Dissertations / Theses on the topic 'Functional conservation'
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Pridham, Phillip. "Functional conservation of transcription activation mechanisms." Thesis, University of Nottingham, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.395631.
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Caufield, J. Harry. "Interactomics-Based Functional Analysis: Using Interaction Conservation To Probe Bacterial Protein Functions." VCU Scholars Compass, 2016. http://scholarscompass.vcu.edu/etd/4580.
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The emergence of genomics as a discrete field of biology has changed humanity’s understanding of our relationship with bacteria. Sequencing the genome of each newly-discovered bacterial species can reveal novel gene sequences, though the genome may contain genes coding for hundreds or thousands of proteins of unknown function (PUFs). In some cases, these coding sequences appear to be conserved across nearly all bacteria. Exploring the functional roles of these cases ideally requires an integrative, cross-species approach involving not only gene sequences but knowledge of interactions among their products. Protein interactions, studied at genome scale, extend genomics into the field of interactomics. I have employed novel computational methods to provide context for bacterial PUFs and to leverage the rich genomic, proteomic, and interactomic data available for hundreds of bacterial species.
The methods employed in this study began with sets of protein complexes. I initially hypothesized that, if protein interactions reveal protein functions and interactions are frequently conserved through protein complexes, then conserved protein functions should be revealed through the extent of conservation of protein complexes and their components. The subsequent analyses revealed how partial protein complex conservation may, unexpectedly, be the rule rather than the exception. Next, I expanded the analysis by combining sets of thousands of experimental protein-protein interactions. Progressing beyond the scope of protein complexes into interactions across full proteomes revealed novel evolutionary consistencies across bacteria but also exposed deficiencies among interactomics-based approaches. I have concluded this study with an expansion beyond bacterial protein interactions and into those involving bacteriophage-encoded proteins.
This work concerns emergent evolutionary properties among bacterial proteins. It is primarily intended to serve as a resource for microbiologists but is relevant to any research into evolutionary biology. As microbiomes and their occupants become increasingly critical to human health, similar approaches may become increasingly necessary.
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Oddo, Julia C. (Julia Christine). "Exploring the functional conservation of muscleblind (Mbl) proteins." Thesis, Massachusetts Institute of Technology, 2015. http://hdl.handle.net/1721.1/101357.
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Thesis: S.M., Massachusetts Institute of Technology, Department of Biology, 2015.Cataloged from PDF version of thesis.
Includes bibliographical references (pages 54-59).
Muscleblind (Mbl) is an evolutionarily conserved family of proteins involved in many aspects of RNA metabolism, including alternative splicing. Disruption of Muscleblind in several animals lends to a variety of defects and disease, including the multi-systemic disorder Myotonic Dystrophy (DM). Though much is known about the involvement of Muscleblind in DM, there is much basic knowledge of the protein's function to be discovered. We approach this problem by exploring the functional conservation of a diverse subset of Muscleblind homologs. The functions of Muscleblinds from a basal metazoan, Trichoplax adhaerens, a primitive chordate, Ciona intestinalis, and the model organisms, Drosophila melanogaster and Caenorhabditis elegans were compared to human Muscleblind-like (MBNL). The zinc finger RNA-binding domains are the most conserved region between homologs, suggesting a conserved role in RNA binding and splicing regulation. To test this, we used splicing reporter assays with validated human MBNL-regulated mini-genes and performed RNA sequencing experiments in mouse embryonic fibroblasts (MEFs). Additionally, we accessed the subcellular localization of the homologs to determine conservation of extra-nuclear functions. Reporter assays in HeLa cells showed that the homologs can positively and negatively regulate splicing. Our RNA-seq experiments led us to discover hundreds of endogenously regulated splicing events, including the identity of the transcripts, direction of splicing regulation, types of splicing events, and the magnitude of alternate exon inclusion in the spliced mRNAs. Additionally, we identified a spectrum of splicing events, from those uniquely regulated by a single Muscleblind, to events regulated by all Muscleblinds, and, characterized the variation in splicing activity that exists between homologs. A subset of events regulated by mammalian Muscleblind were oppositely regulated by non-mammalian homologs. Muscleblinds show nuclear-cytoplasmic localization, which suggests conservation in extra-nuclear functions. In conjunction with exon and intron sequences, this information provides a future tool to discover conserved and novel RNA regulatory elements used by diverse Muscleblinds to regulate splicing and in putative cytoplasmic functions. These data could also be used to determine functionally important residues in Muscleblind proteins and help us better understand the protein family.
by Julia C. Oddo.
S.M.
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Edwards, Martin Tavis. "Comparative prokaryotic genomics : conservation of functional and spatial context." Thesis, Birkbeck (University of London), 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.428024.
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Maloney, Victoria Jane. "Function, functional conservation and interactions of the membrane-bound endo-1,4-beta-glucanases orthologous to Korrigan." Thesis, University of British Columbia, 2010. http://hdl.handle.net/2429/24242.
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Plant endoglucanses (E.C. 3.2.1.4) encompass multi-gene families across several plant clades, all belonging to the glycosyl hydrolase 9 (GH9) family. One class of GH9 enzymes is unique in that all members possess sequences that encode an N-terminal membrane-anchoring domain. This class of enzymes, termed membrane-bound endo-1,4-beta-glucanases, is the focus of this thesis. The most extensively studied enzyme was first discovered in Arabidopsis and was given the name KORRIGAN (KOR) because of the dwarfed phenotype and cellulose deficiency apparent in plants exhibiting KOR gene mutations. Research has principally focused on Arabidopsis and other non-tree species and the possible role that the enzyme might play in primary cell wall development and cellulose synthesis. However, very little research with KOR has been conducted on trees and secondary cell wall development. Consequently, I investigated the effects of mis-regulating KOR in hybrid poplar and white spruce. I was able to demonstrate that the down-regulation of the hybrid poplar KOR gene increases the crystallinity of the secondary cell wall cellulose and affects the relationship between cellulose and the hemicellulose cell wall components. Concurrently, we were the first to isolate and characterize the KOR gene and suppress KOR gene activity in white spruce. Expression of white spruce KOR in Arabidopsis kor1-1 mutants demonstrated that the gene is able to rescue the mutant phenotype, providing evidence for functional equivalence. Additionally, suppression of the gene in white spruce reduced growth and cellulose content. Since KOR has been demonstrated to be required in cells undergoing cellulose synthesis, we investigated whether or not the KOR protein and the cellulose synthase complex (CSC) interact. Although we were not able to provide evidence for any KOR-protein interaction, we were able to disprove the hypothesis that KOR interacts with CesA7, a member of the secondary cell wall CSC. Collectively, the expression, functional characterization, and interaction data suggest that KOR does not function in direct contact with the CSC, but rather that it plays a role in the later stages of cell wall development, presumably in the relaxation of the stresses around the cellulose microfibril or in the separation of putative cellulose macrofibrils.
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Hua, Jiale. "Glimm type functional and one dimensional systems of hyperbolic conservation laws /." access abstract and table of contents access full-text, 2009. http://libweb.cityu.edu.hk/cgi-bin/ezdb/thesis.pl?phd-ma-b23749921f.pdf.
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Thesis (Ph.D.)--City University of Hong Kong, 2009."Submitted to Department of Mathematics in partial fulfillment of the requirements for the degree of Doctor of Philosophy." Includes bibliographical references (leaves 88-95)
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Habberfield, Michael William. "Functional connectivity for wildlife populations across spatially complex landscapes." Thesis, State University of New York at Buffalo, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10163822.
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Integrating animal movement information with the spatial analysis of landscape structure is critical for restoring biological communities in spatially-structured landscapes. This integration can be accomplished by focusing on functional connectivity—a landscape’s potential for the movement of organisms among resource patches—in relation to the spatial and structural connectivity of landscape elements. I carried out three investigations in order to examine how landscape structure interacts with the ecological factors associated with animal movement processes, and thereby produce actionable outcomes for the restoration of wildlife populations. This work combined population- and individual-level data of dispersing wildlife to better resolve the influence of spatial structure on functional connectivity. First, I used a meta-analysis to quantify the relationship between structural and functional connectivity for a broad scope of animal species. Second, I assessed the influence of landscape position and habitat density on colonization, movement, and population dynamics of wood frogs (Lithobates sylvatica) within a network of restored vernal pools. Third, I experimentally evaluated dispersal and habitat selection of green frogs (Lithobates clamitans) within this vernal pool system.
The meta-analysis demonstrated that universal scaling relationships of species and the landscapes they are moving through interact as key drivers mediating the level of functional connectivity afforded to wildlife by structural connectivity. Mark-recapture data revealed rapid colonization of the restored vernal pool network by wood frogs, with subsequently moderate levels of frog movement among neighboring pools. Local pool density interacted with the colonization process and terrestrial habitat availability to limit wood frog productivity within a pool cluster. Experimental dispersal data for green frogs artificially translocated within the pool network showed key differences between movement in familiar and novel environments. Differing movement behaviors and habitat selection patterns indicated that a habitat patch for this species is on the scale of a pool cluster rather than an individual pool. Together, the observed spatial dynamics of these vernal pool amphibians contribute a framework for improving amphibian dispersal modeling, potential responses to rapid environmental changes, and predicting colonization and subsequent population dynamics in restored systems. The results of this dissertation improve our understanding of how spatial structure interacts with organism-specific factors to produce observed patterns of functional connectivity.
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Grant, Alesha. "Functional Conservation of Interferon Antagonism among Flaviviruses| Zika Virus Targets Human STAT2." Thesis, Icahn School of Medicine at Mount Sinai, 2017. http://pqdtopen.proquest.com/#viewpdf?dispub=10270604.
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Flaviviruses are a diverse group of emerging arboviruses capable of infecting an extraordinarily broad range of vertebrate and invertebrate hosts. Nearly half of the viruses in this rapidly expanding genus have been reported to be pathogenic for humans, as well as other vertebrates. The spectrum of human disease includes asymptomatic and febrile illnesses, rash, arthralgia, encephalitis and hemorrhagic fever. The recent outbreak of Zika virus (ZIKV) has uncovered pathology in the form of microcephaly and Guillain-Barré syndrome, cementing the importance of flaviviruses as emerging human pathogens. All vector-borne flaviviruses studied thus far have to overcome type I interferon (IFN) antiviral responses in order to replicate and cause disease in vertebrates. The non-structural protein NS5 is a potent and specific antagonist of IFN signaling for human pathogenic flaviviruses such as dengue virus (DENV), yellow fever virus (YFV), West Nile virus (WNV), and tick-borne encephalitis viruses (TBEVs). Intriguingly, each of these viruses exhibits different mechanisms of IFN antagonism, highlighting the complicated evolutionary nature of flaviviruses. This thesis work presents novel insights into the NS5-mediated antagonism of IFN signaling for several underexamined flaviviruses. Notably, all NS5 proteins examined were able to inhibit IFN-induced gene expression in a mammalian system, indicating a functional conservation of IFN antagonism for flavivirus NS5 proteins. However, mechanistically NS5 function was diverse. Of great interest, ZIKV NS5 bound to the human, but not mouse, IFN-regulated transcriptional activator STAT2 and targeted it for proteasomal degradation. This phenomenon may explain the requirement for IFN deficiency in order to observe ZIKV pathogenesis in mice. Furthermore, the mechanism of ZIKV NS5 resembles that of DENV NS5, but not that of its closer relative Spondweni virus (SPOV). However, unlike DENV NS5, ZIKV NS5 did not require the E3 ubiquitin ligase UBR4 to induce STAT2 degradation. Consequently, flavivirus NS5 proteins exhibit a remarkable functional convergence in IFN antagonism, albeit by virus-specific mechanisms. The potent antagonism of human IFN responses by neglected flaviviruses such as SPOV and Usutu virus (USUV), coupled with similar ecologies to that of known human flavivirus pathogens, suggests their potential for broad emergence into the human population.
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Henscheid, Kristy L. "Functional conservation and RNA binding of the pre-mRNA splicing factor U2AF65 /." view abstract or download file of text, 2007. http://proquest.umi.com/pqdweb?did=1400950821&sid=5&Fmt=2&clientId=11238&RQT=309&VName=PQD.
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Thesis (Ph. D.)--University of Oregon, 2007.Typescript. Includes vita and abstract. Includes bibliographical references (leaves 129-141). Also available for download via the World Wide Web; free to University of Oregon users.
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McOwen, Chris. "The integration of phylogenetic and functional trait information into monocot biodiversity conservation." Thesis, University of St Andrews, 2012. http://hdl.handle.net/10023/3659.
