Thesis (PhD)--Stellenbosch University, 2003. / ENGLISH ABSTRACT: The aims of this study were to investigate genetic issues pertaining to the conservation of the Knysna seahorse, Hippocampus capensis, and to determine the phylogenetic placement of this endangered estuarine species among marine seahorses. This was accomplished by focusing on three aspects of the taxonomy: the interspecific level; the inter-population level; and the intra-population level. To determine which species are closely related to H. capensis, and how the evolutionary history of this lineage relates to that of other seahorses, sequence data derived from four gene fragments (the nuclear RPI and Aldolase and the mitochondrial 16S rRNA and cytochrome b genes) were used to determine the phylogenetic relationships among 30 species belonging to the genus Hippocampus. There were marked differences in the rate of evolution among these gene fragments, with Aldolase evolving the slowest and the mtDNA cytochrome b gene the fastest. Among individual partitions, the RPI gene recovered the highest number of nodes supported by >70% bootstrap values from parsimony analysis, and >95% posterior probabilities from Bayesian inference. The combined analysis based on 2317 nucleotides resulted in the most robust phylogeny. A distinct phylogenetic split was identified between the pygmy seahorse, H. bargibanti, and a clade including all other species. Three species from the western Pacific Ocean included in this study, namely H. bargibanti, H. breviceps, and H. abdominalis, occupy basal positions in the phylogeny. This and the high species richness in the region suggest that the genus probably originated in this region. There is also fairly strong molecular support for the remaining species being subdivided into three main evolutionary lineages: two West Pacific clades and a clade of species present in both the Indo-Pacific and the Atlantic Ocean, which includes H. capensis. The phylogeny obtained herein suggests that seahorses belonging to the latter clade colonised the Atlantic Ocean at least twice, once before the closure of the Tethyan Seaway, and once afterwards. Phylogenies reconstructed using mitochondrial DNA gene fragments (l6S rRNA, cytochrome band 382 bp of the rapidly evolving control region) indicate that H. capensis is closely related to an Indian Ocean lineage of H. kuda and a Red Sea lineage of H. fuscus. Other lineages closely associated with these taxa include H. kuda from the West Pacific, the East Atlantic species H. algiricus, the West Atlantic species H reidi, the East Pacific species H ingens, and the Hawaiian species H fisheri. No control region alleles were shared among H capensis and any of the marine seahorses, suggesting that the Knysna seahorse is phylogenetically distinct. The evolutionary history of H capensis, and the extent of gene flow between its three known populations, were investigated using control region sequences from 138 specimens. Most samples were obtained by taking fin clips; this method was studied on captive seahorses and no negative effects were found. Similarly high levels of genetic diversity were found in two of the wild populations (Knysna and Keurbooms Estuaries), whereas diversity in the third population (Swartvlei Estuary) was lower. Although most haplotypes are shared among at least two populations, based on the haplotype frequency distributions the three assemblages constitute distinct management units. The extant population structure of H capensis suggests that the Knysna seahorse originated in the large Knysna Estuary. The presence of seahorses in the two smaller estuaries is either the result of a vicariance event at the beginning of the present interglacial period, or colonisation of the estuaries via the sea, or a combination of the two. Population genetic parameters of the Knysna population and those of two populations of closely related marine seahorses (H kuda from the Philippines and H fuscus from the Red Sea) were similar, suggesting that the Knysna population is not genetically impoverished, despite its comparatively small area of occupancy. / DEUTSCHE ZUSAMMENFASSUNG: Die hier prasentierte wissenschaftliche Studie beschaftigte sich mit genetischen Themen relevant flïr den Artenschutz des Knysna Seepferds, Hippocampus capensis, und