Thesis (MSc)--Stellenbosch University, 2008. / ENGLISH ABSTRACT: The Greater Cederberg Biodiversity Corridor (GCBC) is a large-scale conservation corridor situated in the south-western region of South Africa. Delineation of the GCBC was largely based on by vegetation data. The relevance of the GCBC for the conservation of the reptilian fauna in the area south of 31°S and west of 21°E is assessed in the present study. This entailed determining the GCBC’s coverage of regional reptile diversity patterns and assessing its potential conservation significance during possible climate induced changes in reptile distributions. Reptile species point distribution data from the preliminary (2007) SARCA (South African Reptile Conservation Assessment) database was used. Under-representation of the Tankwa Karoo in the dataset required a field survey of this region. Additionally, the biogeographical influence of the arid Tankwa Karoo Basin on the distribution of reptiles in the south-western districts of South Africa was investigated. Turnover across the Basin is high, species richness is lower than in surrounding mountainous areas and there are no species endemic to the area. The Tankwa Karoo Basin acts as a dispersal barrier for many reptile species occurring in the surrounding more mesic areas. At the same time, the ranges of a number of typical northern, arid adapted species extend southward along the Tankwa Plains. A number of species range extensions in the region are reported. Patterns of endemism, species richness and turnover were plotted from the point distribution data at quarter and eighth degree square resolution. Extensive sampling bias towards reserves and populated areas is apparent from the reptile species richness plots. This pattern is more pronounced for snakes than lizards. Reptile richness is particularly high along the north-south section of the Cape Fold Mountains and also relatively high along the south-western coast, peaking in the Lambert’s Bay area. The majority of the 20 reptile species endemic to the study area are associated with one of two identified centres of endemism: the Greater Cederberg area, or the narrow coastal zone stretching from the Lambert’s Bay area to the Cape Peninsula. An additional third set of endemics comprised of melanistic forms restricted to a number of different refugia, notably, Landroskop, the Cape Peninsula, Sladanha-Langebaan region, Piketberg Mountains and a confined area along the western section of the Cape Fold Mountains. Species richness and endemism patterns co-vary within the study area. Biotic regions were identified through hierarchical clustering of grid cells according to shared species occurrences. A Northern, Southern, Central and Western biotic region was identified. Classification tree methodology (CART) and Canonical Correspondence Analysis (CCA) were used to characterise defined biotic regions in terms of selected environmental variables. Four sets of species assemblages are described on the basis of these biotic regions – two major and two minor ones. Of the major assemblages the Northern assemblage can be described as an arid zone one and the Southern assemblage as a mesic zone one. The minor Central assemblage, comprising mainly rock-dwelling forms, represent evolutionary leftovers as a result of climate change induces cycles of contraction and expansion of arid and mesic faunas. The other minor one, the West Coast assemblage could be considered a sub-assemblage of the Northern one, with particular adaptation to the coastal climate. Environmental characterisation of the biotic regions reveals that these groupings are supported by an environmental signal. The contiguity of four distinct sets of reptiles, each with its own set of environmental requirements, in this relatively small geographic area clearly indicates that the southwestern region of South Africa is biogeographically complex. The GCBC incorporates the largely coinciding centres of endemism and richness along the West Coast and the greater Cederberg area. Although the centre of endemism for melanistic reptile forms, in the Saldanha-Langebaan area, falls just south of the GCBC boundary, the Corridor fulfils the requirements for effective conservation of reptiles in the area to a large degree. The north-south dispersal pathways provided by the Corridor along the Cape Fold Mountains is believed to be adequate to buffer climate change effects, however there is concern about its ability to contribute to the persistence of the assemblage associated with the narrow coastal zone in the west. / AFRIKAANSE OPSOMMING: Die Groter Cederberg Biodiversiteit Korridor (GCBK) is ‘n grootskaalse bewaringskorridor wat in die suid-westelike deel van Suid-Afrika