Data from: Tunicates and not cephalochordates are the closest living relatives of vertebrates

Tunicates or urochordates (appendicularians, salps and sea squirts), cephalochordates (lancelets) and vertebrates (including lamprey and hagfish) constitute the three extant groups of chordate animals. Traditionally, cephalochordates are considered as the closest living relatives of vertebrates, with tunicates representing the earliest chordate lineage. This view is mainly justified by overall morphological similarities and an apparently increased complexity in cephalochordates and vertebrates relative to tunicates. Despite their critical importance for understanding the origins of vertebrates, phylogenetic studies of chordate relationships have provided equivocal results. Taking advantage of the genome sequencing of the appendicularian Oikopleura dioica, we assembled a phylogenomic data set of 146 nuclear genes (33,800 unambiguously aligned amino acids) from 14 deuterostomes and 24 other slowly evolving species as an outgroup. Here we show that phylogenetic analyses of this data set provide compelling evidence that tunicates, and not cephalochordates, represent the closest living relatives of vertebrates. Chordate monophyly remains uncertain because cephalochordates, albeit with a non-significant statistical support, surprisingly grouped with echinoderms, a hypothesis that needs to be tested with additional data. This new phylogenetic scheme prompts a reappraisal of both morphological and palaeontological data and has important implications for the interpretation of developmental and genomic studies in which tunicates and cephalochordates are used as model animals.

被囊动物（Tunicates，即尾索动物亚门Urochordates）包含尾海鞘（Appendicularians）、樽海鞘（Salps）与海鞘（Sea squirts），头索动物（Cephalochordates，即文昌鱼Lancelets）以及脊椎动物（Vertebrates，涵盖七鳃鳗Lamprey与盲鳗Hagfish），三者构成现存脊索动物的三大类群。传统观点认为，头索动物是脊椎动物现存最近的近亲，而尾索动物则代表最原始的脊索动物支系。该观点主要依据整体形态相似性，以及相较于尾索动物，头索动物与脊椎动物的复杂程度明显更高。尽管脊索动物类群关系研究对于理解脊椎动物起源至关重要，但相关系统发育研究所得出的结果始终模棱两可。本研究借助尾海鞘类（Appendicularian）异体住囊虫（Oikopleura dioica）的基因组测序数据，构建了包含14种后口动物（Deuterostomes）与24种作为外类群（outgroup）的慢速演化物种的系统基因组数据集（phylogenomic dataset），该数据集涵盖146个核基因（共33800个经明确比对的氨基酸位点）。本研究通过对该数据集的系统发育分析，提供了强有力的证据，证明尾索动物而非头索动物才是脊椎动物现存最近的近亲。脊索动物单系群（Chordate monophyly）假说仍未得到确证：尽管统计支持度未达显著水平，但头索动物意外地与棘皮动物（Echinoderms）聚为一支，该假说仍需更多数据加以验证。这一新的系统发育框架促使研究者重新审视形态学与古生物学数据，同时对于以尾索动物和头索动物作为模式动物的发育学及基因组学研究的解读具有重要意义。