Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: 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. / AFRIKAANSE OPSOMMING: Die fenotipe van 'n individu is dikwels gebruik as die diskriminerende faktor in kenmerkende spesies. Maar, met die ontwikkeling van meer akkurate molekulêre tegnieke, word die genotipe van spesies toenemend gebruik as die voorkeur-metode in taksonomiese klassifikasie. Die onversoenbaarheid van genetiese en morfologiese eienskappe kom voor in ‘n verskeidenheid taksa, dit kan wees as gevolg van die invloed wat die omgewing het op die morfologiese en funksionele aspekte van ‘n spesie. Selektiewe druk beїnvloed dikwels doeltreffende funktionaliteit van 'n spesie in 'n bepaalde habitat eerste, en gevolglik word morfologiese karakters wat voorsiening maak vir optimale funktionaliteit geselekteer. Indien geneties uiteenlopende spesies woon in 'n bepaalde omgewing, kan konvergensie in morfologie en soortgelyke werksverrigtinge ontwikkel. Histories, is akkedis spesiesbeskrywings hoofsaaklik gebaseer op eksterne morfologieë, en kan dus misklassifikasie tot gevolg hê wat kan lei tot foutiewe taksonomie van spesies met konvergente morfologieë. In die huidige verhandeling, is die verband tussen die morfologie, werksverrigtingsvermoë, dieët en gedrag ondersoek, in vergelyking met die omgewing en die genetiese verwantskappe van Suider-Afrikaanse sandakkedisse. Die werksverrigtingsvermoë en gepaardgaande morfologiese eienskappe word verwag om te meer verband te hou met die omgewing, en dus nie in noue verband te wees met die genetiese verwantskappe nie. Om hierdie verwagtinge te ondersoek, is 'n multi-dissiplinêre benadering geneem, en genetiese, morfologiese en werksverrigtingontledings is gedoen in vergelyking met dieët, gedrags-en omgewings-ontleding. In die eerste hoofstuk, is die skakel tussen die habitat openheid en die akkedis bauplans ondersoek en die teenwoordigheid van konvergente morfologieë binne hierdie groep akkedisse word ten toon gestel. Hierdie konvergensies het gelei tot foutiewe klassifikasie van twee sandspesies, en taksonomiese hersiening binne die gesin word bespreek. Die tweede hoofstuk ondersoek die verband tussen werksverrigting en gepaardgaande morfologiese eienskappe, en die samestelling van die dieët van die lede van die Nucras genus. Die derde hoofstuk identifiseer die verband tussen die roofdier ontsnapping strategieë, morfologieë en werksverrigtingsvermoë van die Meroles genus. Die vierde hoofstuk ondersoek die intraspesifieke, inter-bevolkingsverskille in morfologieë en ondersoek die verband tussen die morfologiese groepe en die bevolking genetiese groepe binne die Pedioplanis lineoocellata spesies kompleks. Die finale hoofstuk identifiseer hoe die aanpassings na 'n nuwe habitat kan plaasvind oor 'n relatief kort tydperk, en die morfologiese eienskappe, funksionele aspekte en die bevolking genetiese struktuur word ondersoek in vergelyking met die omgewingsanalise van plantegroei en substraat tussen die bevolkings van Meroles knoxii. Die gevolgtrekking is dat die morfologiese en funksionele aspekte van die Suider- Afrikaanse sandakkedisse nader verwant is aan die omgewing, veral die mikrohabitat struktuur, as aan hul genetiese verwantskappe. Toekomstige werk op hierdie groep akkedisse moet ‘n multidisiplinêre benadering behels siende dat verskillende selektiewe drukke 'n rol speel in die vorming van die morfologie en werksverrigtingsvermoë van hierdie akkedisse, in vergelyking met selektiewe drukke wat die genotipes van die akkedisse beinvloed.

