Thesis (PhD (Botany and Zoology))--Stellenbosch University, 2011. / ENGLISH ABSTRACT: African greenbuls are an ideal model system with which to explore different hypothesis that may underlie observed patterns of lineage diversification. Among those few hypotheses amenable to falsification by phylogenetic methods concerning the diversification of the southern and east African biota, three can be singled out because of their verifiable predictions: the Plio-Pleistocene refugia, montane speciation and the gradient hypotheses. I used phylogenetic and population genetics methods to reconstruct the diversification history of three African greenbul species/species complexes (Pycnonotidae) in southern and east Africa. My study established that most of the greenbul diversification took place in Plio- Pleistocene and the primary mechanism appears to be climatic cycling, yet dispersal and vicarince too have shaped the population genetic structure. The pattern of diversification observed in the three study taxa/species complexes differs substantially and can mostly be explained by the Pleistocene refuge hypothesis. The study did not support the montane speciation hypothesis as articulated by Roy (1997) for some of the montane Andropadus taxa. Phylogeographic and population genetics analyses on the grey-olive greenbul found a close association between palaeodrainage systems and swampy areas (seeps) as an important habitat configuration for diversification of lineages restructured to these patchy habitats. Historical demographic analysis on Sombre greenbul revealved evidence for putative eastern and southern coastal forest refugia. Further, this study revealed the complex nature of East African biogeography, and two possible routes of dispersal from Albertine Rift refugia to the Eastern Arc and East African coastal forest in the Yellow-streaked greenbul complex. / AFRIKAANSE OPSOMMING: Afrika greenbuls is 'n ideale modelstelsel wat gebruik kan word om verskillende hipotese rakend die waargenome patrone van lyndiversifisering te verken. Onder dié paar hipoteses met betrekking tot die diversifisering van die suidelike en oos Afrika biota wat ontvanklik is vir vervalsing deur filogenetiese metodes, kan drie uitgesonder word as gevolg van hulle verifieerbare voorspellings: die Plio-Pleistoseen toevlugs-, bergspesiasie- en die gradiënt hipoteses. Ek gebruik filogenetiese en bevolkingsgenetiese metodes om die diversifikasiegeskiedenis van die drie Afrikaanse greenbul spesies / spesiekomplekse (Pycnonotidae) te rekonstrueer in die suidelike en oos Afrika. My studie bevind dat meeste van die greenbul diversifikasie plaasgevind het in Plio- Pleistoseen en die primêre meganisme blyk klimaatsverandering te wees alhoewel verspreiding en vikariansie ook bygedra het tot die algemene bevolkingstruktuur. Die waargenome patroon van diversifikasie in die drie studie taxa / spesiekomplekse verskil aansienlik van mekaar maar kan meestal verklaar word deur die Pleistoseen toevlugshipotese. Die studie het egter geen ondersteuning gevind vir die bergspesiasiehipotese soos verwoord deur Roy (1997) vir 'n paar van die berg Andropadus taxa nie. Filogeografiese- en bevolkingsgenetiese ontledings op die grys-olyf greenbul het 'n noue verband gevind tussen palaeodreineringstelsels en moerasgebiede (syferwater) as' n belangrike habitatdrywer vir diversifisering van lyne wat gestruktureer is rondom verbreekte habitatte. Historiese demografiese analises op die Sombre greenbul het moontlike oostelike en suidelike kuswoud heenkomes uitgewys. Hierdie studie het ook die komplekse aard van Oos- Afrika biogeografie ontbloot, asook twee moontlike roetes van verspreiding vanaf die Albertine Rif na die Oostelike Ark asook Oos-Afrika kuswoude in die geel-gestreepte greenbul-kompleks.

