Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: As the pace of climate change has begun to accelerate so too has it become clear that the direct impacts thereof are likely to have profound consequences for many island systems. Moreover, it has also been suggested that climate change will exacerbate the effects of many invasive species, so further impacting both diversity and ecosystem functioning. Forecasts for such interactions have been most pronounced for the Southern Ocean islands, which are home to a wide variety of endemic species. This thesis is about such interactions and their specific impacts on a key endemic, the black-faced sheathbill (Chionis minor) on the Prince Edward Islands. Of increasing concern is how invasive rodent populations in the Southern Ocean may be responding to global climate change, as ameliorating conditions on these islands are forecast to decrease thermal and resource restrictions on rodents. However, firm evidence for changing rodent populations in response to climate change, and demonstrations of associated impacts on the terrestrial environment, are entirely absent for the region. In Chapter 2 of this thesis, these relationships are explored for invasive house mice (Mus musculus) on Marion Island. Using spatially explicit capture-recapture modeling, it is determined that mouse populations across a range of habitats have increased over time. Owing to an extended breeding season, made possible by ameliorating conditions brought on by climate change, the total number of mice on the island at annual peak density more than doubled over the past decade. It is also demonstrated that mice directly reduce invertebrate densities, with biomass losses up to two orders of magnitude in some habitats. Because of the importance of invertebrates to nutrient cycling on the island, such changes are likely to have significant ecosystem-level impacts. In Chapter 3 the focus expands to examine how increasing mouse impacts and other outcomes of climate change are affecting the ecology of the black-faced sheathbill. It has been established that invasive house mice are capable of suppressing the populations of several seabird species in the Southern Ocean. However, mouse impacts on the region’s few island endemic land-birds remain largely unexplored. Further, a significant effect of climate change may be realized by altering interspecific interactions, specifically food webs. A significant portion of sheathbill diets is derived from rockhopper penguins, a species currently under a climate-change-driven decline, which may have significant effects on sheathbills. The study found that terrestrial invertebrates are no longer a significant prey resource for sheathbills on Marion Island, and that sheathbills have effectively been displaced from a formerly important winter food resource by mice. In response, the number of sheathbills foraging in king penguin colonies increased. Moreover, a reduced rockhopper penguin population lead to significant declines in both the number and proportion of sheathbills foraging in rockhopper penguin colonies. The sum result was a significant decline in the body condition of female sheathbills. Rather than decrease reproductive output, sheathbills responded by decreasing clutch size and producing significantly fewer male nestlings. While population estimates did not detect a reduction in the number of sheathbills, population projections suggest that the population is in decline, with the reproductive population declining faster than the absolute population. There is need for greater study of island species, as for even relatively well-studied taxa such as birds many aspects of ecology remain significantly less studied when compared to species occurring on continents. For example, basal metabolic rate (BMR) is a fundamental characteristic of all endotherms, yet only a handful of island birds have had their BMR measured, and fewer still to a level that allows intraspecific analysis. In Chapter 4 the BMR of black-faced sheathbills on Marion Island was measured to determine whether the unique phylogenetic position and ecology of sheathbills equate to a unique BMR when allometrically compared to other birds. It was found that the BMR of sheathbills is typical for a bird of its size. However, significant intraspecific variation was found to occur, with differences in habitat quality a likely driver. The results of the study show that the combined effects of climate change and invasive species can have significant consequences for terrestrial endemics in the Southern Ocean. Further, the long-term changes observed in sheathbills make clear the need for improved documentation and study of island species in general, as many of the responses observed in this study are significant but subtle and would not have been evident without detailed knowledge of species ecology and vital rates. Giving greater focus to insular biota is imperative to understanding their current status and ecology as well as establishing a barometer against which further global change can be measured and mitigation measures evaluated. Specific conservation responses for the black-faced sheathbill on Marion Island include the provision of nest boxes at king penguin colonies, and eradication of house mice. The latter would have long-term benefits for the species, invertebrates, ecosystem functioning generally, and likely also for important seabirds such as several species of albatrosses whose chicks are being increasingly preyed on by mice. Eradication would, however, be difficult and expensive, and with substantial potential non-target effects, including on sheathbills, that would have to be carefully managed. In the absence of local mouse eradication, and with ongoing climate change, specific management of the sheathbill population through the provision of supplementary nesting sites seems the most appropriate conservation action. It should therefore be examined in small-scale trials to ascertain the likelihood of unintended consequences. Importantly, the maintenance of Prince Edward Island as largely free of invasive species is key to the conservation of the local black-faced sheathbill subspecies, Chionis minor marionensis, endemic to the Prince Edward Island group. / AFRIKAANSE OPSOMMING: Soos die tempo van klimaatsverandering begin om te versnel, het dit ook duidelik geword dat die direkte impak daarvan waarskynlik ernstige gevolge vir