Masters Degrees (Genetics)
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Browsing Masters Degrees (Genetics) by Author "Grobler, J. P."
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Item Open Access Cross-species microsatellite markers for the detection of hybrids in the genus connochaetes(University of the Free State, 2013-07) Wessels, Letecia; Grobler, J. P.; Kotze, A.; Ehlers, K.Black wildebeest (Connochaetes gnou), a species endemic to South Africa, experienced two bottlenecks in the last century and the number of animals ultimately decreased to approximately 300. These bottlenecks led to a decrease in the genetic diversity of black wildebeest populations across South Africa. An additional threat to the genetic integrity of the black wildebeest was discovered between the 1960s and late 1980s, when researchers noted that hybridization between blue and black wildebeest occurs and that these hybrid animals are fertile. Identification of the hybrid individuals is crucial and various molecular techniques were researched, with microsatellite markers proving to be the most successful. The aim of the current study was to investigate the effectiveness of previously identified cross-species microsatellite markers and statistical approaches for the identification of hybrid herds and individuals on various Nature Reserves in the Free State Province as well as privately owned game farms in and around the Province. Two previously identified diagnostic microsatellite markers (BM1824 and ETH10) were used to screen the populations for putative hybrids. The genetic diversity of the black wildebeest populations studied supported earlier findings showing lower genetic diversity in black wildebeest compared to blue wildebeest. The addition of new reference material in the current study revealed that some of the alleles previously assumed to be unique to a specific species were in fact shared between the two species. This reinforced the need to use more reference populations of adequate size. Nominally blue wildebeest alleles were found in five populations on different game farms and Nature Reserves. The presence of these alleles could be an indication that hybrids are present at these localities or alternatively, support the finding that the number and distribution of reference populations should be increased. Assignment of populations to specific clusters using different software programmes revealed that, due to the large amount of genetic material shared between blue and black wildebeest, no clear assignment of individuals to a specific cluster could be obtained. Molecular analysis of two known hybrid animals did indicate that the two microsatellite markers chosen were able to identify first generation hybrids and possibly even second generation hybrids. The study also investigated the persistence of introgression of blue wildebeest genetic material into black wildebeest populations using simulation software. The simulation tests revealed that introgressed alleles could still be detected after ten generations of backcrossing. This has serious implications for the management of hybrid populations. Various recommendations can be made in terms of the future management and conservation of black wildebeest on Nature Reserves and game farms. The most practical approach for dealing with hybrid animals would first be to develop additional molecular techniques for the accurate identification of populations that contain hybrid animals. Positively identified hybrid populations should be kept separate and no introductions of these animals should be made into pure populations. A more drastic approach would be to cull animals with hybrid ancestry. This would however have serious implications on the already reduced level of genetic diversity in the black wildebeest populations. The most pragmatic approach for dealing with hybrid populations would be to keep pure blue and black wildebeest in protected areas and allow black wildebeest with moderate introgression on game ranches exclusively used for sport hunting.Item Open Access Genetic connectivity, population dynamics and habitat selection of the southern ground hornbill (Bucorvus leadbeateri) in the Limpopo province(University of the Free State, 2011-03) Theron, Nicholas Terence; Kotze, A.; Grobler, J. P.; Jansen, R.Southern ground hornbills (Bucorvus leadbeateri) (SGH) are co-operative breeders that occur in groups of 2-9 individuals. Long life spans, large territory sizes (100km²), and low reproductive rates render these birds vulnerable to threats such as loss of habitat, persecution for their habit of breaking windows through territorial aggression, poisoning and loss of suitable nesting sites. As a result, SGH are listed as vulnerable in the red data book of South Africa as well as globally. The main objective of this study was to contribute to our overall understanding of the ecology and biology of the SGH for conservation planning. Data collection was completed in the nonprotected, semi-arid landscape of the Limpopo Valley from June 2008 - September 2009. The seasonal habitat use by a group of SGH, seasonal abundance (numbers) and biomass (volume) of invertebrates using pitfall and sweep net methods was investigated. Furthermore, a total of eight groups and 23 birds were captured in the Limpopo Valley and different statistical analysis were performed to investigate levels of inbreeding, relatedness, sex-biased dispersal and the effects the recent re-colonisation has had on the genetic structure of SGH in the Limpopo Valley. Finally the genetic variation of