Dissertations / Theses on the topic 'Cave biogeography'

The morning duet calls of eastern tarsiers (Tarsius spp.) in North Sulawesi were recorded and analyzed to examine the effects of geography and geologic history on their call structure. Tarsius species exhibit interspecifically variable duet calls shown to correlate with species differentiation and distribution. They are distributed across Sulawesi, a biogeographically complex island in the Indonesian archipelago, where tectonic activity and multiple glaciations during the Pleistocene generated and modified barriers to their dispersal and gene flow. Recordings were made at ten locations from November of 2012 through June of 2014. Two locations were categorized as mainland, while eight island locations were categorized as either shallow or deep, according to the distance and bathymetric depth separating them from the mainland. The first hypothesis was that tarsier calls on islands separated by depths of less than 130 meters would be more strongly correlated to calls found on the mainland than would the calls from islands separated by deeper water, due to dispersal and possible hybridizations during glaciations. There was a higher degree of similarity between the mainland locations and the shallow water islands than was found between the deep water islands and either shallow water islands or the mainland. The second hypothesis was that a stepping stone pattern of colonization would be evidenced in the acoustic structure of tarsiers from the Sangihe Arc, with each island showing vocalizations more similar to its immediate neighbors than to other islands. Since tarsiers were not found to be present on two of the islands, it was not possible to trace the entire arc as planned. It was found, however, that Sangihe (the largest island and the farthest north of the islands) was the most acoustically unique, as expected. Both genetic drift and environmental factors play a role in evolving animal communication, but I hypothesize that it is more likely the former at work in this case, as the habitats are similar, and I found no strong evidence of short term habitat adaptations or frequency partitioning. The spectral and temporal structure of the duet calls on the mainland and shallow water islands showed no clear geographical bias or patterns, suggesting that panmixia and hybridization during recurring glaciations may function in preventing subdivisions among the populations.

Witsenia is a monospecific genus of the putatively basal group, the woody Iridaceae. This upright iris has extremely long black and yellow flowers ( see fig. 1) that are thought to have been pollinated by an extinct Sunbird. The role of the unusual black floral colouration is investigated as this colour is seldom associated with bird pollination. This plant typically exists in discreet and restricted populations in wet habitats in the South Western Cape (South Africa). The restricted nature of the plant is peculiar as it occurs in either low or high altitudes, yet appears to be extremely sensitive to altitude. Popular belief suggests that Witsenia maura occurs in the Peninsula only, and results from this study show the Peninsula population to be genetically separate from other populations, reflecting a long term separation. Samples from nine populations are sequenced to investigate haplotypic variation within the species, and dispersal of ancestral populations. This thesis investigates the current knowledge of Witsenia, its ecology, history and distribution. An examination of flowers under UV light reveals the first evidence of UV nectar guides in an ornithophilous flower. Conservation issues are also addressed, and it is established that although small and apparently shrinking due to global warming, populations are nonetheless viable if managed properly. A molecular study of the species and examinination of its variation revealed exceptional haplotype diversity. This diversity can best be explained by swamps acting as refugia during interglacial periods.

Os roedores Cricetidae (Myomorpha, Muroidea) são representados por cinco subfamílias: Arvicolinae, Cricetinae, Neotominae, Tylomyinae e Sigmodontinae. Os Sigmodontinae, por sua vez, são os representantes sul-americanos com a quase totalidade das espécies pertencentes a esta subfamília. Representa o mais diversificado grupo de mamíferos da América do Sul, o que significa aproximadamente 20% da mastofauna do continente. Algumas contribuições marcaram as pesquisas paleontológicas dos Sigmodontinae sul-americanos, como os registros do naturalista dinamarquês Peter Lund, que coletou grande número de material nas grutas e cavernas de Lagoa Santa, Minas Gerais. Todavia, os dados paleontológicos são escassos quando comparados à diversidade atual dos roedores sigmodontíneos. Com relação à região do Parque Nacional Serra da Capivara, no estado do Piauí, conhecida pelas descobertas arqueológicas e paleontológicas, numerosos restos de mamíferos de pequeno porte foram recuperados de grutas e abrigos calcários, entre eles os roedores Sigmodontinae, objeto do presente trabalho Os materiais estudados provenientes de três localidades da região (Toca do Gordo do Garrincho, Toca do Barrigudo e Toca do Serrote das Moendas) foram identificados e descritos. São registrados aqui: Bibimys labiosus, Necromys lasiurus, Cerradomys sp., Holochilus sciureus, Pseudoryzomys simplex, Calomys sp. e Wiedomys sp. Aspectos ecológicos e biogeográficos de cada táxon também foram considerados para discutir aspectos paleoambientais da região, destacando-se o primeiro registro de B. labiosus para o Quaternário do nordeste brasileiro, sugerindo uma distribuição paleobiogeográfica diferente da atualmente conhecida para espécie. Assim, contribuímos com novos registros de sigmodontíneos para a Serra da Capivara, ampliando o conhecimento sobre o grupo no Quaternário do nordeste do Brasil e mostrando que os materiais recuperados na região apresentam grande potencial para fornecer esclarecimentos sobre a dinâmica biogeográfica dos Sigmodoninae ao longo do Quaternário.<br>The Cricetidae rodents (Myomorpha/Muridae) are composed by five groups: Arvicolinae, Cricetinae, Neotominae, Tylomyinae and Sigmodontinae. The Sigmodontinae are the South American representatives with almost all Cricetidae species in this subfamily. They are the most diverse mammalian taxon in South America, which means about 20% of South American mammalian fauna. Some important contributions marked the Sigmodontinae paleontological researches in south American, as the records of the Danish naturalist Peter Lund, who collected numerous materials in Lagoa Santa caves, Minas Gerais. However, the paleontological data are scarce when compared to current sigmodontinae diversity. In relation to the region of Serra da Capivara National Park, State of Piauí, is known by archaeological and paleontological researches, and there many remains of small mammals were recovered from caves and rock shelter, between them the Sigmodontinae rodents are the object of this study. Remains of the Sigmodontinae from three shelters in the region (Toca do Gordo do Garrincho, Toca do Barrigudo e Toca do Serrote das Moendas) that were identified and described. The taxa identified is: Bibimys labiosus, Necromys lasiurus, Cerradomys sp., Holochilus sciureus, Pseudoryzomys simplex, Calomys sp. e Wiedomys sp. Ecological and biogeographical feature from each taxon were evaluated to discuss the feature paleoenvironment from region, with the first quaternary record from B. labiosus in Brazilian northeast, that suggest a different paleobiogeographic range from currently know. Therefore, we contributed through new Sigmodontinae records from Serra da Capivara, expanding the quaternary sigmodontinae knowledge from Brazilian northeast and showing that there are a large potential for clarify the Sigmodontinae biogeographic dynamic.