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It is now widely acknowledged that a high proportion of the world's species are threatened with global extinction in the near future. Conserving all endangered species is impractical due to limited financial resources and manpower. Therefore, there is a real need to understand the mechanisms behind the extinction process in order to develop a proactive rather than reactive conservation strategy. Furthermore, given these limitations there is a need to be selective, prioritising species or areas not just on the basis of extinction risk or the number of species present, but with consideration for their role within the ecosystem. In this thesis, I investigate three aspects of current global extinction: What causes species to become threatened, how we should prioritise those that are, and how such information can be translated into area-based conservation priorities. Firstly, I developed models of plant extinction risk in relation to environmental (anthropogenic, climatic, and physical) variables and used them to show that non- randomness in extinction risk is highly influenced by interactions between the plants traits and their environment. Incorporating such interactions, my models were able to explain ~30% of the variation in plant extinction risk. Results from this large-scale comparative study suggest the biological traits that increase species' susceptibility are dependent upon local environmental conditions. Secondly, I looked at how much unique evolutionary history, a proxy for species value, will be lost under current extinction patterns, whilst investigating how effective current conservation methods are at prioritising species based on their evolutionary value. The results are not promising; species threatened with extinction had disproportionately high quantities of unique evolutionary history. Furthermore, the IUCN Red List makes no allowance for this, for example, species considered Critically Endangered, the highest threat status under the IUCN Red List, may not necessarily be the most evolutionary unique. Finally, I looked at the relationships among species richness, versity (FD) and phylogenetic diversity (PD) as measures of biodiversity and therefore the conservation value of an area. It was found species richness is generally a good surrogate for FD and PD. However, agricultural development and climatic variation bring out discrepancies between species richness, FD and PD, challenging the claim of interchangeability of different diversity measures, with potential consequences for conservation planning.
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Vaughan, Ritchie Catherine. "Group Analysis of Collaborative Conservation Partnerships." Thesis, Virginia Tech, 2011. http://hdl.handle.net/10919/76805.
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Collaborative conservation partnership frequency is increasing in natural resources management; however, few successful examples exist in the United States. These groups seek to address land stewardship through cooperative, communicative, bottom-up approaches that engage local stakeholders. A better understanding of member characteristics and successful group characteristics may enhance collaborative conservation partnership outcomes.
A survey was conducted to quantify partnership member characteristics and advertising mediums. Results were compared with the National Woodland Owner Survey. Collaborative conservation partnership members tend to be well-educated, middle-aged, upper-middle class individuals with large landholdings. They span previously identified family forest owner clusters but may be classified as earlier adopters by Diffusion of Innovations theory. Word-of-mouth is the most common way members learn about partnership opportunities.
Qualitative data was analyzed to identify key features related to the ability to achieve group goals. Multi-disciplinary literature review points to the likely influences of leadership, task type, social capital, resource inputs, processes, and temporal change attributes on collaborative conservation partnership goal achievement. Key informant interviews demonstrate that resource and social capital inputs derive disproportionately from particular actors, partnerships need flexibility to adapt to changes in available resources, leaders establish partnership activity levels, social capital is the foundation of resource access, and groups are diverse in the ways they deal with context-specific tasks, resources, and processes.
Overall, collaborative conservation partnerships demonstrate potential to positively influence land stewardship and technology transfer. Growth requires expanding membership, establishing partnerships as a legitimate conservation medium, and maintaining diverse groups tailored to local contexts.Master of Science
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Buschbeck, Elke Karin Ursula 1967. "Conservation of "magnocellular" neurons of the dipteran optomotor pathway: Evolutionary and functional implications." Thesis, The University of Arizona, 1994. http://hdl.handle.net/10150/278434.
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In Diptera, small-field retinotopic neurons supply achromatic motion sensitive neurons in the lobula plate, a region thought to control stabilization of yaw, pitch, and roll during flight. If different body shapes, and the flight performance associated with them, place specific demands on the design of control pathways, it might be expected that flies with long bodies and high aerodynamic pitch stability would show specific differences in the organization of such magnocellular achromatic networks. Striking differences emerge in the comparison of 9 species. Tipulids and culicids possess small non-stratified lobula plates, containing only 2-3 large diameter neurons. In syrphids, all VS cells have wide diameters and overlapping fields covering 2-3 times more of the mosaic than those of calliphorids. In asilids (robber flies) vertical cells cannot be identified. Despite these differences, we observe a conserved relationship between terminals of lamina afferents with neurons in the medulla.
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Grambo, Andrew A. "Functional design opportunities for water conservation through native landscape restoration in southwestern Idaho, U.S.A." Virtual Press, 2004. http://liblink.bsu.edu/uhtbin/catkey/1286422.
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This creative project inspected the design of water conserving landscapes by restoring native vegetation. Water conserving design principles discovered in the background research were applied to the redesign of the Old Fort Boise Park in Parma, Idaho. Important issues that were explored included discussing the need for water conserving landscape designs that result in functional spaces that meet the needs of intended users. The main focus of water conservation was implemented by using native plants that typically require less water than non-native species. The project developed a park master plan that could demonstrate to Idaho residents that native plants, when carefully sited, result in lower maintenance, aesthetically pleasing visual qualities, environmentally sensitive performances and could be integrated into landscapes on private or public properties. Rather than viewing the Idaho native plants as unattractive and dull, this project explored the idea that under cultivation and as part of the site character a carefully designed water conserving naturalized landscape has a beauty unsurpassed by traditional landscapes. The park redesign also employed educational and interpretive systems wherein native plants were highlighted and identified. These educational and interpretive systems could assist park users, especially local residents, in familiarizing themselves with many of the beautiful native species that are common in the surrounding deserts, prairies, hills and mountains. The creative project examined one particular site, while it developed principles and concepts applicable to other sites throughout the Great Basin Region.Department of Landscape Architecture
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Wishart, Marcus J. "A comparative phylogeographic approach toward defining functional units for the conservation of biodiversity in lotic ecosystems." Connect to this title online, 2002. http://www4.gu.edu.au:8080/adt-root/public/adt-QGU20031125.103610/.
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Illergård, Kristoffer, Anni Kauko, and Arne Elofsson. "Why are polar residues within the membrane core evolutionary conserved?" Stockholms universitet, Institutionen för biokemi och biofysik, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-68378.
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Here, we present a study of polar residues within the membrane core of alpha-helical membrane proteins. As expected, polar residues are less frequent in the membrane than expected. Further, most of these residues are buried within the interior of the protein and are only rarely exposed to lipids. However, the polar groups often border internal water filled cavities, even if the rest of the sidechain is buried. A survey of their functional roles in known structures showed that the polar residues are often directly involved in binding of small compounds, especially in channels and transporters, but other functions including proton transfer, catalysis, and selectivity have also been attributed to these proteins. Among the polar residues histidines often interact with prosthetic groups in photosynthetic-and oxidoreductase-related proteins, whereas pro-lines often are required for conformational changes of the proteins. Indeed, the polar residues in the membrane core are more conserved than other residues in the core, as well as more conserved than polar residues outside the membrane. The reason is twofold; they are often (i) buried in the interior of the protein and (ii) directly involved in the function of the proteins. Finally, a method to identify which polar residues are present within the membrane core directly from protein sequences was developed. Applying the method to the set of all human membrane proteins the prediction indicates that polar residues were most frequent among active transporter proteins and GPCRs, whereas infrequent in families with few transmembrane regions, such as non-GPCR receptors. Proteins 2011; 79: 79-91.authorCount :3
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Siqueira, Campos Felipe. "Functional and Phylogenetic Diversity of Amphibians in the Brazilian Atlantic Forest: Implications for a Systematic Conservation Planning." Doctoral thesis, Universitat de Barcelona, 2018. http://hdl.handle.net/10803/586284.
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Biodiversity patterns are results of ecological and evolutionary processes. Understanding the forces shaping biodiversity patterns help to predict the responses of ecosystems to environmental change. Considering the role of amphibian species in the functioning of ecosystems, we explored how their functional, phylogenetic and taxonomic relations can be incorporated into spatial decision-making in the Brazilian Atlantic Forest. We used these considerations for developing an integrative strategy based on species dispersal patterns, threats and conservation status, susceptibility to climate change, functional trait evolution and cost-effective conservation. In this line, we organized this thesis in 10 chapters distributed into five sections. We used different dimensions of the amphibians' ecological niches regarding morphology, life history, and behaviour. Our findings highlighted that functional trait-based approaches can be efficient strategies for conserving species in endangered ecosystems. Atlantic Forest reserves are failing to protect threatened species, and anticipated climate change can also be threatening the currently protected species. Therefore, we introduced new priorities for landscape assessments using ecological connectivity under current and future conditions. In the near future, most species can become threatened and tend to disperse towards areas with milder temperatures at high altitudes/latitudes, reducing their geographical ranges. By framing evolutionary ecology into conservation science, we revealed that phylogenetic metrics can be relevant tools for functional landscape planning. Using evolutionary history of functional traits, we also determined the species adaptation across different taxonomic lineages. In addition, under a complementarity-based analysis, we showed a practical suggestion to represent taxonomic indicator groups and estimates of land values. We designed an innovative assessment strategy, showing that prioritization models focused on different dimensions of biodiversity can incorporate cost-benefit relationships through payment for ecosystem services schemes. From theory to practice, our study suggests an eco- evolutionary framework regarding the usefulness of amphibian conservation from regional to global scales.Los patrones de biodiversidad son resultado de procesos ecológicos y evolutivos. Comprender las fuerzas que determinan estos patrones ayuda a predecir la respuesta de los ecosistemas al cambio ambiental. Considerando el papel de las especies de anfibios en el funcionamiento de los ecosistemas, exploramos cómo sus relaciones funcionales, filogenéticas y taxonómicas pueden ser incorporadas en la toma de decisiones espaciales en el Bosque Atlántico brasileño. Utilizamos estas consideraciones para desarrollar una estrategia basada en patrones de dispersión de especies, amenazas y estado de conservación, susceptibilidad al cambio climático, evolución de rasgos funcionales y conservación rentable. En esta línea, organizamos esta tesis en 10 capítulos distribuidos en cinco secciones. Según diferentes dimensiones ecológicas basadas en morfología, ciclo de vida y comportamiento de anfibios, mostramos que el uso de los rasgos funcionales puede ser eficiente para la conservación de especies en ecosistemas en peligro de extinción. Las reservas del Bosque Atlántico no son suficientes para sus especies amenazadas, y las especies actualmente protegidas sufren efectos del cambio climático. Por lo tanto, proponemos prioridades de conservación usando conectividad ecológica para condiciones actuales y futuras. En un futuro pr6ximo, la mayoría de las especies pueden verse amenazadas y tienden a dispersarse hacia áreas con temperaturas más suaves, a altitudes y latitudes elevadas, reduciendo sus rangos geográficos. Empleando la ecología evolutiva en la conservación, revelamos que métricas filogenéticas pueden ser herramientas relevantes para la planificación funcional del paisaje. Según la historia evolutiva de los rasgos funcionales, determinamos la adaptación de las especies en diferentes linajes taxonómicos. Además, bajo un análisis de complementariedad, representamos grupos taxonómicos indicadores y valores economicos de la tierra. Diseñamos modelos de priorización centrados en diferentes dimensiones de la biodiversidad, incorporando relaciones de coste-beneficio a través de esquemas de pago por servicios ecosistémicos. De la teoría a la práctica, nuestro estudio sugiere un marco eco-evolutivo con respecto a la utilidad de la conservación de anfibios desde escalas regionales a globales.
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Sales, Joshua Dong Pinliang. "Determining the suitability of functional landscapes and wildlife corridors utilizing conservation GIS methods in Denton County, Texas." [Denton, Tex.] : University of North Texas, 2007. http://digital.library.unt.edu/permalink/meta-dc-3920.
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Zeng, Shuai, and 曾帥. "Predicting functional impact of nonsynonymous mutations by quantifying conservation information and detect indels using split-read approach." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2014. http://hdl.handle.net/10722/198818.
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The rapidly developing sequencing technology has brought up an opportunity to scientists to look into the detailed genotype information in human genome. Computational programs have played important roles in identifying disease related genomic variants from huge amount of sequencing data.
In the past years, a number of computational algorithms have been developed, solving many crucial problems in sequencing data analysis, such as mapping sequencing reads to genome and identifying SNPs. However, many difficult and important issues are still expecting satisfactory solutions. A key challenge is identifying disease related mutations in the background of non-pathogenic polymorphisms. Another crucial problem is detecting INDELs especially the long deletions under the technical limitations of second generation sequencing technology.
To predict disease related mutations, we developed a machine learning-based (Random forests) prediction tool, EFIN (Evaluation of Functional Impact of Nonsynonymous mutations). We build A Multiple Sequence Alignment (MSA) for a querying protein with its homologous sequences. MSA is later divided into different blocks according to taxonomic information of the sequences. After that, we quantified the conservation in each block using a number of selected features, for example, entropy, a concept borrowed from information theory. EFIN was trained by Swiss-Prot and HumDiv datasets. By a series of fair comparisons, EFIN showed better results than the widely-used algorithms in terms of AUC (Area under ROC curve), accuracy, specificity and sensitivity. The web-based database is provided to worldwide user at paed.hku.hk/efin.
