The fundamental objective of conservation genetics is the identification of the basic units of conservation. Central to this objective is the reconstruction of the adaptive and evolutionary history of populations to evaluate their conservation status. Evolutionary history involves both microevolutionary and macroevolutionary processes and adaptive history is the evolution of specific characters to selective ecological processes in differential heterogeneous environments. Neutral DNA markers such as mitochondrial DNA, minisatellites and microsatellites are most often used for reconstructing history and identifying conservation units. This thesis examined three biological systems: 1) an African cichlid, 2) Canadian moose populations and 3) eastern North American wolves and coyotes to test two hypotheses. Firstly, neutral DNA markers can be used to accurately reconstruct the evolutionary history of populations. Secondly, neutral DNA markers are concordant with adaptive distinctiveness in reconstructing the adaptive history of populations. Few studies have examined these relationships. Lake Magadi tilapia showed discordant patterns between adaptive morphological, physiological and behavioural characters and genetic structure assessed with mitochondrial DNA. I propose this discordance has resulted from selection acting on mitochondrial DNA that has often been assumed to be "neutral". Neutral DNA markers accurately reflected the known history of the moose populations but discordant patterns were observed between neutral and functional loci indicating the former may not accurately reflect adaptive variation. DNA profiles of eastern wolves and coyotes showed a significant conflict in the interpretation of mtDNA and microsatellite data compared to previous genetic studies that examined wolf taxonomy. The data were consistent with the hypothesis of a North American-evolved wolf. Coyote-like mtDNA was not of coyote origin but represented divergent but related sequences of a North American wolf lineage independent of the gray wolf (C. lupus). Under this new model of eastern wolf evolution, we also identified the hybrid origin of eastern coyotes, contrary to previous interpretations, and genetically characterised different wolf "types" within Ontario. These findings could not reject the first hypothesis as neutral markers were used to reconstruct the histories of the three biological systems. However, the findings identified that it is important to ensure the neutrality of DNA markers and that samples are representative of the taxa under investigation. The findings in this thesis did not support the second hypothesis, as neutral DNA markers were not concordant with adaptive characters, i.e. morphology, physiology and functional genetic markers. / Thesis / Candidate in Philosophy