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The six floristic biomes in the Western Cape Province (W.C.P.), namely the Fynbos, Afromontane Forest, Thicket, Grassland, Nama and Succulent Karoo Biomes (Low and Rebelo, 1996), are not only diverse with regard to the variety of plant species and communities occurring there, but also contain a wide diversity of animal species, biogeographical zones, landscapes and natural features, both within the terrestrial and aquatic (freshwater and marine) context. In addition to the topographical diversity of the Cape Fold Mountains, the coastal zone and lowlands, and their transition into surrounding habitats, the W.C.P. experiences a wide climatic diversity too. These features have resulted in an extensive and complex diversity of habitat types which partly explain the rich biological diversity within the W.C.P. Past climatic changes on a global scale have also influenced ecological systems and processes within the W.C.P. to the extent where it is believed that vicariant speciation processes and events during global climatic changes have resulted in evolutionary driving forces that have had significant impacts on the biodiversity within the biogeographical boundaries of the W.C.P. (Vrba, 1985).

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Acanthodactylus arabicus, Acanthodactylus aureus, Acanthodactylus bedriagai, Acanthodactylus blanci, Acanthodactylus blanfordii, Acanthodactylus boskianus boskianus, Acanthodactylus boskianus asper, Acanthodactylus boskianus euphraticus, Acanthodactylus boueti, Acanthodactylus busacki, Acanthodactylus cantoris, Acanthodactylus dumerili dumerili, Acanthodactylus dumerili exiguus, Acanthodactylus erythrurus erythrurus, Acanthodactylus erythrurus belli, Acanthodactylus erythrurus lineomaculatus, Acanthodactylus felicis, Acanthodactylus gongrorhynchatus, Acanthodactylus grandis, Acanthodactylus guineensis, Acanthodactylus haasi, Acanthodactylus longipes, Acanthodactylus maculatus, Acanthodactylus masirae, Acanthodactylus micropholis, Acanthodactylus opheodurus, Acanthodactylus orientalis, Acanthodactylus pardalis, Acanthodactylus robustus, Acanthodactylus savignyi, Acanthodactylus schmidti, Acanthodactylus schreiberi schreiberi, Acanthodactylus schreiberi syriacus, Acanthodactylus scutellatus scutellatus, Acanthodactylus scutellatus hardyi, Acanthodactylus spinicauda, Acanthodactylus tilburyi, Acanthodactylus tristrami, Acanthodactylus yemenicus, Adolfus africanus, Adolfus alleni, Adolfus jacksoni, Adolfus vauereselli, Algyroides fitzingeri, Algyroides marchi, Algyroides moreoticus, Algyroides nigropunctatus nigropunctatus, Algyroides nigropunctatus kephallithacius, Australolacerta australis, Australolacerta rupicola

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Southern Africa has the richest reptile diversity in Africa, with a fauna that currently exceeds 490 species. Present rates of discovery, which for lizards are still comparable to those in the early phases of exploration, indicate that the fauna may approach, if not exceed, 600 species. Lizards form the dominant component (60.9%) of the reptile fauna. The 578 recognised taxa (species and subspecies) were described by 101 authors, of which 12 authors were responsible for 12 or more taxa and together named 68.9% of the total taxa. The five most productive authors were, in order: A. Smith, W. Peters, D. Broadley, J. Hewitt, and V. FitzSimons. The contributions of these authors, the growth in herpetological studies in the last 25 years, and the importance of regional surveys in the development of biogeographic models, are summarised. Over 50 species of reptile have very restricted distributions (less than 3 quarter-degree grid squares) and may be of conservation concern. Despite national rhetoric evincing concern for the biodiversity crisis, there has been a recent decline in herpetological posts and manpower.

