Dissertations / Theses on the topic 'Biology, Ecology'

Tub (Trigla lucerna), Red (Aspitrigla cuculus) and Grey (Eutrigla gurnardus) gurnards exhibit a distinct reproductive cycle. The spawning periods of Tub, Red and Grey gurnard occur from March to July, February to August and February to July respectively. The spawning periods of all three species commence at a minimum sea temperature (approximately 8°C) with the onset of increasing daylength and cease with the onset of decreasing daylength. A highly significant correlation was found between absolute fecundity and total weight of all three species. The relative fecundities of the three species are similar, 234-414 per g body weight for Tub, 271-377 per g body weight for Red and 306-551 per g body weight for Grey gurnard. The ovaries of Tub, Red and Grey gurnard can be characterised as asynchronous ovaries. Histological and ultrastructural studies reveal that these three species have similar oocyte development patterns. There was no hiatus or gap observed in the recruitment of oocytes from the PGP into the SGP or between the different oocyte developmental stages. Two types of yolk inclusions are formed: Lipid vesicles which appear in the mid and outer cortex indicate the initiation of the SGP and later migrate to the inner cortex and coalesce into a single lipid mass and protein yolk granules which initially form as small granules in the outer cortex of the cytoplasm. On maturation they fuse into large granules packing the cortical cytoplasm. In all three species Crustaceans and Teleosts are the preferred prey. Red gurnard had the broadest diet, Grey gurnard had the narrowest. The lowest diet overlap was observed between Grey and Red and the highest between Grey and Tub gurnards. This considerable diet overlap occurring between Grey and Tub gurnard may lead to interspecific competition for food.

Bistability, in which a system has two stable states, is a common property of many dynamic systems. This thesis explores the properties of such systems across a range of length scales, from gene circuits to ecosystems. Cells often store memories of environmental stimuli using bistable gene circuits. High fidelity memory storage requires that a state has a long lifetime. However, an underappreciated aspect of stable memory is that the distance from a bifurcation could determine how sensitive a state is to perturbations in the extracellular environment. We predict that cell memory should become increasingly sensitive to perturbations near a bifurcation and test this idea in three different gene circuits: a toggle switch, the yeast galactose utilization network, and the E. coli lactose utilization network. In a second study, we explore how the environmental context in which two species interact can influence their mode of interaction. Two species in nature often form reciprocally beneficial partnerships termed mutualisms, but in certain environmental regimes the species might shift to competing with one another for resources. This mutualism-competition transition has been understudied in experimental ecosystems. Using a synthetic yeast cross-feeding mutualism, we modulate the degree to which two partners rely on each other by supplementing the cells with variable amounts of nutrients. Surprisingly, we find that as the amount of supplemented nutrients is increased, the system passes through eight qualitatively distinct dynamic regimes: extinction, obligatory mutualism, obligatory/facultative mutualism, facultative mutualism, parasitism, amensalism, competition, and competitive exclusion. In a third study, we probe how population growth dynamics can influence the probability of evolutionary rescue. Natural populations frequently face harsh environments in which their death rate exceeds their birth rate and population size tends toward zero. In such scenarios, populations can either go extinct, migrate to a better habitat, or adapt to the harsh environment. Natural populations often exhibit an “Allee effect,” in which populations grow slowly at low density due to struggles with such behaviors as finding a mate or collective hunting. We hypothesize that the presence of an Allee effect could impede evolutionary rescue and confirm this hypothesis in a model laboratory yeast ecosystem.
Biophysics

Machine learning has been a source for continuous methodological advances in the field of computational learning from data. Systems biology has profited in various ways from machine learning techniques but in particular from network inference, i.e. the learning of interactions given observed quantities of the involved components or data that stem from interventional experiments. Originally this domain of system biology was confined to the inference of gene regulation networks but recently expanded to other levels of organization of biological and ecological systems. Especially the application to species interaction networks in a varying environment is of mounting importance in order to improve our understanding of the dynamics of species extinctions, invasions, and population behaviour in general. The aim of this thesis is to demonstrate an extensive study of various state-of-art machine learning techniques applied to a genetic regulation system in plants and to expand and modify some of these methods to infer species interaction networks in an ecological setting. The first study attempts to improve the knowledge about circadian regulation in the plant Arabidopsis thaliana from the view point of machine learning and gives suggestions on what methods are best suited for inference, how the data should be processed and modelled mathematically, and what quality of network learning can be expected by doing so. To achieve this, I generate a rich and realistic synthetic data set that is used for various studies under consideration of different effects and method setups. The best method and setup is applied to real transcriptional data, which leads to a new hypothesis about the circadian clock network structure. The ecological study is focused on the development of two novel inference methods that exploit a common principle from transcriptional time-series, which states that expression profiles over time can be temporally heterogeneous. A corresponding concept in a spatial domain of 2 dimensions is that species interaction dynamics can be spatially heterogeneous, i.e. can change in space dependent on the environment and other factors. I will demonstrate the expansion from the 1-dimensional time domain to the 2-dimensional spatial domain, introduce two distinct space segmentation schemes, and consider species dispersion effects with spatial autocorrelation. The two novel methods display a significant improvement in species interaction inference compared to competing methods and display a high confidence in learning the spatial structure of different species neighbourhoods or environments.

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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
O conceito de sucessão ecológica, que possui um potencial integrador no ensino de Ecologia, vem passando por diversas transformações desde que foi desenvolvido. Para entendê-lo faz-se necessária a compreensão de outros conceitos tais como, o de população, de ecossistemas, de relações entre os seres vivos e o de habitat. O entendimento deste processo justifica-se, pois, por meio dele, torna-se possível compreender a dinâmica vegetacional, essencial, dentre outras coisas, para a prática de restauração de áeras degradadas. Mesmo diante da importância desse conceito, muitas vezes, evidencia-se que aspectos necessários para o seu entendimento, como o caráter dinâmico das comunidades são apresentados de maneira distorcida, enfatizando-se inclusive a existência de um clímax estável. Assim, tendo em vista a importância desse conceito, objetivou-se neste trabalho analisar como os alunos ingressantes em um curso de Licenciatura em Ciências Biológicas o compreenderam, visando obter um indicador que auxilie na definição de estratégias didáticas que levem em consideração suas concepções alternativas. Foi dada preferência a esse público, pois esses futuros professores de Biologia, ainda no primeiro ano de graduação, carregam muitos dos conceitos aprendidos no Ensino Médio e ainda não sofreram intervenção sobre o assunto no nível superior. Para entender as concepções apresentadas pelos respondentes foam analisados livros didáticos e apostilas utilizadas por eles durante o Ensino Médio, bem como textos históricos sobre o conceito. Além disso, foi elaborado um diagrama semiótico, o qual auxiliou na análise dos esquemas elaborados pelos graduandos. Na análise dos manuais didáticos verificou-se que esse conceito geralmente é apresentado de maneira dogmática, simplista e fragmentada, desconsiderando-se...
The ecological succession concept, which has a potential integrator in the ecology teaching, has undergone several transformations since it was developed. To understand it is necessary to know other concepts suc as the population, relationship between living and habitat. The understanding of this process is justified because, through this, it's possible to understand the vegetation dynamics, essential, among other things, the practice of land reclamation. Even considering the importance of this concept, many times, it's clear that elements necessary for its understanding, as the communities' dynamic nature are presented in a distorted way, including emphasis on existence of a stable climax. Thus, in view of the importance of this concept, this study aimed to examine how newly admitted students (pre-service teachers' education in Biology's graduation) understand it, to obtain an indicator to assist in the strategies teaching definition that take into account their misconceptions. We choose this audience, because these future biology's teachers, in first year of graduation, they carry many of the concepts learned in high school and they haven't received intervention of college studies. To understand the concepts presented by the respondents were analyzed textbooks and handout used by them during high school, as well as historical texts about the concept. In addition, we constructed a semiotic diagram, which helped in the analysis of the schemes prepared by undergraduates. In the textbooks analysis we found that the concept is often presented in a dogmatic, simplistic and fragmented way, disregarding the complexity of the phenomenon. Moreover, the prospects of few researchers were explored in these materials, leaving a clear predilection for Clements' deterministic theories, over the Gleason's... (Complete abstract click electronic access below)

Fungal endophytes associated with leaves of woody plants are thought to be diverse and abundant, especially in tropical forests. However, associations of endophytes with tropical woody angiosperms have not been characterized in detail. In this dissertation, I assess: (1) the scale of endophyte biodiversity in a tropical forest; (2) ecological, temporal, and host-mediated factors influencing endophyte abundance in leaves of tropical trees; (3) utility of endophyte morphospecies as functional taxonomic units; and (4) the nature of endophyte-host interactions. To characterize endophyte biodiversity, I measured endophyte richness in asymptomatic leaves of two distantly related, but co-occurring, host species in lowland forest in central Panama. I found that endophytes are highly diverse within leaves, plants, and host species, and that they demonstrate both host preference and spatial heterogeneity. To determine factors influencing abundance of tropical endophytes, I assessed effects of inoculum abundance, duration of exposure to inoculum, phylogenetic position of host, and leaf traits (e.g., chemical and structural defenses) on rates of endophyte infection. I found that endophyte abundance is sensitive to inoculum abundance in the short term, but to duration of exposure over the long term. In turn, inoculum abundance is sensitive to canopy cover, time of day, and time since precipitation. Generally, neither leaf traits nor phylogenetic position of hosts is related to rates of endophyte infection: endophytes occur with consistently high abundance and diversity among representatives of 14 orders of angiosperms. To assess utility of morphospecies as taxonomic units, I compared diversity and taxonomic composition among morphospecies of endophytes as delineated using several criteria, and among species as inferred using nrDNA data. I found that conservatively designated morphospecies can approximate species boundaries as defined by nrDNA data for diverse Ascomycota. Finally, I examined effects of endophytes on (1) minimum leaf conductance, a measure of water loss from leaves under drought conditions; and (2) leaf mortality and necrosis in the presence of a foliar pathogen for a focal host. I found that endophytes may cost their hosts by increasing water loss under conditions of severe drought, but that they also may play an important role in host defense against pathogens.