Thesis (PhD)--Stellenbosch University, 2013. / Australian Acacia species are an important group of invaders and are known to form dense monospecific cultures in invaded habitats. Despite the ecological and economic importance of invasive acacias, little is known about their invasive biology both from an ecological and evolutionary perspective. Molecular genetic methods have increasingly become important in identifying source populations for invasive species and determining the population genetic structure of these populations. This thesis applied molecular tools to understand the invasion ecology of Acacia pycnantha and its rhizobial symbionts as a model system of Australian Acacia introductions. Specific objectives were to: reconstruct the molecular phylogeny of invasive and native populations of populations of Acacia pycnantha and identify the native provenance of A. pycnantha; identify microsatellite markers for Acacia pycnantha and other invasive Australian acacias based on transferring microsatellite markers developed for A. mangium, A. saligna, Paraserianthes lophantha and universal chloroplast microsatellites developed from tobacco; assess the introduction dynamics of Acacia pycnantha in South Africa and identify the source populations in the species’ native range ; and determine which nitrogen fixing symbionts nodulate A. pycnantha and determine whether A. pycnantha brought its symbionts along from its native range or acquired them in the invasive range. Nuclear and chloroplast DNA sequence data were used to reconstruct phylogeographic relationships between native and invasive A. pycnantha populations. The chloroplast phylogeny showed that Australian populations of A. pycnantha are geographically structured into two previously informally recognized lineages (representing wetland and dry land forms). Habitat fragmentation is probably the result of cycles of aridity and abundant rainfall during the Pleistocene0. The invasive population in Portugal was found to be the wetland form while South African populations were found to be predominantly wetland form although some dryland forms were identified. Thirty microsatellites out of the forty nine tested microsatellites successfully amplified across all species tested (A. implexa, A. longifolia, A. melanoxylon, A. pycnantha and A. podalyriifolia). High Transfer rates varied between 85% for microsatellites developed for A. mangium to 50% for those developed in A. saligna. Although transfer rates were high only twelve microsatellites (24%) out of the fifty tested were polymorphic while the chloroplast microsatellites showed no polymorphism. The low level of polymorphic loci calls for development of more microsatellites in this genus especially for species that have high commodity value. Nuclear microsatellites revealed three genetic groupings with substantial admixture in the native range (1. wetland Victoria and South Australia populations; 2. dryland Victoria and Flinders Range population; and 3. New South Wales). Admixture in the native range may have occurred as a result of reforestation exercises. Acacia pycnantha has been widely used in rea forestation projects in Australia because of its fast growth rate and ease of germination. Admixed populations were most - likely introduced to South Africa thus establishment of A. pycnantha may have been facilitated by already admixed propagules in the invasive range. Extensive admixture in the native range made it difficult to identify source populations of invasive A. pycnantha found in South Africa. The rhizobial symbionts of A. pycnantha were identified, showing that this species utilizes a wider suite of symbionts in its invasive range than its native range and there is support for both the co-introduction and host jumping hypotheses. This creates substantial opportunities for horizontal gene transfer between previously allopatric bacterial lineages, with as yet unknown consequences for plant and bacterial invasions.

The aim of this project was to try to find the mode of action of azadirachtin in cultured cells, and to compare its cytotoxicity with some well-known phytochemical pesticides. The results presented here showed that azadirachtin was toxic to the cultured insect cells used (Sf9 and C6/36, derived respectively from Spodoptera frugiperda and Aedes albopictus) even in very low concentrations with an EC50 for the Spodoptera cells estimated at 5x10-9 M, but that the mammalian fibroblast cell line L929 was little affected except at concentrations greater than 10-4M. The other major neem terpenoids, nimbin and salannin, showed low toxicity towards the cultured cells. The neurotoxic pyrethrum showed little effect against the cultures, except for some slight stimulatory effect on growth at 10-8 M. Rotenone, known to inhibit the electron transport chain, effectively inhibited the growth of both insect and mammalian cells. Nicotine, another neurotoxic phytochemical, had little effect on the growth of the cultured cells. It was concluded that while cell growth assessment is not appropriate for all phytochemical pesticides, it is useful for those, such as azadirachtin and rotenone, whose effect is on the essential mechanisms of insect cells in general. Rotenone was used as a positive control to investigate if azadirachtin had its effect on respiration of the cells. Only at the highest feasible concentration of azadirachtin, was there a slight but significant (15%) reduction of respiration which was the same in both insect and mammalian cells. As expected, rotenone inhibited both insect and mammalian cells even at concentrations as low as 10-11 M. When the effects of azadirachtin on the cell cycle were examined by means of cell cytometry, it was shown that the compound arrested the cell-cycle in G2/M phase, and that the effect was related to the concentration. Microscopy confirmed that there was a three-fold increase in the mitotic index after 2 hours of exposure of 2x10-6 M azadirachtin. The similarity of the of the nuclear profiles and cell-cycle distribution to Sf9 cells treated with colchicine, a well-known antimitotic phytochemical, suggested there was a similarity of action between the two compounds.

This thesis describes the original and significant development of a hierarchical statistical framework in order to realign fine-scale spatial covariate data. An example of the utilisation of this framework is given within the context of biodiversity modelling. Biodiversity is of utmost importance to the correct functioning of ecosystems and the provision of services vital to humanity. Understanding of the impacts on biodiversity by environmental drivers and pressures can help appropriate responses to be taken, to mitigate, halt or reverse damage to habitats. Therefore, linking biodiversity measures with explanatory covariates in statistical models can help understand these relationships and the extent to which certain drivers and pressures are responsible for environmental change. When modelling biodiversity, the scale at which the variables are measured should be considered. Where data are measured at different scales, a situation of misalignment arises. Misaligned data may be subject to measurement error, which can influence the resultant model, if the data are not realigned. In order to realign covariate data, two transformation approaches can be implemented. The first method is to aggregate the response data to the level of the explanatory covariates. The second method is to downscale the covariate data to the response locations. This realignment process is more complex than aggregation of the response, since it requires the uncertainty estimation of the downscaled covariate predictions. The developed framework has possible further applications in fine-scale uncertainty estimation of model covariates, where the scale at which the covariates are given is coarser than that at which the response data are available. Chapter 1 provides an introduction to the main issues and challenges in the thesis: biodiversity, data measurement, modelling techniques, scale and data realignment. The three case studies used in the development of the hierarchical framework are also introduced. Data from Loch Leven on underwater plants are analysed in chapter 2. Carabid data from ten rural locations are considered in chapter 3. In the final case study in chapter 4, coverage abundance data from sites the Countryside Survey across Great Britain are modelled. In chapter 5 the data from chapter 4 are used as the impetus; a hierarchical framework for realigning covariate data is developed and a simulation is created in order to assess its performance relative to the non-realigned model. Chapter 6 provides a summary of the case studies as well as discussion of the main issues and proposals for additional development.

