Thesis (PhD)--University of Stellenbosch, 2008. / Bibliography. Also available via the Internet.

Thesis (MSc)--University of Stellenbosch, 2006. / Bibliography. Also available via the Internet.

Thesis (MA)--University of Stellenbosch, 2006. / Bibliography. Also available via the Internet.

A dissertation submitted to the School of Geography, Archaeology and Environmental Studies, Faculty of Science at the University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Master of Science. Johannesburg, 2016. / The Crocodile River East in Mpumalanga Province, South Africa, has seen three major floods in a twenty-four-month period, specifically January 2011, January 2012 and January 2013. The damage included the loss of life, damage and/or loss of public or private properties, agricultural land loss, and damage to biodiversity and river geomorphology. The purpose of this study was to understand the consequences and risks to livelihoods and river basin systems due to flooding of the river. The study focused on a segment of the Crocodile River East, between Riverside and Tekwane. The study used historic hydro-climatic data for the Crocodile River to determine the critical threshold for past flood events and to predict the extent of future flood events. Hydrological modelling coupled with the HEC-RAS hydraulic model enabled the simulation of these future flood events. The use of orthophotos and digital elevation models (DEMs) allowed for a spatial representation of the areas affected during the flood events. Flood hazard maps and flood risk maps were then developed for the identified flood events within a Geographical Information System (GIS). The maps enabled the identification of high risk and flood prone areas along this segment of the Crocodile River Basin. The results showed that when discharge reaches 241.75 m3/s, both locations (Riverside and Tekwane) are at risk to flooding. This is therefore the threshold for which the two locations are likely to be flooded. This study provides a methodology to determine the spatial extent of past and modelled future river flood events. As such, outcomes of this study may aid in the understanding of flood hazard extent and flood prone areas, and may thus help catchment management authorities and institutions in flood reconstruction and flood risk management. The employed methodology can aid effective spatial planning, and can also be extended at the basin scale through integration with the existent flood warning system to gain an estimate of flood extent and flood risk. / TG2016

A thesis submitted to the Faculty of Science, University of the Witwatersrand, in fulfilment of the requirements for the degree of Doctor of Philosophy. Johannesburg, 2015. / It is recognised that tooth loss as a consequence of oral diseases affects quality of life in humans. This has directed studies towards biological tooth replacement in vivo. In humans and other mammals, tooth replacement occurs only once (diphyodonty) as opposed to non-mammalian vertebrates where tooth replacement continues throughout life (polyphyodonty). Detailed knowledge of tooth initiation, development and morphology amongst vertebrates and especially amniotes, is necessary to understand the tooth replacement process. Crocodilians provide an interesting model for tooth replacement studies as they also exhibit thecodonty. Regulation of polyphyodonty has not been genetically defined, and it is uncertain whether the molecular mechanisms of continuous tooth replacement are similar to those involved in the primary dentition. The aim of this study was therefore to analyse crocodilian odontogenesis in detail, with the aid of light microscopy and CT scans, in order to provide a structural framework for molecular processes regulating polyphyodonty. Crocodile probes to bmp4 and pitx2 were designed, generated and labelled for use in in situ hybridisation. The expression patterns of pitx2 and bmp4 in embryos and hatchlings of the polyphyodont Nile crocodile (Crocodylus niloticus) were examined at different stages of tooth development. Histologically crocodilian tooth development appears similar to mammals. Interesting variations include the initiation of odontogenesis in the ectomesenchyme, the presence of dental placodes, the ‘null generation teeth’, the two different bell-stage tooth germs and the tooth-family organisation. A direct 1:1 relationship between the status of the erupted tooth and the developmental phase of the replacement tooth was not seen. However in more mature teeth, the replacement tooth germs were at a more advanced developmental stage than those associated with less mature teeth. Molecular data revealed that pitx2 was expressed in the oral epithelium and the dental placode. Bmp4 expression was not evident in the dental placode, but was localised in the odontoblasts of early bell stage tooth germs. Pitx2 and bmp4 were expressed in both the odontoblast and ameloblast layers in late bell stage tooth germs. Expression of pitx2 and bmp4 is conserved across vertebrates and pitx2 may play a role in initiation of primary and successional teeth.