Thesis (MSc)--Stellenbosch University, 2013.<br>ENGLISH ABSTRACT: In the present study I examined the phylogeography of the rupicolous Cape girdled lizard, Cordylus cordylus. Samples were collected across the species distribution range from 63 localities in the Eastern and Western Cape and Free State provinces of South Africa, yielding a total sample size of 207 specimens. Four DNA loci, two nuclear (PRLR, PTPN12) and two mitochondrial (16S rRNA, ND2), were sequenced. Bayesian inference, maximum likelihood and maximum parsimony methods were employed to test evolutionary relationships among populations, followed by population structure analyses, divergence time estimations and niche modelling. My results confirm the species monophyly and revealed the presence of two distinct clades. Clade 1 comprised specimens from the western and southern portions of the Western Cape coast, while clade 2 comprised specimens from the southern and eastern Cape coast and adjacent interior of the Eastern and Western Cape and Free State provinces. An area of sympatry between the two clades was observed in the Breede river valley. The divergence time estimates revealed an Early Pliocene (4.31 Ma), Late Miocene (6.01 Ma) divergence for each of the two clades retrieved. Phylogeographic data suggest that clade 1 is younger (lower haplotypic and nucleotide diversity), in comparison to clade 2. Furthermore, the niche modelling shows that C. cordylus occupies a wide range of unfavourable habitats. The absence of marked phylogeographic patterning within clades is very uncharacteristic for a rupicolous vertebrate species. The ecological pliability and generalist nature of C. cordylus presumably contributed to the observed phylogeographic pattern and have facilitated the absence of within clade differentiation. Moreover, I suggest that microclimatic variables, rather than geographic barriers influence the genetic structuring of C. cordylus.

Beetles comprise not only the most diverse group of insects, but also contribute significantly to vital ecological functions. A quantitative formula to determine the optimal level of investment in the beneficial beetle conservation is still not available. I aim to establish specific attention to beetles and their role in tropical island ecosystems in small archipelago in Indonesia. The study aims to give further insights into beetle diversity patterns on islands in the Kepulauan Seribu Marine National Park and on Java, and how island isolation and area affect assemblage composition. My research also provides insights into the effects of anthropogenic activities on beetle diversity on these islands. A first important result is the substantial number of highly abundant island species and a high number of unique island species found in the study areas, indicating islands as potentially important for the global conservation of genetic resources. My results also highlight the highly varied results relating to the use of two different types of traps, pitfall traps and FITs, for sampling beetles. It underscores the need for complementary trapping strategies using multiple methods for beetle community surveys in tropical islands. When testing the equilibrium theory of island biogeography using beetle assemblages, the overall results of this study chiefly support the classic theory of island biogeography. My works also highlight the impacts of anthropogenic activities. The positive effects of such human activities on the overall species richness of beetles are clearly reflected in my result. More island beetle species encountered chiefly in settlement areas than forest species. However, when comparing the type of forest habitat on the islands, undisturbed forests harbour a higher number of unique species than disturbed forests. Finally, this study suggests that the diversity of herbivorous beetles on islands is strongly affected by the different levels of forest cover encountered.

This study aims at explaining the distribution and composition of the southern Cape forests, the largest forest complex in southern Africa. These are the only forests in southern Africa which are actively and scientifically managed for their products and values. Population growth due to forestry, agricultural and economic development and a growing tourism industry exerts increasing pressures on the natural environment of the southern Cape coast and therefore affect the dynamics and conservation of the forests. Conservation and sustained utilization of the forests require a sound knowledge of the composition, structure and dynamics of the forests. This study was aimed at an understanding of the biogeography of the forests at the landscape level in order to isolate those variables which contributed to the present distribution and composition of the forests. Determinants of the forest location pattern in the southern Cape were identified as rainfall above 500 mm, which determines the potential limits of the forests, and the bergwind fire pattern, which determines the actual forest distribution. Fires driven by the hot, dry, northwesterly, föhnlike bergwinds interacted with the terrain physiography since prehistorical times and the forests persisted in topographic shadow areas. The largest forests in the area therefore occur on the coastal platform at the foot of the mountains, in the river valleys and on the coastal scarp. Forests in the mountains, with high rainfall, are small and scattered. The results have shown that the bergwind driven fires control the distribution of forests which have important implications for the understanding of forest dynamics and for conservation management of forests in multiple-use management systems. Forest composition at the landscape level was studied by means of plant species lists. A species list for the southern Cape forests was annotated with information on the growth form, breeding system, propagule type, forest type, moisture tolerance, abundance and spread in the study area, and the distribution range in southern Africa, of each species. Analyses of the list showed that the species/family ratios for the southern Cape forest flora are very low, that woody plants have mostly fleshy propagules and herbaceous plants mostly dry propagules, and that several species have adaptations to adverse conditions. The species richness and composition, and floristic similarity and relationships were compared between the southern Cape forest flora and the floras of 13 other forests representing particular geographic regions in southern Africa. Forest size explained relatively little of the variation in species richness of the forests. Stepwise multiple regression analyses indicated that the number of dispersal corridors, the proximity to other forests and mean altitude explained most of the variation in number of woody species, whereas the number of landscape types and dispersal corridors explained most of the variation in number of herbaceous species. The high similarity between the southern Cape forest flora and those of the forests along the escarpment from the eastern Cape to northern Transvaal, and the southern attenuation of species suggest that the forests were once continuous. It is suggested that the Sundays river valley east of Port Elizabeth isolated the southern Cape forests from those to the east already during the Pliocene or earlier.

Thesis (MSc)--Stellenbosch University, 2013.<br>This study examined the biogeography and taxonomic status of the Cape legless skink, Acontias meleagris species complex using phylogenetic analyses, population genetics, demographic history aspects, time of lineage diversification estimation, environmental statistic analyses and a morphological evaluation. A total of 231 specimens from 55 localities were collected from the entire known distribution range of the A. meleagris complex throughout the Eastern, Northern and Western Cape, South Africa. Partial sequence data were collected from two mitochondrial DNA loci, 16S rRNA and cytochrome oxidase subunit one (COI), and one protein-coding nuclear DNA locus, exophilin 5 (EXPH 5). DNA sequences were analyzed for phylogenetic methods and biogeographical dating, while population genetic analyses were conducted on the COI sequences. Geographical boundaries amongst cryptic lineages were determined and evolutionary drivers of cladogenesis within the species complex were inferred. Marked genetic structure was observed within the A. meleagris complex, and five clades were retrieved, most of which were statistically well supported. These five clades were also evident within the haplotypic analyses and were characterized by demographic stability. Lineage diversification and the current biogeographical patterning observed for lineages within the A. meleagris species complex reflect the impact of sea level oscillations on historical coastal habitat availability. Additional historical evolutionary drivers within this subterranean species complex were inferred and discussed. The five clades within this species complex were considered discrete species, characterised by phylogenetic and biogeographic distinctiveness. While, morphological characters that could be used to identify the five species demonstrated widespread overlap for morphometric and meristic characters as well as colour pattering. Consequently, the phylogenetic species concept was employed for a taxonomical revision of A. meleagris sensu lato. Here, three of the previously recognised subspecies A. m. meleagris, A. m. orientalis and A. m. orientalis–'lineicauda' were elevated to full species, and two new species A. caurinus sp. nov. and A. parilis sp. nov. were described.<br>National Research Foundation (NRF)

