Data from: Genomic signature of natural and anthropogenic stress in wild populations of the waterflea Daphnia magna: validation in space, time and experimental evolution

Natural populations are confronted with multiple selection pressures resulting in a mosaic of environmental stressors at landscape level. Identifying the genetic underpinning of adaptation to these complex selection environments and assigning causes of natural selection within multidimensional selection regimes in the wild is challenging. The water flea Daphnia is a renown ecological model system with its well-documented ecology, the possibility to analyze subfossil dormant egg banks, and the short generation time allowing an experimental evolution approach. Capitalizing on the strengths of this model system, we here link candidate genome regions to three selection pressures, known to induce micro-evolutionary responses in Daphnia magna: fish predation, parasitism, and land-use. Using a genome scan approach in space, time and experimental evolution trials, we provide solid evidence of selection at genome level under well-characterized environmental gradients in the wild and identify candidate genes linked to the three environmental stressors. Our study reveals differential selection at genome level in Daphnia populations and provides evidence for repeatable patterns of local adaptation in a geographic mosaic of environmental stressors fueled by standing genetic variation. Extensive, parallel genetic evolution at a genome-wide scale implies high evolutionary potential, relevant to understand the dynamics of trait changes in natural populations and their impact on community and ecosystem responses through eco-evolutionary feedbacks.

自然种群面临多重选择压力，在景观尺度上形成了环境胁迫因子的镶嵌格局。鉴定适应这些复杂选择环境的遗传基础，并明确野外多维选择体系中自然选择的成因，极具挑战性。水蚤属（Daphnia）是广为人知的生态模型系统，其生态学特征已有充分研究，可开展亚化石休眠卵库分析，且世代周期短，适配实验进化研究方案。本研究充分利用该模型系统的优势，将候选基因组区域与三种已知能诱导大型溞（Daphnia magna）产生微进化响应的选择压力相关联：鱼类捕食、寄生作用与土地利用变化。通过整合空间、时间维度的基因组扫描方法与实验进化试验，我们在野外已充分表征的环境梯度下，获得了基因组水平选择作用的可靠证据，并鉴定出与三种环境胁迫因子相关的候选基因。本研究揭示了水蚤种群基因组水平的差异化选择，并证明在由现有遗传变异驱动的环境胁迫地理镶嵌格局中，本地适应存在可重复的模式。全基因组范围内广泛的平行遗传进化表明其具有较高的进化潜力，这对于理解自然种群的性状变化动态，以及它们通过生态进化反馈对群落与生态系统响应产生的影响具有重要意义。