Genomic Journeys into a Lost World: ‘Ancient Fishes’ Illuminate the Genetic Basis of Vertebrate Development and Evolution

Using examples from diverse developmental pathways and processes, I will demonstrate that comparative genomic, developmental, transcriptomic, and epigenomic analyses using holosteans as "bridge species" are indispensable for connecting the disparate sets of genes, gene regulatory elements, and morphologies among distant vertebrate lineages. The structure and content of the genome of our main holostean model species, the spotted gar (Lepisosteus oculatus), is representative of the bony vertebrate ancestor and retained numerous genes differentially lost in other lineages. The ‘evolutionary inertia’ of holostean genomes particularly facilitates the identification of gene regulatory elements, revealing the deep homology of regulatory landscapes among vertebrates. Holosteans are thus powerful Evo-Devo models that illuminate vertebrate evolution, development, disease, and regeneration.