den phylogenetischen Beziehungen dieser ausschliesslich in Estuaren (Flussmtindungen) vorkommenden gefahrdeten Art mit den im Meer lebenden Seepferden. Die folgenden taxonomischen Einheiten wurden verglichen: Arten, Populationen und Sub-Populationen. Urn festzustellen, welche Arten nah mit H. capensis verwand sind, und wie die Evolution dieser Gruppe sich von der anderer Seepferdgruppen unterscheidet, wurden genetische Sequenzen von vier Genen (den nuklearen RPI und Aldolase und den mitochondrischen 16S rRNA und Cytochrom b Genen) von 30 Seepferdarten verwendet und phylogenetische Beziehungen rekonstruiert. Betrachtliche Unterschiede wurden festgestellt hinsichtlich der Geschwindigkeit in der Mutationen stattgefunden haben: Aldolase mutierte am langsamsten und Cytochrom b am schnellsten. Eine auf RPI Sequenzen basierende Phylogenie hatte die hëchste Anzahl von Gabelungspunkten, die sowohl von parsimonischen Analysen, als auch von bayesischer Inferenz untersttitzt wurden. Die robusteste Phylogenie wurde jedoch gefunden, wenn Sequenzen von allen vier Genen kombiniert wurden (im ganzen 2317 Nukleotide). Eine betrëchtliche genetische Distanz wurde zwischen dem Pygmaen-Seepferd, H. bargibanti, und einer Gruppe, die aus allen anderen Arten bestand, gefunden. Drei Arten vom westlichen Pazifik, namlich H. bargibanti, H. breviceps und H. abdominalis, hatten basale Positionen in der Phylogenie. Das, und der Artenreichtum dieser Region, sind Anzeichen daflïr, dass Seepferde mëglicherweise ursprtinglich aus dem westlichen Pazifik stammen. Es wurde weiterhin gefunden, dass alle tibrigen Seepferdarten in drei Hauptgruppen unterteilt werden kannen: die Verbreitungsgebiete zweier dieser Gruppen beschranken sich hauptsachlich auf den westlichen Pazifik, aber die dritte Gruppe kommt sowohl im Indo-Pazifik, also auch im Atlantik vor (H. capensis ist mit dieser letzteren Gruppe assoziiert). Es gibt gute Anzeichen dafllr, dass die Seepferde der letztgenannten Gruppe den Atlantik mindestens zweimal kolonisiert haben, einmal vor der Schliessung der tethyschen Seeverbindung, und einmal danach. Phylogenien, die ausschliesslich mit mitochondrischen Genen rekonstruiert wurden (16S rRNA, Cytochrom b und 382 Nukleotide der schnell-mutierenden Kontollregion), zeigen, dass H capensis sehr nah verwandt mit H kuda aus dem Indischen Ozean und H fuscus aus dem Roten Meer ist. Andere nah verwandte Arten sind H kuda from westlichen Pazifik, H algiricus vom ëstlichen Atlantik, H reidi vom westlichen Atlantik, Hingens vom ëstlichen Pazifik, sowie die in Hawaii vorkommende Art H fisheri. Keine der Kontrollregionallele, die in H capensis gefunden wurden, kamen in anderen Arten vor. Dies zeigt, dass das Knysna Seepferd eine eigenstandige Art ist, und Paarungen mit anderen Arten nicht vorkommen. Die Evolutionsgeschichte von H capensis, und das Ausmass von genetischem Austausch zwischen den drei Populationen dieser Art, wurden untersucht, indem Kontrollregionsequenzen von 138 Individuen analysiert wurden. Die meisten Proben stammten von Flossenschnitten; diese Methode wurde zuvor an in Gefangenschaft lebenden Seepferden ausprobiert, und es wurden keine negativen Folgeerscheinungen beobachtet. Genetische Diversitat war ungefahr gleich hoch in zwei der Populationen (Knysna und Keurbooms Estuare), aber eine deutlich niedrigere Diversitat wurde in der dritten Population gefunden (Swartvlei Estuar). Obwohl die meisten Allele in mindestens zwei Populationen gefunden wurden, sind die drei Populationen unterschiedliche genetische Einheiten, eine Schlussfolgerung, die hauptsachlich auf Unterschiede in der relativen Haufigkeit der Allele beruht. Die Populationsstruktur von H capensis deutet darauf hin, dass diese Art ihren Ursprung im Knysna Estuar hat. Die Prasenz von Seepferden in den beiden anderen Estuaren ist entweder das Resuitat von Vikarianz (eine Spaltung der urspri.inglichen Population) zu Beginn der jetzigen Interglazialzeit, oder Kolonisierung der Estuare durchs Meer, oder eine Kombination beider Szenarios. Populationsgenetische Parameter der Knysna Population und die zweier Populationen von nah verwandten Arten (H kuda aus den Philippinen und H fuscus aus dem Roten Meer) zeigten keine grossen Unterschiede. Dies deutet darauf hin, dass das Knysna Seepferd trotz seines vergleichbar