Fire is a natural component of, and serves as a tool for, the restoration of forested ecosystems worldwide; however, disturbance due to fire also has been implicated in the proliferation of invasive species. How these fires affect occupancy and use of the forest by wildlife is of great concern, in particular, the differential response of non-native and native species. In the North American Southwest, prior to European settlement, frequent wildfires helped to maintain forest structure. We examined the effect of a large wildfire on an introduced population of the Abert's squirrel (Sciurus aberti) that has invaded the high elevation forests inhabited by the critically endangered Mt. Graham red squirrel (Tamiasciurus fremonti grahamensis). We found that introduced Abert's squirrels were more common than native red squirrels in burned areas. Abert's squirrels did not abandon burned areas but nested, foraged, and did not adjust their home range size in burned areas. This suggests that invasive Abert's squirrels are better able to exploit burned areas than native red squirrels and that fire can favor non-native species. This interaction between non-native species, native species, and fire adds new insight into the complexities of conservation and restoration of ecosystems and helps to inform conservation activities worldwide.

Masters of Science / Thermophilic bacteriophages provide simple model systems for understanding biochemical and biological adaptation mechanisms at elevated temperatures. The essential objectives of this study were to characterise the physicochemical properties of select Geobacillus bacteriophages and to sequence their complete genomes. The later objective is believed to be an essential prerequisite to the engineering of a sitespecific integration vector for the stable cloning of exogenous genes into host bacteria. Bacteriophages were assayed at 55oC by the agar overlay technique using dry Karoo soils as source material. A pure strain of bacteriophage called GV1 (for Geobacillus stearothermophilus virus 1) was isolated with the strain Geobacillus stearothermophilus TAU3A1. Plaques were medium sized (2 to 4 mm diameters), with regular contour, clear, and without resistant cells. Host range specificity study showed that GV1 was lytic on thirteen thermophilic Bacillus-like strains tested, including strains of Geobacillus stearothermophilus, G. thermoglucosidasius, B. licheniformis, Anoxybacillus idirlerensis, and A. kuwalawohkensis. However, GV1 failed to infect a mesophilic strain of Bacillus megaterium. TEM analysis of semipurified particles revealed that the phage belongs to the family of Siphoviridae. Morphological characteristics included a long tail of approximately 100 nm and a hexagonal head of approximately 50 nm diameter. Viability and stability studies showed that the phage was best maintained at -80oC in PMN buffer supplemented with 20% glycerol. It was stable at a pH range of 5.5 to 7.5 and MgCl2 and CaCl2 concentration of 0.001 M. hermostability experiments, conducted over short periods of time, showed that GV1 was stable over the temperature range 50 to 75oC, with optimum at 55oC. The study of phage-host interactions showed that phage articles inhibited the initial growth of infected cultures in the first six hours post-infection, presumably while mature phages were released. This was followed by a steady recovery of the growth rate. Atempts to obtain pure particles and to extract and sequence phage DNA were unsuccessful due to the low titer nature of the phage.

I studied the spatial distribution of South African avian species richness from the viewpoint that humans are a substantial modifying force on earth, and have also modified the historical spatial distribution of species richness. The main aim of the thesis is to investigate the way in which humans have modified avian species richness patterns in South Africa at the quarter-degree square (QDS) resolution, which is a phenomenon that has been either overlooked, or not completely clarified, in many previous studies of the same region and data at the same resolution. In particular, I investigated hypotheses that were proposed to explain the maintenance of a positive relationship between native species richness and human population density in the face of negative human impacts. Further, I investigated which of the possible anthropogenic and natural environmental factors determine spatial distribution in exotic bird species. Highlighted from these studies are that substantial positive and negative human influences on bird species richness distribution patterns are observable at the QDS resolution, that there are differences between common native birds and rare native birds with regard to their relationships with anthropogenic environmental conditions and exotic bird species, and that the particular combination of environmental covariates that is important for the spatial distributions of exotic species is taxon- and scale-dependent. Even though these results have contributed much towards our understanding on how human modifications have affected species richness patterns, this thesis leaves some unanswered questions. Finer resolution studies and temporal studies are needed to examine many of these questions. Further, an interdisciplinary approach incorporating politics and economics into ecological studies is needed to enhance our understanding of the factors that modify the distribution of humans and their associated threats and benefits to species richness. / Dissertation (MSc)--University of Pretoria, 2010. / Zoology and Entomology / unrestricted

