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

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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.