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The phenotype of an individual has often been used as the descriminating factor in distinguishing species. However, with the advent of more precise molecular techniques, the genotype of species is increasingly being used as the preferred method in taxonomic classifications. Many taxa have recently been demonstrated to be incongruent in terms of their genetic and morphological groupings, and this may due to the influence that the environment may have on the morphological and functional aspects of a species. Selective pressures often act upon the performance of a species within a particular habitat first, and then selection for the morphological characters that allow for optimal performance occurs. Should genetically disparate species inhabit a particular environment, convergence in morphologies and performance may evolve. Historically, lizard species descriptions were based primarily on external morphologies, and thus misclassfication of species may have occurred due to mistakenly grouping species with convergent morphologies together. In the current dissertation, the links between morphology, performance capacities, diet and behaviour is explored in comparison to the environment and genetic relationships of southern African lacertid lizards. The performance capacities and associated morphological traits were expected to be more closely linked with the environment, and not closely linked with genetic relationships. To investigate these expectations, a multidisciplinary approach was taken, and genetic, morphological and performance analyses were done and compared with dietary behavioural and environmental analyses. In the first chapter, the link between habitat openness and the lizard bauplans is investigated and the presence of convergent morphologies within this group of lizards is uncovered. These convergences are shown to have resulted in misclassification of two lacertid species, and taxonomic revisions within the family are discussed. The second chapter explores the link between performance and associated morphological traits, and the dietary composition of the members of the Nucras genus. The third chapter identifies the link between the predator escape strategies employed by the members of the Meroles genus, and their morphologies and performance capacities. The fourth chapter explores the intraspecific, inter-population differences in morphologies and investigates the link between the morphological groupings and the population genetic groupings within Pedioplanis lineoocellata. The final chapter identifies whether adaptation to a novel habitat can occur over a relatively short period of time, and the morphological traits, functional aspects, and population genetic structure is investigated in conjunction with environmental analyses of vegetation and substrate between the populations of Meroles knoxii. It was concluded that the morphological and functional aspects of the southern African lacertid lizards are more closely related to the environment, particularly the microhabitat structure, than to their genetic relationships, and that future work using this group of lizards should involve a multidisplinary approach as different selective pressures are playing a role in shaping the morphologies and performance capacities of these lizards, compared to those that are acting upon the genotypes of the lizards.

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Molecular phylogenetic analyses of southern African lacertid lizards (Eremiadini) using mitochondrial and nuclear markers revealed two examples of generic assignments incompatible with monophyletic clades. Australolacerta Arnold 1989, a genus endemic to South Africa and to which two isolated species have been referred, is paraphyletic at the generic level. In addition, the species Ichnotropis squamulosa Peters 1854 was found to be embedded within the genus Meroles. To resolve the paraphyly in Australolacerta we erect a new genus, Vhembelacerta Edwards, Branch, Herrel, Vanhooydonck, Measey, & Tolley, gen. nov., to accommodate Lacerta rupicola FitzSimons 1933. To maintain a monophyletic Ichnotropis Peters 1854, Ichnotropis squamulosa Peters 1854 is transferred to Meroles Gray 1838, now named Meroles squamulosus comb. nov. Where necessary the genera affected by these actions are re-characterized.

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Convergent evolution can explain similarity in morphology between species, due to selection on a fitness-enhancing phenotype in response to local environmental conditions. As selective pressures on body morphology may be strong, these have confounded our understanding of the evolutionary relationships between species. Within the speciose African radiation of lacertid lizards (Eremiadini), some species occupy a narrow habitat range (e.g. open habitat, cluttered habitat, strictly rupicolous, or strictly psammophilic), which may exert strong selective pressures on lizard body morphology. Here we show that the overall body plan is unrelated to shared ancestry in the African radiation of Eremiadini, but is instead coupled to habitat use. Comprehensive Bayesian and likelihood phylogenies using multiple representatives from all genera (2 nuclear, 2 mitochondrial markers) show that morphologically convergent species thought to represent sister taxa within the same genus are distantly related evolutionary lineages (Ichnotropis squamulosa and Ichnotropis spp.; Australolacerta rupicola and A. australis). Hierarchical clustering and multivariate analysis of morphological characters suggest that body, and head, width and height (stockiness), all of which are ecologically relevant with respect to movement through habitat, are similar between the genetically distant species. Our data show that convergence in morphology, due to adaptation to similar environments, has confounded the assignment of species leading to misidentification of the taxonomic position of I. squamulosa and the Australolacerta species.

