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多样性，长期以来学界多依托气候与地质历史背景下的空间模型对其成因进行阐释。然而，真正决定物种在生态系统内演化与种间互作模式的，是适应性遗传多样性。本研究整合基因组扫描（genome scans）、群体遗传学（population genetics）以及基于测序的系统地理学分析（sequenced-based phylogeographic analyses），针对亚马孙鱼类白胸斧脂鲤（Triportheus albus）的基因组中受选择区域与中性进化区域的空间分布与生态格局展开探究。本研究采用覆盖5条亚马孙主要河流、3种水化学环境的采样方案，结合352个核标记（nuclear markers）与2个线粒体DNA基因（mitochondrial DNA genes），评估环境梯度作为亚马孙生物多样性驱动因子的作用。研究发现，在克拉通来源的黑色、清澈水体以及安第斯山脉来源的白色水体中，存在伴随基因流与环境隔离的强烈趋异自然选择。此外，我们发现两类水体交界区域所呈现的强化选择与群体遗传结构，其推动生物多样性产生的效果，较河流系统的空间布局与异域生物地理历史更为显著。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假设提出了挑战。同时，该研究对于全球最具多样性与标志性的生态系统之一的生物多样性评估与进化潜能研究，具有重要的参考价值。