Dissertation (PhD)--University of Stellenbosch, 2007. / ENGLISH ABSTRACT: The taxonomic status of southern Africa’s rupicolous crag lizards (genus Pseudocordylus) was investigated. As considerable confusion exists in the literature regarding the type specimens and type localities of the various taxa, resolution of these problems were considered the starting point of the study. Examination of museum specimens allowed for the designation of lectotypes, alloparalectotypes and/or paralectotypes. Of particular relevance to this study was the rediscovery of Andrew Smith’s type specimens of P. m. melanotus and P. m. subviridis. Restriction of the type locality of P. m. subviridis, based on entries in Smith’s diary and journal, allowed for the confirmation of previous interpretations and definitions of the two taxa. The geographical distribution of the various taxa and populations was determined using an extensive locality database. Two kinds of molecular markers, namely allozymes and mitochondrial DNA, were used in an attempt to resolve taxon boundaries within the P. melanotus species complex. The allozyme analysis indicated that P. m. melanotus might be polyphyletic and comprised of two unrelated lineages. Furthermore, fixed allelic differences between parapatric populations of P. m. melanotus and P. m. subviridis, and between sympatric populations of P. m. subviridis and P. langi, suggested that all three forms might be considered full species, with the possibility of more cryptic species present in the complex. Pseudocordylus transvaalensis differed from most other populations by 1-3 fixed allelic differences, but was indistinguishable from the Nkandhla district (central KwaZulu-Natal) population of P. m. melanotus. There were no heterozygous individuals in a sample from Monontsha Pass (Qwa-Qwa), a population reportedly comprising P. m. melanotus and P. m. subviridis, as well as intermediates, and all specimens were assignable to P. m. subviridis. The allozyme study was, however, based on phenetic principles and for further taxonomic resolution a cladistic approach was required. An mtDNA analysis (16S rRNA gene) using Maximum Parsimony, Maximum Likelihood and Bayesian analyses was therefore conducted to determine phylogenetic relationships among species and subspecies and to re-assess the taxonomic status of forms in the P. melanotus species complex. The mtDNA analysis corroborated most of the results obtained in the allozyme analysis. Firstly, P. langi was again found to be basal. With the addition of P. microlepidotus and P. spinosus to the ingroup, it is now apparent that P. langi is the basal species in the genus. (Recent studies have indicated that P. capensis and P. nebulosus are not congeneric with Pseudocordylus.) Secondly, the 16S rRNA results confirm that P. m. melanotus, as presently construed, is comprised of two clades that are not sister groups. The northern populations of P. m. melanotus (Sabie and Lochiel) form a fairly deeply divergent clade that may represent a separate species. The Nkandla population was, however, found to cluster with the other southern P. m. melanotus populations and not with P. transvaalensis as was the case in the allozyme electrophoretic analysis. However, the most surprising result of the 16S rRNA analysis was the finding that both P. microlepidotus and P. spinosus are embedded within P. m. subviridis. This suggests that these two species evolved from within P. m. subviridis and may have been separated only recently, with rapid morphological divergence occurring, but with limited genetic differentiation. It is suggested that all of the above three taxa be provisionally treated as full species. There was also morphological support for the uniqueness of all groupings indicated by the mtDNA analysis. Pseudocordylus transvaalensis is characterized by its large size, unique dorsal and gular (black) colour patterns, as many as three horizontal rows of lateral temporal scales, a series of small scales posterior to the interparietal scale, and usually two subocular scales behind the median subocular on either side of the head. The various populations currently classified under the name P. melanotus are more difficult to separate, but P. m. melanotus and P. m. subviridis usually differ as follows: frontonasal divided in P. m. melanotus, undivided in P. m. subviridis (and most Northern melanotus); lateral temporals in two rows, upper more elongate versus single row of much elongated scales; longitudinal rows of dorsolaterals closely-set versus widely separated; femoral pores of females pit-like versus deep with secretory plug. Northern melanotus differs from Southern melanotus in usually having an undivided frontonasal scale and seldom having a small scale present behind the frontonasal. Pseudocordylus langi has unique dorsal and gular colour patterns (including a series of blue spots on the flanks), granular dorsals with 6-9 paravertebral rows of enlarged flat scales, high total numbers of femoral pores (25-34) and usually only five (smooth not keeled or ridged) infralabial scales on either side of the head. Pseudocordylus spinosus also has unique dorsal and gular colour patterns, spinose lateral scales, frontonasal longer than wide and excluded from the loreal scales, low total femoral pore counts (6-9), and females (not only males) have differentiated femoral scales. Both Principal Components Analysis (PCA) and Canonical Discriminant Analysis (CDA) distinguished four groups, namely P. transvaalensis, P. langi, P. spinosus and a