A thesis submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Doctor of Philosophy. Johannesburg, South Africa. August 2014 / Unable to load abstract.

Thesis (MSc)--Stellenbosch University, 2008. / ENGLISH ABSTRACT: The Greater Cederberg Biodiversity Corridor (GCBC) is a large-scale conservation corridor situated in the south-western region of South Africa. Delineation of the GCBC was largely based on by vegetation data. The relevance of the GCBC for the conservation of the reptilian fauna in the area south of 31°S and west of 21°E is assessed in the present study. This entailed determining the GCBC’s coverage of regional reptile diversity patterns and assessing its potential conservation significance during possible climate induced changes in reptile distributions. Reptile species point distribution data from the preliminary (2007) SARCA (South African Reptile Conservation Assessment) database was used. Under-representation of the Tankwa Karoo in the dataset required a field survey of this region. Additionally, the biogeographical influence of the arid Tankwa Karoo Basin on the distribution of reptiles in the south-western districts of South Africa was investigated. Turnover across the Basin is high, species richness is lower than in surrounding mountainous areas and there are no species endemic to the area. The Tankwa Karoo Basin acts as a dispersal barrier for many reptile species occurring in the surrounding more mesic areas. At the same time, the ranges of a number of typical northern, arid adapted species extend southward along the Tankwa Plains. A number of species range extensions in the region are reported. Patterns of endemism, species richness and turnover were plotted from the point distribution data at quarter and eighth degree square resolution. Extensive sampling bias towards reserves and populated areas is apparent from the reptile species richness plots. This pattern is more pronounced for snakes than lizards. Reptile richness is particularly high along the north-south section of the Cape Fold Mountains and also relatively high along the south-western coast, peaking in the Lambert’s Bay area. The majority of the 20 reptile species endemic to the study area are associated with one of two identified centres of endemism: the Greater Cederberg area, or the narrow coastal zone stretching from the Lambert’s Bay area to the Cape Peninsula. An additional third set of endemics comprised of melanistic forms restricted to a number of different refugia, notably, Landroskop, the Cape Peninsula, Sladanha-Langebaan region, Piketberg Mountains and a confined area along the western section of the Cape Fold Mountains. Species richness and endemism patterns co-vary within the study area. Biotic regions were identified through hierarchical clustering of grid cells according to shared species occurrences. A Northern, Southern, Central and Western biotic region was identified. Classification tree methodology (CART) and Canonical Correspondence Analysis (CCA) were used to characterise defined biotic regions in terms of selected environmental variables. Four sets of species assemblages are described on the basis of these biotic regions – two major and two minor ones. Of the major assemblages the Northern assemblage can be described as an arid zone one and the Southern assemblage as a mesic zone one. The minor Central assemblage, comprising mainly rock-dwelling forms, represent evolutionary leftovers as a result of climate change induces cycles of contraction and expansion of arid and mesic faunas. The other minor one, the West Coast assemblage could be considered a sub-assemblage of the Northern one, with particular adaptation to the coastal climate. Environmental characterisation of the biotic regions reveals that these groupings are supported by an environmental signal. The contiguity of four distinct sets of reptiles, each with its own set of environmental requirements, in this relatively small geographic area clearly indicates that the southwestern region of South Africa is biogeographically complex. The GCBC incorporates the largely coinciding centres of endemism and richness along the West Coast and