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，进而在景观尺度上形成由多种环境胁迫因子（environmental stressors）构成的镶嵌分布格局。识别这类复杂选择环境下适应的遗传基础（genetic underpinning），并明确野外多维选择机制（multidimensional selection regimes）下自然选择的驱动成因，极具挑战性。水蚤属（Daphnia）是广负盛名的生态模型系统，其生态学特征已有详实研究记录，可通过亚化石休眠卵库（subfossil dormant egg banks）开展相关分析，且世代周期较短，便于开展实验演化研究。本研究依托该模型系统的独特优势，将候选基因组区域与三类已知可诱导大型溞（Daphnia magna）产生微演化（micro-evolutionary）响应的选择压力相关联：鱼类捕食、寄生作用与土地利用扰动。本研究通过整合空间、时间维度与实验演化试验的基因组扫描（genome scan）方法，在野外已被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，并鉴定出与三类环境胁迫因子相关的候选基因。本研究揭示了溞属种群基因组水平上的差异化选择，并证实了在由现存遗传变异（standing genetic variation）驱动的环境胁迫因子地理镶嵌格局中，局部适应存在可重复的模式。全基因组范围内广泛存在的平行遗传演化现象，暗示了极高的演化潜力，这对于理解自然种群的性状变化动态，以及通过生态-演化反馈（eco-evolutionary feedbacks）解析其对群落与生态系统响应的影响具有重要参考价值。