The nuclear small subunit rRNA gene (SSU or 18S) is a marker frequently used in phylogenetic and barcoding studies in Amoebozoa, including Myxomycetes. Despite its common usage and the confirmed existence of divergent copies of ribosomal genes in other protists, the potential presence of intra-individual SSU variability in Myxomycetes has never been studied before. Here we investigated the pattern of nucleotide polymorphism in the 5' end fragment of SSU by cloning and sequencing a total of 238 variants from eight specimens, each representing a species of the dark-spored orders Stemonitidales and Physarales. After excluding singletons, a relatively low SSU intra-individual variability was found but our data indicate that this might be a widely distributed phenomenon in Myxomycetes as all samples analyzed possessed various ribotypes. To determine if the occurrence of multiple SSU variants within a single specimen has a negative effect on the circumscription of species boundaries, we conducted phylogenetic analyses that revealed that clone variation may be detrimental for inferring phylogenetic relationships among some of the specimens analyzed. Despite that intra-individual variability should be assessed in additional taxa, our results indicate that special care should be taken for species identification when working with closely related species.

核小亚基rRNA基因（SSU或18S）是在变形虫（包括粘菌）中经常用于系统发育和条形码研究的标记。尽管普遍使用它，并在其他生物中证实存在核糖体基因的不同拷贝，但以前从未研究过粘菌中个体内部SSU变异性的可能性。在这里，我们通过克隆和测序来自八个标本的238个变体，对SSU的5'末端片段中的核苷酸多态性模式进行了研究，每个变体代表一个暗孢阶Stemonitidales和Physarales。排除单例后，发现相对较低的SSU个体内变异性，但我们的数据表明这可能是粘菌中广泛分布的现象，因为分析的所有样品均具有各种核糖型。为了确定单个标本中多个SSU变体的出现是否对物种边界的界定产生负面影响，我们进行了系统进化分析，结果表明克隆变异可能会对推断的某些标本之间的系统发生关系产生不利影响。尽管应在其他分类单元中评估个体内部的变异性，但我们的结果表明，在与密切相关的物种合作时，应特别注意物种识别。