General Patterns of Diversity in Major Marine Microeukaryote Lineages

Microeukaryotes have vital roles for the functioning of marine ecosystems, but still some general characteristics of their current diversity and phylogeny remain unclear. Here we investigated both aspects in major oceanic microeukaryote lineages using 18S rDNA (V4–V5 hypervariable regions) sequences from public databases that derive from various marine environmental surveys. A very carefully and manually curated dataset of 8291 Sanger sequences was generated and subsequently split into 65 taxonomic groups (roughly to Class level based on KeyDNATools) prior to downstream analyses. First, we calculated genetic distances and clustered sequences into Operational Taxonomic Units (OTUs) using different distance cut-off levels. We found that most taxonomic groups had a maximum pairwise genetic distance of 0.25. Second, we used phylogenetic trees to study general evolutionary patterns. These trees confirmed our taxonomic classification and served to run Lineage Through Time (LTT) plots. LTT results indicated different cladogenesis dynamics across groups, with some displaying an early diversification and others a more recent one. Overall, our study provides an improved description of the microeukaryote diversity in the oceans in terms of genetic differentiation within groups as well as in the general phylogenetic structure. These results will be important to interpret the large amount of sequence data that is currently generated by High Throughput Sequencing technologies.

微型真核生物（Microeukaryotes）对海洋生态系统的功能运行具有关键作用，但目前其现有多样性与系统发育的诸多通用特征仍有待阐明。本研究借助公共数据库中源自各类海洋环境调查的18S rDNA（V4–V5高变区）序列，针对主要海洋微型真核生物支系的上述两方面展开探究。我们构建了一套经严格人工注释的8291条Sanger序列数据集，并在开展下游分析前，将其划分为65个分类群（基于KeyDNATools工具，大致对应纲级分类单元）。首先，我们计算了遗传距离，并采用不同距离截断阈值将序列聚类为操作分类单元（Operational Taxonomic Units，OTUs）。研究结果显示，多数分类群的最大成对遗传距离为0.25。其次，我们通过构建系统发育树探究整体演化模式，这些系统发育树不仅验证了我们的分类学划分，还可用于绘制时间谱系（Lineage Through Time，LTT）图。LTT分析结果表明，不同类群的分支演化动力学存在显著差异：部分类群呈现早期多样化特征，而另一些类群的多样化进程则相对较晚。总体而言，本研究从类群内遗传分化与整体系统发育结构两个维度，优化了对海洋微型真核生物多样性的认知与描述。上述研究结果对于解读当前高通量测序（High Throughput Sequencing）技术所产生的海量序列数据具有重要的参考价值。