With increasing demands on limited water resources and unavailability of suitable dam sites, it is essential that available storage works be carefully planned and efficiently operated to meet the present and future water needs.This research report presents an attempt to: i) use Artificial Neural Networks (ANN) for the simulation of the Crocodile water resource system located in the Mpumalanga province of South Africa and ii) use the model to assess to what extent Kwena dam, the only major dam in the system could meet the required 0.9m3/s cross border flow to Mozambique. The modelling was confined to the low flow periods when the Kwena dam releases are significant. The form of ANN model developed in this study is the standard error backpropagation run on a daily time scale. It is comprised of 32 inputs being four irrigation abstractions at Montrose, Tenbosch, Riverside and Karino; current and average daily rainfall totals for the previous 4 days at the respective rainfall stations; average daily temperature at Karino and Nelspruit; daily releases from Kwena dam; daily streamflow from the tributaries of Kaap, Elands and Sand rivers and the previous day’s flow at Tenbosch. The single output was the current day’s flow at Tenbosch. To investigate the extent to which the 0.9m3/s flow requirement into Mozambique could be met, data from a representative dry year and four release scenarios were used. The scenarios assumed that Kwena dam was 100%, 75%, 50% and 25% full at the beginning of the year. It was found as expected that increasing Kwena releases improved the cross border flows but the improvement in providing the 0.9m3/s cross border flow was minimal. For the scenario when the dam is initially full, the requirement was met with an improvement of 11% over the observed flows.

Borealosuchus Brochu 1997 was erected for a group of Late Cretaceous through early Eocene eusuchian crocodyliform species formerly assigned to Leidyosuchus Lambe 1907. Borealosuchus wilsoni was originally described by Mook (1959) based solely on a dorsoventrally crushed skull from the early Eocene (Wasatchian) Green River Formation of Wyoming, and assigned to Leidyosuchus. Later analyses referred specimens from the late Paleocene and middle Miocene to the species (Brochu, 1997). In phylogenetic analyses, Borealosuchus has been retrieved as either a basal crocodylian (e.g., Salisbury and Willis, 1996; Brochu, 1997; Wu et al., 2001; Buscalioni et al., 2011; Brochu et al., 2012; Narváez et al., 2016) or a close crocodylian outgroup (e.g. Benton and Clark, 1988; Pol et al., 2009; Turner and Pritchard, 2015). More exact phylogenetic placement of Borealosuchus remains unclear. Borealosuchus wilsoni is stratigraphically the youngest species of Borealosuchus, and one of the most completely known, and as such, it figures prominently in ongoing debates over the phylogenetic relationships and origin of crown group Crocodylia. Given its long stratigraphic range in the literature, the question of whether specimens currently referred to B. wilsoni all pertain to a single species is open. This study focuses on a more thorough description of the skeletal morphology of Eocene Borealosuchus, and a revision of the taxonomy of this assemblage, including the conspecific nature of Wasatchian Borealosuchus wilsoni and middle Eocene (Bridgerian) fossils referred to Borealosuchus wilsoni, including material of Diplocynodon stuckeri Mook 1960. A phylogenetic re-assessment of B. wilsoni will hopefully provide further resolution within Borealosuchus and among other closely related taxa. Specimens were coded with a matrix of 190 morphological characters and subjected to phylogenetic analysis. The diversity of Borealosuchus during the Eocene has been underestimated and specimens from the Bridgerian are diagnosable and distinct from those of the preceding Wasatchian stage. A new species will be erected to contain this material. The erection of a new species of Eocene Borealosuchus renders the holotype of D. stuckeri non-diagnostic at the species level, and a new holotype USNM 12990 is designated for Bridgerian Borealosuchus. Some specimens assigned to Brachyuranochampsa eversolei and Crocodylus affinis may also be referable to Borealosuchus. The addition of new material to Borealosuchus increases the diversity of this group during the Eocene.

The Nile crocodile Crocodylus niloticus currently has an extensive range throughout the African continent and Madagascar, though fossil and subfossil remains show that its historic range was considerably larger and included parts of the Sahara Desert, Mediterranean coast, and Arabian Peninsula. Recent molecular studies have yielded genetically distinct populations of C. niloticus, leading to the possibility that C. niloticus is actually multiple cryptic species, while morphological variation remains unassessed. This study compares skulls of C. niloticus to other members of the genus Crocodylus in dorsal view using geometric morphometrics to evaluate intraspecific and interspecific variation. The morphometric analysis is coupled with a geographic analysis to determine if the species is morphologically variable by geographic region as well as a model-based cluster analysis to determine and morphological clusters irrespective of other factors. These analyses indicate that C. niloticus exhibits populational variation that exceeds almost every other species of Crocodylus, with differences between geographic regions statistically disctinct. These results support the presence of a cryptic species complex. Additionally, an osteological description of Crocodylus niloticus is provided.