To solve the second problem, we developed Linux-based software, SPLindel that detects deletions (especially long deletions) and insertions using second generation sequencing data. For each sample, SPLindel uses split-read method to detect the candidate INDELs by building alternative references to go along with the reference sequences. And then we remap all the relevant reads using both original references and alternative allele references. A Bayesian model integrating paired-end information was used to assign the reads to the most likely locations on either the original reference allele or the alternative allele. Finally we count the number of reads that support the alternative allele (with insertion or deletions comparing to the original reference allele) and the original allele, and fit a beta-binomial mixture model. Based on this model, the likelihood for each INDEL is calculated and the genotype is predicted. SPLindel runs about the same speed as GATK and DINDEL, but much faster than DINDEL. SPLindel obtained very similar results as GATK and DINDEL for the INDELs of size 1-15 bps, but is much more effective in detecting INDELs of larger size.
Using machine learning method and statistical modeling technology, we proposed the tools to solve these two important problems in sequencing data analysis. This study will help identify novel damaging nsSNPs more accurately and efficiently, and equip researcher with more powerful tool in identifying INDELs, especially long deletions. As more and more sequencing data are generated, methods and tools introduced in this thesis may help us extract useful information to facilitate identification of causal mutations to human diseases.published_or_final_version
Paediatrics and Adolescent Medicine
Doctoral
Doctor of Philosophy
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Sales, Joshua. "Determining the Suitability of Functional Landscapes and Wildlife Corridors Utilizing Conservation GIS Methods in Denton County, Texas." Thesis, University of North Texas, 2007. https://digital.library.unt.edu/ark:/67531/metadc3920/.
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Denton County's unique cultural and natural landscape has undergone dramatic transformations during the past two centuries due to agricultural, urban and suburban processes which accelerated the loss and removal of native habitat and wildlife. This research sought out to identify the remaining natural areas which retain their natural features and support wildlife. Research methodology included fundamental principles of Conservation Planning, Geographical Information Systems, and Habitat Evaluation Procedures for identifying remnant functional landscapes and wildlife corridors. The final results suggest that Denton County's rural landscape retains the functional properties and elements suitable for habitat conservation and wildlife corridors, while also pointing to the fundamental obstacles to conservation posed by continued growth and private landownership.
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Wang, Xi [Verfasser], H. W. [Akademischer Betreuer] Mewes, and John [Akademischer Betreuer] Parsch. "Detection and evolutionary analysis of functional conserved non-coding sequences in higher plants by integrating evolutionary and functional conservation / Xi Wang. Gutachter: John Parsch. Betreuer: H.-W.Mewes." München : Universitätsbibliothek der TU München, 2012. http://d-nb.info/1025337816/34.
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Gustafsson, Susanne. "Population genetic analyses in the orchid genus Gymnadenia : a conservation genetic perspective." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl [distributör], 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3305.
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Nardi, Laura Verfasser], Alexander von [Akademischer Betreuer] [Kienlin, and Paolo [Akademischer Betreuer] Belardi. "A survey methodology for conservation and reconversion of functional buildings after 1950 / Laura Nardi ; Alexander von Kienlin, Paolo Belardi." Braunschweig : Technische Universität Braunschweig, 2019. http://d-nb.info/1191365417/34.
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Awade, Marcelo. "Padrões de movimentação de uma espécie de ave em paisagens fragmentadas e seus efeitos para a conectividade funcional: uma abordagem hierárquica." Universidade de São Paulo, 2009. http://www.teses.usp.br/teses/disponiveis/41/41134/tde-11122009-135213/.
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Um dos maiores impactos antrópicos aos ecossistemas terrestres é a fragmentação do habitat. Este processo afeta fortemente os padrões de movimentação das espécies, implicando em alterações consideráveis na conectividade entre as manchas de habitat remanescentes. Por sua vez, isso interfere na distribuição espacial e na dinâmica das populações de uma espécie. Nesta dissertação, foram estudados alguns aspectos dos movimentos rotineiros e dispersivo de Pyriglena leucoptera, uma espécie de ave endêmica da Mata Atlântica. Estes dois tipos de movimentação atuam em escalas distintas, afetando diferentemente os parâmetros que regulam a estrutura das populações. Com o uso da técnica de playback, foi verificado se a capacidade desta espécie atravessar áreas abertas, em movimentos rotineiros entre fragmentos, é afetada pela distância entre eles. A partir desta relação, foram obtidas probabilidades de cruzar áreas abertas, as quais foram usadas para parametrizar índices de conectividade funcional (um binário e outro probabilístico) baseados na teoria dos grafos. Em uma abordagem de seleção de modelos, estes dois índices de conectividade mais um outro estrutural (i.e. área do fragmento) foram comparados para se estabelecer qual deles melhor prediz a incidência de P. leucoptera em fragmentos florestais. Quanto aos movimentos dispersivos, foram realizados experimentos de translocação e telemetria para verificar se a dispersão desta espécie em áreas fragmentadas é afetada pela distância entre os fragmentos, assim como para averiguar se este efeito é diferente entre os sexos. Os resultados mostraram que distância entre os fragmentos florestais limita tanto a movimentação rotineira, quanto a dispersiva para esta espécie. Na escala dos movimentos rotineiros, verificou-se que fragmentos distanciados a mais de 45 m estão totalmente isolados. A incidência da espécie foi melhor descrita pelo índice de conectividade funcional probabilístico (PCS), mostrando que a conectividade é fundamental para se compreender a distribuição espacial da espécie, sendo que este atributo da paisagem deve ser visto de forma probabilística. Ademais, a dispersão foi enviesada para fêmeas, as quais possuíram maior propensão a emigrar, assim como foram mais eficientes em sua movimentação pela matriz. As conseqüências deste viés foram discutidas, destacando-se que, em áreas altamente fragmentadas, a probabilidade de colonização de áreas desocupadas diminui, bem como o fluxo gênico entre as populações da espécie pode estar comprometido. Portanto, ambos os tipos de movimento devem ser considerados para que se possa compreender mais precisamente os efeitos da conectividade do habitat para a sobrevivência de uma espécie em paisagens fragmentadas. Por fim, foi sugerido um modelo hierárquico de estrutura populacional, a fim de integrar as informações obtidas pelos dois tipos de movimentação em uma única estrutura conceitual. Esse modelo possui um grande potencial para ser usado no planejamento e manejo ambiental.Habitat fragmentation is one of the major human impacts on terrestrial ecosystems. This process highly affects the species movement pattern, implying in considerable alterations on the connectivity between the remaining habitat patches. Consequently, it interferes in the spatial distribution and in the population dynamics of species. In this dissertation, some aspects of the routine and dispersal movements of Pyriglena leucoptera, an endemic bird of the Atlantic rainforest, were studied. These two movement types act in distinct scales, affecting, differently, the parameter regulating the structure of the populations. Using the playback technique, we verified if the gap-crossing capacity of this species, by routine movements, is affected by gap width. From this relation, we obtained gap-crossing probabilities, which were used to parameterize functional connectivity indices (one binary and one probabilistic) based on graph theory. In a model selection approach, these two indices plus another structural one (i.e. patch area) were compared to establish which one is the best to predict P. leucopteras incidence in forest fragments. About the dispersal movements, we done translocation and telemetry experiments to investigate if the species dispersal ability in fragmented landscapes is affected by the distance between forest patches, and to verify if there are sexual differences in this effect. The results showed that distance between forest patches limits both the routine movements and the dispersal one to this species. In the routine movements scale, we verified that patches are completely isolated when the gap width is higher than 45 m. The species incidence was better described by the probabilistic connectivity index (PCS), evincing that it is essential to consider connectivity to understand the spatial distribution of P. leucoptera, and this attribute must be viewed in its probabilistic form. Furthermore, dispersal is female-biased, since females are more prone to emigrate and were more efficient in their movement in the matrix. We discussed the consequences of this sex-bias, highlighting that, in severely fragmented landscapes, the colonization probability of empty patches is decreased and the genetic flux between populations should be imperiled. Thus, to comprehend the effects of habitat connectivity on species survival in fragmented landscapes, both movement types must be considered. Finally, we suggested a hierarchically structured population model in order to integrate the two movement type information in one conceptual framework. This model has a great potential to be used in environmental planning and management.
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Mayhew, Rebekah Jane Watts. "The species and functional composition of bird communities in regenerating tropical forests." Thesis, University of Stirling, 2017. http://hdl.handle.net/1893/27894.
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The widespread threat of species extinctions caused by the destruction and degradation of tropical primary forest (PF) could potentially be mitigated by the expansion of regenerating secondary forest (SF). However, the conservation value of SF remains controversial, and is dependent on many site- and landscape-scale factors, such as habitat age and isolation. The aim of this thesis was to assess the role that SF can play in conserving forest bird communities in central Panama. We study a chronosequence of SF aged 20 – 120-years-old, with sites either isolated from or connected to extensive PF. Our results suggest that SF supports high levels of avian species diversity, and similar community composition to PF. Whilst forest age plays a small role in determining compositional similarity to PF, connectivity to extensive PF was the main determinant of community composition. However, despite high species richness and complex community composition, some specialist PF bird species were consistently absent from SF, and isolated PF. The functional diversity of bird communities did not vary substantially across the forest age and isolation gradient, although we did find some inter-guild differences; with distinct responses in communities of avian insectivores and frugivores. Isolation caused shifts in the trophic traits of insectivores, but resulted in alterations in the dispersal traits of frugivores. The response of bird and tree community composition to forest age and isolation was similar, although isolation had a stronger impact on bird communities. Bird diversity and composition tracked changes in forest structure over succession. When examining the role of birds in seed-dispersal networks, we found bird gape width was the key predictor of seed size consumed. Large-gaped birds consume a wider variety of seed-sizes than small-gaped birds, and small-seeded trees attract a greater number of bird species than large-seeded trees. These results imply high levels of redundancy among small-gaped avian frugivores and small-seeded plant species, but low levels of redundancy among large-seeded plant species and their avian dispersers. This suggests that large-seeded plants may be most at risk of dispersal failure following any change in avian frugivore assemblages. Together, these results suggest that SF can play a key role in sustaining most tropical biodiversity, and in maintaining ecosystem services. Our findings emphasise the importance of integrating SF into conservation strategies to support and buffer tropical PF habitats.
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Bankroff, Timothy J. "Arthropod community response to high-intensity, low-frequency cattle grazing events and pasture succession." Miami University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=miami1417541806.
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Smith, Joanne. "Agri-environment schemes and soil biodiversity: assessing the conservation, biodiversity and functional value of arable field margins for soil macrofauna." Thesis, University of Reading, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.486322.
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Leclerc, Camille. "Biodiversité endémique insulaire face aux changements globaux : état des lieux dans un contexte de conservation." Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLS507.
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Les changements globaux, du fait de l’empreinte humaine, sont associés à de nombreux déclins de populations et de disparitions d'espèces, et ce, notamment au sein des systèmes insulaires. L'importante biodiversité abritée par de tels écosystèmes est particulièrement vulnérable aux pressions anthropiques en raison de diverses caractéristiques (p. ex. syndrome d’insularité, faible redondance fonctionnelle, isolement géographique des îles). En dépit de cette vulnérabilité accrue, peu d’études se sont jusqu'à lors intéressées à ces systèmes comme modèle d’étude pour évaluer les patrons de menaces sur les différentes facettes de la diversité (taxonomique, fonctionnelle, et phylogénétique). Pourtant, un tel travail permettrait d’améliorer notre compréhension des menaces qui pèsent au sein des îles. Dans ce sens, l’objectif de cette thèse est de décrire les patrons de diversité endémique insulaire dans le contexte actuel des changements globaux et dans un contexte futur de changements climatiques, en explorant les différentes facettes de la diversité. Une finalité de ce travail est de mettre en évidence des priorités éventuelles de conservation pour ces écosystèmes particulièrement vulnérables. Nous avons abordé l'ensemble de ce travail de thèse à une grande échelle à l’aide de deux bases données recensant les îles mondiales et les espèces qui y sont endémiques. Dans une première partie, nous avons caractérisé les menaces pesant sur les écosystèmes insulaires à l'échelle globale, et prospecté également leurs distributions au sein de différents groupes taxonomiques et régions insulaires. Dans une deuxième partie, nous avons analysé l'incidence des menaces sur la biodiversité endémique insulaire et en particulier sur la composante fonctionnelle. Dans une troisième partie, nous avons identifié les régions insulaires à forte représentativité de la biodiversité endémique menacée au travers de différentes facettes et prospecté leurs niveaux de protection via les aires protégées et les menaces les affectant. Dans une dernière partie, nous avons étudié la vulnérabilité future des îles et de la biodiversité endémique face au changement climatique à l’échéance 2050. À la lumière de nos résultats (identification de menaces majeures dont l'importance varie suivant les groupes taxonomiques, les régions insulaires et également les dimensions de biodiversité considérées), nous avons discuté de l’implication des changements globaux pour la biodiversité endémique insulaire dans un contexte de conservation. Cette thèse révèle l’importance d’intégrer de multiples menaces (et leurs associations) et dimensions de diversité pour les approches de changements globaux et de conservationGlobal changes, because of human activities, are associated with numerous population declines and species extinctions, which are especially pronounced in island systems. The important biodiversity of such ecosystems is particularly vulnerable to anthropogenic pressures because of several characteristics (e.g. island syndrome, low functional redundancy, island geographical isolation). Despite this increased vulnerability, few studies have so far looked at these systems as a study model for assessing patterns of threats to the different facets of diversity (taxonomic, functional, and phylogenetic). However, such work would improve our understanding of islands threats. In this sense, the aim of this PhD thesis is to describe patterns of insular endemic diversity in the current context of global changes and in a future climate change context, by exploring different facets of diversity. The purpose of this work is to highlight potential conservation priorities for these particularly vulnerable ecosystems. We have addressed all of this thesis work on a large scale using two databases of worldwide islands and endemic species. In a first part, we characterized threats to island ecosystems at a global scale and also explored their distributions within different taxonomic groups and island regions. In a second part, we analyzed the impact of threats on the functional component of island endemic biodiversity. In a third part, we have identified priority areas for insular endemic biodiversity representativeness and conservation across different dimensions of biodiversity and explored their levels of protection through protected areas and threats affecting them. In a last part, we studied the future vulnerability of islands and endemic biodiversity to climate change by 2050 based on endemic mammals. In the light of our results (identification of major threats whose importance varies according to the taxonomic groups, the island regions and also the dimensions of biodiversity considered), we discussed the implications of global changes for island endemic biodiversity in a conservation context. This PhD thesis reveals the importance of integrating multiple threats and diversity dimensions for global changes and conservation approaches
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Kongor, Raphael Yuniwo. "Plant response to habitat fragmentation : clues from species and functional diversity in three Cape lowland vegetation types of South Africa." Thesis, Stellenbosch : University of Stellenbosch, 2010. http://hdl.handle.net/10019.1/4604.