Floating sulphur biofilms have been observed to occur on sulphate-containing natural systems and waste stabilization ponds. It has been postulated that these biofilms form on the surface of the water because sulphate reducing bacteria present in the bottom layers of the water body reduce sulphate to sulphide which then diffuses upwards and is oxidized under the correct redox conditions to sulphur by sulphide oxidizing bacteria. Very little information exists on these complex floating systems and in order to study them further, model systems were designed. The Baffle Reactor was successfully used to cultivate floating sulphur biofilms. Conditions within the reactor could be closely scrutinized in the laboratory and it was found that sulphate levels decreased, sulphide levels increased and that sulphur was produced over a period of 2 weeks. The success of this system led to it being scaled-up and currently a method to harvest sulphur from the biofilm is under development. It is thought that biofilms are highly complex, heterogeneous structures with different bacteria distributed in different layers. Preliminary work suggested that bacteria were differentially distributed along nutrient and oxygen gradients within the biofilm. Biofilms are very thin structures and therefore difficult to study and Gradient systems were developed in an attempt to spatially separate the biofilm species into functional layers. Gradient Tubes were designed; these provided a gradient of high-sulphide, low oxygen conditions to high-oxygen, low-sulphide conditions. Bacteria were observed to grow in different layers of these systems. The Gradient Tubes could be sectioned and the chemical characteristics of each section as well as the species present could be determined. Silicon Tubular Bioreactors were also developed and these were very efficient at producing large amounts of sulphur under strictly controlled redox conditions. Microscopy and molecular methods including the amplification of a section of Ribosomal Ribonucleic acid by Polymerase Chain Reaction were used in an attempt to characterize the populations present in these biofilm systems. Denaturing Gradient Gel Electrophoresis was used to create band profiles of the populations; individual bands were excised from the gels and sequenced. Identified species included Ectothiorhodospira sp., Dethiosulfovibrio russensis, Pseudomonas geniculata, Thiobacillus baregensis and Halothiobacillus kellyi.

Seasonal occurrence and activity of heterotrophic nanoflagellates (HNANO or heteroflagellates) and bacteria were studied in a sheltered brackish water embayment of Chesapeake Bay wetlands (Virginia, USA) over a three year period (1981 - 1984). Epifluorescence direct counts and Scanning and Transmission Electron Microscopy (SEM and TEM) techniques were used for the description of organisms, enumeration, and biomass determinations. Seasonal bacterial growth rates and growth and grazing rates of bactivorous HNANO were estimated using diffusion chambers equipped with Nuclepore polycarbonate membrane filters in natural salt marsh tidal pools. Environmental monitoring of nanoplankton populations revealed a seasonal pattern of bacterial abundances with temperature while heteroflagellate abundances and growth rates showed no seasonal pattern nor correlation with fluctuations in bacterial densities. Heteroflagellate populations were dominated by 34 to 50 (mu)m('3) sized monads, choanoflagellates, bodonids, and Paraphysomonas sp., all found in varying abundances throughout the year. Blooms were concurrent with extended low tide or specific bacterial populations (i.e., cyanobacteria) typical of spring and autumn periods. Heteroflagellate growth in diffusion chambers reflected the environmental blooms and increased diversity of low water assemblages. Growth and grazing rates of heteroflagellates at ambient densities thus could account for 20 to 80% of daily bacterial carbon production. Although heteroflagellate ingestion rates did not regulate seasonal bacteria densities or vice versa, maximum growth of bacteria and heteroflagellates in chambers was closely coupled. Heteroflagellate grazing activity may regulate the rate of bacterial production by preventing substrate limitation and maintaining the population in an active growth phase. The seasonal study demonstrated the dynamic nature of nanoplankton populations during autumn and spring transitional periods. SEM photomicroscopy revealed that the dominant component of spring blooms may be composed of several members of the loricate choanoflagellate family, Acanthoecidae. Using modified EM techniques, eleven Acanthoecidae choanoflagellates species, identified from spring in situ chamber experiments, were described. In situ growth and grazing rates for the spring chamber populations ranged from 0.023 h('-1) to 0.196 h('-1) and 40 to 210 bacteria h('-1) respectively. These high rates represent an opportunistic response to optimum conditions and an expression of maximum grazing potential. (Abstract shortened with permission of author.).

Phytoplankton embraces a large diversity of life forms, from pioneer oxygenic photosynthetic cyanobacteria to a broad spectrum of phylogenetically distant eukaryotic organisms. In many of the evolutionary branches, colonial organisms have appeared. The evolutionary reasons for the transition to larger sizes are not yet fully understood, but multicellularity is thought to be one of its consequences. Phytoplankton ecological success or failure, under certain conditions is the result of a balance between gains and losses. Unicellular and colonial organisms have to adapt their respective functional traits related to photosynthesis, resource acquisition, and predation, to changes in the environment. The advantages of a certain life-form (unicellular or colonial), could, hence, rely in the relevance of gain processes (light, nutrient related traits), or of losses as main drivers of phytoplankton evolution. Despite coloniality could suppose an opportunity in finding new paths to succeed, previous knowledge pointed to larger phytoplankton cells as worse competitors for nutrients than smaller cells and hence, as the size of the colonies may start to become a constraint for nutrient uptake and utilization. However, other issues changing with size can become advantageous for colonial phytoplankton. For example, large flagellate colonies can move and hence cover a greater space of resources likely to be exploited than small unicellulars, and also can have a larger storage capacity. Large cells (and colonies in particular) can take more advantage of the production of external enzymes since colonial forms, specially mucilaginous ones, could maintain exoenzymes close to the cells in this external matrix. In summary, any strategy by which there is not a proportional increase in the need for nutrients as body size enlarges can be regarded as a competitive advantage for colonial organisms. Besides, a possible advantage for large unicellulars and colonies could be related to the top-down control of the systems by grazers, as smaller unicellulars are subject of grazing by both, small and large filter feeders, whereas large colonies can override the edible size spectrum of some. Also the aggregation of cells to form large colonies harder to gulp or filter by zooplankton is considered a relative widespread defense strategy. The ubiquitousness of colonial forms of phytoplankton and its endurance until today is the basis for believing that there has been a significant selection for it in the ancient unicellular world. Yet it is difficult to guess what the main drivers for coloniality have been, Can we find out the selective forces favoring multicellular colonial forms in phytoplankton? Understanding the ecological advantage that colonial forms could hold in phytoplankton was the main objective of this thesis.
Los orígenes de los organismos que componen la comunidad fitoplanctónica se remontan a distintos eventos endosimbióticos; por ello, una de las principales características del fitoplancton es una enorme diversidad que atañe tanto en sus atributos morfológicos y fisiológicos como en sus formas de vida. A pesar de que la multicelularidad en algunas especies de fitoplancton podría suponer una estrategia para asegurar la conservación de la línea germinal, o para generar un medio interno estable que proteja a las células que forman la colonia del cambiante ambiente que la rodea, actualmente se desconoce el motivo que pudo haber favorecido la transición desde la unicelularidad a la colonialidad. Sin embargo, la existencia de organismos coloniales evolutivamente más avanzados en los que se observa una diferenciación celular y división de tareas, podrían empezar a definir una estrategia de vida compleja y jerarquizada más allá de la simple agregación celular. La gran variedad de formas, tamaños y configuraciones presentadas por las células y colonias, es una muestra de que no hay una estructura óptima, sino un gran abanico de posibilidades exitosas para afrontar los obstáculos a los que estos organismos se enfrentan durante su ciclo de vida. Por otro lado, el paso de una forma de vida unicelular a una colonial en los organismos fitoplanctónicos, implica un número de condicionantes ecológicos que determinan cuándo y cómo las formas coloniales pueden ser más viables. En cualquier caso, el hecho de que las formas unicelulares y coloniales sean ubicuas en el fitoplancton y hayan perdurado durante millones de años, nos da a entender que deben existir ciertas ventajas ecológicas conferidas por la colonialidad. Este trabajo se centra en investigar en qué modo los organismos coloniales han llegado a compensado las desventajas derivadas de la agregación para haberse convertido en una alternativa evolutivamente exitosa a la unicelularidad.

