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

Baited pitfall traps were used to sample the lizard fauna at Birdlings Flat on Kaitorete Spit, Canterbury. Four species had been recorded previously from this area; Leiolopisma maccanni Patterson and Daugherty, Leiolopisma nigriplantare polychroma Patterson and Daugherty, Leiolopisma lineoocellatum (Dumeril and Dumeril) and Hoplodactylus maculatus (Gray). Three of these species (L. maccanni, L. n. polychroma and H. maculatus) were captured during the course of the study. The aim of this present study was to examine the nature of the ecological relationship among these three species at Birdlings Flat. Capture data indicated that L. maccanni was almost entirely confined to the dunelands while L. n. polychroma was associated exclusively with shrublands on old dune ridges behind the sand dunes. H. maculatus' distribution encompassed both of these major habitats. Separation on the basis of habitat was thought to be the most important niche variable for these two diurnal skinks. There was some temporal separation in activity of these two species, with L. maccanni active earlier in the day than L. n. polychroma. However, there was a high degree of overlap in the activity periods of these two species. Temporal differentiation between the nocturnal gecko H. maculatus and the two diurnal skinks is thought to be an important means by which these species coexist. The most common prey items consumed by all three species were Diptera, Araneae, C. propinqua seeds, Hemiptera, unidentified arthropod eggs, Coleoptera and Hymenoptera. Dietary differences between the two skink species were apparent although these differences appeared to be related to the preferred habitats of the respective species. Density estimates for L. maccanni varied between 1050/ha and 1850/ha while L. n. polychroma density varied between 200/ha and 400/ha. The density of H. maculatus was not calculated but appeared to be intermediate to the density of the two skink species. The apparent disappearance of L. lineoocellatum from an area where they were once relatively common is cause for concern. There is no obvious reason for this decline although it may be related to the combined impacts of predation, collection and habitat disturbance.

Nonmammalian vertebrates possess some unusual features in their hormonal systems/ when compared to mammals. As a consequence, they can make an important contribution in investigations concerning the fundamental mechanisms operating in endocrinology. Such studies concerning androgens include inter alia their effects on developmental aspects in the brain of birds and related singing behaviour; the role of neural enzymes in reproductive processes in fish; and the relation between androgens and the stages of spermatogenesis in amphibia, The present thesis examines the biochemistry of androgens in the Australian lizard Tiliqua rugosa. The major compounds studied were testosterone and epitestosterone, which are known to be present in high concentrations in the plasma of the male animal. Previous investigations are expanded, particularly in the areas of steroid identification and testicular biosynthesis. In addition, preliminary studies on the metabolism in the brain (and other tissues) and plasma protein binding are reported. The presence of epitestosterone as a major free androgen in the plasma of the male lizard was confirmed. Other steroids were found in the sulphate fraction. Testosterone sulphate was the most rigorously identified compound, while some evidence was also found for the presence of conjugated 5-androstene-3β,17-diols, etiocholanolone and dehydroepiandrosterone (DHA). Epitestosterone does not appear to be extensively conjugated in this animal. Steroids were not found to be conjugated as glucuronides. The identification studies employed a novel method of electrochemical detection of steroids. This technique was investigated and extended in the current thesis. Biosynthetic studies were carried out on androgen interconversions in the testis, in vitro. The major enzyme activities detected were 17α-arid 17β-oxidoreductases (17α-OR and l7β-OR) and 3β-hydroxysteroid dehydrogenase (3β-HSD)/isonerase. No evidence was found for the presence of a steroid-17-epimerase that would directly interconvert testosterone and epitestosterone. The 17-oxidoreductases were found to be dependent on the cofactor NBDFH. Testosterone appears to be formed mainly via the 4-ene pathway, whereas epitestosterone is formed from both the 4- and 5-ene routes. The compound 5-androstene-3β, 17α-diol was found to be an intermediate in the synthesis of epitestosterone from DHA. Temperature was found to significantly affect 17α-OR activity (maximum at 32°C). In contrast,17β-OR activity was independent of this factor in the testis. Androgen metabolism in the testis was found to be regulated by cofactors, temperature and season. The major enzyme activities found in the male brain were 17α- and 17β-OR. 3βHSD/isomerase was not found; however a low activity of 5α-reductase was identified. Aromatase activity was not positively identified, but preliminary results suggest that it may be present at low levels. The 17-oxidoreductases were widespread throughout the brain. The 17α-OR was significantly lower in the forebrain than other brain sections. The 170-OR activity did not vary significantly throughout the organ, although there was a trend for its activity to be higher in the midbrain region (containing the hypothalamus in these sections). The concentration of endogenous steroids in brain tissue was estimated by radioimmunoassay. Epitestosterone was found throughout the organ structure, whereas testosterone was found mainly in the midbrain (containing hypothalamic regions in these sections). Correlations between enzyme activities and steroid concentrations in brain regions suggested that the main function of 17α-OR is to produce epitestosterone, whereas the 17β-OR may catalyse a more reversible reaction in vivo. Temperature was found to significantly affect both 17α- and 17β-OR activities in the brain. In contrast to the testis, the maximum activity of the brain enzymes occurred at 37°C. The level of 17α-OR activity in the male lizard (100 nmol/g tissue/h) is the highest reported for this enzyme in vertebrates. Both activities were found to be quantitatively similar in the whole brain homogenates of male and female animals, and did not vary seasonally when examined in the male. The 17-oxidoreductases were also found in most other tissues in T.rugosa, including epididymis, adrenal, kidney and liver (but not blood). This suggests that the high activities of both 17α-OR and 17β-OR are dominant features of the steroid system in this animal. The formation of 11-oxygenated compounds was found in the adrenal, in addition to the formation of polar metabolites in the kidney and liver (possibly polyhydroxylated and conjugated steroids). A preliminary investigation into the plasma binding of androgens was carried out. The insults suggest that there are several binding sites for testosterone; one with high affinity and low capacity; the other with low affinity and high capacity. Binding experiments were carried out at 32°C. At this temperature, specific binding was greater than at 25 or 37°C. From the results of competition studies it was suggested that epitestosterone (with a K(i)= 3 X 10 (-6)M for testosterone binding) regulates the binding of testosterone (K(i)=10(-7)M) and hence the concentrations of the latter steroid as a free compound in plasma. In general, the study has shown that the biochemistry of androgens in the reptile T.rugosa is largely similar to that found in other vertebrates. The major difference is a greatly increased activity of 17α-OR, which causes a higher concentration of 17α-compounds to be present in the tissues of this lizard. The physiological roles for epitestosterone are not yet clear. However it appears from this study that this steroid regulates testosterone concentrations in several tissues by either steroidogenic or binding mechanisms. Several major influences on this regulation include temperature, availability of cofactors and seasonal effects.