There is an increasing understanding of the influence seabirds have on island food webs globally, which often arises from the trans-boundary input of nutrients. Seabird-derived nutrients, primarily in the form of guano, can have significant effects on island communities by increasing primary productivity and then indirectly influencing other species. However, there are few studies looking at how the influence of seabirds permeates island food webs to higher trophic levels, in particular within the United Kingdom, which holds globally significant populations of seabirds. To understand the extent to which seabirds influence islands, the size of the seabird population must be first reliably determined. With an increasing seabird population size and density the effects of seabirds on land increases concomitantly. The Atlantic puffin Fratercula arctica is a difficult species to reliably monitor, given its underground presence from the use of burrows and its notoriously erratic attendance at colonies. This study looks firstly at a novel method to monitor the Atlantic puffin using time-lapse photography. Time-lapse photography provides a way to derive an estimate of population size from counts of individuals, by repeated photographs across a period of time with relatively low cost and from areas normally considered inaccessible. The results showed there was a significant and positive relationship between the maximum numbers of Atlantic puffins observed and the size of the population; further work is required though to reduce the error associated with population size estimates. Data from high temporal resolution time-lapse photography shows how the attendance of Atlantic puffins at the colony varies over different temporal scales. Given the variability in sampling intensity the study stresses the need for standardised sampling intensity with the use of photography to monitor Atlantic puffins. Secondly, this study showed how the presence of two seabird species, the Atlantic puffin and the great skua Stercorarius skua, alters island food webs. These seabird species are likely to change plant community diversity, relative to areas without seabirds. The chemical concentration of grasses inside seabird colonies was also altered: grasses had significantly higher concentrations of nitrogen and also had higher values of δ15N, relative to areas without seabirds. These chemical alterations suggest that nutrients from seabirds are incorporated into local vegetation. Furthermore, samples of hair from rabbits and sheep found within puffin colonies also had significantly higher values of δ15N, suggesting that nutrients travel from seabirds into secondary consumers, via ornithogenic forage. An additional study on the transfer of nutrients within island food webs showed how ornithogenic nutrients deposited on an island in the Baltic Sea were incorporated into house martins, via aquatic insects. These studies, along with an understanding of seabird population size, suggest that the impact of seabirds on island food webs may be considerable and have large consequences for island conservation and management.

Interactions between above ground and root-feeding herbivores can be influenced by changes in plant traits, such as tissue chemistry and morphology. Environmental heterogeneity and perturbations also affect these plant-mediated interactions. Climate change is a multi-faceted phenomenon; increases in atmospheric carbon dioxide (CO2) concentrations lead to increased global mean temperature and an associated higher frequency of extreme weather events. These factors can potentially perturb ecosystem function by altering both plant–herbivore and herbivore–herbivore interactions. A detailed understanding of whether above–belowground interactions are affected by climate change remains lacking. In an attempt to fill knowledge gaps in this understudied area of ecology, this thesis investigates, through a series of glasshouse experiments, the effects of elevated CO2 and other aspects of climate change, such as altered phenology, on the interspecific interaction between the aboveground large raspberry aphid (Amphorophora idaei) and the root feeding larvae of the vine weevil (Otiorhynchus sulcatus), mediated by the shared raspberry (Rubus idaeus) host-plant. Under ambient climate conditions, reciprocal feeding facilitation was observed to occur between aphids and vine weevil larvae feeding on raspberry, with the presence of one increasing the abundance of the other herbivore, and vice versa. This occurred regardless of plant cultivar and order of herbivore arrival on the plant. It is likely that this facilitative relationship is driven by over-compensatory plant growth in response to herbivory. Although tougher, adult vine weevils show a feeding preference for leaves grown in elevated CO2. Herbivory may be more influential than CO2 in determining plant–herbivore interaction outcomes. Aphids affect plant intraspecific competition to a greater extent than elevated CO2 by altering plant biomass of both infested and non-infested plants. In conclusion, this particular plant–herbivore system would seem to be relatively robust in the face of possible future CO2 concentration scenarios.

Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Invasive alien plants have had diverse ecological and social impacts on recipient ecosystems and are a major problem for land managers. Successful management demands an understanding of the ecology of invading taxa. The invasive status and impacts are documented for Prosopis populations in South Africa. However, unresolved taxonomic issues, the extent of hybridization, the applicability of morphology as a species identification approach, and the role that some traits plays in the invasion success have not been studied. This creates a gap that hinders implementation of effective management policies. In this thesis I use a phylogenetic approach to determine the taxonomic make-up of invasive Prosopis populations in South Africa (Chapter 2) and compare the results to morphological identification (Chapter 3). I also look at seedling growth rates in the context of variation in genome size and seed size (Chapter 4). Almost all regions invaded by Prosopis are characterized by taxonomic uncertainty exacerbated by the ease of inter-specific hybridization. In Chapter 2 I aim to resolve taxonomic issues of invasive Prosopis populations in South Africa using a phylogenetic approach. In addition, I aim to unravel the extent of hybridization and the species involved in South Africa. Here, I found that Prosopis populations in South Africa comprise both reported and previously unreported species, indicating a need for a reassessment of the identity of invasive taxa. Hybridization is prevalent and all confirmed species are involved. These findings call for a rethink of legislation and management approaches, e.g. the selection of classical biological control agents. Overall the extent of hybridization indicates that Prosopis species in South Africa comprise a freely inter-breeding population typical of a syngameon. Proper morphological identification of invasive species is crucial for ecological studies and management of invasions. In Chapter 3, I use the total evidence approach to assess whether morphological approaches for identification are adequate for identifying Prosopis species in South Africa. I found that Prosopis taxa in South Africa cannot be reliably distinguished using existing morphological keys. This is likely due mainly to the proliferation of hybrids with a diverse morphology. Therefore, molecular tools are crucial for confirming any morphological identities and for determining the presence of any unreported species. Genome size and seed size have been reported to be associated with invasiveness in a number of plant groups, but not often in a system with multiple hybrids like Prosopis. In Chapter 4, I first investigate the relationship between genome size and seed size in invasive populations of Prosopis spp. in South Africa and secondly I investigate how genome and seed sizes influence germination and early growth. Here I found that genome size loses its distinctness, being diluted in hybridizing populations, but can still be used to assess hybridization events themselves. Large seed size seems to be important for invasiveness as it positively influences germination and early growth. This thesis confirms the taxonomic conundrum of Prosopis species in invasive ranges. This coupled with inadequacy of morphological identification calls for a global study involving native and invasive range taxa to clarify the existing confusions. In view of the presence of unreported Prosopis species in South Africa and extensive hybridization, a rethink of the current legislation and control is needed. / AFRIKAANSE OPSOMMING: Uitheemse indringer plante het grootskaalse ekologiese en sosiale impakte op die ekosisteme wat hulle indring en stel 'n groot uitdaging vir bestuurders van natuurlike hulpbronne. Suksesvolle bestuur en bestryding van indringer plante verg deeglike kennis oor hulle ekologie. Die indringer status en impakte van Prosopis populasies in Suid Afrika is reeds voorheen beskryf. Nieteenstaande, die problematiese taksonomie, die omvang van hibridisasie, die waarde van morfologiese identifikasie, en die rol wat sekere eienskappe speel in die sukses van hierdie groep is nog nie bestudeer nie. Daar is dus 'n gaping in kennis wat die effektiewe beheer van die groep in Suid Afrika belemmer. In hierdie tesis pas ek 'n filogenetiese benadering toe om die taksonomiese verwantskappe van Prosopis populasies in Suid Afrika te bepaal (Hoofstuk 2) en vergelyk my resultate met morfologiese identifikasie sleutels (Hoofstuk 3). Ek ondersoek ook saailing groei tempos in die konteks van variasie in genoom en saad groote in die groep (Hoofstuk 4). Bykans alle areas in Suid Afrika waar Prosopis voorkom word gekenmerk deur taksonomiese onsekerheid, verder bemoeilik deur die gemak waarmee spesies vrylik hibridiseer. Ek vind dat beide bekende en voorheen-onbeskryfde Prosopis spesies in Suid Afrika aangetref word en beklemtoon die behoefte om die identiteit van spesies in die land te hersien. Hibridisasie kom algemeen voor tussen alle spesies teenwoordig in Suid Afrika. Hierdie bevindinge beklemtoon dat wetgewing en beheermaatreêls hersiening benodig, byvoorbeeld in die toepassing van biologiese beheer. In samevatting kom dit voor asof hibridisasie gelei het tot 'n vrytelende Prosopis groep in Suid Afrika, tipies van 'n singameon. Ordentlike morfologiese identifikasie van indringer spesies is belangrik in enige ekologiese studie en die implementering van doeltreffende beheermaatreëls. In Hoofstuk 3 gebruik ek ʼn ‘totale bewys’ benadering om vas te stel of morfologiese eienskappe alleenlik genoegsaam is om Prosopis spesies in Suid Afrika korrek te kan identifiseer. Ek vind dat spesies nie geloofwaardig geïdentifiseer kan word nie, heel moontlik as gevolg van wydverspreide hibridisasie tussen alle spesies teenwoordig in die land. Genoom en saad groote is voorheen geassosieer met die indringer aard van verskeie plant groepe. In Hoofstuk 4 ondersoek ek die verwantskap tussen genoom en saad groote. Tweedens bepaal ek die invloed van genoom en saad groote op ontkieming en vroeë groei eienskappe van Prosopis. My bevindinge toon dat, terwyl die kenmerklikheid van genoom groote verloor word as gevolg van hibridisasie, dit steeds hibridisasie gebeurtenisse per se kan identifiseer. Groot sade het ook ʼn positiewe invloed op die ontkieming en vroeë groei eienskappe van Prosopis. Die tesis bevestig die taksonomiese onduidelikheid van indringer Prosopis taksa in Suid Afrika. Tesame met die onakkuraatheid van morfologiese sleutels beklemtoon my bevindinge die behoefte vir ʼn dringende wêreldwye studie op indringer en inheemse populasies van Prosopis om taksonomiese onsekerhede op te klaar. Die identifikasie van nuwe spesies in Suid Afrika beklemtoon ook die behoefte om huidige wetgewing en beheer van die groep in die land te hersien.

