MSc., Faculty of Science, University of the Witwatersrand, 2011 / The role of phylogeny and environmental influences on behaviour were investigated in two sub-species of Rhabdomys dilectus: R. d. chakae and R. d. dilectus. I compared populations of the two sub-species that occur about 70 km apart in superficially similar grasslands, south of Johannesburg (Walkers Fruit Farms) and at Irene in Gauteng Province, South Africa. The vegetation characteristics of the localities were assessed by measuring aerial cover, cover density, amount of dead material, and the maximum and minimum plant height. I studied the maintenance (non-social) and social behaviour of the sub-species in captivity. Three maintenance behaviours were studied: diel activity in an open arena, activity in an enclosed maze and in a modified plus maze. Social behaviour was studied by investigating the stress response of juvenile males after removal from their family groups and being placed in a plus maze, and the tolerance of unfamiliar same-sex consub-specifics in staged dyadic encounters. My results indicate that there were differences in the vegetation at the localities, most notably in the level of cover, which was greater at Irene (R. d. dilectus) than at Walkers Fruit Farms (R. d. chakae). Both sub-species displayed similar activity profiles (diurnal and crepuscular) and similar levels of activity in an enclosed maze. However, R. d. dilectus showed high levels of anxiety in an open arena and in a plus maze. The sub-species showed similar social behaviours: males of both sub-species that were removed from their family groups at the onset of weaning showed a lower stress response compared to the social sister species R. pumilio. Social interactions of same-sex intra-sub-specifics were mostly similar between the sub-species but there were slight discrepancies in behaviour associated with mating. Surprisingly, there were higher levels of amicability in all dyads than predicted by the solitary lifestyle of the two sub-species in nature. Behavioural differences (anxiety response) may be due to divergence in allopatry because of differences in vegetation characteristics. The similarities in activity profile and social behaviours could be explained by phylogenetic inertia or by similar selection pressures in similar environments.

ABSTRACT Environmentally-induced stereotypic behaviour (SB) results from the chronic impact of captivity on brain development and function and, consequently, on behaviour. My study sought to determine group- and individual-level predictors and correlates of SB in the striped mouse, Rhabdomys dilectus, and to identify the mechanisms underlying the stereotypic phenotype. This aim was addressed by collecting cross-sectional and longitudinal behavioural and physiological data from a combination of wild-caught (WC) and captive-born (CB) striped mice born and reared in different social and environmental conditions. First, I examined the group-level effects of rearing conditions. Results confirmed the genetic contribution to SB performance in striped mice, and furthermore indicated that (1) striped mice weaned at or later than their natural weaning age are less likely to develop SB than striped mice weaned prematurely; (2) striped mice reared biparentally showed significantly less SB as adults than striped mice reared by their mothers alone; (3) striped mice raised from weaning in enriched conditions were four times less likely than standard-housed individuals to develop SB, an effect which endured after enriched-housed striped mice were transferred to standard housing; and (4) birth origin predicts the emergence of SB in striped mice, with those WC individuals trapped as adults being relatively protected from the development of SB compared with both WC individuals trapped as juveniles and CB striped mice. I also showed that (1) WC striped mice were more fearful and less active than CB animals, but that these traits did not covary with SB, and (2) WC striped mice were less perseverative and behaviourally more flexible than CB animals, traits that did covary with SB. Second, I characterized the developmental trajectory of SB in a large group of CB, standard-housed striped mice, and then investigated potential individual-level predictors, mediators, and correlates of SB in these animals. Measures of perseveration, activity, and anxiety/fearfulness assessed in juveniles before the development of SB did not predict which animals later developed SB, but stereotypic adults were more active and more perseverative than nonstereotypic individuals. Whilst preweaning developmental maturity did not predict which striped mice later developed SB, striped mice showing accelerated development in the preweaning period were likely to show SB at an earlier age, at a higher frequency, and potentially with reduced variability, effects which persisted into adulthood. In conclusion, my study shows that more naturalistic rearing environments reduce the incidence of SB, an effect mediated by genetic factors and possibly also by experience-dependent alterations in forebrain function. However, further work is necessary to explore whether the association between forebrain function and SB expression in striped mice is causal because, whilst environments which decrease perseverative tendencies also reduce SB, I found no evidence that such tendencies predict which striped mice later develop SB.

