International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.2, 54-62 http://ecoevopublisher.com/index.php/ijmec 54 Research Insight Open Access Phylogenetic Reconstruction and Genomic Adaptive Evolution inSinipercaspp. Chengmin Sun1, RudiMai 2 1 Center for Tropical Marine Fisheries Research, Hainan Institute of Tropical Agricultural Resouces, Sanya, 572025, Hainan, China 2 Tropical Biological Resources Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China Corresponding author: rudi.mai@hitar.org International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.2 doi: 10.5376/ijmec.2025.15.0006 Received: 18 Jan., 2025 Accepted: 24 Feb., 2025 Published: 06 Mar., 2025 Copyright © 2025 Sun and Mai, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Sun C.M., and Mai R.D., 2025, Phylogenetic reconstruction and genomic adaptive evolution in Siniperca spp., International Journal of Molecular Ecology and Conservation, 15(2): 54-62 (doi: 10.5376/ijmec.2025.15.0006) Abstract Siniperca or Chinese perch is a freshwater fish family indigenous to East Asia, of great economic value and ecological particularity. Though of great significance in aquaculture, the phylogenetic histories of the Siniperca genus are unclear due to morphological convergence and a dearth of molecular data. We rebuilt the genome-wide single-copy orthologous genes-based phylogenetic framework of Siniperca and inferred divergence times between species using a molecular clock model in this study. We further performed comparative genomics to identify expansions of gene families, positive selection signals, and adaptive evolutionary trajectories linked with ecological specialization. Several genetic candidates for environmental tolerance, immune response, and sensory systems were detected, suggesting lineage-specific adaptation to various freshwater environments. This study not only illuminates the phylogenetic history of Siniperca, but also reveals the genetic mechanism of its adaptive divergence, providing theoretical evidence for species conservation, utilization of resources, and molecular breeding in aquaculture. Keywords Siniperca; Phylogenetic reconstruction; Comparative genomics; Adaptive evolution; Freshwater fish 1 Introduction The Siniperca genus is a family of freshwater fish endemic to East Asia in the Sinipercidae family. It contains some of its species such as S. chuatsi, S. scherzeri, S. kneri, and S. undulata, which are found mainly in the Yangtze, Pearl, and Amur river basins. They are carnivorous species, solitary, and prefer clean, slow-moving freshwater environments. Despite their ecological divergence, their phylogenetic relationships and placements within the genus are controversial due to convergent morphological features coupled with limited molecular markers (Liang et al., 2019; Zhang et al., 2023). Advances in genome sequencing coupled with phylogenomic methods in the past few years have paved new ways in resolving these taxonomic ambiguities as well as their evolution. Siniperca chuatsi (mandarin fish) and S. scherzeri are two of the most valuable Chinese freshwater aquaculture species, with high consumer demand and excellent meat quality, and they grow rapidly. The production of S. chuatsi has been more than 300,000 tons each year, becoming China's pillar of carnivorous fish production (Zhao et al., 2017; Chen et al., 2020). However, high-level production has brought with it new issues, including more frequent outbreak of disease, reduced genetic variation, and depression in inbreeding. They have generated growing interest in using molecular technologies like whole-genome selection, marker-assisted breeding, and genome-wide association studies to improve desirable traits including disease resistance, growth rate, and feed efficiency (Chen et al., 2020). A good understanding of the evolutionary and genetic basis of these traits is required to guide upcoming breeding programmes. Phylogenetic analysis forms the foundation of understanding speciation, the evolution of traits, and the conservation of biodiversity. In this genomics era, having the capability to combine high-throughput sequencing with phylogenomics enables scientists to have the ability to uncover ancient evolutionary relationships and identify genomic regions under selection. In Siniperca spp., where there has been ecological divergence and niche specialization, the integration of phylogenetic reconstruction and adaptive evolution analysis encapsulates how these fishes evolve to respond to environmental stresses such as temperature, turbidity, and prey availability. In addition, investigations of positively selected genes and fast-evolving gene families can reveal genetic
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