P. melanotus/subviridis/microlepidotus cluster. A separate CDA of all P. melanotus populations partly distinguished between Southern melanotus and P. m. subviridis, and largely separated Northern melanotus; whereas a CDA of P. transvaalensis showed that all three allopatric populations are 100% distinguishable in morphological space. A Nested Clade Analysis indicated that fragmentation as well as range expansion played a role in the distribution of the P. melanotus species complex. This may be explained by climatic oscillations (high-low temperatures and wet-dry cycles) during the Cenozoic that caused habitat expansion and contraction. Based on the topology of the mtDNA phylogram it is apparent that the genus Pseudocordylus originated along the eastern escarpment. A P. langi-like ancestor may have had an extensive range along the eastern escarpment, with the Maloti-Drakensberg forming the southern limit of its range. During a subsequent rise in global temperatures, range contraction and fragmentation took place, leaving an isolated population in the south and one in the north. The southern population survived unchanged in the Maloti-Drakensberg refugium, but the northern population was forced to adapt to the warmer conditions. Thereafter, the northern form expanded its range again, but during a subsequent cooler period, range contraction occurred, resulting in an isolated north-eastern population in the Sabie-Lochiel area in Mpumulanga (Northern melanotus) and a western population. Relationships in the latter clade are not sufficiently resolved to allow further reconstruction of biogeographic history, but it is clear that a P. m. subviridis-like form became isolated in the south where it eventually came into contact with P. langi at high elevations. Pseudocordylus m. subviridis eventually extended its range southwestwards into the inland mountains of the Eastern Cape and Cape Fold Mountains to give rise to the P. microlepidotus complex. This cycle of range expansion and contraction may also account for the isolated populations at Suikerbosrand, Nkandhla district, and in the Amatole-Great Winterberg mountain region. Furthermore, it is suggested that P. spinosus originated from a P. m. subviridis-like ancestral population that became isolated on the lower slopes of the Drakensberg where terrestrial predation pressure resulted in a quick shift in morphology from fairly smooth body scales to a more spiny morphology. / AFRIKAANSE OPSOMMING: Die taksonomiese status van suidelike Afrika se rotsbewonende krans-akkedisse (genus Pseudocordylus) is ondersoek. Omdat daar aansienlike verwarring in die literatuur bestaan met betrekking tot die tipe monsters en die tipe lokaliteite van die verskillende taksa, is die oplossing van hierdie probleme as die beginpunt van hierdie studie geneem. Die bestudering van akkedismonsters in museums het dit moontlik gemaak om lektotipes, alloparalektotipes en/of paralektotipes aan te wys. Van besondere belang vir hierdie studie is die herontdekking van Andrew Smith se tipe monsters van P. m. melanotus en P. m. subviridis. Die beperking van die tipe lokaliteit van P. m. subviridis, gebaseer op inskrywings in Smith se dagboek en joernaal, het dit moontlik gemaak om vorige interpretasies en definisies van die twee taksa te bevestig. Die geografiese verspreiding van die verskillende taksa en bevolkings is bepaal deur middel van ’n omvattende lokaliteit databasis. Twee soorte molekulêre merkers, naamlik allosieme en mitokondriale DNS, is gebruik in ʼn poging om uitsluitsel te verkry oor die takson-grense binne die P. melanotus-spesiekompleks. Die allosiem-analise het daarop gedui dat P. m. melanotus moontlik polifileties mag wees en uit twee onverwante stamboom-vertakkings kan bestaan. Verder het vaste alleliese verskille tussen parapatriese bevolkings van P. m. melanotus en P. m. subviridis, en tussen simpatriese bevolkings van P. m. subviridis en P. langi, daarop gedui dat al drie vorme as volledige spesies beskou kan word, met die moontlikheid dat meer kriptiese spesies in die kompleks teenwoordig kan wees. Pseudocordylus transvaalensis het van die meeste ander bevolkings verskil met 1-3 vaste alleliese verskille, maar was ononderskeibaar van die bevolking van P. m. melanotus van die Nkandhla distrik (sentraal KwaZulu-Natal). Daar was slegs homosigote individue in ʼn steekproef van Monontsha Pas (Qwa-Qwa), ʼn bevolking wat volgens die literatuur P. m. melanotus en P. m. subviridis, sowel as intermediêre omvat, en alle monsters was toekenbaar aan P. m. subviridis. Die allosiemstudie is egter gebaseer op fenetiese beginsels en vir verdere taksonomiese oplossing is ʼn kladistiese benadering vereis. ʼn Mitokondriale DNS-analise (16S rRNS geen) wat gebruik maak van Maksimum Parsimonie-, Maksimum Waarskynlikheids- en Bayes-analises is daarom uitgevoer om die filogenetiese verwantskappe tussen spesies en subspesies te bepaal en om die taksonomiese status van vorme in die P. melanotus-spesiekompleks te herondersoek. Die mtDNS-analise het die meeste van die resultate van die allosiem-analise bevestig. Eerstens, P. langi is weer bevind om basaal te wees. Met die byvoeging van P. microlepidotus en P. spinosus tot die binne-groep het dit nou duidelik geword dat P. langi die basale spesie in die genus is. (Onlangse studies het aangedui dat P. capensis en P. nebulosus nie kongeneries met Pseudocordylus is nie.) Tweedens, die 16S rRNS resultate bevestig dat P. m. melanotus, soos tans vasgestel, saamgestel is uit twee klade wat nie sustergroepe is nie. Die noordelike bevolkings