This project will investigate the utility of using ultra conserved elements of the genome (UCEs) as primary data for genetic and evolutionary studies of populations and species. UCEs are regions of the genome that rarely change, and that are shared across very divergent organismal groups (from humans to lizards). Thus, UCEs could potentially provide hundreds to thousands of data points that are universal across large taxonomic groups for analysis. This project will capture and sequence the DNA of 2,386 UCE areas of the genome across 18 species (from three organismal classes) in order to test the utility and power of UCEs as universal data markers for organismal population studies.
UCE's will provide a unique and important new tool for in-depth genetic studies of biodiversity and evolution while also helping to address problems in conservation biology and wildlife management. Development of UCE-based approaches may: produce data from thousands of genes across entire orders and classes of organisms; enable previously impossible apples-to-apples comparisons of genomic diversity among thousands of species at a time; and provide quantum increases in speed and decreases in cost for population genomic studies. This project will support a bioinformatics training workshop in Alaska, release all data and source code to the public, and publish results in peer-reviewed journals.
This project is demonstrating that ultraconserved elements (UCEs) and their flanking DNA are useful genomic markers for studying populations and species. These markers are highly conserved regions of the genome, so they can provide hundreds to thousands of marker loci that are universal and thus comparable across large taxonomic groups. This project captured and sequenced ~4,000 UCE loci from diverse species in three organismal classes (birds, mammals, and reptiles) to test the usefulness of UCEs as universal population genomic markers. This project also conducted a bioinformatics training workshop in Alaska, is releasing all data and source code to the public, and is publishing results in peer-reviewed journals. UCE loci provide an important new tool for in-depth genetic studies of biodiversity and evolution while also helping to address problems in conservation biology and wildlife management. UCE-based approaches allow researchers to use the exact same genetic toolkit for broad groups of organisms. The overall approach produces data from thousands of single-copy, homologous (orthologous) loci across entire orders and classes of organisms, enables previously impossible apples-to-apples comparisons of genomic diversity among thousands of species at a time, and provides quantum increases in speed and decreases in cost for population genomic studies. In this work, we used one set of DNA tools to discover and describe genetic variation within and among species of birds, mammals, and reptiles. This specific information is now available for these species, which can be used for a variety of purposes, and lays the foundation for future workers who want to use this toolkit to directly compare data from other species to data we have accumulated or who want to develop similar toolkits for other groups of organisms.
