Latitudinal environmental variations driving local adaptation of the P. argenteus population along the coast of China

The distribution of Pampus argenteus, commonly known as silvery pomfret, spans a wide geographic range and diverse habitats, making spatial distance and environmental variations potential factors affecting its population structure. We re-sequenced 117 draft genomes of P. argenteus from six coastal populations in China. Genetic analyses revealed limited genetic differentiation across most genomic regions, yet the Mantel test identified 21 100-Kb sliding windows and 1,607 single nucleotide polymorphisms (SNPs) within these windows, who’s linearized Fst showed significant correlation with latitudinal environmental variations, such as daylight duration, sea surface temperature, and salinity. This suggests potential local adaptations driven by environmental factors in P. argenteus populations. 17 genes within these windows are involved in regulating neuron activity, suggesting that genetic variations in these genes may influence the nervous system's response to environmental cues along the latitude gradient, potentially shaping migratory and spawning behaviors in different silvery pomfret stocks. Moreover, six of these neuronal genes are associated with vertebrate circadian clock regulation, implying the importance of light-dark cycles in driving adaptive evolution in these populations. The majority (96.01%) of candidate SNPs were mapped to non-coding regions, which likely contain regulatory elements affecting transcription and translation. Additionally, 14 transcriptional and translational factors were found within these windows. These findings suggest that local adaptation in silvery pomfrets along the Chinese coast may involve alterations in gene expression rather than functional changes in genes themselves.

银鲳（Pampus argenteus，英文名silvery pomfret）的分布范围涵盖广阔地理区域与多样生境，空间距离与环境变异因此成为影响其种群结构的潜在驱动因素。本研究对取自中国6个沿海种群的117份银鲳草图基因组进行重测序。遗传分析结果显示，多数基因组区域的遗传分化程度较低；通过曼特尔检验（Mantel test）分析，我们在21个100kb滑动窗口及其包含的1607个单核苷酸多态性（single nucleotide polymorphisms, SNPs）中发现，这些窗口内的线性化F统计量（Fst）与纬度相关环境变量（如日照时长、海面温度及盐度）呈显著相关性。该结果提示银鲳种群可能存在由环境因素介导的局部适应性演化。上述滑动窗口内的17个基因参与神经元活动调控，提示这些基因的遗传变异可能影响神经系统对纬度梯度环境信号的响应，进而塑造不同银鲳种群的洄游与产卵行为模式。此外，其中6个神经元基因与脊椎动物生物钟（circadian clock）调控功能相关，这表明光暗周期在推动该种群适应性演化过程中具有重要作用。候选SNPs中的绝大多数（96.01%）被注释到非编码区域，这类区域通常包含影响转录（transcription）与翻译（translation）的调控元件。此外，上述滑动窗口内还鉴定出14个转录翻译因子。上述研究结果表明，中国沿海银鲳的局部适应性演化可能主要通过基因表达调控的改变实现，而非基因本身的功能变异。