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Dissertation presented for the degree of Doctor of Philosophy (PhD)
at
Stellenbosch University.Thesis (PhD (Conservation Ecology and Entomology))--University of Stellenbosch, 2010.
ENGLISH ABSTRACT: The South African Cape lowlands have been severely transformed and reduced to fragments embedded in matrices of various activities. With the need to prioritise conservation efforts, information on the conservation worthiness and management of these fragments is required. This study aimed to better understand how fragmentation affects the Cape lowland vegetation patterns and dynamics and more specifically, to determine if, and if so to what extent these fragments contribute to regional plant diversity and more importantly their functionality. The novel approach adopted focused on plant functional traits, which are better predictors of ecosystem response to global change than individual species. Species were sampled at four scales in four sites of decreasing sizes, including: a mainland and three fragments of three Cape lowland vegetation types i.e. Atlantis Sand Fynbos (ASF), Swartland Shale Renosterveld (SSR) and Langebaan Dune Strandveld (LDS). Traits such as dispersal, pollination, breeding mode and longevity were selected based on relevance to species’ and plantfunctional types’ (PFTs) responses to fragmentation. The findings revealed different effects on species richness and PFTs. The effect of reduced patch size on species richness was more evident in ASF where fragments below 600 ha had significantly fewer species than the mainland. This effect was not unequivocal in SSR and LDS due to several confounding factors (notably the grazing history of the sites). The SSR fragment grazed by indigenous herbivores had significantly more species than the ungrazed sites. Also, the largest LDS fragment grazed by livestock had significantly more species than the ungrazed mainland, indicating that grazing rather than fragment size influences species richness, although the smallest fragments of these two vegetation types had significantly fewer species than the larger fragments. Species turnover and complementarity were high for all three vegetation types, reflecting the degree of habitat heterogeneity and high contribution of beta diversity to overall gama diversity. The effect of reduced patch size was higher on PFT diversity than on PFT richness, with Langebaan Dune Strandveld where habitat fragmentation was more recent being the least affected of the three vegetation types. This indicates a degree of functional redundancy in the Cape lowlands, which is important for ecosystem resistance and resilience. The ASF mainland and the largest fragment had higher PFT diversity than the medium-sized and the smallest fragments; the mainland had also higher PFT diversity than all the fragments combined. Similarly, the smallest SSR fragment had significantly lower PFT diversity and richness than the other sites. The grazed SSR fragment had higher PFT richness and diversity than the ungrazed mainland and smallest fragment, indicating the role of grazing in maintaining renosterveld vegetation. The PFTs absent from the different sites were mostly short-distance dispersed dioecious and non-dioecious species, and some with highly specialised pollination systems. This suggests that dispersal and pollination are vital functional attributes for the persistence of the studied fragmented ecosystems. Habitat fragmentation effects plant community composition and ecological functions in the Cape lowlands, a conclusion supported also by the revealed significant trait-convergence and divergence assembly patterns. These communities result from various fragmentation filters that operate at different spatial-temporal scales and selecting species with suitable responses. All three vegetation types are susceptible to fragmentation, albeit at varying degree. The fragmentation effect was confounded by the sampling and temporal scales, the nature of disturbance regime, and the traitmediated differences in species’ response. The role of the surrounding matrix on fragment connectivity and gene flow appears to be of crucial importance, hence mitigation measures focusing on improving connectivity between patches, monitoring threatened taxa, and promoting dispersal and pollination have been recommended.
AFRIKAANSE OPSOMMING: Suid-Afrika se Kaapse laagland het dramaties verander en weggekwyn tot fragmente wat in matrikse van verskeie bedrywighede veranker is. Gedagtig aan die voorkeuraandag wat bewaringspogings tans geniet, is inligting oor die bewaringswaardigheid en bestuur van hierdie fragmente nodig. Hierdie studie stel dit ten doel om beter begrip te vorm van hoe fragmentasie die plantegroeipatrone en -dinamiek in die Kaapse laagland raak, en meer bepaald om vas te stel óf, en indien wel, in watter mate, hierdie fragmente tot streeksplantdiversiteit en -funksionaliteit bydra. Die ongewone studiebenadering konsentreer op funksionele kenmerke van plante, wat beter aanwyser van ekosisteemreaksie op wêreldwye verandering is as individuele spesies. Spesiemonsters is op vier skale by vier terreine van wisselende grootte ingesamel, wat insluit moederstrook en drie fragmente van elk van drie plantegroeisoorte in die Kaapse laagland, naamlik Atlantis-sandfynbos (ASF), Swartland-skalierenosterveld (SSR) en Langebaan-duinestrandveld (LDS). Kenmerke soos verspreiding, bestuiwing, voortplantingsmetode en lewensduur is gekies op grond van die tersaaklikheid daarvan vir spesies en plantfunksionele tipes (PFT’s) se reaksie op fragmentasie. Die studie bring verskillende uitwerkings op spesie-oorvloed en PFT’s aan die lig. Wat spesie-oorvloed betref, was die uitwerking van kleiner strookgrootte (“patch size”)duideliker te sien by ASF, waar fragmente kleiner as 600 ha beduidend minder spesies as die moederstrook bevat het. Hierdie uitwerking kon nie so duidelik by SSR en LDS waargeneem word nie weens verskeie strengelingsfaktore, veral die weidingsgeskiedenis van die terreine. Die SSR-fragment waarop inheemse herbivore gewei het, het beduidend meer spesies as die onbeweide terreine bevat. Voorts het die grootste LDS-fragment waarop vee gewei het heelwat meer spesies as die onbeweide moederstrook gehad, wat daarop dui dat weiding eerder as fragmentgrootte spesie-oorvloed beïnvloed, hoewel die kleinste fragmente van hierdie twee plantsoorte steeds aansienlik minder spesies as die groter fragmente bevat het. Spesie-omset en -aanvullendheid was hoog vir ál drie plantsoorte, wat aanwyser is van die mate van habitat-heterogeniteit en die groot bydrae wat betadiversiteit tot algehele gammadiversiteit lewer. Die uitwerking van kleiner strookgrootte was duideliker te bespeur op PFT-diversiteit as PFT-oorvloed – in dié verband het LDS, waar habitatfragmentasie mees onlangs plaasgevind het, die ligste van die drie plantsoorte afgekom. Dít dui op mate van funksionele oorbodigheid in die Kaapse laagland wat belangrik is vir ekosisteemweerstandigheid en -gehardheid. Die ASF-moederstrook en die grootste ASF-fragment het hoër PFT-diversiteit getoon as die medium- en kleinste fragmente; die moederstrook het in werklikheid oor hoër PFT-diversiteit as ál die fragmente saam beskik. Insgelyks het die kleinste SSR-fragment beduidend minder PFT-diversiteit en -oorvloed as die ander terreine getoon. Die beweide SSR-fragment was hoër in PFT-oorvloed én -diversiteit as die onbeweide moederstrook en die kleinste fragment, wat die rol van weiding in die instandhouding van renosterveldplantegroei beklemtoon. Die PFT’s wat nié op die verskillende terreine voorgekom het nie, was meestal tweehuisige en nietweehuisige spesies wat oor kort afstande versprei, en sommige spesies met hoogs gespesialiseerde bestuiwingstelsels. Dít dui daarop dat verspreiding en bestuiwing noodsaaklike funksionele kenmerke vir die voortbestaan van die bestudeerde gefragmenteerde ekosisteme is. Habitatfragmentasie raak die samestelling en ekologiese funksies van plantgemeenskappe in die Kaapse laagland. Dié gevolgtrekking word ook gerugsteun deur die bewese patrone van beduidende kenmerkkonvergensie (“trait convergence”) en divergensiesamekoms (“divergence assembly”). Hierdie plantgemeenskappe spruit uit verskeie fragmentasiefilters wat op verskillende ruimte-tydskale funksioneer, en wat spesies met geskikte reaksies kies. Ál drie plantsoorte is ontvanklik vir fragmentasie, hoewel in wisselende mate. Die fragmentasie-uitwerking is beïnvloed deur monsterinsameling- en tydskale, die soort versteuringsbedeling, en die kenmerkbemiddelde (“traitmediated”) verskille in spesiereaksie. Die rol van die omringende matriks op fragmentverbondenheid en geenvloei blyk van die allergrootste belang te wees, en dus word temperingsmaatreëls aanbeveel wat daarop gemik is om verbondenheid tussen stroke te verbeter, bedreigde taksa te moniteer, en verspreiding en bestuiwing aan te help.
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Zolkewitz, Michael Alan Bien Walter F. "The use of assisted succession to restore the globally imperiled dwarf pine-oak forests of the New Jersey Pinelands : an investigation of the functional and structural recovery of an abandoned gravel pit /." Philadelphia, Pa. : Drexel University, 2010. http://hdl.handle.net/1860/3290.
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Krishnakumar, Pritesh [Verfasser], Roland [Akademischer Betreuer] Dosch, Michael [Gutachter] Kessel, and Dirk [Gutachter] Görlich. "Functional conservation of germ plasm organizers Bucky ball in zebrafish and Drosophila Oskar / Pritesh Krishnakumar ; Gutachter: Michael Kessel, Dirk Görlich ; Betreuer: Roland Dosch." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2018. http://d-nb.info/1173420746/34.
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Leung, Yeung-Yeung [Verfasser], and Christoph [Akademischer Betreuer] Schuster. "Functional conservation of the AKT kinase action on the synaptic vesicle release machinery between Drosophila and rat / Yeung-Yeung Leung ; Betreuer: Christoph Schuster." Heidelberg : Universitätsbibliothek Heidelberg, 2016. http://d-nb.info/1180735838/34.
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Leung, Yeung-Yeung Verfasser], and Christoph M. [Akademischer Betreuer] [Schuster. "Functional conservation of the AKT kinase action on the synaptic vesicle release machinery between Drosophila and rat / Yeung-Yeung Leung ; Betreuer: Christoph Schuster." Heidelberg : Universitätsbibliothek Heidelberg, 2016. http://d-nb.info/1180735838/34.
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Leung, Yeung-Yeung [Verfasser], and Christoph M. [Akademischer Betreuer] Schuster. "Functional conservation of the AKT kinase action on the synaptic vesicle release machinery between Drosophila and rat / Yeung-Yeung Leung ; Betreuer: Christoph Schuster." Heidelberg : Universitätsbibliothek Heidelberg, 2016. http://d-nb.info/1180735838/34.
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Bauduin, Sarah. "Integrating functional connectivity and climate change in the design of protected area networks." Doctoral thesis, Université Laval, 2016. http://hdl.handle.net/20.500.11794/26897.
