Tsagkogeorga Georgia, Turon Xavier, Hopcroft Russell R, Tilak Marie-Ka, Feldstein Tamar, Shenkar Noa, Loya Yossi, Huchon Dorothée, Douzery Emmanuel J P, Delsuc Frédéric
Université Montpellier 2, Institut des Sciences de l'Evolution (UMR 5554), CC064, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France.
BMC Evol Biol. 2009 Aug 5;9:187. doi: 10.1186/1471-2148-9-187.
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.
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.
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.
被囊动物最近被揭示为脊椎动物现存的近亲。然而，尽管有超过2500种已被描述的物种，它们进化历史的细节仍然模糊不清。从分子角度来看，被囊动物的系统发育关系大多是基于对18S rRNA序列的分析进行研究的，这些分析表明几个主要分支与传统的纲级分类不一致。尽管如此，关键类群如单鳃类、尾海鞘纲和海樽纲的系统发育关系和分类地位仍存在很大不确定性。
从以前未采样的被囊动物物种中获得了30条新的完整18S rRNA序列，特别关注进化速率高的类群。更新后的18S rRNA数据集已根据rRNA二级结构所施加的同源性约束进行了比对。采用了系统发育重建的概率框架来适应这种核糖体标记的特殊进化动态。在考虑进化过程中位点特异性异质性的非参数CAT混合模型以及适应茎区补偿性替换发生的RNA特异性双峰模型下进行了详细的贝叶斯分析。我们的结果支持将被囊动物分为三个主要分支：1）鳃鳃亚纲+海樽纲+单鳃亚纲，2）尾海鞘纲，3）固鳃亚纲，但尾海鞘纲的位置无法得到确切解决。我们的研究还表明，除了似乎进化缓慢的柄海鞘科外，大多数单鳃亚纲以极高的速率进化，涉及它们18S rRNA二级结构的变化。这种极端的速率异质性使得无法确定单鳃亚纲的确切系统发育位置。最后，最适合的二级结构和CAT混合模型表明海樽纲中的磷海鞘目和火体虫目之间是姐妹群关系。
基于使用目前核糖体分子可用的最现实进化模型和前所未有的分类采样进行的系统发育分析，为被囊动物提供了一个更新的系统发育框架。对18S rRNA基因的详细分析明确了主要的被囊动物类群，并揭示了主要谱系之间截然不同的进化动态。然而，该基因在由鳃鳃亚纲+海樽纲+单鳃亚纲和海鞘科+柄海鞘科组成的分支内的分辨能力似乎有限，这些分支被划定为低分辨率区域。这些局限性强调了开发新的核标记以进一步解决脊索动物进化中这个关键类群的系统发育的必要性。