geleë is. Die grense van GCBK is gebasseer op plantegroei data. In die huidige studie word die betekenis van die GCBK vir die bewaring van die reptiel fauna in die gebied suid van 31°S en wes van 21°O assesseer. Die mate waartoe die GCBK die patrone van reptieldiversiteit in die streek inkorporeer, asook die korridor se potensiaal om voorsiening te maak vir reptiel verspreidingsgebiede wat moontlik as gevolg van potensiële omgewingsverandering kan verskuif. Die beskikbare puntverspreidingsdata van die voorlopige (2007) SARCA (South African Reptile Conservation Assessment) databasis is gebruik. Swak verteenwoordiging van die Tankwa Karoo in die datastel het ‘n veldopname van die gebied genoodsaak. Verder is die biogeografiese invloed van die ariede Tankwa Karoo Kom op die verspreidingspatrone van reptiele in die suid-westelike deel van Suid-Afrika ook ondersoek. Die spesie omset van beide Noord na Suid en Wes na Oos oor die Tankwa is hoog, die spesierykheid is aansienlik laer as in die omringende bergagtige gebiede en daar is geen spesies wat endemies is tot die Tankwa Karoo nie. Die Tankwa Karoo Kom dien as ‘n barieêre teen spreiding vir sommige reptielspesies wat in die omringende gematigde gebiede voorkom. Terselfdertyd reik die verspreidings van ‘n aantal tipiese droogte aangepasde spesies vanuit die noorde suidwaarts langs die Tankwa Vlaktes. Nuwe verspredingsrekords wat ‘n paar spesies se gebiede uitbrei word ook raporteer. Die puntverspreidingsdata is geruik om die patrone van endemisme, spesierykheid en omset op kwart- en agtstegraad resolusie te plot. Spesierykheid kaarte toon ‘n duidelike neiging tot deegliker opnames in reservate en bewoonde gebiede. Hierdie patroon is meer opmerklik vir slange as akkedisse. Reptielrykheid is besonders hoog langs die noord-suid as van die Kaapse Plooiberge en ook relatief hoog langs die suid-wes kus met ‘n maksimum in die Lambertsbaai omgewing. Die meerderheid van die 20 reptielspesies wat endemies is aan die studie area is met een van twee geïdentifiseerde sentrums van endemisme geassosieer: die Groter Cederberg area óf die nou kussone wat vanaf Lambertsbaai tot Kaappunt strek. ‘n Derde stel endemiese spesies wat uit melanistiese vorme bestaan, is beperk tot ‘n aantal refugia, naamlik, Landroskop, Kaappunt, Saldanha- Langebaan omgewing, Piketberg berge en ‘n beperkte area langs die westelike dele van die Kaapse Plooiberge. Spesierykheid en endemisme patrone stem grootliks ooreen binne die studie area. Roosterselle is op grond van gedeelde spesiesamestellings met behulp van ‘n hieragiese groeperingsmetode (Incremental Sum of Squares) gegroepeer. Vier bio-areas, nl. ‘n Noordelike-, Suidelike-, Sentrale en Westelike bio-area is identifiseer. Klassifikasieboom metodologie (Classification and Regression Trees, CART) asook Kanoniese Annalises (Cannonical Correspondence Annalysis, CCA) is gebruik om hierdie geografiese areas in terme van ‘n aantal omgewingsveranderlikes te karakteriseer. Vier spesieversamelings, twee groter en twee kleiner versamelings, is in ooreenstemming met hierdie vier areas geïdentifiseer. Die Noordelike en Suidelike spesieversamelings is die groteres en kan beskryf word as die faunas van onderskeidelik ‘n ariede en gematigde sone. Die kleiner Sentrale versameling bestaan hoofsaaklik uit rots-lewende spesies en mag die evolusionêre oorblyfsels verteenwoordig van ariede en gematigde faunas waarvan die verspreidings herhaaldelik as gevolg van klimaatsveranderingsiklusse uitgebrei en gekrimp het. Die Weskus versameling is ook ‘n kleiner een en kan as ‘n sub-versameling van die Noordelike een beskou word, maar spesifiek tot die kus klimaat aangepas. Die klassifikasie van hierdie bio-areas word ondersteun deur die analiese van die omgewingsveranderlikes. Die feit dat vier kenmerkende versamelings reptiele, elk met sy besondere omgewingsvereistes, in hierdie relatief klein geografiese area ontmoet, dui daarop dat die suid-westelike deel van Suid-Afrika biogeografies kompleks is. Die GCBK inkorporeer die grootliks ooreenstemmende sentrums van endemisme en rykheid wat langs die Weskus en in die groter Cederberg area voorkom. Alhoewel die sentrum van melanistiese endemiese spesies, in die Saldanha-Langebaan omgewing, net buite die grense van die Korridor val, voldoen die GCBK grootliks aan die vereistes vir die effektiewe bewaring van reptiele in die gebied. Die voorsiening van noord-suid verspreidingsweë langs die Kaapse Plooiberge binne die Korridor word beskou as voldoende om die gevolge van klimaatsverandering te buffer. Daarinteen is daar kommer oor die vermoeë van die GCKB om ‘n doeltreffende bydrae te maak tot die voortbestaan van die spesieversameling wat met die nou kussone langs die Weskus geassosieer is.

