Phylogenomics of worm-like lophotrochozoans and platyzoans (Nemertea, Gastrotricha, Gnathostomulida)

散轮藻是基于分子生物学数据提出的三个主要的两侧对称类群之一，包括几个蠕虫样类群。这些分类群之间的关系仍然没有得到解决。然而，最近的结果显示出一些进展，尽管除了将星虫和Echiura置于环节动物门之外，还没有实质性的支持。环节动物门、纽形动物门和帚形动物门似乎彼此密切相关，软体动物门和腕足动物门。另一方面，扁形虫被列为Lophotrochozoa的姐妹群。此外，扁形虫的包容性仍然是有争议的，除其他原因外，由于所有分类群都表现出长分支的事实。因此，虽然似乎有两个主要的蠕虫状分支，但需要更多的新数据来测试并最终证实这些结果。因此，为了解决和测试不同的假设有关纽形动物和扁形动物EST数据库使用454技术应生成纽形动物，gnathotomulid和两个gastrotrichs。后者应得到完整的线粒体基因组的补充。从EST数据库中获取直系同源序列进行系统发育分析需要探索不同的策略。此外，长分支问题的扁形动物类群应彻底调查使用新的方法，如节点的节点一致的方法，如PABA或NDI结合Wilcoxon签署秩检验，新的长分支分数，主成分分析，热图，聚类算法和时间隐马尔可夫模型。这些分析将揭示基因的不同特性，例如组成偏差，对系统发育重建的影响，以及如果扁形虫是一个单系群，包括长分支类群。

Lophotrochozoa, one of the three major bilaterian taxa proposed based on molecular data, comprises several worm-like taxa. The relationship of these taxa to each other is still unresolved. However, recent results show some progress, though without substantial support yet except for the placement of Sipuncula and Echiura within Annelida. Annelida, Nemertea and Phoronida seems to be closely related to each other, Mollusca and Brachiopoda. Platyzoa, on the other hand, are placed as the sister group to Lophotrochozoa. Furthermore, the inclusiveness of Platyzoa is still controversial, among other reasons, due to the fact that all taxa exhibit long branches. Thus, though there seem to be two major worm-like clades new and more data are wanted to test and eventually corroborate these results. Therefore, to address and test the different hypotheses concerning Nemertea and Platyzoa EST databases using 454 technologies shall be generated for a nemertean, a gnathotomulid and two gastrotrichs. The latter ones shall be complemented by complete mitochondrial genomes. Different strategies shall be explored to obtain ortholog sequences from EST databases for phylogenetic analyses. Furthermore, the long branch problem of the platyzoan taxa shall be thoroughly investigated using novel methods such as node-by-node congruence approaches like PABA or NDI in combination with Wilcoxon signed rank tests, new long branch scores, principal component analyses, heat maps, cluster algorithms and temporal hidden Markov models. These analyses shall reveal the impact of different properties of the genes, e.g. compositional biases, on the phylogenetic reconstruction as well as if Platyzoa is a monophyletic group comprising long branched taxa.