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. Ra...

本研究聚焦哺乳动物的高阶系统发育关系，对40余个物种的完整线粒体DNA（mtDNA）序列开展详细分析。我们针对多项已提出的超目亲缘关系假说的支持证据进行检验。为此，本研究采用了多种新近开发的算法方法，辅以更为成熟的分析手段。全新的成对检验结果表明：在忽略不变位点的情况下，几乎所有受试基因组的氨基酸频率均存在极为显著的变化证据。我们将针对不变位点进行修正的LogDet氨基酸距离与自举法、邻接法（Neighbor Joining）相结合，以修正标准进化模型的违反情形。为对进化速率较慢的位点赋予合理权重，我们通过"位点剥离法"将进化速率更快的位点从数据集中移除。该操作导致绝大多数分析方法所得到的最优拓扑树发生改变。不同方法对多数假说的自举支持度差异悬殊，仅有极少数假说能获得本数据集的一致支持。Ra...