Masters Degrees (Genetics)
Permanent URI for this collection
Browse
Browsing Masters Degrees (Genetics) by Author "Ehlers, K."
Now showing 1 - 5 of 5
Results Per Page
Sort Options
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 DNA profiling from the crop content of sarcophagidae spp. larvae(University of the Free State, 2017-01) Barnard, Adri Marlene; Wessels, L.; Ehlers, K.; Brink, S. L.English: Morphological analysis of insect evidence plays a significant role in crime scene investigation. With the influence of DNA analysis in forensic cases, which now also plays a key role in forensic entomology, more emphasis has been placed on a dual preservation goal when collecting insect evidence. Previous studies indicated that it might be possible to identify the last meal of sarcophagid maggots using gut content combined with DNA profiling. For gut content analysis it is imperative to be familiar with the internal morphology as well as maggot gastric emptying. However, insufficient information is available on the morphology of Sarcophaga cruentata maggot alimentary canals as well as the rate of maggot gastric emptying. Also, considering the use of insects for both PMI and DNA analysis, the current preservation methods are not necessarily suitable for maggot preservation for DNA analysis of the crop content. Various preservation methods were examined for optimal preservation of both morphology and gut content. In order to understand gastric emptying, the internal gut structures and movement of food through the gut was examined. Fully fed maggots were removed from the food source and hot water killed at 3 hour intervals for up to 30 hours to investigate gastric emptying. Crop content DNA analyses were performed to attempt identification and DNA profiling of the maggots’ last meal. Due to the inhibiting effect of formalin on DNA analysis and the extensive dehydration of prolonged ethanol storage, -80°C was investigated for sample preservation which generally provided good results. Inconsistent results were obtained using the various preservation and DNA analysis combinations tested. Sarcophagidae gut morphology analysis indicated gross anatomical similarity to Chrysomya megacephala. External tracking of food movement proved difficult. After digestive tract dissection it was found that the mid- and hindgut coiled around each other. Due to the coiled structure of the gut, the exact location of the food bolus could therefore not be determined without dissection. The expected gastric emptying was not consistently observed with pronounced variability in results. Nevertheless, it was observed that the maggot crops were completely empty by 30 hours post removal from food source. DNA profiling of the crop content supported previous findings, although only partial STR profiles were obtained. It is unlikely that full profiles will be obtained when analyzing gut content due to the degraded nature of the food source, as well as the effect of digestive enzymes present in the maggot saliva regurgitated onto the food source. Various recommendations can be made based on the results. At crime scenes maggots should be killed in warm water (± 60°C for 30 seconds), dried on paper towel and stored in 80% ethanol while transported to the laboratory. Samples should be removed from the ethanol within 24 hours after collection, dried and stored individually in microcentrifuge tubes at -80°C (or similar low temperatures) until analysis is performed. During analysis samples should be handled on ice, ensuring the integrity of the sample, as it was found that samples defrosted rapidly after removal from the -80°C storage. It is further recommended to use commercially available kits when analyzing maggot gut samples due to the additional clean-up steps present in the kits. These clean-up steps aid in limiting the addition of fats and lipids from the maggot internal structures that could inhibit downstream DNA analysis of samples. Overall this study reinforced the possibility of using maggot crop content for providing STR profiles of the victim and/or perpetrator. Although only partial STR profiles were obtained, it indicated that, with further investigation and optimization, this is an interesting avenue for future research with many unexplored avenues for aiding in crime scene investigation.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 Insights into the genetics of the Ground Pangolin (Smutsia temminckii)(University of the Free State, 2013-02) De Beer, Christle; Kotzé, A.; Dalton, D.; Ehlers, K.; Jansen, R.English: Little is known about the molecular genetic variation of Ground Pangolin populations in South Africa. In this study it was attempted to assess the genetic diversity of the populations, but this could not be achieved due to insufficient cross‐species markers amplification. It should, however, be emphasized that the molecular work done in this study is novel, and that the results found during this research are key foundations for future studies. During sample collection it was found that three main populations of Ground Pangolins exist in South Africa in the Eastern, Western and Central parts of the country. Isolation protocols have been optimized, and it has been shown that noninvasive samples yield good quality and quantity DNA that is usable for down‐stream applications and perform as well as invasive samples. The PCR protocol was optimized, and the results from the optimization chapter will be of assistance when species‐specific markers are optimized. This study has also shown the need for the development of species‐specific markers, and the use of said markers will give a better indication of the genetic diversity of the Ground Pangolin populations in South Africa. From the statistical analysis it would seem that there are some correlations between the three sampling localities which may indicate a population divergence at some point. Based on the genetic diversity results, it appears that the diversity within Ground Pangolin populations is much lower based on the markers tested than in Malayan Pangolin populations. This will however have to be confirmed with species‐specific markers.