Faculty of Science School of Biology 9410199j TEL: 011 673 8139 / I studied the sociality and activity patterns of free-living ice rats Otomys sloggetti robertsi. The ice rat is a medium-sized, diurnal, herbivorous rodent, endemic to the alpine habitats of the southern Drakensberg and Maluti Mountains in southern Africa. These environments are characterized by sub-zero temperatures in winter and high levels of solar radiation in summer, and snow can be expected at any time of the year. Previous research by other scientists indicated that the physiology of ice rats is more similar to congeners living at lower altitudes, and, instead the taxon has morphological and behavioural adaptations for coping with the temperature extremes in its environment. Predator pressure on ice rats was negligible in my study site, making the ice rat an ideal model for testing how environmental factors influence sociality and activity patterns. Sociality was investigated by using direct observations and through experimental manipulations. Colonies comprised 4-17 individuals with several reproductively active males and females. Colony members had a high degree of home range overlap, whereas interactions between colony members were rare and usually resulted in agonistic behaviour. Ice rats responded aggressively to experimentally-caged colony members positioned in different parts of their own colony and these were treated with the same level of aggression as were strangers. Moreover, colony members competed aggressively for better-quality introduced food, particularly in winter. From direct observations of male-female interactions, it appeared that ice rats mate promiscuously, which is most likely a consequence of the multi-male and multi-female colonies. Females spent long periods of time belowground with unweaned young which emerged aboveground independently at four weeks of age. The first litter born in a season dispersed at sexual maturity (males±14 weeks; females±9 weeks), but, since I did not observe the behaviour of litters born later in the breeding season, I was not able to tell if these dispersed as well. I excavated the burrow systems of ice rats and found an intricate interlinking underground tunnel system with sometimes more than 25 entrance holes and 1-2 nesting chambers, which would provide a thermoneutral refuge for the ice rats at night as well as during adverse weather conditions. Because the ratio of the number of animals in the colony to III the number of nest chambers exceeded one, I predicted that huddling occurs belowground, which was confirmed by video recordings of nest chambers. Diurnal aboveground activity patterns of ice rats were influenced by prevailing environmental conditions, which resulted in synchronous aboveground appearance of members in a colony. The summer activity pattern was bimodal, dominated by foraging and sun basking behaviour aboveground, with animals retreating belowground to escape high temperatures and radiation levels prevalent around midday. Ice rats utilized the warmer temperatures throughout the day in winter for aboveground foraging and basking. Otomys s. robertsi displays a spatial shift in its social system: colony members huddle belowground but display temporal territoriality aboveground. Such a social system is contrary to predictions previously made for this taxon (i.e. they live as family groups). Ice rat relatives living at lower altitudes mainly occur as non-social aggregations and one relative, the vlei rat O. irroratus, also displays temporal territoriality. Although sociality is common in rodents inhabiting temperate environments in the northern hemisphere, these rodents do not show territoriality at other times. I conclude that the social system of ice rats, in the absence of significant predation pressure, is determined by a combination of 1) environmental factors driving communal thermoregulation and 2) phylogenetic constraints imposed by competition for limited food resources.

