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.

解析物种种群的遗传结构，可为基因流、遗传漂变与适应性进化等核心生态与进化过程提供深入洞察。此类推断对于寄生虫类群尤为关键，因为明晰其种群结构可阐明流行病学与协同进化动态。本研究聚焦于杆状芽孢杆菌（*Pasteuria ramosa*）的种群遗传结构——该菌为一类感染水蚤属（*Daphnia*）浮游甲壳动物的寄生虫。此研究体系已成为宿主-寄生虫互作研究的经典模型，同时也是负频率依赖选择（negative frequency-dependent selection，又称‘红皇后’动态（Red Queen dynamics））介导协同进化的典型范例。为获取P. ramosa的样本，我们利用欧洲与西亚大部分分布区内25处池塘沉积物中的天然孢子库，对一组水蚤宿主开展了人工感染实验。本研究借助12个多态性可变数目串联重复序列（variable number tandem repeat, VNTR）位点，检测到不同采样池塘间以及同一池塘内部均存在丰富的遗传多样性，且该多样性呈现地理分区结构。池塘内部的宿主基因型间同样存在遗传结构分化，但该模式因采样位点而异：部分位点的P. ramosa可划分为不同的宿主特异性谱系，而另一些位点则因重组作用，使得不同感染表型间的遗传变异发生了重组洗牌。全采样范围内呈现距离隔离（isolation-by-distance）模式，主成分分析（principal components analysis）结合普氏旋转（Procrustes rotation）分析结果表明，遗传变异格局与地理分布格局具有高度一致性。本研究结果支持‘杆状芽孢杆菌是一类与其宿主紧密协同进化的地方性寄生虫’这一假说。本研究成果可为该经典模型体系的既往研究提供重要背景支撑，并为未来的研究假说构建提供参考依据。