baie eilande gaan hê. Verder word dit is ook voorgestel dat klimaatsverandering die gevolge van baie indringerspesies sal vererger, so ʼn verdere impak het op beide diversiteit en die funksionering van die ekosisteem. Voorspellings vir sulke interaksies is die meeste uitgespreek vir die Suidelike Oseaan-eilande, wat ook die tuiste van 'n wye verskeidenheid van endemiese spesies is. Hierdie tesis is oor sulke interaksies en hul spesifieke impak op 'n sleutel endemiese spesie is, die swart gesig skedebek (Chionis minor) op die Prince Edward-eilande. ʼn Groter bron van bekommernis is hoe uitheemse knaagdier bevolkings in die Suidelike Oseaan kan reageer teenoor globale klimaatsverandering, aangesien toestande op die eilande voorspel word om hitte en hulpbron beperkings vir knaagdiere te verminder. Maar, ferm bewyse vir die verandering van knaagdier bevolkings in reaksie op klimaatsverandering, en demonstrasies van gepaardgaande impakte op die terrestriële omgewing, is heeltemal afwesig vir die streek. In Hoofstuk 2 van hierdie tesis, word hierdie verhoudings ondersoek vir indringende huis muise (Mus musculus) op Marion-eiland. Ruimtelik vang-terugvang modelle word gebruik om vas te stel dat die muis bevolkings oor 'n verskeidenheid van habitatte mettertyd toegeneem het. As gevolg van 'n uitgebreide broeiseisoen as gevolg van die verligting van toestande gebring deur klimaatsverandering, het die totale aantal muise op die eiland by die jaarlikse hoogtepunt digtheid meer as verdubbel oor die afgelope dekade. Dit is ook getoon dat muise die digtheid van ongewerweldes direk verminder het, met biomassa verliese tot twee ordes in sommige habitatte. As gevolg van die belangrikheid van die ongewerweldes vir voedingstof sirkulering op die eiland, behoort sulke veranderinge waarskynlik 'n beduidende ekosisteem-vlak impak te hê. In Hoofstuk 3 word die fokus verbreed om te sien hoe die verhoging van die muis impakte en ander uitkomste van klimaatsverandering die ekologie van die swart gesig skedebek beïnvloed. Daar is vasgestel dat indringende huis muise in staat is om die bevolkings van verskeie spesies seevoëls te onderdruk in die Suidelike Oseaan. Maar die muis impak op die streek se paar eiland endemiese land voëls bly grootliks onverken. Verder kan 'n beduidende uitwerking van klimaatsverandering verwesenlik word deur die wysiging van interspesifieke interaksies, veral voedselwebbe. 'n Beduidende gedeelte van skedebek dieet word gekry van Geelkuifpikkewyne, 'n spesie wat tans onder 'n klimaat-veranderinggedrewe agteruitgang is, wat ook 'n beduidende uitwerking het op die skedebek. Die studie het gevind dat terrestriële ongewerweldes nie meer 'n beduidende prooi hulpbron vir die skedebek op Marion-eiland is nie, en dat die skedebek effektief is verplaas uit 'n voorheen belangrike winter kos hulpbron deur muise. In reaksie hierop het die aantal skedebekke wat kos soek in die koning pikkewyn kolonies toegeneem. Verder, 'n verlaagde Geelkuifpikkewyn bevolking lei tot 'n beduidende afname in beide die aantal en persentasie van skedebekke wat kos soek in Geelkuifpikkewyn kolonies. Die gevolg was 'n beduidende afname in die liggaamstoestand van die vroulike skedebekke. Eerder as ʼn afname van reproduksie, het skedebekke gereageer deur 'n vermindering in die aantal eiers en produseer aansienlik minder manlike kuikens. Terwyl bevolking skattings nie 'n afname in die aantal skedebekke kan vind nie, dui bevolking projeksies daarop dat die bevolking besig is om af te neem, met die voortplanting bevolking wat vinniger daal as die absolute bevolking. Daar is 'n behoefte vir 'n groter studie van eiland spesies, omdat selfs vir betreklik goed bestudeerde groepe soos voëls baie aspekte van die ekologie aansienlik minder bestudeer bly in vergelyking met spesies op die vastelande. Byvoorbeeld, basale metaboliese tempo (BMT) is 'n fundamentele kenmerk van alle endotermiese diere, maar net 'n handjievol van die eiland voëls het hul BMT laat meet, en nog minder tot 'n vlak wat dit moontlik maak intraspesifieke analise. In Hoofstuk 4 was die BMT van die swart gesig skedebek op Marion-eiland gemeet om te bepaal of die unieke filogenetiese posisie en ekologie van skedebekke gelyk aan 'n unieke BMT wanneer allometries vergelyk word met ander voëls. Daar is gevind dat die BMT van skedebekke tipies is vir 'n voël van sy grootte. Daar is egter belangrike intraspesifieke variasie gevind, met verskille in habitat kwaliteit as 'n waarskynlike verduideliking. Die resultate van die studie toon dat die gekombineerde effek van klimaatsverandering en indringerspesies beduidende gevolge vir terrestriele inheemse spesies in die Suidelike Oseaan kan hê. Verder maak die lang-termyn veranderinge waargeneem in skedebekke dit duidelik dat die behoefte aan verbeterde dokumentasie en studie van die eiland spesies in die algemeen, omdat baie van die reaksies waargeneem in hierdie studie betekenisvol is, maar subtiel en sou nie gewees het sonder gedetailleerde kennis van die spesies ekologie van die spesie nie. Om ʼn groter fokus op die insulêre biota te plaas is noodsaaklik om hul huidige status en die ekologie te begryp, sowel as om 'n barometer waarteen verdere globale verandering gemeet kan word en versagtende maatreëls geëvalueer. Spesifieke bewaring antwoorde vir die swart gesig skedebek op Marion-eiland sluit in die voorsiening van nes bokse by koning pikkewyne, en die uitwissing van huis muise. Laasgenoemde sou lang-termyn voordele vir die spesie en ongewerweldes hê, asook funksionering van die ekosisteem in die algemeen, en waarskynlik ook vir belangrike seevoëls soos verskeie spesies van albatrosse wie se kuikens toenemend geëet word deur muise. Uitwissing sou egter moeilik en duur wees, en het 'n aansienlike potensiaal vir nieteiken effekte, insluitend op skedebekke, wat sal versigtig moet bestuur word. In die afwesigheid van plaaslike muis uitwissing, en met voortdurende verandering van die klimaat, spesifieke bestuur van die skedebek bevolking deur die voorsiening van aanvullende broeiplekke blyk die mees geskikte bewaringsaksie. Dit moet dus ondersoek word in 'n kleinskaal proewe om die waarskynlikheid van onbedoelde gevolge te bepaal. Wat belangrik is die instandhouding van Prince Edward Eiland as grootliks vry van indringerspesies en is die sleutel tot die bewaring van die plaaslike swart gesig skedebek subspesie, Chionis minor marionensis, endemies aan die Prince Edward Eiland groep.

Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: The phenotype of an individual has often been used as the descriminating factor in distinguishing species. However, with the advent of more precise molecular techniques, the genotype of species is increasingly being used as the preferred method in taxonomic classifications. Many taxa have recently been demonstrated to be incongruent in terms of their genetic and morphological groupings, and this may due to the influence that the environment may have on the morphological and functional aspects of a species. Selective pressures often act upon the performance of a species within a particular habitat first, and then selection for the morphological characters that allow for optimal performance occurs. Should genetically disparate species inhabit a particular environment, convergence in morphologies and performance may evolve. Historically, lizard species descriptions were based primarily on external morphologies, and thus misclassfication of species may have occurred due to mistakenly grouping species with convergent morphologies together. In the current dissertation, the links between morphology, performance capacities, diet and behaviour is explored in comparison to the environment and genetic relationships of southern African lacertid lizards. The performance capacities and associated morphological traits were expected to be more closely linked with the environment, and not closely linked with genetic relationships. To investigate these expectations, a multidisciplinary approach was taken, and genetic, morphological and performance analyses were done and compared with dietary behavioural and environmental analyses. In the first chapter, the link between habitat openness and the lizard bauplans is investigated and the presence of convergent morphologies within this group of lizards is uncovered. These convergences are shown to have resulted in misclassification of two lacertid species, and taxonomic revisions within the family are discussed. The second chapter explores the link between performance and associated morphological traits, and the dietary composition of the members of the Nucras genus. The third chapter identifies the link between the predator escape strategies employed by the members of the Meroles genus, and their morphologies and performance capacities. The fourth chapter explores the intraspecific, inter-population differences in morphologies and investigates the link between the morphological groupings and the population genetic groupings within Pedioplanis lineoocellata. The final chapter identifies whether adaptation to a novel habitat can occur over a relatively short period of time, and the morphological traits, functional aspects, and population genetic structure is investigated in conjunction with environmental analyses of vegetation and substrate between the populations of Meroles knoxii. It was concluded that the morphological and functional aspects of the southern African lacertid lizards are more closely related to the environment, particularly the microhabitat structure, than to their genetic relationships, and that future work using this group of lizards should involve a multidisplinary approach as different selective pressures are playing a role in shaping the morphologies and performance capacities of these lizards, compared to those that are acting upon the genotypes of the lizards. / AFRIKAANSE OPSOMMING: Die fenotipe van 'n individu is dikwels gebruik as die diskriminerende faktor in kenmerkende spesies. Maar, met die ontwikkeling van meer akkurate molekulêre tegnieke, word die genotipe van spesies toenemend gebruik as die voorkeur-metode in taksonomiese klassifikasie. Die onversoenbaarheid van genetiese en morfologiese eienskappe kom voor in ‘n verskeidenheid taksa, dit kan wees as gevolg van die invloed wat die omgewing het op die morfologiese en funksionele aspekte van ‘n spesie. Selektiewe druk beїnvloed dikwels doeltreffende funktionaliteit van 'n spesie in 'n bepaalde habitat eerste, en gevolglik word morfologiese karakters wat voorsiening maak vir optimale funktionaliteit geselekteer. Indien geneties uiteenlopende spesies woon in 'n bepaalde omgewing, kan konvergensie in morfologie en soortgelyke werksverrigtinge ontwikkel. Histories, is akkedis spesiesbeskrywings hoofsaaklik gebaseer op eksterne morfologieë, en kan dus misklassifikasie tot gevolg hê wat kan lei tot foutiewe taksonomie van spesies met konvergente morfologieë. In die huidige verhandeling, is die verband tussen die morfologie, werksverrigtingsvermoë, dieët en gedrag ondersoek, in vergelyking met die omgewing en die genetiese verwantskappe van Suider-Afrikaanse sandakkedisse. Die werksverrigtingsvermoë en gepaardgaande morfologiese eienskappe word verwag om te meer verband te hou met die omgewing, en dus nie in noue verband te wees met die genetiese verwantskappe nie. Om hierdie verwagtinge te ondersoek, is 'n multi-dissiplinêre benadering geneem, en genetiese, morfologiese en werksverrigtingontledings is gedoen in vergelyking met dieët, gedrags-en omgewings-ontleding. In die eerste hoofstuk, is die skakel tussen die habitat openheid en die akkedis bauplans ondersoek en die teenwoordigheid van konvergente morfologieë binne hierdie groep akkedisse word ten toon gestel. Hierdie konvergensies het gelei tot foutiewe klassifikasie van twee sandspesies, en taksonomiese hersiening binne die gesin word bespreek. Die tweede hoofstuk ondersoek die verband tussen werksverrigting en gepaardgaande morfologiese eienskappe, en die samestelling van die dieët van die lede van die Nucras genus. Die derde hoofstuk identifiseer die verband tussen die roofdier ontsnapping strategieë, morfologieë en werksverrigtingsvermoë van die Meroles genus. Die vierde hoofstuk ondersoek die intraspesifieke, inter-bevolkingsverskille in morfologieë en ondersoek die verband tussen die morfologiese groepe en die bevolking genetiese groepe binne die Pedioplanis lineoocellata spesies kompleks. Die finale hoofstuk identifiseer hoe die aanpassings na 'n nuwe habitat kan plaasvind oor 'n relatief kort tydperk, en die morfologiese eienskappe, funksionele aspekte en die bevolking genetiese struktuur word ondersoek in vergelyking met die omgewingsanalise van plantegroei en substraat tussen die bevolkings van Meroles knoxii. Die gevolgtrekking is dat die morfologiese en funksionele aspekte van die Suider- Afrikaanse sandakkedisse nader verwant is aan die omgewing, veral die mikrohabitat struktuur, as aan hul genetiese verwantskappe. Toekomstige werk op hierdie groep akkedisse moet ‘n multidisiplinêre benadering behels siende dat verskillende selektiewe drukke 'n rol speel in die vorming van die morfologie en werksverrigtingsvermoë van hierdie akkedisse, in vergelyking met selektiewe drukke wat die genotipes van die akkedisse beinvloed.