Citrus is grown in almost all countries with a sub-tropical or tropical climate. Africa produces about 7% of global citrus production representing 67 362 564 tonnes in the 2003-04 season. Of these countries, South Africa is the most important citrus producer with the bulk of its fruit being exported to mainly European countries. Although South Africa is the world’s fourteenth biggest producer, it is currently ranked third in terms of global export volumes. An increase in the number of foodborne disease outbreaks over the past few decades has been related to the shift towards consumption of fresh produce and growing world trade. Other factors include changing demographic profiles, changing farm practises, extensive distribution and handling networks, increased consumption of unprocessed products, emergence of new pathogens and more effective detection methods. Shigella spp., Listeria monocytogenes, Hepatitis virus, Caliciviridae virus, Salmonella spp., Escherichia coli and Vibrio cholera are some of the microorganisms implicated in disease outbreaks caused by the consumption of fresh produce. This dissertation focuses on citrus fruit safety and a selected foodborne pathogen, Salmonella enterica serovar Typhimurium. Salmonella has been implicated in several outbreaks associated with the consumption of unpasteurized orange juice, mangoes, cantaloupes, sprouts and tomatoes. S. enterica sv. Typhimurium is also a water-borne pathogen, and its importance in agricultural irrigation and packhouse wash water was also studied. The presence of S. enterica sv. Typhimurium in biofilms in packhouse water and on fruit was finally investigated since biofilms are known to harbour a number of these pathogens. Biofilm formation was monitored in the warm water dip tank using a photo acoustic monitoring device and confirmed by scanning electron microscopy and enumeration. Water sources, i.e. bathroom, handwash stations, irrigation water and warm water baths had high total viable bacterial counts and faecalassociated contamination. Biofilms also formed within the packhouse dip tank at an increased rate. The Polymerase Chain Reaction (PCR) was used to investigate the presence of Salmonella in the citrus export chain. No Salmonella spp. could be detected. S. enterica sv. Typhimurium survived for up to four weeks on the surface of citrus fruit under simulated export conditions. However, Salmonella is not able to survive uninterrupted cold storage conditions for a period longer than two or three weeks. Scanning Electron Micrographs showed that Salmonella is capable of attaching to and colonizing the citrus fruit surface and is able to be incorporated into existing biofilms in warm water tanks of packhouses. This study showed that Salmonella can thrive in packhouse water and potentially be a continuous source of contamination for fruit moving through the infected warm water dip tank. Everyone participating in fruit production, storage and post-harvest handling of fresh fruit should be involved in ensuring quality and safety, since events in the orchard can affect storage life, and incorrect handling during marketing may nullify all previous efforts of quality maintenance. To minimize the occurrence of these pathogens in the fruit chain from production to consumption, several basic good agricultural practices and food safety systems needs to be incorporated and managed correctly. / Dissertation (MSc)--University of Pretoria, 2009. / Microbiology and Plant Pathology / unrestricted