Student Number : 9613963J - PhD thesis - School of Animal, Plant and Environmental Sciences - Faculty of Science / Animals living in cold environments show physiological, morphological and behavioural adaptations to low temperatures. The African ice rat, Otomys sloggetti robertsi, which is endemic to the southern African Drakensberg and Maluti mountains above 2000m, is an interesting exception since, unlike most alpine small mammals, it does not hibernate or display torpor and is physiologically poorly adapted to low temperatures. It is a strict herbivore, feeding on a low quality diet. Ice rats do show some morphological (e.g. short tails) and behavioural (e.g. communal huddling; constructing underground burrows) adaptations, but little else is known about their biology, particularly how they maximise energy gain to meet thermoregulatory requirements, especially during cold periods. Since feeding represents the primary method of energy gain in endotherms, I studied aspects of the foraging biology of ice rats, including gut structure, foraging patterns and habitat choice. The gut structure of O. s. robertsi is well adapted for a high fibre, herbivorous diet and shows broad similarities with those of its mesic- and arid-occurring relatives. However, O. s. robertsi showed increased dimensions of several foregut organs which may be adaptations for increased energy uptake and/or poor diet quality in alpine environments. Furthermore, females had a larger stomach as well as a longer caecum, small and large intestine in summer than in winter but the gut of males was unaffected; such sexual asymmetry may be related to increased energy requirements of females during pregnancy and lactation. Environmental influences on the aboveground behaviour of O. s. robertsi were investigated by recording the duration of behaviours as well as sequential transitions among behaviours. Ice rats spent most of their day foraging and basking, and much time was spent in their underground burrows. Seasonal comparisons revealed that ice rats spent significantly more time acquiring energy through foraging in winter, whereas they remained below ground for longer periods of time during the middle of the day in summer to escape extreme heat and solar radiation. To understand how low temperatures and predation influenced foraging patterns, the behaviour of ice rats was studied in summer and winter in a population where predators were minimal and in another population which experienced higher levels of predation. Ice rats are central place foragers that travel short distances to forage and display significant seasonal variation in their foraging patterns. In the absence of predation risk, ice rats generally returned to a central place with forage, even though returning to a burrow after foraging in winter was energetically costly. However, these costs must be weighed against the benefits of avoiding exposure to low temperatures by feeding under cover as well as the loss of collected food and possible injury associated with aggressive interactions with conspecifics. Under moderate predation pressure in both seasons, ice rats followed a central place foraging strategy to minimise predation risk, always returning to a burrow entrance with forage collected elsewhere. However, when no perceivable threat was observed, ice rats displayed ‘optimal’ foraging patterns in summer similar to those recorded in the absence of predation pressure and only returned to a burrow with forage as distance from that burrow increased, suggesting that ice rats display facultative foraging decision making in response to multiple environmental cues. The distribution of occupied ice rat burrows was correlated against several environmental factors to determine microhabitat requirements. Ice rat burrows were situated in close proximity to herbaceous and wetland plants, but away from woody vegetation, suggesting that habitat choice is related to the presence of food plants and reduction of shade, facilitating short travel distances during foraging as well as promoting basking. Despite the physiological shortcomings of ice rats, the gut structure, foraging behaviour, and habitat choice of the taxon are adapted for life in cold alpine habitats, most likely by maximising energy intake. Similarities in foraging behaviour and habitat use between O. s. robertsi with its closely-related arid-occurring relative Parotomys spp. suggest phylogenetic influences, but it is possibly more a reflection of similar phenotypic responses to the extreme habitats inhabited by these otomyines.