Thesis (PhD)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Freshwater organisms, such as crabs (Crustacea: Decapoda: Brachyura), are useful in studies examining inland historical biogeographic patterns and speciation because they are isolated to specific drainage systems, which often serve as barriers to gene flow. The Afrotropical freshwater crab fauna (Potamonautidae) present ideal organisms for investigating hypothesis relating to evolutionary histories because they occur on continental Africa (sub-Sahara) and islands. However, there is a great deal of undiscovered freshwater crab diversity, especially with the prevalence of undiscovered cryptic lineages, which are poorly studied among freshwater crabs, leading to uncertain regional diversity. In this research, multiple genetic (mt- and nuDNA) markers were used to infer the phylogenetic relationships and the biogeographical histories of the Afrotropical freshwater crab superfamily, Potamonautidae. Divergence time estimations were used to infer biogeographic histories, to ascertain whether speciation could be linked to past geologic and / or climatic events. Two widely distributed Potamonautes species complexes were targeted for the investigation of regional cryptic species diversity. In Chapter 2, the intraspecific phylogenetic variability within Potamonautes perlatus sensu lato occurring on the Cape Fold Mountain range (South Africa) was examined, with sampling localities occurring in western- and southern flowing drainages. Previous research suggested possible cryptic speciation within this species complex; however, no tangible inferences could be made because of analytical constraints. Two major clades were recovered: one corresponding to western flowing drainages and another to southern flowing drainages. Moreover, three cryptic lineages were recovered: P. perlatus sensu stricto, restricted to western flowing drainages, and two geographically discrete novel cryptic lineages from the southern flowing drainages, described as P. barbarai sp. nov and P. barnardi sp. nov., with divergence (±2.61 Mya) linked to Pleistocene climatic events. Subsequent to the recovery of the two novel lineages from the Cape Fold Mountain range, the Pleistocene climatic events. Subsequent to the recovery of the two novel lineages from the Cape Fold Mountain range, the revision of the P. clarus / P. depressus species complex from the Tugela and uMkomazi drainages (Drakensberg Mountain range, South Africa) was conducted. This species complex was previously found to comprise at least five cryptic lineages (Chapter 3). A coalescent multilocus (three mt- and three nuDNA) Bayesian species delimitation method was used, and an additional three cryptic lineages were recovered, bringing the total to eight species (two already described as P. clarus and P. depressus), with divergence having occurred approximately 10.3 Mya. Following the recent discovery of novel freshwater crab lineages in the mountainous areas of Mozambique and Malawi, a sampling trip to the Zimbabwean Highlands was undertaken, where a novel freshwater crab species was discovered and described as P. mutareensis, highlighting the need to sample high-lying regions (Chapter 4). Furthermore, two additional novel lineages from Mozambique (P. bellarussus sp. nov.) and the Mpumalanga Province in South Africa (P. flavusjo sp. nov) were described (Chapter 5). In Chapter 6, increased taxon sampling, with additional specimens acquired from various museums and personal collections was used to obtain a better resolution of the phylogeny of the Afrotropical Potamonautidae and to infer the ancestral affinities of the two sub-families, Deckeniinae and Potamonautinae. The Potamonautidae were found to have speciated eastward from West Africa, with a late Cretaceous divergence (±107 – 96.04 Mya). The Potamonautinae originated in West Africa (three genera), while the paraphyletic Potamonautes and Platythelphusa had East African affinities. Potamonautes was not monophyletic, comprising several fragmented geographic clades, which may suggest that this genus requires revision. Nevertheless, the overall speciation within the Potamonautidae reflects past geological and climatic events, such as rifting and uplift episodes and the contraction of forests, which occurred from the Tertiary onwards.

