Mammalian evolution: timing and implications from using the LogDeterminant transform for proteins of differing amino acid composition

We explore the tree of mammalian mtDNA sequences, using particularly the LogDet transform on amino acid sequences, the distance Hadamard transform, and the Closest Tree selection criterion. The amino acid composition of different species show significant differences, even within mammals. After compensating for these differences, nearest-neighbor bootstrap results suggest that the tree is locally stable, though a few groups show slightly greater rearrangements when a large proportion of the constant sites are removed. Many parts of the trees we obtain agree with those on published protein ML trees. Interesting results include a preference for rodent monophyly. The detection of a few alternative signals to those on the optimal tree were obtained using the distance Hadamard transform (with results expressed as a Lento plot). One rearrangement suggested was the interchange of the position of primates and rodents on the optimal tree. The basic stability of the tree, combined with two calibration points (whale/cow and horse/rhinoceros), together with a distant secondary calibration from the mammal/bird divergence, allows inferences of the times of divergence of putative clades. Allowing for sampling variances due to finite sequence length, most major divergences amongst lineages leading to modern orders, appear to occur well before the Cretaceous/Tertiary (K/T) boundary. Implications arising from these early divergences are discussed, particularly the possibility of competition between the small dinosaurs and the new mammal clades.

本研究探讨哺乳动物线粒体DNA（mitochondrial DNA）序列的系统发育树构建，尤其采用了针对氨基酸序列的LogDet变换（LogDet transform）、距离阿达马变换（distance Hadamard transform），以及最近树选择准则（Closest Tree selection criterion）。不同物种的氨基酸组成存在显著差异，即便在哺乳类类群内部亦是如此。在校正此类组成差异后，最近邻自举法（nearest-neighbor bootstrap）分析结果显示，该系统发育树整体具备局部稳定性；但当移除大量恒定位点时，少数类群的拓扑结构会出现较为明显的重排。我们构建的系统发育树的多数拓扑分支与已发表的蛋白质最大似然树（Maximum Likelihood tree，ML）结果一致。本次研究得到的一项有趣结果，支持啮齿类为单系群（rodent monophyly）。通过距离阿达马变换分析，我们检测到最优树之外存在少量其他系统发育信号，其结果以伦托图（Lento plot）呈现。其中一种被提出的拓扑重排方式，为最优树上灵长类与啮齿类的位置互换。结合两个校准点（鲸/牛分歧时间与马/犀牛分歧时间）以及源自哺乳类/鸟类分歧的远端次级校准点，基于该树的基本稳定性，我们可以推断推定演化支的分歧时间。考虑到有限序列长度带来的抽样方差，现代哺乳类各目所属支系间的多数主要分歧事件，均远早于白垩纪/第三纪（K/T）界线时期。本研究还讨论了此类早期分歧所带来的研究启示，尤其是小型恐龙与新兴哺乳类演化支之间的竞争可能性。