Rozprawy doktorskie na temat „Reptile populations”

Reptile populations are suffering substantial global losses and roads are identified as one of the leading threats to their persistence. Currently, efforts to mitigate this threat are being implemented with various levels of success. I studied the effectiveness of exclusion structures (i.e., fencing) at preventing reptiles from gaining access to the road, and reducing road mortality. I also examined if population connectivity structures (i.e., ecopassages) were effective at reducing habitat and population fragmentation and allowing individuals to access habitats, resources, and mates on both sides of a major road (4 lane highway). I found that the fence was ineffective at preventing reptiles from gaining access to the road; however, reptiles were observed using the ecopassages to cross the road. Behavioural trials testing painted turtles’ (Chrysemys picta) willingness to use an ecopassage demonstrated that refusal was twice more likely than use of an ecopassage. I also examined the potential for roads to pose a physiological threat to roadside populations of reptiles by examining corticosterone (CORT), a stress hormone linked to negative health effects in cases of elevated levels over the long-term. To assess if individuals living near a major road had higher CORT levels than individuals from a less impacted population, I developed a novel means of measuring CORT from painted turtle claws in partnership with Dr. Gabriela Mastromonaco (Toronto Zoo). With long-term CORT levels considered as a proxy for chronic physiological stress, I did not find evidence that populations near roads had altered stress levels. However, this seminal study will provide the framework for further examination of more species, including species-at-risk, and a better understanding of effects of anthropogenic environments on wildlife health. As road ecologists strive to expand our understanding of the threats roads pose to reptiles, it is important that this field spans multiple disciplines, so that we can both understand the direct and indirect threats that roads cause and develop effective mitigation that preserves biodiversity within our anthropogenic landscape.

Orientador: Ricardo Jannini Sawaya
Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: A ecologia de populações investiga os fatores que levam a variação das taxas vitais e, consequentemente, no número de indivíduos. Isso inclui testar hipóteses sobre aspectos da história de vida das espécies e entender os fatores que podem modular a dinâmica populacional. No entanto, a obtenção de dados para testar hipóteses pode ser difícil para populações que apresentam probabilidades de detecção < 1, como anfíbios e répteis. A marcação e recaptura é amplamente usada para estimar a detecção e inferir aspectos de dinâmica populacional e testar hipóteses ecológicas. Neste trabalho empregamos a teoria de marcação e recaptura para testar hipóteses relacionadas à ecologia e conservação de populações de anfíbios e répteis. Utilizamos o programa MARK para implementar modelos de populações abertas e fechadas incorporando a probabilidade de detecção dos indivíduos, para obter estimativas de sobrevivência, e outros parâmetros populacionais usando máxima verossimilhança. Organizamos esta tese em quatro capítulos. Iniciamos enfatizando a importância da probabilidade de detecção, além de simular cenários hipotéticos para demonstrar a relação entre esforço de campo, tamanho ótimo amostral e viés amostral. Em seguida comparamos o efeito de duas técnicas de marcação, o corte de artelhos e o implante de microchips, sobre a sobrevivência individual do sapo ferreiro, Hypsiboas faber. No terceiro capítulo estimamos a sobrevivência e o crescimento populacional da jararaca-ilhoa, Bothrops insularis incorporando emigração temporária aos modelos. Além do estudo de taxas vitais e de dinâmica nas populações, a alocação de energia e suas consequências na sobrevivência individual podem ser testadas com modelos de marcação e recaptura. Assim, no quarto e último capítulo consideramos dois caracteres sexuais presentes no sistema de acasalamento dos lagartos, o tamanho da mandíbula e a coloração chamativa, para comparar as estimativas de sobrevivência entre machos e fêmeas do lagarto cauda de chicote, Cnemidophorus cf. ocellifer. . De forma geral, observamos que a probabilidade de detecção individual nos sistemas estudados foi baixa e condizente com a detecção de vertebrados em ambientes tropicais. Além disso, a inclusão de covariáveis na investigação de parâmetros vitais e no processo de detecção é fundamental para o melhor entendimento dos fatores que explicam a dinâmica de uma população. Especificamente observamos que: (i) demonstramos que as taxas que não incorporam a detecção são enviesadas em relação às estimativas que consideram a detecção, (ii) as estimativas de sobrevivência foram similares em indivíduos de Hypsiboas faber marcados com ablação de artelhos e microchips , (iii) Bothrops insularis apresentou baixa probabilidade de sobrevivência anual e crescimento populacional anual negativo. Por fim, (iv) machos maiores do lagarto Cnemidophorus cf. ocellifer apresentaram sobrevivência mensal menor do que machos menores, mas o oposto foi observado para as fêmeas
Abstract: Population ecology aims to search for factors that lead to variation in vital rates and consequently, in the number of individuals. This includes testing hypotheses about natural history traits and threats to populations. However, obtaining data to test hypotheses is challenging because following individuals in the field can be difficult, especially for amphibians and reptiles, where detection probabilities are often < 1. Mark-recapture methods are widely used to estimate detection probabilities and to test ecological hypothesis. Here we used mark-recapture methods to test hypotheses related to ecology and conservation of amphibian and reptile populations. We implemented open- and closed-population models in Program MARK, to account for detection probabilities and to calculate survival estimates and other population parameters. We organized this dissertation into four chapters. In the first chapter we emphasize the importance of considering detection probabilities besides simulating hypothetical scenarios to show the relationship between field effort, sample size and precision. In the second chapter we used a Cormack-Jolly-Seber model to compare the effect of two amphibian marking techniques, toeclipping and PIT tagging, on survival in the blacksmith tree frog, Hypsiboas faber. In the third chapter our goal was to estimate survival and population growth of the golden lancehead, Bothrops insularis accounting for temporary emigration using Pollock's Robust Design. Besides the study of vital rates and population dynamics, energy allocation and its consequences for survival are testable with mark-recapture models. Thus, in the last chapter we used two traits from the lizard mating system, namely jaw size and courtship coloration, to compare survival estimates between males and females of the whiptail lizard, Cnemidophorus cf. ocellifer. In summary we observed that detection probability on the studied populations were low and similar to other vertebrate populations from the tropics. However, including covariates in estimation models of vital rates and detection is important to obtain more accurate results to explain population dynamics. Specifically we conclude that (i) return rates were biased low in relation to survival estimates that account for detectability, (ii) the estimates of survival were similar between toe-clipped and PIT tagged individuals of Hypsiboas faber, (iii) Bothrops insularis showed low survival probability and negative annual population growth. And (iv) larger Cnemidophorus cf. ocellifer males showed lower monthly survival probability than smaller males but the opposite was found for females
Doutorado
Ecologia
Doutor em Ecologia

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.

