Department of Biology, The National University of Ireland, Maynooth, Ireland School of Earth Sciences, University of Bristol, United Kingdom
Department of Genetics, Evolution and Environment, University College London, United Kingdom School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom.
Genome Biol Evol. 2016 Jan 5;8(2):330-44. doi: 10.1093/gbe/evv261.
Placental mammals comprise three principal clades: Afrotheria (e.g., elephants and tenrecs), Xenarthra (e.g., armadillos and sloths), and Boreoeutheria (all other placental mammals), the relationships among which are the subject of controversy and a touchstone for debate on the limits of phylogenetic inference. Previous analyses have found support for all three hypotheses, leading some to conclude that this phylogenetic problem might be impossible to resolve due to the compounded effects of incomplete lineage sorting (ILS) and a rapid radiation. Here we show, using a genome scale nucleotide data set, microRNAs, and the reanalysis of the three largest previously published amino acid data sets, that the root of Placentalia lies between Atlantogenata and Boreoeutheria. Although we found evidence for ILS in early placental evolution, we are able to reject previous conclusions that the placental root is a hard polytomy that cannot be resolved. Reanalyses of previous data sets recover Atlantogenata + Boreoeutheria and show that contradictory results are a consequence of poorly fitting evolutionary models; instead, when the evolutionary process is better-modeled, all data sets converge on Atlantogenata. Our Bayesian molecular clock analysis estimates that marsupials diverged from placentals 157-170 Ma, crown Placentalia diverged 86-100 Ma, and crown Atlantogenata diverged 84-97 Ma. Our results are compatible with placental diversification being driven by dispersal rather than vicariance mechanisms, postdating early phases in the protracted opening of the Atlantic Ocean.
非洲兽总目（例如象和食蚁兽）、异关节总目（例如犰狳和树懒）和真兽亚纲（所有其他胎盘哺乳动物），它们之间的关系是争议的主题，也是对系统发育推断界限的辩论的试金石。以前的分析支持了这三个假说，导致一些人得出结论，由于不完全谱系分选（ILS）和快速辐射的复合效应，这个系统发育问题可能无法解决。在这里，我们使用基因组规模的核苷酸数据集、microRNAs 以及对三个先前发表的最大氨基酸数据集的重新分析，表明胎盘类的根位于 Atlantogenata 和真兽亚纲之间。尽管我们在早期胎盘进化中发现了 ILS 的证据，但我们能够拒绝先前的结论，即胎盘的根是一个无法解决的硬多分支。对先前数据集的重新分析恢复了 Atlantogenata+Boreoeutheria，并表明矛盾的结果是由于进化模型拟合不佳造成的；相反，当进化过程得到更好的建模时，所有数据集都集中在 Atlantogenata 上。我们的贝叶斯分子钟分析估计，有袋动物与胎盘动物的分化发生在 157-170 Ma 之间，冠真兽类的分化发生在 86-100 Ma 之间，冠 Atlantogenata 的分化发生在 84-97 Ma 之间。我们的结果与胎盘多样化是由扩散而不是隔离机制驱动的观点是一致的，这发生在大西洋早期漫长扩张的早期阶段之后。