kleinen Verbreitungsgebietes nicht unter geringer genetischer Diversitat leidet. / AFRIKAANSE OPSOMMING Die doelwitte van hierdie studie was om die Knysna seeperdjie, Hippocampus capensis, te ondersoek relatief tot die spesie se bewaring asook om die filogenetiese posisie van hierdie bedreigte estuariene spesie binne mariene seeperdjies te bepaal. Drie aspekte van die taksonomie word ondersoek: interspesie verwantskappe, interbevolking verwantskappe en intra-bevolking verwantskappe. Om te bepaal watter spesies na verwant is aan H capensis, asook om die evolusionêre geskiedenis van hierdie groep met die van ander groepe te vergelyk, word nukleotieddata van vier ONS fragmente (die nukleêre RPI intron en Aldolase, en die mitochondriale 16S rRNA en sitokroom b fragmente) van 30 spesies van die genus Hippocampus gebruik. Aansienlike verskille in die tempo van evolusionêre verandering tussen hierdie ONS fragmente word gevind: Aldolase was die stadigste en die mitochondriale sitokroom b die vinnigste. Die RPI intron het die meeste knoesteringe gehad wat ondersteun word deur hoë stewelvasgordnommers (>70%) van parsimoniese analises en hoë agterwaarskynlikheide (>95%) van Bayesiese gevolgtrekkinge. Die kombineerde analise wat 2317 nukleotiede ingesluit het, het die beste filogenie geproduseer. 'n Besliste filogenetise verdeling was gevind tussen die pigmee seeperdjie, H bargibanti, en 'n groep wat al die ander spesies ingesluit het. Drie spesies van die westelike Stille Oseaan wat in hierdie studie ingesluit is, H bargibanti, H breviceps en H abdominalis, neem primitiewe posisies in die filogenie in. Dit, en die hoë spesiesrykdom in daardie gebied dui aan dat dit moontlik is dat die genus in die westelike Stille Oseaan ontstaan het. Daar is ook taamlike goeie molekulêre ondersteuning dat al die ander spesies in drie evolusionêre hoofgroepe verdeel kan word: twee groepe wat hoofsaaklik in die westelike Stille Oseaan voorkom, en 'n groep van spesies wat in die Stille Oseaan, die Indiese Oseaan en in die Atlantiese Oseaan voorkom, wat H capensis insluit. Die filogenie wat hier gevind is dui aan dat seeperdjies van hierdie laas genoemde groep die Atlantiese Oseaan minste twee keer gekoloniseer het, een keer voor die sluiting van die Tetiese Seepad, en een keer daarna. Filogenies wat met mitochondriale ONS fragmente gerekonstrueer is (16S rRNA, sitokroom b en 382 nukleotide van die vinnig evolveerende kontrolestreek) dui aan dat H capensis na verwant is aan 'n groep van H kuda wat in die Indiese Oseaan voorkom en H fuscus van die Rooi See. Ander groepe wat na verwant is aan hierdie takson is H kuda van die westelike Stille Oseaan, H algiricus van die Oos Atlantiese Oseaan, H reidi van die Wes Atlantiese Oseaan, en die Hawaiise spesie H fisheri. Geen kontrolestreek allele was gedeel tussen H capensis en enige mariene seeperdj ie spesies; dit dui aan dat die Knysna seeperdjie filogeneties verskillend is. Die evolusionêre geskiedenis van H capensis, en die omvang van die genetiese interaksies tussen sy drie bekende bevolkings, word ondersoek met kontrolestreek nukleotieddata van 138 monsters. Die meeste van hierdie monsters was verkry deur vinknipsels; hierdie metode was getoets op seeperdjies in gevangenskap en geen negatiewe gevolge was gevind nie. Genetiese diversiteit was omtrent dieselfde in twee van die natuurlike bevolkings (Knysna en Keurbooms Estuariums), maar diversiteit in die derde bevolking (Swartvlei Estuarium) was laër. Alhoewel die meeste allele gedeel was tussen ten minste twee bevolkings, dui die verspreiding van allelfrekwensies aan dat die drie bevolkings aparte bestuurseenhede is. Die ekstante bevolkingsstruktuur van H capensis dui aan dat die Knysna seeperdjie in die groot Knysna Estuarium ontstaan het. Die teenwordigheid van seeperdjies in die twee kleiner estuariums is óf die resultaat van 'n vikariansie voorval aan die begin van hierdie interglasiale tydperk, óf kolonisasie van die estuariums deur die see, óf 'n kombinasie van albei. Bevolkingsgenetiese parameters van die Knysna bevolking en van twee bevolkings van na verwante seeperdjie spesies (H kuda van die Filippyne en H fuscus van die Rooi See) was soortgelyk, wat aandui dat die Knysna bevolking nie geneties verarm is nie, alhoewel dit 'n betreklik kleiner streek bewoon.