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Eremiadinae, one of three subfamilies of Lacertidae, are distributed throughout Asia and Africa. Previous phylogenetic studies suggested that one of the main groups of Eremiadinae (the Ethiopian clade) consist of two clades with predominately East-African and South-African distribution. Yet, especially the latter one, which includes the genera Pedioplanis, Meroles, Ichnotropis, Tropidosaura and Australolacerta, was not well supported in the molecular phylogenetic analysis. In this study, we analysed the phylogenetic relationships among the genera of the ‘South African clade’ to assess whether this group actually forms a highly supported clade and to address questions concerning the monophyly of the genera. We sequenced sections of the widely used mitochondrial genes coding for 16S rRNA, 12S rRNA and cytochrome b (altogether 2045 bp) as well as the nuclear genes c-mos, RAG-1, PRLR, KIF24, EXPH5 and RAG-2 (altogether 4473 bp). The combined data set increased the support values for several nodes considerably. Yet, the relationships among five major lineages within the ‘South African clade’ are not clearly resolved even with this large data set. We interpret this as a ‘hard polytomy’ due to fast radiation within the South African lacertids. The combined tree based on nine marker genes provides strong support for the ‘South African Clade’ and its sister group relationship with the ‘East African Clade’. Our results confirm the genus Tropidosaura as a monophylum, while Ichnotropis is paraphyletic in our trees: Ichnotropis squamulosa appears more closely related to Meroles than to Ichnotropis capensis. Furthermore, the monophyly of Meroles is questionable as well. Based on our results, I. squamulosa should be transferred from Ichnotropis into the genus Meroles. Also, the two species of Australolacerta (A. australis and A. rupicola) are very distantly related and the genus is perhaps paraphyletic, too. Finally we propose a phylogeographical scenario in the context of palaeoclimatic data and compare it with a previously postulated hypothesis.

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Climatic conditions changing over time and space shape the evolution of organisms at multiple levels, including temperate lizards in the family Lacertidae. Here we reconstruct a dated phylogenetic tree of 262 lacertid species based on a supermatrix relying on novel phylogenomic datasets and fossil calibrations. Diversification of lacertids was accompanied by an increasing disparity among occupied bioclimatic niches, especially in the last 10 Ma, during a period of progressive global cooling. Temperate species also underwent a genome- wide slowdown in molecular substitution rates compared to tropical and desert-adapted lacertids. Evaporative water loss and preferred temperature are correlated with bioclimatic parameters, indicating physiological adaptations to climate. Tropical, but also some popu- lations of cool-adapted species experience maximum temperatures close to their preferred temperatures. We hypothesize these species-specific physiological preferences may con- stitute a handicap to prevail under rapid global warming, and contribute to explaining local lizard extinctions in cool and humid climates.

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The evolutionary diversification of many terrestrial vertebrate groups is strongly linked to climatic events in the Cenozoic, the period from 65 Million years ago to today when modern animals first appeared. I investigated the effects of Cenozoic climate change on the taxonomic and morphological diversification of the Old World lizard family Lacertidae, with particular emphasis on the African radiation. African lacertids exhibit an unusual pattern of diversification, in which their highest species richness occurs in deserts north and south of the equator, despite being spread throughout the continent. This disparity is particularly surprising given that desert lacertids are thought to be evolutionarily younger than their mesic-dwelling relatives, suggesting increased diversification rates in arid habitats. To identify the evolutionary factors underlying this pattern, I use a combination of phylogenetic, morphological and ecological techniques. In Chapter 1, I apply Bayesian methods and fossil-based calibrations to molecular sequence data to construct a time-calibrated phylogeny for Lacertidae. I estimate that the family arose in the early Cenozoic, with the majority of their African radiation occurring in the Eocene and Oligocene. In Chapter 2, I describe changes in lacertid body shape across biomes and substrates, and find widespread morphological convergence in similar habitat types. I suggest that in addition to foraging demands, fluctuating and extreme climatic conditions, largely driven by precipitation and temperature, contribute to morphological convergence across independent arid-dwelling clades. Finally, I test if ancestral transitions in ecology, morphology, and rates of diversification temporally coincide with paleoclimatic events in the Cenozoic. I use High Resolution X-ray Computed Tomography to characterize changes in the skull related to life in arid habitats, and apply maximum likelihood methods to test if the origins of those traits temporally coincide with significant shifts in habitat, diversification rates and climatic changes. My results show that African lacertids experienced three major peaks in diversification, accompanied by the evolution of suites of arid-adapted morphological traits. These changes coincide with climatic shifts in Africa, including the transition from closed forests to open grasslands and savanna in the late Oligocene, prior to the peak temperatures of the mid-Miocene Climatic Optimum, and following the formation of the Benguela current leading to hyper-aridity in southern Africa. I conclude that deserts are important centers for reptile evolution, but that expected changes in climate due to global warming may outpace the ability of arid-dwelling species to adapt and persist in the future.