Thesis (MSc)--University of Stellenbosch, 2010. / ENGLISH ABSTRACT: This study examines the phylogeography of the southern African vlei rat, Otomys irroratus using the mtDNA cyt b gene and chromosomal data derived using G-, and C-banding, Ag-NOR staining and fluorescence in situ hybridization (FISH using flow sorts of Myotomys unisulcatus). A total of N = 102 specimens were used from the Western Cape, Eastern Cape, Northern Cape, Free State, Mpumalanga and KwaZulu-Natal provinces of South Africa. Of the N = 102, N = 55 comprised fresh material while N = 47 comprises museum material obtained from the Durban Natural Science Museum of South Africa. Cytogentic analysis of N = 55 specimens collected from seven localities in South Africa revealed intra-specific variation resulting from two rearrangements, namely pericentric inversions and heterochromatin variation. Of the 55 specimens that were analyzed 47% contained inversions or centromeric shifts on four autosomes (OIR1, OIR4, OIR6 and OIR10) which were present singly in specimens (i.e. none of the specimens contained all four inversions concurrently). These inversions were present in both homozygous and heterozygous state over a wide geographic range suggesting that they are floating polymorphisms. Given the potential role of inversions in post-mating isolation (through production of aneuploid gametes), the prevalence of inversions as floating polymorphisms in the vlei rats suggest that they are probably retained in the population through suppression of recombination in the inverted regions of the chromosomes. In addition, differences between populations is due to the presence or absence of heterochromatic arms (and not inversions), which cause variation in the NFa (40 – 49) and supernumerary B chromosomes, resulting in the variation in diploid number (2n = 28 – 32). Analysis of N = 55 specimens revealed Ag-NORs on 7 autosomal pairs 1, 2, 5, 7, 8 and 9 proximal to the centromere on the short arm of the chromosome. Pair 8 also displayed Ag-NOR at the distal end of the long arm of the chromosome in individuals from the Free State province. Pair 3 showed two Ag- NORs occurring proximal to the centromere on the short arm and on the terminal end of the long arm, respectively. I obtained 953bp of mtDNA cyt b from fresh material and 400bp from museum material. Using maximum parsimony and Bayesian inference two main clades were retrieved. Clade A specimens occur mainly in the Western and Eastern Cape provinces of South Africa. Clade B specimens occur in the Eastern Cape, Free State, KwaZulu-Natal, Northern Cape and Mpumalanga provinces of South Africa. The mean sequence divergence between the main clades (A and B) is 7.0% and between sub-clades comprising clade B is 4.8%, while within clade A the sequence divergence was 1.91%. Nested clade analysis revealed allopatric fragmentation within O. irroratus. Chromosomal characters also support the two evolutionary lineages as clade A has pericentric inversions which occur as floating polymorphisms which are absent in clade B. Clade B in turn is fixed for a complex tandem fusion rearrangement which is absent from clade A. Divergence date estimates indicate that the two clades separated around 1.1 MYA, which coincides with climate changes since the late Pliocene/Pleistocene epochs. Cladogenesis within this species complex could therefore have been influenced by habitat fragmentation. A full taxonomic review of O. irroratus is therefore warranted by this study. / AFRIKAANSE OPSOMMING: Die suider Afrikaanse vlei rot, Otomys irroratus word gekenmerk deur fenotipiese konservatisme regoor die spesie se verspreiding en het groot chromosomale variasie met diploied chromosoom getalle wat reeks vanaf 2n = 23 tot 2n = 32. Hierdie variasie binne O. irroratus het gelei tot die beskrywing van drie chromosomale groupe naamlik die A sitotipe wat gekenmerk word deur 'n akrosentriese komplement. Die tweede groep wat die B sitotipe genoem word besit ten minste agt chromosoom pare met heterokromatiese kort arms, onderwyl die derde group (die C sitotipe) vier chromosoom pare het met heterokromatiese kort arms. Hierdie studie bestudeer die bevolkings genetika struktuur van O. irroratus deur 102 monsters te analiseer wat gekollekteer was regoor die spesie se verspreiding binne Suid-Afrika en die mitochondriale merker sitokroom b sowel as chromosoom fluoressent hibridisasie te gebruik. Ek het 55 monsters van sewe lokaliteite binne Suid-Afrika sitogeneties geanaliseer deur gebruik te maak van G- en C-bandbepaling asook die hibridisasie patrone geproduseer deur die vloeisorteerde chromosoome van Myotomys unisulcatus. Die analise het gewys dat 47% van die monsters perisentromeriese inversies besit het, wat slegs aangetref was of die outosome OIR1, OIR4, OIR6 en OIR10. Hierdie inversies was nooit almal teenwoordig binne dieselfde monster nie en was gevind in beide heterosigotiese en homosigotiese vorm. Die inversies kom ook voor oor 'n wye verspreiding wat daarop aandui dat dit swerwende polymorfisme is. Omdat inversies lei tot die produksie van aneuploiede gamete speel hulle 'n belangrike rol in post-parings reproduktiewe isolasie, die verskyning van swerwende inversies binne vlei rotte dui dus daarop dat hulle onderhou word binne populasie verband deur die onderdrukking van rekombinasie in die gedeeltes van die chromosoom. Verdere verskille tussen populasies behels die voorkoms of afwesigheid van heterochromatiese kort arms wat (nie inversies) wat lei tot die variasies in die Nfa (40 – 49). Die variasie in diploied getal (2n = 28 – 32) is eksklusief as gevolg van B chromosoome. Ag-NOR banding het ook gewys dat daar twee evolusionêre lyne binne O. irroratus voorkom. Verder het filogenetiese analise van al die monsters verkryg deur volgorde-bepaling met behulp van maksimale parsimonie en Bayesian afleiding twee klades geidentifiseer. Klade A diere kom voor