Thesis (PhD)--University of Stellenbosch, 2002. / ENGLISH ABSTRACT: In the present study, the systematic status, aspects of the evolutionary biology and phylogenetic relationships among species of the African freshwater crab genus Potamonautes in South Africa are examined. Systematic research between allopatric populations of P. brincki, using allozyme and morphometric data has revealed the existence of a new undescribed freshwater crab species occurring in mountain streams of the Cape Peninsula. This species is described in the present study. In addition, the diagnostic value of carapace dentition patterns in the taxonomy of freshwater crabs is explored among two toothed river crab species from South Africa. The latter study utilized P. warreni and P. unispinus where considerable variation in the dentition pattern of the former species has been recorded. Fixed differences in allozyme loci demonstrated that these two taxa should indeed be considered separate, yet closely related species, while the morphometric data failed to reveal this taxonomic separation. The holotype of P. warreni is re-described. The relationship of hybrid taxa between P. depressus and P. clarus populations are investigated. Evident from this study is that populations that occur equidistant from the two parental taxa have undergone extensive introgressive hybridization. Considering the pronounced sequence divergence and the occurrence of fixed allozyme loci between populations, it is postulated that the hybrid populations should be considered to be on a unique evolutionary trajectory worthy of conservation. The population genetic structure of P. calcaratus is examined as this species is unique in its occupation of water holes. Results demonstrate that the genetic population structure is the result of recent colonization and moderate gene flow among populations. Phylogenetic relationships between the southern African freshwater crab fauna is investigated with the use of sequence data from two mitochondial genes (12 S rRNA and 16 S rRNA), allozymes and morphology in an attempt to firstly, test the usefulness of freshwater crabs as biogeographic indicators, secondly to explore the relationship among hybrid taxa, and thirdly to examine Bott's (1955) subgeneric divisions. Results demonstrated that freshwater crabs can be used as biogeographic indicators, that hybrid taxa are phylogenetic ally closely related and that Bott's subgeneric divisions have no systematic basis. Among the three data sets, the sequence data provided the best resolution, while the phylogenetic inferences derived from the allozyme data and the morphology was limited. / AFRIKAANSE OPSOMMING: In hierdie studie word die sistematiek, aspekte van die evolusionêre biologie en filogenetiese verwantskappe tussen spesies van die varswater krap genus Potamonautes ondersoek in Suid Afrika. Navorsing op geografies geisoleerde populasies van P. brincki word met behulp van allosieme en morfometriese data ondersoek en dui daarop dat daar 'n nuwe onbeskryfde spesie op die berge van die Kaapse Skiereiland voorkom. Die nuwe spesies word beskryf in hierdie studie. Die diagnostiese waarde van tand patrone in varswater krappe word tussen twee spesies P. warreni en P. unispinus ondersoek. Genetiese data dui daarop dat alhoewel P. warreni morfologies baie naverwant is aan P. unispin us, is genoegsame verskille in allosiem lokusse wat daarop dui dat die twee taksa volwaardige spesies is. Die holotipe van P. warreni word herbeskryf. Die verwantkap tussen populasies van twee hibried taksa, P. depressus en P. clarus, word ondersoek. Resultate van hierdie studie dui daarop dat noemenswaardige verskille voorkom tussen die twee hibridie taxa en dat die hibriede populasies geneties verskillend is. 'n Argument word aangevoer vir die beskerming van hibriede taksa. Die populasie genetika van P. calcaratus word ondersoek en vergelyk met vorige studies. Die data dui daarop dat minimale geen vloei tusses populasies is en dat die populasie struktuur waarskynlik die resultaat is van onlangse kolonisasie. Die filogenetiese verwantskap tussen die suider Afrikaanse krappe word ondersoek met DNA, allosieme en morfologiese karakters met drie hoofdoele. Eerstens om die gebruik van varswater krappe as biografiese indikatore te toets. Tweedens om die verwantskap van hibriede taksa te ondersoek, en derdens om die status van Bott (1955) se subgenera te bepaal. Resultate dui daarop aan dat varswater krappe wel gebruik kan word as biografiese indikatore. Hibridieserende taxa naverwant is derdens en dat Bott se subgenera geen taksonomiese basis het nie. Die DNA data het die beste resolusie gebied vir die filogenetiese vrae, terwyl die allosieme en morfologiese data 'n laer resolusie bedied het, en meer beperk was.