In this thesis, I investigate the phylogeny and evolution of Lerista, a clade of more than 75 species of scincid lizards, distributed in arid, semi-arid, and seasonally dry habitats throughout Australia. Among extant tetrapods, Lerista is exceptional in comprising a large number of closely-related species displaying prodigious variability of body form; several species possessing well-developed, pentadactyl limbs resemble typical non-fossorial scincids in body proportions, while many other species exhibit varying degrees of limb reduction and body elongation, including two that are highly elongate and entirely limbless. The extensive variation in limb morphology observed among species, incorporating at least 20 distinct phalangeal configurations, has prompted some authors to identify Lerista as the best available model for studying limb reduction in squamates. Nonetheless, lack of a well-resolved phylogeny has impeded investigation of the pattern and mode of limb reduction and loss within the clade. The primary goal of my research was to furnish a comprehensive phylogenetic hypothesis for Lerista, enabling more sophisticated study of the evolution of limb morphology and body form in this clade than has previously been possible. A recent phylogenetic analysis of mitochondrial DNA sequences for a series of Australian Sphenomorphus group scincids (including two species of Lerista) recovered several well-supported, major clades, although these were generally separated by relatively short branches associated with low support values. Applying a recently described methodology for inferring lineage-level polytomies, I use ATP synthetase-β subunit intron sequences and the existing mitochondrial DNA data set (with sequences for additional taxa) to assess the hypothesis that the poorly resolved basal relationships within the Australian Sphenomorphus group are a consequence of the major clades having originated essentially simultaneously. Phylogenetic analyses of the separate mitochondrial DNA and intron sequence data reveal a number of congruent clades, however, the relationships among these clades indicated by the two data sets are generally incongruent. Although this may be partly ascribed in to error in estimating phylogenetic relationships due to insufficient data, some incongruence is evident when uncertainty in inferred relationships is allowed for. Moreover, the congruent clades are typically separated by very short branches, several having a length insignificantly different from zero. These results suggest that initial diversification of Australian Sphenomorphus group scincids was rapid relative to the substitution rates of the mitochondrial DNA and intron fragments considered, if not essentially simultaneous. The pattern and rate of limb reduction in Lerista are investigated, employing a nearly complete phylogeny inferred from nucleotide sequences for a nuclear intron and six mitochondrial genes. Ancestral digit configurations reconstructed assuming this phylogeny indicate at least ten independent reductions in the number of digits from a pentadactyl condition, including four independent losses of all digits, three from pentadactyl or tetradactyl conditions. At the highest rate, complete loss of digits from a pentadactyl condition is estimated to have occurred within no more than 3.6 million years. Patterns of digit loss for the manus and pes are consistent with selection for preserving hindlimb utility as the limbs are reduced, and suggest that intermediate digit configurations exhibited by extant species do not represent transitory stages in a continuing process of limb reduction. An increase in the relative length of the body is demonstrated to precede digit loss in lineages experiencing substantial reduction of the limbs, supporting the hypothesis that limb reduction and loss is a consequence of the adoption of lateral undulation as a significant locomotory mode. However, less extensive limb reduction may proceed in the absence of body elongation, perhaps due to a decrease in absolute body size. The exceptionally high frequency and rate of limb reduction in Lerista emphasise the potential for rapid and dramatic evolutionary transformation of body form in squamates. The substantial divergence of relative limb and body length evident within Lerista is more readily explained by the correlated progression model of phenotypic transformation than the independent blocks model. At each step in the attainment of a limb-reduced, elongate body form, alterations to the relative length of the limbs are accompanied by changes in relative snout-vent length (or vice versa) enabling the maintenance of locomotory ability. Nonetheless, some dissociation of hindlimb reduction and body elongation is possible, emphasising the potentially variable intensity of functional constraints and, accordingly, that the independent blocks model and correlated progression are extremes of a continuum of models (each invoking a different degree of functional integration) and do not describe discrete categories of phenotypic change. An increase in the extent of seasonally dry and arid habitats coincident with the origination of Lerista would have facilitated limb reduction and body elongation by furnishing an environment conducive to the adoption of fossorial habits, however, trends toward a limbless, highly elongate body form may be attributed primarily to the very low probability of re-elaborating reduced limbs. Such asymmetry in the probabilities of possible phenotypic changes may be a significant cause of evolutionary trends resulting in the emergence of higher taxa. / Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2008

In this thesis, I investigate the phylogeny and evolution of Lerista, a clade of more than 75 species of scincid lizards, distributed in arid, semi-arid, and seasonally dry habitats throughout Australia. Among extant tetrapods, Lerista is exceptional in comprising a large number of closely-related species displaying prodigious variability of body form; several species possessing well-developed, pentadactyl limbs resemble typical non-fossorial scincids in body proportions, while many other species exhibit varying degrees of limb reduction and body elongation, including two that are highly elongate and entirely limbless. The extensive variation in limb morphology observed among species, incorporating at least 20 distinct phalangeal configurations, has prompted some authors to identify Lerista as the best available model for studying limb reduction in squamates. Nonetheless, lack of a well-resolved phylogeny has impeded investigation of the pattern and mode of limb reduction and loss within the clade. The primary goal of my research was to furnish a comprehensive phylogenetic hypothesis for Lerista, enabling more sophisticated study of the evolution of limb morphology and body form in this clade than has previously been possible. A recent phylogenetic