the species in the rest of Africa was determined using samples from Kenya, Tanzania and three populations in South Africa namely the Limpopo Valley, Kruger National Park (KNP) and Kwa Zulu-Natal (KZN). Genetic analysis revealed SGH have retained comparatively high levels of genetic diversity, even though there are indications of genetic bottlenecks in the Limpopo, KNP and Kenyan populations. The SGH populations studied were grouped into two clusters corresponding to the geographic origin of samples. The birds from Tanzania and Kenya clustered together while the KNP and KZN birds clustered together with the Limpopo population grouping more or less equally between the Kenyan/Tanzanian and South African populations. A large percentage of genetic variation was found within populations while among population variation was low, indicating there is little molecular evidence for the presence of SGH subspecies. The overall home range of one group was approximately 20 000 ha while seasonal home ranges varied between 5000 ha in winter to 13 500 ha in summer. The response of organisms to environmental variables in this extremely seasonal habitat was further revealed by the positive correlations found between the number of invertebrates with mean monthly maximum and minimum temperatures, and the volume of invertebrates with mean monthly rainfall. No significant differences were found between numbers and volume of invertebrates per order, between sites, which was expected in this homogenous vegetation type dominated by mopani shrub and trees (Colophospermum mopane). The re-colonisation of the Limpopo Valley was shown to have occurred by a number of unrelated individuals. This was demonstrable by very low levels of inbreeding and average relatedness of the population, as well as the favourable levels of heterozygosity across age and sex categories. Within group relatedness was high with juveniles related to at least one parent from their natal group. Insights were also gained into the breeding behaviour of SGH, providing evidence for the first time that SGH are not as monogamous as previously thought, with two instances of extra pair copulations recorded between four groups. This study shows that a holistic approach combining genetic techniques, radio telemetry studies and ecological principles has great potential to further investigate SGH, thereby contributing to the preservation of this enigmatic species of the savannah biome.Item Open Access Genetic diversity in the Afrikaner cattle breed(University of the Free State, 2014) Pienaar, Lené; Grobler, J. P.; Neser, F. W. C.; Scholtz, M. M.; Ehlers, K.𝑬𝒏𝒈𝒍𝒊𝒔𝒉 This study was a first attempt to use microsatellite markers to determine the genetic diversity in an indigenous cattle breed, namely the Afrikaner. It was also the first study to combine genetic markers and pedigree analysis to estimate the genetic variability within an indigenous cattle breed. The objectives of the study were to estimate genetic diversity and inbreeding levels within the breed and to utilize the results to preserve and ultimately improve the genetic resources offered by the breed. A total of 1214 stud animals (representing 28 herds) and 166 commercial animals (nine herds) from different geographical areas within and adjoining South Africa were included in this study. Animals were genotyped at the two major animal molecular laboratories in South Africa, with both using the same standardized 11 marker microsatellite set. Estimates of genetic diversity did not support the hypothesis of significant loss of genetic diversity in the Afrikaner breed. Heterozygosity estimates ranged from 0.737-0.456 within individual populations, with an overall heterozygosity estimate of 0.568 for the Afrikaner breed. Assignment methods (based on STRUCTURE software) revealed a real structure consisting of four genetic populations (K=4). No consistent pattern of significant differentiation between stud- and commercial herds could be identified. Pedigree information, based on a total of 244714 recorded animals from 1940 to 2011, were analysed to determine the mean level of inbreeding (F), effective population size (Ne), generation interval, effective number of founders (fe), effective number of ancestors (fa) and average relatedness (AR). The average inbreeding coefficient calculated was 1.83% and the effective population size computed using the increase in the individual rate of inbreeding was estimated at 167.54. A total of 84138 animals (34.4%) were inbred to some degree. The effective numbers of founders and ancestors were 288 and 226 respectively, with an average relatedness of 0.44% and with results confirming a total of six complete generations. The average generation interval for the whole population was calculated as 6.554 ± 3.883 years. It is concluded that a moderate to high degree of variation is still present within the Afrikaner cattle breed, despite the recent decline in numbers of this indigenous breed. Levels of inbreeding appear to be at acceptable and at manageable levels. The current study provided results than can be utilized by farmers and breeders’ society to conserve the Afrikaner and develop the breed to its full potential.Item Open Access Genetic management of the baboon population in the Suikerbosrand Nature Reserve(University of the Free State, 2012-10-12) Bubb, Annesca; Ehlers, K.; Kotze, A.; Grobler, J. P.Genetic management has become a critical part of the overall management of nonhuman primate populations. This dissertation describes a genetic analysis of the chacma baboon population