Crawford Nicholas G, Parham James F, Sellas Anna B, Faircloth Brant C, Glenn Travis C, Papenfuss Theodore J, Henderson James B, Hansen Madison H, Simison W Brian
Center for Comparative Genomics, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA.
John D. Cooper Archaeological and Paleontological Center, Department of Geological Sciences, California State University, Fullerton, CA 92834, USA.
Mol Phylogenet Evol. 2015 Feb;83:250-7. doi: 10.1016/j.ympev.2014.10.021. Epub 2014 Nov 4.
Molecular analyses of turtle relationships have overturned prevailing morphological hypotheses and prompted the development of a new taxonomy. Here we provide the first genome-scale analysis of turtle phylogeny. We sequenced 2381 ultraconserved element (UCE) loci representing a total of 1,718,154bp of aligned sequence. Our sampling includes 32 turtle taxa representing all 14 recognized turtle families and an additional six outgroups. Maximum likelihood, Bayesian, and species tree methods produce a single resolved phylogeny. This robust phylogeny shows that proposed phylogenetic names correspond to well-supported clades, and this topology is more consistent with the temporal appearance of clades and paleobiogeography. Future studies of turtle phylogeny using fossil turtles should use this topology as a scaffold for their morphological phylogenetic analyses.
龟类亲缘关系的分子分析推翻了主流的形态学假说，并推动了新分类学的发展。在此，我们提供了首个龟类系统发育的基因组规模分析。我们对代表总共1,718,154bp比对序列的2381个超保守元件（UCE）位点进行了测序。我们的样本包括代表所有14个公认龟类科的32个龟类分类单元以及另外6个外类群。最大似然法、贝叶斯法和物种树方法产生了一个单一的解析系统发育树。这个稳健的系统发育树表明，所提出的系统发育名称对应于得到充分支持的分支，并且这种拓扑结构与分支的时间出现和古生物地理学更为一致。未来使用化石龟进行龟类系统发育研究时，应将这种拓扑结构作为其形态学系统发育分析的框架。