Thesis (MSc)--Stellenbosch University, 2000. / ENGLISH ABSTRACT: This thesis investigates the population structure of a number of ungulate species occurring within Rooipoort private reserve. Specifically the study serves to make estimates of the ratio of males to females and calves to cows within each species population under observation, based on the data collected. Data were also analysed to ascertain the distribution patterns of the species in question, in relation to vegetation type and habitat. Distribution data were additionally compared to distribution data collected at an earlier period on Rooipoort, to determine whether any change has occurred in distribution patterns of the ungulates concerned. Through analysis of both sex/age data and distributional data, one of the main objectives of the study was to determine the most appropriate time of the year, length of time and managment costs involved to undertake sex/age counts on Rooipoort. Results of the study were also compared to existing population models of ungulates on the reserve. Results obtained from data concluded that a single monthly sex/age count or, in some cases, even three consecutive monthly counts, to determine age ratios, would be insufficient to deliver a reliable estimate of population structure. A number of counts would have to be carried out throughout the year in order to make reliable estimates. Distribution data revealed that all habitat/vegetation types on Rooipoort would have to be covered in order to effectively sample all of the species in question. / AFRIKAANSE OPSOMMING: Gegewens is ook ontleed om die verspreidingspatrone van hoefdiersoorte te bepaal met betrekking tot plantegroeitipe en habitat. Die verspreidingsdata is ook vergelyk met vorige ..studies wat op Rooipoort gedoen is om te. bepaal. of enige. veranderings in die verpreidingspatrone van die hoefdiere onder bespreking plaasgevind het. Een van die hoof doelwitte van die studie was om.. deur ontleding. van beide die geslags/ouderdom data en die verspreidingsdata, die mees geskikte tye van die jaar, die tydsduur en bestuurskoste te bepaal, om geslags/ouderdomstellings op Rooipoort uit te voer. Resultate van die studie is ook met vertroude populasiemodelle op die reservaat vergelyk. Die dataontledings het aangeduidat 'n enkele maandlikse geslags/ouderdoms telling, of, In sekere gevalle, selfs drie agtereenvolgende maandlikse tellings, om ouderdomsverhoudings te bepaal, nie voldoende sal wees om 'n vertroubare beraming van die bevolkings struktuur te maak. n' Aantal tellings moet gedurende die yaar uitgevoer word om vertroubare beramings te kan doen. Verspreidingsdata het bevestig dat alle habitate en plantegroeitipes op Rooipoort bemonster moet word om alle spesie effektief te bemonster.

