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Thesis (PhD)--University of Stellenbosch, 2003. / ENGLISH ABSTRACT: The geographic genetic population structure and evolutionary history of the African four-striped mouse, Rhabdomys pumilio, was investigated using mitochondrial (mtDNA) cytochrome b gene (1140 bp) and control region (994 bp) sequences and a combination of cytogenetic banding techniques (G- and C-banding), and fluorescence in situ hybridization. Two cytotypes (2n = 46 and 2n = 48) were identified by cytogenetic analysis. No evidence of diploid number variation within populations was found nor were there differences in gross chromosome morphology, or subtle interchromosomal rearrangements at levels detected by ZOO-FISH. The comparative painting data (using the complete suite, N = 20, of Mus musculus chromosome specific painting probes) show that 10 mouse chromosomes have been retained as chromosomal arms, or intact chromosome blocks within the R. pumilio genome, six produced double signals, while the remaining four hybridized to three or more R. pumilio chromosomes. In total, the 20 mouse chromosome paints detected 40 segments of conserved synteny. Their analysis revealed eight R. pumilio specific contiguous segment associations, a further two that were shared by R. pumilio and other rodents for which comparable data are available, the Black (Rattus rattus) and Norwegian (Rattus nONegicus) rats, but not by the Chinese hamster, Cricetulus grise us. The results suggest that mouse chromosomes 1, 10, and 17 have undergone extensive rearrangements during genome evolution in the murids and may be useful markers for enhancing our understanding of the mode and tempo of chromosome evolution in rodents. Following initial studies using control region sequences, the phylogeographic appraisal of R. pumilio was done using cytochrome b gene sequences. Analyses based on a variety of analytical procedures resulted in the detection of two major mtDNA lineages that correspond roughly to the xeric and mesic biotic zones of southern Africa. One clade comprises specimens with 2n = 48, and the other representatives of two cytotypes (2n = 48 and 2n = 46). The mean sequence divergence (12.0%, range 8.3% -15.6%) separating the two mtDNA clades is comparable to among-species variation within murid genera suggesting their recognition as distinct species, the prior names for which would be R. dilecfus and R. pumilio. Low sequence divergences and the diploid number dichotomy within the mesic lineage support the recognition of two subspecies corresponding to R. d. dilecfus (2n = 46) and R. d. chakae (2n = 48). The data do not support subspecific division within the nominate, R. pumilio. Molecular dating places cladogenesis of the two putative species at less than 5 million years, a period characterised by extensive climatic oscillations which are thought to have resulted in habitat fragmentation throughout much of the species' range. / AFRIKAANSE OPSOMMING: Die geografiesebevolkingsstruktuur en evolusionêre verwantskappe binne die Afrika streepmuis, Rhabdoys pumilio, is ondersoek deur middel van mitochondriale ONS volgordebepaling van die geenfragment sitochroom b (1140 basispare) en die reguleerstreek (994 bp) in kombinasie met sitogenetiese tegnieke (G- en Cbandkleuring en f1uoreseerende in situ hibridisasie). Twee sitotipes (2n = 46 en 2n = 48) is geidentifiseer deur sitogenetiese analasie. Geen bewys van variasie in die 2n chromosoomgetal binne bevolkings is gevind nie. Verder is daar ook geen verskil in die morfologies struktuur van chromosome aanwesig binne bevolkings nie. Vergelykende data (verkry met behulp van die N = 20 Mus musculus chromosoomspesifiekepeilers) dui daarop dat 10 muis chromosome behoud gebly het as chromosoomarms of chromosoomblokke binne die R. pumilio genoom. Ses peilers het dubbel seine gelewer terwyl die oorblywende vier peilers gehibridiseer het aan drie of meer R. pumilio chromosome. In totaal het die 20 muischromosoomverwe 40 konserwatiewe segmente geidentifiseer. Die analise dui agt R. pumilio spesifieke aaneenlopende segmentassosiasies aan, met 'n addisionele twee wat deur R. pumilio en ander muisagtiges vir wie vergelykende data beskikbaar is, byvoorbeeld die swart (Rattus rattus) en Noorweegse (R. norvegicus) rot maar nie die Chinese hamster, Cricetulus grise us, gedeel word. Die resultate stel voor dat muischromosoom 1, 10 en 17 ekstensiewe herrangskikkings ondergaan het gedurende die genoom evolusie binne die Muridae en dat hulle waarskynlik waardevolle merkers kan wees om beide die patroon en tempo van chromosome evolusie in muisagtiges verder te kan verstaan. Die filogeografiese verwantskappe binne R. pumilio is ondersoek deur middel van ONS volgordebepalings van die reguleerstreek asook sitochroom b. Die resultate van hierdie studie het twee divergente mitochondriale ONS eenhede ontdek wat gekorreleer kan word met xeriese en mesiese klimaatsones binne suidelike Afrika. Een groep bestaan uit diere met 2n = 48, terwyl die ander genetiese groep twee sitotipes (2n = 46 en 2n= 48) insluit. 'n Gemiddelde genetiese divergensie van 12.0% (varieer tussen 8.3% - 15.5%) verdeel die twee mtDNS-groepe en is vergelykbaar met tussenspesievariasie binne ander muisagtige genera, wat moontlik daarop dui dat twee verskillende spesies teenwoordig is; die voorgestelde name is R. di/ectus en R. pumilio. Lae genetiese divergensie binne die mesiese groep versterk die moontlike teenwoordigheid van twee subspesies, R. d. di/ectus (2n = 46) en R. d. chakae (2n = 48). Die data verleen egter nie steun aan die divisie binne R. pumilio nie. Molekulêre datering van die twee spesies dui daarop dat die divergensie ten minste 5 miljoen jaar gelede plaasgevind het. Die periode was gekarakteriseer deur ekstensiewe klimaatsossilasies, wat gely het tot habitat fragmentasie in die spesie se verspreidingsgebied.