in die Wes en Oos-Kaap provinsies van Suid-Afrika terwyl klade B diere voorkom in die Oos-Kaap, Vrystaat, KwaZulu-Natal, Noord-Kaap en Mpumalanga provinsies onderskeidelik van Suid-Afrika. Die gemiddelde volgorde-bepalings verskille beloop 7% tussen die twee hoof klades (A en B) en tussen sub-klades 4.8%, terwyl binne klade A die verskille slegs 1.91% beloop het. Analise van die verwantskap tussen die klades het gewys dat allopatriese fragmentasie heel waarskynlik gelei het tot die populasie genetiese struktuur binne O. irroratus. Chromosoom karakters onderskraag die twee evolusionêre lyne waar klade A slegs perisentriese inversies besit wat swerwend wat ontbreek in klade B. Klade B op sy beurt besit 'n komplekse tandemme fusie wat glad nie voorkom in klade A nie. Molekulêre datering het verder gewys dat die twee klades omtrent 1.1 miljoen jaar gelede versprei het, wat ooreenstem met die klimaats veranderinge wat sedert die Peioceen en Pleistoceen plaasgevind het. Klade vorming binne die spesies komples kan daarom as gevolg van habitat fragmentasie plaasgevind het. Hierdie studie dus noodsaak 'n volle taksonomiese ondersoek van O. irroratus ten einde vas te stel hoeveel spesies binne die komplex voorkom.

The ecology and life history of the vlei rat, Otomys irroratus (Brants, 1827), were studied in a population on the Van Riebeeck Nature Reserve near Pretoria. Two main procedures were used to collect the basic information and material for the project. First, a permanent live-trapping grid was established where 333 animals were captured, marked, released, and recaptured over a period of 26 months, Second, snap-trapping and live-trapping were conducted elsewhere in the study area for supplementary material. Because Otomys angoniensis Wroughton, 1906, a sibling species of 0. irroratus, also occurred in the study area and grid, it was necessary to define the differences in morphology and ecological distribution between the two species. The ecology and life history of 0. irroratus are described and discussed in regard to the following major topics: taxonomy and morphology, distribution, population dynamics, reproduction, postnatal growth and development, activity, behavior, and economic importance. In addition to the presently used means of distinguishing 0. irroratus and 0. angoniensis, it was found that the hind foot length of the two species differed, being 29-34 mm in 0. irroratus and 25-28 mm in O. angoniensis. The baculum of the two species was also found to be distinct in both shape and size. In Southern Africa 0. irroratus occurs primarily in the grassland subregion of the Southern Savanna biotic zone, while O. angoniensis occurs primarily in the woodland subregion of the same biotic zone. The preferred habitats of the two species on the study grid were determined. There was little overlap of niches and each species had a high degree of association with a different veld type, O. irroratus being associated with the more mesic habitat. The population size of O. irroratus reached a peak in May and a low in September. The population also fluctuated considerably from one year to the next, with rainfall possibly being the main contributing cause. The ratio of juveniles, subadults, and adults fluctuated primarily in respect to the season when the young were born. The sex ratio did not depart significantly from 1:1. Males comprised 49,5 per cent of the total and females 50,5 per cent. The rate of disappearance after one month from first capture was 41 per cent, indicating that a large number of transients and individuals dispersing from their birth site were involved. The overall rate of disappearance, excluding the high first month rate of disappearance, was 3,1 per cent per month. The mortality rate appeared to be at its highest between August and September when the food and cover were of very poor quality and quantity. This was also the period when males demonstrated a significant loss in body weight. The major factors causing mortality appeared to be flooding of the habitat and owl predation. Floods not only reduced the population but significantly interrupted breeding. Otomys irroratus was one of the most prominent prey species of both barn and grass owls. The major factors causing mortality appeared to be flooding of the habitat and owl predation. Floods not only reduced the population but significantly interrupted breeding. Otomys irroratus was one of the most prominent prey species of both barn and grass owls. Recapture data revealed that the mean home range size was 1 443m2, while that of males (1 730 m2) was highly significantly different (P<O,Ol) from that of females (1 252m2). Home range size decreased significantly in winter but only slightly in relation to a doubling of the population size. Of 18 individuals recaptured after a flood, 12 (66,7 per cent) had returned to their previously determined home range. Despite a small mean litter size (2,33) and relatively long gestation period (about 40 days), the long breeding season (nine months) and precocial birth, rapid development, and nipple-clinging behavior of the young together give O. irroratus a good reproductive potential. Several litters of young were reared. They are precocial at birth and