The place of functional genetics and population genomics within conservation genetics

This thesis explores questions about genetic markers within the field of conservation genetics. It first engages accepted conservation genetic theory and applies 'traditional' genetic techniques including microsatellite and mtDNA analysis to inform conservation management of the Australian native species mala (Lagorchestes hirsutus). These genetic markers suggest multiple founder effects within the captive population and that captive management may benefit from translocation. However, they are poorly suited to answering other important questons such as the degree of adaptation to captivity. The thesis then investigates the types of genetic markers commonly used in conservation and explores the factors that may affect one alternate marker, the major histocompatibility complex (MHC) with a meta-analysis. It finds the relationship between MHC and microsatellite markers is significant but not simply predictive and that more work may be required in order to understand MHC diversity in threatened species As MHC may be an ideal genetic marker for a number of conservation scenarios, we then attempt to develop a novel method for genotyping MHC that can be used on a large number of vertebrate species. This method is based on tagged degenerate primers and genotyping by 454 sequencing. During this chapter both the molecular biology and bioinformatics components of early next generation sequencing techniques are explored. This method fails. Finally, the thesis explores the emerging field of population genomics and attempts to use a population genomic technique, RAD-TAG sequencing, to look for disruptive selection associated with land clearing in native scincid lizard Cunningham's skink (Egernia cunninghami). This is a question pertinent to wider conservation efforts because of possible associations between disruptive selection and outbreeding depression. Using RAD-TAG methods we were able to find some evidence of disruptive selection occurring at small temporal and spatial scales. This final analysis allows for a reflection on the changes in conservation genetics stemming from the sequencing revolution, which coincided with the period of this thesis, and for suggesting future directions based on the outcomes of these studies.