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Several specimens of different genera of Lacertid lizards were collected during a 4-week-trip into the Limpopo Province of South Africa. Depending on their habitat members of the different species occurred within different reptile species assemblages. On the Soutpansberg specimens of Nucras intertexta were recorded in unusual habitat and a genetic study shall resolve their systematic position. No Lacertids were recorded in the high altitudes of the Blouberg and Wolkberg, which is most probably attributed to sampling artifacts.

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Intraspecific variation in morphology, colouration, pholidosis, and tail loss rate of up to 80 specimens of the endemic Soutpansberg rock lizard Australolacerta rupicola were assessed from 2005 to 2007. These were analysed together with data from the type specimen and eleven additional specimens from an earlier study (1979–1985). In comparison with other lacertids, this species exhibits only a feeble sexual dichromatism. Analyses of morphometric characters show the existence of sexual size dimorphism, with females growing to greater snout–vent lengths and males having larger heads. Additionally, adult males have significantly more femoral pores than females. Compared to adults, juveniles have proportionally larger heads. The frequencies of regenerated tails did not show significant differences between the tested groups. All differences described are discussed in the light of the ecology of this species.

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The Soutpansberg situated in north-eastern South Africa was investigated with respect to its reptile species diversity, geographic range of the species and habitat utilisation. Typical inselberg characteristics are discussed in the context of the herpetofauna and compared with the Blouberg, an isolated mountain range to the west of the Soutpansberg. Possible biogeographic links between the species assemblage of the Soutpansberg and adjacent areas are discussed in the context of present geological and climatic conditions within the area. The Soutpansberg reptile community clearly shows effects of isolation. The mistbelt and the grassland on the summits, which both withstood climatic oscillations in the past, harbour the majority of species and most of the endemic taxa in particular. Hence, these areas are of significant ecological value for the reptile community. Rocky habitats and the cooler and moister climate on the mountain provide exceptional conditions within this area. Most of the Soutpansberg endemics exhibit a rupicolous lifestyle and a large number of species are adapted to mesic conditions. A high proportion of Afromontane species was detected. Furthermore, eastern coastal and Lowveld elements exert an influence on the species composition whereas the Kalahari elements are of lesser importance. Tropical forest species are completely absent. The Soutpansberg harbours more endemics (nine taxa) compared to the Blouberg (three taxa) due to its larger size and the resultant decreased risk of extinction.

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Foraging mode of the endemic Soutpansberg rock lizard (Australolacerta rupicola) was determined by (1) measuring the number of movements per minute (MPM) and the percentage time spent moving (PTM); and (2) analysing faecal samples. Furthermore, these criteria were related to diet composition, proportion of attacks initiated while moving and foraging substrate. The results are discussed in comparison to the foraging modes of 20 other lacertid species. Values for MPM and PTM as well as faecal analysis indicate an active foraging strategy for A. rupicola. Although rock living, this species mostly forages in leaf litter where it is well camouflaged while actively searching for sedentary prey. Even in comparison to other active foragers of the family Lacertidae, A. rupicola displays the prototypic behaviour of a widely foraging lizard with very high PTM and very low MPM.