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Unsustainable use of wildlife is a global conservation challenge. Understanding ecosystem specific patterns of wildlife exploitation is key to addressing this challenge. This thesis explores the nature of wildlife exploitation in and around Ugalla Game Reserve in western Tanzania. The reserve is divided into Ugalla east and Ugalla west tourist hunting blocks. First, I assessed the status of wildlife in the hunting blocks. Overall, estimates of wildlife population parameters suggested that Ugalla west was somewhat more exploited than Ugalla east. Second, I looked at the degree to which the hunting blocks experienced illegal wildlife hunting (poaching) and factors behind this. The spatial distribution of poaching signs and household interviews revealed that poaching was widespread, more so in Ugalla west than Ugalla east. Proximity to the reserve encouraged poaching, although bushmeat consumption increased with distance from the reserve. A wide range of bushmeat species was favoured, but the common species were impala Aepyceros melampus, dik-dik Madoqua kirkii and common duiker Sylvicapra grimmia. Availability of alternative sources of animal protein, agricultural production and income had significant influences on poaching. Different forms of poaching were specialist activities largely independent of each other. To address poaching, the main focus of attention has been on creating wildlife management areas (WMAs) along with allowing legal subsistence hunting by the communities around the reserve. Third, I assessed the impact of legal subsistence hunting on the wildlife species, and showed that it is not well managed and wildlife populations are contracting. This leaves WMAs as a potentially viable option for the conservation of Ugalla. Therefore, lastly, I identified and recounted some options for promoting the sustainability of WMAs. This thesis presents the first detailed assessment of wildlife exploitation in Ugalla, thus contributing to the existing body of knowledge on tackling the bushmeat crisis in Africa.

Individuals within a species often compete for resources in both space and time. In dominance hierarchies individuals with the greatest competitive ability will occupy prime locations during optimal periods to increase efficiency in gathering a resource. Subdominant individuals with low competitive abilities may be forced to reside in habitats of poor quality relative to dominant individuals. In this study I examined the long term patterns of giant kokopu distribution, movement, growth, habitat use, and social interaction between fish in relation to invertebrate drift (food supply). The habitat quality and abundance of food along a one km section of Alex�s Creek was monitored for a two year period. Though the physical structure of Alex�s Creek was relatively homogenous there were significant spatial differences in the density of drifting invertebrates sampled between riffles and pools over this long temporal period. In general, more drifting invertebrates were sampled in riffles of relatively long length and area. Within Alex�s Creek the distribution of giant kokopu, Galaxias argenteus, was determined by patchy distributions of food supply, specific physical factors of pools, and interactions between fish in dominance hierarchies. Over the 20 month study period, the most important biotic factor determining fish biomass was the total number of drifting invertebrates within pools while the most important abiotic factor determining fish abundances within pools was the pool size (surface area). The growth rate of individual fish correspondingly varied between fish residing within pools of different quality. Growth rates were higher for individual fish residing in pools with a relatively high density of drifting invertebrates. The differences in individual growth rates of giant kokopu may determine when fish leave a particular habitat patch (pool) and move to a new one. Fish that moved had lower growth rates (before moving) than fish that remained resident within home pools. Overall the movement of giant kokopu within Alex�s Creek was very restricted due to a relatively consistent distribution of food, however there were differences in the mobility of giant kokopu among different social ranks. The most dominant fish in pools were largely sedentary while fish ranked directly below fish 1 (i.e. fish 2 and 3 in social hierarchies) were relatively mobile. The ability of dominant fish to exclude subdominant fish from the most preferred feeding positions during optimal feeding times had consequences for overall giant kokopu activity. Under normal food supply conditions dominant fish were predominantly nocturnal and maintained large home ranges at night. Conversely subdominant fish occupied large home ranges by day, but were generally not observed at night. When the food supply was limited the utilization of pools was determined by social rank. Dominant fish from each pool increased daytime activity, home range size, aggressiveness, and the capture of food items offered by day while simultaneously reducing the spatial and temporal activity and habitat use of subdominant fish. These results indicate that behavioral changes in large dominant fish influence and reduce the amount of resources available to subdominant fish.