van P. m. melanotus (Sabie en Lochiel) vorm ʼn redelik diep divergente klaad wat ʼn afsonderlike spesie mag verteenwoordig. Dit is egter bevind dat die Nkandla bevolking saamgegroepeer het met die ander suidelike P. m. melanotus-bevolkings en nie met P. transvaalensis soos wat die geval was in die allosiem-elektroforetiese analise nie. Die mees verbasende resultaat van die 16S rRNS-analise was egter die bevinding dat beide P. microlepidotus en P. spinosus genestel was binne P. m. subviridis. Dit dui daarop dat hierdie twee spesies kon ontwikkel het vanuit P. m. subviridis en slegs onlangs van mekaar geskei het, toe vinnige morfologiese splitsing voorgekom het, maar met beperkte genetiese differensiasie. Dit word voorgestel dat al drie die bogenoemde taksa voorlopig as volledige spesies beskou word. Daar was ook morfologiese steun vir die uniekheid van al die groeperings wat die mtDNS-analise uitgewys het. Pseudocordylus transvaalensis kan uitgeken word aan sy bogemiddelde grootte, unieke dorsale en (swart) kleurpatrone op die keel, so veel as drie horisontale rye lateraaltemporale skubbe, ʼn reeks klein skubbe agter die interpariëtale skub, en gewoonlik twee subokulêre skubbe agter die middelste subokulêre skub op beide kante van die kop. Die verskillende bevolkings wat tans geklassifiseer word as P. melanotus is moeiliker om van mekaar te skei, maar P. m. melanotus en P. m. subviridis verskil gewoonlik soos volg: frontonasale skub in twee gedeel in P. m. melanotus, heel in P. m. subviridis (en in die meeste Noordelike melanotus); lateraal-temporale skubbe in twee rye, die boonste ry met verlengde skubbe teenoor ʼn enkele ry verlengde skubbe; longitudinale rye van dorsolaterale skubbe naby aan mekaar teenoor ver uit mekaar; femorale porieë van wyfies klein en vlak teenoor diep met sekreterende proppe. Noordelike melanotus verskil van Suidelike melanotus deurdat hulle gewoonlik ʼn heel frontonasale skub het en daar selde ʼn klein skub teenwoordig is agter die frontonasale skub. Pseudocordylus langi het unieke dorsale en keel-kleurpatrone (wat ʼn reeks blou kolle op die sye insluit), granulêre dorsale skubbe met 6-9 rye vergrote plat skubbe langs die rugsteen, ʼn groot totale aantal femorale porieë (25-34), en gewoonlik net vyf (glad, ongerif) infralabiale skubbe op elke kant van die kop. Pseudocordylus spinosus het ook unieke dorsale en keel-kleurpatrone, skerp laterale skubbe, frontonasale skub langer as wyd en nie in kontak met die loreale skubbe nie, klein totale aantal femorale porieë (6-9), en wyfies (nie net mannetjies nie) het gedifferensieerde femorale skubbe. Die Hoof-komponent Analise (HKA) en die Kanonieke Diskriminant Analise (KDA) het albei vier groepe geïdentifiseer, naamlik P. transvaalensis, P. langi, P. spinosus en ʼn P. melanotus/subviridis/microlepidotus groepering. ʼn Aparte KDA van alle P. melanotus bevolkings het gedeeltelik onderskei tussen Suidelike melanotus en P. m. subviridis, en die Noordelike melanotus is grootliks van die ander onderskei; terwyl ʼn KDA van P. transvaalensis daarop gedui het dat al drie allopatriese bevolkings 100% onderskeibaar in morfologiese ruimte is. ʼn Genestelde Klaad-Analise het aangedui dat fragmentasie, sowel as gebiedsuitbreiding, ʼn rol gespeel het in die verspreiding van die P. melanotus-spesiekompleks. Dit kan moontlik verklaar word deur die klimaatswisselinge (hoë-lae temperature en nat-droë siklusse) gedurende die Senosoikum wat habitat-uitbreiding en –verkleining veroorsaak het. Gebaseer op die topologie van die mtDNS filogram is dit duidelik dat die genus Pseudocordylus al langs die oostelike platorand ontstaan het. ʼn Voorouer soortgelyk aan P. langi kon ʼn uitgebreide gebied al langs die oostelike platorand gehad het, met die Maloti-Drakensberg wat die suidelike limiet van hierdie gebied gevorm het. Gedurende ʼn daaropvolgende toename in globale temperature het gebiedsverkleining en fragmentasie plaasgevind, wat ʼn geïsoleerde bevolking in die suide en een in die noorde tot gevolg gehad het. Die suidelike bevolking het onveranderd oorleef in die Maloti-Drakensberg skuilplek (“refugium”), maar die noordelike bevolking is geforseer om aan te pas in die warmer toestande. Daarna het die noordelike vorm se gebied weer uitgebrei, maar gedurende ʼn daaropvolgende koeler periode het gebiedsverkleining weer plaasgevind, met die gevolg dat daar ʼn geïsoleerde noord-oostelike bevolking in die Sabie-Lochiel-area in Mpumalanga (Noordelike melanotus) en ʼn bevolking in die weste was. Verwantskappe in die laasgenoemde klaad is nie voldoende opgelos om verdere rekonstruksie van die biogeografiese geskiedenis moontlik te maak nie, maar dit is duidelik dat ʼn vorm soortgelyk aan P. m. subviridis geïsoleer geraak het in die suide waar dit eindelik op hoë liggings in kontak gekom het met P. langi. Die gebied van P. m. subviridis is ook later suidweswaarts uitgebrei tot in die binnelandse berge van die Oos-Kaap en Kaapse Plooiberge om tot die ontstaan van die P. microlepidotuskompleks aanleiding te gee. Hierdie siklus van gebiedsuitbreiding en verkleining kan ook ʼn verklaring bied vir die geïsoleerde bevolkings by Suikerbosrand, Nkandhla distrik, en in die Amatole-Groot Winterberg-streek. Verder word voorgestel dat P. spinosus ontstaan het uit ʼn voorouerlike bevolking soortgelyk aan P. m. subviridis wat geïsoleerd geraak het op die laer hange van die Drakensberg waar die druk van aardsbewonende roofdiere tot ʼn vinnige verandering in morfologie vanaf redelik gladde liggaamskubbe tot ʼn meer skerppuntige morfologie gelei het.

