Data from: A novel approach to parasite population genetics: experimental infection reveals geographic differentiation, recombination, and host-mediated population structure in Pasteuria ramosa, a model bacterial parasite of Daphnia

The population structure of parasites is central to the ecology and evolution of host-parasite systems. Here, we investigate the population genetics of Pasteuria ramosa, a bacterial parasite of Daphnia. We used natural P. ramosa spore banks from the sediments of two geographically well-separated ponds to experimentally infect a panel of Daphnia magna host clones whose resistance phenotypes were previously known. In this way, we were able to assess the population structure of P. ramosa based on geography, host resistance phenotype and host genotype. Overall, genetic diversity of P. ramosa was high, and nearly all infected D. magna hosted more than one parasite haplotype. On the basis of the observation of recombinant haplotypes and relatively low levels of linkage disequilibrium, we conclude that P. ramosa engages in substantial recombination. Isolates were strongly differentiated by pond, indicating that gene flow is spatially restricted. Pasteuria ramosa isolates within one pond were segregated completely based on the resistance phenotype of the host—a result that, to our knowledge, has not been previously reported for a nonhuman parasite. To assess the comparability of experimental infections with natural P. ramosa isolates, we examined the population structure of naturally infected D. magna native to one of the two source ponds. We found that experimental and natural infections of the same host resistance phenotype from the same source pond were indistinguishable, indicating that experimental infections provide a means to representatively sample the diversity of P. ramosa while reducing the sampling bias often associated with studies of parasite epidemics. These results expand our knowledge of this model parasite, provide important context for the large existing body of research on this system and will guide the design of future studies of this host-parasite system.寄生虫种群结构是宿主-寄生虫系统生态学与进化研究的核心议题。本研究聚焦于大型水蚤（Daphnia magna）的寄生细菌——拉莫巴斯德菌（Pasteuria ramosa）的种群遗传学。我们使用采自两个地理间隔较远的池塘沉积物中的天然拉莫巴斯德菌孢子库，对一批已知抗性表型的大型水蚤宿主克隆株开展人工感染实验。借此，我们得以从地理分布、宿主抗性表型及宿主基因型三个维度解析拉莫巴斯德菌的种群结构。整体而言，拉莫巴斯德菌的遗传多样性较高，且几乎所有被感染的大型水蚤体内均携带不止一种寄生虫单倍型。基于重组单倍型的检出以及相对较低的连锁不平衡水平，我们推断拉莫巴斯德菌存在频繁的基因重组现象。不同池塘来源的菌株存在显著的遗传分化，表明其基因流存在空间限制。单个池塘内的拉莫巴斯德菌菌株完全按照宿主的抗性表型进行分化——据我们所知，目前尚无关于非人类寄生虫出现此类现象的研究报道。为验证人工感染实验与天然拉莫巴斯德菌菌株感染的可比性，我们对其中一个源池塘来源的天然感染大型水蚤的种群结构进行了分析。研究发现，同一源池塘来源、对应相同宿主抗性表型的人工感染与天然感染样本之间无显著差异，这表明人工感染实验可用于代表性地采样拉莫巴斯德菌的多样性，同时规避寄生虫流行病学研究中常见的采样偏差问题。本研究结果深化了我们对这一模式寄生虫的认知，为该宿主-寄生虫系统已有的大量研究提供了重要的研究背景，同时将为该系统未来的相关研究设计提供指导。