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

建立良好的系统发育关系是我们理解进化和分类群内部和之间进化变化的基础。最近的进展，特别是在转录组测序和从头组装的转录组的非模式生物，允许一个前所未有的组合推断系统发育关系和潜在的基因组变化。这远远不止是重建种族隔离。基因组无形态，如分类单元或进化枝特异性基因，可以确定为每个恢复的单系群。此外，通过评估基因的功能与基因本体论的进化机制，潜在的分支可能会阐明。在这个项目中，我将采用转录组数据集的系统发育和功能分析相结合，研究两个有趣的情况下，分支与节肢动物的深刻进化转变。第一个是从甲壳类祖先到六足类的转变。在这里，重点将放在Cephecarida和Branchiopoda，两个分类群的关键，以解决仍然有争议的姐妹组的六足动物的问题。第二个是从一个spinicaudata类的祖先，枝角类在鳃足类，这是与重要的生活史变化（如周期性孤雌生殖的进化）和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，以揭示基因组变化的相对时间和程度。所有分析将基于27个转录组的测序和从头组装：三个cephalocarid和六个branchiopod物种，每个物种有三个单独测序的发育阶段。

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.