A biogeographic analysis of the seaweed flora of the area from Lüderitz to Cape Agulhas was undertaken. Biogeographic patterns were reviewed across 15 geographic regions. A TWINSPAN analysis showed a clear division of the area into two separate species communities. These two communities are the Benguela province, and the western overlap region between the Benguela and Agulhas provinces. The western overlap region was found to be the most diverse. Diversity was shown to decrease with a decrease in latitude. Patterns in endemism among the brown seaweeds follow this trend. In contrast to this, red and green endemics increase with a decrease in latitude. Shore distribution patterns were reviewed, and demonstrated an increase in diversity with a progression down the shore. Among the red seaweeds, this increase, with greater depth was considerable. Species distribution patterns in both shore and shore pool zones were found to follow the same pattern, except for a drop in species in the subtidal fringe pools, which this study concluded was a meaningless concept. These results have been reviewed in relation to present conservation areas along this shore, and future recommendations were made for location of sites for the conservation of seaweed. These were the formation of reserves between Lüderitz and Port Nolloth, between Yzerfontein and Melkbosstrand, and from Scarborough to Cape Hangklip. In some of these areas existing reserves need to make policy adjustments while in others reserves need to be established for the conservation of both diversity and uniqueness of seaweed species.

Many evolutionary processes are influenced by spatio-temporal environmental variation, including speciation, genetic divergence among populations, and evolutionary change in physiology, morphology and behaviour. However, despite the extensive environmental data available from Geographic Information Systems (GIS) most evolutionary biologists and conservationists have not taken advantage of this data until recently. The general objective of this thesis was to integrate and expand the use of geospatial methods in evolutionary biology (biogeography, phylogeography and systematics) and conservation research. This general objective was accomplished through three specific objectives spread over six chapters, which compromised both methodological developments and their application in a series of case studies on Western Palearctic herpetofauna. This thesis explored and successfully used a number of promising new geospatial methods in combination with more traditional molecular analyses. Such integrative approaches will ultimately allow us to better consider and examine the range of potential histories underlying both inter and intraspecific divergence patterns.<br>Molts processos evolutius estan influïts per variació ambiental-, incloent l’especiació, espai-temporal, divergència genètica entre poblacions, així com el canvi evolutiu en fisiologia, morfologia i comportament. No obstant això, malgrat l'àmplia quantitat de dades ambientals disponibles en els Sistemes d'Informació Geogràfica (SIG), la majoria dels biòlegs i conservacionistes no han aprofitat aquestes dades fins fa poc. L'objectiu general d'aquesta tesi és integrar i ampliar l'ús de mètodes geoespacials en biologia evolutiva (biogeografia, filogeografia i sistemàtica) i recerca de conservació. Aquest objectiu general es va aconseguir a través de tres objectius específics dividits en 6 capítols, els quals inclouen tant un desenvolupament metodològic i la seva aplicació en una sèrie de casos d'estudi espaciotemporals de herpetofauna paleárctica occidental. Aquesta tesi explora i utilitza de manera reeixida nous mètodes geoespacials en combinació amb anàlisis moleculars tradicionals. Aquests enfocament combinats ens permeten avaluar i examinar de millor manera les diverses possibles històries que hi ha al darrere patrons divergents inter i intraespecífics.<br>Muchos procesos evolutivos están influidos por variación ambiental espaciotemporal, incluyendo la especiación, divergencia genética entre poblaciones, así como el cambio evolutivo en fisiología, morfología y comportamiento. Sin embargo, a pesar de la amplia cantidad de datos ambientales disponibles en los Sistemas de Información Geográfica (SIG), la mayoría de los biólogos y conservacionistas no han aprovechado estos datos sino hasta hace poco. El objetivo general de esta tesis es integrar y ampliar el uso de métodos geoespaciales en biología evolutiva (biogeografía, filogeografía y sistemática) e investigación de conservación. Este objetivo general se logró a través de tres objetivos específicos divididos en 6 capítulos, los cuales incluyen tanto un desarrollo metodológico y su aplicación en una serie de casos de estudio espaciotemporales de herpetofauna paleárctica occidental. Esta tesis explora y utiliza de manera éxitosa nuevos métodos geoespaciales en combinación con análisis moleculares tradicionales. Estos enfoque combinados nos permiten evaluar y examinar de mejor manera las diversas posibles historias que subyacen en patrones divergentes inter e intraespecíficos.