Thesis (PhD (Botany and Zoology)) -- University of Stellenbosch, 2008. / Afrosoricida is a 65 million years old (my) eutherian order that together with the Tubulidentata (aardvark) and Macroscelidea (elephant shrews) form the Afroinsectiphillia, a subclade of Afrotheria. It includes two families – Chrysochloridae (nine genera of golden moles) and Tenrecidae (11 genera of tenrecs) – that collectively represent ~59% of the afrotherian generic diversity. This study presents the first comprehensive cytogenetic comparison between members of these two families (seven genera and 11 species/subspecies of golden moles, and two genera and 11 species of tenrecs) using G- and C-banding and chromosome painting. All detected rearrangements are interpreted in a strict cladistic framework. In the case of Chrysochloridae, this provides evidence for a sister relationship between Chrysochloris and Cryptochloris, the monophyly of the Amblysomus genus, and for the elevation of A. hottentotus meesteri to specific rank. The detection of telomeric-like repeats in the centromeres of all chromosomes of the Amblysomus species/subspecies but not in those of A. h. meesteri further strengthens its recognition as a distinct species. Parsimony analysis of chromosomal rearrangements within Tenrecidae, the second Afrotheria assemblage studied, showed that rearrangements which could be interpreted as Whole Arm Reciprocal Translocations (WARTs) were more likely to be the result of Robertsonian translocations. Four interspecific associations are recovered within Microgale that are consistent with morphological and molecular characters. It was also possible to infer ancestral karyotypes for the Chrysochloridae, Oryzorictinae and the two tenrecid genera, Oryzorictes and Microgale. Given the relatively high karyotypic diversity observed among some Microgale species and the prevailing debates on chromosomal evolution and regional palaeoenvironmental fluctuations, it is suggested that Microgale be added to the list of taxa where structural rearrangements are likely to have played a role in speciation. Using Genbank sequences and a relaxed Bayesian clock method, we estimate the age of the family Chrysochloridae at ~28.5 my and that of the genus Microgale at ~9.9 my. Based on these dates, it can be shown that most of the evolutionary branches are characterized by a slow rate of chromosomal change, but that markedly high rates are observed in some Microgale species and to a lesser extent in the lineage leading to A. robustus. The rates of chromosomal evolution and other cytogenetic features highlighted in this study are discussed in light of recent advances in understanding the molecular mechanims that underpin changes to genomic architecture.

Thesis (DSc (Botany and Zoology))—-Stellenbosch University, 2008. / The south-western Cape is a unique region of southern Africa with regards to generally low soil nutrient status, winter rainfall and unusually species-rich temperate vegetation. This region supported a diverse large herbivore (> 20 kg) assemblage at the time of permanent European settlement (1652). The lowlands to the west and east of the Kogelberg supported populations of African elephant, black rhino, hippopotamus, eland, Cape mountain and plain zebra, ostrich, red hartebeest, and grey rhebuck. The eastern lowlands also supported three additional ruminant grazer species - the African buffalo, bontebok, and blue antelope. The fate of these herbivores changed rapidly after European settlement. Today the few remaining species are restricted to a few reserves scattered across the lowlands. This is, however, changing with a rapid growth in the wildlife industry that is accompanied by the reintroduction of wild animals into endangered and fragmented lowland areas. These reintroductions, together with the realisation that we have limited knowledge of the functional role of native large herbivores in the fynbos ecosystem, provided the rationale for this study. Questions on large herbivore ecology were addressed at three different spatial scales. At the biome level, the reason for the absence of three ruminant grazers from the western lowlands was investigated. It was hypothesised that the absence of adequate high quality fodder in the form of C4-grass during the hot and dry summers made it impossible for buffalo, blue antelope, and bontebok to survive on the western lowlands. The results from carbon isotope analysis of late prehistoric, historic and contemporary large herbivore remains were consistent to this Summer Nutritional Stress Hypothesis. I found that eland, elephant, grey rhebuck, ostrich, and red hartebeest (all species that historically occurred in both coastal lowlands) can survive with very little (< 15%) C4 grass in their diet. In contrast, bontebok utilized at least 43% C4 grass biomass in what was considered their natural habitats. At a regional level, I tested the hypothesis that the large herbivores avoid nutrient-poor sandstone, sand, and limestone fynbos shrublands in favour of the more nutrient-rich shale renosterveld habitats. Support for this Renosterveld Preference Hypothesis was found by means of dung count surveys, which showed that both eland and bontebok readily utilize renosterveld, but avoid sandstone and limestone fynbos. In the latter they only utilize grassy microhabitats such as karstic sinkhole depressions. The same hypothesis was addressed in a novel way by using strontium isotope analysis and concluded that the technique needs more refinement for it to produce reliable results. At a landscape level, interactions between fire and grazing by native large herbivores in relation to renosterveld vegetation dynamics were addressed. I conclude that the disappearance of the native herbivores probably had little bearing on the putative structural changes in renosterveld (grassland-shrubland dynamics). Support was found for the notion that a high fire frequency followed by intense grazing by livestock could have converted original renosterveld grasslands to unpalatable shrublands. Herbivory by native grazers/browsers, or the release from it, cannot by itself bring about the vegetation-state (structural) changes in renosterveld patches which had already been altered to herbivoretolerant plant communities. However, in combination with fire, the presence or absence of large herbivores can change the trajectory of the system among the alternative structural states.