the greater Cederberg area. Although the centre of endemism for melanistic reptile forms, in the Saldanha-Langebaan area, falls just south of the GCBC boundary, the Corridor fulfils the requirements for effective conservation of reptiles in the area to a large degree. The north-south dispersal pathways provided by the Corridor along the Cape Fold Mountains is believed to be adequate to buffer climate change effects, however there is concern about its ability to contribute to the persistence of the assemblage associated with the narrow coastal zone in the west. / AFRIKAANSE OPSOMMING: Die Groter Cederberg Biodiversiteit Korridor (GCBK) is ‘n grootskaalse bewaringskorridor wat in die suid-westelike deel van Suid-Afrika geleë is. Die grense van GCBK is gebasseer op plantegroei data. In die huidige studie word die betekenis van die GCBK vir die bewaring van die reptiel fauna in die gebied suid van 31°S en wes van 21°O assesseer. Die mate waartoe die GCBK die patrone van reptieldiversiteit in die streek inkorporeer, asook die korridor se potensiaal om voorsiening te maak vir reptiel verspreidingsgebiede wat moontlik as gevolg van potensiële omgewingsverandering kan verskuif. Die beskikbare puntverspreidingsdata van die voorlopige (2007) SARCA (South African Reptile Conservation Assessment) databasis is gebruik. Swak verteenwoordiging van die Tankwa Karoo in die datastel het ‘n veldopname van die gebied genoodsaak. Verder is die biogeografiese invloed van die ariede Tankwa Karoo Kom op die verspreidingspatrone van reptiele in die suid-westelike deel van Suid-Afrika ook ondersoek. Die spesie omset van beide Noord na Suid en Wes na Oos oor die Tankwa is hoog, die spesierykheid is aansienlik laer as in die omringende bergagtige gebiede en daar is geen spesies wat endemies is tot die Tankwa Karoo nie. Die Tankwa Karoo Kom dien as ‘n barieêre teen spreiding vir sommige reptielspesies wat in die omringende gematigde gebiede voorkom. Terselfdertyd reik die verspreidings van ‘n aantal tipiese droogte aangepasde spesies vanuit die noorde suidwaarts langs die Tankwa Vlaktes. Nuwe verspredingsrekords wat ‘n paar spesies se gebiede uitbrei word ook raporteer. Die puntverspreidingsdata is geruik om die patrone van endemisme, spesierykheid en omset op kwart- en agtstegraad resolusie te plot. Spesierykheid kaarte toon ‘n duidelike neiging tot deegliker opnames in reservate en bewoonde gebiede. Hierdie patroon is meer opmerklik vir slange as akkedisse. Reptielrykheid is besonders hoog langs die noord-suid as van die Kaapse Plooiberge en ook relatief hoog langs die suid-wes kus met ‘n maksimum in die Lambertsbaai omgewing. Die meerderheid van die 20 reptielspesies wat endemies is aan die studie area is met een van twee geïdentifiseerde sentrums van endemisme geassosieer: die Groter Cederberg area óf die nou kussone wat vanaf Lambertsbaai tot Kaappunt strek. ‘n Derde stel endemiese spesies wat uit melanistiese vorme bestaan, is beperk tot ‘n aantal refugia, naamlik, Landroskop, Kaappunt, Saldanha- Langebaan omgewing, Piketberg berge en ‘n beperkte area langs die westelike dele van die Kaapse Plooiberge. Spesierykheid en endemisme patrone stem grootliks ooreen binne die studie area. Roosterselle is op grond van gedeelde spesiesamestellings met behulp van ‘n hieragiese groeperingsmetode (Incremental Sum of Squares) gegroepeer. Vier bio-areas, nl. ‘n Noordelike-, Suidelike-, Sentrale en Westelike bio-area is identifiseer. Klassifikasieboom metodologie (Classification and Regression Trees, CART) asook Kanoniese Annalises (Cannonical Correspondence Annalysis, CCA) is gebruik om hierdie geografiese areas in terme van ‘n aantal omgewingsveranderlikes te karakteriseer. Vier spesieversamelings, twee groter en twee kleiner versamelings, is in ooreenstemming met hierdie vier areas geïdentifiseer. Die Noordelike en Suidelike spesieversamelings is die groteres en kan beskryf word as die faunas van onderskeidelik ‘n ariede en gematigde sone. Die kleiner Sentrale versameling bestaan hoofsaaklik uit rots-lewende spesies en mag die evolusionêre oorblyfsels verteenwoordig van ariede en gematigde faunas waarvan die verspreidings herhaaldelik as