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.

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.

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.

Drosophila females remate generating an opportunity for sperm competition. Normally the second male to mate sires the majority of progeny; however, conspecific sperm precedence is the phenomena whereby the male of the same species as the female fathers the majority of the progeny regardless of mating order. I surveyed D. simulans laboratory strains carrying D. mauritiana P-element insertions (IG lines) for their ability to sire progeny when second to mate. I found significant variation in the proportion of progeny sired by IG lines, with lines showing sperm competitive breakdown (P2< 0.5). I identified two loci that account for conspecific sperm precedence between D. simulans and D. mauritiana. 81 candidate genes were identified and narrowed down the list on the basis of differences in male reproductive tract gene expression to five (P< 0.05) or eight (P<0.1) genes. A larger concentration of differentially regulated genes within the 89B position was found. Using coding sequence data I identified 10 genes as candidate conspecific male precedence genes. Genes in the 89B region come to light as candidates for future functional studies of conspecific male precedence.

The condition which is now known as lead poisoning was familiar even in ancient times. Hippocrates (370 B.C.) was probably the first to associate lead with certain symptoms, such as severe attack of colic in a man who extracted metals. The symptoms of lead poisoning were more clearly defined in the first century A.D. by Dioscorides, “the drinking of litharge (red lead) causes oppression to the stomach, belly, and intestines, by its severe pressure; it suppresses the urine, while the body swells and acquires an unsightly leaden line”. He also speaks of paralysis and delirium as consequences of the ingestion of lead.

Cleft palate is a common congenital anomaly, and it is dealt with by a variety of scientific groups. The medical profession is concerned about cleft palate because it is of sufficiently frequent occurrence to distress many people. Knowledge of the mechanisms and materials involved in palate development might be useful in designing preventive measures for prenatal care. The cleft palate condition is of interest to embryologists because it so often turns up in the list of defects caused by various teratogenic agents, and a better understanding of this defect would help in assessing the specific defects of a teratogenic substance.

