The Colpodea form a major clade of ciliates that are often found in environmental DNA sequencing studies. They are united by similar somatic ciliature, but differentiated by complex oral structures. Although there are four well supported colpodean subclades, there is disagreement in molecular phylogenetic inferences about their branching order. Using available nuclear SSU-rRNA sequences, we evaluated if the bursariomorphids or the platyophryids are sister to the remaining colpodeans. We inferred the “platyophryids-early” topologies using different alignment and masking methods, but constrained analyses could not reject the “bursariomorphids-early” topology. Both bursariomorphids and platyophryids clades have a similar number of nucleotide positions shared with the outgroup, and both are interconnected with the outgroup in phylogenetic networks. Based on these discordant results, it is hard to determine which clade branched off first, although the “platyophryids-early topology” is also supported by mitochondrial SSU-rRNA data. We also offer different reference alignments that can be used to phylogenetically place short- and long-read data from environmental DNA sequencing studies, and we propose some tentative evolutionary and ecological interpretations of those placements.

Colpodea形成了主要的纤毛虫，在环境DNA测序研究中经常发现。它们通过相似的体细胞纤毛而结合在一起，但是通过复杂的口腔结构来区分。尽管有四个支撑良好的colpodean子小节，但是在分子系统发育学上关于它们的分支顺序并不一致。使用可用的核SSU-rRNA序列，我们评估了bursariomorphids或platyophryids是否是其余colpodeans的姐妹。我们使用不同的比对和掩蔽方法推论了“鸭嘴兽-早期”拓扑，但是受约束的分析不能拒绝“蛇s子-早期”拓扑。囊囊梭菌和侧柏囊进化枝都具有与外群共享的相似数目的核苷酸位置，并且两者在系统发育网络中都与外群互连。基于这些不一致的结果，尽管线粒体SSU-rRNA数据也支持“鸭嘴兽-早期拓扑”，但很难确定哪个进化枝首先分支。我们还提供了不同的参考比对，可用于系统地放置环境DNA测序研究中的短读和长读数据，并且我们对这些放置提出了初步的进化论和生态学解释。