Thesis (PhD (Botany and Zoology))--Stellenbosch University, 2008. / ENGLISH ABSTRACT: The worldwide movement of biota is of substantial concern for the conservation of biodiversity. The movement of species takes place at three different scales. These are translocations of indigenous species within their natural distribution ranges, the translocation of species outside their natural distribution ranges within geopolitical boundaries (i.e. extralimital introductions) and the translocation of species outside geopolitical boundaries and their natural distribution ranges (i.e. extraregional introductions). Ungulates are extensively translocated at each of these scales and each scale of translocation is expected to have different impacts on biodiversity. Ungulates are translocated for conservation purposes such as reintroducing species to places where they have previously gone extinct and to mitigate inbreeding in small, isolated populations. Ungulates are also extensively translocated for economic and recreational reasons, such as for sport hunting. Translocations for sport hunting include indigenous, extralimital and extraregional species. Concerns for translocations of indigenous species are largely for the loss of genetic diversity through the mixing of genetically distinct populations, and concerns for extralimital and extraregional translocations are for impacts on indigenous biodiversity such as through herbivory, competition, hybridization and disease transmission. This thesis investigates the extent of ungulate introductions globally and at a finer resolution in South Africa. It investigates the pathways, drivers and impacts of ungulate introductions and it also investigates the use of surrogates for genetic distinctiveness for advising the translocation of indigenous ungulates. The study finds that ungulate translocations have been extensive and have lead to the homogenization of ungulate assemblages in countries globally and at a quarter-degree grid-cell resolution in South Africa. Zoos were identified as a potential introduction pathway for extraregional ungulates globally and in South Africa extraregional introductions have made ungulate assemblages more different; whereas large numbers of extralimital introductions have made ungulate assemblages more similar. The homogenization of ungulate species in South Africa has increased with time, due to increased numbers of translocations, particularly of extralimital species. In South Africa translocations have most recently been made to high-income areas with high human population density and high livestock density; whereas in the 1960s ungulates were introduced to areas species poor for indigenous ungulates and marginal for livestock. In South Africa, long distance translocations of indigenous species extralimitally has resulted in extensive range expansions of a magnitude greater than predicted range changes as a result of predicted climate change. When the use of surrogates of genetic distinctiveness for advising translocations was investigated for Africa, the East African rift valley was found to be important in delineating genetic distinctiveness and translocations across this feature should be prevented. Major rivers in Africa also showed potential for delineating genetic distinctiveness in ungulates, but relevant phylogeographic data are needed to confirm this. Sufficient evidence for the impacts of non-indigenous ungulates on biodiversity both in South Africa and globally is lacking despite substantial concern for their impacts. It is suggested that to demonstrate the impacts of non-indigenous ungulates exclosure and enclosure experiments should be used and population declines in indigenous species should be shown. / AFRIKAANSE OPSOMMING: Verskuiwing van plante en diere wêreldwyd lei tot groot kommer in gevolge die bewaring van biodiversiteit. Verskuiwings vind op drie skale plaas, naamlik, die verskuiwing van inheemse spesies binne hulle natuurlike verspreidingsgebied, die verskuiwing van spesies buite hul natuurlike verspreidingsgebied maar binne landsgrense (d.w.s. buite limiet verskuiwings), en die verskuiwing van spesies buite hul natuurlike verspreidingsgebied en buite landsgrense (d.w.s. buite grondgebied verskuiwings). Grootskaalse verskuiwing van hoefdiere vind op al drie skale plaas. Verskuiwing op elk van die skale sal na verwagting biodiversiteit verskillend beïnvloed. Hoefdiere word ook vir bewaringsdoeleindes verskuif, bv. die herbevolking van ‘n gebied waar die spesies uitgesterf het, asook om genetiese probleme wat gepaardgaan met klein bevolkingsgroottes te vermy. Hoefdiere word ook verskuif vir ekonomiese- en ontspannings