analysis of mitochondrial DNA sequences for a series of Australian Sphenomorphus group scincids (including two species of Lerista) recovered several well-supported, major clades, although these were generally separated by relatively short branches associated with low support values. Applying a recently described methodology for inferring lineage-level polytomies, I use ATP synthetase-β subunit intron sequences and the existing mitochondrial DNA data set (with sequences for additional taxa) to assess the hypothesis that the poorly resolved basal relationships within the Australian Sphenomorphus group are a consequence of the major clades having originated essentially simultaneously. Phylogenetic analyses of the separate mitochondrial DNA and intron sequence data reveal a number of congruent clades, however, the relationships among these clades indicated by the two data sets are generally incongruent. Although this may be partly ascribed in to error in estimating phylogenetic relationships due to insufficient data, some incongruence is evident when uncertainty in inferred relationships is allowed for. Moreover, the congruent clades are typically separated by very short branches, several having a length insignificantly different from zero. These results suggest that initial diversification of Australian Sphenomorphus group scincids was rapid relative to the substitution rates of the mitochondrial DNA and intron fragments considered, if not essentially simultaneous. The pattern and rate of limb reduction in Lerista are investigated, employing a nearly complete phylogeny inferred from nucleotide sequences for a nuclear intron and six mitochondrial genes. Ancestral digit configurations reconstructed assuming this phylogeny indicate at least ten independent reductions in the number of digits from a pentadactyl condition, including four independent losses of all digits, three from pentadactyl or tetradactyl conditions. At the highest rate, complete loss of digits from a pentadactyl condition is estimated to have occurred within no more than 3.6 million years. Patterns of digit loss for the manus and pes are consistent with selection for preserving hindlimb utility as the limbs are reduced, and suggest that intermediate digit configurations exhibited by extant species do not represent transitory stages in a continuing process of limb reduction. An increase in the relative length of the body is demonstrated to precede digit loss in lineages experiencing substantial reduction of the limbs, supporting the hypothesis that limb reduction and loss is a consequence of the adoption of lateral undulation as a significant locomotory mode. However, less extensive limb reduction may proceed in the absence of body elongation, perhaps due to a decrease in absolute body size. The exceptionally high frequency and rate of limb reduction in Lerista emphasise the potential for rapid and dramatic evolutionary transformation of body form in squamates. The substantial divergence of relative limb and body length evident within Lerista is more readily explained by the correlated progression model of phenotypic transformation than the independent blocks model. At each step in the attainment of a limb-reduced, elongate body form, alterations to the relative length of the limbs are accompanied by changes in relative snout-vent length (or vice versa) enabling the maintenance of locomotory ability. Nonetheless, some dissociation of hindlimb reduction and body elongation is possible, emphasising the potentially variable intensity of functional constraints and, accordingly, that the independent blocks model and correlated progression are extremes of a continuum of models (each invoking a different degree of functional integration) and do not describe discrete categories of phenotypic change. An increase in the extent of seasonally dry and arid habitats coincident with the origination of Lerista would have facilitated limb reduction and body elongation by furnishing an environment conducive to the adoption of fossorial habits, however, trends toward a limbless, highly elongate body form may be attributed primarily to the very low probability of re-elaborating reduced limbs. Such asymmetry in the probabilities of possible phenotypic changes may be a significant cause of evolutionary trends resulting in the emergence of higher taxa. / Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2008

Reptiles are polyphyletic, and previous studies of renal anatomy and physiology in reptiles have covered a wide diversity of species of different phylogeny and habitat. To date, no study has examined the renal morphology and function of a group of closely related reptiles from different environments, yet this design has a number of advantages. Firstly, phylogenetic effects are reduced while adaptive specialisations in renal function or structure can be elucidated, and secondly, the variation in renal form and function between closely related species may be quantified in an effort to appreciate better the variation between more distantly related species. In this thesis, kidney morphology and renal function were studied in three Western Australian agamid lizards inhabiting environments differing in the availability of water. These key species were Pogona minor, Ctenophorus nuchalis and Ctenophorus salinarum. The renal anatomy of the three key lizards was characterised by determining glomerular diameter, volume density, surface area and number in each. Allometric relationships between kidney, colon and body mass were investigated in these and an additional 11 species of agamid lizard. Patterns of response to osmotic challenge were recorded by measuring renal variables such as urine flow rate, glomerular filtration rate and fractional reabsorption of filtrate among the three key species, and concurrent measurements of circulating arginine vasotocin in P. minor and C. nuchalis allowed the response of this hormone to homeostatic imbalance in these species to be gauged. The gross morphology and the glomerular characteristics of the kidneys was remarkably similar between species. Glomerular number and other characters varied as a function of body size rather than species, contrasting with reports in the literature suggesting that a given species has a particular number of glomeruli. ... Thus, kidney morphology is constrained among species and the response of each species to osmotic perturbation is similar. However, the mechanisms underlying antidiuresis and the hormonal control of this process differ subtly between species, and there is some evidence to suggest that P. minor is more adapted to a mesic environment than the other two lizards examined in this study. The hypothesis that renal form and function reflect the environment in which a lizard lives therefore receives partial support, although the reptilian bauplan is able to mitigate many of the forces that could potentially lead to renal specialisation.