L’étude de la composition isotopique de l’oxygène de l’émail des dents de vertébrésconstitue une méthode fiable de reconstitution des paléotempératures, grâce àl’interdépendance entre le δ18O de l’apatite des dents, le δ18O des fluides corporels, del’eau ingérée et la température du milieu. L’amélioration et la miniaturisation des techniquesanalytiques a permis d’augmenter la résolution du signal reconstitué, depuis les variations detempérature sur de grandes échelles de temps jusqu’aux variations saisonnières durant laformation de la dent. Cependant, ces variations du δ18O de la dent ne sont pas uniquementdépendantes des variations de température du milieu, mais peuvent également êtreaffectées par d’autres paramètres climatiques, comme la répartition des précipitations aucours de l’année, ou biologique, comme le mode de minéralisation de la dent, l’alimentation,la physiologie de l’animal ou des migrations.Les paramètres biologiques peuvent être estimés dans le cas de taxons possédantdes parents proches dans la faune actuelle. Par exemple, la connaissance des processus deformation et de minéralisation des dents de bovinés actuels permet d’interpréter le signalisotopique de l’oxygène enregistré dans les dents de bovinés fossiles. Ainsi, l’analyse dedents de Bison priscus provenant de l’aven de Coudoulous (Lot, France) a permis dereconstituer les variations saisonnières de température au cours de l’avant-dernier épisodeglaciaire (MIS 6) au Pléistocène moyen, lorsque la région servait de terrain de chasse àHomo neanderthalensis. Le climat était à cette époque plus froid de 4°C en moyenne, maisavec des saisons nettement plus contrastées. Ainsi, si les températures estivales étaientidentiques aux valeurs actuelles, les températures hivernales étaient plus basses de 6-7°C.En milieu marin, les variations saisonnières de température affectent uniquement leseaux de surface. Les plaques dentaires de myliobatidés, un groupe de raies pélagiquesvivant principalement entre 0 et 100 mètres de profondeur, sont un outil potentiel pourreconstituer la paléosaisonnalité. L’étude de plaques dentaires de Myliobatis et deRhinoptera actuels montre que la composition isotopique des dents de ces animauxenregistre des variations de température et de δ18O des eaux de surface. Ainsi, il est doncpossible de reconstituer les caractéristiques des masses d’eau traversées par l’animal. Cetoutil a également un intérêt paléoécologique car il permet de mettre en évidence d’éventuelscomportements migratoires, comme chez certains myliobatidés actuels. L’étude despécimens d’Aetomylaeus provenant du Pliocène de Montpellier (Hérault, France) montredes températures 5°C plus élevées par rapport aux v aleurs actuelles. / The oxygen isotopic composition of the vertebrate tooth enamel is a reliable proxy toreconstruct paleotemperatures based on the dependence of the δ18O of the tooth apatite onthe δ18O of body fluids, on the δ18O of the drinking water, and on the environmentaltemperature. The improvement and the miniaturization of the analytical procedures allowedincreasing the resolution of the reconstructed signal, from paleotemperature variations overgeological times to seasonal variations during the tooth growth. However seasonal variationsof the enamel δ18O do not only depend on temperature variations but can also be influencedby other climatic parameters such as rainfall distribution over the year, or by biological andecological parameters such as tooth mineralization process, diet, physiology or migratorypatterns.Biological parameters can be estimated based on the study of extant relatives inmodern faunas. For example, data on tooth formation and mineralization processes inmodern bovids allow a better understanding of the oxygen isotopic signal recorded in fossilbovid teeth. Thus reconstruction of seasonal variations of temperature during the penultimateglacial episode (MIS 6) has been made possible from the analysis of Bison priscus teethfrom the aven of Coudoulous (Lot, France). Climate was 4°C colder during the middlePleistocene when Europe was still Homo neanderthalensis hunting ground, and seasonswere more contrasted than today. Summer temperatures were similar to modern values, butwinter temperatures were 6-7°C colder.In marine environments, seasonal variations of temperature only affect surfacewaters. Myliobatids are pelagic rays living mostly between 0 and 100 m depth, thus theoxygen isotopic composition of myliobatid dental plates is a potential proxy to reconstruct thepaleoseasonality. The isotopic analysis of modern Myliobatis and Rhinoptera samplesconfirmed that variations of the sea-surface temperature (SST) and the δ18O of seawater arerecorded in the δ18O of myliobatid teeth. Thus it is possible to reconstruct the variations ofseawater temperature during a part of the animal’s life, but it also allows pointing outmigratory patterns in some myliobatid species. Reconstructions of seasonal variations ofSST during the middle Pliocene in Montpellier (Hérault, France) from the δ18O of myliobatiddental plates yielded paleotemperatures 5°C higher than modern values.