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Le rapide déclin actuel de la biodiversité est inquiétant et les activités humaines en sont la cause directe. De nombreuses aires protégées ont été mises en place pour contrer cette perte de biodiversité. Afin de maximiser leur efficacité, l’amélioration de la connectivité fonctionnelle entre elles est requise. Les changements climatiques perturbent actuellement les conditions environnementales de façon globale. C’est une menace pour la biodiversité qui n’a pas souvent été intégrée lors de la mise en place des aires protégées, jusqu’à récemment. Le mouvement des espèces, et donc la connectivité fonctionnelle du paysage, est impacté par les changements climatiques et des études ont montré qu’améliorer la connectivité fonctionnelle entre les aires protégées aiderait les espèces à faire face aux impacts des changements climatiques. Ma thèse présente une méthode pour concevoir des réseaux d’aires protégées tout en tenant compte des changements climatiques et de la connectivité fonctionnelle. Mon aire d’étude est la région de la Gaspésie au Québec (Canada). La population en voie de disparition de caribou de la Gaspésie-Atlantique (Rangifer tarandus caribou) a été utilisée comme espèce focale pour définir la connectivité fonctionnelle. Cette petite population subit un déclin continu dû à la prédation et la modification de son habitat, et les changements climatiques pourraient devenir une menace supplémentaire. J’ai d’abord construit un modèle individu-centré spatialement explicite pour expliquer et simuler le mouvement du caribou. J’ai utilisé les données VHF éparses de la population de caribou et une stratégie de modélisation patron-orienté pour paramétrer et sélectionner la meilleure hypothèse de mouvement. Mon meilleur modèle a reproduit la plupart des patrons de mouvement définis avec les données observées. Ce modèle fournit une meilleure compréhension des moteurs du mouvement du caribou de la Gaspésie-Atlantique, ainsi qu’une estimation spatiale de son utilisation du paysage dans la région. J’ai conclu que les données éparses étaient suffisantes pour ajuster un modèle individu-centré lorsqu’utilisé avec une modélisation patron-orienté. Ensuite, j’ai estimé l’impact des changements climatiques et de différentes actions de conservation sur le potentiel de mouvement du caribou. J’ai utilisé le modèle individu-centré pour simuler le mouvement du caribou dans des paysages hypothétiques représentant différents scénarios de changements climatiques et d’actions de conservation. Les actions de conservation représentaient la mise en place de nouvelles aires protégées en Gaspésie, comme définies par le scénario proposé par le gouvernement du Québec, ainsi que la restauration de routes secondaires à l’intérieur des aires protégées. Les impacts des changements climatiques sur la végétation, comme définis dans mes scénarios, ont réduit le potentiel de mouvement du caribou. La restauration des routes était capable d’atténuer ces effets négatifs, contrairement à la mise en place des nouvelles aires protégées. Enfin, j’ai présenté une méthode pour concevoir des réseaux d’aires protégées efficaces et j’ai proposé des nouvelles aires protégées à mettre en place en Gaspésie afin de protéger la biodiversité sur le long terme. J’ai créé de nombreux scénarios de réseaux d’aires protégées en étendant le réseau actuel pour protéger 12% du territoire. J’ai calculé la représentativité écologique et deux mesures de connectivité fonctionnelle sur le long terme pour chaque réseau. Les mesures de connectivité fonctionnelle représentaient l’accès général aux aires protégées pour le caribou de la Gaspésie-Atlantique ainsi que son potentiel de mouvement à l’intérieur. J’ai utilisé les estimations de potentiel de mouvement pour la période de temps actuelle ainsi que pour le futur sous différents scénarios de changements climatiques pour représenter la connectivité fonctionnelle sur le long terme. Le réseau d’aires protégées que j’ai proposé était le scénario qui maximisait le compromis entre les trois caractéristiques de réseau calculées. Dans cette thèse, j’ai expliqué et prédit le mouvement du caribou de la Gaspésie-Atlantique sous différentes conditions environnementales, notamment des paysages impactés par les changements climatiques. Ces résultats m’ont aidée à définir un réseau d’aires protégées à mettre en place en Gaspésie pour protéger le caribou au cours du temps. Je crois que cette thèse apporte de nouvelles connaissances sur le comportement de mouvement du caribou de la Gaspésie-Atlantique, ainsi que sur les actions de conservation qui peuvent être prises en Gaspésie afin d’améliorer la protection du caribou et de celle d’autres espèces. Je crois que la méthode présentée peut être applicable à d’autres écosystèmes aux caractéristiques et besoins similaires.The world is facing worrisome declines in biodiversity. Species extinction rates have increased as a direct consequence of human activities. Protected areas have been implemented around the world in an effort to counter biodiversity loss. Although protected areas are part of the solution, they should be designed systematically in a way to maximize their effectiveness. Enhancing functional connectivity between protected areas is one way to increase their effectiveness. Climate change is disrupting environmental conditions globally. It is a threat to biodiversity that until recently was not often integrated into protected area design. Climate change has been shown to impact species movements, and therefore landscape functional connectivity. Some studies have suggested that enhancing functional connectivity between protected areas can also help species cope with climate change impacts. My thesis presents a methodology to design protected area networks while accounting for climate change and functional connectivity. My study area is located in the natural region of Gaspésie in Québec (Canada). The endangered Atlantic-Gaspésie population of woodland caribou (Rangifer tarandus caribou) was used as the focal species to define functional connectivity. This small population is in long-term decline due to predation and habitat change, but climate change may become an additional threat. First, I built a spatially explicit individual-based model to explain and simulate caribou movement. I used sparse VHF data available at the time of the study to select and parameterize a movement model using a pattern-oriented modeling strategy. My best model reproduced most of the movement patterns defined from the observed data. This model improved the understanding of the movement drivers for the Atlantic-Gaspésie caribou. It also provided spatial estimates of caribou landscape use in the Gaspésie region. I concluded that sparse data were sufficient to fit individual-based models when coupled with a pattern-oriented modeling strategy. Second, I estimated how climate change and conservation activities may impact caribou movement potential. I used the individual-based model to simulate caribou movements in hypothetical landscapes representing the impacts of various climate change scenarios and conservation activities. Conservation activities represented the implementation of new protected areas in Gaspésie, according to the scenario developed by the government of Québec, and the restoration of secondary roads inside protected areas. Climate change impacts on vegetation, as defined in my scenarios, reduced caribou movement potential. Road restoration was able to mitigate these negative effects whereas the implementation of the new protected areas did not improve caribou movement potential. Third, I presented a methodology to design effective protected area networks and proposed new protected areas to implement in Gaspésie to conserve biodiversity in the presence of climate change. I created a large sample of protected area networks expanding the existing network to reach an areal target of 12%. I then calculated an ecological representativeness index and two measures of functional connectivity over time for each network. Functional connectivity measures represented the overall access to the protected areas and the movement potential in them for the Atlantic-Gaspésie caribou. I used movement potential estimates for the current time period and for the future under different climate change scenarios to represent functional connectivity. The protected area network I proposed maximized the trade-off between the three network features I calculated. In this thesis I examined Atlantic-Gaspésie caribou movements under different environmental conditions, including climate change impacted landscapes. These results helped define new protected areas for the Gaspésie region that will protect the caribou population over time. I believe this thesis gives new insights on the Atlantic-Gaspésie caribou movement behavior, as well as on the management actions that could be taken in Gaspésie to improve conservation of caribou and of other species. I believe this methodology could be applied to other ecosystems with similar characteristics and needs.
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Kirkpatrick, Lucinda. "Bat exploitation of Sitka Spruce plantations : impacts of management on bats and nocturnal invertebrates." Thesis, University of Stirling, 2016. http://hdl.handle.net/1893/25312.
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Plantations are widespread throughout temperate regions, and the area of plantation land cover is predicted to get larger in the future. Interest in ensuring sustainable plantation management is also growing, as it is increasingly recognised that productive areas should play a role in biodiversity conservation. Plantation landscapes can comprise the majority of forested cover in some countries, but taxon-specific guidance can be lacking, due to plantations often being under surveyed. Therefore, despite substantial incentives existing to ensure that plantations meet various ecological criteria, plantation managers lack the information necessary to implement effective management plans. Many bat species have undergone widespread declines in recent decades, attributed to habitat loss and fragmentation, particularly of forested habitat. In many temperate countries, historical deforestation has resulted in very low native tree cover, and subsequently, considerable replanting with non-native commercial coniferous plantations has taken place. Species specific habitat surveys have often demonstrated avoidance of conifer plantations by bats, which has been attributed to a lack of roosts and low invertebrate prey abundance. Furthermore, widespread lepidopteran declines have been partly attributed to afforestation with non-native conifer, but moth associations with commercial coniferous plantations are usually only studied for pest species. Bats present a particular challenge in plantation landscapes; tree cover is important to many species to a greater or lesser extent, and in the United Kingdom, destruction of a roost site is illegal, regardless of whether it was deliberate or accidental. However, the extent to which bats associate with non-native commercial plantations is relatively unexplored. This is the first study to explicitly test bat associations with Picea sitchensis plantations (using acoustic detectors, trapping and radio tracking), and shows that, contrary to expectations, they may be an important habitat for breeding populations of Pipistrellus spp., particularly P. pygmaeus. High levels of activity were recorded for both P. pygmaeus and P. pipistrellus, despite little difference in dipteran abundance between different stand types, both species preferentially foraged in felled or less dense stands. This suggests that bats preferentially forage in areas with less acoustic and physical clutter, which will increase foraging efficiency. The impacts of felling in non-native commercial coniferous plantations on foraging activity was tested, for the first time, using a Before – After – Control – Impact experimental design. Bat activity (specifically P. pipistrellus and Nyctalus) increased after felling, particularly in smaller stands. In contrast felling had significant, negative impacts on moth abundance, species richness and diversity, and these effects remain after constraining for functional trait similarity. Reductions in richness and diversity in response to felling were similarly large for both rare and abundant species. Therefore, while bats may benefit from clear fell practices, albeit as long as the size of patches is small, moth populations could benefit from a shift towards other forestry methods, iv such as continuous cover forestry. These results also have implications for the recent, but increasing practice of siting wind turbines in commercial coniferous plantations, as pre-installation preparation involves clearing small patches of forest which may attract foraging bats; post felling monitoring should be carried out to examine potential impacts on bat populations. The presence of broadleaf trees in and around plantations significantly increased moth richness, mostly through increased occurrence of rare species. Broadleaf woodlands (defined as land spanning more than 0.5 ha, with trees higher than 5m and a combined cover of shrubs, bushes and trees above 10%), also had higher functional redundancy than plantation sites. For a diverse moth population to persist in plantation landscapes, preserving remnant patches of broadleaf trees is essential. There was little difference in bat activity between broadleaf woodlands and plantation sites. However, bat abundance, particularly that of reproductively active females, was greater in broadleaf sites compared to plantations. This was particularly true for Myotis and Nyctalus spp., very few of which were trapped in commercial plantations. Therefore, although reproductively active female Myotis bats are present in the surrounding landscape, they do not appear to associate with plantations themselves. This may reflect a lack of roost availability; both P. pygmaeus and P. pipistrellus preferentially form large maternity colonies in buildings, but for Myotis and Nyctalus spp. which roost switch regularly and often use trees, it is unlikely many suitable roosts exist within the plantations themselves. Many substantial P. pygmaeus maternity colonies were identified in and around Galloway forest, with some holding more than 500 individuals. All maternity colonies were in buildings, and most inhabited (and one uninhabited) buildings within the plantation contained a roost. Although females occasionally used old or dead deciduous trees as temporary roosts, there was no evidence of roosting in crop trees such as P. sitchensis. During this study, the Forestry Commission installed 36 bat boxes; within 6 months over 90% had been used, with a number of harems found inside. This fast uptake compared with bat use of boxes in other locations reflects the paucity of appropriate structures for either roost or harem use in commercial plantations. Twelve bats were captured while foraging, tagged with small radio transmitters, and followed for between 2 and 6 nights during 2014 and 2015. All but one tagged female preferentially foraged within the plantation, with individuals selecting equally riparian habitats and felled stands. Tagged females which roosted furthest from the plantation had the largest home ranges; one individual flew nearly 40km each night to reach foraging areas distant from her roost, suggesting that the food availability within the plantation was sufficient to render such a long journey energetically viable. v These results have important implications for bat populations in and around commercial coniferous plantations. Far from being avoided by bats, plantation landscapes may constitute an important habitat type for both P. pygmaeus and P. pipistrellus, likely due to the high abundance of nematoceran diptera in plantation woodlands. Furthermore, plantation forests support a similar richness of moth species to urban and agricultural woodlands, including a number of declining species of special conservation concern. A list of management recommendations to benefit both bat and moth populations in commercial plantations is presented at the end of this thesis.
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Zielke, Barbara [Verfasser], and Thomas [Akademischer Betreuer] Stamminger. "The HCMV encoded mRNA-export factor pUL69 : functional conservation within the Betaherpesvirinae and identification of mRNA-targets during infection / Barbara Zielke. Betreuer: Thomas Stamminger." Erlangen : Universitätsbibliothek der Universität Erlangen-Nürnberg, 2012. http://d-nb.info/1022737279/34.
