the genomic foundation of convergent phenotypes (Regev et al., 2015; Csilléry et al., 2018). Figure 2 Genomic structure and sequence information of the Sinipercagenus (Adopted from Liang et al., 2019) 5 Analysis of Adaptive Evolutionary Mechanisms at the Genomic Level 5.1 Selective pressures from ecological factors such as temperature, water environment, and diet Siniperca members are dispersed in diverse freshwater ecosystems throughout China and possess impressive ecological adaptations to temperature, water quality, and diet. Siniperca members vary from subtropical low-oxygen water to cold oxygen-rich rivers in northern China and possess physiological and metabolic distinctions. Genomic analysis indicates that metabolic genes underwent rapid evolutionary rates, allegedly an adaptation to their carnivorous diet as well as environmental sensitivity (Han, 2024). Ecological stresses such as temperature fluctuations, fluctuating dissolved oxygen, and nutrient differences apparently have exerted positive pressure on energy metabolism genes, oxidative stress response genes, and nutrient uptake genes (Huang, 2020; Bafna et al., 2021). Aside from that, adaptive evolution can also be facilitated through events of gene loss to prefer against duplicative functions in new habitats, a process that occurs within aquatic and flying mammals but which also might be promoted to Sinipercaspecies (Langer et al., 2018).
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