Data from: Capturing the population structure of microparasites: using ITS-sequence data and a pooled DNA approach

The internal transcribed spacer (ITS) region of nuclear ribosomal DNA is a common marker not only for the molecular identification of different taxa and strains, but also for the analysis of population structure of wild microparasite communities. Importantly, the multicopy nature of this region allows the amplification of low-quantity samples of the target DNA, a common problem in studies on unicellular, unculturable microparasites. We analysed ITS sequences from the protozoan parasite Caullerya mesnili (class Ichthyosporea) infecting waterflea (Daphnia) hosts, across several host population samples. We showed that analysing representative ITS-types [as identified by statistical parsimony network analysis (SPN)] is a suitable method to address relevant polymorphism. The spatial patterns were consistent regardless of whether parasite DNA was extracted from individual hosts or pooled host samples. Remarkably, the efficiency in detecting different sequence types was even higher after sample pooling. As shown by simulations, an easily manageable number of sequences from pooled DNA samples are sufficient to resolve the spatial population structure in this system. In summary, the ITS region analysed from pooled DNA samples can provide valuable insights into the spatial and temporal dynamics of microparasites. Moreover, the application of SPN analysis is a good alternative to the well-established neighbour-joining method (NJ) for the identification of representative ITS-types. SPN can even outperform NJ by joining most of the singleton sequences to representative sequence clusters.细胞核核糖体DNA的内部转录间隔区（ITS）是一类常用分子标记，不仅可用于不同类群与菌株的分子鉴定，还可用于解析野生微型寄生虫群落的种群结构。重要的是，该区域的多拷贝特性可实现靶标DNA低含量样本的扩增——这也是单细胞、不可培养微型寄生虫研究中普遍存在的难题。我们对多个宿主种群样本中，感染水蚤（溞属，Daphnia）宿主的原生动物寄生虫梅氏考氏虫（Ichthyosporea纲）的ITS序列展开了分析。研究结果表明，利用经统计简约网络分析（SPN）鉴定的代表性ITS型开展分析，是探究相关多态性的适宜方法。无论寄生虫DNA提取自单个宿主还是混合宿主样本，其空间分布模式均保持一致。值得注意的是，对混合样本进行分析后，不同序列类型的检测效率甚至更高。正如模拟实验所证实，仅需从混合DNA样本中获取少量易于操作的序列，即可解析该系统的空间种群结构。综上，从混合DNA样本中分析得到的ITS区域序列，可为微型寄生虫的时空动态研究提供极具价值的见解。此外，在鉴定代表性ITS型方面，SPN分析是相较于成熟邻接法（NJ）的优质替代方案，其甚至可将绝大多数单例序列归入代表性序列簇中，表现更优。