<p>Glaucoma is a chronic ocular neuropathy and a leading cause of blindness worldwide. Primary open-angle glaucoma (POAG) is the most common subtype with an estimated 2 million affected individuals in the Unites States. POAG is a heritable complex trait. Understanding the genetics of POAG may increase our ability to predict disease onset and help elucidate the underlying biological mechanisms responsible for the development of the disease. With this overall goal, three different approaches are presented here.</p><p>First, the genetics of an important POAG-associated trait, central corneal thickness (CCT), was investigated using genome-wide single nucleotide polymorphism (SNP) data available from the NEIGHBOR and GLAUGEN consortia to identify novel POAG candidate genes. Twenty previously published CCT-associated SNPs were tested for association with both CCT (N = 1,117) and POAG (N = 6,470). While several of these variants were significantly associated with CCT in our dataset (top SNP = rs12447690, near ZNF469 (beta = -5.08 µm/allele; p = 0.001), none were associated with POAG. A CCT genome-wide association study was conducted. Using a p-value threshold of </p><p>1X10-4, 50 candidate SNPs were tested for association with POAG. One SNP, rs7481514, within the NTM gene was significantly associated with POAG in a low tension subset of cases (odds ratio (OR) = 1.28; p = 0.001). Additionally, SNPs in the CNTNAP4 gene showed suggestive evidence of association with POAG (top SNP = rs1428758; OR = 0.84; p = 0.018). A gene expression analysis showed evidence of NTM and CNTNAP4 gene expression in relevant ocular tissues. This study suggests previously reported CCT loci do not increase POAG susceptibility. However, by using a two-step gene mapping approach, the cell adhesion molecules, NTM and CNTNAP4, were identified as potential POAG candidate genes in a subset of cases.</p><p>The second study aimed to identify functional alleles within a POAG candidate gene. Previous association studies identified a significant association between POAG and the SIX6 locus (top SNP = rs10483727, OR = 1.32, p = 3.87X10-11). SIX6 plays a role in ocular development and has been associated with the morphology of the optic nerve. Sequencing of the SIX6 coding and regulatory regions in 262 POAG cases and 256 controls identified six nonsynonymous coding variants. Of these six, five were rare (minor allele frequency (MAF) < 0.002) and one, Asn141His (rs33912345), was a common variant that showed a significant association with POAG (OR = 1.27, p = 4.2X10-10) in the NEIGHBOR/GLAUGEN dataset. These variants were tested in an in vivo zebrafish complementation assay to evaluate ocular metrics. Five of the six alleles had a functional effect on the protein. These five variants, found primarily in POAG cases, were hypomorphic or null, while a sixth variant, found only in controls, was benign. One variant in the SIX6 enhancer increased expression of the SIX6 gene and disrupted its regulation. Using optical coherence tomography, the retinal thickness of POAG with and without the common SIX6 risk allele, Asn141His (rs33912345), was measured. Patients who are homozygous for the SIX6 risk allele (His141) have a statistically thinner retinal nerve fiber layer than patients homozygous for the SIX6 non-risk allele (Asn141). These results in combination with previous SIX6 work, leads us to hypothesize that SIX6 risk variants disrupt the development of the neural retina and result in a reduced number of retinal ganglion cells generated during development, thereby increasing the risk of glaucoma-associated vision loss later in life.</p><p>Next, the transcriptional landscape of three POAG-related tissues; the trabecular meshwork, the cornea, and the ciliary body; were evaluated using an RNA sequencing (RNA-seq) approach. Tissues were selected from two fetal and four adult human donor samples with no known history of ocular disease. Deep RNA-seq was performed, and the total number of paired reads per sample ranged from 32,137,380 to 59,784,117. A descriptive analysis was conducted and included the identification of the top most expressed genes in each tissue and the distribution of gene expression values. Additionally, gene expression of selected POAG candidate genes (CDKN2B, CDKN2A, CDKN2B-AS, SIX6, SRBD1, ATOH, CAV1, CAV2, ELOVL5, and TMCO1) was evaluated. Most of these genes showed high expression values in the trabecular meshwork and cornea. ATOH was only found to be expressed in the fetal TM and, interestingly, SIX6 was shown to be highly expressed in the adult and fetal ciliary body. CDKN2B-AS was not found to be expressed in any of the tissues evaluated. Finally, the RNA-seq data was used to identify potential novel isoforms of these candidate genes. Using a stringent threshold, five novel isoforms were identified in CDKN2B, SRBD1, and SIX6. The data generated as part of this study can be used to develop novel hypotheses, guide future work, and is broadly applicable for ocular research because the tissues included in this analysis are essential for normal vision and play important roles in ocular diseases.</p><p>In this dissertation, three different approaches (assessment of a quantitative risk factor, candidate gene functional analysis, and the assessment of the transcriptional landscape of relevant ocular tissues) were used to study the common blinding disorder, primary open-angle glaucoma. Continued research in this field is essential. There is a need for increased functional follow-up of genetic association studies in order to identify true causal susceptibility genes and improve our understanding of POAG biology. Additionally, researchers should focus on building and implementing accurate prediction models to increase POAG diagnosis rates and preemptive treatment.</p> / Dissertation

<p> Advancing age of the global population is resulting in an increase in the accumulation of age-related pathologies. Many potential molecular and cellular causes of aging are still being debated. Endogenous retroelements are a class of mobile DNA elements that have coexisted in the genomes of virtually every eukaryotic organism for much of evolution. Recent work indicates that retrotransposons are active in advanced age but their impact on aging has not been explored in detail. Evidence is accumulating to suggest that retrotransposon-mediated events are a potential source of genomic change that can influence aging. In this study I took advantage of a unique yeast model system to characterize aging in cells with or without Ty1 retroelements. I identify here a novel role of retroelements in extending yeast chronological lifespan in certain media conditions, rather than observing an anticipated pro-aging effect. This effect was correlated with changes in factors known to influence aging such as mitochondrial function, reactive oxygen species, and sensitivity to a chemical inhibitor of nutrient sensing pathways. These results demonstrate that the presence of these retroelements have unforeseen direct or indirect roles in influencing cellular processes relevant to lifespan. The ability of retrotransposons to regulate cellular functions has not been well investigated, in contrast to the ability of cellular pathways to regulate retrotransposons. The work here broadens our perspective on the role retrotransposons have in host cells to influence certain aspects of eukaryotic aging.</p>

