An Li, Meng Qinglei, Dong Xuesa, Zhu Shuren, Wang Chao, Xu Xiao, Feng Xiuyun, Liu Yuqing, Yan Jiaren, Zhang Longgang
Department of Genetics and Breeding, Shandong Freshwater Fisheries Research Institute, Jinan, China.
J Fish Biol. 2025 Aug 12. doi: 10.1111/jfb.70128.
The snakehead (Channa argus) is an economically important freshwater fish species. Understanding how geographical isolation affects population differentiation is important for understanding the processes that shape biodiversity. We examined four wild populations [Dongping Lake (DP), Nansi Lake (NS), Yihe River (YH) and Yellow River Estuary (HH)] and an aquaculture population [Weishan Lake (WL)] in Shandong Province using whole-genome resequencing for the first time. This approach provided deeper insights of genetic variation compared to previous studies with lower genome coverage. We identified single nucleotide polymorphisms (SNPs) and insertion-deletion (InDel) variants among the five populations. A total of 106,172 DNA variants were located in the exonic gene region, with 53,415 causing nonsynonymous mutations, 9757 resulting in frameshift mutations and 2345 leading to a loss or gain of stop codons. Polymorphic information content (PIC) analysis showed moderate polymorphism across all populations, with an increase over the past decade, likely due to reduced human interference. Genetic diversity indexes (H, H, H' and π) showed minimal variation among populations, suggesting similar environmental pressures and low levels of inbreeding. F values indicated that the WL and NS populations met the neutral expectation of heterozygosity, whereas other populations exhibited higher heterozygosity potentially due to geographical factors. Phylogenetic tree analysis, principal component analysis (PCA) and population structure analysis confirmed genetic clustering aligned with geographical distribution. The F values indicated moderate genetic differentiation, with gene flow observed between the DP and WL populations likely due to artificial introductions. The WL population exhibited strong signs of artificial selection. Functional enrichment analysis revealed adaptive differentiation in osmoregulation-related genes in the HH population, whereas the WL population showed selective pressure in genes related to oxygen transport in the blood, suggesting the influence of aquaculture and environment on genetic adaptation. This study highlights the role of geographical isolation in population differentiation and emphasizes the importance of habitat connectivity in maintaining gene flow and genetic diversity. The findings indicate no significant human-induced isolation in the major water bodies of Shandong Province, which benefits the conservation of C. argus and provides valuable insights for the sustainable management of wild populations.
乌鳢（Channa argus）是一种具有重要经济价值的淡水鱼类。了解地理隔离如何影响种群分化对于理解塑造生物多样性的过程至关重要。我们首次对山东省的四个野生种群[东平湖（DP）、南四湖（NS）、沂河（YH）和黄河口（HH）]以及一个养殖种群[微山湖（WL）]进行了全基因组重测序。与之前基因组覆盖度较低的研究相比，这种方法能更深入地洞察遗传变异。我们在这五个种群中鉴定出单核苷酸多态性（SNP）和插入缺失（InDel）变异。共有106,172个DNA变异位于外显子基因区域，其中53,415个导致非同义突变，9757个导致移码突变，2345个导致终止密码子的缺失或增加。多态信息含量（PIC）分析表明所有种群均具有中等多态性，且在过去十年中有所增加，这可能是由于人类干扰减少所致。遗传多样性指数（H、H、H'和π）表明种群间差异极小，这表明环境压力相似且近亲繁殖水平较低。F值表明WL和NS种群符合杂合度的中性预期，而其他种群可能由于地理因素表现出较高的杂合度。系统发育树分析、主成分分析（PCA）和种群结构分析证实了与地理分布一致的遗传聚类。F值表明存在中等程度的遗传分化，DP和WL种群之间观察到基因流，这可能是由于人工引入所致。WL种群表现出强烈的人工选择迹象。功能富集分析揭示了HH种群中与渗透调节相关基因的适应性分化，而WL种群在与血液中氧气运输相关的基因中表现出选择压力，这表明养殖和环境对遗传适应的影响。本研究强调了地理隔离在种群分化中的作用，并强调了栖息地连通性在维持基因流和遗传多样性方面的重要性。研究结果表明山东省主要水体中不存在显著的人为诱导隔离，这有利于乌鳢的保护，并为野生种群的可持续管理提供了有价值的见解。
