Data from: Natural selection in the water: freshwater invasion and adaptation by water color in the Amazonian pufferfish

Natural selection and ecological adaptation are ultimately responsible for much of the origin of biodiversity. Yet the identification of divergent natural selection has been hindered by the spatial complexity of natural systems, the difficulty in identifying genes under selection and their relationship to environment, and the confounding genomic effects of time. Here we employed genome scans, population genetics and sequence-based phylogeographic methods to identify divergent natural selection on population boundaries in a freshwater invader, the Amazonian pufferfish, Colomesus asellus. We sampled extensively across markedly different hydrochemical settings in the Amazon Basin and use ‘water color’ to test for ecological isolation. We distinguish the relative contribution of natural selection across hydrochemical gradients from biogeographic history in the origin and maintenance of population boundaries within a single species and across a complex ecosystem. We show that spatially distinct population structure generated by multiple forces (i.e. water color and vicariant biogeographic history) can be identified if the confounding effects of genetic drift have not accumulated between selective populations. Our findings have repercussions for studies aimed at identifying engines of biodiversity and assessing their temporal progression in understudied and ecologically complex tropical ecosystems.自然选择与生态适应，是绝大多数生物多样性起源的核心动因。然而，歧化自然选择（divergent natural selection）的识别工作长期受到多重因素制约：自然系统的空间复杂性、受选择基因及其与环境关联的识别难度，以及时间所带来的混淆性基因组效应。本研究采用基因组扫描、群体遗传学及基于序列的系统发育地理学方法，针对淡水入侵物种亚马孙河鲀（Colomesus asellus）的种群边界开展歧化自然选择识别。研究团队在亚马孙盆地内多个差异显著的水化学环境中开展了大范围采样，并以‘水色’作为指标检验生态隔离效应。本研究旨在区分：在单一物种种群边界的起源与维持过程中，以及在复杂生态系统尺度下，沿水化学梯度的自然选择与异域生物地理历史各自的相对贡献。研究表明，若选择性种群间未积累遗传漂变的混淆效应，则可识别由多重作用（即水色与异域生物地理历史）形成的空间差异化种群结构。本研究结果对于旨在识别生物多样性驱动引擎，并评估研究不足、生态复杂的热带生态系统中这些驱动因子的时间演化进程的相关研究，具有重要参考价值。