Dissertation (PhD)--University of Stellenbosch, 2006.<br>ENGLISH ABSTRACT: The central goal in macroecology is to determine species diversity patterns across ecological gradients. Altitudinal and latitudinal patterns in species richness are often assumed to be analogous. Furthermore, the primary mechanisms underlying richness patterns along these two gradients might be similar. To date, few studies have tested whether the hypotheses proposed to explain latitudinal richness variation apply to patterns across altitude. This study therefore tests several hypotheses proposed to explain patterns in species diversity (i.e. ambient energy, productivity, area and geometric constraints) and their underlying mechanisms using altitudinal gradients in epigaeic ant and beetle species richness in the Greater Cederberg Biodiversity Corridor (GCBC) (Western Cape, South Africa). The study was conducted across an altitudinal gradient that was laid out from sea level to the top of a mountain (approximately 2000 m above sea level) and down the other side thereof. First, it was determined how the ant and beetle assemblages differ between the main vegetation types included in the transect and which environmental variables might underlie these differences. Thereafter, the variation in species richness and range size patterns of the two groups was investigated across the full altitudinal gradient. This is the first study that tests the applicability of two mid-domain models across such an altitudinal gradient using both complete and partial assessments. The models explained large proportions of the variance in range sizes across three domains but the ranges could have been constrained to show peaks in the middle of the domains due to the way in which the boundaries of the domains were selected. By contrast, the mid-domain models were not important in explaining species richness patterns, which suggests that they cannot explain diversity across the gradient. The species richness patterns of the two groups did not show the predicted mid-altitudinal peak. Moreover, it was demonstrated that different processes structure ant and tenebrionid assemblages across the same altitudinal transect. Ant species diversity was highly correlated to contemporary climatic variables, while historical factors appear to play a more important role in structuring tenebrionid beetle assemblages. Furthermore, support was found for the species energy theory in the ant assemblages, as well as for two of its underlying mechanisms, namely the more individuals hypothesis and the niche position mechanism. These results suggest that there are likely to be substantial and complex changes to ant assemblages under the predicted climate change scenarios for the region. Given the crucial role played by this group in ecosystem functioning (e.g. myrmecochory) it is suggested that these responses are not likely to be a response solely to vegetation changes, but might also precipitate vegetation changes. This study also forms the basis of a long-term monitoring programme to establish baseline data for the epigaeic ants and tenebrionids and to monitor changes in these communities due to climate change.<br>AFRIKAANSE OPSOMMING: Een van die sentrale idees in makro-ekologie is om die patrone in spesies diversiteit oor ekologiese gradiënte te ondersoek. Verder word daar aangeneem dat spesie rykheidspatrone oor hoogte- en breedtegradiënte analoog is aan mekaar en dat die primêre onderliggende meganismes van die patrone dieselfde kan wees oor hierdie twee gradiënte. Tot dusver het min studies getoets of die voorgestelde hipoteses wat breedtegradiënte in spesie rykheid verduidelik van toepassing is op hoogtegradiënte. Hierdie studie toets dus verskeie van hierdie hipoteses (aanvoelbare temperatuur, produktiwiteit, area en geometriese beperkinge) en hulle onderliggende meganismes in mier en kewer spesie rykheid in die Groter Cederberg Biodiversiteits Korridor (GCBK) (Wes Kaap, Suid Afrika). Die studie is uitgevoer oor ‘n hoogtegradiënt wat vanaf see vlak tot ongeveer 2000 meter bo seevlak en weer aan die ander kant van die berg af uitgelê is. Eerstens is daar bepaal hoe die mier en kewer diversiteit verskil tussen die hoof planttipes wat oor die hoogtegradiënt voorgekom het en watter omgewingsveranderlikes daarvoor verantwoordelik is. Daarna is die variasie in spesie rykheid en area van verspreiding van die twee groepe ondersoek oor die hele hoogtegradiënt. Hierdie is die eerste studie wat die toepaslikheid van twee mid-domein modelle oor so ‘n hoogtegradiënt toets met behulp van volledige en gedeeltelike ondersoeke. Die modelle het baie van die variasie in area van verspreiding verduidelik oor drie domeine maar die areas van verspreiding kon beperk gewees het om pieke in die middel van die domeine te vorm as gevolg van die manier waarop die grense van die domeine gekies is. In teenstelling, het die modelle nie spesie rykheid verduidelik nie en dus kan hulle nie spesie diversiteit oor hierdie gradiënt verduidelik nie. Die spesie rykheidspatrone van die twee groepe het nie die verwagte piek by midhoogte gewys nie. Verder het verskillende prosesse mier en kewer groeperings oor die hoogtegradiënt gestruktureer. Mier diversiteit was hoogs gekorroleer met kontemporêre klimaatsveranderlikes, terwyl historiese faktore belangriker was vir die kewers. Die spesie-energie teorie was ondersteun deur die data, asook die meer individue hipotese en die nis posisie meganisme. Hierdie resultaat dui daarop dat daar moontlik komplekse veranderinge in mier groeperings gaan plaasvind soos die klimaat verander. Miere vervul belangrike ekologiese prosesse in ekosisteme, wat beteken dat die laasgenoemde verandering nie bloot net gaan plaasvind as gevolg van veranderinge in die plantegroei nie, maar dat hulle self ook veranderinge kan veroorsaak. Hierdie studie vorm ook die basis van ‘n langtermyn moniteringsprogram om basislyn data vir hierdie twee ekologies belangrike groepe vas te stel en om veranderinge wat in hierdie gemeenskappe plaasvind, as gevolg van klimaatsverandering, te monitor.

L'archipel indonésien abrite 1218 espèces de poissons d'eau douce disséminées sur 14 000 îles. Englobant trois ensembles géographiques majeurs (Sundaland, Wallacea, Sahul) séparés par deux transitions faunistiques majeures (lignes de Wallace et de Lyddeker), les îles indonésiennes présentent des niveaux hétérogènes de richesse spécifique résultant de divers antécédents géologiques et paléoécologiques. Sundaland abrite 68% du nombre total d’espèces de poissons d’eau douce et constitue l’une des faunes les plus menacées au monde. Contrairement à Wallacea qui résulte d'une mise en place précoce par subduction autour de 40 Mya, Sundaland (Bornéo, Sumatra et Java) a acquis sa configuration moderne au cours des 5 derniers Mya grâce à une combinaison de fragmentation continentale et de subduction. L’état alarmant de l’ichtyodiversité de Sundaland, associé à des lacunes importantes en matière de taxonomie et de connaissances de la distribution des espèces, plaide en faveur d’une réinterprétation moderne au moyen de méthodes standardisées et basées sur l’ADN. L'ichtyodiversité de Java, en particulier, est la plus menacée et la moins connue de Sundaland. Cette thèse vise à répondre à deux questions principales: (1) Les code-barres ADN constituent-ils une approche appropriée pour caractériser l'ichtyodiversité de Java? (2) L’histoire géologique et paléoécologique de Java est-elle un bon prédicteur des profils de diversité et de la structure génétique de la population? Les principaux résultats obtenus sont les suivants: 1) d’importants écarts entre la liste de référence des poissons d’eau douce de Java fondée sur des données historiques et une réévaluation moderne au moyen de code-barres à ADN. Les raisons invoquées sont le biais taxonomique lié à l'inventaire interrompu de l'ichthyofaune de Java au cours des 3 derniers siècles et la raréfaction de plusieurs espèces ciblées par la pêche artisanale. (2) Une réévaluation basée sur l’ADN des limites et de la distribution des espèces pour les genres Nemacheilus et Rasbora a indiqué deux nouveaux taxons, plusieurs cas de diversité cryptique et plusieurs cas d’attribution erronée de populations aux niveaux de l’espèce. Les aires de distribution des espèces semblent être beaucoup plus limitées que considéré précédemment et questionne les modalités de persistance des espèces dans des paysages en mutation. (3) Une évaluation basée sur l'ADN, grace aux code-barres ADN, de la structure génétique des populations de trois espèces largement répandues à Java met en évidence des niveaux élevés de diversité cryptique et des divergences génétiques profondes entre lignées mitochondriales géographiquement restreintes et ne se chevauchant pas. Conformément à une fragmentation liée à la montée des arcs volcaniques à Java qui a entraîné un déclin à long terme de la taille effective de la population, cette tendance plaide en faveur du statut de conservation sensible de ces lignées mitochondriales. Les résultats présentés ici soulignent les avantages d'utiliser une approche standardisée et basée sur l'ADN pour la caractérisation rapide d'une faune mal connue et ouvrir de nouvelles perspectives pour la conservation de l'ichtyofaune de Java et de Bali<br>The Indonesian archipelago hosts 1218 freshwater fish species disseminated across 14,000 islands. Encompassing three majors geographic assemblages (Sundaland, Wallacea, Sahul) separated by two majors faunistic transitions (Wallace and Lyddeker lines), Indonesian islands display heterogeneous levels of species richness resulting from diverse geological and paleoecological histories. Sundaland itself hosts 68% of the total number of freshwater fish species and constitutes one of the world’s most endangered fauna worldwide. By contrast with Wallacea that results from an early settlement through subduction around 40 Mya, Sundaland (Borneo, Sumatra and Java) has acquired its modern configuration during the last 5 Mya through a combination of continental fragmentation and subduction. The alarming state of Sundaland ichthyodiversity, combined with major taxonomy and distribution knowedge gaps, urges for a modern reapparaisal through standardized DNA-based methods. The ichtyodiversity of Java in particular, is the most threatened and the less known of Sundaland. This dissertation aims at addressing two main questions: (1) Is DNA barcoding a suitable approach to characterize the ichthyodiversity of Java? (2) Is the geological and paeloecological history of Java a good predictor of diversity patterns and population genetic structure? The main results evidence: (1) large discrepancies between the checklist of the Java freshwater fishes based on historical records and a modern re-appraisal through DNA barcodes. Reasons invoqued are the taxonomic bias related to the interrupted inventory of Java ichthyofauna during the last 3 centuries and the rarefaction of several species targeted by artisanal fisheries. (2) A DNA-based reappraisal of species boundaries and distribution for the genera Nemacheilus and Rasbora indicated two new taxa, several cases of cryptic diversity and several cases of wrong assignement of populations to the species levels. Species range distributions appear to be much more restricted than previously thoughts and question the persistence of these species in changing landscapes. (3) A DNA-based assessment through DNA barcodes of the population genetic structure of three widespread species in Java evidences high levels of cryptic diversity and deep genetic divergences among geographically restricted and non-overlapping mitochondrial lineages. Consistent with a fragmentation related to the rise of volcanic arches in Java that prompted a long-term declines of historical effective population size, this pattern argue for the sensitive conservation status of these mitochondrial lineages. The results presented here highlights the benefits of using a standardized DNA-based approach for the fast characterization of a poorly known fauna and open new perspectives in the conservation of the ichtyofauna of Java and Bali