The Convention on International Trade in Endangered Species of Wild Fauna and Flora (C.I.T.E.S.) has always recognized Osteolaemus tetraspis osborni (Schmidt, 1919) as a geographic subspecies of the African dwarf-crocodile, taxonomically distinguished from the subspecies Osteolaemus tetraspis tetraspis Cope, 1861. These two subspecies are primarily based on anatomical evidence that is not visible on a whole living animal. The subspecies distinction is the internal degree of boniness of the septum between the two external nostrils. This character must be examined by dissection of the animal’s head. Therefore it is desirable that some reliable and diagnostic kind of externally visible identification character (such as coloration, measuring head proportions, or counting scales) should be searched for. Otherwise, any individual Osteolaemus tetraspis animal must be partly dissected to see what subspecies it is. In this thesis, approximately a dozen different external characters (mostly counting scales or rows of scales) are independently tested and compared with each other in an effort to determine which of them is the most useful as an identification tool for separating the Osteolaemus t. osborni subspecies from the O. t. tetraspis taxon. If none of these scalation details are found to be 100% reliable as a predictor of the appropriate geographic taxon, then some additional factors become relevant, such as their comparative difficulties in physically performing the investigation. Some kinds of scale-counts are easier to define and record than others. The new sample is 68 African dwarf-crocodiles, of which 53 are geographically in the COAST (O. t. tetraspis) taxon, and 15 are from the INTERIOR (O. t. osborni). The data was collected by field-work in numerous African nations, and the expedition sampled and travelled across the C.I.T.E.S. subspecies boundary between these two taxa in several ways. In comparison with earlier published reports about scalation characters in the Osteolaemus tetraspis species, this new sample is relatively large, and has remarkably good precision about locality data. Further, this expedition (the Zoer Osteolaemus Project, 2006-2007) exercised extreme care to apply clear definitions for the various characters (scale-counts, row-counts, etc.). Based on good samples, and on the high quality scalation data collected in 2006-2007 in Africa, it is concluded that none (zero) of these dorsal and ventral skin characters (with the possible exception of the two kinds of ventral scale-counts, for which the INTERIOR sample was only 3 animals) yield satisfactory results for discriminating subspecies of dwarfcrocodiles in the general part of the continent that was examined. All of these many kinds of scalation features fail to 100% reliably predict the correct subspecies (COAST or INTERIOR) outcome. Some characters never (0,00%) work, while other characters work part of the time, but not one gives the level of predictability that is required by C.I.T.E.S. for quick and accurate taxonomic identification in Osteolaemus tetraspis with these two subspecies as regulated taxa. All of the literature scalation characters required detailed special examination procedures, usually involving physically handling the animal. This thesis invents and recommends a new kind of character which has the advantage that just looking at the dorsal surface of the crocodile is often sufficient, and sometimes it can be done through a telescope. For this “permit-free” scalation character, properly taken photographs can include the normal (tourist at the zoo) view from the side and slightly above. It is not necessary to look straight down at the animal, as long as the number of transverse rows on the base of the neck, and along the length of the body, and on the proximal half of the tail can be counted. Neither the old nor the new characters work 100% of the time, and although the permitfree count of transverse rows on the dorsum is slightly more predictive than any of the others, even this new method yields remarkably poor results. However, given a large enough sample (for example bushmeat or stuffed animals or flat hornback hides passing through a local market over a long period of time), it is predicted that an interesting indication of subspecies identification could, in a statistical way, possibly be obtained. In the final analysis, though, African dwarf-crocodile scale-counts do not appear to support the model of two taxa in Osteolaemus tetraspis as a species, and therefore they do not support the inclusion of Osteolaemus tetraspis osborni as a regulated taxon on the C.I.T.E.S. list of crocodilians. AFRIKAANS : Het CITES verdrag (“Convention on International Trade in Endangered Species of Wild Fauna and Flora”) heeft Osteolaemus tetraspis osborni (Schmidt, 1919) altijd erkent als een geografische ondersoort van de Afrikaanse dwergkrokodil, die onderscheiden kan worden van Osteolaemus tetraspis tetraspis Cope, 1861. Deze twee ondersoorten zijn primair gebaseerd op anatomisch bewijs dat niet zichtbaar is op een puntgaaf en levend dier. Het onderscheid tussen de ondersoorten is de interne graad van het aanwezig bot van de afscheiding tussen de twee uitwendige neusgaten. Dit karakter zal moeten worden onderzocht middels een autopsie op het hoofd van het dier. Daarom is het wenselijk dat er gezocht wordt naar