Abstract

The sediment requirements for freshwater pearl mussel (Margaritifera margaritifera) recruitment, in 18 rivers in the counties of Västra Götaland, Örebro, Värmland and Västmanland in Sweden, were investigated. The top 4 cm of sediment in the rivers was analysed in terms of size, distribution and organic compound within the fine sediment. The aims of the study were to determine whether there is a relation between sediment particle size compound and freshwater pearl mussel recruitment as well as between organic compound in fine sediment and recruitment of mussels. The study shows that there is a significant difference in the amount of organic silt between non-recruitment and recruitment sites with a higher percentage of organic silt in recruitment sites. There is also a legible difference between the amounts of silt per sample between non-recruitment sites and recruitment sites where there was significantly more silt in sediment samples of non-recruitment sites. With the exception of fine sediment, no significant difference was found between non-recruitment and recruitment sites regarding size class distribution.

Sammanfattning

Sedimentkraven för rekrytering hos flodpärlmussla (Margaritifera maragaritifera) i 18 svenska vattendrag belägna i Västra Götalands, Örebro, Värmlands och Västmanlands län undersöktes. Vattendragens översta 4 cm sediment analyserades gällande storlek, fördelning och organisk sammansättning i finsedimentet. Målen med studien var att fastställa huruvida det finns förhållanden mellan sedimentets partikelstorleksammansättning och rekrytering av flodpärlmussla samt mellan finsedimentets organiska sammansättning och rekrytering av musslor. Studien visar en signifikant skillnad i organiskt finsediment mellan icke-rekryteringsplatser och platser med rekrytering där rekryteringsplatser hade högre procentuell andel organiskt finsediment. En signifikant skillnad påvisades också mellan andel finsediment per sedimentprov där sedimentprov från icke-rekryteringsplatser innehöll en högre procentuell andel finsediment. Förutom gällande finsediment påvisades ingen signifikant skillnad i sedimentets storleksdistribution mellan rekryterings- och icke-rekryteringsplatser.

The Tachinidae is a taxonomically and ecologically diverse clade of parasitoids for which evolutionary and ecological relationships with hosts are largely unknown. Here, I employed a multidisciplinary approach to evaluate the determinants of patterns of host use in the Tachinidae. First, I examined spatio-temporal variation in the tachinid-dominated parasitoid assemblage of one lepidopteran species Grammia geneura . The parasitoid assemblage and parasitism rates varied dramatically among and within sampling sites, seasons, and years. I show that this variability may be a function of habitat-specific parasitism and indirect interactions between this host and other Macrolepidoptera through shared tachinid parasitoids. I then experimentally examined the host selection process in the tachinid Exorista mella. Host movement was an important elicitor of attack behavior. Flies also responded to odors associated with food plants of their host. Experienced flies attacked hosts more readily than did inexperienced flies. Based on these results, I proposed a host selection scenario for this tachinid species. E. mella also teamed to associate colors with hosts and avoided deterrent models that they had experienced. However, I failed to find evidence for odor learning. Learning of host-associated cues by E. mella may allow this parasitoid to take advantage of abundant host populations and maintain host-searching efficiency in an unpredictable environment. To examine how host-associated characteristics evolved in the Tachinidae, I reconstructed the evolutionary relationships within the subfamily Exoristinae using molecular data. Phylogenetic analyses generally supported recent classifications. Analyses of host-related characters indicated that tachinids show great evolutionary lability in behavior, morphology, and host range. Finally, I sampled host species to assess the determinants of tachinid community structure and host range. Several host characteristics were found to affect tachinid species richness. These patterns may be due to the opportunistic use of abundant hosts by polyphagous tachinids, enemy-free space provided by well-defended hosts, and the process of host location. Patterns of tachinid host use varied significantly with sample size, host diet breadth, host gregariousness, plant form, and host morphology. Taken together, these studies indicate high levels of plasticity in tachinid-host associations. This may be responsible for their ecological and evolutionary success.

All organisms must interact with and adapt to their surrounding environment. There are myriad ways in which species accomplish this; ultimately resulting in the vast diversity of life on earth today. Changes in the environment can have profound impacts on an organisms' ability to compete and utilize their surroundings. Plants are particularly impacted by local environmental differences because of the fact that they are immobile. This environmental variation exists at both large and small spatial scales. For example, on larger scales, forces such as fire and grazers can remove dominant plant competitors. on smaller scales, variation in resource availability (e.g. light, nutrients, water) may benefit more phenotypically plastic species. to better understand how changes in the environment, on both large and small spatial scales, I established a two part study using milkweed (Asclepias spp.) as a model system. in the first chapter, I ask how fire, large grazers, and nutrients have affected milkweed abundance over relatively long time and large spatial scales. Here I found that most milkweed species increase in abundance with burning alone but expressed species-specific responses to other treatment combinations. This indicates that milkweed species have likely experienced unique fluctuations in abundance as fire and large herbivores moved across the landscape. The second aspect of this research focuses in on a single year and relatively small spatial scales. Here, using common milkweed (A. syriaca), I ask how environmental variation shapes spatial structuring of phenotypes within fine-scale physical distance and how genotypes impact phenotypes. I found that environment, not genotype, had a relatively larger role on fine-scale phenotypic variation. Combined, these results have implications for understanding the role of large and small scale environmental variations in plant phenotypes and plant abundance.

A community of benthic cladocerans (Crustacea) from the River Thames at Twickenham, comprising seven chydorid and two macrothricid species, was studied. The species present were Alona affinis, A. quadrangularis, A. rectangula, Disparalona rostrata, Leydigia leydigi, Pleuroxus uncinatus, P. trigonellus, Iliocryptus sordidus and Macrothrix laticornis. A general trend, among the chydorid species, of a midsummer peak in abundance followed by a rapid decline was noted. Alona affinis, A. rectangula and Pleuroxus uncinatus also exhibited an autumn peak in abundance. The Iliocryptus sordidus (Macrothricidae) population did not follow this pattern. Birth and death rates were calculated for the populations of Alona affinis, Disparalona rostrata and Leydigia leydigi. Results obtained from qualitative sampling of rivers in Southeast England, and from a survey of the literature, indicated the presence of a taxocene of benthic cladocerans characteristic of the unvegetated substrate of lakes and rivers. The life histories of Disparalona rostrata and Leydigia leydigi were examined in detail. The number and duration of adult and juvenile instars, duration of egg development and mean length of life were determined at four temperatures. A study of the relationship between egg volume and parent length for Alona affinis, Disparalona rostrata and Leydigia leydigi revealed a highly significant positive regression of egg volume on parent length. The life cycle strategy of the Chydoridae as a whole was examined and found to differ from that of both the large and small planktonic Cladocera. Like the small planktonic cladocerans, the Chydoridae produce large young relative to their size at maturity. However, unlike these, the Chydoridae exhibit curtailment of growth after maturity and in this resemble the large planktonic Cladocera. The annual production of the benthic chydorid community in the River Thames, Twickenham was calculated and was found to be 0.876g C m^-2 in 1982.

In Chapter one I introduce the subject of geographic profiling, its use in criminology and its previous application to biology. I go on in Chapter two to examine the original model and develop a likelihood-based approach to fit the parameters to data from 53 UK invasive species. GP performs well on this novel problem, and outperforms other simple spatial modelling techniques. Using simulations I show that GP is particularly efficient at locating sources when there is more than a single source. Chapter three develops a Bayesian approach using Dirichlet Processes to account for the problem of multiple sources. This model was developed in collaboration with Robert Verity. This new Bayesian model outperforms the original model used in criminology and offers a range of additional information from the data. The Bayesian GP model is then used to determine the sources of malaria outbreaks in Cairo. These developments significantly improve and extend the theory and application of GP. In Chapter four I discuss the possible shapes of dispersal functions. I conduct a review of the literature and find a geometric mistake in the way linear distributions have been extracted from two-dimensional data. The correct back-transformation allows these dispersal distributions to be properly generated. Using this information; ecologists, conservationists and resources managers can now apply GP to real world problems and effectively allocate limited resources to locate sources of species invasions and disease outbreaks. I go on in Chapter five to develop a method for fitting the primary parameter sigma from the point pattern data and run simulations to show the effectiveness of this new approach. In Chapter six I illustrate the application of GP to three problems, one in criminology, one in ecology and one in epidemiology. I finish by summarising the work in this thesis and discussing the potential future developments and applications of GP.

