Date of Graduation


Document Type


Degree Type



Eberly College of Arts and Sciences



Committee Chair

David A Ray


Retrotransposons including CR1 (Chicken Repeat 1) elements mobilize in a genome in a way that makes them useful for phylogenetic analysis and species identification. This study was designed to identify lineages of CR1 elements in the genomes of forensically important carrion fly species and to further characterize the one element, Sarcophaga bullata CR1B, though genome walk techniques.;Using conserved oligonucleotide primers, CR1 fragments from several carrion fly taxa were amplified, cloned and sequenced, and the recovered sequences were analyzed to identify different lineages of elements. A variety of retrotransposon families were recovered that exhibit similarity to known retrotransposon families from other dipterans (e.g. mosquitoes, Drosophila). We also provide evidence that several of these lineages may have given rise to taxon-specific subfamilies that have been recently active in carrion fly genomes.;The final reconstructed sequence from the S. bullata CR1B genome walk is presumed to be the complete Open Reading Frame 2 (ORF2) portion of the element containing both the reverse transcriptase (RT) and endonuclease (EN) domains. These domains were used to identify conserved amino acid regions in the recovered consensus via comparison to known non-LTR retrotransposons. A phylogenetic analysis of the RT domain revealed the recovered ORF in S. bullata compares favorably with previously documented CR1-like elements.;This work will serve as the basis for additional analyses targeted at developing a simple, efficient marker system for the identification of forensically important carrion flies. The fast turnaround time possible for this system will also help to make it an extremely useful tool. Though much work will be needed to completely develop the method, the data presented here lays the groundwork for future efforts.