Conservation genetics at the species boundary: Case studies from African and Caribbean crocodiles (genus: Crocodylus)

This dissertation presents an examination of boundaries within and between species using the combined tools of mitochondrial and nuclear genetic markers. Such marker systems provide specific levels of resolution which, when combined, have the ability to clarify patterns of evolution at local, regional and continental geographic scales. The perspective afforded by this approach is brought to bear on the conservation and management of the true crocodiles in Africa and the Caribbean.; The first chapter provides a detailed history of problems in crocodile taxonomy and how one can hope to address some of the threats to members of this group, using the tools of conservation genetics. In order to explore the hypothesis of the monophyly of the widespread type species, Crocodylus niloticus, the Nile crocodile, a phylogeographic analysis based on data from 5 mitochondrial and 4 nuclear regions is presented in Chapter 2. The findings suggest a deep and early split between crocodile lineages in East and West Africa rendering the species Crocodylus niloticus paraphyletic and indicating two distinct species of true crocodile currently inhabiting Africa. In chapter three, populations of Crocodylus niloticus are examined at a finer level, using microsatellite markers to evaluate levels of population identity and differentiation. Measures of population differentiation (Fst and Rst) depict low levels of interpopulation dispersal and suggest a close association between populations and regional drainage systems. The assignment test allows for clear identification of individuals from source populations in Kenya, Zimbabwe, South Africa and Madagascar, and will provide a valuable enforcement mechanism for monitoring trade in Nile crocodile products.; Chapter four examines the presence and extent of a hybrid zone between two protected species of Caribbean crocodiles using both mitochondrial and nuclear markers. The results demonstrate that, although some hybrid individuals can be identified using morphological characters, additional hybrids are detected by multilocus genotyping. In addition, the molecular markers indicate a unidirectional pattern of hybridization and suggest that it is a relatively localized occurrence. Chapter five provides a review of the use of genetic markers for crocodile conservation and their application at differing scales to elucidate meaningful boundaries for the maintenance of biodiversity.