Members of the genus Paramecium (Ciliophora, Oligohymenophorea) are widespread ciliates able to colonize many fresh, brackish and marine water environments around the globe. Despite they have been historically used in a variety of research fields, ranging from genomics to ecology, their evolutionary origin and genetic structure remains elusive for most valid species. There are currently 19 valid species distributed in 5 subgenera, which can have restricted to cosmopolitan distribution patterns. However, their true biodiversity and biographical distribution are blurred by evidences of cryptic species within most of these valid species. Here, we inferred a 18S rDNA-based time-calibrated tree to determine the evolutionary origin of extant Paramecium lineages and intra-genus phylogenetic relationships. Next, we used two common computational species delimitation algorithms (PTP and mPTP) to analyze a population-level (cytochrome oxidase subunit I [COI]) phylogeny to predict the existence of independent evolutionary unities (IEUs) within valid Paramecium morphospecies. Our data suggest that, some cosmopolitan Paramecium may have emerged prior to the Cretaceous period (before the complete separation of the continents), thus, explaining their wide distribution pattern. We found that the diversity of cryptic species may be higher than previous though and that most of the valid Paramecium species should be, in fact considered as complexes of species, composed each by IEUs that can co-occur within restricted or wide geographical areas. Moreover, our data indicate that these species delimitation algorithms (PTP and mPTP) may be of great assistance to uncover the diversity of cryptic species within Paramecium (or any other microeukaryote) by indicating potential candidates for more in detail future studies of taxonomists through integrative taxonomy frameworks.

中文翻译：

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草履虫谱系的属内进化时间和隐藏的遗传多样性（Ciliophora：Oligohymenophorea）

草履虫属 (Ciliophora, Oligohymenophorea) 的成员是分布广泛的纤毛虫，能够在全球许多淡水、咸水和海水环境中定居。尽管它们历来被用于从基因组学到生态学的各种研究领域，但对于大多数有效物种而言，它们的进化起源和遗传结构仍然难以捉摸。目前有 19 个有效物种分布在 5 个亚属中，可能仅限于世界性分布模式。然而，它们真正的生物多样性和传记分布被大多数这些有效物种中隐匿物种的证据所模糊。在这里，我们推断了一个基于 18S rDNA 的时间校准树，以确定现存草履虫谱系的进化起源和属内系统发育关系。下一个，我们使用两种常见的计算物种定界算法（PTP 和 mPTP）来分析种群水平（细胞色素氧化酶亚基 I [COI]）系统发育，以预测有效草履虫形态种中独立进化单位 (IEU) 的存在。我们的数据表明，一些世界性草履虫可能在白垩纪之前（在大陆完全分离之前）出现，从而解释了它们的广泛分布模式。我们发现隐性物种的多样性可能比以前更高，并且大多数有效的草履虫物种实际上应该被视为物种的复合体，每个物种都由可以在有限或广阔的地理区域内共同发生的 IEU 组成。而且，