With temperatures rising globally, assessing the possible impacts of the changing climate becomes more and more urgent. Ectotherms are excellent indicators of potential climatic ramifications on biodiversity because of their heavy reliance on the environment for their thermoregulation. Studies have historically looked at thermal tolerance values to establish predictive models for population and species extinctions. In chapter 1, we looked at recent studies that suggest that thermal tolerance may be a plastic trait and test the effects empirically. Most studies are based on captive lizards acclimated to laboratory conditions that do not necessarily reflect natural environments, and if thermal tolerance is plastic and affected by the recent thermal history of the animal, then the data may not be accurate. We tested the critical thermal maximum of the western fence lizard, Sceloporus occidentalis, in all four seasons, both under field (same-day) and short (two-day) lab-acclimated conditions. We found that thermal tolerance varied seasonally, with the lowest values in the summer in both same-day and two-day acclimated lizards. Additionally, we found that the thermal tolerance of lizards tested on the same day was higher in spring than in fall, but two days of acclimation to lab conditions eliminated this difference. We also tested the thermal tolerance of lizards housed at several constant acclimation temperatures for one or three weeks and compared these values to those of lizards housed in a terrarium allowing thermoregulation, and to same-day lizards. While the thermal tolerance of all lab-acclimated lizards was higher than that of same-day lizards, there was no significant difference in thermal tolerance among any of the acclimation treatments. Overall, our results show that thermal tolerance may be plastic in some situations in S. occidentalis, but that this species overall shows little plasticity in response to acclimation. In chapter 2, we evaluated the thermal environment of S.occidentalis using operative temperature models. Using operative temperature models combined with field lizard body temperatures and a lab-determined selected body temperature range, we evaluated the thermal environment of Sceloporus occidentalis to identify habitat quality, thermoregulatory effectiveness, and thermal exploitation index. Additionally, we used two predictive climate change models at a 1°C and 2°C increase to project the potential changes in habitat quality in the future. The thermal quality was highest for shady microhabitats, lowest for sunny microhabitats, and intermediate for mixed sunny/shady microhabitats. S. occidentalis were able to maintain their body temperatures in their Tset range for 6 hours, indicating the ability to exploit multiple microhabitats. Neither climate change scenario (1°C or 2°C increase) placed S. occidentalis at risk of extinction, likely because the coastal field site has a relatively mild climate. However, both scenarios greatly decreased the thermal quality of the environment, causing S. occidentalis to lose up to 2.5 hours of activity time per day. This highlights that even animals that inhabit mild climates are likely to experience sub-lethal effects of climate change.

Humans have tried to separate themselves from nature and to gain an understanding of what it means to be human, through studies of nature. Ideas of human nature have political and ideological implications, and are thus important in providing information about what it means to be human and what the relation to animals and the environment "ought" to be like. The ideology of human nature makes the world hence meaningful and points out what kind of actions regarding environmental issues are appropriate. The understanding of human nature and the human relationship with nature is culturally and historically produced. Humans' cultural conception thus also influences what kind of relationships are seen as desirable with particular animals. Different animals are seen as having different relations to humans, relations in which all animals are not seen as being equal. Some animals are defined edible, others are defined as companions.

Greater knowledge of the rough-toothed dolphin, Steno bredanensis, is needed to effectively contribute to conservation and management efforts for this species. The primary purpose of this research was to describe ecological and biological parameters for S. bredanensis that will be useful in future assessments of population stress. Several approaches were used to study S. bredanensis, including investigations of free-ranging populations, dead specimens, and captive individuals. Free-ranging rough-toothed dolphins distributed near small oceanic island environments were found to be more commonly sighted in-shore than off-shore. In the Windward islands of French Polynesia, this species preferred water depths of 1000 to 2000m and a distance of 1.8 to 5.5 km from the barrier reef. Group sizes ofrough-toothed dolphins sighted in French Polynesia range between 1 and 35 individuals with a mean size of 12.1. Endocrinology data for S. bredanensis was established in captive healthy and stranded individuals. Ranges and means were provided for progesterone, testosterone, cortisol and thyroid hormones. Changes in thyroid hormone concentrations were reflective of health status and testosterone appeared to be suppressed in ill individuals. Reproduction in S. bredanensis was investigated by determining the size and age range that this species attains sexual and physical maturity. Female rough-toothed dolphins attain sexual maturity by 9 to 10 years of age and males between 5 and 10 years at a similar length of approximately 216 cm. Physical maturity is generally reached at an older age and larger size for both males and females. Ecologically healthy and unheahhy populations of S. bredanensis were described in this investigation and these fmding will be useful in assessing future threats to this species.

Bibliography: leaves 82-89. Rampion mignonette is an annual to short-lived perennial agricultural weed from the Mediterranean region, first found in vineyards at Clare, South Australia, in 1986. The biology and ecology of rampion mignonette was studied to provide a basis for its integrated control and management. The study includes a literature review, maps of world and Australian distribution and drawings showing plant habit and details. A field survey found that rampion mignonette showed little migration and that containment and population reduction could be achieved by careful management including both chemical and cultural techniques. Common herbicides were also found to be effective in controlling the weed. An experiment established that it is unlikely to become a major weed of broadacre crops and pastures in the South Australian dryland farming system. It does however have the potential to compete with grapevines and reduce grape yields.

Benthic foraminifera inhabiting the mudflats of the Eden Estuary, NE Scotland, exhibited a single annual peak in abundance at both high (270 individuals 10 cm⁻²) and low shore (210 individuals 10 cm⁻²) intertidal sampling stations during June 2000. The increased total abundance coincided with reproduction in the two dominant foraminiferal species Elphidium williamsoni (May) and Haynesina germanica (June) at both sites. Benthic diatom biomass, measured as chlorophyll c, peaked at the high intertidal site during March and April 2001 (36 and 37 mg m cm⁻², respectively) and at the low intertidal site in June2000 (45 mg m cm⁻²). The high intertidal foraminiferal populations appeared to display a lagged response to increases in chlorophyll c. Multivariate statistics suggest that abiotic factors control the abundance of foraminifera at the high intertidal site. At the low intertidal site, total foraminiferal abundance demonstrated an almost immediate response to increased chlorophyll c and multivariate statistics suggested biotic factors are more important in controlling foraminiferal species abundance here. Ingestion rates of ¹³C-Iabelled benthic diatoms over a five-day experimental period were high (e.g. enrichment values for Elphidium were recorded as 687 ± 121 % after 1 day) in intertidal benthic foraminifera. Laboratory observations of E. williamsoni demonstrated rapid asexual reproduction (within 3 days) and growth rates of up to 14 µm day⁻¹ were estimated. Three benthic foraminiferal species E. williamsoni, H germanica and E. oceanensis ingest motile benthic diatoms as a food resource on the intertidal mudflats of the Eden Estuary. Novel application of natural abundance stable isotope (δ¹³C and δ¹⁵N) techniques demonstrated the trophic position of intertidal benthic foraminifera, confirming that they largely ingest and assimilate organic matter derived from benthic diatoms. Foraminifera have largely been overlooked in meiofaunal studies, but play a significant role in the rapid transfer of autotrophic carbon to higher trophic levels within benthic marine food webs.