Despite long-term study, the mechanism explaining the parapatric distribution of two Australian reptile ticks species, Bothriocroton hydrosauri and Amblyomma limbatum, is not understood. This project aimed to use molecular genetic data to investigate aspects of the population biology of these two tick species, such as population structure and dispersal, to gain further insights into the cause and maintenance of this parapatric boundary. I developed and subsequently tested for Mendelian inheritance a suite of B. hydrosauri and A. limbatum species-specific microsatellites markers. Pedigree analysis showed one B. hydrosauri locus and all of the A. limbatum loci to be inherited in a non-Mendelian manner. Thus I could not investigate A. limbatum population structure and focused solely on B. hydrosauri. The first part of this study tested predictions of a model formulated to explain B. hydrosauri transmission dynamics. The “ripple” model, based on detailed ecological and behavioural data on B. hydrosauri and Tiliqua rugosa, B. hydrosauri’s most common host, predicts higher relatedness among larvae than among nymphs or adults on a host, and significant spatial autocorrelation in larvae extending further than for the later life stages. The model also predicts that adult ticks are likely to encounter related partners and that this will generate inbreeding within the population. I tested those predictions using nine microsatellite loci on a sample of 848 ticks (464 larvae, 140 nymphs and 244 adults) collected from 98 T. rugosa hosts at the northern edge of B. hydrosauri’s distribution range. My data did support all of the predictions of the “ripple” model and indicated that the dynamics of transmission among hosts play an important role in parasite population structure. The second part of this project focused on investigating the population genetic structure of B. hydrosauri at the edge of its geographic range and testing the predictions of a population model derived to explain B. hydrosauri’s parapatric boundary with A. limbatum. The “ridge and trough” model suggested the tick population was organised spatially into a series of “ridges” where tick density was high and “troughs” where it was low. Genetically, the expectation was to find clusters of more closely related individuals associated with the ridges. Cluster analysis of microsatellite allele frequencies and analysis of molecular variance of mitochondrial haplotype frequencies revealed the presence of four genetic clusters within a sample of 244 B. hydrosauri adults. As the highly genetically divergent clusters had overlapping distributions, and in some cases were syntopic, the genetic population structure predicted for these ticks by the “ridge and trough” model was not observed. Several explanations were considered for the observed B. hydrosauri genetic population structure, but syntopy of the clusters suggested that assortative mating is the most likely. I speculated that the clusters have formed in allopatry, when the environment was extremely heterogeneous, such that the ticks (and their hosts) were confined to isolated patches of high-quality habitat. Given sufficient time, this could have resulted in reproductive incompatibility between ticks occupying different patches. The population structure I uncovered indicates subsequent secondary recontact of divergent groups. Although my study allowed for a better understanding of B. hydrosauri biology and population structure, the reasons for the parapatric distributions of B. hydrosauri and A. limbatum are still unclear. Further research should focus on investigating the population genetic structure of A. limbatum at the edge of its range, as well as on performing a larger-scale study of B. hydrosauri population genetic structure and a more detailed investigation of the applicability of the “ridge and trough” model to this tick species. Moreover, it will be useful to inspect the population structure of both these species within the centers of their ranges and compare these findings with population structure found at the edge of the range.

Thesis (Ph. D.)--University of Oregon, 2001.
Typescript. Includes vita and abstract. Includes bibliographical references (leaves 121-147). Also available for download via the World Wide Web; free to University of Oregon users.

