Amrine-Madsen Heather, Koepfli Klaus-Peter, Wayne Robert K, Springer Mark S
Department of Biology, University of California, Riverside 92521, USA.
Mol Phylogenet Evol. 2003 Aug;28(2):225-40. doi: 10.1016/s1055-7903(03)00118-0.
Higher-level relationships within, and the root of Placentalia, remain contentious issues. Resolution of the placental tree is important to the choice of mammalian genome projects and model organisms, as well as for understanding the biogeography of the eutherian radiation. We present phylogenetic analyses of 63 species representing all extant eutherian mammal orders for a new molecular phylogenetic marker, a 1.3kb portion of exon 26 of the apolipoprotein B (APOB) gene. In addition, we analyzed a multigene concatenation that included APOB sequences and a previously published data set (Murphy et al., 2001b) of three mitochondrial and 19 nuclear genes, resulting in an alignment of over 17kb for 42 placentals and two marsupials. Due to computational difficulties, previous maximum likelihood analyses of large, multigene concatenations for placental mammals have used quartet puzzling, less complex models of sequence evolution, or phylogenetic constraints to approximate a full maximum likelihood bootstrap. Here, we utilize a Unix load sharing facility to perform maximum likelihood bootstrap analyses for both the APOB and concatenated data sets with a GTR+Gamma+I model of sequence evolution, tree-bisection and reconnection branch-swapping, and no phylogenetic constraints. Maximum likelihood and Bayesian analyses of both data sets provide support for the superordinal clades Boreoeutheria, Euarchontoglires, Laurasiatheria, Xenarthra, Afrotheria, and Ostentoria (pangolins+carnivores), as well as for the monophyly of the orders Eulipotyphla, Primates, and Rodentia, all of which have recently been questioned. Both data sets recovered an association of Hippopotamidae and Cetacea within Cetartiodactyla, as well as hedgehog and shrew within Eulipotyphla. APOB showed strong support for an association of tarsier and Anthropoidea within Primates. Parsimony, maximum likelihood and Bayesian analyses with both data sets placed Afrotheria at the base of the placental radiation. Statistical tests that employed APOB to examine a priori hypotheses for the root of the placental tree rejected rooting on myomorphs and hedgehog, but did not discriminate between rooting at the base of Afrotheria, at the base of Xenarthra, or between Atlantogenata (Xenarthra+Afrotheria) and Boreoeutheria. An orthologous deletion of 363bp in the aligned APOB sequences proved phylogenetically informative for the grouping of the order Carnivora with the order Pholidota into the superordinal clade Ostentoria. A smaller deletion of 237-246bp was diagnostic of the superordinal clade Afrotheria.
胎盘类动物内部的高级关系以及胎盘类动物的根源，仍然是有争议的问题。胎盘类进化树的解析对于哺乳动物基因组计划和模式生物的选择很重要，对于理解真兽类辐射的生物地理学也很重要。我们针对一种新的分子系统发育标记——载脂蛋白B（APOB）基因第26外显子的1.3kb片段，对代表所有现存真兽类哺乳动物目的63个物种进行了系统发育分析。此外，我们分析了一个多基因串联序列，其中包括APOB序列以及先前发表的一个数据集（Murphy等人，2001b），该数据集包含三个线粒体基因和19个核基因，从而得到了42种胎盘类动物和两种有袋类动物的超过17kb的比对序列。由于计算上的困难，先前对胎盘类哺乳动物的大型多基因串联序列进行的最大似然分析使用了四重奏迷惑法、不太复杂的序列进化模型或系统发育限制来近似完整的最大似然自展分析。在这里，我们利用一个Unix负载共享工具，对APOB数据集和串联数据集进行最大似然自展分析，采用GTR + Gamma + I序列进化模型、树二分重连分支交换法，且不设系统发育限制。对两个数据集进行的最大似然分析和贝叶斯分析都支持北方真兽高目、灵长总目、劳亚兽总目、异关节总目、非洲兽总目和鳞甲目（穿山甲 + 食肉目）等超目分支，以及真盲缺目、灵长目和啮齿目等目的单系性，而这些最近都受到了质疑。两个数据集都在鲸偶蹄目内恢复了河马科和鲸目之间的关联，以及在真盲缺目内刺猬和鼩鼱之间的关联。APOB显示出对灵长目内跗猴型下目和类人猿下目之间关联的有力支持。使用两个数据集进行的简约法、最大似然法和贝叶斯分析都将非洲兽总目置于胎盘类辐射的基部。采用APOB来检验胎盘类进化树根的先验假设的统计检验拒绝了以鼠形亚目和刺猬为根的情况，但无法区分以非洲兽总目基部、异关节总目基部为根，或者在大西洋兽类（异关节总目 + 非洲兽总目）和北方真兽高目之间为根的情况。在比对的APOB序列中363bp的直系同源缺失对于将食肉目和鳞甲目归为超目分支鳞甲目具有系统发育信息价值。237 - 246bp的较小缺失是非洲兽总目超目分支的诊断特征。