The incidental introduction of alien phytophagous insects and mites has become quite a common event in the world owing to intensive commercial exchanges of plants and goods and ever-increasing tourist traffic. There is evidence that this phenomenon is increasing, in spite of the control measures of the EU phytosanitary system in order to minimize unintentional introductions. The introduction of an alien species in a new ecosystem and the interaction between an alien species and the autochthonous species usually has many disadvantages. The alien species can dominate the invaded ecosystems and eventually become an invasive species due also to the absence or paucity of natural enemies. These invasions can affect the native species that become less common or threatened with extinction. Apart from the environmental impacts alien species are known for their economic and health impacts. In this study were investigated mostly 3 recently introduced alien species in Italy, namely Tuberocephalus (Trichosiphoniella) tianmushanensis Zang (Hemiptera Aphididae), Cydalima perspectalis (=Glyphodes) (Walker, 1859) (Lepidoptera Crambideae), the box caterpillar and Phenacoccus defectus Ferris (Rhynchota Pseudococcidae). The first chapter is a background of invasive ecology and presents with graphs the high number of alien species introduced in Europe the last years.. The second chapter is dealing with Tuberocephalus (Trichosiphoniella) tianmushanensis Zang, an Asiatic heteroecious species so far not recorded in Italy. This species was collected in the University Botanical Garden of Padova in spring 2012. On May 30, 2012 reddish-pink galls, with aphids inside, were observed on the leaves of two Prunus subhirtella cv. pendula trees (Rosaceae) (Weeping Higan Cherry), about 40 years old. Once mounted on slides the aphids were identified as Tuberocephalus (Trichosiphoniella) tianmushanensis Zang. The purposes of this study were to collect data on species distribution over the territory, by monitoring ornamental cherry trees in the Veneto region, to observe the phenology and biology of the Asiatic aphid, to study the life-cycle in screen houses and outdoors, to verify if its secondary host plant was an Artemisia sp., as reported in bibliography. Another aspect of the work was to provide an overview of the species belonging to the genus Tuberocephalus so far described, by consulting the available literature. It was made an effort to gather all the currently available information for each species, its distribution and information on their biology mainly regarding the first and secondary host plants. Results showed that Tuberocephalus (T.) tianmushanensis, is now considered acclimatized in our environment. The aphid is closely related to the presence of its primary host Prunus subhirtella v. pendula with pink flowers. The aphid can carry on two generations on Prunus and can induce two types of leaf galls. The gall A is induced by the fundatrix, while the gall B is induced by the fundatrigeniae. The trial of colonization on Artemisia vulgaris, failed for the second successive year so possibly Artemisia vulgaris is not the secondary host plant of the aphid, as reported in literature. The third chapter concers Cydalima perspectalis (Lepidoptera, Crambiidae) (Walker, 1859), an asiatic pest of Buxus. It was reported for the first time in Europe in Germany in 2007. In Italy it was detected in 2011, in Lombardy, Como province. In a very short time it invaded the other northern regions and was recorded in Veneto in 2012. The larvae feed on leaves and shoots of the box trees and the infestations lead to defoliation of the plants. The objective of this study was to investigate the phenology of C. perspectalis. More precisely we examined the biological cycle of life, the number of molts and the overwintering stage. In addition host plants were monitored by regular samplings, from late winter to late fall to collect data on species distribution over the territory. The life-cycle was studied in screen houses and in the field, to investigate the role of potential predators and parasitoids. Additionally experiments were conducted with pheromones traps with the purpose of checking, monitoring and collecting data on species distribution over the territory, finding any possible differences based on climate, checking the potential differences between types of traps. According to the results of 2014 and 2015 in the Veneto Region C. perspectalis develops three generations / year. In 2014 the overwintering larvae started their activity early in February until mid-April while in 2015 one month later until end of April probably due to different climate conditions between these years. C. perspectalis overwinters in a silk cocoon in-between the leaves as a larva of 2nd instar and the number of larval instar is 5. The number of captures from the sex pheromones traps was low. No differences were observed between the two types of pheromones. C. perspectalis has spread quickly in our environment proving that it has acclimatized. So far, it seems there has been no adaptation by indigenous natural enemies (parasitoids) to C. persectalis. The next chapter is focued on the difficulty to separate the Phenacoccus solani Ferris and P. defectus Ferris (Hemiptera: Pseudococcidae). They are morphologically similar and the microscopic morphological characters of the adult female alone are not enough. In order to resolve their identity, a canonical variates morphological analysis of 199 specimens from different geographical origins and host plants and a molecular analysis of the CO1 and 28S genes were performed. The morphological analysis supported synonymy of the two species, as although the type specimens of the "species" are widely separated from each other in the canonical variates plot, they are all part of a continuous range of variation. The molecular analysis showed that P. solani and P. defectus are grouped in the same clade. On the basis of the morphological and molecular analyses, P. defectus is synonymized under the senior name P. solani, syn. n. Finally a zoogeographic analysis of the Greek scale insects fauna (Hemiptera, Coccoidea) was carried out with the aim to highlight how many alien scale insects species are so far present in the Greek territory. According to the last data, the scale insect fauna of whole Greek territory comprehends 207 species; a total of 187 species are recorded in mainland Greece and minor islands, whereas only 87 scale species are known so far in the island of Crete. The most numerous families are the Diaspididae, with 86 species in total, followed by Coccidae, with 35 species and by Pseudococcidae, with 34 species. The results of a first zoogeographical analysis of scale insect fauna of mainland Greece and the island of Crete is also presented. Five scale species, respectively four in mainland Greece and one in Crete, are considered as endemic. This analysis demonstrated that alien scale insects, introduced and acclimatized a long time ago or recent invaders, make up 30% of the Greek scale insects fauna.<br>Tra le specie di Phenacoccus neartiche, P. defectus Ferris, P. solani Ferris è P. solenopsis Tinsley condividono l’insolito carattere morfologico dell’assenza di pori pentaoculari è sono morfologicamente simili da rendere difficile l’ identificazione. Il problema della loro identificazione è stato evidenziato da diversi autori (McKenzie, 1967; Williams & Granara de Willink, 1992; Culik & Gullan, 2005; Pellizzari & Porcelli, 2013), benché sia generalmente riconosciuto che P. solenopsis possieda un maggior numero di pori multiloculari e un circulus di maggiori dimensioni rispetto alle altre due specie; inoltre quest’ultima è una specie bisessuale mentre le altre due si riproducono per partenogenesi. Le tre specie di cocciniglie condividono diverse piante ospite. In accordo con Hodgson et al. (2008) ci sono elementi che supportano l’ipotesi che si tratti di varianti di una singola specie. Per definire meglio il loro status tassonomico, abbiamo amplificato mediante PCR e sequenziato il frammento di DNA ‘barcode’ di P. solani, P. solenopsis, e P. defectus.