Die Vegetationskomposition und –struktur, beispielsweise die unterschiedliche Architektur von Bäumen, Sträuchern, Gräsern und Kräutern, bietet ein großes Spektrum an Habitaten und Nischen, die wiederum eine hohe Tierdiversität in den Savannensystemen des südlichen Afrikas ermöglichen. Dieses Ökosystem wurde jedoch über Jahrzehnte weltweit durch intensive anthropogene Landnutzung (z.B. Viehwirtschaft) nachhaltig verändert. Dabei wurden die Zusammensetzung, Diversität und Struktur der Vegetation stark verändert. Überweidung in Savannensystemen führt zu einer Degradation des Habitates einhergehend mit dem Verlust von perennierenden Gräsern und krautiger Vegetation. Dies führt zu einem Anstieg an vegetationsfreien Bodenflächen. Beides, sowohl der Verlust an perennierenden Gräsern und krautiger Vegetation sowie der Anstieg an vegetationsfreien Flächen führt zu verbesserten Etablierungsbedingungen für Sträucher (z.B. Rhigozum trichotomum, Acacia mellifera) und auf lange Sicht zu stark verbuschten Flächen. Die Tierdiversität in Savannen ist hiervon entscheidend beeinflusst. Mit sinkender struktureller Diversität verringert sich auch die Tierdiversität. Während der Einfluss von Überweidung auf die Vegetation relativ gut untersucht ist sind Informationen über den Einfluss von Überweidung auf die Tierdiversität, speziell für Reptilien, eher spärlich vorhanden. Zusätzlich ist sehr wenig bekannt zum Einfluss auf die Populationsdynamik (z.B. Verhaltensanpassungen, Raumnutzung, Überlebensrate, Sterberate) einzelner Reptilienarten. Ziel meiner Doktorarbeit ist es den Einfluss von Überweidung durch kommerzielle Farmnutzung auf die Reptiliengemeinschaft und auf verschiedene Aspekte der Populationsdynamik der Echse Pedioplanis lineoocellata lineoocellata zu untersuchen. Hinsichtlich bestimmter Naturschutzmaßnahmen ist es einerseits wichtig zu verstehen welchen Auswirkungen Überweidung auf die gesamte Reptiliengemeinschaft hat. Und zum anderen wie entscheidende Faktoren der Populationsdynamik beeinflusst werden. Beides führt zu einem besseren Verständnis der Reaktion von Reptilien auf Habitatdegradation zu erlangen. Die Ergebnisse meiner Doktorarbeit zeigen eindeutig einen negativen Einfluss der Überweidung und der daraus resultierende Habitatdegradation auf (1) die gesamte Reptiliengemeinschaft und (2) auf einzelne Aspekte der Populationsdynamik von P. lineoocellata. Im Teil 1 wird die signifikante Reduzierung der Reptiliendiversität und Abundanz in degradierten Habitaten beschrieben. Im zweiten Teil wird gezeigt, dass P. lineoocellata das Verhalten an die verschlechterten Lebensbedingungen anpassen kann. Die Art bewegt sich sowohl häufiger als auch über einen längeren Zeitraum und legt dabei größere Distanzen zurück. Zusätzlich vergrößerte die Art ihr Revier (home range) (Teil 3). Im abschließenden Teil wird der negative Einfluss von Überweidung auf die Populationsdynamik von P. lineoocellata beschrieben: In degradierten Habitaten nimmt die Populationsgröße von adulten und juvenilen Echsen ab, die Überlebens- und Geburtenrate sinken, währen zusätzlich das Prädationsrisiko ansteigt. Verantwortlich hierfür ist zum einen die ebenfalls reduzierte Nahrungsverfügbarkeit (Arthropoden) auf degradierten Flächen. Dies hat zur Folge, dass die Populationsgröße abnimmt und die Fitness der Individuen verringert wird, welches sich durch eine Reduzierung der Überlebens- und Geburtenrate bemerkbar macht. Und zum anderen ist es die Reduzierung der Vegetationsbedeckung und der Rückgang an perennierenden Gräsern welche sich negativ auswirken. Als Konsequenz hiervon gehen Nischen und Mikrohabitate verloren und die Möglichkeiten der Reptilien zur Thermoregulation sind verringert. Des Weiteren hat dieser Verlust an perennierender Grasbedeckung auch ein erhöhtes Prädationsrisikos zur Folge. Zusammenfassend lässt sich sagen, dass nicht nur Bäume und Sträucher, wie in anderen Studien gezeigt, eine bedeutende Rolle für die Diversität spielen, sondern auch das perennierende Gras eine wichtige Rolle für die Faunendiversität spielt. Weiterhin zeigte sich, dass Habitatdegradation nicht nur die Population als gesamtes beeinflusst, sondern auch das Verhalten und Populationsparameter einzelner Arten. Des Weiteren ist es Reptilien möglich durch Verhaltensflexibilität auf verschlechterte Umweltbedingen zu reagieren.
In semi-arid savannah ecosystems, the vegetation structure and composition, i.e. the architecture of trees, shrubs, grass tussocks and herbaceous plants, offer a great variety of habitats and niches to sustain animal diversity. In the last decades intensive human land use practises like livestock farming have altered the vegetation in savannah ecosystems worldwide. Extensive grazing leads to a reduction of the perennial and herbaceous vegetation cover, which results in an increased availability of bare soil. Both, the missing competition with perennial grasses and the increase of bare soils favour shrub on open ground and lead to area-wide shrub encroachment. As a consequence of the altered vegetation structure and composition, the structural diversity declines. It has been shown that with decreasing structural diversity animal diversity decline across a variety of taxa. Knowledge on the effects of overgrazing on reptiles, which are an important part of the ecosystem, are missing. Furthermore, the impact of habitat degradation on factors of a species population dynamic and life history, e.g., birth rate, survival rate, predation risk, space requirements or behavioural adaptations are poorly known. Therefore, I investigated the impact of overgrazing on the reptile community in the southern Kalahari. Secondly I analysed population dynamics and the behaviour of the Spotted Sand Lizard, Pedioplanis l. lineoocellata. All four chapters clearly demonstrate that habitat degradation caused by overgrazing had a severe negative impact upon (i) the reptile community as a whole and (ii) on population parameters of Pedioplanis l. lineoocellata. Chapter one showed a significant decline of regional reptile diversity and abundance in degraded habitats. In chapter two I demonstrated that P. lineoocellata moves more frequently, spends more time moving and covers larger distances in degraded than in non-degraded habitats. In addition, home range size of the lizard species increases in degraded habitats as shown by chapter three. Finally, chapter four showed the negative impacts of overgrazing on several population parameters of P. lineoocellata. Absolute population size of adult and juvenile lizards, survival rate and birth rate are significantly lower in degraded habitats. Furthermore, the predation risk was greatly increased in degraded habitats. A combination of a variety of aspects can explain the negative impact of habitat degradation on reptiles. First, reduced prey availability negatively affects survival rate, the birth rate and overall abundance. Second, the loss of perennial plant cover leads to a loss of niches and to a reduction of opportunities to thermoregulate. Furthermore, a loss of cover and is associated with increased predation risk. A major finding of my thesis is that the lizard P. lineoocellata can alter its foraging strategy. Species that are able to adapt and change behaviour, such as P. lineoocellata can effectively buffer against changes in their environment. Furthermore, perennial grass cover can be seen as a crucial ecological component of the vegetation in the semi-arid savannah system of the southern Kalahari. If perennial grass cover is reduced to a certain degree reptile diversity will decline and most other aspects of reptile life history will be negatively influenced. Savannah systems are characterised by a mixture of trees, shrubs and perennial grasses. These three vegetation components determine the composition and structure of the vegetation and accordingly influence the faunal diversity. Trees are viewed as keystone structures and focal points of animal activity for a variety of species. Trees supply animals with shelter, shade and food and act as safe sites, nesting sites, observation posts and foraging sites. Recent research demonstrates a positive influence of shrub patches on animal diversity. Moreover, it would seem that intermediate shrub cover can also sustain viable populations in savannah landscapes as has been demonstrated for small carnivores and rodent species. The influence of perennial grasses on faunal diversity did not receive the same attention as the influence of trees and shrubs. In my thesis I didn’t explicitly measure the direct effects of perennial grasses but my results strongly imply that it has an important role. If the perennial grass cover is significantly depleted my results suggest it will negatively influence reptile diversity and abundance and on several populations parameters of P. lineoocellata. Perennial grass cover is associated with the highest prey abundance, reptile diversity and reptile abundance. It provides reptiles both a refuge from predators and opportunities to optimise thermoregulation. The relevance of each of the three vegetation structural elements is different for each taxa and species. In conclusion, I can all three major vegetation structures in the savannah system are important for faunal diversity.