Thesis (MTech (Nature Conservation))--Cape Peninsula University of Technology, 2016. / Lions are threatened across their natural range. The Kgalagadi Transfrontier Park (KTP), comprising the Kalahari Gemsbok National Park (KGNP; South Africa) and Gemsbok National Park (GNP; Botswana), is a stronghold for the species. Population size and demography of lions in the KGNP has been addressed in four historic studies. Studies in mid-1970 and 1990 reported a female biased population whereas in 2010 the sex structure was skewed towards males (56%). The bias in sex ratios towards males was first observed in cubs and sub-adults in 2001 and later, in 2010, throughout the population. Furthermore, in the 2010 assessment of the lion population, a smaller proportion of cubs (< 2 yrs) were observed in comparisons to the preceding studies (10% vs. ≥ 23%). The skew in age and sex structures that were observed in the KGNP led to concerns over the long-term sustainability of the greater KTP lion population. The lion population carries further risks associated with the stochastic, arid environment, in which the KTP lion population persists. Human-lion conflict on the borders of the KTP and anthropogenic alterations of the environment further threaten lion demographic stability.

Black rhinoceroses (Diceros bicornis) are endangered; there are only ~5000 individuals remaining worldwide. Consequently, black rhinos are managed as a metapopulation in southern Africa. This means that even though several sub-populations of black rhinos are geographically separated, they are managed as a single population. This is achieved by interchanging genetic material between the sub-populations. The main aim of the metapopulation management approach is to increase black rhino numbers in the sub-region. The Rhino Management Group (RMG), formed in 1989, was tasked with setting scientifically defensible demographic targets for the remaining black rhino sub-populations in southern Africa. In the same year, the RMG set fecundity rate at 25% and stated that each black rhino sub-population should achieve a minimum growth rate of 5% per year. The black rhino population in the Hluhluwe-iMfolozi Park (HiP), KwaZulu-Natal, South Africa, is of international importance as it has historically been a significant donor population for the translocation of black rhinos to establish new subpopulations elsewhere in the sub-region. However, the black rhino population at HiP is performing poorly in terms of reproductive success. My study was initiated to assess the reproductive life-histories of the black rhino population at HiP and to determine whether the population was meeting the demographic targets set by the RMG. I also wished to assess the use of space by black rhinos in HiP as a potential explanation for the observed reproductive output. Detailed life-history information for known black rhinos (n = 120) was used to investigate reproductive success between 1998 and 2012. The mean age at sexual maturity (ASM) was determined as 12 years, which is higher than the ASM found in black rhino populations that are considered to be performing poorly (ASM = ~ 7 years). The intercalving interval (ICI) was three years, nine months; this was also longer than the ICI of most black rhino populations. Further, the 2012 black rhino population at HiP had a growth rate of 6.4%, and the population comprised 60% adults, 23% sub-adults and 13% juveniles. Such demographics are usually observed in stable populations and it is possible that poor habitat quality could be resulting in the delayed ASM and longer ICI’s at HiP. In addition, 5% of the population is removed annually as part of the Black Rhino Range Expansion Program (BRREP) to establish new sub-populations. This could also be negatively influencing the reproductive performance of the HiP population. To determine the home range and habitat use of black rhinos at HiP, field data from 13 individual adult black rhinos (n = 9 females and 4 males) over a two-year period (2011-2012) were analyzed. Black rhino female home ranges were slightly smaller (15.4 ± 12.9 km²) than the home ranges of males (23.3 ±14.0 km²) and both sexes utilized similar habitats in the centre of the park. In addition, both the male and female black rhinos were found closer to rivers and drainage lines than expected. However, the assessment of black rhino space use in HiP was limited by a small sample size, making inferences of the impact of space use on reproductive success difficult. Nevertheless, my study suggests that food availability likely influences the location and sizes of black rhino home ranges at HiP. I believe that my study forms the first step in understanding the factors that influence the reproductive success and habitat use patterns of the current black rhino population at HiP. The information produced by my study should enable park management to identify future research to be conducted at HiP, which will yield more robust data for making informed black rhino management decisions at HiP and elsewhere.