gevolg van klimaatsveranderingsiklusse uitgebrei en gekrimp het. Die Weskus versameling is ook ‘n kleiner een en kan as ‘n sub-versameling van die Noordelike een beskou word, maar spesifiek tot die kus klimaat aangepas. Die klassifikasie van hierdie bio-areas word ondersteun deur die analiese van die omgewingsveranderlikes. Die feit dat vier kenmerkende versamelings reptiele, elk met sy besondere omgewingsvereistes, in hierdie relatief klein geografiese area ontmoet, dui daarop dat die suid-westelike deel van Suid-Afrika biogeografies kompleks is. Die GCBK inkorporeer die grootliks ooreenstemmende sentrums van endemisme en rykheid wat langs die Weskus en in die groter Cederberg area voorkom. Alhoewel die sentrum van melanistiese endemiese spesies, in die Saldanha-Langebaan omgewing, net buite die grense van die Korridor val, voldoen die GCBK grootliks aan die vereistes vir die effektiewe bewaring van reptiele in die gebied. Die voorsiening van noord-suid verspreidingsweë langs die Kaapse Plooiberge binne die Korridor word beskou as voldoende om die gevolge van klimaatsverandering te buffer. Daarinteen is daar kommer oor die vermoeë van die GCKB om ‘n doeltreffende bydrae te maak tot die voortbestaan van die spesieversameling wat met die nou kussone langs die Weskus geassosieer is.

Thesis (PhD)--Stellenbosch University, 2010. / ENGLISH ABSTRACT: Biological invasions are a growing threat to biodiversity, trade and agriculture in South Africa. Though alien reptiles and amphibians (herpetofauna) are not currently a major issue, escalating problems worldwide and increased trade in South Africa suggest a possible increase in future problems. In this thesis I explore practical measures for risk assessment implementable under national legislation. I began by documenting record-keeping and legislative differences between provinces in South Africa. This revealed some serious deficiencies, complicating attempts to compile accurate inventories and discern import trends. International trade data, however, revealed an exponential increase in the number of imports to South Africa over the last 30 years. Characterising the abundance of species in this trade is important as species introduced in large numbers pose a higher establishment risk. In South Africa, I found a tendency for venomous and expensive species to be traded in low numbers, whereas species that are easy to breed and handle, or that are colourful or patterned are traded in higher numbers. Unlike South Africa, California and Florida have had a large number of well-documented herpetofaunal introductions. These introductions were used to verify the role of several key predictors in species establishment. I first evaluated the role of each variable separately. I examined different approaches for bioclimatic modelling, the predictive power of different sources of distribution data, and methods of assigning a climate-match score. I also present the first test of Darwin’s naturalization hypothesis for land vertebrates using two new phylogenies inferred for native and introduced reptiles in California and Florida. I then used boosted regression trees (BRT) to infer the relative contribution of each factor to species establishment success. Results from the BRTs were incorporated into a user-friendly spreadsheet model for use by assessors inexperienced in complex modelling techniques. Introduction effort was found to be the strongest contributor to establishment success. Furthermore, species with short juvenile periods were more likely to establish than species that started breeding later, as were species with more distant relatives in regional biotas. Average climate match and life form were also important. Of the herpetofaunal groups, frogs and lizards were most likely to establish, while snakes and turtles established at much lower rates, though analysis of all recorded herpetofaunal introductions shows slightly different patterns. Predictions made by the BRT model to independent data were relatively poor, though this is unlikely to be unique to this study and can be partially explained by missing data. Though numerous uncertainties remain in this field, many can