L'examen des statuts sytematiques a permis de distinguer deux especes de scincidae et dans les populations du gesco l. Lugubris, cinq clones parthenogenetiques diploides ou triploides, une lignee bisexuee et certains individus issus d'une hybridation entre ces deux groupes. Une analyse micro-evolutive de plus de 6000 individus montre que, malgre la repartition des iles sur une tres grande surface marine, les capacites de dispersion ne permettent pas l'isolement de populations. Les resultats obtenus sont confrontes aux donnees acquises sur deux groupes d'invertebres remarquables par leur radiations en polynesie francaise

In order to explore the conservation ecology of frogs and lizards in the Sarapiqui region of Costa Rica, I compared populations and communities among forest fragments and La Selva Biological Station, as well as across 35 years of sampling at La Selva. Species richness in nine fragments combined was 85% of that found in La Selva, and community composition varied among sites and by fragment size class. Although communities in fragments differed fundamentally from those in intact forest, the high diversity observed across all fragments indicates that preserving a network of small forest patches may be of great conservation value to the herpetofauna of this region. According to data from past studies at La Selva, most common species of leaf-litter frogs and lizards demonstrated significant decreases in density over the 35-year period. My findings may represent either natural population fluctuations or sweeping faunal declines at this site.

Thesis (M.S.)--Michigan State University. Dept. of Fisheries and Wildlife, 2006.
Title from PDF t.p. (viewed on Nov. 20, 2008) Includes bibliographical references (p. 118-124). Also issued in print.

Globally, as many as 30% of amphibians and 23% of reptile species are threatened and require urgent conservation action. The major threats are primarily caused by anthropogenic activities. This research aimed to investigate the impacts of two anthropogenic threats, over-exploitation and habitat changes on herpetofaunal populations in Hong Kong. Platysternon megacephalum has been heavily depleted because of severe hunting pressure for the food and pet trades. Low densities of individuals and few remaining intact populations have limited our ability to study their ecology. I conducted mark-recapture and radio-telemetry studies on P.megacephalum populations in five streams in Hong Kong, one of which was free from trapping, over 34 months (2009–2011) to investigate the impacts of illegal trapping on populations of P.megacephalum and their spatial ecology and growth. Illegal trapping was associated with the absence of large adults, smaller body sizes of adults and skewed ratios of juveniles to adults. Home ranges were relatively small with a mean 100% minimum convex polygon 996m2. Males moved longer distances than females and both sexes moved longer distances in wet seasons. P.megacephalum was highly aquatic, preferring to stay in pools, and their microhabitat preferences were affected by stream width and depth, and substrate types. Juvenile P.megacephalum grew rapidly, with growth declining after attainment of sexual maturity. The average ages of sexual maturation were eight years for females. Illegal trapping remains the major threat to P.megacephalum populations and I recommend that regulatory personnel identify key streams and patrol regularly against illegal trapping to safeguard remaining populations. In Hong Kong, large areas of primary forest have been replaced by secondary forests and plantations, and changes in tree species composition have often led to alteration of associated plant and animal communities. I examined the herpetofaunal assemblages in secondary forests and exotic Lophostemon confertus plantations. Amphibian abundances were higher in secondary forests while reptile abundance, species richness of amphibian and reptiles were similar. Secondary forests provided better habitats for amphibians and I recommend the planting of a mixture of native tree species and the thinning of exotic trees in future plantation management efforts in South China. Our knowledge about the effectiveness of different herpetofaunal survey methods in Southeast Asia is limited. To fill the information gap, I examined the effectiveness of three survey methods, including transect surveys, pitfall traps and coverboards, for sampling terrestrial herpetofauna. Transect surveys were most effective at sampling species richness and pitfall traps were most efficient in capturing high numbers of reptiles. The results of this study will aid researchers in assessing the feasibility of and choosing herpetofaunal survey methods in Southeast Asia. Despite the severe threats that herpetofauna are facing, our understanding of their ecology and conservation needs remains limited. More research and the initiation of monitoring programs for herpetofauna, strengthened enforcement of existing regulations, and proper habitat management are crucial for the conservation of herpetofauna in South China.
published_or_final_version
Biological Sciences
Doctoral
Doctor of Philosophy