Elephants (Loxodonta africana, Blumenbach) are recognised as keystone herbivores and ecosystem engineers in African ecosystems due to the noticeable impact they have on plant communities. This impact can influence other animal taxa and ecosystem processes, especially within enclosed systems. I investigated the effects of elephants in four vegetation types and the cascade effect on three associated taxa and two ecosystem processes at five sites with elephants and five paired sites without elephants in the Eastern Cape Province, South Africa, between April 2005 and July 2007. In grassland habitats, the physical structure of the vegetation was neither enhanced nor degraded in the presence of elephants. Within the locally important Thicket Biome, elephant browsing transformed relatively homogeneous stands of vegetation into more heterogeneous units. However, although seeds from thicket plant species were recorded in elephant dung, elephants did not promote the viability and germination success of these plants. In addition, elephant foraging on aloes caused declines in their populations. By contrast, the size of bushclumps was not reduced in the presence of elephants in bushclump savanna. The associated insect, bird and mammal communities appeared to benefit from elephant foraging in all vegetation types assessed, whereas vegetation patch dynamics and soil surface processes were neither enhanced nor degraded in the presence of elephants. I conclude that, at current densities, elephants do not (in most cases) negatively affect plant and animal communities or ecosystem processes in enclosed reserves. However, elephants have only been present at each site for a relatively short period and it is likely that their impact will be cumulative, increasing over time in these closed systems. Thus, future research along a continuum of elephant density and time since re-introduction is recommended.

Leopards (Panthera pardus) are the most common large predators, free roaming outside of protected areas across most of South Africa. Leopard persistence is attributed to their tolerance of rugged terrain that is subject to less development pressure, as well as their cryptic behaviour. Nevertheless, existing leopard populations are threatened indirectly by ongoing transformation of natural habitat and directly through hunting and conflict with livestock farmers. Together these threats may further isolate leopards to fragmented areas of core natural habitat. I studied leopard habitat preferences, population density, diet and the attitudes of landowners towards leopards in the Little Karoo, Western Cape, South Africa, an area of mixed land-use that contains elements of three overlapping global biodiversity hotspots. Data were gathered between 2010 and 2012 using camera traps set up at 141 sites over an area of ~3100km², GPS tracking collars fitted to three male leopards, scat samples (n=76), interviews with landowners (n=53) analysed in combination with geographical information system (GIS) layers. My results reveal that leopards preferred rugged, mountainous terrain of intermediate elevation, avoiding low-lying, open areas where human disturbance was generally greater. Despite relatively un-fragmented habitat within my study area, the leopard population density (0.75 leopards/100km²) was one of the lowest yet recorded in South Africa. This may reflect low prey densities in mountain refuges in addition to historical human persecution in the area. Currently local landowners are more tolerant of leopards than other wildlife species with incidents of conflict involving leopards being rare relative to black-backed jackals (Canis mesomelas), baboons (Papio hamadryas), caracals (Caracal caracal) and porcupine (Hystrix africaeaustralis). Although current levels of conflict between leopards and stock farmers are low, leopards do depredate livestock, which constitute 10-15% of their diet. Improved livestock husbandry measures and co-operation between conservation authorities and farmers are necessary to mitigate such conflict and balance economic security with biodiversity conservation in the region. Leopards are the only remaining top predators throughout much of the Little Karoo and the Western Cape and as such are predicted to play a critical role in ecosystem structure and the survival of other species. Current high levels of connectivity between areas of suitable leopard habitat bode well for the conservation status of leopards within this region and future conservation efforts need to ensure that narrow corridors linking such habitat are preserved. The potential for leopards to serve as both an umbrella and a flagship species for biodiversity conservation suggests that long term monitoring of this population would be a conservation priority for the Little Karoo.