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Daily activity patterns of the endemic Soutpansberg rock lizard (Australolacerta rupicola) and ecologically similar syntopic lizards were analysed to assess potential niche partitioning. Data to evaluate the temporal niche included time and temperature, and niche overlap was determined over three different sample plots using the Pianka-Index. Altogether, 11 other lizard species and four snake species were recorded at the sample plots. Australolacerta rupicola showed a large overlap in the spatial niche with Trachylepis varia and Platysaurus relictus and in the trophic niche with T. varia, however, the maximum activity period of A. rupicola fell into periods of low activity by P. relictus and T. varia and vice versa. These patterns were most pronounced when the different sample plots were analysed separately. The asynchronous activity cycles are probably the result of avoidance of competition for food in the case of the active foragers A. rupicola and T. varia, whereas different thermal preferences driven by physiological constraints appear to be more relevant when comparing A. rupicola and P. relictus. Individual numbers of the usually abundant species T. varia and P. relictus decreased in A. rupicola habitats and it is posted that the latter species resides in less climatically favourable habitats, thus avoiding competition with other rupicolous lizards.

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Aim To map and assess the richness patterns of reptiles (and included groups: amphisbaenians, crocodiles, lizards, snakes and turtles) in Africa, quantify the overlap in species richness of reptiles (and included groups) with the other terrestrial vertebrate classes, investigate the environmental correlates underlying these patterns, and evaluate the role of range size on richness patterns. Location Africa. Methods We assembled a data set of distributions of all African reptile species. We tested the spatial congruence of reptile richness with that of amphibians, birds and mammals. We further tested the relative importance of temperature, precipitation, elevation range and net primary productivity for species richness over two spatial scales (ecoregions and 1° grids). We arranged reptile and vertebrate groups into range-size quartiles in order to evaluate the role of range size in producing richness patterns. Results Reptile, amphibian, bird and mammal richness are largely congruent (r = 0.79–0.86) and respond similarly to environmental variables (mainly productivity and precipitation). Ecoregion size accounts for more variation in the richness of reptiles than in that of other groups. Lizard distributions are distinct with several areas of high species richness where other vertebrate groups (including snakes) are species-poor, especially in arid ecoregions. Habitat heterogeneity is the best predictor of narrow-ranging species, but remains relatively important in explaining lizard richness even for species with large range sizes. Main conclusions Reptile richness varies with similar environmental variables as the other vertebrates in Africa, reflecting the disproportionate influence of snakes on reptile richness, a result of their large ranges. Richness gradients of narrow-ranged vertebrates differ from those of widespread taxa, which may demonstrate different centres of endemism for reptile subclades in Africa. Lizard richness varies mostly with habitat heterogeneity independent of range size, which suggests that the difference in response of lizards is due to their ecological characteristics. These results, over two spatial scales and multiple range-size quartiles, allow us to reliably interpret the influence of environmental variables on patterns of reptile richness and congruency.

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Aim Body size is instrumental in influencing animal physiology, morphology, ecology and evolution, as well as extinction risk. I examine several hypotheses regarding the influence of body size on lizard evolution and extinction risk, assessing whether body size influences, or is influenced by, species richness, herbivory, island dwelling and extinction risk. Location World-wide. Methods I used literature data and measurements of museum and live specimens to estimate lizard body size distributions. Results I obtained body size data for 99% of the world`s lizard species. The body size–frequency distribution is highly modal and right skewed and similar distributions characterize most lizard families and lizard assemblages across biogeographical realms. There is a strong negative correlation between mean body size within families and species richness. Herbivorous lizards are larger than omnivorous and carnivorous ones, and aquatic lizards are larger than non-aquatic species. Diurnal activity is associated with small body size. Insular lizards tend towards both extremes of the size spectrum. Extinction risk increases with body size of species for which risk has been assessed. Main conclusions Small size seems to promote fast diversification of disparate body plans. The absence of mammalian predators allows insular lizards to attain larger body sizes by means of release from predation and allows them to evolve into the top predator niche. Island living also promotes a high frequency of herbivory, which is also associated with large size. Aquatic and nocturnal lizards probably evolve large size because of thermal constraints. The association between large size and high extinction risk, however, probably reflects a bias in the species in which risk has been studied.