at the Suikerbosrand Nature Reserve. The aim of this study was to apply genetic data as a credible tool to contribute to the conservation and management of chacma baboons at Suikerbosrand Nature Reserve. The specific objectives included individual identification, determining genetic relationships and levels of gene flow within- and among the fourteen troops, and to construct a genetic database with individual genotypes of the whole population. A secondary objective of this study was to determine whether it would be feasible to extract DNA from fecal samples collected from a sleeping site and then use the genetic profiles to determine the number of individuals in that specific troop. The current population is estimated to be between 611 and 764 animals. The sleeping site of the Diepkloof troop was used for this part of the study. A panel of eleven human microsatellite markers was used for DNA analysis. DNA profiles from all the blood samples were successfully constructed and could be used to estimate genetic relationships. The level of genetic diversity in the Suikerbosrand baboon population did not differ significantly from that in the outgroup. Thus, the reintroduction of new individuals into the population to maintain acceptable levels of diversity is not an immediate priority. High levels of gene flow were observed between the troops, especially the troops located in the central part of the reserve. In order to ensure high DNA quality from fecal samples collected at the sleeping site, the collection method for fecal samples were optimized (A manuscript based on the work in this section has been accepted for publication in the European Journal of Wildlife Research). The profiles obtained from the fecal samples that were collected at the Diepkloof site corresponded with two of the thirteen profiles from the reference database. The estimated size of the Diepkloof troop is thirty seven individuals. The results show that non-invasive sampling could be a promising alternative for future research on the reserve, as the samples can be used to determine individual profiles. The genetic data collected can be combined with ecological and behavioral information collected form future research to further understand the population structure of the Suikerbosrand chacma baboons and changes that might occur in the population.Item Open Access Genetic origins of the introduced pea weevil (Bruchus pisorum) population in Ethiopia(University of the Free State, 2012) Scheepers, Loraine Cornelia; Grobler, J. P.English: This study aimed to determine the origin of pea weevils (Bruchus pisorum) in Ethiopia and to determine the current population structure across that country. The pea weevil is presently a widely distributed pest of peas in Ethiopia, causing huge financial losses. Conflicting hypotheses exist on the origin of B. pisorum in Ethiopia. It was possibly introduced to Ethiopia sometime in the 1970s, or it might have occurred historically in the area in very low numbers. The methodology of this study consisted of finding populations of pea weevils across the globe and then comparing these populations with the population currently found in Ethiopia. Specimens were obtained from Ethiopia, the USA, Germany and Australia. Gene sequences of pea weevils from China and Japan were also downloaded from GenBank to serve as reference material. DNA was extracted, amplified and sequenced using standard protocols, with the exception of the USA sample which was composed of museum specimens that demanded a non-destructive DNA extraction method. Three gene regions were used in this study: the Elongation Factor 1alpha (EF-1α), Cytochrome oxidase subunit one (COX1) and Cytochrome b (Cytb). The COX1 and Cytb sequence data provided insight into a possible source population of pea weevils in Ethiopia, whereas results from EF-1α were uninformative. Pea weevils from the USA were identified as a possible direct source, but it should be noted that these pea weevils are not endemic to the USA. The possibility of an endemic population of pea weevils in Ethiopia is also discussed. Tests for differentiation indicated that there was some differentiation between the Ethiopian subpopulations. This variation is discussed with reference to possible multiple sources of introduction for the current population in Ethiopia, genetic drift since introduction, and the possibility of a mixture of endemic and introduced genetic material in B. pisorum in Ethiopia.Item Open Access Patterns of genetic diversity in vervet monkeys (Chlorocebus aethiops) from the south eastern regions of South Africa(University of the Free State, 2012-07) Coetzer, W. G.; Grobler, J. P.; Turner, T. R.Vervet monkeys (Chlorocebus aethiops) are one of the most widely distributed primate species in Africa. The aim of this study was to determine the level of genetic differentiation among conspecific vervet monkey populations in the south-eastern regions of South Africa, as part of a bigger project to determine levels of differentiation across South Africa. For this purpose, samples were taken from four localities in the Free State Province (Soetdoring Nature Reserve (NR), Gariep Dam NR, Sandveld NR and the Parys area), four Eastern Cape locations (Tsolwana NR, Baviaanskloof NR, Shamwari Private Game Reserve (PGR) and the Nelson Mandela Metropolitan University (NMMU) campus, Port Elizabeth), three Kwa-Zulu Natal location (St. Lucia area) and one Limpopo Province locality. Genetic differentiation was quantified using sequence data from a portion of the mtDNA control region. Twelve