With 226-343 individual/ha, population density of Chelodina longicollis in the dams of the University of Western Sydney-Hawkesbury Richmond campus were in the range of other studies around Australia. Their size extremes (24.3 -223.3 mm) were within the range of previous studies, and the overall sex ratio was skewed toward males. The annual growth rates varied and were weakly correlated with animal size. Scute shedding occurred between September and April and peaked in December. Turtles were generally in excellent condition, indicating that sufficient food resources were available in local habitats. Only 3.4% of the population were in poor condition and few animals (8.8 %) carried signs of past injury. No gross abnormalities were recorded, however, there has been low levels of recruitment to the population compared with other Australian studies. Despite a maximum distance dams sampled of 2.8 km and ample evidence of interchange between dams, there was a great variation in animal size, cohort structure, sex ratio among dams. There are a range of factors which have the potential to bias sampling results. Turtles were not influenced by a dominance hierarchy or by the presence of eels, however, they appeared to be capable of avoidance behaviour when nets are set at a specific location. Different cohorts were caught differentially and this varied with month, season and year. In addition, catchability varied among cohorts. Juveniles were least likely, and sub-adult males were most likely, to be recaptured. In some dams there was evidence that animals moved at random while in others movement did not conform to this pattern. These results could not be accounted for in terms of dam size, physical structure of the dam or the distribution and abundance of vegetation.
Master of Science (Hons)

The sand lizard (Lacerta agilis) reaches the northern periphery of its distribution in south-central Sweden, where small, isolated relict populations occur in pine heath forests on sandy sediments. Modern forestry and fire suppression have reduced the amount of suitable open habitat for the species in this area and seem to be important for its decline. Main objectives of this thesis were to evaluate the efficiency of different management strategies, and if the sand lizard can function as an umbrella species for biodiversity conservation. Over a 16-year period, the estimated annual numbers of adult females in each of two study populations fluctuated between 23 and 3. Simulations of stochastic future population growth showed that the risk of extinction was highly dependent on population growth rate, which in turn was strongly affected by juvenile survival as indicated by elasticity analysis. Simulations of population growth for 50 years showed that the quasi-extinction risk (threshold ≤ 10 females) was > 56% for patches ≤ 1 ha; which is the observed average size of suitable habitat for inhabited patches during a 10-year period. In managed metapopulation networks with highly co-fluctuating local populations, among-population dispersal was not important to reduce extinction risks over a 50-year horizon. In the field the preferred microhabitat of sand lizards was successfully restored using tree felling and patch-soil scarification. The lizards gradually colonized the restored patches, and 16 years after restoration, sand lizards where mainly found there. Pine-heath area, and patch area within individual pine heaths, were of major importance for long-term population persistence at regional and landscape scales, respectively. Analyses of nested species subsets and an umbrella index suggest that the sand lizard can be a useful cross-taxonomic umbrella species on both scales for other red-listed species.

Elucidating the factors that drive variation in the abundance and distribution of organisms is central to ecology. Variables that explain the spatial variation in the abundance of organisms primarily include environmental (e.g., temperature and precipitation) and biotic factors (e.g., competition, predation, and parasitism). An important mechanism influencing the spatial distribution of organisms, at least at small spatial scales, is habitat selection. Traditionally, habitat selection theory has assumed that animals select habitat based on their ability to acquire depletable resources within that habitat, especially food. Ectotherms, however, may instead select habitat based on their ability to process food within the habitat, given the strong dependence of body temperature (and performance) on environmental temperature in this group. The major objective of my thesis was to determine whether energy gain, habitat selection, and population density were driven primarily by food availability or by temperature in ectotherms. I used Sceloporus jarrovii lizards as a study species because these lizards occur at high densities and in similar habitat across a broad altitudinal range. In Chapter 1, I tested the prediction, central to the thermal coadaptation hypothesis, that juvenile lizards prefer body temperatures that maximize their net energy gain. I also tested whether lizards shifted their preferred body temperatures to correspond to the optimal temperature for different energetic states, as per Huey’s (1982) energetics model. In Chapter 2, I determined whether the home range size and density of lizards shifted in response to manipulations of food availability and/or thermal quality within a site. In Chapters 3 and 4, I determined whether mean body condition, individual growth rate, and population density were driven by food availability or thermal quality. In Chapter 3, I visited 32 study sites over a 1,550 m altitudinal range within a year; whereas in Chapter 4, I food-supplemented five out of 10 study sites where I performed mark-recapture over a period of three years. Overall, my thesis demonstrates that both food availability and thermal quality of the habitat drive energy gain, habitat selection, and population density. Juvenile S. jarrovii preferred body temperatures that maximized net energy gain, regardless of energetic state. Although they did not shift their preferred body temperature range depending on energetic state, the difference in the optimal temperature for net energy gain between states (0.4°C), may have been too small to warrant a change in behaviour. Within a site, S. jarrovii increased their home range size and occurred at higher densities as natural food availability increased, and decreased their home range size and occurred at lower densities as the thermal quality under the rocks increased. This suggests that S. jarrovii respond to food availability and thermal quality at different scales, selecting territories based on thermal quality and home ranges based on food availability. Over 32 sites, the abundance of S. jarrovii increased with food availability, whereas the mean body condition increased and the rate at which lizards attained their maximum body size decreased with elevation (at lower thermal quality). In the three-year study, mean body condition and individual growth rate decreased and population density increased with thermal quality, but the strength of the relationship depended on natural food availability. Overall, both food availability and thermal quality of the habitat drive energy gain, habitat selection, and population density; however, thermal quality is often the stronger driver. Thus, improvements to habitat selection models should incorporate habitat thermal quality to improve predictions on how ectotherms distribute themselves on a landscape.

The Pleistocene land bridge islands in the Aegean Sea make an ideal natural experimental system for testing how island age, area and isolation affect genetic variation. My research focuses on the population genetics of the Aegean wall lizard Podarcis erhardii (Lacertidae, Reptilia), which because of its wide distribution, and poor dispersal abilities is a sensitive indicator of fragmentation history. I predict that genetic diversity will be positively correlated with island area and negatively correlated with age. I also predict that island characteristics, host genetic variability or grazing may impact parasite prevalence. Findings showed that larger islands maintained more genetic diversity than smaller islands and older islands have higher mite loads. Geographic distance was unrelated to genetic divergence. Tick prevalence was significantly associated with past grazing practices. This study provides a unique opportunity to disentangle factors that may influence the retention of genetic diversity and prevalence of ectoparasites in natural populations.