Le développement des activités industrielles et agricoles du siècle dernier a eu pour conséquence le rejet de substances chimiques dans l’environnement, qui contaminent les écosystèmes, et peuvent s’accumuler dans les plantes, les sédiments, et le long des chaînes alimentaires. Il apparait primordial d’effectuer une évaluation du risque écologique associé à la présence de ces composés dans les milieux naturels et les espèces sentinelles sont des outils judicieux pour déterminer l’exposition des individus et évaluer les conséquences sur les organismes. Les amphibiens et les reptiles possèdent des caractéristiques écologiques et biologiques qui les rendent potentiellement intéressants en tant qu’espèces sentinelles. L’objectif des études présentées dans cette thèse est de déterminer la disponibilité de certaines substances dans l’environnement, et d’évaluer les effets de la contamination environnementale sur les organismes en utilisant plusieurs espèces de reptiles et d’amphibiens, (i) en mesurant les niveaux de polluants accumulés dans les tissus d’espèces de reptiles ; (ii) en évaluant l’influence d’un habitat contaminé sur la morphologie d’adultes de crapaud commun (Bufo bufo) ; (iii) en mesurant de manière expérimentale l’impact d’une molécule fréquemment retrouvée dans l’environnement sur le développement de têtards de crapaud commun. Nos résultats montrent d’une part que les reptiles accumulent efficacement les polluants organiques et les éléments traces métalliques dans leurs tissus, et permettent d’évaluer efficacement la contamination globale d’une zone, mais aussi de mettre en évidence des pollutions ponctuelles localisées. D’autre part, nos travaux montrent une influence de l’habitat agricole sur la morphologie du crapaud commun, potentiellement causé par la présence de contaminants dans ces milieux. Enfin, nous avons pu mettre en évidence un effet de concentrations faibles d’AMPA, métabolite principal du glyphosate, sur le développement de têtards de crapaud commun. Les amphibiens constituent donc des organismes efficaces pour étudier l’impact de la contamination de l’environnement sur les caractéristiques individuelles. Nos travaux montrent ainsi l’utilité de certaines espèces de reptiles et d’amphibiens comme espèces sentinelles de la présence de contaminants dans l’environnement et de leur impact potentiel sur les organismes. Les travaux en écotoxicologie qui portent sur ces organismes restent trop rares, et il est impératif de développer la recherche dans ce domaine, pour participer de manière efficace à l’évaluation du risque environnemental. / The development of industrial and agricultural activities over the last century has resulted in the release of chemicals into the environment, which contaminate ecosystems and can accumulate in plants, sediments and across food webs. As such, it is essential to conduct an assessment of the ecological risk associated with the presence of these compounds in natural environments. Achieving this can be aided through the study of sentinel species, which can be used to determine exposure rates of individuals and assess how these subsequently impact wildlife. Amphibians and reptiles display ecological and biological characteristics that may make them particularly attractive as sentinel species. The collection of studies presented in this thesis aims to determine the availability of contaminants in the environment and estimate the effects of this on individual traits of living organisms. Across several species of reptiles and amphibians we, (i) measured levels of pollutants accumulated in the tissues of several reptile species ; (ii) assessed how contaminated habitats impact the morphology of adult common toads (Bufo bufo) ; and (iii) experimentally measured the influence of a molecule frequently detected in the environment on common toad tadpoles’ growth. Results show that reptiles efficiently accumulate organic pollutants and metal trace elements in their tissues, and thereby allow efficient evaluation of the global contamination of an area, as well as the occurrence of localized pollution events. In addition, our work shows an influence of the agricultural habitat on the morphology of adult common toads, which is potentially a consequence of the presence of chemicals in these environments. Finally, we were able to demonstrate an effect of low concentrations of AMPA, the main metabolite of glyphosate, on the development of common toad tadpoles. Amphibians are therefore efficient organisms to study the impact of environmental contamination on individual characteristics. Our work shows the usefulness of certain species of reptiles and amphibians as sentinel species for the presence of contaminants in the environment, and their potential impact on organisms. Ecotoxicological studies on these organisms remain too scarce, and it is imperative to develop research in this field, to participate effectively in the assessment of environmental risk.