redes, o.a. vir sportjag, en sluit verskuiwings op al drie skale in. Kommer oor verskuiwings binne ‘n spesies se verspreidingsgebied rus hoofsaaklik op die verlies van genetiese diversiteit a.g.v. die vermenging van vorig genetiese eiensoortige bevolkings, terwyl op die ander twee skale kommer hoofsaaklik gebaseer is op die impakte van kompetisie, interteling, predasie, herbivoor effek, en die verspreiding van parasiete op inheemse biodiversiteit. Hierdie proefskrif ondersoek die omvang van hoefdier verskuiwings globaal asook in Suid Afrika. Die verskuiwingsweë, oorsake en impakte van verskuiwings word hier ondersoek, asook die maatstawwe van genetiese eiensoortigheid om advies oor verskuiwings te verskaf. Die bevindings toon op ekstensiewe verskuiwing van hoefdiere wat eenvormigheid van hoefdier spesiesamestellings wêreldwyd bevorder het, sowel as op ‘n kwartgraad skaal in Suid Afrika. Dieretuine is geïdentifiseer as ‘n potensiële bron van buite grondgebied verskuiwings. In Suid Afrika het buite grondgebied verskuiwings hoefdier spesiesamestellings minder eenvormig gemaak, terwyl buite limiet verskuiwings hoefdier samestellings binne Suid Afrika meer eenvormig gemaak het. Eenvormigheid in hoefdier spesiesamestellings het met tyd in Suid Afrika toegeneem as gevolg van ‘n toename in veral buite limiet verskuiwings. In Suid Afrika is verskuiwings mees onlangs na hoë-inkomste gebiede met hoë menslike bevolkingsen veëdigthede gemaak. In die sestiger jare is hoefdiere egter verskuif na gebiede waar min inheemse hoefdiere voorgekom het en wat marginaal was vir veëboerdery. In Suid Afrika het langafstand buite limiet verskuiwings versoorsaak dat die verspreidingsgebiede van sekere hoefdier spesies groter is as wat die geval sal wees met voorspelde klimaatsveranderinge. Waneer surogaat inligting gebruik word om genetiese verskille tussen bevolkings te identifiseer om verskuiwings te adviseer, word die Oos Afrika Rift vallei geïdentifiseer as ‘n belangrike breuk tussen bevolkings. Verskuiwings oor die vallei moet verkieslik nie plaasvind nie. Groot riviere in Afrika speel ‘n soortgelyke rol, maar verdere genetiese inligting is nodig om dit te bevestig. Alhoewel kommer oor die impak van verskuiwings groot en teoreties verdedigbaar is, bestaan daar te min konkrete bewyse vir die impakte in Suid Afrika. Daar word voorgestel dat manipuleringseksperimente uitgevoer moet word om impakte te demonstreer, en dat aandag veral gegee moet word aan die demonstrasie van impakte op inheemse spesies.

This PhD thesis seeks to consider conifer forestry stream corridor design in relation to both in-stream and riparian zone biodiversity and functioning. The contribution, availability and source of basal resources within varying corridor conditions are the focus of this project. This approach is combined with surveys of community diversity on a number of key trophic scales in order to determine how the corridor characteristics and their associated resource availability, affects community structure. The effects of varying design and management of the riparian buffer zones within afforested stream systems on in-stream and overall habitat diversity and functioning remains largely unknown. Although guidelines have been implemented for several years (Forest and Water Guidelines, Forestry Commission), recommendations, although based on sound assumptions, are subjective assessments and tend not based on scientific research or data. As such, the premise of this project is to consider a variety of corridor physical parameters adjacent to low-order streams within two afforested catchments in South-West Scotland, between 2003 and 2005, in order to contribute to the understanding of system functioning within the limitations of forestry land-use and management. A number of different approaches were employed in order to define the proportional contributions of allochthonous and autochthonous material within the benthos of the stream systems. This was done in order to define resource availability, biofilm characteristics, stream functioning and the role of corridor design in influencing resource availability. Yet, despite significant autochthonous productivity, allochthonous organic matter was the primary resource utilised by many taxa. However, conversely, light regime was found to be fundamental in shaping production and community structure within these ecosystems. Consequently, here I explore a number of different trophic scale responses to riparian conditions in order to define the biotic responses to variation of resource availability, with the aim of contributing information which may aid in design and management of afforested riparian zones.