Thesis (PhD (Zoology))--University of Stellenbosch, 2009. / ENGLISH ABSTRACT: The Cape Floristic Region (CFR) is a biodiversity hotspot in South Africa, threatened by climate change and various other processes. The Greater Cederberg Biodiversity Corridor (GCBC) is a conservation area incorporating both public and private land, providing a practical and effective solution to conserve biodiversity in the CFR. This area is also home to two of the eight melanistic cordylid lizard species found in south-western South Africa. One of the herpetological conservation targets identified for the GCBC was an understanding of the ecology of melanistic cordylid populations with particular reference to global environmental change. Most melanistic cordylids occur in cool coastal and montane localities, and it was suggested that melanism has a thermoregulatory function in these species. The first aim of this study was to determine the climatic conditions with which melanistic cordylids are currently associated. Several melanistic cordylid populations showed a distinct association with a high incidence of fog and cloud cover, underscoring the thermal melanism hypothesis, which predicts that melanistic lizards should occur in cool environments. Several other populations, however, did not show such an association. The next aim was thus to compare habitat use and morphology among 10 melanistic cordylid populations. Individuals of the northern population of Pseudocordylus capensis and the Cordylus peersi population occurred in the warmest environments, used significantly higher rock formations, and had relatively longer limbs than those of other melanistic populations. Having a morphology that allows for flexibility in habitat use, may enable species such as P. capensis to overcome the constraints of melanism in warm environments. Being melanistic may result in decreased activity times in warm environments. The variation in habitat thermal quality and daily activity patterns of two melanistic cordylid species with different morphologies and habitat preferences, occurring sympatrically, was investigated. During summer, high rocks provided a better thermal quality habitat to P. capensis than small rocks, and P. capensis had a longer activity period than C. oelofseni. This suggests that the thermal opportunities provided by high rock enables P. capensis to increase its activity time. The impact of terrestrial and aerial predators can help shape body armour in lizards, with those species more exposed to aerial predators being faster and less armoured, and those more exposed to terrestrial predators being more heavily armoured. The degree of body armour in melanistic cordylids and their non-melanistic relatives was investigated. Melanistic members of the cordylus-niger-oelofseni and C. polyzonus clades had less armour than their non-melanistic relatives, supporting the prediction that melanistic cordylids basked more and were more exposed to aerial predators than non-melanistic lizards. An increase in body armour in C. peersi indicated exposure to terrestrial predators, whereas P. capensis had a reduction in body armour, indicating exposure to aerial predators. Little body armour, together with a slender morphology and long limbs, may thus enable this species to move with ease on large boulders and scale vertical surfaces to successfully avoid predators. Pseudocordylus capensis displayed much greater movement rates during activity than other cordylids. A less sedentary foraging strategy may be a prerequisite for life on large, barren rock surfaces where food availability may be low or not uniformly distributed. Both males and females of this species also had large home ranges, a unique phenomenon for cordylids. Space use of males only overlapped marginally, but extensive overlap among males and females and among females, respectively, was observed. Due to the constraining effect of climate on the distribution of most melanistic populations, melanistic cordylids should be considered as priority species for conservation. While P. capensis is pre-adapted for survival in warm climates, it is dependent on the availability of suitable habitats. The GCBC would thus play an important role in the conservation of this species’ habitat. / AFRIKAANSE OPSOMMING: Die Kaapse Blommeryk (KBR) is ‘n “biodiversity hotspot” in Suid-Afrika wat deur klimaatsverandering en verskeie ander prosesse bedreig word. Die Groter Cederberg Biodiversiteitskorridor (GCBK) is ’n bewaringsarea wat beide openbare en privaatgrond inkorporeer, en ’n praktiese en effektiewe oplossing tot die bewaring van biodiversiteit in die KBR bied. Twee van die ag melanistiese gordelakkedisse wat in suidwestelike Suid-Afrika aangetref word, kom ook hier voor. Een van die herpetologiese bewaringsdoelwitte vir die GCBK was om insig oor die ekologie van melanistiese gordelakkedis populasies met verwysing na globale omgewingsveranderinge in te win. Die meeste melanistiese gordelakkedisse kom in koel kus- en berggebiede voor, en daar is voorgestel dat melanisme ‘n termoregulerende funksie by hierdie spesies het. Die eerste doel van die studie was om die huidige klimaatstoestande waarmee melanistiese gordelakkedisse geassosieer word, te bepaal. Verskeie melanistiese gordelakkedis-populasies het ‘n duidelike assosiasie met mis en wolkdekking getoon, wat die termiese melanisme hipotese se voorspelling dat melanistiese akkedisse in koue omgewings moet voorkom, ondersteun. Verskeie ander populasies, het egter nie so ‘n assosiasie getoon nie. Die volgende doel was om habitatgebruik en morfologie tussen 10 melanistiese gordelakkedispopulasies vergelyk. Individue van die noordelike populasie van Pseudocordylus capensis en Cordylus peersi het in die warmste omgewings voorgekom, het relatief langer ledemate gehad en beduidend hoër rotsformasies as ander melanistiese populasies benut. ’n Morfologie wat buigsame gebruik van die habitat toelaat, kan sommige spesies soos P. capensis in staat stel om die beperkinge van melanisme in ‘n warm omgewing te oorkom. In warm omgewings mag melanisme tot ’n afname in aktiwiteitstye lei. Variasie in termiese kwaliteit van die habitat en daaglikse aktiwiteitspatrone van twee melanistiese spesies, met verskillende morfologieë en habitatvoorkeure, wat simpatries voorkom is bestudeer. Gedurende somer het hoë rotse ‘n beter termiese kwaliteit habitat aan P. capensis verskaf as die klein rotse, en P. capensis het ‘n langer aktiwiteitsperiode as C. oelofseni gehad. Dit stel voor dat die termiese geleenthede wat deur hoë rotse verskaf word, P. capensis in staat stel om sy aktiwiteitsperiode te verleng. Die invloed van terrestriële en lugpredatore kan help om liggaamspantser in akkedisse te vorm. Spesies wat hoofsaaklik aan lugpredatore blootgestel is, is vinniger en het minder pantser, terwyl spesies wat hoofsaaklik aan terrestriële predatore blootgestel is, meer pantser het. Die graad van pantser in melanistiese gordelakkedisse en hulle nie-melanistiese naasverwantes is ondersoek. Melanistiese lede van die cordylus-niger-oelofseni en C. polyzonus klades het minder pantser as hulle nie-melanisties naasverwantes gehad, en ondersteun die voorspelling dat melanistiese gordelakkedisse meer in die son gebak het en meer aan lupredatore blootgestel was. ’n Toename in pantser by C. peersi dui op blootstelling aan terrestriële predatore, terwyl P. capensis die minste pantser van alle melanistiese gordelakkedisse het, wat dui op blootstelling aan lugpredatore. Min beskerming, tesame met ‘n lenige morfologie en lang ledemate, mag dus hierdie spesie toelaat om gemaklik oor groot rotse en vertikale oppervlaktes te beweeg en roofdiere suksesvol te vermy. Pseudocordylus capensis het groter bewegingstempo’s tydens aktiwiteit as ander gordelakkedisse getoon. ‘n Meer beweeglike voedingstrategie mag ook ‘n voorvereiste wees vir ‘n lewe op groot, leë klipoppervlaktes waar voedselbeskikbaarheid dalk laag kan wees en nie eweredig versprei is nie. Beide mannetjies en wyfies het ook groot tuisgebiede gehad, ’n unieke verskynsel by gordelakkedisse. Mannetjies se ruimtes het slegs marginaal oorvleuel, terwyl daar heelwat oorvleueling tussen mannetjies en wyfies se ruimtes was. As gevolg van die beperkende invloed van klimaat op die verspreiding van die meeste melanistiese populasies, moet melanistiese gordelakkedisse as prioriteitspesies vir bewaring beskou word. Terwyl P. capensis pre-aangepas is vir oorlewing in warm klimate, is hierdie spesie afhanklik van die beskikbaarheid van gepaste habitatte. Die GCBK sal dus ’n belangrike rol vervul in die bewaring van die habitat van hierdie spesie.