Thesis (PhD (Botany and Zoology))—University of Stellenbosch, 2009. / Females of many bird species prefer to mate with males exhibiting elaborate ornamentation, which serves as an indicator of male quality. Such ornaments, called secondary sexual traits, could act as signals to females that males could confer direct and/or indirect genetic benefits (when offspring inherit superior genes), on offspring. In particular, it has been suggested that these signals relate to male ability to resist infections, as only high quality individuals are able to invest both in high immune defence and elaborate ornament expression. The ostrich (Struthio camelus) is the largest living bird and is a member of the family of flightless birds, the ratites. They are sexually dimorphic, males displaying black plumage, and a pink-coloured neck and bill; whereas females display dull-brown plumage (both sexes have white feathers). Little is known about the mating system of ostriches: they are promiscuous and in the wild, males and females have multiple partners. The communal nesting system of ostriches is unique in that only the major female and major male provide parental care, in the form of incubation and guarding the offspring until independence. Furthermore, a remarkable feature of cohorts is that offspring may differ greatly in size, and these size differences are likely to have a genetic basis arising from differing parental genotypic differences. As a trade-off between immune response and life-history traits has been documented in various bird species, I examined the relationships between male secondary sexual traits (and specifically colouration) and maternal investment; levels of immunocompetence in both parents and chicks; and chick growth. This study showed that females invest more at the egg stage in response to traits involved in the male courtship display: the colour of the neck, white and black body feathers, and the brightness of black feathers. As these traits, which are exposed during the courtship display as well as during male-male interactions, were related to male immune responses, I suggest that only high quality males will be able to display their condition optimally. Chicks with higher growth rates were found to have intermediate responses to stimulation of their humoral immune system with diphtheria and tetanus vaccines, suggesting that not only fitness benefits, but also costs are associated with mounting an immune response; and that variation in humoral responses and growth rates relates to how individuals trade off these costs and benefits. In addition, chick humoral responses were found to be related to the humoral response of both parents, but through different antibody responses (maternal responses to tetanus and paternal responses to diphtheria), suggesting that this component of the immune system is heritable. As the colouration of white feathers predicted chick growth rates, as well as a male’s ability to raise an antibody response, I suggest that this visual cue could serve as a signal to females of male humoral immunocompetence, therefore forming the basis of mate choice whereby females could increase the fitness of their offspring through higher growth rates.

Thesis (PhD (Botany and Zoology))--Stellenbosch University, 2008. / Endocrine disruption is an alteration of the chemical messaging processes in the body. The value of studies‐ and monitoring of endocrine disruption using techniques included in the field of toxicogenomics is undoubtedly supported by scientific literature over the past four decades, as is demonstrated in Chapter 1 where I review relevant literature on the topic. Clearly, well sustained bio‐monitoring will include studies both in vitro and in vivo, and very well on transcriptional and translational levels. Animals are providing good models for in vivo studies to report or monitor endocrine disruption. It is imperative though to first understand such an animal’s biology, especially its endocrine system, and characterize what is considered “normal” for a species before engaging in endocrine disrupting exposures. A multitude of studies report endocrine disruption in relation to reproductive systems, with more recent work illustrating alteration of metabolism related to thyroidogenic disruption within the last decade. It is therefore essential to consider sex determination and ‐differentiation when studying sentinel species. Apart from the obvious academic interest in the matter of sex differentiation, altered patterns of sex differentiation in certain appropriate species provide for a very convincing endpoint in monitoring estrogenic endocrine disruption. As I approach to study a potential sentinel species for the southern African subcontinent, I set forward to study aspects of endocrine disruption influencing the reproductive system in a piece‐meal manner, starting with estrogenic endocrine disruption as this is the best studied facet of the endocrine disruption hypothesis to date. Yet, one learn from vast amounts of literature that in cases where sex is not exclusively determined by the genetic fraction of an individual, a number other characteristics may very well be used to determine estrogenic disruption in ecosystems. Quantitative production of the egg yolk precursor protein (vitellogenin) resides under these characteristics, and in the proposed sentinel, South African tilapiine, Oreochromis mossambicus phenotypic sex can be altered by environmental sex determination. The present study therefore targeted firstly the product most often used in tier I screening processes, vitellogenin (VTG). Specimens of O. mossambicus were cultured for this purpose from wild breeding stock, sampled at 5 day intervals and the transcription levels of vitellogenin gene (vtg) studied in those. Hereby, Chapter 2 describes the cloning of partial vtg gene and subsequent temporal expression of vtg quantitatively in O. mossambicus. To shed light on the state of gonadal differentiation sub‐samples were subjected to histology, illustrated in Chapter 3. In addition the quantitative vtg responses has been described in this study at a transcriptional level, both of adult males and juveniles subjected to low and very high levels of natural estrogens. In addition, a 3 kb 5’ flanking region of vtg was cloned and sequenced, and several putative binding sites identified for transcription factors of vtg, including several estrogen responsive elements (EREs). These indicate the expected regulational process of vtg by estrogens. Subsequently I measured the transcription levels of the only enzyme capable of aromatizing androgens into estrogens, Cytochrome P450 19 (cyp19) as has been characterized in Chapter 3. For stable binding of an estrogen to an ERE, binding of the ligand to its specific nuclear receptor (Estrogen receptor, ESR) is required. Since E2 is known to have different mechanisms of action in vertebrates, the expression levels of the ESRs were evaluated in our sample set after cloning 3 different homologues of ESR in O. mossambicus. The results on this matter is discussed in Chapter 4 and provides in addition to data on vtg and cyp19 a platform of “normal” transcription levels of these candidate genes involved in estrogenic endocrine disruption of O. mossambicus. Ultimately, characterization of those candidate genes involved extensively in phenotypic sex, contribute to our understanding of sex determination and differentiation in this species in a small way.