Thesis (PhD) - Stellenbosch University, 2011. / ENGLISH ABSTRACT: The Albertine Rift is characterized by a heterogeneous landscape which may, at least in part, drive the exceptional biodiversity found across all taxonomic levels. Notwithstanding the biodiversity and beauty of the region, large areas are poorly understood because of political instability with the inaccessibility of most of the region as a contributing factor. The majority of studies in the Albertine Rift have focussed on charismatic mega fauna, with other taxa receiving less attention. One of the taxonomically and numerically more abundant small mammal genera is the genus Praomys, an African endemic with a wide distribution range spanning most of west, central and east Africa. Four species are typically recognized from the Albertine Rift namely P. degraaffi, P. jacksoni, P. misonnei and P. verschureni. In this study I used a combination of DNA sequence data (mitochondrial control region, mitochondrial cytochrome b and 7th intron of the nuclear ß-fibrinogen gene) as well as morphometric data (traditional and geometric) to investigate the systematics of the Praomys taxa occurring in the Albertine Rift. To allow meaningful DNA assessments and in an attempt to identify potential drivers of diversifications, other Praomys species were also included from public sequence data bases for comparisons. The main focus was on P. jacksoni (the numerically most abundant taxon; also, up to 2005, all Praomys in the Albertine Rift were mostly collected as “jacksoni”) and P. degraaffi (an Albertine Rift endemic). A surprising finding was the presence of P. mutoni; this represents a range extension for this species into the Albertine Rift. Distinct evolutionary lineages were found in both P. jacksoni (confirmed by sequence data as well as morphometrics) as well as P. degraaffi (based only on sequence data; insufficient samples precluded a full morphometric investigation). These lineages (in both P. jacksoni as well as P. degraaffi) appear to be separated along a north – south gradient; however, further investigations should confirm this. To further investigate the genetic patterns at local scales across the Albertine Rift, as well as introgression between species as revealed by sequence data, a species-specific microsatellite library was developed for P. jacksoni. Twelve polymorphic markers were identified of which nine also amplified in P. degraaffi. Introgression was confirmed between the two focal species with almost 20% of the individuals analysed being jacksoni-degraaffi hybrids. This is perhaps not so surprising given that there is considerable overlap in their ranges (between ~ 1500 m a.s.l. to 2450 m a.s.l.) as well as the relative ages of the species (the divergence time between these two species were estimated at 3.8 Mya). The presence of distinct lineages within each of these species was confirmed by microsatellite analyses (these lineages diverged approcimately at same time at ca. 3.4 Mya). As suggested by sequence and morphometric data, these lineages had a largely north – south distribution but with considerable overlap in the central Albertine Rift in the vicinity of Lake Kivu. The phylogeographic patterns obtained for both focal species were not consistent with the physical barriers such as the rivers, lakes or mountains, nor were they exclusively associated with Pleistocene phenomena such as the change of the course of the rivers or uplift; rather, the lineages predate the Pleistocene and fall firmly in the Pliocene (>3 Mya). Biogeographically, the north - south location of lineages with a centrally - located contact zone could be a result of parapatric speciation due to habitat fragmentation or past climate change, followed by secondary contact. Barcoding using genetic information provides a useful tool to identify unknown taxa, cryptic diversity or where different life stages are difficult to identify. From an invasion biology perspective, it allows for the rapid identification of problem taxa against a known data base. By adopting such a barcoding approach (senso lato), the presence of three invasive rodents was confirmed in the Democratic Republic of the Congo (DRC); these are Rattus rattus (black rat), R. norvegicus (Norway rat) and Mus musculus domesticus (house mouse). A comparison with global data available for these species revealed two possible introduction pathways namely via the shipping port at Kinshasa/Matadi (with strong links to Europe) and via the slave trade routes in the east (strong links to the Arab world and the east). Of these three taxa, only R. rattus is currently documented from the DRC although the others have received mention in the gray literature. These findings draw attention to the lack of any official policy regarding biosecurity in the DRC, and argue for the development of strict control measures to prevent further introductions. / AFRIKAANSE OPSOMMING: Die Albertine Rift word gekenmerk deur 'n heterogene landskap wat kan, ten minste gedeeltelik, die uitsonderlike biodiversiteit wat oor al die taksonomiese