Doctoral Degrees (Genetics)
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Browsing Doctoral Degrees (Genetics) by Author "Dalton, D. L."
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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 Linking geographic origin and mitogenomes of the ground pangolin in southern Africa(University of the Free State, 2021-11) Du Toit, Zelda; Grobler, J. P.; Kotze, A.; Dalton, D. L.; Jansen, R.The order Pholidota includes the most trafficked mammal species globally. The family Maninae with recognized species are categorized as Endangered and Critically Endangered on the IUCN Red List of Threatened Species. Due to the sharp decline in Asian pangolin numbers, the shift was towards the African pangolin species, to meet the demand in Asia and in Africa. Subsequently, the status of Smutsiinae has been revised by the IUCN and varies between Vulnerable and Endangered. This study contributes to clarify the genetic status of the four African pangolin species using molecular technologies. The first part of the study aimed to assemble mitogenomes of the four African pangolin species using NGS technologies. Whole mitogenomes were assembled and compared with published mitogenomes available in online databases. Mitogenomes were only available for six of the eight pangolin species. Our results showed different genome lengths for the four species: Temminck’s pangolin (16 558 bp), giant pangolin (16 540 bp), white-bellied pangolin (16 565 bp) and black-bellied pangolin (16 649 bp). Three distinctive clusters were observed supporting three genera. The first cluster consisted of the Asian pangolins (Manis), the second cluster was the African tree pangolins (Phataginus) and the third cluster represented the African ground pangolins (Smutsia). There were also two insertions found in the control region of the black-bellied pangolin which could indicate a recent mutation or selection event. The second part of the study focused on the development of species-specific STRs for Temminck’s pangolin and in combination with previous developed mtDNA markers the aim was to assess the population structure across the distribution range in southern Africa. Three mtDNA loci were analysed (Co1, Cytb, control region) with 30 STRs. A total of 62 individuals from six countries were included in the study. The results showed little to no geographical differentiation across the identified sampling locations. This indicates high levels of gene flow between the populations. Three distinctive clusters were observed within the different sampling areas. This could indicate inherited ancestral traits in juveniles with dispersal into new home ranges following a stepping stone model. Temminck’s pangolin has been reported to cover vast distances in search of new home ranges or territories. This study provides the first account of a combination of mtDNA and STR markers to investigate possible geo-referencing of Temminck’s pangolin in southern Africa. It is evident that the mtDNA and STRs markers used in this study, are not robust enough to discriminate between different sampling locations or populations. Further in-depth investigations, including whole genome analysis and SNPs are recommended. A more comprehensive sampling strategy is required to include all areas within the distribution range as well as more individuals for an in-depth genome analyses.