Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria).
Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria).
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系统基因分析支持海龟作为姊妹鸟类和鳄鱼（Archosauria）的位置。
DOI：
10.1186/1741-7007-10-65
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发表时间：
2012-07-27
期刊：
影响因子：
5.4
通讯作者：
Delsuc F
中科院分区：
文献类型：
--
作者：
Chiari Y;Cahais V;Galtier N;Delsuc F
长期以来，龟类的形态特征阻碍了它们在龟类生殖系统中的准确定位。用于解决这一重大进化问题的分子数据迄今为止仅限于少数标记和/或分类群。这些研究支持了相互矛盾的拓扑学，将海龟定位为所有其他爬行动物的姐妹群，蜥蜴类（蜥蜴和蛇），主龙类（鸟类和鳄鱼）或鳄鱼。基因组规模的数据已被证明是有用的，在解决其他有争议的遗传问题，但没有这样的足够的数据集尚未提供给阿托。在这项研究中，我们使用下一代测序技术从四只海龟、一只凯门鳄、一只蜥蜴和一只肺鱼的血液、肝脏或颌骨中获得了七个新的转录组。我们使用了一个基于16种脊椎动物分类群的248个核基因（187，026个核苷酸位点）的基因组数据集来解决海龟的起源。最大似然和贝叶斯串联分析和物种树的方法下进行的核苷酸和氨基酸取代过程的最现实的模型明确支持海龟作为一个姐妹组的鸟类和鳄鱼。使用更简单的模型的核苷酸取代的连接和物种树重建方法导致的人工分组的海龟和鳄鱼，最有可能是因为在第三个密码子位置的取代饱和。宽松的分子钟方法估计大约在2.55亿年前海龟和祖龙之间的分歧。现存龟类的最新共同祖先，对应于侧颈龟和隐颈龟的分裂，估计发生在大约1.57亿年前的上侏罗纪时期。这是一个比以前报道的更新的估计，并质疑有争议的下侏罗纪化石作为现存海龟辐射的一部分的解释。这些结果提供了一个系统发育的框架和时间尺度，以解释的独特的形态，发育和分子特征的海龟内的阿托特斯的演变。
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. In this study, we used next-generation sequencing to obtain seven new transcriptomes from the blood, liver, or jaws of 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. 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.
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影响因子：
10.7
作者：
Castresana, J
通讯作者：
Castresana, J
影响因子：
2.7
作者：
Benson, Roger B. J.;Domokos, Gabor;Reisz, Robert R.
通讯作者：
Reisz, Robert R.
影响因子：
10.7
作者：
Drummond, Alexei J.;Suchard, Marc A.;Rambaut, Andrew
通讯作者：
Rambaut, Andrew
影响因子：
3.3
作者：
Castoe TA;Hall KT;Guibotsy Mboulas ML;Gu W;de Koning AP;Fox SE;Poole AW;Vemulapalli V;Daza JM;Mockler T;Smith EN;Feschotte C;Pollock DD
通讯作者：
Pollock DD
影响因子：
4.5
作者：
Degnan JH;Rosenberg NA
通讯作者：
Rosenberg NA