published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

Wong Ka Lok. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2001. / Includes bibliographical references (leaves 121-129). / Abstracts in English and Chinese. / Acknowledgments --- p.i / Abstract --- p.ii / Table A --- p.v / Table B --- p.vi / Table of Contents --- p.vii / Abbreviations --- p.xi / Chapter Chapter 1 --- Molecular authentication of endangered crocodiles and snakes / Chapter 1.1 --- Introduction --- p.1 / Chapter 1.2 --- Traditional method of snake and crocodile identification / Chapter 1.2.1 --- Morphology --- p.7 / Chapter 1.2.2 --- Chemical Analysis --- p.9 / Chapter 1.3 --- Molecular Technology in Authentication / Chapter 1.3.1 --- Polymerase Chain Reactions (PCRs) --- p.11 / Chapter 1.3.2 --- Random-primed amplification reaction --- p.12 / Chapter 1.3.3 --- Sequence Characterized Amplified Region (SCAR) --- p.13 / Chapter 1.3.4 --- PCR-RFLP --- p.13 / Chapter 1.3.5 --- DNA sequencing --- p.14 / Chapter 1.4 --- Objectives and strategies of the study --- p.15 / Chapter Chapter 2 --- Materials and General Methods / Chapter 2.1 --- Reagents and Buffers / Chapter 2.1.1 --- Buffers for Total DNA Extraction --- p.17 / Chapter 2.1.2 --- Reagents for Agarose Gel Electrophoresis --- p.17 / Chapter 2.1.3 --- Reagents for Plasmid DNA Preparation --- p.18 / Chapter 2.1.4 --- Medium for Bacterial Culture --- p.18 / Chapter 2.1.5 --- Reagents for Preparation of Competent Cells --- p.19 / Chapter 2.2 --- DNA Isolation / Chapter 2.2.1 --- Extraction of DNA from meats --- p.20 / Chapter 2.2.2 --- Extraction of DNA from blood --- p.20 / Chapter 2.3 --- Phenol/Chloroform Extraction --- p.21 / Chapter 2.4 --- Ethanol Precipitation --- p.22 / Chapter 2.5 --- DNA Concentration/Purity Estimation --- p.22 / Chapter 2.6 --- Mitochondrial DNA amplification --- p.23 / Chapter 2.7 --- Random-Primed Polymerase Chain Reactions --- p.24 / Chapter 2.8 --- SCAR for Snake samples --- p.24 / Chapter 2.9 --- SCAR for Crocodile samples --- p.25 / Chapter 2.10 --- Restriction fragment length polymorphism analysis --- p.25 / Chapter 2.11 --- Agarose Gel Electrophoresis of DNA --- p.26 / Chapter 2.12 --- Purification of PCR product --- p.26 / Chapter 2.13 --- Preparation of Escherichia coli Competent Cells --- p.27 / Chapter 2.14 --- Ligation and transformation of E. coli --- p.27 / Chapter 2.15 --- Plasmid preparation --- p.28 / Chapter 2.16 --- Screening of Plasmid DNA by Restriction Digestion --- p.29 / Chapter Chapter 3 --- DNA sequencing of snakes & construction of snake database / Chapter 3.1 --- Introduction --- p.30 / Chapter 3.2 --- Materials and methods / Chapter 3.2.1 --- Snake samples --- p.32 / Chapter 3.2.2 --- "DNA Extraction, mitochondrial gene amplification and DNA sequencing" --- p.33 / Chapter 3.2.3 --- Construction of database --- p.33 / Chapter 3.3 --- Results / Chapter 3.3.1 --- Cytochrome b gene amplification and sequencing --- p.34 / Chapter 3.3.2 --- Gene amplification and sequencing of 16S rRNA --- p.42 / Chapter 3.3.3 --- Cytochrome b sequence database --- p.50 / Chapter 3.3.4 --- 16S rRNA sequence database --- p.53 / Chapter 3.4 --- Discussion / Chapter 3.4.1 --- Cytochrome b and 16S rRNA genes of snake species --- p.55 / Chapter 3.4.2 --- Cytochrome b and 16S rRNA databases --- p.55 / Chapter Chapter 4 --- Application of PCR-RFLP and SCAR in snake species identification / Chapter 4.1 --- Introduction --- p.57 / Chapter 4.2 --- Material and Methods / Chapter 4.2.1 --- DNA extraction and PCR-RFLP --- p.58 / Chapter 4.2.2 --- RAPD and SCAR --- p.58 / Chapter 4.3 --- Results / Chapter 4.3.1 --- PCR-RFLP of cytochrome b genes of snakes --- p.59 / Chapter 4.3.2 --- PCR-RFLP of 16S rDNA --- p.61 / Chapter 4.3.3 --- RAPD & SCAR analysis --- p.67 / Chapter 4.4 --- Discussion --- p.72 / Chapter Chapter 5 --- "Application of DNA sequencing, PCR-RFLP and SCAR to identify crocodile species" / Chapter 5.1 --- Introduction --- p.74 / Chapter 5.2 --- Materials and methods / Chapter 5.2.1 --- "Crocodile, human and four animal samples" --- p.75 / Chapter 5.2.2 --- "DNA Extraction, mitochondrial gene amplification and DNA sequencing" --- p.75 / Chapter 5.2.3 --- PCR-RFLP and SCAR --- p.76 / Chapter 5.3 --- Results / Chapter 5.3.1 --- Isolation of crocodiles DNA --- p.77 / Chapter 5.3.2 --- Isolation of DNA from Human and four animal species --- p.78 / Chapter 5.3.3 --- Cytochrome b gene amplification and sequencing --- p.78 / Chapter 5.3.4 --- 16S rRNA gene amplification and sequencing --- p.84 / Chapter 5.3.5 --- PCR-RFLP of cytochrome b --- p.89 / Chapter 5.3.6 --- PCR-RFLP of 16S rRNA --- p.91 / Chapter 5.3.7 --- SCAR primers for four crocodile species --- p.93 / Chapter 5.4 --- Discussion --- p.97 / Chapter Chapter 6 --- A case report - authentication of animal samples using DNA sequencing / Chapter 6.1 --- Introduction --- p.99 / Chapter 6.2 --- Material and methods / Chapter 6.2.1 --- Materials --- p.101 / Chapter 6.2.2 --- DNA Extraction and sequencing --- p.101 / Chapter 6.3 --- Result and discussion / Chapter 6.3.1 --- Cytochrome b gene sequencing --- p.102 / Chapter 6.3.2 --- Sequence homology among samples and meats obtained from the market --- p.111 / Chapter 6.3.3 --- Identity of samples B & D --- p.113 / Chapter Chapter 7 --- General Discussion / Chapter 7.1 --- Advantages and weakness of DNA technology --- p.116 / Chapter 7.2 --- Choosing appropriate molecular markers --- p.118 / Chapter 7.3 --- Further suggested work --- p.119 / Chapter 7.4 --- Conclusion --- p.119 / References --- p.121 / Appendix --- p.130

Many herpetofaunal species are imperiled, and the causes of this are often a synergy of multiple factors. In wetlands specifically, two of the possible determinants of species occurrence and faunal community assemblage are fish presence and wetland permanence, which are not always correlated. Twenty wetlands were sampled in Jonathan Dickinson State Park, Florida, USA to observe how wetland herpetofaunal communities vary with fish, wetland permanence and other environmental factors. Herpetofaunal communities with and without fish were significantly different from one another and differences between herpetofaunal communities were primarily due to the contribution of four species of frogs, two generalist ranids and two specialist hylids. Wetland permanence had no observable effect on community structure. Fishless wetlands were significantly more species-rich and possessed higher numbers of individuals even for species that occurred in both fishless and fish wetlands, regardless of their permanence. These findings have implications for wetlands restoration and herpetofaunal conservation. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2014. / FAU Electronic Theses and Dissertations Collection

L’Algérie est un cas d’école en matière d’ignorance en biodiversité. A ce jour, on ne dispose d'aucun inventaire complet pour aucun taxon ni aucun atlas à l’échelle du pays ! Pourtant, l’Algérie est d’une grande importance pour la biodiversité mondiale. La façade littorale de l’Algérie fait partie du hostpot de biodiversité mondial qui est le pourtour méditerranéen et compte plusieurs points rouges de biodiversité régionaux. Par ailleurs, la partie saharienne contient une diversité d’organismes endémiques adaptés aux fortes conditions de sécheresse. Les autorités algériennes déploient un projet ambitieux pour la conservation en fixant 50 % de la surface du pays comme objectif pour les aires protégées ! Mais, l’emplacement de ces aires protégées et leur gestion n’obéit pas à des critères basés sur une bonne connaissance de la diversité, mais sont plutôt panifiés à dire d’expert. L’objectif général de cette thèse c’est l’étude de la distribution de l’ignorance en biodiversité en Algérie en se concentrant sur les « Linnean, Wallacean et Darwinian Shortfalls » et de contribuer à