Thesis (PhD (Botany and Zoology))--University of Stellenbosch, 2007. / Improved anti-predator protection has been postulated to be the primary advantage of sociality in the family Herpestidae. Therefore, the yellow mongoose, Cynictis penicillata, is considered an anomaly in the family because it may den socially with conspecifics, cooperating in the rearing of young and territory defence, but inevitably forages alone. I studied the communicative and anti-predator behaviour of a population of yellow mongooses which exhibited a lower degree of sociality than populations studied elsewhere. The yellow mongoose’s flexible social nature was evident in its vocal repertoire. Although its vocal repertoire was smaller and less context-specific than those of social mongooses, it had a large proportion (over 50%) of affiliative vocalizations, suggesting that individuals show a higher degree of cooperation than strictly solitary species. During predator encounters yellow mongooses used a simple urgency-based alarm call repertoire, indicating high and low urgency threat with two separate call types. The social environment strongly affected the alarm communication of yellow mongooses – vocal alarms were displayed almost exclusively by individuals in a group, whereas the visual alarm (a raised tail) was displayed by solitary individuals, when predators were outside the range from which they were potentially dangerous. This was a clear demonstration of the ‘audience effect’ – a phenomenon whereby animals adjust their communicative signals depending on the audience that is present. Until this study, the audience effect has only been demonstrated in obligate social species. The yellow mongoose’s social flexibility was further reflected in its territorial scent marking behaviour. In contrast to high density populations, where subordinate individuals contribute significantly to territory defence and scent marking, only the dominant male marked and defended territory borders in this low density population. Dominant males appeared to overmark the small number of cheek marks that females deposited, especially during the breeding season, which suggests that cheek marks were used in mate guarding. The yellow mongoose showed less flexibility in responses to conspecifics while foraging: the presence of group members appeared to make foragers more nervous, as individuals increased vigilance and decreased foraging success when group members were nearby. This could not be attributed to foraging competition, which happened very rarely. Yellow mongooses relied on a form of vigilance that allowed them to continue foraging while remaining alert, which contrasted with meerkats, Suricata suricatta, that had to interrupt foraging in order to be vigilant. The foraging patterns of yellow mongooses and meerkats differed markedly, and both species appeared to be inflexible in these patterns. I have proposed, therefore, that rigid vigilance patterns of vigilance are the reason why yellow mongooses forage alone, despite showing other cooperative tendencies. This study highlights that the selective forces acting on group living and group foraging are very different, and that the group-size effect – which postulates that individual vigilance declines as group size increases – may not be applicable to species adapted to solitary foraging.

Thesis (DSc)--University of Stellenbosch, 1959 / Published in the Annals of the University of Stellenbosch, Vol. 35, Sect. A, No.4 (1959) / ENGLISH ABSTRACT: The ontogeny of the cloacal region of Ascaphus is described from limited larval material (beginning approximately at the stage of hind-limb bud development). A comprehensive series of Bufo angusticeps larvae and late pre-larval embryos were used for comparison. The adult and/ or late larval conditions of the cloacal region in Ascaphus, Bufo, Bombina, Leiopelma, Rana and Xenopus arc compared. The rods of Noble supporting the cloaca in Ascaphus and the tendinous sheet connecting these with the epipubis are shown to be modifications of an interfemoral ligament present, with thickened lateral margins, in all the Anura studied. The cloacal lips differentiate early in metamorphosis in Ascaphus and Bufo and bear similar relations to the interfemoral ligament in these and other Anura, so that they are apparently homologous. The posterior part of the urodaeum is lengthened in the adult male Ascaphus to form the "tail" (phallus). The hind-limb anlagen of Ascaphus appear directly beneath the spinal myomeres and immediately behind the posterior tips of the abdominal muscle cords. In Ascaphus, Bufo and Bombina the abdominal muscles (metamerically disposed in Ascaphus and Bufo) are initially attached posteriorly to the spinal myomeres but are separated from them anteriorly. lt is probable that the mm. compressores cloacae are derived from the hind-limb anlagen. In all Anura examined, including members of all the South African families, the a. ischiadica and n. ischiadicus have a small muscle (designated m. circumflexor arteriae) associated with them; it is presumably capable of compressing the artery against the nerve. The cloacal region of Ascaphus appears to be less specialized than that of Rana and Xenopus, contrary to what is generally believed for the last two genera. Bufo, particularly and Bombina have undergone less specialization. / No Afrikaans abstract available.

Dissertation (PhD)--University of Stellenbosch, 2007. / ENGLISH ABSTRACT: South Africa, Lesotho and Swaziland are home to an endemic group of dwarf chameleons (Bradypodion). They are small, viviparous, insectivorous, arboreal lizards, found in a variety of vegetation types and climatic conditions. Previous work on Bradypodion pumilum suggests prolonged breeding and high fecundity which is very unusual for a viviparous lizard inhabiting a Mediterranean environment. It has been suggested that the alleged prolonged reproduction observed in B. pumilum may be a reproductive adaptation to life in a fire-prone habitat. In addition, Chamaesaura anguina a viviparous, arboreal grass lizard also occurs in the fire-frequent fynbos and exhibits an aseasonal female reproductive cycle with high clutch sizes; highly unusual for the Cordylidae. With the observation of two species both inhabiting a fire-driven environment and exhibiting aseasonal reproductive cycles with high fecundity, it was thought that this unpredictable environment may shape the reproductive strategies of