Evolutionary and Functional Impacts of Short Interspersed Nuclear Elements (SINEs) Revealed Via Genomic Assessment of Felid CanSINEs Open Access
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Short interspersed nuclear elements (SINEs) are a type of class 1 transposable element that comprise over 10% of mammalian genomes, and play a vital role in genome structure and gene function. SINEs have also been promoted as valuable evolutionary markers at the population, species, genus and familial strata. While SINEs are prolific throughout Mammalia, historically SINE-based inquiry has primarily occurred amongst primates, rodents and cetaceans. Recent developments in genomic resources enable high-throughput investigations of SINEs within a variety of mammalian lineages. Publication of domestic dog, (Canis familiaris), and domestic cat (Felis catus) whole genome sequences in 2005 and 2007 respectively provide references sequences for comparative investigations of the Carnivora order specific SINE family, CanSINEs. This dissertation explores the evolutionary implications CanSINES within the Felidae (cat) family, a charismatic carnivoran clade of 38 species that includes biomedical model organisms, companion animals, and ecologically imperiled species. Capitalizing on the relative conservation of chromosome arrangements among Felidae species, comparative genomics methods were used to find CanSINE insertions that were initially located in domestic and exotic species across the entire Felidae family and in other Feliform suborder representatives. Comparative analyses of CanSINEs elucidate many aspects of SINE biology including: characterization of two Feliform specific SINE subfamilies, the phylogenetic consistency of CanSINE insertion loci, the evolutionary distribution of loci in divergent species following rapid speciation, a non-random retrotransposition process wherein new inserts occur at specified DNA motifs, and the utility of both presence/absence data and sequence data derived from SINE inserts for de novo phylogenetic reconstruction. The methods employed in this dissertation allow prior assumptions regarding the functional and evolutionary activity of mammalian SINEs to be evaluated empirically, ultimately providing a framework for the study of transposable elements in all mammals.