Odronitz Florian, Kollmar Martin
Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg, 37077 Goettingen, Germany.
Genome Biol. 2007;8(9):R196. doi: 10.1186/gb-2007-8-9-r196.
The evolutionary history of organisms is expressed in phylogenetic trees. The most widely used phylogenetic trees describing the evolution of all organisms have been constructed based on single-gene phylogenies that, however, often produce conflicting results. Incongruence between phylogenetic trees can result from the violation of the orthology assumption and stochastic and systematic errors.
Here, we have reconstructed the tree of eukaryotic life based on the analysis of 2,269 myosin motor domains from 328 organisms. All sequences were manually annotated and verified, and were grouped into 35 myosin classes, of which 16 have not been proposed previously. The resultant phylogenetic tree confirms some accepted relationships of major taxa and resolves disputed and preliminary classifications. We place the Viridiplantae after the separation of Euglenozoa, Alveolata, and Stramenopiles, we suggest a monophyletic origin of Entamoebidae, Acanthamoebidae, and Dictyosteliida, and provide evidence for the asynchronous evolution of the Mammalia and Fungi.
Our analysis of the myosins allowed combining phylogenetic information derived from class-specific trees with the information of myosin class evolution and distribution. This approach is expected to result in superior accuracy compared to single-gene or phylogenomic analyses because the orthology problem is resolved and a strong determinant not depending on any technical uncertainties is incorporated, the class distribution. Combining our analysis of the myosins with high quality analyses of other protein families, for example, that of the kinesins, could help in resolving still questionable dependencies at the origin of eukaryotic life.
生物体的进化历史通过系统发育树来表示。描述所有生物体进化的最广泛使用的系统发育树是基于单基因系统发育构建的，然而，这些系统发育树常常产生相互矛盾的结果。系统发育树之间的不一致可能源于直系同源假设的违背以及随机和系统误差。
在此，我们基于对328种生物体的2269个肌球蛋白运动结构域的分析重建了真核生物生命树。所有序列均经过人工注释和验证，并被分为35个肌球蛋白类别，其中16个是此前未曾提出过的。所得的系统发育树证实了一些主要类群已被接受的关系，并解决了有争议的和初步的分类问题。我们将绿藻植物门置于眼虫纲、囊泡虫类和不等鞭毛类分离之后，我们提出内阿米巴科、棘阿米巴科和盘基网柄菌目的单系起源，并为哺乳动物和真菌的异步进化提供了证据。
我们对肌球蛋白的分析允许将来自特定类别树的系统发育信息与肌球蛋白类别进化和分布的信息相结合。与单基因或系统发育基因组分析相比，这种方法有望带来更高的准确性，因为直系同源问题得到了解决，并且纳入了一个不依赖于任何技术不确定性的强决定因素，即类别分布。将我们对肌球蛋白的分析与其他蛋白质家族（例如驱动蛋白家族）的高质量分析相结合，可能有助于解决真核生物生命起源时仍有疑问的相关性问题。