be lessened by applying case by case rules rather than generalising across all herpetofaunal groups. The purpose for import and potential trade volume of a species will influence the threat it poses. Considering this in conjunction with a species’ environmental tolerances and previous success of species with similar life histories, should provide a reasonable and defendable estimate of establishment risk. Finally, a brief summary of the potential impacts of introduced alien herpetofauna is provided in the thesis. / AFRIKAANSE OPSOMMING: Indringer spesies hou ‘n al groter bedreiging in vir die biodiversiteit, handel en landbou van Suid- Afrika. Alhoewel uitheemse reptiele en amfibieërs (herpetofauna) tans nie ‘n groot bedreiging in Suid-Afrika is nie, dui groeiende probleme wêreldwyd asook 'n toename in plaaslike handel op moontlike toekomstige probleme. In hierdie tesis, ondersoek ek praktiese metodes vir risikobepaling wat onder nasionale wetgewing toegepas kan word. Ek begin deur die verskille in stoor van rekords en wetgewing tussen provinsies te dokumenteer. Hierdie proses het ernstige tekortkominge uitgewys, wat pogings om akkurate inventarisse saam te stel en invoertendense te bepaal, bemoeilik. Internasionale handelsdata het egter getoon dat daar ‘n eksponensiële toename in die hoeveelheid invoere na Suid-Afrika oor die laaste 30 jaar was. Die hoeveelheid spesies in hierdie handel is belangrik omdat spesies wat in groot hoeveelhede ingevoer word, ‘n hoër vestigingsrisiko het. In Suid-Afrika is ‘n tendens gevind vir handel in giftige en duur spesies teen lae hoeveelhede, terwyl spesies wat maklik teel, maklik hanteer kan word en kleurvol is of mooi patrone het, in groter hoeveelhede mee handel gedryf word. Kalifornië and Florida, in teenstelling met Suid-Afrika, het ‘n hoë aantal goed-gedokumenteerde gevalle van herpetofauna wat in die natuur vrygestel is. Hierdie introduksies was gebruik om die rol van verskeie belangrike faktore in die vestiging van populasies te bepaal. Eerstens het ek die rol van elke faktor apart ondersoek. Ek het verskillende benaderinge vir bioklimatiese model-bou ondersoek, die akuraatheid van verskillende bronne van distribusiedata getoets en drie metodes om ‘n “climate match score” te bereken, voorgestel. Ek bied ook die eerste toets van Darwin se naturalisasie-hipotese vir landwerveldiere aan, deur gebruik te maak van twee nuwe filogenieë wat ek gebou het vir inheemse en ingevoerde reptiele in Kalifornië en Florida. Ek het verder gebruik gemaak van “boosted regression trees” (BRT) om die relatiewe bydrae van elke faktor tot die vestigings-potensiaal van spesies te bepaal. Resultate van hierdie BRTs was ingekorporeerd in ‘n gebruikersvriendelike ontledingstaat wat deur bestuurders, onervare in komplekse modelboutegnieke, gebruik kan word. Invoer-hoeveelheid was die faktor wat die sterktste bygedra het tot suksesvolle vestiging. Verder is spesies met kort jeugperiodes en dié met verlangse familie in streeks-biotas, meer geskik om suksesvol te vestig. Gemiddelde klimaatooreenstemming en lewensvorm was ook belangrik. Paddas en akkedisse was die mees waarskynlikste van die herpetofauna groepe om populasies te vestig, terwyl slange en skilpaaie teen laer tempo’s populasies gevestig het, alhoewel analise van alle gedokumenteerde gevalle van herpetofauna-invoerings wêreldwyd effens verskillende tendense toon. Voorspellings wat deur die BRT-model vir onafhangklike data gemaak is was redelik swak, alhoewel hierdie resultaat onwaarskynlik nie uniek aan die studie is nie, en word gedeeltelik verduidelik deur die gebrek aan data. Alhoewel talle onsekerhede steeds bestaan, kan dié verminder word deur geval-tot-geval reëls toe te pas eerder as om vir herpetofauna as ‘n groep te veralgemeen. Die doel van invoer en potensiële handel-volumes van ‘n spesie, sal die bedreiging wat die spesie toon, bepaal. Hierdie faktore moet saam met omgewingstoleransie en voorafgaande sukses van spesies met soortgelyke lewenswyses oorweeg word, om ‘n aanvaarbare en verdedigbare beraming van vestigingsrisiko te gee. Laastens, word ‘n kort opsomming van die effekte wat uitheemse herpetofauna mag hê, verskaf.