Data from: Riverscape genomics of a threatened fish across a hydroclimatically heterogeneous river basin

Understanding how natural selection generates and maintains adaptive genetic diversity in heterogeneous environments is key to predicting the evolutionary response of populations to rapid environmental change. Detecting selection in complex spatial environments remains challenging, especially for threatened species where the effects of strong genetic drift may overwhelm signatures of selection. We carried out a basinwide riverscape genomic analysis in the threatened southern pygmy perch (Nannoperca australis), an ecological specialist with low dispersal potential. High-resolution environmental data and 5162 high-quality filtered SNPs were used to clarify spatial population structure and to assess footprints of selection associated with a steep hydroclimatic gradient and with human disturbance across the naturally and anthropogenically fragmented Murray–Darling Basin (Australia). Our approach included FST outlier tests to define neutral loci, and a combination of spatially explicit genotype–environment association analyses to identify candidate adaptive loci while controlling for the effects of landscape structure and shared population history. We found low levels of genetic diversity and strong neutral population structure consistent with expectations based on spatial stream hierarchy and life history. In contrast, variables related to precipitation and temperature appeared as the most important environmental surrogates for putatively adaptive genetic variation at both regional and local scales. Human disturbance also influenced the variation in candidate loci for adaptation, but only at a local scale. Our study contributes to understanding of adaptive evolution along naturally and anthropogenically fragmented ecosystems. It also offers a tangible example of the potential contributions of landscape genomics for informing in situ and ex situ conservation management of biodiversity.

解析自然选择如何在异质环境中产生并维持适应性遗传多样性，是预测种群对快速环境变化的演化响应的核心所在。在复杂空间环境中检测选择信号仍颇具挑战，对于受胁物种而言更是如此——这类物种的强烈遗传漂变效应可能掩盖选择的分子印记。我们针对受胁物种南矮鲈（*Nannoperca australis*）开展了全流域河川景观基因组学分析，该物种为扩散能力较弱的生态特化类群。我们借助高分辨率环境数据与5162个经过高质量过滤的单核苷酸多态性（Single Nucleotide Polymorphism, SNPs），明确了澳大利亚墨累-达令盆地这一受自然与人为活动双重破碎化影响的区域的空间种群结构，并评估了与陡峭水文气候梯度及人为干扰相关的选择印记。本研究采用的分析方法包括：通过固定指数（Fixation Index, FST）离群值检测界定中性位点，结合空间显性基因型-环境关联分析识别候选适应性位点，同时校正景观结构与种群共享历史带来的影响。研究结果显示，种群的遗传多样性水平较低，且呈现出显著的中性种群结构，这与基于河流空间层级结构及物种生活史所预期的结果相符。与之形成对比的是，在区域与局域尺度上，与降水和温度相关的变量均为推定适应性遗传变异的最重要环境替代指标。人为干扰同样会影响适应性候选位点的遗传变异，但这种影响仅存在于局域尺度。本研究有助于解析受自然与人为活动双重破碎化的生态系统中的适应性演化过程，同时也为景观基因组学如何为生物多样性的就地保护与迁地保护管理提供科学依据提供了切实可行的范例。