Doutoramento em Biologia
O papel ecológico das gorgónias (Octocorallia: Alcyonacea) nos fundos marinhos rochosos é mundialmente reconhecido. Contudo, a informação acerca da ecologia e biologia das espécies de gorgónias nas zonas temperadas do NE Atlântico é manifestamente escassa, especialmente tendo em consideração as actuais perturbações globais, regionais e locais. Nos fundos rochosos da costa algarvia até aos 30 m, verificouse que várias espécies de gorgónias são abundantes e frequentes, nomeadamente Eunicella labiata, Eunicella gazella, Eunicella verrucosa, Leptogorgia lusitanica e Leptogorgia sarmentosa. As populações de gorgónias são co-dominadas por diferentes espécies que apresentaram elevados índices de associação, indicando reduzidos níveis de competição entre elas. Em todo o caso, a estrutura dos povoamentos diferiu com as condições locais. Todas as espécies evidenciaram padrões de distribuição semelhantes ao longo do gradiente de profundidade, i.e. a abundância aumenta significamente com a profundidade após os 15 m. A profundidades mais baixas (até aos 15 m), a distribuição das gorgónias parece ser condicionada por factores abióticos e pela competição com algas. Com efeito, os padrões de distribuição espacial das espécies de gorgónias na costa algarvia são determinados pela interacção de pressões naturais e antropogénicas (ex. pesca). Ainda que as colónias de maior tamanho não tenham sido restritas a áreas menos pescadas, em áreas mais perturbadas pela pesca, a distribuição dos tamanhos das colónias estava maioritariamente desviada para tamanhos mais pequenos. Os efeitos das perturbações naturais nas populações de gorgónias foram evidenciados pela ocorrência de padrões demográficos distintos em áreas vizinhas sujeitas a níveis semelhantes de pressões antropogénicas. Estes estudos demonstraram, ainda, que os efeitos na distribuição de frequências de tamanho das colónias são dependentes das espécies de gorgónias em causa: Eunicella labiata não parece ser afectada; Leptogorgia sarmentosa é tendencialmente afectada por pressões antropogénicas; Eunicella gazella e Leptogorgia lusitanica aparentam ser afectadas, quer por pressões naturais, quer por pressões antropogénicas. Os efeitos verificados nos padrões da distribuição de frequências de tamanho, particularmente a tendência para o desvio destas frequências para tamanhos mais pequenos em áreas sujeitas a perturbações, poderão ter consequências para a biodiversidade dos fundos sublitorais rochosos na costa algarvia. Com efeito, o presente estudo apoia o paradigma geral de que os corais são habitats que suportam comunidades de elevada biodiversidade e abundância. Num dos poucos estudos que examinam a relação entre as gorgónias e as suas comunidades de invertebrados epibentónicos, foi verificado que as gorgónias (Eunicella gazella e Leptogorgia lusitanica) sustentam comunidades ricas (11 phyla, 181 taxa) e abundantes (7284 indivíduos). Estas comunidades são dominadas por anfípodes, mas os poliquetas tiveram um grande contributo para os níveis elevados de biodiversidade. Verificou-se, igualmente, que o tamanho da colónia desempenha um papel fundamental na biodiversidade, na medida em que as colónias de menor tamanho apresentaram um contributo mais baixo, comparativamente às médias e grandes. Ainda que ambas as gorgónias partilhem a maioria das espécies amostradas, 11 e 18 taxa foram exclusivos de Eunicella gazella e Leptogorgia lusitanica, respectivamente (excluindo indivíduos com presenças únicas). No entanto, a maioria destes taxa eram ou pouco abundantes ou pouco frequentes. A excepção foi a presença de planárias (Turbellaria) de coloração branca nas colónias de Eunicella gazella, provavelmente beneficiando do efeito de camuflagem proporcionado pelos ramos com a mesma coloração. Com efeito, a complementaridade entre as comunidades epibentónicas associadas a ambas as gorgónias diminuiu quando usados os dados de presença/ausência, sugerindo que os padrões de biodiversidade são mais afectados pelas alterações na abundância relativa das espécies dominantes do que pela composição faunística. As comunidades de epifauna bentónica associadas a estas gorgónias não só apresentaram valores elevados de ®-diversidade, como de ¯- diversidade, resultantes de padrões intrincados de variabilidade na sua composição e estrutura. Ainda que o conjunto de espécies disponíveis para colonização seja, na generalidade, o mesmo para ambos os locais, cada colónia apresenta uma parte deste conjunto. Na sua totalidade, as colónias de gorgónias poderão funcionar como uma metacomunidade, mas a estrutura das comunidades associadas a cada colónia (ex. número total de espécies e abundância) parecem depender dos atributos da colónia, nomeadamente superfície disponível para colonização (altura, largura e área), complexidade e heterogeneidade (dimensão fractal e lacunaridade, respectivamente) e cobertura epibentónica “colonial” (ex. fauna colonial e algas macroscópicas; CEC). Numa primeira tentativa para quantificar a relação entre as gorgónias e os invertebrados epibentónicos a elas associados (em termos de abundância e riqueza específica), verificou-se que a natureza e a intensidade destas relações dependem da espécie hospedeira e variam para os grupos taxonómicos principais. No entanto, independentemente do grupo taxonómico, a riqueza específica e a abundância estão significativamente correlacionadas com a CEC. Com efeito, a CEC provavelmente devido a um efeito trófico (aumento da disponibilidade alimentar directo ou indirecto), combinado com a superfície disponível para colonização (efeito espécies-área) foram as variáveis mais relacionadas com os padrões de abundância e riqueza específica. Por outro lado, ainda que a complexidade estrutural seja frequentemente indicada como um dos factores responsáveis pela elevada diversidade e abundância das comunidades bentónicas associadas a corais, a dimensão fractal e a lacunaridade apenas foram relevantes nas comunidades associadas a Leptogorgia lusitanica. A validade do paradigma que defende que a complexidade estrutural promove a biodiversidade poderá ser, então, dependente da escala a que se realizam os estudos. No caso das gorgónias, o efeito da complexidade ao nível dos agregados de gorgónias poderá ser muito mais relevante do que ao nível da colónia individual, reforçando a importância da sua conservação como um todo, por forma a preservar a diversidade de espécies hospedeiras, o seu tamanho e estrutura. Actividades antropogénicas como a pesca, podem, ainda, ter efeitos negativos ao nível da reprodução de espécies marinhas. Analogamente ao verificado para os padrões de distribuição espacial das populações de gorgónias na costa algarvia, a informação relativa à sua reprodução é igualmente escassa. Os estudos realizados em populações de Eunicella gazella a 16m de profundidade, demonstraram que o desenvolvimento anual das estruturas reprodutivas é altamente sincronizado entre os sexos. A razão entre sexos na população foi de 1.09 (F:M), encontrando-se perto da paridade. A espermatogénese estende-se por 6 a 8 meses, enquanto que a oogénese é mais demorada, levando mais de um ano para que os oócitos se desenvolvam até estarem maduros. Antes da libertação dos gâmetas, foi observada uma elevada fecundidade nas fêmeas (27.30§13.24 oócitos pólipo−1) e nos machos (49.30§31.14 sacos espermáticos pólipo−1). Estes valores encontram-se entre os mais elevados reportados à data para zonas temperadas. A libertação dos gâmetas (não há evidência de desenvolvimento larvar, nem à superfície da colónia, nem no seu interior) occorre em Setembro/ Outubro, após um período de elevada temperatura da água do mar. As fêmeas emitem oócitos maduros de elevadas dimensões, retendo, todavia, os oócitos imaturos que se desenvolvem apenas na época seguinte. Ainda que o efeito da pesca nas populações de gorgónias da costa do Algarve seja perceptível, às taxas actuais, o mergulho recreativo não aparenta afectar seriamente estas populações. Contudo, sendo uma indústria em expansão e conhecendo-se a preferência de mergulhadores por áreas rochosas naturais ricas em espécies bentónicas, futuramente poderá vir a afectar estes habitats. A monitorização de mergulhadores na costa algarvia mostrou que a sua maioria (88.6 %) apresenta comportamentos que podem impactar o habitat, com uma taxa média de contactos de 0.340§0.028 contactos min−1. Esta taxa foi mais elevada em mergulhadores com moderada experiência e na fase inicial do mergulho (0–10 min). Os contactos com as barbatanas e mãos foram comuns, resultando, maioritariamente, na resuspensão do sedimento, mas geralmente apresentando um impacto reduzido. Todavia, a fauna também foi afectada, quer por danos físicos, quer pela interacção com os mergulhadores, e num cenário de expansão significativa desta actividade, os impactos na fauna local poderão aumentar, com consequências para os ecossistemas de fundos rochosos da costa sul de Portugal. Na sua globalidade, a informação recolhida nos estudos que contemplam esta tese, por ser em grande parte totalmente nova para a região, espera-se que contribua para a gestão da zona costeira do Algarve.
The ecological role of gorgonians (Octocorallia: Alcyonacea) in marine rocky bottoms is worldwide recognized, but the knowledge on the ecology and biology of NE Atlantic temperate species is insufficient, considering current global, regional and local threats. In the rocky bottoms of the Algarve several gorgonians were abundant and frequent down to 30 m, namely Eunicella labiata, Eunicella gazella, Eunicella verrucosa, Leptogorgia lusitanica and Leptogorgia sarmentosa. There is a high association of several gorgonian species that co-dominate assemblages, indicating low levels of competition among species. Nevertheless, gorgonian assemblages differed in structure, depending on local conditions. All species evidenced a similar depth pattern, i.e. abundance significantly increased with depth below 15 m. At shallower waters (up to 15 m), the distribution of gorgonians may be constrained by abiotic factors and competition with algae. Indeed, the spatial patterns of gorgonian populations along the southern coast of Portugal were driven by the interaction of both natural and anthropogenic pressures (namely fishing). Although larger colonies were not restricted to the sites with lower fishing pressure, gorgonian populations sampled in more intensively fished areas generally presented skewed distributions towards small sizes. The effects of natural disturbance events on the structure of gorgonian populations were evidenced by distinct demographic patterns in nearby areas under similar anthropogenic pressure. The present studies also showed that the effect of disturbance on size-frequency distribution of gorgonian populations is species-dependent: Eunicella labiata does not seem to be affected; Leptogorgia sarmentosa is likely affected mainly by anthropogenic pressures; Eunicella gazella and Leptogorgia lusitanica seem to be affected by both kinds of stress. The effects on sizefrequency distributions patterns, namely the trend to skewed distribution towards small sizes under disturbance may have consequences for biodiversity of rocky sublittoral areas of the Algarve coast. Indeed, the present study supports the general paradigm that corals are habitats of enhanced abundance and biodiversity. In one of the few studies examining the relationship between gorgonians and their associated non-colonial epifaunal assemblages, gorgonians (Eunicella gazella and Leptogorgia lusitanica) were found to support rich (11 phyla, 181 taxa) and abundant (7284 individuals) assemblages. The present study supports the general paradigm that corals are habitats of enhanced abundance and biodiversity. In one of the few studies examining the relationship between gorgonians and their associated non-colonial epifaunal assemblages, gorgonians (Eunicella gazella and Leptogorgia lusitanica) were found to support rich (11 phyla, 181 taxa) and abundant (7284 individuals) assemblages. These epifaunal assemblages were dominated by amphipods, but polychaetes had a relevant contribute to diversity. Colony size was found to have a relevant role on biodiversity patterns, with small size colonies contributing the least for overall biodiversity. Although both gorgonians shared most of the species collected, 11 and 18 taxa were exclusively associated with Eunicella gazella and Leptogorgia lusitanica, respectively (without considering singletons). Nevertheless, most of these exclusive taxa were either rare or uncommon. The exception was the presence of white flatworms Turbellaria in Eunicella gazella colonies probably taking advantage of crypsis with the white Eunicella gazella branches. Indeed, complementarity in the epifaunal assemblages associated with the two gorgonian hosts decreased when data was analysed after presence/absence transformation, suggesting that patterns of biodiversity are more affected by changes in the relative abundance of dominant species rather than in faunal composition. Gorgonian epifaunal assemblages not only showed high values of ®-diversity but intricate patterns of variability in their composition and structure leading to high ¯-diversity. Although the total pool of species available in gorgonian colonies appears to be the same in both sites analysed, each colony yields a rather small set of this species pool. All together, the colonies may act as a metacommunity, but the structure of the assemblage in each colony (e.g. total number of species, dominance) apparently depends upon host attributes, namely the surface available for colonization (colony height, width and area), complexity and heterogeneity (fractal dimension and lacunarity respectively) and “colonial” epibiont cover (e.g. colonial fauna and macroscopic algae; CEC). In a first attempt to explicitly quantify the link between gorgonians and the abundance and species richness of associated non-colonial epifaunal invertebrates, the nature and intensity of these relationships were found to be not only host-dependent but varied from one taxonomic group to another. In all faunal groups associated with the two gorgonian hosts analysed, the species richness and abundance were strongly correlated with CEC. In fact, CEC possibly due to a trophic effect (direct or indirect enhancement of food availability) combined with the surface available for colonization (species-area effect) were the strongest predictors of species richness and abundance. On the other hand, although structural complexity is usually indicated as the main driver for the rich and abundant coral-associated assemblages, fractal dimension and lacunarity were only relevant for the assemblages associated with Leptogorgia lusitanica. The validity of the paradigm that structural complexity enhances biodiversity may be scaledependent. In the case of gorgonians, the effect of complexity at the “garden” level may be much more relevant than at the individual colony level reinforcing the need for the conservation of gorgonian aggregation areas as a whole in order to preserve host diversity and size structure. On the other hand, although structural complexity is usually indicated as the main driver for the rich and abundant coral-associated assemblages, fractal dimension and lacunarity were only relevant for the assemblages associated with Leptogorgia lusitanica. The validity of the paradigm that structural complexity enhances biodiversity may be scale-dependent. In the case of gorgonians, the effect of complexity at the “garden” level may be much more relevant than at the individual colony level reinforcing the need for the conservation of gorgonian aggregation areas as a whole in order to preserve host diversity and size structure. Anthropogenic activities like fishing may also have a negative impact on reproduction. Likewise the lack of information on distribution patterns of gorgonian assemblages and their role on local biodiversity patterns, no information was available for the Algarve coast concerning reproductive patterns of main gorgonian species. The annual development of reproductive structures in Eunicella gazella populations (16m depth) was highly synchronized between sexes. The sex ratio of the population was 1.09 (F:M) being close to parity. The spermatogenic cycle extended for six to eight months, but the oogenic cycle was much longer, taking more than one year for mature oocytes to develop. Prior to spawning, high fecundity was observed in females (27.30§13.24 oocytes polyp−1) and males (49.30§31.14 sperm sacs polyp−1). These values are amongst the highest values reported to date in temperate gorgonians. Broadcast spawning of the gametes (no evidence of surface or internal brooding) occurred in September/October after a period of high sea surface temperatures during summer. Females release large sized mature oocytes but retain immature oocytes that develop only in the next season. Although the effect of fishing on gorgonian assemblages in the Algarve coast is apparent, at current rates, scuba diving does not seem to seriously affect gorgonians. However, this is a growing industry and the preference of scuba divers for natural rocky areas with diverse fauna is well known, which put these habitats under threat. The monitoring of scuba divers in the Algarve showed that most of them (88.6 %) have behaviours that can impact the habitat, presenting a mean contact rate of 0.340§0.028 contacts min−1 (§SE). This rate was higher in scuba divers with moderate experience, and in the initial part of the dive (0–10 min). Contacts with fins and hands were common, mainly resulting in sediment re-suspension, but generally presenting low impact. However, fauna was also affected by physical damage and interactions, and under a scenario of significant expansion of this activity, the impacts on local fauna may increase with consequences for the sublittoral rocky ecosystems of the Algarve coast. Overall, the information gathered in this thesis, most of it completely new for the region, is expected to have a major contribution for the management of the Algarve coast.