Student Number : 9905625D - MSc dissertation - School of Animal, Plant and Environment Science - Faculty of Science / Stereotypic behaviours are repetitive invariant behaviours that serve no obvious purpose and are common in both domestic and non-domestic captive animals. Stereotypies are regarded as indicators of poor welfare although the growing body of work pertaining to these behaviours has challenged many previously held notions of stereotypy. The most widely accepted, although frequently contested, hypothesis used to explain stereotypies is the coping hypothesis, which states that animals perform stereotypies to cope with the stress of adverse environments. The aim of my study was to investigate the fitness effects of stereotypy, and whether or not environmental enrichment protocols were effective in reducing or eliminating stereotypy in the adult striped mouse Rhabdomys pumilio. Both of these experiments were designed to evaluate the coping hypothesis. I intentionally used wild caught and F1 individuals to eliminate any potential captive selection bias that may exist in extant captive populations that could affect interpretation of fitness. For the first aim, 40 breeding pairs were assigned to one of four treatments: 1) stereotypic female and stereotypic male (S-S); 2) stereotypic female and non-stereotypic male (S-NS); 3) non-stereotypic female and stereotypic male (NS-S); and 4) non-stereotypic female and non-stereotypic male (NS-NS). Compared to non-stereotypic females, stereotypic striped mice females had better reproductive output, including larger litter size, higher growth rate, higher litter survival, shorter interlitter interval and shorter time to first litter. Reproductive success was higher in S-S and S-NS pairs, indicating that genetic and maternal effects jointly determined fitness in striped mice. Unlike other published research, maternal mass was not a predictor of fitness. For the second aim, I housed 20 non-stereotypic and 20 stereotypic striped mice (equal sex ratio) in barren cages for 60 days, and transferred them to enriched cages, and repeated this experiment with striped mice housed initially in enriched cages and transferred to barren cages. While there was a measurable reduction in stereotypy in individuals transferred from barren to enriched environment cages, no increase in stereotypy was noted in striped mice transferred from enriched to barren cages. These findings appear to concur with the coping hypothesis, that stereotypies become perseverative (e.g. bad habits) and difficult to disrupt. Non-stereotypic striped mice were not influenced by the swap. I conclude that the expression of stereotypy is a potential sign of positive welfare and that it may be worthwhile to specifically elicit stereotypic behaviours in order to improve the welfare, and in certain cases, breeding success, of captive animals. Moreover, I maintain that where necessary, effort should be applied to combating stereotypies before they arise, rather than attempting to eliminate them once they have actually developed.