Variation in sex ratio among clutches of eggs from different females is common in reptiles with TSD, but the mechanisms that cause this variation are unknown. In an effort to shed light on these mechanisms, we first critically review literature that examines variation in temperature-dependent sex determination (TSD) within species. Genetic variation in TSD and maternal effects on TSD are two major mechanisms that have received attention. We outline the types of experiments and data required to demonstrate that a) genetic variation, b) maternally derived steroids, or c) both factors influence variation in sex ratio among clutches. Next, we compare allele frequencies between populations of Chelydra serpentina that differ in thermosensitivity of sex determination and identify population differentiation in putative TSD genes.

Serovare von Salmonella enterica subspecies enterica sind im allgemeinen pathogen für Mensch und andere Säugetiere. In dieser Arbeit habe ich anhand eines “Multilocus Sequences Typing” Typisierungsschemas die Populationsstruktur einer der am häufigsten auftretenden Serovaren dieser Subspecies, das aus Menschen und Schlachttieren isolierte Serovar Newport charakterisiert. Dieses Schema wurde auch für die Charakterisierung von Isolaten derselben Subspecies aus humanen Dauerträgern und Reptilien verwandt, um zu bestimmen, ob Isolate aus diesen Quellen sich in ihrer Populationstruktur von denjenigen unterscheiden, die aus anderen Quellen isoliert wurden. Multilocus Sequences Typing ist eine weitgehend für die Untersuchung der Evolution und Populationsstruktur von einen breiten Spektrum von Organismen verwendete Technik. 400 - 600 bp lange Fragmente von 7 Haushaltsgenen wurden sequenziert, und jede einzelne Sequenz jedes einzelnen Gens wurde eine Allelnummer zugeordnet. Jede einzelne Allelkombination wurde einem Sequenztyp zugeordnet. Die so gewonnenen Daten wurden weiter analysiert. Drei “Lineages”, Newport-I, Newport-II und Newport-III, wurden innerhalb dieses Serovars identifiziert, die jeweils aus Menschen in Europa, Tieren und Menschen in Nordamerika isoliert wurden. Der Multiresistenz-Phänotyp wurde häufiger in Newport II gefunden, während die meisten Newport III Isolate pan-sensitiv waren. Verglichen mit anderen Serovaren war die Anzahl von “Lineages” innerhalb Newport höher als bei Enteritidis, Kentucky und Typhimurium, aber niedriger als bei Paratyphi B. Das heisst, die Serovare von S. enterica subspecies enterica variieren stark in ihrer Populationsstruktur. Die Sequenztypen in Isolaten aus humanen Dauerträgern waren im allgemeinen am häufigsten in Isolaten von klinischen Patienten und Tieren vorhanden. In der Mehrheit der Serovaren waren die meisten Isolate aus Patienten und Tieren genetisch identisch mit solchen, die aus gesunden Trägern isoliert wurden. Die genetische Variabilität war zwischen Isolaten aus diesen Quellen vergleichbar. Diese Ergebnissen deuten daraufhin, dass Salmonellen aus Dauerträgern sowie Isolate aus Patienten und Tieren derselben Population angehören. Die meisten Serovare aus Reptilienisolaten waren genetisch identisch mit denen von Menschen und warmblütigen Tieren. In den Serovaren Bovismorbificans, Decatur, Miami und Oranienburg hingegen waren die meisten Isolate aus Reptilien genetisch anders als Isolate aus anderen Wirten. Allerdings wurden nur wenige Isolate der Serovaren Bovismorbificans, Decatur und Miami aus Reptilien und nur wenige Isolate der Serovaren Oranienburg aus anderen Quellen getestet; eine grössere Anzahl von Isolaten müsste daher untersucht werden, um festzustellen ob diese genetischen Unterschiede statistich signifikant sind oder nicht.
Serovars of Salmonella enterica subspecies enterica are generally pathogenic to humans and other mammals. In this study, I examined the population structure of one of the most common serovars of this subspecies isolated from humans and food animals, serovar Newport, using a multilocus sequence typing scheme. This scheme was also used to analyze isolates of this subspecies from chronic human carriers and reptiles to determine whether isolates from these sources represent distinct populations than those from other hosts. Multilocus sequence typing has extensively been used to study evolution and population structure of a wide range of organisms. 400-600 bp fragments of 7 housekeeping genes were sequenced and every unique sequence of each gene fragment was given a distinct allele number. Each unique combination of alleles was assigned a distinct sequence type number. The data were used in further analyses. Three lineages, namely Newport-I, Newport-II and Newport-III were identified within serovar Newport which were associated to European humans, animals and humans in North America, respectively. Multidrug resistance phenotypes were most common in Newport-II whereas most isolates in Newport-III were pan-susceptible. When compared to other serovars, the numbers of lineages within Newport were higher than for Enteritidis, Kentucky and Typhimurium but lower than for Paratyphi B. Therefore, serovars of S. enterica subspecies enterica vary greatly in their population structures. The sequence types observed for isolates from chronic human carriers were generally the most common among human-clinical and animal isolates. Most isolates from non-carrier humans plus animals were genetically identical to the carried isolates within most serovars. Genetic diversity was also comparable between isolates from these sources. These results suggest that salmonellae from chronic human carriers belong to the same population as isolates from non-carrier humans and animals. For most serovars, most isolates from reptiles were genetically identical to those from humans or other warm blooded animals. However, in serovars Bovismorbificans, Decatur, Miami and Oranienburg, most reptile isolates were genetically distinct from isolates from other hosts. Only few reptile isolates were tested from Bovismorbificans, Decatur and Miami and only few non-reptile isolates were tested from Oranienburg, and in larger numbers of such isolates would be needed to determine whether these differences are statistically significant.