The invasion of Acacia mearnsii in the Kouga catchment, Eastern Cape, South Africa, has various negative impacts on the ecosystem. These impacts include: reduced species richness, increased water use, increased nutrients and increased N cycling rates. The native shrubby fynbos vegetation has adapted to the acidic nutrient poor soils and Mediterranean climate of the Kouga Mountains. Fynbos, however, is currently being out competed by the much taller Acacia mearnsii trees, due to their competitive nature and ability to fix nitrogen, thereby enriching the soil. The invaded sections of the valley bottoms and lower hill slopes are characterised by an almost complete monoculture of Acacia mearnsii, with very few fynbos species still present. The Department of Water and Environmental Affairs sponsored Working for Water programme started clearing Acacia mearnsii in 1996 in the Kouga Mountains. Cleared sites have remained bare for long periods, indicating that soil properties are not favourable for indigenous propagule re-establishment. The aim of this research was to assess how A. mearnsii invasion and clearing affect fynbos recovery through its impact on soils. This was done by characterising vegetation and soil properties on fynbos, infested and cleared slopes. Vegetation cover for various growth forms was determined and a species list was compiled for each plot. The slope angle, surface hardness, litter cover, bare ground cover and soil depth were measured in the field, whereas water repellency, particle size and the chemical composition were measured in the laboratory. Furthermore, the plant establishment capacity of soils from fynbos, infested and cleared slopes was calculated. This was done by germinating fynbos seeds and growing fynbos plants in soils from the various slopes. The effect that invasion and clearing has on soil erosion was quantified using erosion plots on fynbos, infested and cleared slopes. The invasion and clearing of Acacia mearnsii led to an increase in soil nutrients, especially nitrogen, phosphorus, potassium, carbon and manganese. Furthermore, soils became more acidic, with increased water repellency and reduced surface hardness. The vegetation changed to a tree-dominated structure, replacing the native species. Native plant germination was relatively unaffected by invasion and clearing, with an increase in germination just after clearing. Plant growth of a native grass, Themeda triandra, and herb, Helichrysum umbraculigerum, has increased on soils from cleared slopes. This study showed that soil movement increased on slopes which are invaded and cleared of Acacia mearnsii, with erosion rates doubling on invaded slopes

This dissertation is primarily an applied statistical modelling investigation, motivated by a case study comprising real data and real questions. Theoretical questions on modelling and computation of normalization constants arose from pursuit of these data analytic questions. The essence of the thesis can be described as follows. Consider binary data observed on a two-dimensional lattice. A common problem with such data is the ambiguity of zeroes recorded. These may represent zero response given some threshold (presence) or that the threshold has not been triggered (absence). Suppose that the researcher wishes to estimate the effects of covariates on the binary responses, whilst taking into account underlying spatial variation, which is itself of some interest. This situation arises in many contexts and the dingo, cypress and toad case studies described in the motivation chapter are examples of this. Two main approaches to modelling and inference are investigated in this thesis. The first is frequentist and based on generalized linear models, with spatial variation modelled by using a block structure or by smoothing the residuals spatially. The EM algorithm can be used to obtain point estimates, coupled with bootstrapping or asymptotic MLE estimates for standard errors. The second approach is Bayesian and based on a three- or four-tier hierarchical model, comprising a logistic regression with covariates for the data layer, a binary Markov Random field (MRF) for the underlying spatial process, and suitable priors for parameters in these main models. The three-parameter autologistic model is a particular MRF of interest. Markov chain Monte Carlo (MCMC) methods comprising hybrid Metropolis/Gibbs samplers is suitable for computation in this situation. Model performance can be gauged by MCMC diagnostics. Model choice can be assessed by incorporating another tier in the modelling hierarchy. This requires evaluation of a normalization constant, a notoriously difficult problem. Difficulty with estimating the normalization constant for the MRF can be overcome by using a path integral approach, although this is a highly computationally intensive method. Different methods of estimating ratios of normalization constants (N Cs) are investigated, including importance sampling Monte Carlo (ISMC), dependent Monte Carlo based on MCMC simulations (MCMC), and reverse logistic regression (RLR). I develop an idea present though not fully developed in the literature, and propose the Integrated mean canonical statistic (IMCS) method for estimating log NC ratios for binary MRFs. The IMCS method falls within the framework of the newly identified path sampling methods of Gelman & Meng (1998) and outperforms ISMC, MCMC and RLR. It also does not rely on simplifying assumptions, such as ignoring spatio-temporal dependence in the process. A thorough investigation is made of the application of IMCS to the three-parameter Autologistic model. This work introduces background computations required for the full implementation of the four-tier model in Chapter 7. Two different extensions of the three-tier model to a four-tier version are investigated. The first extension incorporates temporal dependence in the underlying spatio-temporal process. The second extensions allows the successes and failures in the data layer to depend on time. The MCMC computational method is extended to incorporate the extra layer. A major contribution of the thesis is the development of a fully Bayesian approach to inference for these hierarchical models for the first time. Note: The author of this thesis has agreed to make it open access but invites people downloading the thesis to send her an email via the 'Contact Author' function.

Permafrost disturbances, including active layer detachments (ALDs), have occurred both recently and historically at Cape Bounty, Melville Island. These recent and relict ALDs were studied to determine their short- and long-term landscape effects. Six relict detachments showed altered vegetation and site characteristics, despite 60 or more years of recovery. Of the environmental variables studied, including soil moisture, soil temperature, and active layer depth, soil moisture showed the greatest changes in disturbed zones. These were attributed to the concavity of disturbance, which allows for more snow accumulation. Two vegetation types influenced by moisture regimes, polar desert and mesic heath, were compared to determine the role of moisture in recovery. The best indicators of disturbance differed in areas of different moisture regimes, with canopy height showing increases in disturbed mesic heath zones, while Normalized Difference Vegetation Index (NDVI) values increased in polar desert disturbances. Ultimately, the comparison of vegetation in disturbed and undisturbed zones revealed differences to be highly localized and minimal. Remote sensing was utilized to compare the effects of recent and relict disturbances as seen on satellite and airborne imagery. Vegetation was classified using NDVI, and zonal separation of these values in ALDs revealed the upper scar areas and lower toe zones contained significantly different NDVI values. The upper scar values were similar to undisturbed control areas, as blocks of vegetation in these areas often contain unmodified vegetation, which later helps with revegetation. The lower toe zone displayed both elevated and lower NDVI values, as material accumulates in these areas but often in a complex with bare soil. Remote sensing techniques also allowed for site characterization of disturbances, with physiographic factors including slope and flow properties determined through satellite imagery. Slope values ranged from 3 to 13 degrees in each disturbance, but were found to be slightly lower in relict disturbances, as recovery and revegetation have reduced these slopes. Flow paths were identified in ALDs, however similar patterns were also identified in surrounding undisturbed landscapes. Given the small scale of many ALDs, it is difficult to characterize the nature of the changes associated with these events, particularly for relict ALDs.<br>Thesis (Master, Geography) -- Queen's University, 2011-07-28 11:42:47.636