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Across the globe, reptile species are threatened by anthropogenic activities, including habitat destruction, habitat degradation, expanding human settlements and climate change. Those with restricted ranges are often the most vulnerable due to their limited dispersal capabilities, narrow thermal tolerances and specific habitat requirements. Many of these restricted species are also poorly understood, with a lack of knowledge concerning their ecological and physiological requirements. In order to design effective conservation strategies for these restricted species, these knowledge gaps need to be filled. The aim of this thesis was to gain a deeper understanding on the biology of some of the endemic and restricted reptiles in the Soutpansberg Mountains. This mountain range is located in the Limpopo Province of South Africa and is a unique study area due to its sub-tropical location, habitat heterogeneity and the fact that it is located in the replacement transition zones of three biogeographic subregions. This has led to the mountains supporting extremely high faunal and floral biodiversity and endemism, reptiles being no exception. However, to date there have been few ecological studies into the reptile fauna of the area and the ecological requirements of many of these species are unknown. There are several threats that species from the mountains currently face including habitat destruction, agriculture, silviculture, mining and climate change. This thesis is made up of four main parts: firstly, I investigated the broad scale distribution patterns, climatic requirements and potential interspecific interactions of five of the rupicolous, endemics using ecological niche modelling (Afroedura pienaari; Lygodactylus incognitus: L. soutpansbergensis; Platysaurus relictus and Vhembelacerta rupicola). Results indicated that most species were limited by climatic factors, with the average temperature of the coolest three months having the most influence on the majority of the species, suggesting that they may be negatively affected by climate change in the future. Interspecific interactions between these species are not likely to affect broad-scale distribution patterns. Secondly, I examined the microhabitat requirements and potential niche separation of two, endemic Lygodactylus geckos: L. incognitus and L. soutpansbergensis by recording fine- and broad-scale habitat variables. Results indicated that the two species showed differences in their microhabitat selection, but that interspecific aggression was unlikely to be the factor causing these differences. Instead, their morphology and physiology were likely driving microhabitat selection. This study revealed microhabitat requirements of the two species, knowledge of which is important for future conservation efforts in the area. Next, I investigated the daily activity patterns of the two Lygodactylus geckos by conducting scan surveys along transects in the mountains. Results showed that L. incognitus was more active in cooler temperatures whilst L. soutpansbergensis was more active in warmer conditions. These results suggest that L. incognitus may be more vulnerable than L. soutpansbergensis to the effects of climate change and that physiological studies are required to investigate adaptive capability. Finally, I explored the potential effects climate change will have on the distribution of eleven rupicolous reptiles using ecological niche modelling. These species are likely to have limited dispersal abilities and thus are unlikely to be able to track suitable conditions in the face of climate change; therefore, I also identified potential climatic refugia. Results indicated that four species in particular are likely to be extremely vulnerable to the effects of climate change with large reductions in suitable habitat between current and future projections. The western Soutpansberg may act as a climatic refugia in the future. I recommended that detailed investigations into the physiological requirements of these vulnerable species be performed in order to develop models that are more accurate. Long-term monitoring projects in the mountain should also be executed in order to track these potential range reductions. Ultimately, this thesis resulted in the gain of valuable ecological information on several restricted reptiles of South Africa for which there was previously few data. This information is vital for ongoing conservation assessments and planning in the region. One of the main findings of this thesis is that ongoing anthropogenic pressures will likely have negative effects for the majority of the species studied here.

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Climate change is causing the geographical ranges of some species to track suitable conditions. Habitat specialists, range-restricted species and species with limited dispersal abilities may be unable to track changing conditions, increasing their extinction risk. In response to changing conditions and speciesmovement patterns, there is a need to account for the effects of climate change when designing protected areas and identifying potential climate refugia.We used ecological niche models projected into future climates to identify potential impacts of climate change on the distribution of 11 rupicolous reptile species in the Soutpansberg Mountains, South Africa. Lygodactylus incognitus, Lygodactylus soutpansbergensis, Platysaurus relictus and Vhembelacerta rupicola were identified as being vulnerable to climate change due to substantial reductions in suitable habitat and low spatial overlap between current and future niche envelopes. We identified areas of high conservation importance for the persistence of these species under present-day and projected future conditions. The western Soutpansberg was identified as an area of high conservation priority as it is a potential refuge under future projections. Projecting distributions of vulnerable species into future climate predictions can guide future research and identify potential refugia that will best conserve species with restricted ranges in a world with climate change.