<p> The central focus in evolutionary biology is understanding how environments influence population genetic diversity and divergence through both adaptive and non-adaptive processes. Using a population genomic approach to examine population structure and morphological divergence of black spotted topminnow fish allowed us to survey how populations vary in river environments. Fish throughout the river continuum occupy different habitats that vary in several environmental aspects such as water velocity, predators, prey, and spatial heterogeneity. Body shape and size are great features to focus on for identifying adaptations to local environmental pressures. Shape and size have effects on maneuverability and energy conservation and, due to this, are targets for selection to act upon. Populations in differing habitats have shown variation in body shape and size, although not all species show differences between habitat types, and some species do not show consistent changes in morphological characters.</p><p> A total of 283 fish were sampled from headwater and large river environments in the Gasconade (150 individuals) and Meramec (133 individuals) river systems during the summer months of 2013. Individuals were genotyped, and 5744 single nucleotide polymorphism (SNP) loci were used to analyze population structure. In general, the study supported divergence between the two drainages, but some evidence of mixed ancestry for individuals sampled in the large river environments suggesting incomplete lineage sorting or secondary contact. Substantially more genetic structure was observed in the Gasconade River samples when compared to the Meramec River samples. Headwater populations exhibited clear divergence from larger river populations. Headwater divergence could be attributed to smaller effective population sizes and greater susceptibility to genetic drift. </p><p> Adult individuals were subjected to geometric morphometric analysis. Of the 283 individuals sampled, 175 individuals were large enough for shape and size analysis. Centroid sizes (measure of overall size) confirmed that headwater fish from both river systems were larger than their downstream large river counterparts. As expected, most significant shape variation was found in the sexual dimorphism between males and females, where males have larger dorsal and anal fins than females. With sexual dimorphic characteristics factored out, Gasconade individuals exhibited deeper bodies than that of Meramec individuals, but Meramec fish exhibited longer caudal fins.</p>

Pinus patula is the most widely planted softwood species in Southern Africa and is utilised for various solid wood and pulp and paper products. Tree improvement programmes for forestry species started in Southern Africa during the 1950âs, with an initial focus on volume improvements. The focus for many advanced tree improvement programmes has moved to the improvement of wood properties. This quantitative genetics study utilized half-rotation age P. patula progeny material from a 5 Ã 5 full diallel mating design and additional factorial crosses. A radial wood sample at 1.3 m above ground level from each of 300 trees was used to study a range of wood density, tracheid cross-sectional and -dimension characteristics. A large range of family variation was found for all wood properties. The combining ability analysis indicated that general combining ability was the most predominant effect and that specific combining ability effects were absent for nearly all the investigated wood density and tracheid traits. Reciprocal, maternal and non-maternal effects were also not significant for all but a few traits. Some of the wood properties were influenced by the specific site where trees were grown. Heritability estimates for many of the important wood density and tracheid traits were moderate to high, indicating strong additive genetic control of these properties. Wood density traits were under strong genetic control, with a pith-to-bark increase in wood density traits. Latewood proportion and earlywood density had a strong effect on weighted mean wood density. There were also strong positive correlations for density traits between growth rings, indicating that early selection would be possible. Tracheid cross-sectional properties were also strongly inherited, and strong correlations were found between the cross-sectional traits and calculated pulp and paper traits. Tracheid dimension traits such as tracheid length, width and cellwall thickness had lower heritability estimates than those found for wood density and tracheid cross-sectional traits. These were, however, of higher magnitude than growth trait heritabilities. Several strong positive and negative correlations were found between growth, wood density and tracheid property traits. These negative correlations would make multi-trait selections very problematic. Predicted gains for some of the studied wood properties were substantial, but correlated responses between primary and secondary selection traits were often negative. The structuring of genetic material into wood property specific sub-populations would ensure the improvement of selected important wood properties. These different properties can then be combined by means of controlled pollinations, and be deployed via vegetative propagation. This study has provided novel information on the genetic inheritance of physical wood properties of P. patula grown in Southern Africa, and will allow tree breeders to include some of these properties in breeding programmes.