A thesis submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Doctor of Philosophy, 2017 / Under current and previous global climate change, environments are changing and have changed at a rapid rate. Species with the potential to undergo adaptive radiation are likely to survive environmental change. The genus Rhabdomys is widespread in southern Africa, occurring along the east-west rainfall gradient in South Africa. Rhabdomys may have undergone adaptive radiations in the past, which may have resulted in the current suite of species in various habitats of different aridity. Some Rhabdomys species also occur in sympatry in some locations in South Africa. The aim of my study was to investigate adaptive variation in Rhabdomys by studying the behaviour of 5 populations, representing 3 Rhabdomys species, across South Africa. Using selected taxa, my approach was, firstly, to describe variation in two traits, personality and spatial cogntion, well known for showing environmentally-linked (i.e. adaptive) variation. Secondly, I manipulated the development of exploratory and anxiety behaviour to assess the limits of the adaptive variation (i.e. test the nature of the reaction norm of the characters measured). I first established the taxon-level personality of 4 taxa (2 sympatric) in 5 standard behavioural tests. Generally, the semi-desert living R. pumilio was the boldest together, surprisingly, with R. d. dilectus occurring in grasslands of central South Africa, contradicting previously published results. Comparatively, R. bechuanae from central South Africa and R. dilectus from far north-eastern South Africa, also occurring in grasslands were less bold, even though R. bechuanae is sympatric with R. dilectus in central South Africa. My data indicate adaptive variation at the extreme populations and possibly character displacement in the sympatric populations. In the next chapter, I investigated whether early rearing environment shapes exploratory behaviour and anxiety responses of R. pumilio and R. bechuanae. I predicted that using an interspecies cross-fostering protocol would reveal a gene x environment interaction on behaviour, so that fostered offspring would display an intermediate behaviour phenotype compared to their non-fostered siblings. I showed that a novel rearing environment mostly did not influence the adult behaviour of cross-fostered inidividuals. This indicates genetic constraints on exploratory behaviour and anxiety responses. Next, I tested whether physical rearing environment shapes exploratory behaviour and anxiety responses. I reared semidesert R. pumilio, sympatric R. bechuanae and R. dilectus and allopatric R. bechuanae under either no cover or high cover for 2 generations. The taxa were mostly similar and altering the phyical housing condition did not alter behaviour, but there were small differences between the taxa in exploratory behaviour. In the final experimental chapter, I established whether the environment predicts the spatial cognition in semi-desert R. pumilio, sympatric R. bechuanae and R. dilectus and an allopatric population of R. dilectus from far north-eastern South Africa. The populations showed very similar performance in a modified Barnes maze, indicating a possible phylogenetic constraint on spatial cognition. Overall, my study suggests that there is adaptive variation in personality but not spatial cognition. In contrast to previous studies in the genus, alterations to the social and physical environments failed to separate out genetic and environmental effects (i.e. reaction norm) that would potentially provide the mechanisms for adaptive variation within and between species. The similarity in spatial cognition between taxa and similar responses to environmental modification indicate phylogenetic constraints on traits that were predicted to vary geographically. / XL2018

The striped-mouse, Rhabdomys pumilio, is widely distributed throughout southern Africa within a variety of habitats and rainfall regimes. It is found at sea level in the Eastern and Western Cape regions and at altitudes above 2700 m in the Drakensberg mountains. The attraction of R.pumilio to cultivated land and crops has resulted in extensive damage to plants and cultivated crops. A study of the genetic variation between populations of R.pumilio from different regions of southern Africa was undertaken by protein electrophoresis and randomly amplified polymorphic DNA using the polymerase chain reaction (PCR-RAPD). A cytogenetic study was also undertaken. The mean heterozygosity (H=0.074) for R.pumilio was more than twice that estimated for mammals (H=0.036) while the mean percent polymorphism (P=16.1%) was only slightly higher than the mean percent polymorphism obtained for mammals (P=14.7%). The highest heterozygosities were recorded in the Potchefstroom (H=0 .145) and Zimbabwe (H=0 .118) samples and the lowest mean heterozygosity was recorded in the peninsular Western Cape (H=0. 032). A mean Fst value of 0.459 was obtained, suggesting a high degree of genetic differentiation between the samples of R.pumilio but the negative Fis (-0.01) value emphasized that R.pumilio retained an outbreeding population structure. The similarity coefficient between the samples of R.pumilio using PCR-RAPD's ranged between 0.471 and 0.853 and substantiated the argument for genetic divergence between the samples of R.pumilio. An isolation by distance model for the population genetic structure of R.pumilio was supported by the allozymes (r=0.58, p<0.00l) and PCR-RAPD's (0.75, p<0.00l). Temperature and rainfall also had an influence on the allelic frequency distribution of certain loci of R.pumilio. Rogers (1972) genetic similarity varied between 0.796 and 0.988 while the values for Nei's (1978) unbiased genetic distance varied between 0.000 and 0.189 for the different samples of R.pumilio. Subgrouping of the KwaZulu-Natal samples, the peninsular Western Cape and Eastern Cape samples of R.pumilio was evident with the allozymes. With the PCR-RAPD' s the Zimbabwe sample showed the least similarity to the other samples with a KwaZulu-Natal/Potchefstroom subgroup separating from the less well defined Eastern Cape and Western Cape subgroup. Cytogenetic studies of specimens of R.pumilio from some of the localities in southern Africa revealed a chromosomal number of 2n=48 , while the Potchefstroom and Zimbabwe specimens displayed a chromosomal number of 2n=46. Homology in G-and C-banding was recorded. The allozymes, PCR-RAPD's and chromosomal studies suggested subspecies status for the Zimbabwe population of R.pumilio. The Potchefstroom sample displayed a greater genetic similarity to the remaining South African samples of R.pumilio than the Zimbabwe samples and therefore could not be considered for subspecies status. Although the South African samples of R.pumilio displayed a certain degree of genetic divergence, it was insufficient to warrant subspecies status although evolution in this direction was suggested. / Thesis (Ph.D.)-University of Natal, Durban, 1999.

Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Within southern Africa, the widely distributed four-striped mouse Rhabdomys is parasitized by, amongst others, the host-specific ectoparasitic sucking louse, Polyplax arvicanthis. The present study investigated this parasite-host association from a phylogenetic and phylogeographic perspective utilizing mitochondrial and nuclear DNA markers. The findings support the existence of four species within Rhabdomys (three distinct lineages within the previously recognized arid-adapted R. pumilio and the mesic-adapted R. dilectus). These species have distinct geographic distributions across vegetational biomes with two documented areas of sympatry at biome boundaries. Ecological niche modelling supports a strong correlation between regional biomes and the distribution of distinct evolutionary lineages of Rhabdomys. A Bayesian relaxed molecular clock suggests that cladogenesis within the genus coincides with paleoclimatic changes (and the establishment of the biomes) at the Miocene-Pliocene boundary. Strong evidence was also found that the sucking louse P. arvicanthis consists of two genetically divergent lineages, which probably represent distinct species. The two lineages have sympatric distributions throughout most of the sampled range across the various host species and also occasionally occur sympatrically on the same host individual. Further, the absence of clear morphological differences among these parasitic lineages suggests cryptic speciation. Limited phylogeographic congruence was observed among the two P. arvicanthis lineages and the various Rhabdomys species and co-phylogenetic analyses indicated limited co-divergence with several episodes of host-switching, despite the documented host-specificity and several other traits predicted to favour congruence and co-divergence. Also, despite the comparatively smaller effective population sizes and elevated mutational rates found for P. arvicanthis, spatial genetic structure was not more pronounced in the parasite lineages compared to the hosts. These findings may be partly attributed to high vagility and social behaviour of Rhabdomys, which probably promoted parasite dispersal among hosts through frequent inter-host contact. Further, the complex biogeographic history of Rhabdomys, which involved cyclic range contractions and expansions, may have facilitated parasite divergence during periods of host allopatry, and host-switching during periods of host sympatry. Intermittent contact among Rhabdomys lineages could also have prevented adaptation of P. arvicanthis to specific host lineages, thus explaining the lack of host-specificity observed in areas of host sympatry. It is thus evident that the association between Polyplax arvicanthis and Rhabdomys has been shaped by the synergistic effects of parasite traits, biogeography, and host-related factors over evolutionary time. / AFRIKAANSE OPSOMMING: Binne suidelike-Afrika word die wyd-verspreide gestreepte veldmuis, Rhabdomys, onder andere deur die gasheer-spesifieke ektoparasitiese luis, Polyplax arvicanthis, geparasitiseer. Die huidige studie het hierdie parasiet-gasheer interaksie vanuit ‘n filogenetiese en filogeografiese oogpunt ondersoek deur van beide mitokondriale en nukluêre merkers gebruik te maak. Die bevindinge dui op die bestaan van vier spesies binne Rhabdomys, waaronder drie nuwe genetiese groepe binne die voorheen erkende R. pumilio asook R. dilectus. Hierdie spesies het nie-oorvleulende geografiese verspreidings binne spesefieke plantegroei biome met twee geidentifiseerde areas van simpatriese voorkoms by bioom grense. Ekologiese nis modellering ondersteun ‘n sterk korrelasie tussen biome en die verspreiding van die evolusionêre groepe binne Rhabdomys. ‘n Bayesiaanse verslapte molekulêre klok dui daarop dat kladoginese binne die genus gedurende paleoklimatiese veranderinge, wat tot die totstandkoming van die huidige biome gelei het, by die Mioseen-Plioseen grens plaasgevind het. Sterk bewyse is ook gevind dat die parasitiese luis P. arvicanthis uit twee geneties verskillende groepe, wat heel moontlik afsonderlike