development proceeds rapidly. At birth the incisors are erupted, enabling the young to cling firmly to the nipples of the mother, thereby reducing mortality losses. Most adult behavior patterns are developed before weaning at 13 days of age. Sexual maturity is reached at approximately three months of age. Otomys irroratus is primarily crepuscular, but activity tests conducted in the field and laboratory indicated some activitv throughout the day and night. Individual and social behavior are described and discussed. The vlei rat is shy and retiring in captivity and in nature is not easily captured by the use of snap-traps. Interactions of adults were tested and they were found to be antisocial, with intrasexual aggression occurring when caged. Complex threat and communication patterns exist, a feature of asocial behavior. Mating failed to occur in captivity, probably as a result of their antisocial nature. Marking behavior is very distinctive and, combined with urination and possibly defecation, would appear to be useful in delineating territories. It would also appear from their social habits, marking behavior, and considerable overlap of home ranges that their interactions with conspecifics in nature are represented by a dominance hierarchy. The influence of O. irroratus upon the environment was found to be slight. The species serves as a common prey item for a number of predators and was found to harbor several endo- and ectoparasites of public health importance. / Thesis (DSc)--University of Pretoria, 1973. / gm2013 / Zoology and Entomology / Unrestricted

Thesis (MSc (Botany and Zoology))--Unkiversity of Stellenbosch, 2009. / Phylogeographic genetic structure has been documented for a number of southern African terrestrial taxa. Information regarding geographic population genetic structuring in multiple taxa, with differing life histories, can provide insights into abiotic processes such as vicariance. A fragment of the cytochrome b mitochondrial DNA gene of a plains-dwelling species, Otomys unisulcatus, was sequenced and analysed. Two closely related geographic assemblages were found. The first assemblage (lowland group) contains populations from both the eastern and western parts of the species range, and the second comprises populations from the Little Karoo (central group). The lowland group was shown to be in a state of population expansion after a relatively recent mitochondrial DNA (mtDNA) coalescence, while the genetic signature of the central assemblage was characterized by more genetic diversity indicative of an older lineage/genetic refuge. Areas of higher elevation (namely mountain ranges) appeared to be the main factor limiting gene flow between these two groups. Aridification cycles due to glacial maximum periods probably resulted in increased dispersal leading to the widespread distribution of common haplotypes throughout the lowland group. Morphological variation in skull shape and size has been shown to follow environmental clines in some rodents. Geometric morphometric analyses on the ventral and dorsal views of the craniums of O. unisulcatus were utilised to test whether the population groupings obtained in the genetic analyses would be recovered by morphometric analyses. In addition, it was also investigated which of the environmental factors investigated influenced skull shape and size. The genetic groupings were not recovered for either the cranial shape or size. Size variation in the females correlated positively with annual rainfall, and so by proxy with habitat productivity, indicating that females which inhabited areas with lower rainfall would be larger. The significant relationship between females’ centroid sizes and rainfall was thought to be as a result of the increased nutrient requirement by this gender in the production of offspring. The males did not show a significant correlation between any of the environmental variables and centroid size. There was a significant difference between the skull shapes of the genders, further verifying the sexual dimorphism in the species. Three major clusters were found (according to cranium shape) using a Two-Block Partial Least Squares Analysis (2B-PLS), which relate to the biome boundaries within the species’ range. Variations in shape were attributed to the varying needs for strong masticatory muscles resulting from differing diets. The skull shapes of specimens occurring along the escarpment were intermediate between the first two clusters. Cranial shape in the male dorsal view dataset was significantly correlated with the environmental variables block, possibly due to the much lower minimum temperature in the Sutherland population (a population which was not included in the female analyses). It was concluded that differing diets of individuals in the respective biomes influenced the shape of the cranium of both genders. The sexual dimorphism in the cranium shapes may be as a result of the females digging tunnels (using their teeth) underneath the stick nests. Otomys unisulcatus show high levels of phenotypic plasticity throughout the range and it thus appears that the species can adapt fast to the different environmental variables.

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