Data from: Divergent natural selection with gene flow along major environmental gradients in Amazonia: insights from genome scans, population genetics and phylogeography of the characin fish Triportheus albus

The unparalleled diversity of tropical ecosystems like the Amazon Basin has been traditionally explained using spatial models within the context of climatic and geological history. Yet, it is adaptive genetic diversity that defines how species evolve and interact within an ecosystem. Here we combine genome scans, population genetics and sequenced-based phylogeographic analyses to examine spatial and ecological arrangements of selected and neutrally evolving regions of the genome of an Amazonian fish, Triportheus albus. Using a sampling design encompassing five major Amazonian rivers, three hydrochemical settings, and 352 nuclear markers and two mitochondrial DNA genes, we assess the influence of environmental gradients as biodiversity drivers in Amazonia. We identify strong divergent natural selection with gene flow and isolation by environment across craton (black and clear color) and Andean (white colour) derived water types. Furthermore, we find that heightened selection and population genetic structure present at the interface of these water types appears more powerful in generating diversity than the spatial arrangement of river systems and vicariant biogeographic history. The results from our study challenge assumptions about the origin and distribution of adaptive and neutral genetic diversity in tropical ecosystems. In addition, they have important implications for measures of biodiversity and evolutionary potential in one of the world’s most diverse and iconic ecosystems.

以亚马孙流域为代表的热带生态系统拥有无与伦比的生物多样性，过往学界多依托气候与地质历史背景下的空间模型，对其多样性成因展开阐释。然而，真正决定物种在生态系统内演化与相互作用方式的，是适应性遗传多样性（adaptive genetic diversity）。本研究整合基因组扫描（genome scans）、群体遗传学（population genetics）与基于测序的系统地理学分析（phylogeographic analyses）方法，针对亚马孙鱼类Triportheus albus基因组中受选择区域与中性演化区域的空间与生态分布模式展开探究。本研究采用覆盖5条主要亚马孙河流域、3种水化学类型的采样方案，结合352个核标记与2个线粒体DNA（mitochondrial DNA）基因位点，评估环境梯度作为亚马孙生物多样性驱动因子的影响。本研究发现，在克拉通（craton）来源的黑色与透明清水型水体，以及安第斯山脉（Andean）来源的白色水体之间，存在显著的趋异自然选择，同时伴随基因流与环境隔离效应。此外，本研究发现，在两类水体的交界区域出现的强化选择与群体遗传结构，相较于河流系统的空间布局与异域分化生物地理历史，在生物多样性生成过程中的驱动作用更为显著。本研究结果对热带生态系统中适应性与中性遗传多样性的起源与分布的传统认知提出了挑战。此外，该研究对于全球最具多样性与标志性的热带生态系统之一的生物多样性评估与演化潜力研究，具有重要的参考价值。