Genealogy and traits of living and fossil vertebrates that never left the water
Why exons for phylogenomics?
To assemble exon data matrices from raw reads, whole genomes or transcriptome data bases
What taxa have been sequenced?
The FishLife Collaboration
NSF- DEB - 1541554 Collaborative Research: FishLife: genealogy and traits of living and fossil vertebrates that never left the water
This project will complete the tree of life of all living and fossil fishes, from the early evolutionary radiation of vertebrates to the extraordinary diversity of fishes. This explicit phylogenetic framework will be used for integrating genomic, paleontological, anatomical, functional, and ecological, data with comparative approaches.
Our knowledge of the tree of life for vertebrates, and in particular the species-rich branches of fishes among which sprung a branch that gave rise to tetrapods, has undergone a dramatic transformation in the last five years. Increased phylogenetic resolution has led to identification of new clades among poorly resolved groups of bony fishes but many other groups remain poorly sampled and in dire need of resolution. Likewise, relationships among sharks, rays, and chimaeras are becoming clearer but an integrative and comprehensive phylogeny including cartilaginous and bony fishes has never been resolved. This project will provide such resolution and make possible integrative analysis to elucidate the evolutionary history of all fishes and their connection to tetrapods. For the first time, this project will provide a unified framework that includes fossil and living species for comparative analyses, from sharks to coral reef and deep-sea fishes, and clarify the ancestry and origins of the most popular food and aquarium fishes worldwide. The project will contribute to community-driven scientific efforts, to student training, to web content and app development, and to public outreach. All collections of specimens, data, and results obtained will be placed into a dynamic and open structure to facilitate wide accessibility to the broader scientific and non-scientific communities. High school, undergraduate, graduate, and postdoctoral student training constitute central activities for this project, by implementing internships, workshops, and a student exchange program between institutions. A fish species identification app for smartphones based on image data will be developed and made freely available to the public. Finally, outcomes of this project will form part of a new public exhibit at the National Museum of Natural History’s (Smithsonian) to highlight the value of specimen collections at natural history museums.
The research team blends strengths in collection-based research for all groups of fishes, molecular and morphological phylogenetics, bioinformatics, and comparative analyses. The resolution of phylogenetic relationships among all fishes will empower fundamentally new ways of exploring evolution among basal vertebrates through novel comparative analysis based on the rich data layers compiled by the project. Time-calibrated trees will be used to reveal diversification patterns of the major groups. Image data analysis within the tree framework will promote the discovery of evolutionary patterns in size, shape, and biomechanical function across thousands of species. Using new software tools for comparative analysis and visualization of diversification patterns through time and space, this project will examine character associations of anatomy, life history, habitat and ecology in an attempt to understand the evolutionary radiation in the largest and yet unresolved groups of vertebrates.