The development and implementation of effective species and population-specific management strategies requires population-specific information. To demonstrate the relative extirpation risk associated with various road mortality scenarios for a population of Blanding’s turtles at Canadian Nuclear Laboratories in Chalk River, Ontario, a Population Viability Analysis was conducted. Road mortality of two adult females every ten years resulted in population extirpation within 200 years relative to a stable population not experiencing road mortality. To accommodate informed decision-making for the management of this species at risk, the movement patterns and habitat selection of this Blanding’s turtle population were described. There was no significant difference between males and females in distance moved between relocations in either the spring or the summer, but turtles moved greater distances in the spring than in the summer. Annual and seasonal home range size did not differ between the sexes or between spring and summer periods. A compositional analysis indicated Blanding’s turtles preferred marsh habitats over bog, swamp, lake, and upland. Matched-paired logistic regression was used to determine selection of microhabitat features, such as type of vegetation, in the spring and summer. Turtles preferred sites with warmer air temperatures, shallower water, a higher availability of open water, and greater coverage of emergent and floating vegetation types in the spring period. In the summer period, turtles preferred sites characterized by cooler, deeper water, a higher availability of open water, and greater coverage of emergent and floating vegetation types. This population of Blanding’s turtles appears to be relatively small and the continued threat of road mortality indicates a delicate situation for its persistence. Considering seasonally preferred habitats will best inform management decisions for seasonal work restrictions and future development plans.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
Cnemidophorus littoralis é um lagarto teiídeo ameaçado de extinção, endêmico de restinga e restrito ao estado do Rio de Janeiro, tendo sido encontrado em apenas quatro restingas da região: restinga de Grussaí (limite norte), restinga de Jurubatiba, restinga de Maricá e restinga de Marambaia (limite sul). Devido à sua restrita distribuição, os efeitos da degradação de hábitat e mudanças climáticas são especialmente danosos para os indivíduos dessa espécie, podendo levar a uma extinção local ou até total. A fim de aumentar a gama de informações sobre esta espécie de lagarto, investigamos a sua densidade e o seu tamanho populacional em três áreas de restingas, além de termos registrado as temperaturas às quais estão sujeitos nos diferentes micro-hábitats disponíveis, bem como suas preferências a determinadas estruturas da vegetação, e a situação atual de degradação das restingas, comparando-a com a de anos anteriores. O presente trabalho foi realizado nas restingas de Barra de Maricá (Maricá), Jurubatiba (Macaé) e Grussaí (São João da Barra). Os resultados revelaram uma diferença na estrutura da vegetação entre as três restingas, sendo a de Grussaí a que mais se destaca. Essa restinga é também a que apresenta menor densidade populacional e maior índice de degradação. Por outro lado, a restinga de Jurubatiba foi o local com menor quantidade de distúrbios encontrados, possuindo a maior densidade populacional dentre as três e se caracterizando como a melhor área para manutenção da espécie. O folhiço no bordo de moita foi, no geral, o hábitat mais utilizado pelos lagartos, sendo o período entre 10h00 e 11h00 o que teve maior número de avistamentos. A altura de arbusto demonstrou influenciar negativamente a ocupação dos indivíduos na restinga de Grussaí, enquanto os períodos de observação ao longo do dia influenciaram a detectatibilidade dos indivíduos nas três restingas. As restingas também apresentaram uma temperatura ambiente semelhante ao longo do dia, sendo Maricá a restinga com média mais alta (34,6C), seguida por Grussaí (33,9C) e por último Jurubatiba, com uma média de 33,2C. As temperaturas corpóreas às quais os indivíduos estariam sujeitos nos micro-hábitats disponíveis variaram de 27C (folhiço sobre vegetação) a 42,5C (areia nua), na restinga de Grussaí e de 28C (folhiço no interior de moita) a 32,9C (areia nua) na restinga de Jurubatiba. Uma vez que a estrutura do ambiente influencia na característica termal dos lagartos e, consequentemente, na manutenção das populações, a conservação das restingas e de suas estruturas vegetacionais são indispensáveis para a perpetuação da espécie.
Cnemidophorus littoralis is a teiid lizard endemic to restingas and restrict to the state of Rio de Janeiro, being found only in four restingas: restinga de Grussaí (north limit), restinga de Jurubatiba, restinga de Maricá e restinga de Marambaia (south limit). Its current conservation status is "in danger". Due to its restricted distribution, the effects of hábitat degradation and climate changes are specially harmful to individuals of this species, which may lead to local or even total extinction. In order to raise the level of information about this lizard species, we investigated the population density and population size in three areas of restinga, besides recording the temperatures to which they are subject in different micro-hábitats available as well as their preferences for certain vegetation structures and the current situation of degradation of restingas, comparing it to the previous years. The present study took place in Barra de Maricá (Maricá), Jurubatiba (Macaé) and Grussaí (São João da Barra). The results showed a difference between the vegetation structures of the three restingas, being restinga de Grussaí the most different one. This restinga is also the one with the lowest density and the highest degradation index. On the other hand, restinga de Jurubatiba was the site where we found lowest disturbance, having the highest density among the three and being characterized as the best area for the maintenance of the species. The litter on the edges of bushes was, overall, the hábitat most widely used by lizards, and the period between 10:00 am and 11:00 am was the one when most of the sightings ocurred. Shrub height showed a negative effect on the occupation of the individuals in restinga de Grussaí, while the periods of observation along the day influenced the detectability of individuals in the three restingas. The restingas had similar temperature throughout the day, Maricá being the one with highest average temperature (34,6C), followed by Grussaí (33,9C) and finally Jurubatiba, with 33,2C average. The body temperature to which the individuals were subject in the micro-hábitats ranged from 27C (litter above vegetation) to 42,5C (bare sand) in Grussaí, and from 28C (litter inside shrub) to 32,9C (bare sand) in Jurubatiba. Since environmental structure influences the thermal characteristic of lizards, hence maintaining populations, conservation of restingas and its vegetation structures are essential for the perpetuation of the species

Les 2 populations etudiees sont de chize (deux-sevres) et de julliac (massif central). Les durees d'activite journaliere et annuelle, selon le sexe, sont precisees. Le domaine vital est de 14 m**(2) chez les males, 7 m**(2) chez les femelles. Le comportement alimentaire est decrit, la ration alimentaire s'estime d'apres le poids des individus. La densite de population est plus elevee et plus stable a juillac. La proportion des pontes et les taux de survie sont fournis