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

Thesis (MSc (Botany and Zoology))--University of Stellenbosch, 2005. / The Dwarf Crag Lizard, Pseudocordylus nebulosus, is one of several relict ectotherm species associated with the mistbelt of the Cape folded mountain belt. Prior to this study, it was only known from a single locality in the Hottentots Holland Mountains. In this study, the distribution range and microhabitat preferences of P. nebulosus were determined and resource partitioning among the three melanistic cordylids (C. oelofseni, P. capensis and P. nebulosus), co-occurring in this area, investigated. Using the locality where P. nebulosus was first discovered as centerpoint, surveys were conducted in all directions and the occurrence of all three melanistic species recorded. The previous known range of P. nebulosus, of only 0.04 km2, was extended to 11 km2. Of the three melanistic cordylids, P. nebulosus has by far the smallest range, completely overlapping with the ranges of both the other two melanistic cordylids. Pseudocordylus nebulosus was found to show a distinct affinity for water bodies such as mountain streams and seepage areas. Distinct differences in resource partitioning were found among the three species regarding crevice selection, which will prevent any significant competition during periods of environmental stress. Cordylus oelofseni preferred small crevices at ground level, P. capensis preferred large rock structures high above ground level and P. nebulosus utilized intermediate sized rock structures. Because of its relatively small range and melanistic colour, P. nebulosus could be a key indicator species of environmental change. Although the lack of objective fire management and global warming may be immediate threats to the survival of this species, possible illegal collection due to the easy access via the popular hiking trail in the area, is probably less significant a threat than was previously thought. Although its known range has been extended considerably, it is recommended that the Vulnerable status of P. nebulosus be maintained. This study provides baseline data that could be useful in future monitoring programmes to predict declines and fluctuations. In the second part of this study, the aim is to provide information about sexual dimorphism in P. nebulosus and to discuss the observed variation in sexual size dimorphism among montane cordylids. Data were recorded for all P. nebulosus individuals encountered in the Landdroskop area (Hottentots Holland Mountains), irrespective of size and sex. The total sample of 87 lizards recorded, consisted of 26 adult males, 49 adult females and 12 indeterminates. Size at sexual maturity was determined at 60 mm snout-vent length (SVL) for both sexes. The highly female-biased adult sex ratio recorded for P. nebulosus, is considered to be due to sampling error, gravid females probably basking more than males, making them easier to locate during searches. Generation glands were found to be present in males only and the number present was significantly correlated to body size. Both adult males and adult females possessed active femoral glands, but males had significantly more than females. Females were found to reach larger body sizes than males, but adult males had relatively larger heads than females. No significant difference in scar frequency was found between the male and female samples. Variation in sexual size dimorphism among montane cordylids is discussed and the need for more comprehensive data pointed out. The female-biased sexual size dimorphism in P. nebulosus and its sister species, P. capensis, is tentatively ascribed to fecundity selection for offspring to be large at birth in order to survive in a predictable unfavourable environment at high altitudes. Sexual dimorphism in head size is ascribed to sexual selection, males probably being territorial as in many other cordylids.

Thesis (MSc)--University of Stellenbosch, 2002. / ENGLISH ABSTRACT: Specialized skin scales (generation glands) and undifferentiated skin scales were compared in three species of cordylid lizard, viz. Cordy/us cordy/us, Pseudocordy/us micro/epidotus and P. capensis. These skin derivatives were histologically examined and compared, using data existing in literature (Maderson, 1966; 1967; 1968a) with similar structures in gekkonids. Histological descriptions of cordylid skin structure were the same as those shown for gekkonids. Three types of generation glands were identified in cordylids (Van Wyk & Mouton, 1992), and these proved to be different to those existing in gekkonid species. These three types of generation glands were further compared regarding their ecdysis histology, which proved to be identical, thus, these glands differ only on gross morphological structure. Skin of all three species was also compared with regard to ecdysis, and while the histology of all three was identical, shedding activity was shown to differ in all three species. P. micro/epidotus displayed dormancy in the germinative layer for much longer periods of the year than either of the other two species, while P. capensis displayed very little dormancy. C. cordy/us displayed an intermediate pattern of ecdysis activity and dormancy. Autoradiography was performed on all species in both ecdysis activity and dormancy periods, to compare mitotic activity patterns in these periods. Generation gland activity appeared to correlate well with known testosterone peaks in the testicular cycle in all three species. Asynchrony between generation glands and skin scales was shown in all three species. / AFRIKAANSE OPSOMMING: GENERASIEKLIERE EN VERVELLINGSIKLUSSE IN GORDELAKKEDISSE (SAURIA: CORDYLIDAE) Drie spesies gordelakkedisse, Gordy/us cordy/us, Pseudocordy/us micro/epidofus en P. capensis, se gespesialiseerde velskubbe (generasiekliere) en gewone velskubbe word vergelyk. Hierdie velskubbe word deur histologiese metodes geëksamineer en vergelyk, met gebruik van data wat reeds in die literatuur bestaan (Maderson, 1966; 1967; 1968a), met soortgelyke strukture in Gekkonidae. Histologiese beskrywing van Cordylidae veistruktuur was identies met dié van Gekkonidae. Drie tipes generasiekliere was geïdentifiseer in gordelakkedisse (van Wyk & Mouton, 1992), en hulle verskil gedeeltlik van naverwante strukture in Gekkonidae. Hierdie drie tipes generasiekliere was verder vergelyk met betrekking tot hulle vervellingsiklus histologie, wat identies was. Dus verskil hulle net met betrekking tot hulle vorm. Vel is ook vergelyk met dieselfde metodes. Alhoewel daar geen verskille was met betrekking tot hulle histology nie, was die tye van aktiwiteit van kiem-sellae beduidend verskillend in alle spesies. In P. micro/epidofus het die kiem-sellaag russtadium baie langer geduur as in die ander twee spesies, terwyl P. cepensis amper geen russtadium getoon het nie. G. cordy/us het 'n intermediêre gedragspatroon vertoon tussen aktiewe en rustende fase met betrekking tot sy vervellingsiklus. Outoradiografie is gebruik op elke spesie, in beide aktiewe en rustende vervellingsfases, om verskille in mitotiese aktiwiteit te wys. Generasieklier aktiwiteit blyk te korreleer met pieke van testosteroonvlakke van die testikulêre siklus in al drie spesies. Asinkronie is aangetoon tussen generasiekliere en velskubbe in al drie spesies.