Chez les insectes phytophages, l'adaptation à la plante hôte peut correspondre à l'une des premières étapes de la spéciation. Dans ce contexte, ce manuscrit s'intéresse à Spodoptera frugiperda (Lepidoptera : Noctuidae), un ravageur responsable de dommages importants sur de nombreuses cultures en Amérique et dans les Caraïbes. Spodoptera frugiperda présente deux variants, l'un adapté au riz et l'autre au maïs, et constitue un modèle biologique pertinent pour étudier ce mécanisme. En effet, les deux variants sont morphologiquement identiques, mais ils sont génétiquement différenciés et présentent des différences écologiques et comportementales. L'ensemble de ces caractéristiques suggèrent la présence d'un isolement reproducteur entre les deux variants, qui pourraient alors correspondre à deux espèces différentes. Cependant la présence d'hybrides dans la nature ainsi que des résultats controversés sur le succès d'accouplement entre les deux variants, rendent ambiguë le statut d'espèce de S. frugiperda. L'objectif de ce travail est donc de mieux estimer, à travers une étude intégrative, le niveau de différenciation génétique présent entre les deux variants de S. frugiperda. Grâce à un premier niveau d'analyse, menées à partir de population naturelles, il a été possible de mettre en évidence un niveau de différenciation génétique élevé entre les deux variants, qui est compatible à celui attendu entre deux espèces. Le deuxième niveau d'étude réalisé à partir de population de laboratoire nous a permis de mettre en évidence la présence d'un isolement reproducteur entre les deux variants, se traduisant notamment par une distorsion de ségrégation méiotique des marqueurs moléculaires chez les hybrides. L'ensemble de ces résultats supportent l'hypothèse selon laquelle le variant riz et maïs de Spodoptera frugiperda seraient des entités situées à une étape avancée dans le continuum de la spéciation. / In phytophagous insects, adaptation to host plant could be the first step leading to speciation. In this context, this document focus on moth Spodoptera frugiperda (Lepidoptera: Noctuidae), a pest responsible for serious damages in several crops in the Western hemisphere. Spodoptera frugiperda consists of two host-plant strains, one adapted to rice and the other adapted to maize, which made it a relevant model to study this mechanism. Though the two variants are morphologically identical, they are nonetheless genetically distinguishable and present some ecological and behavioral differences. The species status of S. frugiperda is also highly controversial because hybrids naturally occur in the wild, not to mention the fact of the discrepancies among published results concerning mating success between the two strains. The aim of this thesis is thus to better estimate, through an integrative approach, the level of genetic differentiation between the two variants of S. frugiperda. Starting with natural populations, various phylogenetic methods allowed us to highlight a high level of genetic differentiation between the two variants, compatible with what is expected between distinct species. Furthermore, studies on laboratory populations, including crossing experiments, showed a significant unidirectional bias in inter-strain mating success and the presence of meiotic segregation distortion of molecular markers in hybrid progenies. These results as a whole support the assumption that the two strains of S. frugiperda are well-advanced in the continuum of speciation.

When the agricultural revolution took place, the biodiversity decreased and during the last century more than 90 % of the area of species-rich grasslands has been lost. Fragmentation has occurred with the area lost and insects, e.g. butterflies, suffer because of this. I investigated the impact that surrounding landscapes have on vegetation in species-rich grasslands, by using data from NILS and land use land cover data. I used the area of grassland, forest, water and arable land at radii from 100 m to 40000 m. All landscape structures showed a significant effect on the species density, but at different ranges. Arable and forest were both positive at large radii. Water had a negative effect at short ranges but positive at large ranges. The same was shown for grassland, and that is likely explained by grassland making up a very small proportion of the total area. In conclusion, species density in species-rich grasslands can partly be explained by the surrounding landscape. These results have implication for reserve selection, monitoring and restoration.

The species–area relationship (SAR) has been applied to predict species richness declines as area is converted to human-dominated land covers.In many areas of the world, however, many species persist in human-dominated areas, including threatened species. Because SARs are decelerating nonlinear, small extents of natural habitat can be converted to human use with little expected loss of associated species, but with the addition of more species that are associated with human land uses. Decelerating SARs suggest that, as area is converted to human-dominated forms, more species will be added to the rare habitat than are lost from the common one. This should lead to a peaked relationship between richness and natural area. I found that the effect of natural area on avian richness across Ontario was consistent with the sum of SARs for natural habitat species and human-dominated habitat species, suggesting that almost half the natural area can be converted to human-dominated forms before richness declines. However, I found that this spatial relationship did not remain consistent through time: bird richness increased when natural cover was removed (up to 4%), irrespective of its original extent. The inclusion of metapopulation processes in predictive models of species presence improves predictions of diversity change through time dramatically. Variability in site occupancy was common among bird species evaluated in this study, likely resulting from local extinction-colonization dynamics. Likelihood of species presence declined when few neighbouring sites were previously occupied by the species. Site occupancy was also less likely when little suitable habitat was present. Consistent with expectations that larger habitats are easier targets for colonists, habitat area was more important for more isolated sites. Accounting for the effect of metapopulation dynamics on site occupancy predicted change in richness better than land cover change and increased the strength of the regional richness–natural area relationship to levels observed for continental richness–environment relationships suggesting that these metapopulation processes “scale up” to modify regional species richness patterns making them more difficult to predict. It is the existence of absences in otherwise suitable habitat within species’ ranges that appears to weaken regional richness–environment relationships.