een aantal betrouwbare en diagnostieke vormen van uitwendig zichtbare identificatie karakters (zoals kleuring, het meten van hoofdproporties, of het tellen van schubben). Zo niet, dan zal ieder individueel Osteolaemus tetraspis dier gedeeltelijk moeten worden ontleed om te zien welke ondersoort het betreft. In deze scriptie zijn ongeveer een twaalftal verschillende uitwendige karakters (met name het tellen van schubben of rijen van schubben) onafhankelijk van elkaar getest en onderling vergeleken in een poging om vast te stellen welke van hen het meest bruikbaar is als een middel ter identificatie voor het onderscheiden van de Osteolaemus t. osborni ondersoort en de O. t. tetraspis taxon. Wanneer geen van deze schubbenkleed details als 100% betrouwbaar wordt beschouwd als voorspeller van de van toepassing zijnde taxon, dan worden een aantal aanvullende factoren relevant, zoals de moeilijkheidsgraad van de fysieke uitvoering van het onderzoek. Sommige schubbentellingen zijn eenvoudiger te definiëren en te registreren dan andere. De nieuwe sample bestaat uit 68 Afrikaanse dwergkrokodillen, waarvan er 53 geografisch gezien in de KUST (O. t. tetraspis) taxon zitten en er 15 zijn van het BINNENLAND (O. t. osborni). De gegevens zijn verzameld middels veldwerk in een groot aantal Afrikaanse landen en de expeditie verzamelde op verscheidene manieren gegevens van deze taxa aan beide zijden van de C.I.T.E.S. ondersoorten grens. In vergelijking met eerder gepubliceerde rapporten over schubbenkleed karakters in de soort Osteolaemus tetraspis, is deze nieuwe sample relatief groot en heeft het opvallend nauwkeurige plaatsgegevens. Verder heeft deze expeditie (het Zoer Osteolaemus Project, 2006-2007) voor zeer duidelijke definities gezorgd voor de verschillende karakters (schubbentellingen, rij-tellingen, enz.). Op basis van goede samples en de hoge kwaliteit van de in 2006-2007 in Afrika verzamelde schubbenkleed gegevens, kan worden geconcludeerd dat geen (nul) van deze rug en buik huidkarakters (met mogelijk uitzondering van de twee schubbentelllingen op de buik, waarvan de BINNENLAND sample slechts 3 dieren was) bevredigende resultaten geeft om ondersoorten in dit breedvoerig onderzochte deel van het continent te kunnen onderscheiden. Al deze schubbenkleed kenmerken schieten te kort om 100% betrouwbaar de juiste ondersoort te voorspellen (KUST of BINNENLAND). Sommige karakters werken nooit (0,00%), andere gedeeltelijk, maar geen enkele geeft het door C.I.T.E.S. vereiste niveau van voorspelbaarheid voor een snelle en accurate identificatie van Osteolaemus tetraspis met deze twee ondersoorten als gereguleerde taxa. Alle schubbenkleed karakters uit de literatuur vereisten gedetailleerde en speciale onderzoeksprocedures, waaronder vaak het fysiek hanteren van het dier. Deze scriptie vindt uit en beveelt aan een nieuw karakter, welke het voordeel heeft dat enkel het kijken naar de bovenkant van de krokodil voldoende is en soms met behulp van een verrekijker kan gebeuren. Voor deze “vergunning-vrije” schubbenkleed karakter kunnen fatsoenlijk genomen foto’s het normale (toerist in een dierentuin) aanzicht weergeven van de zijkant en lichtelijk van boven. Het is niet nodig om recht boven het dier naar beneden te kijken, zolang het aantal rijen van de basis van de nek in de lengterichting van het lijf tot ongeveer de helft van de staart kunnen worden geteld. Noch de oude, noch de nieuwe karakters werken in 100% van de gevallen en ondanks dat de “vergunning-vrije” telling van dwars op de bovenkant van het dier lopende rijen een iets betere voorspelling geeft dan alle andere, heeft zelfs deze nieuwe methode opvallend slechte resultaten. Echter, met een sample die groot genoeg is (bijvoorbeeld “bushmeat” of opgezette dieren of huiden, die over een lange periode op lokale markten worden verhandeld) ligt het in de lijn der verwachting dat er een interessante indicatie voor de identificatie van ondersoorten (op een statistische manier) kan worden verkregen. Al met al kan worden gezegd dat schubbentellingen in Afrikaanse dwergkrokodillen niet het model van twee taxa in Osteolaemus tetraspis ondersteunen en daarmee Osteolaemus tetraspis osborni niet erkennen als een gereguleerd taxon in de C.I.T.E.S. lijst van krokodillen. / Dissertation (MSc)--University of Pretoria, 2010. / Animal and Wildlife Sciences / unrestricted

The Eocene Green River and Bridger Formations of Wyoming represent lacustrine and fl uvial environments noteworthy for an extremely diverse crocodylian fauna (at least eight species in seven genera). This paper discusses a fragmentary crocodylian jaw from the Bridger Formation, and also notes possible ecological partitioning among these sympatric crocodylians. The jaw fragment can be assigned confi dently to Borealosuchus based on the exclusion of the splenial from the mandibular symphysis and the presence of occlusal grooves between the alveoli, and it is referred tentatively to Borealosuchus cf. B. wilsoni. To examine the paleoecology of these crocodylians, variables based on habitat, body size, and inferred diet were formulated and species placed within respective categories. The research found that while there were more sympatric crocodylians in the early to mid Eocene of Wyoming than in any present-day biota, direct interspecifi c competition for resources is presumed to have been relatively low.