les réduire. J’ai consacré un chapitre qui a pour but de réduire le Linnean Shortfall en proposant 1) une première checklist des reptiles et amphibiens d’Algérie qui est le fruit d’un examen précis des publications scientifiques sur ces taxons en Afrique du Nord. 2) une première pré-évaluation des statuts de conservations des reptiles et amphibiens d’Algérie pour la production de la première liste rouge nationale. La deuxième partie de ce manuscrit traite la question de l’ignorance de la distribution géographique des espèces. Le but de cette partie est de cartographier l’ignorance qui est la différence entre la diversité la richesse spécifique attendue et la richesse spécifique observée. La richesse spécifique attendue a été modélisée avec deux approches : 1 l’utilisation des modèles de niches avec la méthode de maximum d’entropie (MaxEnt) pour prédire les habitats favorables pour chaque espèce puis additionner les différentes couches binaires de présence des espèces pour calculer la richesse spécifique. 2) l’addition des couches des aires d’occurrences des espèces construite par la méthode du minimum convex polygon pour produire la carte de distribution de la richesse spécifique. Les deux approches ont montré la même tendance à l’échelle nationale, c’est-à-dire la concentration des zones les plus riches sur le long de l’Atlas Saharien et des hauts plateaux qui sont la zone de transition entre le Sahara et la partie méditerranéenne de l’Algérie. L’opposition de la partie saharienne globalement pauvre en espèce et la moitié nord plus riche. En fin, les massifs sahariens du Hoggar et Tassili forment une zone très distincte avec une richesse nettement supérieure par rapport au reste du Sahara. Pour ce qui est des lacunes, dans la Partie nord, la Kabylie, le parc national d’El Kala et la région d’Oran sont assez bien prospectées. Dans le Sahara, seuls quelques points sont assez bien prospectés comme Biskra, Béchar et quelques zones du Hoggar et Tassili. En fin, la troisième partie porte sur la distribution des lignées génétiques dans le Maghreb. Les objectif de cette partie est localiser les zones de sutures entre les lignées génétiques divergentes des populations de l’est et de l’ouest du Maghreb et d’essayer de comprendre les mécanismes qui ont conduit à ce patron de diversité génétique. Pour répondre à ces questions, j’ai effectué une phylogéographie comparées sur 11 espèces de reptiles et amphibiens à distribution continue et large dans le Maghreb. Deux zones de sutures ont été identifiées : une zone à la frontière de l’Algérie et du Maroc, l’autre EN Kabylie à l’ouest de la vallée de la Soummam. Les divergences entre les clades est et les clades ouest ont eu lieu entre la période pré-messinienne jusqu’au à la limite plio-pleistocène et se seraient maintenues dans des refuges climatiques à l’est et à l’ouest du Maghreb. / Algeria is a case study of biodiversity ignorance. To date, there are neither complete inventories for any taxa nor atlas across the country! Yet, Algeria is of great importance for global biodiversity. The coastal area of Algeria is part of the global biodiversity hostpot which is the Mediterranean perimeter and has several regional red spots of biodiversity. Moreover, the Saharan part encompasses a diversity of endemic organisms adapted to the strong conditions of drought. The Algerian authorities are deploying an ambitious project for conservation aiming to reach 50% of the country's surface as protected areas! However, the location of these protected areas and their management don’t obey to a scientific evidence based, but are rather based on experts opinion. The main aim of this thesis is the study of the biodiversity ignorance distribution in Algeria by focusing on the "Linnean, Wallacean, and Darwinian Shortfalls" and to contribute to reduce them. The first chapter aims at reducing the Linnean Shortfall by proposing 1) a first checklist of reptiles and amphibians of Algeria which is the result of an accurate review of scientific publications on these taxa in North Africa. 