spesies verteenwoordig, bestaan. Hierdie genetiese groepe het simpatriese verspreidings oor meeste van die gebestudeerde geografiese area op die verskeie gasheer spesies en mag ook soms simpatries op dieselfde gasheer individu voorkom. Verder dui die afwesigheid van duidelike morfologiese verskille tusssen die parasiet genetiese groepe op moontlike kriptiese spesiasie. Beperkte filogeografiese ooreenstemming is tussen die P. arvicanthis genetiese groepe en die Rhabdomys spesies waargeneem en die vergelykende-filogenetiese analises het aangedui dat daar beperkte gesementlike-divergensie plaasgevind het met verskeie episodes van gasheer-wisseling, ten spyte van die gasheer-spesifieke aard van die parasiete asook verskeie ander kenmerke wat veronderstel is om filogeografiese ooreenstemming en gesementlike-divergensie te bevorder. Ten spyte van die vergelykbaar kleiner effektiewe bevolking groottes en verhoogde mutasie tempo wat vir P. arvicanthis gevind is, is die geografiese genetiese struktuur nie meer gedifferensieёrd in die parasiet groepe as in die gasheer nie. Hierdie bevindinge mag deels verklaar word deur die hoё beweeglikheid asook die sosiale gedrag van Rhabdomys, wat waarskynlik parasiet beweging tussen gashere bevorder deur gereelde tussen-gasheer kontak. Die komplekse biogeografiese geskiedenis van Rhabdomys, wat sikliese inkrimping en uitsetting van die geografiese verspreiding behels het, het heel moontlik parasiet divergensie tydens tydperke van gasheer allopatrie asook gasheer-wisseling tydens tydperke van gasheer simpatrie, gefasiliteer. Tussentydse kontak tussen Rhabdomys genetiese groepe kon aanpassing van P. arvicanthis tot sekere gasheer genetiese groepe verhoed het en verklaar dus die afwesigheid van waargenome gasheer-spesifisiteit in areas van gasheer simpatrie. Dit is dus duidelik dat die assosiasie tussen P. arvicanthis en Rhabdomys deur die sinergistiese uitwerking van parasiet kenmerke, biogeografie, asook gasheer-verwante faktore oor evolusionêre tyd gevorm is. / National Research Foundation (NRF)

Student Number : 0419128X - MSc Dissertation - School of Animal, Plant and Environmental Sciences - Faculty of Science / Reproductive isolation was investigated in two chromosomally distinct populations of Rhabdomys on the Gauteng highveld. The two populations, Midrand (2n = 48) and Irene (2n = 46), occur 15 km apart, with no known contact or hybrid zone between them. Behavioural experiments, comprising male-female dyadic encounters and female preference tests for same-and different-population male odour, were used to test for premating barriers. Aggression levels were highest in different-population than same-population dyads, and females spent more time with odours of males from their own population than of those of the other population. Breeding and postnatal development studies were conducted to establish postmating barriers. Compared to different-population pairs, reproductive success was markedly reduced in different-population pairings, and the few hybrids that were produced did not breed. My studies indicate that behavioural isolation is well-developed between the Midrand and Irene striped mice, and suggest that the mate recognition system has diverged in allopatry, which would reduce gene flow between the two populations. Such divergence supports the findings of mtDNA studies by other workers who proposed that the two chromosomal forms used in my study represent two subspecies of R. dilectus. Previous studies showed that distant striped mice populations (>900km) displayed behavioural divergence and intermediately located populations (~80km) were behavioural compatible but had hybrid failure; the Irene population was used in both studies. In comparison, the behavioural incompatibility between the closely-located Midrand and Irene populations provides support for the reinforcement of previous postmating isolation seen in the intermediately located populations, particularly since no contact or hybrid zone exists between the two forms. However, I cannot rule out other explanations, such as dissimilar ecological conditions, influencing interfertility.

