An examination of the crocodilian mitochondrial control region: Structural and functional units and utility in phylogenetic and phylogeographic analysis

The use of molecular markers for elucidating crocodilian phylogenetic relationships has been ongoing for several decades now. While significant progress has been made in understanding how each of the three major morphological groups of crocodilians are related to one another and to the remainder of Archosauria, issues involving the relationships of the two gharial species to the remainder of the order Crocodylia and understanding phylogeny within the family Crocodylidae remain. In this dissertation, I describe the development of a new marker for examining each of these issues as well as problems involving population level relationships. For representatives of each major crocodilian lineage, the mitochondrial control region is characterized from structural and functional perspectives and then utilized as a marker for the determination of phylogenetic relationships within the Crocodylia and for examining the population dynamics of one species, Crocodylus moreletii. I found that the control region of crocodilians contains several features in common with other vertebrate groups as well as several features that deserve special interest, including a series of heteroplasmic tandem repeats. I also found that the control region appears to be useful in resolving relationships at several levels within the order Crocodylia. Finally, while control region sequences reveal little with regard to phylogeography in C. moreletii, the inclusion of these new data have significantly affected our interpretation of other studies with regard to population structure in this species.