Data from: An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models

BACKGROUND: Tunicates have been recently revealed to be the closest living relatives of vertebrates. Yet, with more than 2500 described species, details of their evolutionary history are still obscure. From a molecular point of view, tunicate phylogenetic relationships have been mostly studied based on analyses of 18S rRNA sequences, which indicate several major clades at odds with the traditional class-level arrangements. Nonetheless, substantial uncertainty remains about the phylogenetic relationships and taxonomic status of key groups such as the Aplousobranchia, Appendicularia, and Thaliacea.

RESULTS: Thirty new complete 18S rRNA sequences were acquired from previously unsampled tunicate species, with special focus on groups presenting high evolutionary rate. The updated 18S rRNA dataset has been aligned with respect to the constraint on homology imposed by the rRNA secondary structure. A probabilistic framework of phylogenetic reconstruction was adopted to accommodate the particular evolutionary dynamics of this ribosomal marker. Detailed Bayesian analyses were conducted under the non-parametric CAT mixture model accounting for site-specific heterogeneity of the evolutionary process, and under RNA-specific doublet models accommodating the occurrence of compensatory substitutions in stem regions. Our results support the division of tunicates into three major clades: 1) Phlebobranchia + Thaliacea + Aplousobranchia, 2) Appendicularia, and 3) Stolidobranchia, but the position of Appendicularia could not be firmly resolved. Our study additionally reveals that most Aplousobranchia evolve at extremely high rates involving changes in secondary structure of their 18S rRNA, with the exception of the family Clavelinidae, which appears to be slowly evolving. This extreme rate heterogeneity precluded resolving with certainty the exact phylogenetic placement of Aplousobranchia. Finally, the best fitting secondary-structure and CAT-mixture models suggest a sister-group relationship between Salpida and Pyrosomatida within Thaliacea.

CONCLUSION: An updated phylogenetic framework for tunicates is provided based on phylogenetic analyses using the most realistic evolutionary models currently available for ribosomal molecules and an unprecedented taxonomic sampling. Detailed analyses of the 18S rRNA gene allowed a clear definition of the major tunicate groups and revealed contrasting evolutionary dynamics among major lineages. The resolving power of this gene nevertheless appears limited within the clades composed of Phlebobranchia + Thaliacea + Aplousobranchia and Pyuridae + Styelidae, which were delineated as spots of low resolution. These limitations underline the need to develop new nuclear markers in order to further resolve the phylogeny of this keystone group in chordate evolution.

背景：近期研究证实，被囊动物（tunicates）是现存与脊椎动物亲缘关系最近的类群。尽管目前已记录超过2500个被囊动物物种，但其演化历史的诸多细节仍不明晰。从分子研究视角出发，学界此前多基于18S核糖体RNA（18S rRNA）序列分析来探究被囊动物的系统发育关系，相关结果已揭示出多个与传统纲级分类框架相悖的主要演化支。不过，诸如无孔目（Aplousobranchia）、幼形纲（Appendicularia）以及樽海鞘纲（Thaliacea）等关键类群的系统发育关系与分类学地位，仍存在大量未明确之处。
结果：本研究从此前未被采样的被囊动物物种中获取了30条全新的完整18S rRNA序列，重点关注了演化速率较高的类群。本研究基于核糖体RNA二级结构所施加的同源性约束，对更新后的18S rRNA数据集完成了序列比对。研究采用了基于概率的系统发育重建框架，以适配该核糖体标记基因独特的演化动态。本研究分别基于考虑演化过程位点异质性的非参数CAT混合模型，以及适配茎区补偿性替换现象的RNA特异性双碱基模型，开展了详尽的贝叶斯分析。研究结果支持将被囊动物划分为三个主要演化支：1）褶海鞘目（Phlebobranchia）+ 樽海鞘纲（Thaliacea）+ 无孔目（Aplousobranchia）；2）幼形纲（Appendicularia）；3）盲海鞘目（Stolidobranchia），但幼形纲的系统发育位置仍无法被明确确定。本研究还发现，绝大多数无孔目类群的演化速率极高，其18S rRNA二级结构亦发生相应改变，但棒海鞘科（Clavelinidae）除外，该类群演化速率相对缓慢。这种极端的演化速率异质性，使得我们无法准确确定无孔目的确切系统发育位置。最后，拟合效果最优的二级结构模型与CAT混合模型结果显示，在樽海鞘纲内部，纽鳃樽目（Salpida）与火体虫目（Pyrosomatida）构成姊妹群关系。
结论：本研究基于当前适用于核糖体分子的最贴合实际的演化模型，结合前所未有的分类学采样广度开展系统发育分析，为被囊动物提供了一套更新后的系统发育框架。针对18S rRNA基因的详尽分析，清晰界定了被囊动物的主要类群，并揭示了不同主要演化支之间迥异的演化动态。不过，该基因的解析能力在褶海鞘目+樽海鞘纲+无孔目演化支，以及腕海鞘科（Pyuridae）+柄海鞘科（Styelidae）类群中存在局限，上述类群被界定为系统发育分辨率较低的区域。这些局限性表明，我们需要开发新的核基因标记，以进一步阐明这一脊索动物演化关键类群的系统发育关系。