Thesis (MSc)--Stellenbosch University, 1998 / Stellenbosch University. Faculty of Science. Dept. of Botany & Zoology. / ENGLISH ABSTRACT: There has been a long-standing need to systematically analyze and classify South African fossil Lacertilia. Although extensive assemblages of fossil lizard and amphibian material from Langebaan on the West Coast and elsewhere exist in museum collections, the fragmentary nature of the material has largely prevented in-depth analyses and identification. In this comparative study the skulls and lower jaws of 7 lizard genera, representing the six extant South African families, were disassembled and the bones analyzed individually. The aim was to compile a comparative database of each bone against which current and future fossil finds could be matched. Detailed descriptions of the isolated elements were given. The results showed that despite some intra-generic variation, unique structural differences do exist in individual bones which may be utilized in the taxonomic assessment of fragmentary fossil material. / AFRIKAANSE OPSOMMING: Daar bestaan lank reeds 'n behoefte vir die sistematiese analise en klassifisering van fossielmateriaal van Suid-Afrikaanse Lacertilia. Alhoewel uitgebreide versamelings van akkedis- en amfibier-fossiele van Langebaan aan die Weskus en elders in museums bestaan, het die fragmentariese aard van die materiaal grootliks diepgaande analises en identifikasie belemmer In hierdie vergelykende studie is die skedels en onderkake van 7 akkedisgenera, wat die ses resente Suid-Afrikaanse families verteenwoordig, gedisartikuleer en elke been individueel geanaliseer. Die doel was om 'n vergelykende databasis van elke been saam te stel waarmee huidige en toekomstige fossielvondse vergelyk kan word. Gedetaileerde beskrywings van die ge'isoleerde elemente word gegee. Die resultate toon dat desondanks 'n mate van intra-generiese variasie, unieke strukturele verskille tussen individuele bene weI bestaan en dat hierdie verskille gebruik kan word om fossielfragmente taksonomies te analiseer.

Thesis (PhD)--Stellenbosch University, 2003. / ENGLISH ABSTRACT: The sungazer, Cordylus giganteus, is an endangered lizard species belonging to the family Cordylidae. It has been speculated that the function of semiochemical communication is performed by two types of skin glands, the femoral glands and the generation glands, which are also found in this family of lizards. Other skin glands and also the cloacal glands are further possible sources of semiochemicals. The investigation of these potential sources of chemical messages in C. giganteus, served as a starting point towards a better understanding of the chemical communication of lizard species belonging to the family Cordylidae. In continuation of this study the femoral gland secretion of the Cape girdled lizard, C. cordylus, was also investigated. Gas chromatography, low resolution GC-MS, GC-HR-MS, MO-TMS derivatisation and retention time comparison were used as analytical techniques in the chemical characterization of the femoral and generation gland secretions of C. giganteus and the femoral gland secretion of C. cordylus. Some compounds were not identified because of their low concentration in the secretions and/or mass spectra could not be obtained for pure compounds because of co-elution with other compounds. Compounds identified in the femoral gland secretion include the following: Carboxylic acids - saturated and unsaturated Alcohols Ketones Aldehydes - saturated and unsaturated Esters - saturated and unsaturated Hydrocarbons - saturated and unsaturated Nitriles Amides - saturated and unsaturated y-Lactones Squalene u-Tocopherol Steroids Quantitative analysis of the femoral and generation gland secretions of a number of sungazers indicated distinct differences between the secretions of males and females (in the case of the femoral gland secretions), but no apparent trend could be found in the differences between the femoral and generation gland secretions of individual lizards of the same gender. Qualitative seasonal differences were however observed in the femoral gland secretions of all individuals of C giganteus. / AFRIKAANSE OPSOMMING: Die ouvolk, Cordylus giganteus, is 'n bedreigde akkedisspesie van die familie Cordilidae. Daar is gespekuleer dat twee soorte velkliere wat by hierdie familie akkedisse voorkom, naamlik die femorale- en generasiekliere, betrokke is by semiochemiese kommunikasie van hierdie diere. Ander velkliere, asook die kliere in die akkedisse se kloaka, is ook potensiele bronne van semiochemiese verbindings. Die bestudering van hierdie potensiele bronne van chemiese boodskappe by C. giganteus is as 'n beginpunt gebruik om die semiochemiese kommunikasie van die akkedisse van die familie Cordilidae beter te verstaan. Ter uitbreiding van hierdie studie is die femorale klierafskeiding van die Kaapse gordelakkedis, C. cordylus, ook ondersoek. Die femorale en generasieklierafskeidings van C. giganteus en die femorale klierafskeidings van C. cordylus is chemies gekarakteriseer deur van analitiese tegnieke, naamlik gaschromatografie, lae resolusie GC-MS, GC-HR-MS, MO- TMS derivatisering en retensietydvergelyking, gebruik te maak. Talle verbindings is nie geidentifiseer nie omdat hulle in 'n baie lae konsentrasie in die afskeidings voorkom, en/of saam met ander komponente elueer, wat veroorsaak dat daar nie massaspektra vir hierdie suiwer komponente verkry kon word nie. Verbindingstipes wat in die afskeidings voorkom, sluit die volgende in: Karboksielsure - versadig en onversadig Alkohole Ketone Aldehiede - versadig en onversadig Esters - versadig en onversadig Koolwaterstowwe - versadig en onversadig Nitriele Amiede - versadig en onversadig y-Laktone Skwaleen a-Tocopherol Steroiede Kwantitatiewe analises van die femorale en generasieklierafskeidings van verskeie ouvolk akkedisse het getoon dat daar duidelike kwantitatiewe verskille tussen die afskeidings van mannetjies en wyfies is (in die geval van die femorale klierafskeidings), maar dat daar geen duidelike patroon in die verskille tussen die femorale en generasieklierafskeidings van individuele akkedisse van dieselfde geslag is rue. Daar is kwalitatiewe seisoenale verskille tussen die femorale klierafskeidings van individue van C. giganteus gevind.