The reproductive ecology of nine aroid species in the rain forests around Kumasi in Ghana was studied. These species included two seasonal geophytes; Amorphophallus johnsonii and Anchomanes difformis, two herbaceous species; Culcasia saxatilis and Culcasia striolata, Four hemi-epiphytic species with terrestrial phases; Cercestis afzelii, Cercestis stigmaticus, Culcasia angolensis and Culcasia parviflora, and one hemi-epiphytic species without a terrestrial phase when mature; Rhaphidophora africana. These aroids are pollinated by beetles and flies. Anchomanes difformis and Culcasia angolensis exhibit floral heating. Trap mechanisms are present in the inflorescences of Amorphophallus johnsonii, both Cercestis species, in Culcasia parviflora and in C.saxatilis. Pollen is psilate or verrucate to bacculate in most species, but echinate in Culcasia angolensis. Ripe infructescences in most species consist of clusters of large orange to red coloured berries, but Rhaphidophora africana develops gravid spadices, with the outer tapetum peeling away to reveal naked seeds in a pulp. The seeds in most of these aroids germinate quickly and produce high percentage germination, but Amorphophallus johnsonii exhibits bimodal germination, with some seeds germinating immediately and others delaying germination until 8 months later. Evidence of berry flesh inhibition was found in Cercestis afzelii. Two main patterns of climbing are displayed by the hemi-epiphytic aroid species, with continuous growth in Culcasia angolensis and Culcasia parviflora and periodic climbing shown by Cercestis afzelii, Cercestis stigmaticus and Rhaphidophora africana. Growth towards dark areas or 'skototropism' is evident in Culcasia angolensis, Culcasia parviflora and to some extent in Cercestis stigmaticus.

Thesis (Ph.D.)--Indiana University, Dept. of Biology, 2006.
"Title from dissertation home page (viewed July 11, 2007)." Source: Dissertation Abstracts International, Volume: 67-08, Section: B, page: 4208. Advier: Keith Clay.

This work focuses on members of the Boletales. This order is comprised of a morphological and ecologically diverse set of species. While the vast majority of species are pileate-stipitate with pores and have a mutualistic nutritional strategy ectomycorrhal (ECM), there are resupinate and gilled species, and saprotrophs and mycoparasites as well. In the first chapter, we review the ecological niche occupied by Boletinellus merulioides. This species was originally considered to be ECM, the symbiont to Fraxinus americana. This hypothesis was rejected, and replaced by the possibility of a mutualism with an F. americana aphid pest, Prociphilus fraxinifolii. We present the first study that observed all three species, since the original publication, the first molecular data for each species, and isotopic fractionation results for B. merulioides and P. fraxinifolii. Additionally, we describe a new morphology for sclerotia of B. merulioides. In total, we are unable to reject the possibility of a facultative mutualism between B. merulioides and P. fraxinifolii.

Chapters two through five review systematics in the Boletineae. Chapter two presents the most comprehensive phylogenetic review of the Boletineae, at the time publication, and remains one of the most inclusive Boletineae phylogenies. Three genes, nuclear large subunit, translation elongation factor 1-alpha, and DNA directed RNA polymerase II largest subunit, were used. This chapter is a summary of Boletineae taxonomy and morphological characteristics, with a clade by clade analysis. We present compelling evidence for the mycoparasitic nutritional mode of Buchwaldoboletus lignicola. Additionally, we found that Chalciporus piperatus, a close relative of B. lignicola, is likely to be a mycoparasite. We present strong evidence that the genus Boletus is limited to single clade that contains approximately 10% of the validly published Boletus species.