Oceanic Islands are natural laboratories for the study of the processes and patterns of dispersion, colonization and ultimately of the appearance of new species. In the Northeast Atlantic, the archipelago of the Azores meets all the requirements to be considered one of the most isolated oceanic island systems. In general terms, the Azorean biota, as other oceanic systems, derives from dispersal chance events. For shallow-water marine benthic organisms, the main mechanisms to overcome the isolation by distance are rafting by non-planktonic life stages and through planktonic larval stages, both of which rely heavily on sea-surface currents to travel. However, and in spite of being under the influence of the western-intensified Gulf Current, the Azorean biota shows an opposite trend, being predominantly derived from the NE Atlantic and the Mediterranean. This apparent paradox has startled many marine biogeographers, who search for answers in the present-day faunal patterns together with those reconstructed through the past geological history of the archipelago. The present study attempts to further contribute to the knowledge of the marine fauna of the Azores, and its biogeographical relationships, using the echinoderms as a model. This animal phylum encloses a diverse group of strictly marine invertebrates found at all latitudes and depths. Furthermore, the echinoderms form one of the most conspicuous elements of both shallow- and deep-sea fauna in the Azores, and both in extant waters and among the fossiliferous outcrops of Santa Maria (37°N23’ 24°45’W), the oldest island in the archipelago. Thus, for a clear biogeographical background it was necessary to construct an updated catalogue of both local extant and fossil echinoderm fauna. During the International Workshops ‘Palaeontology in Atlantic Islands’, held in Santa Maria Island between 2002-2013, new material was collected from Lower Pliocene and Pleistocene deposits. The early Pliocene beds encompass the following taxa: Eucidaris tribuloides, Echinoneus cf. cyclostomus, Clypeaster altus, Echinocyamus pusillus, Echinocardium sp. 1, Echinocardium sp. 2, Schizobrissus sp. and undetermined spatangoids. The Pleistocene outcrops (MISS 5e) included three regular echinoid species, Sphaerechinus granularis, Arbacia lixula and Paracentrotus lividus. The small irregular echinoid Echinocyamus pusillus was also present in the Azorean Pleistocene fauna, a species common as well in the extant coasts of the archipelago. The presence of tropical taxa in the early Pliocene sediments clearly contrasts with the warm temperate taxa found in the Pleistocene and present coasts of the Azores. Updated faunal lists are fundamental in biodiversity and biogeographical studies. Arbaciella elegans is a small cryptic echinoid species that was believed to have a large geographical range from the tropical Atlantic waters of Central Africa to the northern shores of the Azores, Canaries, Northwest Africa and Mediterranean Sea. However, and unlike the Central African material, individuals from the warm temperate waters present a uniform dark color. A morphological and genetic characterization of specimens from the Azores shows that the dark Arbaciella phenotype represents in fact juvenile stages of Arbacia lixula, which implies that A. elegans is circumscribed to the tropical African waters from where it was first described. This study emphasizes the difficulty of constructing faunal lists mirroring true distributions of species or local biodiversity, when rare or cryptic species are involved. The Faculty of Sciencie and Tecnology (University of the Azores), houses hundreds of echinoderm specimens collected over more than 20 years of activity by the former Department of Biology. Three young specimens of the Mediterranean sea star Sclerasterias richardi (Perrier, in Milne-Edwards, 1882), a species previously not known to the Azores, were found among the echinoderm material. These animals were dredged off the south coast of São Miguel Island, at 135 m depth. Sclerasterias richardi is one of two sea star species known to reproduce asexually through fission in the Azores, the other being the shallow-water Coscinasterias tenuispina (Lamarck, 1816). However, S. richardi, though a shelf species, lives at much deeper waters than the latter. S. richardi is also capable of producing long-lived planktotrophic larvae with high dispersal potential to reach remote areas such as the Azores. The presence of S. richardi in Azorean waters in an otherwise thoroughly investigated area does not necessarily imply a recent arrival, as the depths in consideration (80-700 m) are also the least studied in the archipelago. The review of the extant echinoderm fauna of the Azores, based on the related bibliography that has been accumulating over 150 years, complemented with the construction of an important local echinoderm reference collection in the University of the Azores, resulted in a critical reassessment of this significant component of the Azorean marine fauna. Herein are reported 172 species of echinoderms (6 crinoids, 55 ophiuroids, 45 asteroids, 36 holothuroids and 30 echinoids) to the archipelago, most of them inhabiting deep-waters. Although 65 species could be classified as shelf species (<200 m), only 29 occur in shallow-water (≤50 m depth). In general, the echinoderm species from the Azores are characterized by a wide geographical distribution in the Atlantic Ocean, with an additional 37 species occurring as well outside the Atlantic. Only 9 taxa (all deep-water species, >840 m) appear to be restricted to the Azorean waters. Though relatively poorer in number of species, the Azores show similar general trends to what is observed in other Macaronesian archipelagos (i.e. Madeira, Canaries and Selvagens): lack of endemic species, dominance of echinoderm fauna generally associated with rocky shores and species capable of producing planktonic feeding larvae. The relatively low echinoderm diversity could be attributed to the archipelago remoteness, the northern geographical position and to other local features attributed to their relative young volcanic age (e.g., lower habitat diversity). The echinoderm fauna of the Azores encompasses several edible species, though none known to be traditionally harvested. In recent years, fisheries targeting holothurian species have developed dramatically in several European and North African countries, and two of the most common sea-cumber species in the Azores, Holothuria mammata and H. sanctori, are now being commercially harvested in the Northeast Atlantic and in the Mediterranean Sea. The identification of Holothuria species tends to be difficult and time-consuming, and in many cases requires experienced taxonomists. Conversely, the use of PCR-RFLPs to rapidly and inexpensively identify species with no need for taxonomical or genetic expertise could prove a valuable asset. The present work introduces a simple and fast method, using restriction nuclease Sau3AI on 16S rRNA fragments. A simple non-destructive DNA sampling is also presented, using tube feet or oral tentacles, to be applied in genetic studies. The updated faunal list of the echinoderms of the Azores was combined with those from the other areas in an updated distributional catalogue of the shallow-water echinoderms (≤200 m depth) from the North and Central Atlantic, and the Mediterranean Sea, providing the basic framework for the analysis of biodiversity patterns and the construction of a biogeographical model. A total of 891 species belonging to 341 genera of shallow-water echinoderms are presently recorded in the studied areas. The tropical West Atlantic was by far the most biodiverse region (483 species, 210 of which were endemic). The Mediterranean Sea did not emerge as a biodiversity hotspot, revealing similar biodiversity rates as the neighbouring regions of Iberian and NW Africa, but presented significant endemism rate. Among the insular systems, Canaries presented the highest echinoderm biodiversity with 85 species, followed by Cabo Verde with 76. A positive correlation between latitude and the species’ depth range was detected, confirming the Rapoport’s latitudinal gradient. The most common larval development was planktotrophic (119 species), followed by the lecithotrophic (71 species) and aplanktonic (47 species). The relative representation of lecithotrophic and aplanktonic larval development increased towards high latitude areas and decreased as species geographical range increased. Also, the asexual reproduction decreased towards high latitude colder areas and this reduction was correlated with the relative increase of aplanktonic larval mode of development in the same areas. Endemic species were particularly numerous among sediment-associated habitats and broadly distributed species showed no preference for either soft or hard bottoms. Most areas showed a natural decrease of shared species with increasing geographical distance and this was particularly evident in oceanic systems. In these, faunal affinities tended to be related with the nearest continental shores, regardless of the prevailing sea-surface currents. In general, echinoderms proved to be good models for testing biodiversity and biogeographical patterns, though significant gaps were found on the available information.

