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（internal transcribed spacer, 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，还可用于分析野生微寄生虫群落的种群结构。值得关注的是，该区域的多拷贝特性可实现靶标DNA低含量样本的扩增，而这正是单细胞、不可培养微寄生虫研究中的常见难题。我们对感染水蚤（*Daphnia*，溞属）宿主的原生动物寄生虫*Caullerya mesnili*（鱼孢虫纲，Ichthyosporea）的ITS序列展开了分析，样本覆盖多个宿主种群。研究证实，对经统计简约网络分析（statistical parsimony network analysis, SPN）鉴定的代表性ITS型进行分析，是解析相关多态性的可靠方法。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；尤为突出的是，混合样本甚至可提升不同序列型的检测效率。模拟实验结果表明，仅需对混合DNA样本进行少量易操作的测序，即可解析该系统中的空间种群结构。综上，从混合DNA样本中分析ITS区域，可有效揭示微寄生虫的时空动态。此外，相较于成熟的邻接法（neighbour-joining method, NJ），SPN分析是鉴定代表性ITS型的优质替代方案；SPN甚至可通过将绝大多数单例序列归入代表性序列簇，实现优于NJ的分析效果。