Data from: Spatial population genetic structure of a bacterial parasite in close coevolution with its host

Knowledge of a species’ population genetic structure can provide insight into fundamental ecological and evolutionary processes including gene flow, genetic drift, and adaptive evolution. Such inference is of particular importance for parasites, as an understanding of their population structure can illuminate epidemiological and coevolutionary dynamics. Here we describe the population genetic structure of the bacterium Pasteuria ramosa, a parasite that infects planktonic crustaceans of the genus Daphnia. This system has become a model for investigations of host-parasite interactions and represents an example of coevolution via negative frequency-dependent selection (a.k.a. ‘Red Queen’ dynamics). To sample P. ramosa, we experimentally infected a panel of Daphnia hosts with natural spore banks from the sediments of 25 ponds throughout much of the species range in Europe and Western Asia. Using 12 polymorphic VNTR loci, we identified substantial genetic diversity both within and among localities that was structured geographically among ponds. Genetic diversity was also structured among host genotypes within ponds, though this pattern varied by locality, with P. ramosa at some localities partitioned into distinct host-specific lineages, and other localities where recombination had shuffled genetic variation among different infection phenotypes. Across the sample range, there was a pattern of isolation-by-distance, and principal components analysis coupled with Procrustes rotation identified congruence between patterns of genetic variation and geography. Our findings support the hypothesis that Pasteuria is an endemic parasite coevolving closely with its host. These results provide important context for previous studies of this model system and inform hypotheses for future research.

了解一个物种的种群遗传结构，可为解析基因流、遗传漂变与适应性进化等核心生态与进化过程提供关键洞见。这类种群结构解析对于寄生虫类群尤为重要，因为阐明其种群结构可揭示流行病学与协同进化动态。
本研究聚焦于拉莫萨巴斯德菌（Pasteuria ramosa）的种群遗传结构，该菌是一种寄生于溞属（Daphnia）浮游甲壳动物的寄生虫。该研究体系已成为宿主-寄生虫互作研究的经典模型，并代表了通过负频率依赖选择（negative frequency-dependent selection，又称"红皇后"动态）实现协同进化的典型案例。为采集拉莫萨巴斯德菌样本，研究团队利用覆盖欧洲与西亚该物种分布区大部分区域的25个池塘沉积物中的自然孢子库，对一组溞属宿主开展人工感染实验。
本研究利用12个多态性可变数目串联重复序列（Variable Number Tandem Repeats, VNTR）位点，在各采样点及采样点内部均检测到丰富的遗传多样性，且该多样性在池塘间呈现地理结构化分布特征。池塘内宿主基因型间同样存在遗传多样性结构，但该模式因采样点而异：部分采样点的拉莫萨巴斯德菌可划分为不同的宿主特异性谱系，而另一些采样点中重组作用已在不同感染表型间打乱了遗传变异。在整个采样范围内，研究观测到距离隔离模式；结合主成分分析与普氏旋转（Procrustes rotation）的结果显示，遗传变异模式与地理分布模式存在一致性。
本研究结果支持"拉莫萨巴斯德菌是一种与其宿主紧密协同进化的地方性寄生虫"这一假说。上述研究结果为该模型体系的既往研究提供了重要背景，并可为未来研究的假说构建提供参考。