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

Lophotrochozoa是根据分子数据提出的三个主要双边分类群之一，由几个蠕虫样的分类群组成。这些分类群之间的关系仍未解决。然而，最近的结果显示取得了一些进展，尽管除了在安内利达安置西蓬库拉和埃奇乌拉之外，还没有得到实质性的支持。环节动物门、网虫门和腕足动物门之间的亲缘关系似乎很近。另一方面，扁形动物被归类为Lophotrochozoa的姐妹群。此外，在其他原因中，扁形动物的包容性仍然存在争议，因为所有的分类群都表现出长的分枝。因此，尽管似乎存在两个主要的蠕虫状分支，但需要更多新的数据来测试并最终证实这些结果。因此，为了解决和检验使用454技术的线虫和扁形动物EST数据库的不同假设，应该为一个线虫、一个节肢动物和两个胃毛生成EST。后者将由完整的线粒体基因组来补充。应该探索不同的策略来从EST数据库中获得用于系统发育分析的直系同源序列。此外，应该使用新的方法来彻底研究鸭嘴兽分类群的长枝问题，例如逐节的同余方法，如PABA或NDI，结合Wilcoxon符号等级检验、新的长枝分数、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性质，例如组成偏见，对系统发育重建的影响，以及扁形动物是否为由长分支分类群组成的单系群。

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.