Forest carnivores such as the fisher have frequently been the target of conservation concern due to their association with older forests and assumed sensitivity to landscape-level habitat alteration. Although the fisher has been extirpated from most of its former range in the western U.S., it is still found throughout much of northwestern California. However, fisher distribution is still poorly known in the majority of this region where surveys have not been conducted. In order to predict fisher distribution across the region, a multiple logistic regression model was created using data from 682 previously surveyed locations and a GIS vegetation coverage created from satellite imagery. A moving-average function was used to derive landscape level indices of vegetation variables from the GIS layer. Moving averages of canopy closure, tree size class, and percent conifer were found to have strong correlations with fisher presence. Regional gradients as represented by either precipitation or a trend surface derived from spatial coordinates were also significant predictors in the model. The model was validated with new data collected from 240 survey locations and proved to be accurate in predicting fisher presence in unsurveyed areas. The model was used to generate hypotheses as to the mechanisms controlling habitat selection and the scales at which these operate and to evaluate the representation of fisher habitat in existing protected areas. These insights may be valuable in designing conservation reserve networks that insure the long-term viability of forest carnivore populations. / Graduation date: 1998

Mobile, rocky shore species often exhibit distinct but dynamic spatial distribution patterns, such as the occupation of microhabitats and formation of aggregations. These patterns are likely to be influenced by the behavioural patterns of a species, their population dynamics and the consequent benefits of adopting particular patterns at certain times of the year. Using Planaxis sulcatus (Planaxidae) as a model species, this thesis documented spatial and temporal variation in the spatial patterns of this species, and attempted to identify the causes and consequences of these behaviours in the seasonally variable Hong Kong intertidal zone. Activity patterns and snail behaviour during activity influenced the locations and types of spatial patterns formed. Planaxis was active and foraged whilst awash, with activity initiated by the ebbing or rising tides. Activity continued until the rock dried on an ebbing tide, or until snails were submerged by the rising tide. Snails were more active and moved for longer durations in summer than winter. When inactive, Planaxis occupied microhabitats such as cracks and crevices in summer and winter, but in the cooler months snails also formed aggregations on open rock surfaces and around microhabitats such as crevices. The extent of aggregation and number of snails in each aggregation showed strong seasonal variation, being greater in the transition period between summer and winter, and differed between sites, being the greatest at one site at Stanley. Seasonal differences in aggregation patterns may be linked with concurrent variation in Planaxis populations which, as a result of life histories events, had a greater abundance of snails and a larger number of recruits in the summer-winter transition, potentially increasing the chances and likelihood of aggregation formation. Microhabitat occupation in the summer provided physiological benefits to the snails. Compared with snails on open rock surfaces during summer low tides, those in crevices remained cooler and suffered less osmotic stress; while individuals in rock pools experienced lower osmotic but not thermal stress. In summer, aggregated snails suffered higher thermal and osmotic stresses than solitary individuals. The winter aggregations, however, showed little physiological benefits; with aggregations of different sizes having no effect on snail body temperatures, and only weak indications of large aggregations relieving osmotic stress. Winter aggregations, therefore, may be linked to minimizing dislodgement risks due to increased wave action at this time. A computer simulation incorporating seasonal differences in population densities, the likelihood and duration of activity, different topographies and three behavioural “rules” produced spatial patterns similar to those on the shore in terms of aggregation sizes, and the proportions of aggregating and crevice-occupying snails. These variables, therefore, play a role in determining the spatial patterns seen in Planaxis. This simple model did not, however, completely match field observations, suggesting that seasonal and spatial differences in distribution patterns involved more complex processes such as variation in local environmental conditions (temperature, wave action, shore topography) and/or biological factors (population densities, size structures, behavioural variation). Further investigations of these processes may better resolve our understanding of how these patterns form and their potential benefits. / published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

No description available.

The spatial distribution of four species of rorqual whales was studied along the north shore of the Gulf of St. Lawrence during the months of June to October from 1989 to 2000. A research effort of 6511 hours at sea yielded 849 sightings of blue whales (Balaenoptera musculus), 5291 of finback whales (Balaenoptera physalus), 3822 of humpback whales (Megaptera novaeangliae) and 6489 of minke whales (Balaenoptera acutorostrata). Spatial and behavioural data were collected at sea using inflatable boats, and Global Positioning Systems (GPS) were used to obtain accurate positions. These data were plotted and analysed using a Geographic Information System (GIS) to test the hypotheses that patterns of distribution were not random, were associated with bathymetry and reflected specific differences in habitat use. The resulting maps illustrated the clustered distribution of rorqual whales linked to sea-bottom topography, probably associated with areas of local upwelling and increased productivity. Blue and fin whales shared almost the same distribution, humpback whales were found in slightly deeper, offshore waters whereas minke whales were more abundant in shallower waters. Little attention has been given until now to local patterns of distribution in the area and such information can be useful for practical management considerations. The results emphasise the importance of scale in ecological studies of marine mammals and the need for further research using additional oceanographic parameters, in order to better understand habitat selection.

Glaciated areas offer a unique opportunity to study the dispersal of animals . During glaciation the fauna of glaciated areas was either destroyed or forced into ungla iated refugia. ..When the icesheets retreated the glaciated regions were open to reinvasion.