Rainfall is the most important factor limiting primary production, and hence food availability, in ecosystems. This study tests the thesis that, under conditions where rainfall is unpredictable and food supply varies spatially and temporally from year-to-year, physiological energy-saving mechanisms should evolve in animals for which migration is not an option to avoid periods of low habitat productivity. Apart from the normally erratic rainfall patterns characteristic of arid regions, unpredictable seasonal rainfall may also occur in mesic zones as a consequence of climatic phenomena such as the El Niño Southern Oscillations (ENSO). Using two hypothetical models, this study attempts to determine whether the respective evolutionary history of both aridity and ENSO can be detected in the various phenotypic physiological traits of Rhabdomys pumilio from across southern Africa. Model 1 predicts that a gradient of conservatism of physiological traits related to metabolism, will be detectable along an aridity gradient. Model 2 predicts an increase in the conservatism of similar traits correlated with both the aridity gradient and the gradient of negative rainfall anomalies that are associated with the ENSO. Measurements of circadian rhythms of body temperature and oxygen consumption of individuals of R. pumilio collected from six sites across southern Africa showed that the geographic variation in the physiological traits and proximate responses of this species was explained better by Model 2 than by Model 1. Furthermore, for some traits and proximate responses of this species it was shown that, although the stresses associated with unpredictable rainfall occur less frequently in non-desert ENSO-zones, they are nevertheless sufficient to mimic the selection pressures of rainfall unpredictability in arid zones. This study also highlighted the low basal rates of metabolism and the other conservative physiological traits of this species as a whole. The basal metabolic rate of 0.819 mlO₂g/h and the minimum wet thermal conductance of 0.110 mlO₂/g/h/ºC are lower than that predicted by allometry. The circadian amplitude of body temperature of 2.52°C and the circadian amplitude of oxygen consumption of 1.39 mlO₂/g/h were higher than those predicted by allometric equations. These deviations from predicted values were attributed to the adaptedness of this species to the physiological energy stresses associated with unpredictable resource availability in southern Africa. / Thesis (M.Sc.)-University of Natal, Pietermaritzburg, 1998.

MSc (Zoology) / Department of Zoology / The adverse ecological effects of landscape modification by humans are well known and continue to be studied. Habitat disturbances arising from such modifications result in various levels of biodiversity loss. Amongst mammals, large carnivores are usually the first to disappear, leaving a gap in the trophic pyramid. However, ecologically adaptive small carnivores, free from the effects of intraguild predation can readily fill this gap (i.e. mesopredator release). In highly productive disturbed habitats, small mammals may thrive, reaching densities that can support an abundant and diverse suite of small carnivores. After frequent sightings of serval (Leptailurus serval) on the highly disturbed Sasol Synfuels Operations property, three camera trap surveys were conducted between 2014 and 2015 to study its ecology. The resulting data was subsequently used to study the site’s small carnivores. Multispecies occupancy modelling was used to determine detection (p) and occupancy (ψ) probabilities and estimate species richness across the study area. Site-specific covariates were then modelled against abundance values to identify any correlations. Out of 23 small carnivore species predicted to occur on the site, 11 were detected. Spatially, estimated species richness was highest in disturbed habitats, while it was slightly lower in Grassland possibly due to undersampling. Detection and occupancy probabilities were low (except for serval), with interspecies variations. It is suspected that this is the result of survey bias towards serval. The only covariate showing any significant effect was livestock presence, negatively affecting serval occupancy. Estimated species richness was used as a proxy to identify high- or low-predation areas. Within these areas, three vegetation treatments were selected (low, medium and high cover). Small mammal foraging behaviour under varying predation pressures within these treatments was then studied using the giving-up density (GUD) framework. Differences