A subset of the taxa sampled in chapter two was used in the phylogenies presented in chapters three, four, and five. Each of these chapters reviews the phylogenetic placement of traditionally problematic species/genera; Surotius eximius, Harrya chromapes and allies, and the Boletaceae species with longitudinally striated spores. These groups have been in multiple. Our results show that Sutorius and Harrya species are distinct from other Boletacaea species and that the longitudinally striated species have been lumped together. By correcting taxonomic confusion and using a multigene data set we are able to resolve these problematic species, and provide a path for future systematics and evolutionary analysis.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2015.
Cataloged from PDF version of thesis. Each chapter with its own abstract. Each appendix with its own summary.
Includes bibliographical references.
Microbial secondary metabolites are among the most structurally and functionally complex molecules in nature. Lanthipeptides are ribosomally derived peptide secondary metabolites that undergo extensive post-translational modification. Most lanthipeptides are bactericidal but they are also known to act as signaling molecules or morphogenetic peptides, nevertheless the function of many lanthipeptides remains unknown. Prochlorosins are a diverse group of lanthipeptides produced by strains of the ubiquitous marine picocyanobacteria Prochlorococcus and Synechococcus. Unlike other lanthipeptide-producing bacteria, picocyanobacteria utilize an unprecedented mechanism of catalytic promiscuity for the production multiple structurally diverse lanthipeptides using a single biosynthetic enzyme. Also unprecedented is the production of lanthipeptides by single celled, planktonic gram-negative bacteria in a dilute nutrient-limited habitat, which suggests that they may have an unconventional biological function. The overarching goal of this thesis is to further our understanding of the ecology and evolution of the prochlorosins, and provide insights into their biological role in the marine environment. Here, we demonstrate that the prochlorosin genes are widespread in the ocean and that globally distributed populations of marine picocyanobacteria have the genetic potential of producing thousands of different lanthipeptide structures. The diversity of prochlorosin structures provides an interesting model to study the evolutionary forces that drive the creation of new lanthipeptide structures. We present evidence that there is a unique evolutionary interplay between the components of prochlorosin biosynthesis pathway; while the peptide substrates independently expand and diversify within the genome, the catalytically promiscuous biosynthetic enzyme evolves under a strong purifying selection that maintains its substrate tolerant state. This relationship indicates that the lanthipeptide production trait in marine picocyanobacteria might find its evolutionary advantage in the plasticity of the production of multiple cyclic peptides with diverse ring topologies. The remarkable diversity of prochlorosins poses many questions regarding their biological role in the marine environment. In laboratory experiments, we explore of some of the potential bioactivity of the prochlorosins, namely their potential as signaling molecules, antimicrobials and nutrient sources. The results from this exploration open new perspectives for the role of the lanthipeptides in the natural environment - more specifically the oligotrophic ocean.
by Andrés Fernando Cubillos-Ruiz.
Chapter 1. Chapter 2. Chapter 3. Chapter 4. Chapter 5. Appendix A. Appendix B. Introduction -- Evolutionary radiation of lanthipeptides in natural populations of marine picocyanobacteria / Andres Cubillos-Ruiz ; Jessica W. Berta-Thompson ; Jamie Becker ; Sallie W. Chisholm -- Exploring the biological role of prochlorosins / Andres Cubillos-Ruiz ; Jamie Becker ; Yanxiang Shi ; Wilfred van der Donk ; Sallie W. Chisholm -- Amino acid toxicity and tolerance in prochlorococcus / Andres Cubillos-Ruiz ; Audrey Olshefsky ; Sallie W. Chisholm -- Conclusion and future directions -- Proposed molecular mechanism for the expansion and diversification of prochlorosins - Hawaii Ocean experiment : prochlorosin amendment.
Ph. D.

Orientador: Osmar Cavassan
Banca: Luzia Marta Bellini
Banca: Ana Maria de Andrade Caldeira
Resumo: O conceito de sucessão ecológica, que possui um potencial integrador no ensino de Ecologia, vem passando por diversas transformações desde que foi desenvolvido. Para entendê-lo faz-se necessária a compreensão de outros conceitos tais como, o de população, de ecossistemas, de relações entre os seres vivos e o de habitat. O entendimento deste processo justifica-se, pois, por meio dele, torna-se possível compreender a dinâmica vegetacional, essencial, dentre outras coisas, para a prática de restauração de áeras degradadas. Mesmo diante da importância desse conceito, muitas vezes, evidencia-se que aspectos necessários para o seu entendimento, como o caráter dinâmico das comunidades são apresentados de maneira distorcida, enfatizando-se inclusive a existência de um clímax estável. Assim, tendo em vista a importância desse conceito, objetivou-se neste trabalho analisar como os alunos ingressantes em um curso de Licenciatura em Ciências Biológicas o compreenderam, visando obter um indicador que auxilie na definição de estratégias didáticas que levem em consideração suas concepções alternativas. Foi dada preferência a esse público, pois esses futuros professores de Biologia, ainda no primeiro ano de graduação, carregam muitos dos conceitos aprendidos no Ensino Médio e ainda não sofreram intervenção sobre o assunto no nível superior. Para entender as concepções apresentadas pelos respondentes foam analisados livros didáticos e apostilas utilizadas por eles durante o Ensino Médio, bem como textos históricos sobre o conceito. Além disso, foi elaborado um diagrama semiótico, o qual auxiliou na análise dos esquemas elaborados pelos graduandos. Na análise dos manuais didáticos verificou-se que esse conceito geralmente é apresentado de maneira dogmática, simplista e fragmentada, desconsiderando-se... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: The ecological succession concept, which has a potential integrator in the ecology teaching, has undergone several transformations since it was developed. To understand it is necessary to know other concepts suc as the population, relationship between living and habitat. The understanding of this process is justified because, through this, it's possible to understand the vegetation dynamics, essential, among other things, the practice of land reclamation. Even considering the importance of this concept, many times, it's clear that elements necessary for its understanding, as the communities' dynamic nature are presented in a distorted way, including emphasis on existence of a stable climax. Thus, in view of the importance of this concept, this study aimed to examine how newly admitted students (pre-service teachers' education in Biology's graduation) understand it, to obtain an indicator to assist in the strategies teaching definition that take into account their misconceptions. We choose this audience, because these future biology's teachers, in first year of graduation, they carry many of the concepts learned in high school and they haven't received intervention of college studies. To understand the concepts presented by the respondents were analyzed textbooks and handout used by them during high school, as well as historical texts about the concept. In addition, we constructed a semiotic diagram, which helped in the analysis of the schemes prepared by undergraduates. In the textbooks analysis we found that the concept is often presented in a dogmatic, simplistic and fragmented way, disregarding the complexity of the phenomenon. Moreover, the prospects of few researchers were explored in these materials, leaving a clear predilection for Clements' deterministic theories, over the Gleason's... (Complete abstract click electronic access below)
Mestre

Land use change is considered to be one of the biggest threat to global species diversity. In Sweden, abandonment of grazing is one of the most common reasons for decline in species richness in semi-natural grasslands. Today semi-natural grasslands often occur as more or less isolated fragments. The result for species that benefits from grazing is a smaller area of suitable habitat and higher extinction risks and a lowered ability to colonize new areas. Succisa pratensis is a long-lived perennial plant that benefits from grazing and is common in Swedish semi-natural grasslands. I have assessed the performance of Succisa pratensis at various spatial and temporal scales, in a Swedish rural landscape. I performed demographic matrix modelling of populations at grazed and ungrazed sites. A regional level was then added, by incorporating data collected from a large number of populations and habitat types into the matrix models and extinction risks over 50 years were calculated. A dynamic metapopulation model was created and the regional dynamics, in terms of colonisations resulting from long distance dispersal and population extinctions were examined. The effects of management history were incorporated into the model by using historical maps. In addition, I made an analysis of the impact of management history on the distribution and performance of four grassland species, using vegetation maps from 1945 and 2001. Local dynamics of Succisa pratensis was negatively affected by abandonment of grazing. Recorded population sizes were ten times higher in grazed sites than in ungrazed. The turnover rate of the system was estimated to about one extinction or colonisation per year. Both the simulation study and the analyses of vegetation maps suggested a pronounced legacy of management history in Succisa pratensis in the study landscape. Overall, the results of this thesis demonstrate the importance of management history for species in the rural landscape.

This dissertation presents a four year field study on the movement patterns, community dynamics, and management of granivorous wintering grassland sparrows in Arizona. Chapter one focuses on within winter, local scale movement patterns. Recapture statistics and radiotelemetry both showed strong interspecific differences in movement, consistent with the idea that these species may partition niche space according to the regional coexistence mechanism. Both techniques ranked species from most to least sedentary as follows: Cassin's and Grasshopper sparrows, Baird's, Vesper, and Savannah and Brewer's sparrows. Data also indicated that fixed home range movements, and within-species constancy of movement behavior across years and study sites are generally the rule in this group. Correlations between bird abundance and summer rainfall suggest that movement may constrain large scale habitat selection processes. Chapter two presents larger scale movement data from grassland sparrows, along with a general discussion of facultative migration in birds. High between-year abundance fluctuations and low and variable rates of between-year recapture suggest that facultative migration strategies may be the rule in grassland sparrows. The use of alternative wintering sites by individual Grasshopper Sparrows provides direct evidence of limited facultative migration behavior. These patterns contrast with the largely non-facultative migration strategies that are the rule in birds. The evolution of facultative migration strategies is linked with unpredictable temporal variation in the spatial distribution of habitat conditions in the landscape. Chapter three presents three years of data on the effects of spring/summer burning and cattle grazing on wintering grassland sparrows. Vesper and Savannah sparrows responded positively to fire, while Cassin's Sparrows responded negatively. The ecologically and geographically restricted Baird's and Grasshopper sparrows utilized burned areas during the first post-bum winter and did not significantly respond to fire. Both Ammodramus sparrows also utilized the grazed pasture; they were more abundant there than in the ungrazed study area in one year. While field observations and a prior study suggest that heavy grazing can have a strong detrimental effect on Ammodramus sparrows, the results of this study suggest that moderate cattle grazing may be compatible with the conservation of these species.

