| Identifying the units of conservation is an essential first step in designing a successful taxon oriented conservation strategy. In this thesis I propose a scientific framework for identification of conservation units employing a cladistic analysis of molecular characters. Two applications of this proposed framework are presented to illustrate useful laboratory techniques, methods of analysis, and important limitations of this methodology. In chapter 1, an analysis of conservation units for the Caiman crocodilus (common caiman) complex using a character analysis of 12S and 16S ribosomal mitochondrial DNA sequences demonstrates the usefulness of combining limited direct sequencing with allele specific PCR technology. The distribution of characters supports designating three conservation units corresponding to the trinomials Caiman crocodilus crocodilus, C.c. fuscus, and C.c.yacare. Controversies in higher level crocodilian relationships are reviewed in chapter 2. A total evidence analysis of extant rhinoceros is presented in chapter 3 in order to provide context for an assessment of conservation units for Dicerorhinus sumatrensis (Sumatran rhino). In this study I assess the number of conservation units determined by a cladistic analysis of completely sequenced 12S and 16S ribosomal mitochondrial DNA for the allopatric populations of Sumatran Rhinos. Nucleotide sequence data weakly supports separation of the three units. Subjective assessments of the effects of sample size and inferred degrees of divergence support a policy of treating Dicerorhinus sumatrensis as a single conservation unit.;Finally, a summary of the strengths and limitations of this generalized approach to determining conservation is presented. |