Thesis (MTech (Nature Conservation))--Cape Peninsula University of Technology, 2015. / The klipspringer (Oreotragus oreotragus subsp. oreotragus) population became extinct on the Cape Peninsula in 1930. Being re-introduced into Table Mountain National Park (TMNP) in 1999 it became one of the species of special conservation concern to monitor in the Park. Most klipspringer territories are known by Park management but the distribution of all potentially suitable habitats for this species in the Park is not known. The main aim of this study is to produce a distribution range map that is representative of all potentially suitable habitats for the klipspringer within TMNP, through the use of a species distribution modelling tool. Since only presence data were available for this study, a popular presence-only modelling tool namely maximum entropy (MaxEnt) was used. The use of MaxEnt in species distribution modelling has become popular as it has proven to provide robust predictions of a species’ geographic distribution. Klipspringer occurrence data and five environmental variables namely altitude, slope, aspect, vegetation, and distance to urban edge were used as model input. Occurrence data were sourced through existing databases and employing a stratified random sampling technique of dividing the Park into different habitat subtypes to survey the Park for more klipspringer occurrences. These habitat subtypes consisted of a variety of vegetation communities or vegetation types and altitudinal and slope ranges available in the Park. Grid size for all the raster layers used was 10x10 m. Spatial filtering of one point per 100 m² grid was used to eliminate clumping of points. Six models were run at different regularisation multiplier (RM) values namely 0.25, 0.5, default (1), 2, 4 and 7. To assist in better understanding of the spatial extent of the occurrence data and the areas inhabited by the klipspringer, home range analyses were carried out. This was done through kernel density estimation in the Geospatial Modelling Environment (GME). All six bandwidth parameters in GME namely smoothed cross validation (SCV), biased cross-validation (BCV), a second BCV algorithm, plug-in estimator, least squares cross validation and the likelihood cross validation (CVh) were tested. The smoothed cross validation and likelihood cross validation bandwidth algorithms provided the best visual output of klipspringer home ranges and territories. Home range sizes from the SCV output ranged from about 3 – 11 ha across the study area, and home range size for the CVh output ranged from 0.6 – 2.5 ha. The output from the CVh algorithm was interpreted as territories rather than home ranges, as it is based on a univariate kernel unlike, the SCV algorithm that produces rotated bivariate kernels. iv The default regularisation multiplier of 1 provided the best probability distribution output, whilst values lower than the default tended to underestimate the prediction and those values higher than the default were tending towards overestimations. Response curves for the default RM also gave the most ecologically meaningful responses of the klipspringer to each environmental variable. Model evaluation in the form of area under the receiver operating characteristic curve (ROC AUC) showed that all models performed well. Therefore, the choice of the “best” model was based on the ability to provide ecological interpretation, on the shape of the response curve and the probability distribution maps. Consequently, the default RM model was considered the best, with an AUC score of 0.903. Altitude and vegetation contributed the most to suitable habitat and therefore indicates that klipspringer in the Park do prefer high altitudinal areas with the right vegetation to feed on. Suitable altitudinal ranges are from 400 m.a.s.l. and higher and ericaceous fynbos is the most preferred vegetation community. Slope, aspect and distance to urban edge played a less important role in suitable klipspringer habitat. The probability map and an additional binary map produced at the 10 percentile training logistic presence threshold showed that suitable habitat for the klipspringer occurs in all three sections of the Park in different proportions. These maps can be used by Park management to prioritise conservation efforts and future re-introductions. / National Research Foundation

The conservation of leopards in the Eastern Cape Province requires a holistic approach that considers both predator-human interactions as well as the biology of the carnivore. Numerous studies have been conducted on leopards within protected areas; however more information regarding the species is needed outside these areas to facilitate effective management of predators. The spatial ecology of the leopard (Panthera pardus) were studied in the Baviaanskloof and GAENP in the Eastern Cape. The Baviaanskloof is an extensive area of mountainous terrain (approximately 2665km²) which has a mosaic of land uses, and leopards move from conservation areas to farmland where they come into contact and conflict with farmers. This study examined the spatial ecology of leopards living on farmlands adjacent to protected land. The space utilization and activity patterns of six leopards were analysed. These animals were caught and released on farmlands in the Baviaanskloof (n=4) or translocated (n=2) when not possible to release on site. The animals were caught by means of fall-door, walk-in traps and fitted with Vectronic GPS collars that facilitated the collection of high quality GPS fixes from each animal. Data was collected using VHF and UHF telemetry to download data. An understanding of spatial requirements in areas with different land use, and the extent of overlap of space use with other leopards allow, for the first time in the region, the calculation of possible maximum population size. Analysis of range size was carried out using two methods: minimum convex polygon, and Kernel Utilization Distribution. Finally, a key predictor of space use is prey availability. I assessed the prey base using a grid of camera traps. The studied leopards revealed large range utilization with minimal overlap. The activity patterns suggest there is no preference between diurnal and nocturnal activity patterns and the population density was estimated between 0.3 - 1.3 leopards per 100km². Large home range sizes and low population densities suggest that leopards require large areas of suitable habitat, and that conservation efforts need to be extended beyond protected areas to ensure the long-term viability of leopard populations in such areas.