Data from: Using novel phylogenetic methods to evaluate mammalian mtDNA, including amino acid-invariant sites-LogDet plus site stripping, to detect internal conflicts in the data, with special reference to the positions of hedgehog, armadillo, and elephant

We look at the higher-order phylogeny of mammals, analyzing in detail the complete mtDNA sequences of over 40 species. We test the support for several proposed super-ordinal relationships. To this end, we apply a number of recently programmed methods and approaches, plus better established methods. New pairwise tests show that there is highly significant evidence that amino acid frequencies are changing among nearly all the genomes studied when unvaried sites are ignored. LogDet amino acid distances, with modifications to take into account invariant sites, are combined with bootstrapping and the Neighbor Joining algorithm to account for these violations of standard models. To weight the slower evolving sites, we exclude the more rapidly evolving sites from the data using "site stripping". This leads to changing optimal trees with nearly all methods. The bootstrap support for many hypotheses varies widely between methods, and few hypotheses can claim unanimous support from these data. Rather, we uncover good evidence that many of the earlier branching patterns in the placental subtree could be incorrect, and this includes the placement of the root. The tRNA genes, for example, favour a split between the group hedgehog, rodents and Primates versus all other sequenced placentals. Such a grouping is not ruled out by the amino acid sequence data. A grouping of all rodents plus rabbit, the old Glires hypothesis, is also feasible with stripped amino acid data, while rodent monophyly is also common. The elephant sequence allows confident rejection of the older taxon Ferungulata (Simpson 1945). In its place, the new taxa Scrotifera and Fereuungulata is defined. A new likelihood ratio test is used to detect differences between the optimal tree for tRNA versus that for amino acids. While not clearly significant as made, there are indications the test is tending towards significance with more general models of evolution. Individual placement tests suggest alternative positions for hedgehog, and the elephant. There are striking congruence arguments to support elephant and armadillo together, suggesting a superordinal group composed of Xenarthra and African endemic mammals, which in turn may be near the root of the placental subtree. Thus, the analyses while casting doubt on some recent conclusions, are also unveiling some interesting new possibilities.

本研究聚焦哺乳动物的高阶系统发育关系，详细分析了40余个物种的完整线粒体DNA（mtDNA）序列。我们对多项已提出的超目级亲缘关系的支持度进行了检验。为此，我们采用了多种新近开发的分析方法与策略，辅以更为成熟的经典分析方法。全新的成对检验结果显示，在忽略恒定位点的前提下，几乎所有被测基因组的氨基酸频率均存在极显著的演化变化。针对这一违反标准演化模型的情况，我们结合了经恒定位点修正的LogDet氨基酸距离算法、自举法（bootstrapping）以及邻接法（Neighbor Joining）开展分析。为了对演化速率较慢的位点赋予权重，我们通过位点剥离（site stripping）策略移除数据中演化速率较快的位点。这一操作使得绝大多数方法得到的最优系统发育树发生改变。不同分析方法对多数演化假说的自举支持度差异显著，仅有极少数假说能得到本数据集的一致支持。我们的分析揭示了有力证据：胎盘类哺乳动物亚树中的诸多早期分支模式可能并不正确，其中甚至包括类群根节点的位置。例如，转运RNA（tRNA）基因支持刺猬、啮齿类与灵长类构成一支，与其余已测序胎盘类动物形成分化。这一类群划分并未被氨基酸序列数据排除。基于剥离后的氨基酸序列数据，“所有啮齿类与兔类构成单系群”的古老啮型类（Glires）假说同样具备可行性，而啮齿类单系群的结论也较为常见。大象的线粒体序列则可明确推翻旧有的有蹄总目（Ferungulata）分类单元（Simpson 1945）。取而代之的是，我们定义了两个新的分类单元：阴囊兽类（Scrotifera）与真有蹄类（Fereuungulata）。我们采用了全新的似然比检验（likelihood ratio test）来检测转运RNA基因与氨基酸序列对应的最优系统发育树之间的差异。尽管当前检验结果未达到显著水平，但有迹象表明，若采用更具普适性的演化模型，该检验将趋近于显著。个体类群定位检验显示，刺猬与大象的系统发育位置存在多种备选方案。有显著的一致性证据支持大象与犰狳构成姊妹群，这表明由异关节总目（Xenarthra）与非洲特有哺乳动物构成的超目类群可能接近胎盘类亚树的根部。综上，本研究不仅对部分近期的研究结论提出了质疑，同时也揭示了若干颇具研究价值的全新演化可能性。