Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms (file : V4dataset.fna)

file : V4dataset.fna Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms (file : readme_Forster_et_al_BMC) http://dx.doi.org/10.6084/m9.figshare.1264013 Background: High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but in silico analyses of the resulting millions of short amplicons remain a major bottleneck for these approaches. Here, we introduced the analytical and statistical framework of sequence similarity networks, increasingly used in evolutionary studies and graph theory, into the field of ecology to analyze novel pyrosequenced V4 SSU-rDNA sequence data sets in the context of previous studies, including SSU-rDNA Sanger sequence data from cultured ciliates and from previous environmental diversity inventories.Results: Our broadly applicable protocol quantified progress in the description of genetic diversity of ciliates by environmental rRNA amplicons studies, detected a fundamental historical bias, the tendency to recover already known groups, in these surveys, and revealed substantial amounts of hidden microbial diversity. Moreover, network measures demonstrated that ciliates are not globally dispersed, but present strong local patterns at intermediate geographical scale, as observed for bacteria, plants, and animals.Conclusions: Although currently available ‘universal’ primers used for local in-depth sequencing surveys provide little hope to exhaust the significantly higher ciliate (and most likely microbial) diversity than previously thought, sequence similarity networks, since they identify groups of divergence sequences sharing distinctive similarities, offer a promising way to guide the design of novel primers and to further explore such a vast and structured microbial diversity.文件：V4dataset.fna 研究主题：利用序列相似性网络（sequence similarity networks）验证生态学理论：海洋纤毛虫（marine ciliates）展现出与多细胞生物相似的地理扩散模式（关联文件：readme_Forster_et_al_BMC），DOI链接：http://dx.doi.org/10.6084/m9.figshare.1264013 背景：高通量测序技术（high-throughput sequencing technologies）突破了真核微生物多样性分子生态学研究的主要限制，但针对由此产生的数百万条短扩增子（short amplicons）的计算机（in silico）分析仍是该研究路径的主要瓶颈。本研究将进化研究与图论（graph theory）中日益广泛应用的序列相似性网络分析与统计框架引入生态学领域，结合既往已发表的研究数据，分析全新的焦磷酸测序V4区小亚基核糖体RNA（SSU-rDNA）序列数据集，其中包括培养纤毛虫的桑格测序（Sanger sequencing）SSU-rDNA数据以及此前的环境多样性调查数据。 结果：本研究提出的广泛适用分析流程量化了环境rRNA扩增子研究对纤毛虫遗传多样性描述的进展，检测到此类调查中存在的根本性历史偏差——即倾向于检测到已被报道的类群，并揭示了大量隐藏的微生物多样性。此外，网络度量指标（network measures）显示，纤毛虫并非全球扩散，而是在中等地理尺度下呈现出显著的本地分布模式，这与细菌、植物与动物的观测结果一致。 结论：尽管当前用于本地深度测序研究的通用引物（universal primers）几乎无法穷尽比此前预想中更为丰富的纤毛虫（极大概率也涵盖多数微生物）多样性，但序列相似性网络可识别共享独特相似性的分化序列簇，因此为设计新型引物以及进一步探索如此庞大且具有结构化特征的微生物多样性提供了极具前景的途径。