This study deals with the three orders of Squamata (Sauria, Amphisbaenia, Serpentes) of the Orange Free State, South Africa. Following an intensive systematic survey 4 492 specimens have been examined comprising 77 different species and subspecies of which 25% represent new records for the study area. Variation in taxonomically important characters as well as informa- tion on colour, size, habitat, breeding, predators and diet are discussed. Certain taxonomic changes have been made. Distribution maps have been compiled on the basis of eighth-degree-units. Distributional patterns have been analyzed to establish areas of relative homogeneity separated by transitional zones. A causal analysis of the main distribution patterns of the O.F.S. Squamata indicated that rainfall is the major environmental factor influencing distribution. A comparative analysis of the squamate areas has been done with regard to various biogeographic phenomena. / Thesis (Ph.D.)-University of Natal, Pietermaritzburg, 1977.

Os lagartos Tropidurus do grupo torquatus compreendem um conjunto de 15 espécies atualmente reconhecidas que se distribuem pelas áreas abertas da América do Sul cis-Andina. Estas espécies apresentam populações saxícolas e arenícolas, cuja relação não era bem compreendida. O objetivo deste trabalho foi, utilizando cinco marcadores moleculares, dois mitocondriais e três nucleares, propor uma hipótese filogenética robusta. Foi feita a mais extensa cobertura geográfica da distribuição conhecida do grupo, o que proporcionou incluir o maior número possível de populações arenícolas e saxícolas. Juntamente com as análises moleculares, foram feitas contagens de caracteres merísticos e medidas morfométricas de modo a delimitar as linhagens encontradas. Foram incluídas nas análises moleculares 14 das 15 espécies, e para os dados morfológicos, todas as espécies contaram com pelo menos um indivíduo. O gênero Tropidurus não foi recuperado como monofilético. Embora a monofilia do grupo torquatus não tenha sido formalmente testada pela ausência de T. chromatops nas análises moleculares, todas as demais espécies foram recuperadas em um grupo monofilético. Das 14 espécies estudadas, seis provaram-se monofiléticas: T. erythrocephalus, T. hygomi, T. insulanus, T. Montanus e T. mucujensis e T. psammonastes; as demais mostraram-se para- ou polifiléticas. Foram testadas hipóteses de relacionamento entre as populações arenícolas e saxícolas, mostrando que o quadro é bastante complexo, com uma grande plasticidade eco-morfológica, indicada pelos múltiplos eventos de ocupação das áreas arenosos ao longo da América do Sul Cis-Andina. Houve pelo menos 10 eventos independentes de linhagens arenícolas, mostrando uma grande plasticidade eco-morfológica. Entre os clados recuperados, há pelo menos 10 linhagens que podem ser candidatas a espécie, obtidas de clados bem resolvidos e morfologicamente distintos. Os resultados mostraram que muitas das espécies consideradas de ampla distribuição e por isto consideradas de menor preocupação para políticas de conservarção, como T. hispidus, T. oreadicus e T. torquatus, na verdade são constituídas por muitas linhagens microendêmicas que devem receber atenção especial quanto a sua conservação. / As presently understood, the Tropidurus torquatus group comprises 15 lizard species distributed in open areas throughout Cis-Andean South America. These species include saxicolous and psammophilous populations with uncertain phylogenetic relationships. The aim of this work was to provide a comprehensive phylogenetic analysis of the group based on two mitochondrial and three nuclear markers. Our sample represents the most extensive geographic coverage of the group\'s distribution, including the largest possible number of saxicolous and psammophilous populations. Our approach also involve a parallel morphological analysis based on meristic and morphometric data in order to delimit the taxonomic lineages. The phylogenetic analyses included 14 of the 15 species known to date, whereas morphological data were obtained from at least one individual of all nominal species. Our results recovered the genus Tropidurus as non-monophyletic; of the 14 species included in the molecular analyses T. erythrocephalus, T. hygomi, T. insulanus, T. montanus, T. mucujensis and T. psammonastes are monophyletic, whereas all other traditional taxa are apparently para/polyphyletic aggregates. The relationships between psammophilous and saxicolous populations are complex indicating least 10 independent origins of sandy lineages, as well as at least 10 candidate species without available names. Many of the traditional species previously considered widespread, and therefore of minor concern from conservation perspectives, (e.g., T. hispidus, T. oreadicus and T. torquatus) in fact consist of many microendemic lineages that should receive special conservational attention.