Data from: Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

BACKGROUND: The morphological peculiarities of turtles have, for a long time, impeded their accurate placement in the phylogeny of amniotes. Molecular data used to address this major evolutionary question have so far been limited to a handful of markers and/or taxa. These studies have supported conflicting topologies, positioning turtles as either the sister group to all other reptiles, to lepidosaurs (tuatara, lizards and snakes), to archosaurs (birds and crocodiles), or to crocodilians. Genome-scale data have been shown to be useful in resolving other debated phylogenies, but no such adequate dataset is yet available for amniotes. RESULTS: In this study, we used next-generation sequencing to obtain seven new transcriptomes from the blood, liver, or jaws from four turtles, a caiman, a lizard, and a lungfish. We used a phylogenomic dataset based on 248 nuclear genes (187,026 nucleotide sites) for 16 vertebrate taxa to resolve the origins of turtles. Maximum likelihood and Bayesian concatenation analyses and species tree approaches performed under the most realistic models of the nucleotide and amino acid substitution processes unambiguously support turtles as a sister group to birds and crocodiles. The use of more simplistic models of nucleotide substitution for both concatenation and species tree reconstruction methods leads to the artefactual grouping of turtles and crocodiles, most likely because of substitution saturation at third codon positions. Relaxed molecular clock methods estimate the divergence between turtles and archosaurs around 255 million years ago. The most recent common ancestor of living turtles, corresponding to the split between Pleurodira and Cryptodira, is estimated to have occurred around 157 million years ago, in the Upper Jurassic period. This is a more recent estimate than previously reported, and questions the interpretation of controversial Lower Jurassic fossils as being part of the extant turtles radiation. CONCLUSIONS: These results provide a phylogenetic framework and timescale with which to interpret the evolution of the peculiar morphological, developmental, and molecular features of turtles within the amniotes.背景：长期以来，龟类的形态学特征一直阻碍着其在羊膜动物（amniotes）系统发育树中的准确定位。此前用于解答这一重大演化问题的分子数据仅局限于少量分子标记或类群，相关研究得出的系统发育拓扑结构相互矛盾：部分研究将龟类定位为所有其他爬行类的姊妹群，部分则将其置于鳞龙类（lepidosaurs，喙头蜥、蜥蜴与蛇类）、主龙类（archosaurs，鸟类与鳄类）或鳄类（crocodilians）的姊妹群位置。基因组尺度的数据已被证实可用于解决其他存在争议的系统发育问题，但目前尚无适用于羊膜动物的此类高质量数据集。结果：本研究借助下一代测序技术，从4种龟类、1种凯门鳄、1种蜥蜴以及1种肺鱼的血液、肝脏或颌部组织中获取了7套全新的转录组（transcriptome）。我们构建了涵盖16个脊椎动物类群、基于248个核基因（共计187026个核苷酸位点）的系统发育组数据集，以解析龟类的起源问题。在最贴合实际的核苷酸与氨基酸替换模型下开展的最大似然法、贝叶斯联配分析以及物种树构建方法，均一致支持龟类为鸟类与鳄类的姊妹群。若在联配分析与物种树重建中使用更为简化的核苷酸替换模型，则会人为将龟类与鳄类聚为一支，这一现象极有可能源于密码子第三位的替换饱和效应。宽松分子钟（relaxed molecular clock）方法估算得出，龟类与主龙类的分化时间约为2.55亿年前。现生龟类的最近共同祖先（对应侧颈龟亚目（Pleurodira）与曲颈龟亚目（Cryptodira）的分化事件）估算发生于约1.57亿年前的晚侏罗世（Upper Jurassic）。这一分化时间的估算结果早于此前报道，因此对"争议性早侏罗世化石属于现生龟类演化支"的解读提出了质疑。结论：本研究结果为解析羊膜动物框架内龟类独特的形态、发育与分子特征演化提供了系统发育框架与时间标尺。