Copies of author's previously published articles inserted. / Includes bibliographies. / 3 v. : ill. ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / The aim of this thesis is to provide a comprehensive study of the cytology, innervation and blood supply of the pineal complex in Tiliqua rugosa, a large desert dwelling skink (family: Scincidae), commonly known as the sleepy or stumpy-tailed lizard. The study complements the physiological work already reported and expands the knowledge of the epithalamic region in lizards. Various histological techniques, at both light and electron microscopic levels, are utilised. / Thesis (Ph.D.)--University of Adelaide, Dept. of Anatomy and Histology, 1997

Copies of author's previously published articles inserted. / Includes bibliographies. / 3 v. : ill. ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / The aim of this thesis is to provide a comprehensive study of the cytology, innervation and blood supply of the pineal complex in Tiliqua rugosa, a large desert dwelling skink (family: Scincidae), commonly known as the sleepy or stumpy-tailed lizard. The study complements the physiological work already reported and expands the knowledge of the epithalamic region in lizards. Various histological techniques, at both light and electron microscopic levels, are utilised. / Thesis (Ph.D.)--University of Adelaide, Dept. of Anatomy and Histology, 1997

This thesis considers the prevalence and spatial distribution of Salmonella serovars amongst wild endemic lizards on offshore islands around the coast of New Zealand. The mean test prevalence of faecal excretion of Salmonella was 4.7%. Skinks (Scincidae) were more likely (8.5%) to be carriers of Salmonella than geckos (1.6%). Each island was host to between one and three Salmonella serovars that were not found on any other islands in this study. Two exceptions were Salmonella Bousso and Salmonella Mana which were found on two islands within the same geographical area. Based on the findings of this study, different islands are likely to be hosts to different Salmonella serovars which could have implications for future translocations of native lizards. I also assessed the prevalence and spatial distribution of faecal excretion of Salmonella, Aeromonas and Hafnia alvei within Mana Island. The prevalence of Salmonella on Mana Island was estimated at 5.8%. Salmonella was found predominantly in skinks (10.0%) and less often in geckos (4.1%). H. alvei was found at a prevalence of 1.9%. No Aeromonas species were cultured from any of the cloacal swabs, suggesting that the 95% confidence interval for the true prevalence is 0-3%. Each site sampled in this study was host to one or more unique serovar of Salmonella not found at any of the other sites. The results of this study indicate that Salmonella serovars may become established within populations of lizards and is not spread between them. This may be due to a lack of dispersal of lizards between sites, raising important considerations for the translocation of native lizards. I investigated the prevalence of faecal excretion of Salmonella, H. alvei and Aeromonas by New Zealand native lizards from two captive populations. The mean prevalence of faecal excretion of Salmonella in the captive lizards sampled was 11.5%. There was a higher prevalence of Salmonella within captive population A (22.0%) than in population B (3.6%). No Aeromonas was cultured from any of the lizards. H. alvei was found at a prevalence of 5.2%. The prevalence of Salmonella and H. alvei was significantly higher in captive lizards than in wild populations. Captive lizards may, therefore, not be appropriate founders for new populations of wild lizards. Finally I assessed the different efficiencies of two media and two temperatures in isolating six Salmonella serovars from a reptilian source. All serovars grew equally well at 37°C and 27°C. For most serovars XLD agar was the more successful media than MacConkey agar but the success of different culture media depended on the serovar being cultured. Because lizards are frequently host to a wide range of Salmonella serovars, screening samples using multiple microbiological methods is likely to give the best chance of isolating all Salmonella serovars present.