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Kondratyeva, Anna. "Measuring inter-specific diversity. Benefits of species originality indices in community ecology and conservation biology." Thesis, Paris, Muséum national d'histoire naturelle, 2019. http://www.theses.fr/2019MNHN0012.
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L'humanité dépend fortement de la biodiversité et des services qu'elle nous fournit. Pour prévenir la perte de biodiversité et établir des relations durables avec la nature, l'humanité doit gérer et protéger des ressources naturelles. Le problème de "what to protect" n'est pas nouveau, mais il est devenu aujourd'hui plus important que jamais et pourrait être résolu par une utilisation appropriée des mesures de la biodiversité. De nombreuses mesures de biodiversité ont été élaborées au cours des quatre dernières décennies avec l'abondance des espèces comme l'une des unités centrales. Cependant, les études en écologie et évolution nécessitent une description précise des caractéristiques des espèces pour quantifier au mieux la diversité interspécifique, car en effet les espèces ne sont pas équivalentes. Les premières mesures tenant compte des différences biologiques entre les espèces étaient fondées sur les relations phylogénétiques et les valeurs de traits des espèces. Cependant, beaucoup d'entre elles mesurent la diversité d'un ensemble d'espèces et n'indiquent pas la contribution de chaque espèce à la diversité de l'ensemble. Comme une solution à ce problème, d'autres types de mesures sont apparus au début des années 90's, comparant les espèces en fonction de ce qu'elles ont en commun, mais elles ont été mises de côté, classées à tort comme mesures de la diversité. Néanmoins, ces mesures donnent une valeur à chaque espèce et non à l'ensemble des espèces. Dans cette thèse, nous appelons ces mesures des indices d'originalité des espèces. Une espèce est originale si elle possède des valeurs de traits inhabituels par rapport à toutes les autres espèces dans une communauté ou si elle est phylogénétiquement éloignée des autres. Ainsi, les espèces les plus originales sont celles qui contribuent le plus à la diversité de cette communauté. Dans cette thèse, nous avons cherché à démontrer des avantages des mesures d'originalité, en particulier en biologie de la conservation et en écologie des communautés. Tout d'abord, nous examinons la relation entre les concepts de l'originalité, de la diversité et de la rareté des espèces et nous comparons leurs mesures associées. Poursuivant des liens théoriques entre les mesures d'originalité et de diversité, nous proposons une application pratique d'indices d’originalité en deux étapes (et à deux échelles) à un jeu de données réel des espèces végétales. Enfin, nous discutons des principaux points forts et faibles liés aux données sur les espèces, à l'échelle spatiale des études et au choix des mesures d'originalité, impliqués dans l'analyse d'originalité. Un outil prometteur, les mesures d'originalité pourraient être utilisés avec d'autres entités que des espèces, tels que les gènes ou les habitats, et donc élargir notre compréhension et la conservation de la biodiversitéHumanity strongly depends on biodiversity and services it provides. To prevent the biodiversity loss and to establish sustainable relations with nature humanity has to efficently manage and protect natural resources. The problem of “what to protect” is not new but became more important than ever and could be resolved by an appropriate use of biodiversity measures. Many indices of biodiversity have been developed in the last four decades, with species being one of the central units. However, evolutionary and ecological studies need a precise description of species’ characteristics to best quantify inter-species diversity, as species are not equivalent and exchangeable. First measures taking into account species biological differences were based on species phylogenetic relations and trait values. However, many of them measure a diversity of a set of species, and does not indicate the respective contribution of each species to the diversity of the set. To find a remedy to this issue, other type of measures appeared in early 90’s, comparing species through the shared amount of characteristics, but were put aside, erroneously classified as diversity measures too. In this thesis we refer to these measures as species originality indices. A species is original if it possesses unusual trait values compared to all others in a community or if it is distantly related with other species in a community. Thus, the most original species have the greatest contribution to the diversity of that community. In this thesis we sought to demonstrate the benefits of originality metrics, particularly in conservation biology and community ecology. First we review the relation of species originality with concepts of species’ diversity and rarity and we compare their related measures. Following theoretical links between originality and diversity measures we propose a practical application of a two-step (and two-scale) originality framework to a real plant species data. Finally, we discuss main pitfalls and advantages related to species data, spatial scale of a study and the choice of an originality measure. Future studies could use originality measures with other entities than species, such as genes or habitats, and therefore broad the extent of biodiversity assessment and conservation
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Lorel, Claire. "Concilier le développement urbain et agricole avec la conservation de la biodiversité : anticipation de l'empreinte des activités anthropiques sur la biodiversité par une approche fonctionnelle et multi-trophique." Thesis, Paris, Muséum national d'histoire naturelle, 2018. http://www.theses.fr/2018MNHN0009/document.
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La forte croissance des populations humaines a engendré une intensification des milieux, surtout agricoles pour l’alimentation et l’élevage, résultant en une plus grande appropriation de la productivité primaire nette. La productivité primaire étant à la base des réseaux trophiques et écologiques, toute modification de ce processus essentiel est susceptible d’avoir de fortes conséquences sur la biodiversité. Par ailleurs, l’intensification est un processus complexe dont les trois dimensions – intrants, extrants et système – sont rarement étudiées de concert. Le cadre conceptuel et méthodologique HANPP (Human Appropriation of Net Primary Production) proposé par Helmut Haberl et collaborateurs en 2007, a pour objectif de quantifier différents paramètres de l’intensification. Dans un premier temps, les liens entre des composantes d’HANPP et d’autres indices d’intensification (i.e. HNV, IC/ha) ont été explorés afin de mieux interpréter la variabilité d’HANPP et ses composantes. HANPP semble lié à la fois aux dimensions « système » et « extrants » de l’intensité d’usage des sols et apparait comme complémentaire aux autres indicateurs testés. Dans un second temps, je me suis intéressée à la relation entre HANPP et biodiversité, à travers deux taxons complémentaires par leurs fonctions écosystémiques, i.e. les oiseaux et chiroptères. Grâce à l’utilisation de données issues de programmes de sciences participatives en France métropolitaine, j’ai pu montrer que l’intensification : i) diminuait la richesse spécifique, l’abondance et la masse moyenne des communautés de chiroptères, et ii) simplifiait la structure des communautés aviaires par l’abaissement du niveau trophique et de la régularité fonctionnelle, au bénéfice de spécialistes des milieux agricoles. Par ailleurs, j’ai pu observer que la réponse de la biodiversité pouvait grandement varier selon l’indicateur et/ou la facette (taxonomique ou fonctionnelle) étudiée. A travers mes analyses, j’ai pu clarifier les conditions d’utilisation du cadre méthodologique HANPP. J’ai également identifié des régions et types de paysage où l’intensité d’usage des sols peut coexister avec la biodiversité. L’ensemble de ces résultats forme le support à une discussion sur les opportunités pour concilier efforts de conservation et intensificationThe strong growth of Human populations has led to the intensification of land uses and land covers, especially in agricultural lands for food production and livestock, resulting in a higher appropriation of net primary productivity. As primary productivity is the root of food webs and ecological networks, any change in this essential process is likely to have a strong impact on biodiversity. Besides, intensification is a complex process whose three dimensions - inputs, outputs and system - are rarely studied together. The conceptual and methodological framework of HANPP (Human Appropriation of Net Primary Production) proposed by Helmut Haberl and collaborators in 2007, aims to quantify different parameters of intensification. First, I explored the variability of HANPP components and their relationships to other intensification indices (i.e. HNV, IC / ha) to better interpret the variability of HANPP and its components. HANPP seems to be linked to both the "system" and "output" dimensions of land use intensity and appears to complement the other indicators considered. Then, I investigated the relationship between HANPP and biodiversity, focusing on two taxa complementary in their ecosystem functions, i.e. birds and bats. Using data from citizen-science programs occurring in metropolitan France, I showed that intensification: i) decreased species richness, abundance and the average mass of bats, and ii) simplified the structure of avian communities by lowering the average trophic level and functional regularity, to the benefit of farmland specialists. In addition, I observed that the response of biodiversity could widely vary depending on the indicator and / or facet (taxonomic or functional) studied. Through my analyzes, I was able to clarify the conditions of use of the HANPP methodological framework. I also identified areas and types of landscape where land use intensity can coexist with biodiversity. All of these results form the basis for a discussion on opportunities to reconcile conservation efforts with intensification
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Perkkiö, M. (Miia). "Utilitas restauroinnissa:historiallisen rakennuksen käyttötarkoituksen muutos ja funktionaalinen integriteetti." Doctoral thesis, University of Oulu, 2007. http://urn.fi/urn:isbn:9789514286759.
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Abstract The functional usage of historical buildings is essential for their preservation. However, it appears to be very difficult to find satisfactory solutions especially when deciding new uses for them. This research focuses on the problem of the re-use of historical buildings from the point of view of the tasks of architecture and restoration. The aim of this research is, firstly, to examine the history of the re-use of historical buildings and, secondly, to identify the premises for their functional integrity and authenticity, both of which are considered crucial in restorations. Since antiquity the Latin concept utilitas has been referred to as the primary task of architecture: to be useful and functional. In this research the theme of utilitas has been observed through architectural and restoration theories and examples of re-use from different periods. Even if the re-use of old buildings has been common throughout history, it is only since the modern restoration approach of the 19th century that the functionality of historical buildings has been considered important in their preservation. Among restoration debates during the 20th century the functionality and the re-use of historical buildings have been considered only occasionally. However, among theoretical discussions on architecture functionality has been one of the most central themes of the century. Can a historical building be authentic even if its original function has changed? The main issue in the re-use of historical buildings is not to find technical solutions or methodologies, but to understand the more profound intentions for the building. Historical buildings cannot be distinguished from the reality and the requirements of human beings of today. In the restorations there must be an equilibrium between the historical legacy and the requirements of the present. Analyzing historical buildings from the point of view of functional integrity offers not only a new method but also new possibilities to discover planning solutions in the re-use of the historical buildings — respecting both the past and the presentTiivistelmä Historiallisen rakennuksen säilymisen ehto on sen järkevä hyödyntäminen alkuperäisen käyttötarkoituksen loputtuakin. Silti käytön kannalta välttämättömiin muutoksiin suhtaudutaan usein kielteisesti. Tämä tutkimus käsittelee historiallisten rakennusten käyttötarkoituksen muutoksia arkkitehtuurin ja restauroinnin tehtävien näkökulmasta. Siinä pohditaan käyttötarkoituksen muutosten oikeutusta ja restauroinneissa keskeisenä pidettyä autenttisuuden ongelmaa. Samalla pyritään hahmottamaan, mitä tarkoittaa autenttisuuteen liittyvä funktionaalinen integriteetti käyttötarkoituksen muuttuessa. Utilitas-käsitteellä on aina antiikista lähtien viitattu arkkitehtuurin yhteydessä rakennusten funktionaalisuuteen ja käyttökelpoisuuteen. Aihetta on tässä tutkimuksessa käsitelty eri aikojen arkkitehtuuriteorioiden ja historiallisiin rakennuksiin kohdistuneiden käyttötarkoituksen muutosten avulla. Vaikka historiallisia rakennuksia on aina muutettu uusiin tarkoituksiin vasta 1800-luvulla alettiin korostaa käyttötarkoituksen merkitystä historiallisten rakennusten säilymiselle. Historiallisten rakennusten käyttötarkoituksen muutoksiin liittyviin ongelmiin on 1900-luvun restaurointikeskustelussa viitattu kuitenkin vain harvoin. Sen sijaan arkkitehtuurista puhuttaessa rakennuksen funktionaalisuus on ollut yksi keskeisistä aiheista. Suurin ongelma historiallisten rakennusten käyttötarkoituksen muutoksissa on rakennuksen syvempien merkitysten ymmärtäminen, ei teknisten menetelmien ja ratkaisujen puuttuminen. Historiallisia rakennuksia ei voida täysin erottaa todellisuudesta ja ihmisen tarpeista tässä ja nyt. Kysymys on tasapainosta historian ja nykyhetken välillä. Funktionaalisen integriteetin tarkastelu tarjoaa paitsi menetelmän restaurointien arvioimiseen, myös mahdollisuuden löytää uusia ratkaisuja historiallisten rakennusten hyödyntämiseksi samalla sekä historiaa että nykyajan tarpeita kunnioittaen
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BRAGA, Rosana Talita. "Priorização espacial para conservação de Carnívoros (Mammalia) no Brasil." Universidade Federal de Goiás, 2012. http://repositorio.bc.ufg.br/tede/handle/tde/2566.