Humans are modifying the global landscape at an unprecedented scale and pace. As a result, species are declining and going extinct at an alarming rate. Here, I investigate two main aspects of species’ declines: what factors are contributing to their declines and how effective our conservation efforts have been. I assessed one of the main mechanisms for protecting species by looking at the Endangered Species Act (ESA) in the United States. I examined three separate indicators of species declines for different groups of species: range contractions in Canadian imperilled species, declines in abundance in global amphibian populations and increases in temporal variability in abundance in North American breeding birds. I found that change in recovery status of ESA listed species was only very weakly related to the number of years listed, number of years with a recovery plan, and funding. These tools combined explained very little of the variation in recovery status among species. Either these tools are not very effective in promoting species’ recovery, or species recovery data are so poor that it is impossible to tell whether the tools are effective or not. I examined patterns of species’ declines in three different groups in relation to a number of anthropogenic variables. I found high losses of Canadian imperiled bird, mammal, amphibian and reptile species in regions with high proportions of agricultural land cover. However, losses of imperiled species are significantly more strongly related to the proportion of the region treated with agricultural pesticides. This is consistent with the hypothesis that agricultural pesticide use, or something strongly collinear with it (perhaps intensive agriculture more generally), has contributed significantly to the decline of imperiled species in Canada. Global increases in UV radiation do not appear to be a major cause of amphibian population declines. At individual sites, temporal changes in amphibian abundance are not predictably related to changes in UV intensity. Variability in species’ abundance of North American breeding birds, after accounting for mean abundance, is not systematically higher in areas of high human-dominated land cover or climate change. Rather, it appears that areas with a high proportion of human-dominated cover come to have a higher proportion of highly abundant, and thus more variable, species.

It is generally assumed that when natural habitat is converted to human-dominated cover such area is “lost” to its native species. Extinctions will ensue. The literature generally assumes that species are extirpated as natural area is reduced, following the well-known species-area relationship (SAR). However, SARs have consistently over-estimated species losses resulting from conversion of natural habitat to human-dominated land covers. We hypothesize that the overestimation occurs because these area-based models assume that converted habitat is “lost”, eliminating all species. However, in the real world, conversion of natural land cover to human-dominated cover frequently produces new land covers, different from the original habitat, but not necessarily completely inhospitable to biodiversity. We evaluated the responses of total avian richness, forest bird richness and open habitat bird richness to remaining natural area within 991 quadrats, each 100 km2, across southern Ontario. Total bird species richness does not follow SAR predictions; rather, the number of bird species peaks at roughly 50% natural land cover. The richness of forest birds does follow the usual SAR power-law as a function of forested area. In contrast, richness of birds that prefer open-habitat does not increase monotonically with either natural- or human-dominated land cover. However, we can partition human-dominated land cover into an “available human-dominated” component and “lost” habitat. Richness of open-habitat species relates to the amount of available human-dominated cover. Distinguishing three habitat types (natural, available human-dominated, and lost) permits accurate predictions of species losses in response to natural habitat conversion.

Dung beetles is a group of coprophagous beetles in the family Scarabaeidae. Dung beetles have an important function by improving nutrient circulation and biological control of parasites. Dung is a short-lived resource, making dung beetles tied to habitats continuously grazed. Decline in pasture combined with shorter grazing seasons has resulted in a decrease in available dung. Other reasons can be the use of chemicals to control internal parasites on the grazing animals. This has contributed to the fact that half of the dung beetles in Sweden are endangered. The aim of the present study was to analyze data on dung beetles from the County Administration Board in Östergötland and see if species communities have changed between 2001-2019. In addition, the effect of sand as soil type was studied by comparing the species richness between pastures with and without sand. Analysis whether there was any variation among species richness and species communities depending of grazing animals was also performed. Results showed that the number of species had increased over time and that changes in species communities had occurred. Pastures with sand had more species, however, the amount of sand in the nearest surroundings was of less importance. Dung beetles were found to have a preference when choosing dung-type. Pastures with dung from multiple species of grazing animals were found having the highest species richness. Studies on this would clarify even further what seems to favor dung beetles, this could then be applied to other areas to counteract the loss of species.