Artificial retreats are increasingly used to sample animal populations and in attempts to boost animal numbers in degraded habitats. Here, I test potential applications of artificial retreats for lizards inhabiting a coastal environment of high conservation value (Kaitorete Spit, New Zealand). I first conducted a pitfall-trapping survey examining the distribution and relative abundance of lizards in duneland, farmland and shrubland habitats, and tested the influence of trap placement on capture rates. Capture rates of the diurnal skinks Oligosoma maccanni (McCann�s skink) and O. nigriplantare polychroma (common skink) were highest in duneland and farmland, respectively, and were most sensitive to the distance separating traps from the nearest cover (the greater the distance, the lower the capture rate). Captures of O. lineoocellatum (spotted skink) and Hoplodactylus maculatus (common gecko) were rare. Secondly, in separate chapters I test the utility of artificial retreats for monitoring: 1) a preference trial examining relative use of three types of artificial retreats by skinks (O. maccanni and O. n. polychroma) and geckos (H. maculatus); 2) a comparison of the effectiveness of artificial retreats relative to pitfall traps for detecting cryptic and primarily nocturnal geckos (H. maculatus) following translocation; and 3) capture-recapture estimation of population parameters (survival and abundance) of H. maculatus. I found that: 1) geckos strongly preferred retreats made of Onduline over corrugated iron and concrete tiles, whereas skinks exhibited no apparent preferences; 2) artificial retreats were more effective than pitfall traps for detecting geckos following translocation; and 3) monthly survival and recapture probabilities of geckos varied with age-class and over time. Estimated survival was unexpectedly low, possibly due to excessive trap spacing. I developed a new capture-recapture model specifically for population size estimation with data from artificial retreats, which gave estimates that were up to 50% greater than those predicted by conventional capture-recapture models. I caution that permanent placement of artificial retreats in long-term studies may be inappropriate for estimation of population parameters due to potential habitat-enhancement effects and/or altered predation risk. Thirdly, I conducted a capture-recapture field experiment, using a replicated Before-After-Control-impact (BACI) design, to test the relative effects of habitat manipulation (artificial retreat addition) and partial predator removal (by fencing) on annual survival of duneland skink (O. maccanni) populations. Survival increased at sites with predator exclosures, but not at control sites or following the addition of artificial retreats, either alone or in combination with a predator exclosure. The magnitude of the increase in survival for the exclosure-only treatment was small, but sufficient to change the trajectory of an apparently stable population into an increasing one, suggesting that the population is limited by predators. Predator control, but not the addition of artificial retreats, is predicted to benefit O. maccanni. To conclude, the Onduline design developed here appears to be particularly useful for sampling cryptic, terrestrial geckos; however, artificial retreats must be used appropriately to avoid bias arising from habitat-enhancing effects and/or altered predation risk. The restoration value of artificial retreats requires further testing on other species and in areas where natural retreat sites are limited.

