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以及类群内部和之间进化变化的基础。系统发育研究的最新进展，特别是在转录组测序和非模式生物转录组的重新组装方面，使推断系统发育关系和潜在的基因组变化得到了前所未有的结合。这比仅仅重建系统发育要深入得多。基因组无形态，如分类群或分支特异性基因，可以为每一个恢复的单系群识别。此外，通过基因本体评估基因的功能，可以阐明分支发生的进化机制。在这个项目中，我将结合系统发育和转录组数据集的功能分析来研究与节肢动物深刻进化转变相关的两个有趣的枝发生案例。首先是从甲壳类动物祖先到六足动物的过渡。这里的重点将放在头足纲和鳃足纲上，这两个分类群对于解决仍有争议的六足纲姐妹类群的问题至关重要。二是从棘足类祖先到枝足类的过渡，这与重要的生活史变化（如循环孤雌生殖的进化）和可能的大规模基因组变化有关。特别是在这种情况下，系统发育分析将主要作为揭示基因组变化的相对时间和程度的工具。所有的分析将基于27个转录组的测序和重新组装：3个头足类和6个支足类，每个物种有3个单独的发育阶段测序。

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.