Doctoral Degrees (Genetics)
Permanent URI for this collection
Browse
Browsing Doctoral Degrees (Genetics) by Advisor "Kotzé, A."
Now showing 1 - 2 of 2
Results Per Page
Sort Options
Item Open Access The application of new technologies in conservation genetics(University of the Free State, 2016-01) Labuschagne, Christiaan De Jager; Grobler, P.; Dalton, D. L.; Kotzé, A.English: Over the past decade, the development of high-throughput DNA techniques has expanded the scope of conservation genetics and molecular markers have become indispensable tools for the management of wildlife species and populations. There are several molecular markers available for biodiversity analysis, but their selection depends on the objective of the study, the molecular information sought (and reliability thereof) and the facilities and/or resources available. In order to develop and apply new genetic techniques I have decided on using one bird and one mammal species of interest in South Africa. The bird species chosen is the African Penguin (Spheniscus demersus) which has suffered serious population declines and is listed in the IUCN Red Data Book as an endangered species. Due to world-wide attention to rhinoceros conservation and population decline, the white rhinoceros (Ceratotherium simum) was selected as mammal species. Three different markers and their utility in aid of South African wildlife biodiversity conservation were investigated in these diverse species. The complete mitochondrial genome of the African Penguin was sequenced. The Spheniscus demersus mtDNA genome is very similar, both in composition and length, to both the Eudyptes chrysocome and E. minor genomes. This is the first report of the complete nucleotide sequence for the mitochondrial genome of the African Penguin. These results can be subsequently used to provide information for penguin phylogenetic studies and insights into the evolution of genomes. Furthermore, the study reported eight species specific microsatellite markers as well as 31 SNP markers as new molecular tools for the investigation, management and reintroduction of African penguin. Utilising these new tools, the study generated molecular genetic information to verify/complement studbook-based pedigree data from ex-situ populations of African Penguin. In addition, we compared the relative and combined utility of MS and SNP markers for parentage assignment. We found that a combined subset of these two types of markers attained a > 99% correct cumulative parentage assignment probability. This study further reported on 34 novel SNP markers for the white rhinoceros, identified through sequencing of CATS loci as well as SNP enriched libraries. The utility of 33 Single Nucleotide Polymorphisms and 10 microsatellites in isolation and in combination for assigning parentage in captive white rhinoceros were compared. It was found that a combined dataset of SNPs and microsatellites was most informative and showed the highest confidence level. This study thus provides a useful set of SNP and MS markers for parentage and relatedness testing in white rhinoceros. Furthermore, assessment of the utility of SNP and MS markers over multiple (> three) generations and the incorporation of a larger variety of relationships among individuals (e.g. half-siblings or cousins) is strongly recommended. Developed SNP markers could be used to define the genetic mating system of this species, for forensic applications and to determine population structure and variability when other markers prove problematic.Item Open Access Biological clock measures: assessing the association between the circadian and epigenetic clock as predictors of migration phenology and biological aging in wildlife(University of the Free State, 2024) Le Clercq, Louis Stephanus; Dalton, D. L.; Grobler, J. P.; Kotzé, A.This thesis explores the use of biological clocks, studied at the molecular level, in understanding and predicting animal traits that change over time. In particular, the thesis focuses on two biological clocks: the circadian clock and the epigenetic clock. The study aimed to shed light on how these clocks, along with specific genes associated with them, influence traits such as migration patterns in birds and age in animals. In the investigation of circadian clock genes, this thesis presents a detailed review of existing literature, presenting both supporting and conflicting results on the association between clock gene polymorphisms and migration patterns. This review summarized the central hypotheses tested in these studies, identified several candidate genes that have been used, revealed distinct patterns in terms of the taxonomy and phylogeny of studied species, and present new insights into why conflicting results happen as well as what future research is needed. Furthermore, the review emphasizes the importance of considering molecular clock differences between lineages when studying multiple species. The two most studied candidate genes were then tested for associations to phenology in an intra-African migrant, the Diederik cuckoo, and provides the first evidence that phenotypic correlates identified in Eurasian passerine species is conserved for these species. The second part of the thesis delves into epigenetic clocks, examining two widely used methods: methylation and telomere length. A systematic review and meta-analysis were performed to compare the performance of these methods across vertebrate classes. Methylation was found to outperform telomere length in predictive power, with both methods showing promise as biomarkers for age determination in animals. To demonstrate the practical application of epigenetic clocks, the study included the development of a new age determination model on the African cheetah. Six candidate genes were identified, and a model using CpG methylation levels was created using machine learning techniques to refine the model, resulting in accurate age predictions. This approach offers a less invasive means of age estimation for population monitoring. The research also introduces two new PYTHON tools, PAReTT, to incorporate phylogenetic and molecular clock data into ecological and evolutionary reviews, and ABCal, to address potential biases in systematic reviews in evolution and ecology. The thesis concludes by highlighting the broader implications of the study, emphasizing the utility of biological clocks in understanding temporal traits, from annual life events in birds to lifelong aging in mammals. The generated datasets and tools contribute to ecological systematic reviews and individual studies, expanding our knowledge of biological clocks and guiding future research endeavours.