High-throughput sequencing (HTS) metabarcoding is commonly applied to assess phytoplankton diversity. Usually, haplotypes are grouped into operational taxonomic units (OTUs) through clustering, whereby the resulting number of OTUs depends on chosen similarity thresholds. We applied, instead, a phylogenetic approach to infer taxa among 18S rDNA V4-metabarcode haplotypes gathered from 48 time-series samples using the marine planktonic diatoms Chaetoceros and Bacteriastrum as test case. The 73 recovered taxa comprised both solitary haplotypes and polytomies, the latter composed each of a highly abundant, dominant haplotype and one to several minor, peripheral haplotypes. The solitary and dominant haplotypes usually matched reference sequences, enabling species assignation of taxa. We hypothesise that the super-abundance of reads in dominant haplotypes results from the homogenization effect of concerted evolution. Reads of populous peripheral haplotypes and dominant haplotypes show comparable distribution patterns over the sample dates, suggesting that they are part of the same population. Many taxa revealed marked seasonality, with closely related ones generally showing distinct periodicity, whereas others occur year-round. Phylogenies inferred from metabarcode haplotypes enable delineation of biologically meaningful taxa, whereas OTUs resulting from clustering algorithms often deviate markedly from such taxa.

中文翻译：

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通过元条形码对海洋浮游硅藻Chaetoceros和细菌基质中的物种进行检测和划定：使单体型具有生物学意义。

高通量测序（HTS）元条形码通常用于评估浮游植物的多样性。通常，通过聚类将单倍型分组为可操作的分类单位（OTU），由此产生的OTU数量取决于所选的相似性阈值。相反，我们应用了系统发育方法，以海洋浮游硅藻Chaetoceros和Bacteriastrum作为测试案例，从48个时间序列样本中收集的18S rDNA V4-metabarcode单倍型中推断类群。回收的73个分类单元既包含单倍型又包含多态性，后者由高度丰富的优势单倍型和一对至少数的外围单倍型组成。单体和优势单倍型通常与参考序列匹配，从而使分类单元的物种分配成为可能。我们假设优势单倍型中阅读的超丰度归因于协同进化的均质化效应。人口外围单倍型和显性单倍型的读数显示在抽样日期内具有可比的分布模式，表明它们是同一种群的一部分。许多分类单元显示出明显的季节性，而密切相关的分类单元通常表现出明显的周期性，而其他分类单元则全年出现。从元条形码单倍型推断的系统发生学能够描述生物学上有意义的分类单元，而由聚类算法产生的OTU通常与该分类单元明显不同。说明他们属于同一人口。许多分类单元显示出明显的季节性，而密切相关的分类单元通常表现出明显的周期性，而其他分类单元则全年出现。从元条形码单倍型推断的系统发生学能够描述生物学上有意义的分类单元，而由聚类算法产生的OTU通常与该分类单元明显不同。说明他们属于同一人口。许多分类单元显示出明显的季节性，而密切相关的分类单元通常表现出明显的周期性，而其他分类单元则全年出现。从元条形码单倍型推断出的系统发育能够描述具有生物学意义的分类单元，而由聚类算法产生的OTU通常与该分类单元明显不同。