Department of Plant Sciences and Landscape Architecture, University of Maryland, 2112 Plant Sciences Building, College Park, MD 20742, USA.
Mol Ecol. 2011 Jul;20(14):3001-13. doi: 10.1111/j.1365-294X.2011.05110.x. Epub 2011 May 9.
The estimation of species diversity in fungal endophyte communities is based either on species counts or on the assignment of operational taxonomic units (OTUs). Consequently, the application of different species recognition criteria affects not only diversity estimates but also the ecological hypotheses that arise from those observations. The main objective of the study was to examine how the choice and number of genetic markers and species delimitation criteria influence biodiversity estimates. Here, we compare approaches to defining species boundaries in three dominant species complexes of tropical endophytes, specially Colletotrichum gloeosporioides agg., Pestalotiopsis microspora agg. and Trichoderma harzianum agg., from two Amazonian trees: Hevea brasiliensis and H. guianensis. Molecular tools were used to describe and compare the diversity of the different assemblages. Multilocus phylogenetic analyses [gpd, internal transcribed spacer (ITS) and tef1] and modern techniques for phylogenetic species delimitation were overlaid with ecological data to recognize putative species or OTUs. The results demonstrate that ITS alone generally underestimates the number of species predicted by other nuclear loci. These results question the use of ITS and arbitrary divergence thresholds for species delimitation.
真菌内生菌群落物种多样性的评估要么基于物种计数，要么基于操作分类单元（OTUs）的分配。因此，不同物种识别标准的应用不仅会影响多样性估计，还会影响从这些观察中产生的生态假设。本研究的主要目的是检验选择和使用不同遗传标记和物种界定标准如何影响生物多样性估计。在这里，我们比较了三种热带内生菌优势种复合体（胶孢炭疽菌复合群、拟盘多毛孢属和木霉属）在两种亚马逊树种：巴西橡胶树和圭亚那橡胶树中的物种界限定义方法。分子工具被用于描述和比较不同组合的多样性。多基因座系统发育分析（gpd、内部转录间隔区（ITS）和 tef1）和现代种系发生物种界定技术与生态数据叠加，以识别可能的种或 OTUs。结果表明，ITS 单独使用通常会低估其他核基因座预测的物种数量。这些结果对使用 ITS 和任意分歧阈值进行物种界定提出了质疑。