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Previous issue date: 2012-03-02Changes of natural landscape caused by antropic activities are currently the main threats for biodiversity. Thus, the identification of priority areas has become a challenge for conservation biology. The scarcity of financial resources for conservation involves studies for emergency actions, considering important biological aspects, and different components of diversity in order to better allocate the available resources. Furthermore, the costs incorporation of potentially priority areas can display a favorable balance for minimize possible conflicts of interest. Hence, our objectives in this study were to identify priority areas for Carnivore species conservation in Brazil, considering social-economic variables as cost measure for conservation. We also investigate how the taxonomical, functional and phylogenetic diversities of the Carnivore are distributed in the Brazilian territory, in order to identify the set of regions that best represent this three diversity measures. In both cases, we investigate the efficiency of currently established conservation units (CUs), examining whether the current distribution in space of these is better than if they were randomly distributed in Brazil. Our results showed that regions of interest for conservation of species are also important in the social-economical development. Thus, other regions that were not at first priority will be considered important in order to minimize conflicts of conservation. We also found that taxonomic diversity was not the better predictor of functional and phylogenetic diversity. It is necessary the combination of a set of areas to represent these three diversity measures. The UC s are not efficient for all species to represent phylogenetic diversity. In the latter case even the UC s were distributed randomly in Brazilian territory, representing the largest indices of phylogenetic diversity. Thus, it is necessary the addition of new protected areas that complement the previous one. We concluded that it is important to include socio-economic analysis in prioritization, and that studies considering different measures of diversity are important since the species richness may not well represent the other measures of diversity. In conservation plans that incorporate such analysis, the results are more satisfactory for the long-term species protection.
As mudanças da paisagem natural provocadas por atividades antrópicas são atualmente importantes ameaças à biodiversidade. Diante disto, a identificação de áreas prioritárias tem se tornado um desafio para a biologia da conservação. A escassez de recursos financeiros para ações conservacionistas implica em estudos direcionados às ações emergenciais de conservação, que considerem aspectos biológicos importantes e diferentes componentes de diversidade, a fim de estabelecer a melhor possibilidade de alocação dos recursos existentes. Além disto, a incorporação de custos das áreas potencialmente prioritárias pode exibir um balanço favorável para minimizar possíveis conflitos de interesse. Assim, nossos objetivos nesta dissertação foi, indicar áreas prioritárias para conservação de espécies de Carnívoros no Brasil, considerando uma série de variáveis sócio-econômicas (e.g. índice de desenvolvimento humano, demografia urbana, cabeças de gado, dentre outras) como medida de custo para conservação. Também averiguamos como estão distribuídas no território brasileiro, a diversidade taxonômica, funcional e filogenética das espécies deste grupo, a fim de identificar o conjunto de regiões que melhor representam estas três medidas de diversidade. Em ambos os casos, averiguamos a eficiência das Unidades de conservação atualmente instituídas (UC s), analisando se a distribuição atual destas no espaço é melhor do que se tivessem distribuídas ao acaso no Brasil. Nossos resultados mostram que algumas regiões de interesse para conservação de espécies também são importantes no contexto sócioeconômico. Assim, outras regiões que a princípio não eram prioritárias passaram a ser consideradas importantes no intuito de minimizar conflitos de conservação. Encontramos também que a diversidade taxonômica não é um bom preditor de diversidade funcional e filogenética. Assim, é necessária uma combinação de conjunto de áreas para representar estas todas as espécies e as demais medidas de diversidade. As UC s não são eficientes para todas as espécies nem para representar diversidade filogenética. Neste último caso, nem mesmo se as UC s estivessem distribuídas ao acaso no território brasileiro, representariam maiores índices de diversidade filogenética. Sendo assim, é necessário o acréscimo de novas áreas protegidas que complementam as existentes. Concluímos que é importante inserir fatores sócio-economicos nas análises de priorização, e que estudos considerando diferentes medidas de diversidade são importantes pois, a riqueza de espécies pode não representar bem as outras medidas de diversidade. A medida em que os planejamentos de conservação incorporarem análises como estas, os resultados serão mais satisfatórios no que diz respeito a proteção das espécies em longo prazo.
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Rosatti, Natália Bianca. "Perda de originalidade e extinções simuladas de espécies arbustivo-arbóreas de cerrado." Universidade Federal de São Carlos, 2012. https://repositorio.ufscar.br/handle/ufscar/2062.
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Previous issue date: 2012-03-02Universidade Federal de Minas Gerais
Originality measures how different a given species is from all other species regarding either their phylogenetic history or functional traits and may be used to assign conservation priorities. This dissertation is divided into two chapters. In the first chapter, we introduced and defined the phylogenetic and functional originalities, which are still underused. We discussed the advantages of using this approach and showed how it could be used in conservation plans. In the second chapter, we analysed the relationships between phylogenetic, and functional originalities, their relationships with the environment, and their losses under extinction scenarios based on species abundance, fire tolerance, and habitat preference. We placed 100 plots in a cerrado reserve located in central Brazil, sampled all woody plants within the plots, measured 14 functional traits, and measured soil, topography, and fire. We assembled a phylogenetic tree, and a functional dendrogram, with which we calculated the originalities. Phylogenetic- and functional-based originalities were correlated, and both increased towards harsher environments. However, the loss of functional originality was different from random extinctions on the abundance and fire tolerance scenarios, whereas the loss of phylogenetic originality was not. Functional originality seemed to be a better surrogate to be used in conservation strategies, because it was sensitive to differences in species abundances and fire tolerance.
A originalidade mede o quanto uma dada espécie é diferente das outras espécies em uma comunidade com relação à sua história filogenética e aos seus traços funcionais, podendo ser usada para atribuir prioridades de conservação. Este trabalho está dividido em dois capítulos. No primeiro capítulo, nosso objetivo foi introduzir as originalidades filogenética e funcional, medidas ainda pouco conhecidas. Justificamos as razões para o uso dessa abordagem e exemplificamos maneiras de utilizá-la para fins conservacionistas. No segundo capítulo, nosso objetivo foi avaliar a relação entre a originalidade filogenética e a originalidade funcional, a relação de ambas com variáveis ambientais, e suas perdas em cenários de extinções baseados na abundância, tolerância ao fogo e preferência por hábitats, uma maneira objetiva para se tomar decisões com fins conservacionistas. Para isso, em uma reserva de cerrado no Brasil Central, lançamos 100 parcelas, amostramos o componente arbustivoarbóreo e medimos para cada indivíduo 14 traços funcionais. Para cada parcela, coletamos variáveis ambientais de solo, topografia e histórico de fogo. As originalidades filogenética e funcional estiveram correlacionadas, e ambas aumentaram em direção a ambientes mais severos. Entretanto, nas simulações de extinções baseadas na abundância e na tolerância de fogo, a perda de originalidade funcional foi diferente da perda em extinções aleatórias, enquanto que a perda de originalidade filogenética não foi. Originalidade funcional parece ser uma medida mais apropriada para ser utilizada em estratégias de conservação, já que foi sensível a diferença entre as espécies com relação a suas abundâncias e tolerância ao fogo.
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Drucker, Debora Pignatari 1978. "A integração da informação sobre biodiversidade e ecossistemas para embasar políticas de conservação : o projeto Biota Gradiente Funcional como estudo de caso." [s.n.], 2012. http://repositorio.unicamp.br/jspui/handle/REPOSIP/280208.
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Orientadores: Carlos Alfredo Joly, Leila da Costa FerreiraTese (doutorado) - Universidade Estadual de Campinas, Instituto de Filosofia e Ciências Humanas
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Resumo: No Brasil, há numerosas instituições e cientistas que produzem conhecimento sobre nossos ecossistemas e muito já se sabe sobre nossa diversidade biológica. Novas descobertas e orientações para a tomada de decisão baseadas em conhecimento científico podem ser feitas pelo uso da informação que já existe, mas que em grande parte está dispersa, mal documentada e inacessível aos interessados. Uma integração é, portanto, necessária e pode ocorrer tanto por meio da consolidação de dados de estudos semelhantes, de forma a expandir escalas temporais e espaciais de análise, como pela associação de conhecimentos gerados por estudos com diferentes abordagens. Novas tecnologias computacionais que permitem lidar com informações de procedência diversa e características heterogêneas podem contribuir para representar o estado atual do conhecimento do sistema terrestre e para comunicar esse conhecimento entre os diversos atores interessados. Nessa direção, os objetivos deste estudo foram analisar o sistema de informação desenvolvido para o Projeto Temático Biota Gradiente Funcional, como estudo de caso para a integração de dados ecológicos e de biodiversidade, e também discutir as aplicações e limitações desse sistema para a conservação e gestão ambiental. Para isso, proponho um arcabouço para investigar uma infraestrutura de informação sobre biodiversidade e discuto o potencial dessa infraestrutura como objeto-ponte entre ciência e processos de tomada de decisão em conservação e gestão ambiental; analiso também as características de dados ecológicos, boas práticas para documentá-los e algumas ferramentas existentes para gerenciá-los, de forma a promover a integração do conhecimento ecológico, descrevo as etapas de desenvolvimento do sistema de informação para o Projeto Temático Biota e o analiso pelas lentes do arcabouço de investigação proposto. O sistema foi eficiente para gerenciar os dados e metadados do Projeto fornecidos pelos pesquisadores. Foi possível recuperar a informação por consultas integradas tanto ao catálogo de metadados, pelo uso de palavras-chave, quanto à base de dados, pela seleção de variáveis e de parâmetros temporais e espaciais. A possibilidade de consultar qualquer variável de interesse, independentemente da associação com uma entidade taxonômica, configura um sistema de informação sobre biodiversidade original e inovador. No sistema estudado, a base de dados é verdadeiramente genérica: a única restrição é a exigência da informação espacial. Os resultados permitiram concluir que avanços em ferramentas computacionais para gerenciar dados de biodiversidade e ecossistemas permitem análises que potencializam o valor de dados coletados em pesquisas individuais. Para perpetuar iniciativas de desenvolvimento tecnológico, como a do sistema aqui investigado, é necessário empreender mais esforços, no sentido de se promoverem os arranjos institucionais, legislativos e administrativos que atuam como alicerces da infraestrutura da informação e conferem sustentabilidade dos sistemas a médio e longo prazo. Além disso, é preciso capacitar recursos humanos no uso e desenvolvimento desses recursos tecnológicos e promover a sensibilização dos atores envolvidos, a fim de tornar o compartilhamento e a curadoria de dados uma prática amplamente realizada
Abstract: There are numerous scientists and institutions that produce knowledge about Brazilian ecosystems, and a lot is already known about the biological diversity therein. New findings and guidelines for decision making based on scientific knowledge can be made by using information that already exists, but is largely dispersed, poorly documented and inaccessible to users. It is therefore necessary to integrate biodiversity information, which may occur by consolidating data from similar studies in order to expand temporal and spatial analysis scales, or by associating knowledge generated by studies with different approaches. New computer technologies are continuously developed by information scientists, providing opportunities for the Biodiversity Informatics field to improve its capacity of making sense of the growing amount of heterogeneous data of diverse provenance, thus contributing to represent the current state of knowledge on the Earth's Systems and to communicate this knowledge among the various stakeholders. This study aimed at analyzing the information system developed for the Thematic Project Biota Functional Gradient as a case study on biodiversity and ecological data integration, and at discussing the applications and limitations of this system for conservation and environmental management. To this end, I propose a framework for investigating biodiversity information infrastructures and discuss their potential as boundary objects between science and decision making in conservation and environmental management; analyze the characteristics of ecological data, the best practices to document them and some existing tools to manage them in order to promote the integration of ecological knowledge; describe the stages of development of the information system for the Thematic Project Biota and discuss it through the lens of the proposed analytical framework. The information system was efficient to manage data and metadata provided by researchers. Information retrieval was possible by querying the metadata catalog based on keywords, and by querying the database system based on the selection of variables and parameters of space and time. The ability to query any variable of interest, regardless of association with a taxonomic entity, set up an original and innovative information system on biodiversity. In the studied system, the database is truly generic: the only restriction is the mandatory requirement for spatial information. The results showed that advances on computational tools for managing biodiversity and ecosystem data enable analyses that maximize the value of data collected in individual surveys. To perpetuate technological development initiatives such as the system investigated here, it is necessary to undertake further efforts in order to promote institutional arrangements, legislation and administration that act as foundations for information infrastructures and provide sustainability over time. Furthermore, it is necessary to train human resources in the use and development of technological tools, and to promote awareness and a collaborative culture between the actors involved in order to make data sharing and curation widely adopted practices
Doutorado
Aspectos Biológicos de Sustentabilidade e Conservação
Doutor em Ambiente e Sociedade
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Boreau, de Roincé Catherine. "Biodiversité et aménagements fonctionnels en verger de pommiers : Implication des prédateurs généralistes vertébrés et invertébrés dans le contrôle des ravageurs." Phd thesis, AgroParisTech, 2012. http://pastel.archives-ouvertes.fr/pastel-00952799.
