Department of Plant and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden.
Evol Bioinform Online. 2008 May 26;4:193-201. doi: 10.4137/ebo.s653.
The internal transcribed spacer (ITS) region of the nuclear ribosomal repeat unit is the most popular locus for species identification and subgeneric phylogenetic inference in sequence-based mycological research. The region is known to show certain variability even within species, although its intraspecific variability is often held to be limited and clearly separated from interspecific variability. The existence of such a divide between intra- and interspecific variability is implicitly assumed by automated approaches to species identification, but whether intraspecific variability indeed is negligible within the fungal kingdom remains contentious. The present study estimates the intraspecific ITS variability in all fungi presently available to the mycological community through the international sequence databases. Substantial differences were found within the kingdom, and the results are not easily correlated to the taxonomic affiliation or nutritional mode of the taxa considered. No single unifying yet stringent upper limit for intraspecific variability, such as the canonical 3% threshold, appears to be applicable with the desired outcome throughout the fungi. Our results caution against simplified approaches to automated ITS-based species delimitation and reiterate the need for taxonomic expertise in the translation of sequence data into species names.
内转录间隔区（ITS）是核核糖体重复单位的一部分，是基于序列的真菌学研究中用于物种鉴定和亚属系统发育推断的最常用基因座。该区域在种内显示出一定的变异性，尽管其种内变异性通常被认为是有限的，并且与种间变异性明显分开。这种种内和种间变异性之间的划分是自动物种鉴定方法隐含假设的，但种内变异性在真菌界是否确实可以忽略不计仍然存在争议。本研究通过国际序列数据库估计了目前真菌学界可获得的所有真菌的种内 ITS 变异性。在真菌界中发现了明显的差异，而且这些结果与所考虑的分类群的分类归属或营养模式没有直接的相关性。似乎没有一个统一但严格的种内变异性上限，例如经典的 3%阈值，适用于整个真菌界。我们的结果告诫不要简化基于 ITS 的自动化物种划分方法，并再次强调在将序列数据转换为物种名称时需要分类学专业知识。