vlakke gevind word teweeg bring. Nieteenstaande die biodiversiteit en die skoonheid van die streek, is groot gebiede onbekend as gevolg van politieke onstabiliteit met die ontoeganklikheid van meeste van die streek as 'n bydraende faktor. Die meerderheid van studies in die Albertine Rift het gefokus op die charismatiese mega fauna, met ander taxa wat minder aandag ontvang. Een van die taksonomies en numeries meer volop klein soogdier genera is die genus Praomys, 'n Afrika endemiese groep met 'n wye verspreiding wat strek oor die grootste deel van van wes-, sentraal en oos-Afrika. Vier spesies word tipies erken van die Albertine Rift naamlik P. degraaffi, P. jacksoni, P. misonnei en P. verschureni. In hierdie studie het ek 'n kombinasie van DNA volgorde data (mitochondriale beheer streek, mitochondriale sitochroom b en 7de intron van die kern ß-fibrinogeen geen) sowel as morfometriese data (tradisioneel en meetkundig) gebruik om die sistematiek van die Praomys taxa te ondersoek. Om betekenisvolle DNA aanslae toe te laat en in 'n poging om potensiële aandrywers van diversiteit te identifiseer, is ander Praomys spesies van openbare volgorde data basisse vir vergelykings ingesluit. Die hooffokus is op P. jacksoni (die numeries volopste takson, ook, tot en met 2005 is alle Praomys in die Albertine Rift meestal as "jacksoni" versamel) en P. degraaffi ('n Albertine Rift endemiese spesie). 'n Verrassende bevinding was die teenwoordigheid van P. mutoni, dit verteenwoordig' n verspreidingsuitbreiding vir hierdie spesie in die Albertine Rift. Bepaalde evolusionêre ontwikkelingslyne was in beide P. jacksoni (bevestig deur die volgorde data sowel as morfometrie) sowel as P. degraaffi (wat slegs gebaseer is op die volgorde data, onvoldoende monsters verhinder 'n volledige morfometriese ondersoek). Hierdie lyne (in beide P. jacksoni sowel as P. degraaffi) word geskei langs 'n noord - suid gradiënt, maar verdere ondersoeke moet dit bevestig. Om die genetiese patrone op plaaslike skaal oor die Albertina Rift verder te ondersoek, sowel as introgressie tussen spesies soos geopenbaar deur die volgorde data, is 'n spesie-spesifieke mikrosatelliet biblioteek ontwikkel vir P. jacksoni. Twaalf polimorfiese merkers is geïdentifiseer waarvan nege ook amplifiseer in P. degraaffi. Introgressie is bevestig tussen die twee brandpunt spesies met byna 20% van die individue wat ontleed is as jacksoni-degraaffi basters. Dit is miskien nie so verbasend gegee dat daar aansienlike oorvleueling is in hul gebiede (tussen ~ 1500 m bo seespieel tot 2450 m bo seespieel), sowel as die relatiewe ouderdomme van die spesies (die divergensie tussen hierdie twee spesies is geskat op 3,8 Mya). Die teenwoordigheid van verskillende lyne in elk van hierdie spesies is bevestig deur mikrosatelliet ontleding (hierdie lyne het gedivergeer ongeveer 3,4 Mya). Soos voorgestel deur die DNA volgorde en morfometriese data, het hierdie lyne 'n grootliks noorde – suid verspreiding, maar met 'n aansienlike oorvleueling in die sentrale Albertine Rift in die omgewing van die Kivumeer. Die filogeografiese patrone wat vir beide die brandpunt spesies gevind is nie in ooreenstemming met die fisiese struikelblokke soos die riviere, mere of berge nie, en hou ook nie uitsluitlik verband met die Pleistoseen verskynsels soos die verandering van die loop van die riviere nie; die afstammelinge is eerder veel ouer as die Pleistoseen en val binne die Plioseen (> 3 Mya). Biogeografies, die noorde – suid plasing van die lyne met 'n sentraal geleë kontak sone kan die gevolg wees van parapatriese spesiasie te danke aan habitatfragmentasie as gevolg van verandering in die klimaat, gevolg deur 'n sekondêre kontak. Strepieskodering met behulp van genetiese inligting verskaf 'n nuttige instrument om onbekend taxa, kriptiese diversiteit of waar verskillende lewensfases moeilik is om te identifiseer, te identifiseer. Vanuit 'n indringerbiologie perspektief, maak hierdie benadering dit moontlik om vinnige identifikasies van die probleem taksa teen' n bekende data basis te bekom. Deur gebruik te maak van so 'n strepieskoderingsbenadering (senso lato), is die teenwoordigheid van drie indringende knaagdiere bevestig in die Demokratiese Republiek van die Kongo (DRK), naamlik Rattus rattus (swart rot), R. norvegicus (Noorweë rot) en Mus musculus domesticus (huis muis). 'n Vergelyking met die globale data wat beskikbaar is vir hierdie spesies het aan die lig gebring dat twee moontlike betree-roetes bestaan, naamlik via die skeepshawe by Kinshasa / Matadi (met sterk skakels na Europa), en via die slawehandel roetes in die ooste (sterk skakels na die Arabiese wêreld en die ooste) . Van hierdie drie taxa, is tans slegs R. rattus van die Demokratiese Republiek van die Kongo gedokumenteer, hoewel die ander melding ontvang in die grys literatuur. Hierdie bevindinge vestig die aandag op die gebrek aan enige amptelike beleid ten opsigte van biosekuriteit in die Demokratiese Republiek van die Kongo, en argumenteer vir die ontwikkeling van streng beheermaatreëls om verdere indringerspesies te voorkom.