animals inhabiting it. However, detailed reproductive data for B. pumilum were unavailable. The first aim was provide baseline reproductive data for B. pumilum and to discuss the reproductive strategy in relation to a fire-prone environment. To establish the significance of fire in the reproductive strategy of B. pumilum, reproductive data of other Bradypodion species, not inhabiting the fire-prone area was required. The second aim was to provide baseline reproductive data for Bradypodion with discussion on possible scenarios facilitating the evolution of dwarf chameleon reproduction. Bradypodion pumilum specimens were collected in monthly samples from Stellenbosch and Somerset West in the Western Cape, South Africa. Specimens of other Bradypodion species were obtained from South African museums. Data were collected for both sexes of Bradypodion, and sperm storage ability was investigated in B. pumilum. Bradypodion females all showed an aseasonal reproductive cycle with relatively high clutch sizes for their body size and the possibility of individual females producing multiple clutches per year. Male Bradypodion have sperm available the entire year round however, there appears to be an increase in sperm production in autumn and again in spring in B. pumilum. Elements of this bimodal pattern are seen in other Bradypodion species. Dwarf chameleons regardless of habitat and associated climatic conditions are thus able to reproduce through out the year. It has also been demonstrated in B. pumilum that both sexes are able to store sperm and it is expected that other Bradypodion species would posses this character. This type of reproductive strategy is highly unusual for viviparous, temperate-zone lizards. It is likely that the cooling of the climate due to the development of the Benguela current facilitated the transition to viviparity in Bradypodion. Bradypodion may be aseasonal reproducers for a number of reasons. They are of tropical ancestry, they relatively recently inhabited tropical forests, or fluctuations in climate may have caused this. Bradypodion most likely have a high reproductive output due to their intense vulnerability to predation as in other chameleon species. The proposed hypothesis that the unusual reproductive characteristics of B. pumilum (and possibly the ancestral Bradypodion) were due to inhabiting a fire-prone environment now appears an unlikely explanation. However, even if this extraordinary reproduction was not in direct response to fire, the strategy appears beneficial in this type of unpredictable environment. / AFRIKAANSE OPSOMMING: Suid-Afrika, Lesotho en Swaziland huisves ‘n endemiese groep van dwergverkleurmannetjies (Bradypodion). Hulle is klein, lewendbarende, insekvretende, arboreale akkedisse en word gevind in ‘n verskeidenheid van plantegroeitipes en klimaatsomstandighede. Vorige studies op Bradypodion pumilum dui op ‘n verlengde broeiseisoen en hoë fekunditeit, wat ongewoon is vir ‘n lewendbarende akkedis wat in ‘n Mediterreense omgewing voorkom. Daar is voorheen voorgestel dat die skynbare verlengde voortplanting in B. pumilum ‘n aanpassing tot oorlewing in hoogs brandvatbare habitat kan wees. Chamaesaura anguina is ook ‘n lewenbarende, arboreale akkedis wat in fynbos voorkom wat hoogs vatbaar is vir brande en groot werpsels produseer en ‘n aseisoenale voortplantingsiklus in wyfies toon; hierdie patroon is ongewoon vir lede van die Cordylidae. Met die waarneming dat twee species wat in ‘n brandvatbare omgewing voorkom albei aseisoenale voortplantingsiklusse en hoë fekunditeit toon, het die gedagte ontstaan dat hierdie onvoorspelbare omgewing die voortplantingstrategieë van diere wat daarin voorkom, bepaal. Gedetailleerde voortplantingsdata ontbreek egter vir B. pumilum. Die eerste doelstelling van die studie was dus om basisinligting te voorsien oor voortplanting by B. pumilum en om die voortplantingstrategie aan die hand van die brandvatbare omgewing te bespreek. Om die moontlike rol van brand in die vorming van die voortplantingstrategie van B. pumilum te ondersoek, is voortplantingsdata vir ander Bradypodion species wat nie in brandvatbare habitat voorkom nie, nodig. Die tweede doelstelling was dus om basisinligting oor voortplanting by Bradypodion in die breë in te samel, gevolg deur bespreking van moontlike scenarios in die evolusie van voortplanting by dwergverkleurmannetjies. Bradypodion pumilum eksemplare is maandeliks versamel te Stellenbosch en Somerset-wes in die Weskaap, Suid-Afrika. Eksemplare van ander Bradypodion species is vanaf Suid-Afrikaanse museums verky. Data is vir beide geslagte van Bradypodion versamel, en die vermoë tot spermstoring in B. pumilum bepaal. Bradypodion wyfies het almal ‘n aseisonale voortplantingsiklus getoon met relatief hoë werpselgroottes vir hul liggaamsgrootte en daar bestaan die moontlikheid dat individuele wyfies verskeie werpsels per jaar kan lewer. Bradypodion mannetjies produseer sperms dwarsdeur die hele jaar, maar daar blyk tog ‘n toename in spermstoring te wees in die herfs en weer in die lente in B. pumilum. Spore van hierdie bimodale patroon word in ander Bradypodion species gesien. Dwergverkleurmannetjies is dus instaat om dwardeur die jaar voort te plant, ongeag die habitat en geassosieerde klimaatsomstandighede. Daar is getoon dat beide geslagte van B. pumilum sperms kan stoor en daar word verwag dat ander Bradypodion species ook hierdie vermoë het. Hierdie tipe van voortplantingstrategie is ongewoon vir lewendbarende akkedisse van die gematigde sone. Dit is moontlik dat die ontwikkeling van ‘n koue klimaat weens die onstaan van die Benguela-stroom aanleiding gegee het tot die oorskakeling na lewendbarendheid in Bradypodion. Bradypodion mag aseisonale voortplanting toon vir ‘n aantal moontlike redes. Hulle is van tropiese oorsprong, het redelik onlangs tropiese woude betrek, of fluktuasies in klimaat kon ook die oorsaak wees. Bradypodion het waarskynlik hoë voortplantingsuitset omdat hulle besonder kwesbaar is vir predasie, soos dit die geval is by ander verkleurmannetjies. Die aanvanklike hipotese dat die ongewone voortplantingseienskappe van B. pumilum (en moontlik die voorvaderlike Bradypodion) ‘n gevolg is van lewe in ‘n hoogs brandvatbare omgewing, blyk nou ‘n onwaarskynlik te wees. Selfs as hierdie buitengewone voortplantingstrategie nie ‘n direkte gevolg van brandvatbaarheid is nie, blyk die strategie voordelig te wees vir oorlewing in hierdie onvoorspelbare omgewing.