Phylogenetic and functional transcriptome analyses to highlight the evolution of Cephalocarida and Branchiopoda with special focus on Cladocera (Crustacea)

良好的系统发育关系是我们理解进化和类群内部和类群间进化变化的基础。最近在系统基因组研究方面的进展，特别是在转录组测序和非模式生物转录组的从头组装方面的进展，使得推断系统发育关系和潜在的基因组变化成为前所未有的组合。这比仅仅重建系统发展史走得更远。对于每个恢复的单系类群，可以识别基因组同型，例如分类单元或支系特有基因。此外，通过用基因本体论评估基因的功能，可以阐明分支发生的进化机制。在这个项目中，我将使用转录组数据集的系统发育和功能分析相结合的方法来研究节肢动物中与深刻进化转变相关的两个有趣的分支发生案例。首先是从甲壳类祖先到六足类动物的过渡。在这里，焦点将集中在头足纲和支足纲，这两个分类群对于解决六足纲姐妹群的问题至关重要。第二个是从棘尾类祖先向枝角类的转变，这与重要的生活史变化(例如循环孤雌生殖的进化)有关，也可能是大规模的基因组变化。特别是在这种情况下，系统发育分析将主要作为一种工具来揭示基因组变化的相对时间和程度。所有的分析都将基于27个转录体的测序和重新组装：3个头足类和6个鳃足目动物物种，每个物种都有三个单独的发育阶段。

Well founded phylogenetic relationships are the basis for our understanding of evolution and of evolutionary changes within and among taxa. Recent advances in phylogenomic research, in particularly in transcriptome sequencing and the de novo assembly of transcriptomes of non-model organisms, allow an unprecedented combination of inferring phylogenetic relationships and the underlying genomic changes. This goes considerably further than merely reconstructing phylogenies. Genomic apomorphies, such as taxon or clade specific genes, can be identified for each recovered monophyletic group. Furthermore, by assessing the genes' function with gene ontologies the evolutionary mechanisms underlying cladogenesis may be elucidated. In this project, I will employ a combination of phylogenetic and functional analyses of transcriptome datasets to study two interesting cases of cladogenesis associated with profound evolutionary transitions within arthropods. The first is the transition from a crustacean-like ancestor to Hexapoda. Here the focus will be on the Cephalocarida and the Branchiopoda, two taxa crucial to solve the problem of the still controversial sister group of Hexapoda. The second is the transition from a spinicaudatan-like ancestor to Cladocera within Branchiopoda, which was associated with important life history changes (e.g. evolution of cyclic-parthenogenesis) and presumably large-scale genomic changes. Especially in this case, phylogenetic analyses will mainly serve as a tool to uncover the relative timing and extent of genomic changes. All analyses will be based on the sequencing and de novo assembly of 27 transcriptomes: three cephalocarid and six branchiopod species with three separately sequenced developmental stages each.