Over the last years, the sightings of the cubomedusa Carybdea marsupialis have increased in the Mediterranean Sea and this has been linked to an increase in its abundance. Consequently, this phD thesis addresses some questions regarding the possible causes and effects of this phenomenon. Firstly, the taxonomy and distribution of the species have been revised and updated. Moreover, laboratory experiments were conducted to study the development and ecophysiology of this animal. These results were complemented with field studies on the gut contents and trophic markers of C. marsupialis. Finally, the results of a four years monitoring in the coast of Denia (Spain), as well as the sightings of the species reported along the Mediterranean, provided solid evidence on the main factors affecting the distribution of C. marsupialis. Overall, the species seems to be favoured by high nutrient inputs from anthropogenic origin, and other human activities as coastal constructions.
Los avistamientos de la cubomedusa Carybdea marsupialis han aumentado en el Mar Mediterráneo en los últimos años, hecho que ha sido atribuido a un incremento en su abundancia. El objetivo de esta tesis doctoral es responder algunas preguntas relacionadas con las posibles causas y efectos de este fenómeno. En primer lugar, se han actualizado la taxonomía y la distribución de la especie. Además, se han llevado a cabo experimentos relacionados con su desarrollo y ecofisiología. Estos resultados se han complementado con estudios de sus contenidos estomacales y marcadores tróficos en el campo. Finalmente, un monitoreo durante cuatro años en la costa de Denia (España), junto con los avistamientos de esta cubomedusa en el Mediterráneo, han proporcionado evidencias sólidas acerca de los factores principales que afectan la distribución de C. marsupialis. En general, la especie parece verse favorecida por el aporte de nutrientes de origen antropogénico, y por otras actividades humanas como las construcciones costeras.

Thesis (MSc)--Stellenbosch University, 2013.
ENGLISH ABSTRACT: Thaumatotibia leucotreta, the false codling moth (FCM), is a phytosanitary pest in South Africa posing a substantial threat to many of the country’s international export markets. Its pest status is of high importance because it has a wide ecological range and has been reported in all areas where citrus is produced in South Africa. Many methods of control have been implemented, such as chemical and cultural control, mating disruption and sterile insect releases. There was a need to obtain a more accurate understanding of FCM biology on deciduous fruit in South Africa and this then us to pose the questions described in the chapters to follow. The first aim was focused on the possibility of FCM diapause during winter. If FCM were to undergo diapause this could pose further problems for control methods, but knowledge thereof could also assist in more accurate and timely control methods. Considering past research on other Lepidoptera species, four physiological traits were chosen as indicative of a diapause state. Water loss rate, metabolic rate and the supercooling points should be lower if the individuals were in a diapause state, with a higher fat content expected for these individuals. Diapause induction was attempted through a gradual lowering of the environmental temperature in combination with longer nights to simulate overwintering conditions. Diapause was not observed in these experimental individuals. The second aim was to better understand the field biology of FCM. This was studied through in-field flight ability studies and damage assessments on four fruit kinds. Six release dates were used to measure the flight ability. The highest recapture rates were at minimum temperatures above 16°C and maximum temperatures averaging above 30°C, although the recapture rates were not significant in relation to the amount released. The recapture rates in the different fruit kinds were not significantly different, with the amount recaptured at the closest distance of 30 m being significantly more than that of the other distances. This was also only for the last release at the warmest temperatures. Fruit damage assessments were conducted and we were able to rear wild FCM from Granny smith apples, Forelle pears, Larry Ann plums and Satsuma and Clementine citrus cultivars. Citrus infestations had the highest count and a prolonged occurrence compared to the other varieties, due to its later harvest period. The third aim was to study the developmental parameters of FCM in different fruit kinds and an artificial medium. Firstly, FCM did not infest apples, Royal Gala and Pink lady’s, under laboratory conditions. Results were obtained using Forelle pears, Clementines and Thompson seedless grapes. On average the grapes had the shortest FCM developmental time from egg to adult stage, followed by oranges and then pears. Pears had the lowest developmental success rate, with that of oranges and grapes being much higher. Infestations took place at the stalk end of the fruit for the grapes and oranges, with the pears being infested at the calyx end. Future research should include an in-field life cycle, to determine the life cycle of FCM on different economically important fruit kinds under field conditions. The focus could also be shifted to where FCM overwinter, leading to better preventative control leading to lower infestation pressure during harvest periods. This is of utmost importance in an environment where maximum residue levels for pesticides dictate market access.
AFRIKAANSE OPSOMMING: Thaumatotibia leucotreta, die vals kodling mot (VKM) is ‘n fitosanitere pes in Suid Afrika, wat kan lei tot groot finansiele verliese. Die VKM se wye gasheerreeks en die feit dat dit al in al die sitrus verbouings-areas in Suid Afrika opgelet is, maak dit ‘n ernstige pes. Daar word van verskeie beheer metodes gebruik gemaak, insluitend chemiese en kulturele metodes. In sommige areas word daar ook van paaringsontwrigting en steriele insek vrylatings gebruik gemaak en hierdie metodes word gewoonlik met ander gekombineer. Daar is ‘n groot behoefte vir meer inligting omtrent die status van VKM in sagtevrugte in Suid Afrika en het gelei tot die vrae wat in hierdie studie aangespreuk word. Die eerste doelwit was om te bepaal of die VKM wel diapouse ondergaan. Dit sal verskeie beheermetodes belemmer, maar kennis hiervan kan meer gefokusde en gevolglik meer effektiewe beheermaatreels tot gevolg hê. Daar is gekyk na vier fisiologiese eienskappe wat beduidend tot diapouse van ander Lepidoptera spesies is. Daar word verwag dat VKM wat diapouse ondervind ‘n hoër vetinhoud sal he, terwyl die metabolise tempo, “supercooling’ punte en tempo van waterverlies laer sal wees. Hierdie eienskappe kon egter nie by die individue geidentifiseer word nie. Ons het diapouse probeer induseer deur gebruik te maak van ‘n gesimuleerde oorgang na winterstoestande in die laboratorium. Die toestande het toegelaat vir korter dae en laer gemiddelde temperature gedurende beide die dag en nag. Die tweede doelwit waarna gekyk is, is die bepaling van VKM se beweging in die boorde en die vrugskade op verskillende vrugsoorte. Daar kon ‘n duidelike tendens geidentifiseer word in die toename van VKM hervangs by temperature bo ‘n minimum van 16°C en gemiddelde maksimum bo 30°C. Daar was 6 vrylatings periodes, met geen betekenisvolle getalle van hervangs nie. Daar was geen betekenisvolle verskille tussen die hervangsgetalle in die verskillende vrugsoorte nie, alhoewel die 30m lokval ‘n betekenisvol hoër gemiddelde hervangs gehad het, in vergelyking met lokvalle by 60m en 90m. Die hoeveelheid vrugskade is ook gemonitor op Granny smith appels, Forelle pere, Larry Ann pruime en Satsuma en Clementine sitrus kultivars. Die vrugte is na die laboratorium geneem waar die VKM tyd gegee is om uit te broei. Al die vrugsoorte het VKM volwassenes opgelewer, maar die eksperiment kon nie op appels in die laboratorium herhaal word tydens die toets van verkillende onwikkeling stadiums nie. Ons glo dus die VKM wat hier vanaf appels uitgebroei het, is weens sekondere infeksies in die boorde. Die hoogste skadetelling is in die sitrusboord gevind. Die derde doelwit was om die duur van onderskeie ontwikkeling stadiums te bepaal op vier vrugsoorte, sowel as op ‘n kunsmatige medium. Ons het ondervind dat die VKM nie Royal Gala of Pink lady kultivars kan infesteer onder laboratorium toestande nie. Die vrugsoorte wat dus ontwikkeling kon onderhou was Forelle pere, Clementines en Thompson pitlose druiwe. Die ontwikkeling vanaf eier na volwasse stadium was die kortste op druiwe, gevolg deur lemoene en pere. Die pere het die minste VKM onderhou in vergelyking met die lemoene en druiwe. Al die vrugte is binnegedring naby die aansluiting van die stingel aan die vrugte, behalwe die pere wat nader aan die kelk binnegedring is. Toekomstige navorsing sal gefokus moet word op die lewenssiklus in die veld, vir die verskillende vrugsoorte. Daar sal ook gekyk moet word na die spesifieke alternatiewe gashere of plekke waar die VKM kan oorwinter sodat beheer meer voorkomend plaas kan vind. Dit sal infestasie vlakke onderdruk, om veral laer druk tydens oesperiodes te verseker. Dit is uiters belangrik om beheer stategieë te kombineer met die hoeveelheid druk vanaf uitvoermarkte oor maksimum residu vlakke van chemiese middels.