Phylogenetics of early vertebrate genomes: an approach to understanding genomic innovations as sources of phenotypic evolution

脊椎动物具有许多无脊椎动物所不具备的高级表型特征，如复杂的大脑和多样的生理能力。在脊椎动物中，环口动物（无颌鱼类）和软骨鱼类（软骨鱼）在早期分支谱系中占据重要的系统发育位置。然而，我们对脊椎动物基因组学的了解主要局限于骨脊椎动物，即四足动物和硬骨鱼。在这个项目中，我们将利用新兴的基因组和转录组DNA序列以及现有的生物信息学工具，进行大规模的系统发育分析，以检测所有现存脊椎动物祖先获得的基因组成分（如蛋白质编码基因、miRNA、顺式调控元件）。作为这些新因素的来源，我们还将关注发生在脊椎动物进化早期的全基因组复制的时间和模式。为了说明这些新的基因组成分如何促成脊椎动物共有的表型特征，我们将对颅面发育和内分泌学进行合作实验分析。这项研究为理解从前脊椎动物到脊椎动物的转变提供了一个坚实的分子系统发育框架，这被认为是人类基因组建设的主要升级之一。

Vertebrates share a number of advanced phenotypic traits that are not possessed by invertebrates, such as complex brain and diverse physiological capacity. Among vertebrates, cyclostomes (jawless fishes) and chondrichthyes (cartilaginous fishes) occupy crucial phylogenetic positions as early-branching lineages. However, our knowledge of vertebrate genomics is limited mainly to bony vertebrates, namely tetrapods and teleost fishes. In this project, using emerging genomic and transcriptomic DNA sequences and available bioinformatic tools, we will conduct large-scale phylogenetic analyses to detect genomic components (e.g. protein-coding genes, miRNA, cis-regulatory elements) acquired by the ancestor of all extant vertebrates. As a source of such novel factors, we will also focus on timing and mode of whole genome duplications that occurred early in vertebrate evolution. To illustrate how such novel genomic components contributed to phenotypic traits shared by vertebrates, we will perform collaborative experimental analyses on craniofacial development and endocrinology. This study should provide a solid molecular phylogenetic framework to understand the transition from pre-vertebrates to vertebrates which is regarded as one of major upgrades in establishment of the human genome.