碩士<br>高雄醫學大學<br>生物醫學暨環境生物學研究所<br>102<br>Island biogeography theory explains species richness of islands mathematically. The area effect and distance effect of island biogeography theory are also applied for habitat islands, such as urban greenspaces. However, the relationship between mainland (species source) and habitat islands was ignored in many park bird studies due to the lack of a mainland. In order to investigate whether Shoushan plays as a species source for park avifauna in Kaohsiung City, I surveyed bird communities of 26 city parks as well as Shoushan. Besides, I measured landscape characteristics and human disturbances of the 26 city parks and neighborhood areas to assess the influence of these factors on bird communities and specific guilds of these city parks. The results indicated that bird community similarity indices between city parks and Shoushan were significantly related to area size of city parks. When taking Banpingshan as a species source, the trends were similar, but with a relatively smaller P value. The results of stepwise multiple regression indicated that bird species richness and Margalef’s species richness were both positively affected by area size of city parks, percentage of water areas and percentage of greenspaces in neighborhood space. Bird density was positively affected by average number of visitors in the breeding season. Shannon diversity index was positively affected by area size of city parks and percentage of water areas in both seasons, but was negatively affected by canopy cover density in the non-breeding season. In addition, evenness was negatively affected by canopy cover density in the non-breeding season. The influence of landscape characteristics and human disturbances were different among bird guilds of city parks. In conclusion, in addition to Shoushan, Banpingshan also plays as a species source for city park avifauna in Kaohsiung City. Among all, area size of parks is the most important factor that influences bird diversity in city parks. As a result, it is essential to make a park as large as possible, to maintain high habitat diversity, and to increase greenspace percentage in neighborhood space and the connection around large city parks.

Understanding dispersal dynamics is important for conservation of vulnerable species because they effect whether populations recover or disappear following decline or disturbance, especially in species with slow life-histories that cannot replenish quickly. Palm cockatoos have one of the slowest reproductive rates for any parrot, and likely face steep decline in at least one location on Cape York Peninsula (CYP), north-eastern Australia. Traditional methods of measuring dispersal, such as capture and fitting of tracking devices, identification markers or tissue sampling for genetic analyses, are inappropriate in this species due to their susceptibility to stress. While handling chicks for DNA sample collection does not cause harm, locating nests requires too much focused effort at spatial scales relevant for conservation. In this thesis, I assess the utility of cultural methods for determining population connectivity based on published literature, and employ a combination of cultural and genetic methods to assess connectivity among Australian palm cockatoo populations. I then use a landscape ‘resistance’ modelling approach based on electrical circuit theory to identify connectivity corridors. Finally, I use population viability analysis (PVA) to determine the effects of dispersal dynamics on viability for both individual populations and the combined meta-population in Australia. Based on the literature I concluded that geographic variation in cultural behaviour among populations of a species can help fill important knowledge gaps about their population level processes, especially when comparisons to similar species and alternative data are available. My assessments of vocal and genetic variation among populations revealed differentiation among populations on Cape York Peninsula, separating east coast palm cockatoos at Iron Range from other Australian populations with some evidence of gene flow between them. My landscape ‘resistance’ analysis identified the Great Dividing Range as a barrier, and rainforest patches as important corridors for interaction among separate populations. However, the level of connectivity we determined appears not to provide enough support via dispersal to buffer the decline predicted for Iron Range. Furthermore, other populations require much better reproductive success than data suggests for Iron Range if individuals dispersing to there are to be replenished. I emphasise the importance of managing local declines for the preservation of genetic and behavioural diversity in Australian palm cockatoos.

The flightless Cape High-mountain stag beetle genus Colophon (Coleoptera: Lucanidae) is studied. Represented by 17 species, which are restricted to the highest mountain peaks of the Cape Floristic Region in the Western Cape, South Africa, and show a strict association with the fynbos biome. The study aimed to determine the specific and phylogenetic status of the described species of Colophon and to determine the main factors driving their evolution by testing hypotheses of relationship and of a lowland origin. This was achieved by analysing DNA sequence data from three gene regions, the mitochondrial COI and 16S rRNA and the nuclear CAD, using a Maximum Likelihood (ML) and Bayesian approach. Timing of key biogeographical events in the diversification of Colophon was estimated in BEAST. The study also undertook to determine diagnostic larval characters for Colophon species and also to determine their phylogenetic implications for the sub-familial placement of the genus. Lastly, the study aimed to collate biological information on Colophon species so as to make suggestions for their revised conservation status in terms of IUCN and ToPS criteria. Most species of Colophon showed an allopatric distribution, although contact zones between geographically adjacent species are likely. Climate seems to be the main driving factor behind Colophon evolution and the hypothesis of a lowland origin appears to be supported. Larvae are soil-living and feed on humus, a habit unique to the family. There are only small inter-specific differences between larvae, with larval characters contributed little equivocal information from which phylogenetic support for family placement of Colophon could be deduced. The main threats to Colophon survival include overexploitation by commercial collectors, decline in habitat quality and habitat loss due to projected changes in climate. It is suggested that out of the 17 currently described species, eight should be listed as Critically Endangered, seven as Endangered, two as Data Deficient. Lastly, in light of this project‟s findings, it is suggested that future considerations in terms of Colophon research should focus on obtaining more information on their biology, behaviour and population size and in so doing contribute knowledge for the effective conservation management of each species. A taxonomic revision of the species, focusing on the C. stokoei varieties and C. eastmani subspecies, should be done and a complete taxonomic key of all described species compiled. Future fieldwork should focus on sampling the five species that remained elusive during the project, to eventually be included in phylogenetic analyses.<br>Dissertation (MSc)--University of Pretoria, 2013.<br>gm2013<br>Zoology and Entomology<br>unrestricted