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 basin-wide riverscape genomic analysis in the threatened southern pygmy perch (Nannoperca australis), an ecological specialist with low dispersal potential. High-resolution environmental data and 5,162 high-quality filtered SNPs were used to clarify spatial population structure and to assess footprints of selection associated to a steep hydroclimatic gradient and to 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 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进化响应的核心所在。在复杂空间环境中检测选择印记仍颇具挑战，对于受威胁物种而言尤为如此——这类物种中强烈的遗传漂变效应往往会掩盖选择的分子印记。本研究针对受威胁物种南方矮鲈（Nannoperca australis）开展了全流域河流景观基因组学分析，该物种为扩散能力较弱的生态特化种。研究借助高分辨率环境数据与5162个经过严格质控的高质量单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）位点，旨在明确澳大利亚墨累-达令盆地这一兼具自然与人为碎片化特征的区域内的空间种群结构，并评估与陡峭水文气候梯度及人类干扰相关的选择印记。本研究采用的分析方法包括：以FST（Fixation Index）离群位点检测界定中性位点，结合空间显式基因型-环境关联分析鉴定候选适应性位点，同时控制景观结构与共享种群历史的影响。结果显示，种群的遗传多样性水平较低，且存在显著的中性种群结构，这与基于河流空间层级结构与生活史特征的预期相符。与之相对，与降水和温度相关的环境变量，在区域与局域尺度上均为推测性适应性遗传变异的最重要环境替代指标。人类干扰同样会影响适应性候选位点的遗传变异，但该效应仅存在于局域尺度。本研究有助于深化对自然与人为碎片化生态系统中适应性进化过程的认知，同时也为景观基因组学在指导生物多样性原地保护与迁地保护管理方面的潜在应用价值提供了切实例证。