This thesis set out to examine the soils, plants, lichens, invertebrates and common skinks along a gradient of habitat modification. This gradient was represented by ten study sites, of varying management histories, in a mid altitude tall tussock (Chionochloa spp.) grassland in eastern Central Otago. One extreme of the gradient was represented by intact tall tussock plants with a high density of inter tussock vegetation. The other extreme was represented by intensively managed exotic pasture. Native plants, invertebrates and reptiles were present along the entire gradient of modification and there was a clear threshold in the diversity of native plants along the gradient. This threshold was reached after the management practice of ploughing was applied to a site. Sites that had not been ploughed were found to be similar in their native plant diversity, and all unploughed sites had significantly higher native plant diversity than unploughed sites. There was considerable variation in the abundance of individual plant and Coleoptera species along the modification gradient. The most intensively modified sites had the lowest plant diversity, the lowest abundance and diversity of Orthoptera, as well as the lowest abundance of common skinks. Sites with low levels of modification contained a higher abundance of common skinks, and, native forbs, lichens and bryophytes than the more intensively modified sites. With regard to individual plant and Coleoptera species recorded, there were generally not clear thresholds for their presence and absence along the modification gradient. Rather, there was a gradual turnover for most species along the gradient such that the plant and Coleoptera community at opposing ends of the gradient had less species in common sites of similar modification levels. A high proportion of the Coleoptera species observed were present in all sites, suggesting that disturbance has selected for an adaptive generalist life trait, and that the species remaining comprise the resilient portion of the Coleoptera fauna. The relationship between Coleoptera communities and the gradient of modification was scale dependent, with the strongest relationship being observed at the largest scale measured. The hypothesis that faunal diversity and abundance would be best predicted by the structural diversity of the vegetation rather than by plant species diversity was tested. Structural diversity was strongly correlated (p < 0.01) with Coleoptera diversity, and Coleoptera abundance whereas plant species diversity was not. However, plant species diversity was a stronger correlate of common skink abundance than plant structural diversity. The structural diversity of the vegetation has the potential to be measured remotely and could be a correlate for faunal diversity and abundance when undertaking landscape scale studies. This thesis demonstrates that native biota exists within the agricultural environment of the mid-altitude tall tussock (Chionochloa rigida) grasslands of eastern Central Otago despite intensive modification in some areas. The findings suggest that it is possible to integrate the objectives of agriculture and the conservation of some faunal groups especially for the more resilient species. However, this study also indicates that relatively unmodified sites are valuable reservoirs of biodiversity in the mid altitude zone and it is recommended that the limited number of lightly modified sites that remain in the mid altitude zone be conserved.

Artificial retreats are increasingly used to sample animal populations and in attempts to boost animal numbers in degraded habitats. Here, I test potential applications of artificial retreats for lizards inhabiting a coastal environment of high conservation value (Kaitorete Spit, New Zealand). I first conducted a pitfall-trapping survey examining the distribution and relative abundance of lizards in duneland, farmland and shrubland habitats, and tested the influence of trap placement on capture rates. Capture rates of the diurnal skinks Oligosoma maccanni (McCann�s skink) and O. nigriplantare polychroma (common skink) were highest in duneland and farmland, respectively, and were most sensitive to the distance separating traps from the nearest cover (the greater the distance, the lower the capture rate). Captures of O. lineoocellatum (spotted skink) and Hoplodactylus maculatus (common gecko) were rare. Secondly, in separate chapters I test the utility of artificial retreats for monitoring: 1) a preference trial examining relative use of three types of artificial retreats by skinks (O. maccanni and O. n. polychroma) and geckos (H. maculatus); 2) a comparison of the effectiveness of artificial retreats relative to pitfall traps for detecting cryptic and primarily nocturnal geckos (H. maculatus) following translocation; and 3) capture-recapture estimation of population parameters (survival and abundance) of H. maculatus. I found that: 1) geckos strongly preferred retreats made of Onduline over corrugated iron and concrete tiles, whereas skinks exhibited no apparent preferences; 2) artificial retreats were more effective than pitfall traps for detecting geckos following translocation; and 3) monthly survival and recapture probabilities of geckos varied with age-class and over time. Estimated survival was unexpectedly low, possibly due to excessive trap spacing. I developed a new capture-recapture model specifically for population size estimation with data from artificial retreats, which gave estimates that were up to 50% greater than those predicted by conventional capture-recapture models. I caution that permanent placement of artificial retreats in long-term studies may be inappropriate for estimation of population parameters due to potential habitat-enhancement effects and/or altered predation risk. Thirdly, I conducted a capture-recapture field experiment, using a replicated Before-After-Control-impact (BACI) design, to test the relative effects of habitat manipulation (artificial retreat addition) and partial predator removal (by fencing) on annual survival of duneland skink (O. maccanni) populations. Survival increased at sites with predator exclosures, but not at control sites or following the addition of artificial retreats, either alone or in combination with a predator exclosure. The magnitude of the increase in survival for the exclosure-only treatment was small, but sufficient to change the trajectory of an apparently stable population into an increasing one, suggesting that the population is limited by predators. Predator control, but not the addition of artificial retreats, is predicted to benefit O. maccanni. To conclude, the Onduline design developed here appears to be particularly useful for sampling cryptic, terrestrial geckos; however, artificial retreats must be used appropriately to avoid bias arising from habitat-enhancing effects and/or altered predation risk. The restoration value of artificial retreats requires further testing on other species and in areas where natural retreat sites are limited.