Haplotypes were identified within the total sample group. The nucleotide diversity for each grouping was calculated over all loci. Nucleotide diversity ranged from 0 to 0.038% ±0.02. Haplotype frequencies distribution among samples was calculated. An analysis of Molecular Variance (AMOVA) test was conducted and population pairwise FST values were estimated. The AMOVA test revealed that the majority of the genetic diversity occurred among the different groups (52.5%), with only 4.9% of the variation found within populations. The populations were assigned to groups according to geographic origins. The pairwise analysis identified significant levels of genetic variation among populations, with an average FST value of 0.851. These haplotypes were found to coincide with the geographical borders of Provinces. A ML tree was constructed using the haplotype data, and results showed clustering corresponding to geographical borders. A phylogenetic network was constructed, and this showed clustering similar to that found with the ML tree analysis. According to these results it is clear that there is genetic structuring among vervet monkey populations in South Africa. This clustering of populations can be potentially explained by female philopatry and geographical barriers. Female philopatry is a well known occurrence amongst Cercopithecine primates. The occurrence of geographical barriers, such as rivers and mountains had influence on migration rates and genetic structuring. This clustering pattern observed with mtDNA analysis contradicts results from previous studies working with nuclear DNA markers. This can be caused by various factors. Except for female philopatry having an effect on mtDNA differentiation patterns, it should be noted that the faster evolutionary rate of mtDNA vs. nuclear DNA can also cause different genetic patterns. The effective population size of mtDNA is also four-fold smaller than that of nuclear genes, and will also cause skewed results when comparing mtDNA data with nuclear DNA data. No reliable recommendations can be made toward the release of rehabilitated vervet monkeys, as further analysis is needed. It is thus suggested to use both genetic markers in follow-up studies. An increase in sample size from a broader geographical range is also recommended. In addition to further work on patterns of genetic variation, the adaptive significance of observed genetic differences should also be investigated.Item Open Access Population genetic structure of the ground pangolin based on mitochondrial genomes(University of the Free State, 2014-03) Du Toit, Zelda; Grobler, J. P.; Kotzé, A.; Dalton, D. L.English: Temminck’s ground pangolin, S. temminckii, is currently listed as Vulnerable on the IUCN Red Data List. However, their numbers are decreasing due to illegal hunting for bush meat and over-harvesting for traditional use in Africa. Pangolins are also exported to Asia as a delicacy and for use in traditional medicine. Currently, the greatest threat to ground pangolins in southern Africa is electrocution by electric fences on game farms. This project consisted of two parts. The first was to sequence the whole mtDNA genome of Temminck’s ground pangolin to identify gene regions and to determine the evolutionary relationship of the order Pholidota. Results generated using the primer walking method, indicated that the whole mtDNA of Temminck’s ground pangolin is 16,559 bp in length. The phylogenetic analysis shows that the order Pholidota form a sister grouping with the order Carnivora rather than with the order Xenarthra as would be expected. Data suggested a Laurasian origin approximately 87 mya and possible migration into Africa during the Paleocene era around 55 mya. The second part of the study was conducted in order to determine the phylogeography of Temminck’s ground pangolins in southern Africa. Twenty five samples were collected from four countries, namely Namibia, Zimbabwe, Mozambique and South Africa (Mpumalanga and the Northern Cape Provinces). The results obtained indicated a high level of genetic variation within populations and only a few individuals displayed private haplotypes, which resulted in an increase in haplotype diversity. Samples from Zimbabwe and Mozambique (Group 1) clustered together while samples from the Northern Cape and Mpumalanga Provinces of South Africa grouped with samples from Namibia (Group 2), suggesting either an ancestral or recent split between Groups 1 and 2. The BEAST analysis indicated that the two groups shared a recent common ancestor between 2.94 and 1.27 mya across the three gene regions. In addition, it was estimated that the Zimbabwe/Mozambique split occurred between 920 and 710 kya and the Kalahari/Namibia/Mpumalanga split between 1.16 mya and 790 kya. This pattern corresponds to the Mega Kalahari Sand Sea forming a barrier between individuals and populations around that time. This study is the first molecular analysis based on the mitochondrial DNA genome of Temminck’s ground pangolin in southern Africa and it provides an insight into the species’ population genetics across its range in southern Africa. However, additional research into the order Pholidota throughout Africa can assist in better understanding of genetic variation within African pangolin species and populations. Furthermore, such studies will also support the conservation of genetic variation within species and contribute to identifying evolutionary distinct populations to assist in developing effective conservation management plans for the different species of the order Pholidota.