Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms (file : CULTUREid_taxo_GB_V4seq.tab)

file : CULTUREid_taxo_GB_V4seq.tab 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.<br>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.<br>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：CULTUREid_taxo_GB_V4seq.tab 《利用序列相似性网络验证生态学理论：海洋纤毛虫展现出与多细胞生物相似的地理扩散模式》（配套说明文件：readme_Forster_et_al_BMC），DOI：http://dx.doi.org/10.6084/m9.figshare.1264013

背景：高通量测序（High-throughput sequencing）技术打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（amplicon）的硅基分析（in silico）仍是该研究路径的一大瓶颈。本研究将进化生物学与图论中日益常用的序列相似性网络分析与统计框架引入生态学领域，结合既往研究中的相关数据——包括培养纤毛虫的小亚基核糖体RNA基因（SSU-rDNA）桑格测序（Sanger sequencing）数据与此前的环境多样性调查数据集，对新获得的经焦磷酸测序（pyrosequenced）的V4区SSU-rDNA序列数据集展开分析。

结果：本研究开发的通用型分析流程量化了环境rRNA扩增子（rRNA amplicon）研究对纤毛虫遗传多样性描述的进展，在上述调查中检测到一项根本性的历史偏差——即倾向于回收已报道的已知类群，并揭示了大量未被发掘的微生物多样性。此外，网络度量指标显示，纤毛虫并非全球泛布，而是在中等地理尺度下呈现出强烈的局域分布模式，这与细菌、植物和动物的分布特征一致。

结论：尽管当前用于局域深度测序研究的"通用"引物几乎无法穷尽此前预估范围之外的纤毛虫（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具有显著相似性的分化序列类群，因此为指导新型引物设计、进一步探索这种庞大且具有结构特征的微生物多样性提供了极具前景的研究路径。