Understanding the impacts of both natural and anthropogenic landscape features on genetic diversity, population structure and connectivity has important implications for conservation of species living in fragmented environments. Here, I combine population genetic data, detailed land cover information, and computer simulations to explore how landscape shapes genetic structure across two regional populations of the threatened eastern massasauga rattlesnake (Sistrurus catenatus catenatus) in Ontario, Canada: one along the eastern shores of Georgian Bay and the other largely confined to the northern half of the Bruce Peninsula. First I used spatial Bayesian assignment to quantify the genetic population structure within each regional population. I found marked subpopulation structure within eastern Georgian Bay with differentiation of island and mainland snakes, a north-south split within the mainland coinciding with the town of Parry Sound, and evidence of further subdivision within the cluster of snakes north of Parry Sound. In contrast I found no population subdivision within the mainland of the Bruce Peninsula, but genetic distinction of mainland and island snakes. Next, I identified the landscape features that shape spatial genetic structure within regional populations. In eastern Georgian Bay I found local variation in the effect of landscape on populations. North of Parry Sound I found no effect of landscape on inter-individual genetic differentiation, but a strong pattern of isolation-by-distance. In contrast I found that both open water and roads restrict gene flow of snakes south of Parry Sound. I found no evidence of isolation-by-distance or that landscape shape genetic structure within the Bruce Peninsula. Finally I used individual-based, spatially explicit simulations to identify the lag-time associated with the detection of contemporary landscape feature effects on genetic structure of massasaugas, and explore the consequences of using spatially correlated land cover elements in landscape genetic analyses. I found that the genetic consequences of roads could be detected within 2-12 generations when population sizes were small or juvenile dispersal was low. However, I also found that roads could be spuriously identified as impediments to gene flow when spatially correlated features such as water are included in genetic models.
Thesis (Master, Biology) -- Queen's University, 2011-10-14 15:06:35.956

Understanding the events and processes responsible for patterns of within species diversity, provides insight into major evolutionary themes like adaptation, species distributions, and ultimately speciation itself. Here, I combine ecological, genetic and spatial perspectives to evaluate the roles that both historical and contemporary factors have played in shaping the population structure and genetic variation of foxsnakes (Pantherophis gloydi). First, I determine the likely impact of habitat loss on population distribution, through radio-telemetry (32 individuals) at two locations varying in habitat patch size. As predicted, individuals had similar habitat use patterns, but restricted movements to patches of suitable habitat at the more disturbed site. Also, occurrence records spread across a fragmented region were non-randomly distributed and located close to patches of usable habitat, suggesting habitat distribution limits population distribution. Next, I combined habitat suitability modeling with population genetics (589 individuals, 12 microsatellite loci) to infer how foxsnakes disperse through a mosaic of natural and altered landscape features. Boundary regions between genetic clusters were comprised of low suitability habitat (e.g. agricultural fields). Island populations were grouped into a single genetic cluster suggesting open water presents less of a barrier than non-suitable terrestrial habitat. Isolation by distance models had a stronger correlation with genetic data when including resistance values derived from habitat suitability maps, suggesting habitat degradation limits dispersal for foxsnakes. At larger temporal and spatial scales I quantified patterns of genetic diversity and population structure using mitochondrial (101 cytochrome b sequences) and microsatellite (816 individuals, 12 loci) DNA and used Approximate Bayesian computation to test competing models of demographic history. Supporting my predictions, I found models with populations which have undergone population size drops and splitting events continually had more support than models with small founding populations expanding to stable populations. Based on timing, the most likely cause was the cooling of temperatures and infilling of deciduous forest since the Hypisthermal. On a smaller scale, evidence suggested anthropogenic habitat loss has caused further decline and fragmentation. Mitochondrial DNA structure did not correspond to fragmented populations and the majority of foxsnakes had an identical haplotype, suggesting a past bottleneck or selective sweep.
Thesis (Ph.D, Biology) -- Queen's University, 2011-01-11 10:40:52.476

ABSTRACT One cause of declines and extinctions of island species is carnivore introduction. Four carnivores, including the small Indian mongoose (Herpestes auropunctatus), are on the IUCN’s list of 100 of the World's Worst Invasive Alien Species. My thesis summarizes global patterns of carnivore introductions and examines ecological, evolutionary, and management impacts of this mongoose. I study abundances of reptiles and amphibians on mongoose-infested and mongoose-free islands in the Adriatic Sea to determine if factors other than mongoose presence can account for abundance differences. For several reptiles and amphibians, the mongoose is implicated as causing differences. Additionally, I assess species abundance in the small mammal community and activity times of introduced ship rats (Rattus rattus) on the same islands. The mongoose is implicated in a shift in rat activity times, but it is difficult to separate mongoose impacts on small mammal abundance from rat impacts. To manage introduced carnivores, we can exclude, control, or eradicate them. I review literature data on mongoose eradication and control campaigns. I compiled a list of all islands with known mongoose populations and focused on assessing successes, failures, and challenges. The mongoose has been eradicated only on six very small islands. Management at low levels by various techniques has been attempted on many islands, with variable success. On almost all islands of introduction, the mongoose has no potential competitors of similar size. However, on three Adriatic islands where the mongoose was introduced, a similar-sized native carnivore, the stone marten (Martes foina), is present, while on one Adriatic island the small Indian mongoose is the sole carnivore. To see if character displacement occurs in the mongoose when the marten is present, and vice-versa, I examined size variation in the diameter of the upper canine tooth (the prey-killing organ) and skull length in these two species on these islands. Character displacement in both traits was evident for the mongoose but not the marten. Lastly, I developed a simulation model to examine genetic consequences of serial introductions of the small Indian mongoose and found that the potential for population genetic data to determine introduction pathways and sequences is limited.