2) a first pre-assessment of the conservation status of reptiles and amphibians of Algeria for the production of the first national red list. The second part of this manuscript deals with the ignorance of the geographical distribution of species. The purpose of this part is to map the ignorance which is defined as the difference between the expected specific richness diversity and the observed specific richness. The predicted species richness was modelled with two approaches: 1 ecological niche modeling with the maximum entropy method (MaxEnt) to predict the suitable habitats for each species and then add the different binary layers of species presence to calculate the specific richness. 2) Minimum convex polygon method was used to create range maps of each species and were auditioned to obtain predicted species richness. Both approaches have shown the same trend at a national scale: the concentration of the richest areas along the Saharan Atlas and the high plateaux which are the transition zone between the Sahara and the the Mediterranean part of Algeria. The opposition of the Saharan with a low species richness and the northern part with a higher species richness. Finally, the Saharan massifs of the Hoggar and Tassili form a very distinct zone with a much greater wealth compared to the rest of the Sahara. In terms of gaps, in the northern part, Kabylie, El Kala National Park and the Oran region are fairly well surveyed. In the Sahara, only a few points are clearly well prospected as Biskra, Bechar and some areas of the Hoggar and Tassili. The third part deals with the distribution of genetic llineages in the Maghreb. The aim of this section is to locate the phylogeographic breaks between the divergent eastern and western populations of the Maghreb and to try to understand the mechanisms that led to this pattern of genetic diversity. To answer these questions, I carried out a comparative phylogeography on 11 species of reptiles and amphibians with continuous and wide distribution in the Maghreb. Two suture zones have been identified: one zone on the border of Algeria and Morocco, the other in Kabylia west of the Soummam valley. The divergences between the eastern clades and the western clades occurred between the pre-Messinian periods up to the plio-pleistocene boundary and were maintained in climatic refugia in the east and west of the Maghreb.

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.

Magister en Ciencias Biológicas con mención en Genética

Previous studies of the relationship between egg size and the embryonic development time showed a positive correlation between the two variables at interspecies level, thus offering the idea that the evolution of the latter could be a limiting factor for enlarging the size of eggs during evolution. Some research into interspecies and intraspecific level of reptiles doesn't confirm this correlation. At the same time, the relationship between the development time and egg size is influenced by many factors, such as shifts in ontogenetic stages of the embryo at the time of ablation of eggs, due to temperature and humidity, the presence of embryonic diapause during embryogenesis or synchronization of hatching time, of which the authors of previous studies took no account or filtered out inaccurately. I think that most of these factors can be well controlled in intraspecific studies, but, variation in egg size within species also tends to be small, which prevents a reliable test for correlation. The solution can be to compare closely related species with high variability in the size of the eggs, in our case the geckos of the genus Paroedura and family Eublepharidae. I eliminated temperature effects by comparing the time of incubation in two equal constant temperatures. The results show that, in this...