in GUDs were examined using generalised linear mixed models (GLMM). Small mammal trapping in the study area showed that four-striped grass mouse (Rhabdomys sp.; diurnal) and multimammate mouse (Mastomys sp.; nocturnal) were dominant. Nocturnal GUDs were lower than diurnal, which is interesting as four-striped grass mice are more abundant than multimammate mice. This indicates that density alone does not influence GUDs. Additionally, no significant difference in GUDs was observed between predation and vegetation treatments. I suggest that observed GUDs are linked to individual or combined impacts of interspecific differences in foraging behaviour, metabolic requirements or temporal variations in perceived predation pressure. GUDs also varied between surveys, being lower in mid- compared to early winter. This might be attributable to decreased availability of food and greater metabolic requirements in mid-winter. The results show that modified landscapes (such as the study site) can contribute to biodiversity conservation, especially of small carnivores, the adaptability of which allows them to flourish in disturbed habitats. Under favourable conditions, ecologically flexible small mammal species seem to be unaffected by the risks associated with an abundance of small carnivores. While the processes governing the dynamics of predator and prey communities in disturbed systems are not entirely clear, the conservation potential of such areas cannot be ignored and deserves more attention from researchers. / NRF

The main aim of the current study was to determine the prevalence and diversity of potentially zoonotic bacterial genera in accurately identified indigenous rodents from South Africa. Bacterial prevalence and diversity were determined by PCR amplification and sequence analyses. Rodents were molecularly identified by amplification and sequence analysis of the mitochondrial cytochrome b gene region. Three species (Aethomys ineptus, Mastomys coucha and Otomys angoniensis) belonging to murid species complexes were identified. Furthermore, phylogenetic analyses revealed that both the proposed subspecies (R. dilectus dilectus and R. d. chakae) within the recently erected Rhabdomys dilectus occur in Hammanskraal and at the University of Pretoria Experimental farm, both in the Gauteng Province of South Africa. An overall bacterial prevalence of 38.6 % was observed in kidney samples of commensal and natural indigenous rodents after molecular screening with broad range 16S rRNA gene primers. Nucleotide sequence analyses identified a diverse range of bacterial genera namely, Bartonella, Anaplasma, Helicobacter, Burkholderia, Streptococcus, Aerococcus and Lactobacillus. Some members of these genera have been identified as causative agents of human and animal diseases, being transmitted either through environmental contamination or through haematophagous arthropod vectors. Subsequent genus-specific bacterial screening focussed on vector-borne genera identified in the commensal and natural rodent populations sampled. Bartonella prevalence and genetic diversity was compared between a natural and commensal population of the southern multimammate mouse (M. coucha) using two gene regions (Citrate synthase gene and NADH dehydrogenase gamma subunit gene). A significantly higher infection prevalence was detected in the commensal population (92.9 %) as compared to the natural population (56.9 %). No differences however, were detected between infection status and the ectoparasite loads calculated for both rodent populations. Apart from several novel Bartonella strains identified in both M. coucha populations, phylogenetic analyses also identified a species of known zoonotic potential (B. elizabethae) in both populations. The present study represents one of the first to screen indigenous rodents for tick-borne members of the bacterial family Anaplasmataceae. Anaplasma bovis-like DNA was detected in five of the six rodent species sampled (A. ineptus, Lemniscomys rosalia, M. coucha, O. angoniensis and R. dilectus) at an overall prevalence of 39.2 %. The potentially zoonotic Ehrlichia ewingii was detected in M. coucha samples only at a prevalence of 5.3 %. The diverse bacterial genera detected in commensal and natural populations of indigenous rodents comprise members of zoonotic potential and agricultural significance, highlighting the importance of continuous disease surveillance of indigenous rodents. / Dissertation (MSc)--University of Pretoria, 2014. / National Research Foundation (NRF) / Zoology and Entomology / MSc / Unrestricted