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L'intérêt des prédateurs généralistes dans la lutte biologique par conservation est peu étudié en verger de pommiers. Cette thèse visait à déterminer le rôle de prédateurs généralistes invertébrés (principalement carabes et araignées) et vertébrés (mésanges et chauves souris) dans le contrôle de trois ravageurs clés du pommier et de définir les éléments paysagers qui leur sont favorables. Pour cela, nous avons effectué des suivis de populations dans des vergers en agriculture biologique et nous les avons associés à des mesures de prédation des ravageurs par analyse moléculaire des contenus stomacaux et faeces des prédateurs à l'aide d'amorces spécifiques développées à cet effet. Nous montrons que les ravageurs sont consommés dès leur apparition dans les vergers, notamment les pucerons par les araignées de la frondaison, ce qui suggère que ces prédateurs ont un potentiel de régulation important. De plus une complémentarité temporelle semble exister entre araignées et carabes dans le contrôle des tordeuses. L'influence des éléments paysagers intra et extra verger diffère selon les taxa de prédateurs considérés. Ce dernier résultat suggère des compromis dans les aménagements à réaliser pour favoriser leur action et la nécessité d'une meilleure compréhension de leur écologie.
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Lin, Yangchen. "Macroscopic insights from mechanistic ecological network models in a data void." Thesis, University of Cambridge, 2015. https://www.repository.cam.ac.uk/handle/1810/254976.
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Complexity science has come into the limelight in recent years as the scientific community begins to grapple with higher-order natural phenomena that cannot be fully explained via the behaviour of components at lower levels of organization. Network modeling and analysis, being a powerful tool that can capture the interconnections that embody complex behaviour, has therefore been at the forefront of complexity science. In ecology, the network paradigm is relatively young and there remain limitations in many ecological network studies, such as modeling only one type of species interaction at a time, lack of realistic network structure, or non-inclusion of community dynamics and environmental stochasticity. I introduce bioenergetic network models that bring together for the first time many of the fundamental structures and mechanisms of species interactions present in real ecological communities. I then use these models to address some outstanding questions that are relevant to understanding ecological networks at the systems level rather than at the level of subsets of interactions. Firstly, I find that realistic red-shifted environmental noise, and synchrony of species responses to noise, are associated with increased variability in ecosystem properties, with implications for predictive ecological modeling which usually assumes white noise. Next, I look at simultaneous species extinction and invasion, finding that as their individual impacts increase, their combined impact becomes decreasingly additive. In addition, the greater the impact of extinction or invasion, the lesser their reversibility via reintroduction or eradication of the species in question. For modifications of pairwise species interactions by third-party species, a phenomenon that has so far been studied one interaction at a time, I find that the many interaction modifications that occur concurrently in a community can collectively have systematic effects on total biomass and species evenness. Finally, examining a higher level of organization in the form of compartmentalized networks, I find that the relationship between intercompartment connectivity and the impacts of species decline depends considerably on network topology and whether the consumer-resource functional response is prey- or ratio-dependent. Overall, the results vary considerably across model communities with different parameterizations, underscoring the contingency and context dependence of nature that scientists and policy makers alike should no longer ignore. This work hopes to contribute to a growing multidisciplinary understanding, appreciation and management of complex systems that is fundamentally transforming the modern world and giving us insights on how to live more harmoniously within our environment.
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Sonja, Trifunov. "Gazdovanje šumama u zaštićenim područjima u Srbiji i realizacija konzervacionih ciljeva." Phd thesis, Univerzitet u Novom Sadu, Prirodno-matematički fakultet u Novom Sadu, 2019. https://www.cris.uns.ac.rs/record.jsf?recordId=111015&source=NDLTD&language=en.
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U radu je analizirano gazdovanje šumama u zaštićenim područjima u Srbiji,posmatrajući: 1) ekološke efekte gazdovanja, i 2) procese prilagođavanja gazdovanja konzervacionim potrebama. Površina zaštićenih područja je značajno porasla, ali ima malo informacija o njihovom doprinosu u realizaciji konzervacionih ciljeva. Pošto se u većini zaštićenih šumskih područja u Evropi aktivno gazduje, i dozvoljeno je korišćenje drvne biomase, informacije o efektima gazdovanja su neophodne. Glavna barijera u ekološkim evaluacijama gazdovanja je nepostojanje indikatora kojima bi se mogle izmeriti promene u ekosistemu, a koje nastaju kao rezultat primenjenih mera gazdovanja. Poslednjih godina se sve više ističe potencijal primene funkcionalnih indikatora, tj. indikatora koji se oslanjaju na informacije o funkcionalnim karakteristikama vrsta. U radu je stoga primenjen funkcionalni pristup za analizu ekološkog efekta gazdovanja. U te svrhe su odabrane karakteristike koje se povezuju sa sposobnošću vrsta za brzousvajanje ili konzervisanje resursa, tj. određuju odgovor vrsta na promene u dostupnim resursima, a koje, na primer, nastaju usled uklanjanja drvne biomase: visina, specifična površina lista, sadržaj suve materije lista, sadržaj ukupnog azota i ukupnog fosfora. Iste se dovode i u vezu sa primarnom produktivnošću i dekompozicijom, procesima od značaja za očuvanje integriteta ekosistema. Pošto analiza odgovora funkcionalnih indikatora zahteva duži vremenski period posmatranja, u radu je osmišljen drugačiji pristup za izvođenje eksperimenta. U te svrhe su iskorišćeni Landsat satelitski snimci, tj. tri snimka sa vremenskim razmakom od 10 godina: 1994., 2005. i 2015. godina. Izvršena je digitalna klasifikacija snimaka prema sastavu šuma, nakon čega su detektovane promene u sastavu šuma za period od ukupno 20 godina. Ovi podaci su spojeni sa podacima o funkcionalnim karakteristikama vrsta, kako bi se utvrdile promene u funkcionalnoj kompoziciji. Poslednji korak je bio formiranje modela šumske krune, kroz koji je određen intenzitet seče. Koristeći podatke o promenama u gustini krune ipromenama u funkcionalnoj kompoziciji, sproveden je eksperiment, tj. analiza efekta različitih nivoa intenziteta seče na promene u funkcionisanju šumskog ekosistema. Za sprovođenje ovog eksperimenta je odabran samo jedan deo Fruške gore, jer je cilj bio da se osmisli pristup za evaluaciju, prilagođen trenutnom konceptu gazdovan ja zaštićenim šumskim područjima, i ispita njegova praktičnost. Kao propratni podatak ovoj analizi, sprovedena je i komparativna analiza upravljača zaštićenih šumskih područja u Srbiji, kako bi se ispitao nivo ulaganja u konzervacione sposobnosti, kao ključnog procesa u implementaciji konzervacionih ciljeva. U digitalnoj klasifikaciji je postignuta visokapreciznost, sa ukupnom preciznošću 94,5% i Kapa koeficijentom 0,93. Potpuno spektralno razdvajanje je postignuto samo za Q. petraea od Tilia tomentosa, i sastojina ukojima se kao dominantne pojavljuju F. silvatica i Tilia tomentosa. Utvđeno je prodiranje F. moesiaca u šume Q. petraea, i apsolutno širenje vrste Tilia tomentosa, posebno u periodu nakon 2005. godine, a koja prema podacima o karakteristikama vrsta ima najveću kompetetivnu sposobnost u odnosu na druge ispitivane vrste drveća. Rezultati modela gustine krune ukazuju na postepeno proređivanje šume od 1994. ka 2015. godini, sa potpunim nestankom šuma guste krune na prelazu između 1994. i 2005. godine. Utvrđen je značajan efekat proređivanja šume na promene u funkcionalnoj kompoziciji. Sa višim intenzitetom proređivanja, CWM indikator se pomerio od konzervativnih karakteristika ka onima koje ukazuju na dominaciju vrsta sklonih brzom sticanju resursa. Prelaz koji je imao značajnog efekta na promene je prelaz iz šume sa gustinom krune većom od 65% u šumu gustine krune između 50-65%, a što bi moglo ukazivati i na prelaz u drugi režim funkcionisanja ekosistema. Konzervacioni ciljevi su još uvek slabo integrisani u gazdovanje šumama u zaštićenim područjima.In this work, the forest management in protected areas of Serbia was analysed, following: 1) ecologic effects of management and 2) investments in capabilities essential for integration of conservation objectives. The size of protected areas has significantly grown, but there is a little information on their contribution to real conservation goals. Since in most of European protected forest areas is employed active management, the information on ecological effects of management is necessary. The main barrier in ecologic evaluations of managing is the absence of indicators, which could measure the changes in ecosystem, resulting from applied measures. Recently, the potentiality of functional indicators is more emphasized, i.e. indicators, which lean on information about functional traits of species. So, in this work functional approach was taken to analyse ecologic effects of forest management. For this sake were chosen characteristics, which are connected to capabilities of specie s to acquire or conserve resources, i.e. define the answer of the species on changes in available resources, caused by elimination of wooden mass, i.e. logging: height, specific leaf area, leaf dry matter cont ent, nitrogen content and phosphorus content. The same are connected to the processes of significance for conservation of ecosystem integrity (net primary productivity and decomposition). Since the analysis of functional indicators response demands a longer period of observation, another attitude of performing the experiment was conceptualized. For that purpose Landsat satellite image was used, i.e. three images in interval of ten years: 1994, 2005, and 2015. A digital image classification of forest composition was performed, after which the changes in forest composition were detected over the period of 20 years. These data were then connected with the data on functional characteristics of species to determine changes in functional composition. The last step was forming of forest canopy density model, through which was determined the intensity of logging. Using data on changes of forest canopy density model and changes in functional composition, an experiment was performed, i.e. analysis of effects of different levels of logging intensity on changes in forest ecosystem function. For the performing of this experiment was chosen just a part of Fruska gora, as the goal was to try to construct the evaluation approach, adapted to momentary concept of managing in protected forest areas and inspect its feasibility. As an accompanying data with this analysis was performed a comparative analysis of protected forest area managers in Serbia, to examine the level of investments in conservation capabilities, as the key process in implementing conservation goals.
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Lizée, Marie-Hélène. "Diversité, organisation spatiale et fonctionnelle des communautés de papillons (lépidoptères, rhopalocères) en milieu urbain et périurbain : Rôle des espaces artificialisés en terme de conservation et de connectivité." Thesis, Aix-Marseille 1, 2011. http://www.theses.fr/2011AIX10153.
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Au regard de la variété d’enjeux (économiques, sociétaux et environnementaux) que recouvrent les espaces de nature soumis au développement humain, il apparait urgent de comprendre les déterminants de leur fonctionnement. En effet, même si elles ne constituent pas des lieux prioritaires de conservation pour les espèces rares et menacées, les zones urbanisées sont loin d’être dépourvues de biodiversité. Cependant, cette biodiversité et les processus écologiques en œuvre demeurent mal connus. Il s’agit ici d’utiliser les communautés de Rhopalocères (papillons de jour) comme grille de lecture des paysages urbains et périurbains. A partir de l’étude des communautés de papillons (et accessoirement d’oiseaux) en région PACA, l’objectif principal de ce travail est ainsi de mettre en évidence les patrons d’organisation de ces communautés afin comprendre les facteurs conditionnant les assemblages d’espèces en milieu urbain et périurbain. Situé en région méditerranéenne qui constitue un espace original d’un point de vue biogéographique, ce travail a porté sur des terrains d’étude permettant d’aborder deux expressions différentes du processus d’urbanisation touchant le territoire provençal : (i) le village de Lauris (84), caractéristique d’un arrière-pays méditerranéen « en voie de métropolisation » ; et (ii) l’agglomération marseillaise (13), 2ème ville la plus peuplée de France. A partir de l’analyse des assemblages d’espèces de quatre habitats (friches, jardins privés, vignes, forêts), les travaux menés sur la commune de Lauris se sont intéressés à la réponse des communautés de Rhopalocères face aux changements de la disponibilité en habitats dans une mosaïque paysagère en mutation. Les résultats ont ainsi révélé des variations en termes de structure et de composition fonctionnelle, soulignant tant l’influence du contexte paysager que du type d’habitat sur l’organisation de ces communautés. Cette étude a également soulevé l’intérêt du compartiment jardin en tant que réservoir de biodiversité. Les travaux ont ensuite été orientés sur la question de la biodiversité hébergée par les espaces artificialisés en ville. Pour cela 24 parcs publics de la ville de Marseille ont été étudiés. Il a été possible de démontrer comment les traits fonctionnels des espèces (papillons et oiseaux) permettaient de prédire leur répartition le long d’un gradient d’urbanisation. Les différents travaux menés sur l’agglomération marseillaise ont également révélé l’importance de l’échelle paysagère et des dynamiques spatiales régionales (dispersion et colonisation) sur l’organisation des assemblages d’espèces. Les communautés de Rhopalocères apparaissent fortement conditionnées par le degré d’isolement des parcs vis-à-vis des massifs semi-naturels, soulevant l’idée d’une alimentation des assemblages intra-urbains par un pool d’espèces régional situé en périphérie. Cette hypothèse est d’ailleurs appuyée par la distribution imbriquée des espèces (nested subsets) entre les parcs, où les sites les plus pauvres en termes de composition spécifique constituent des sous-échantillons des sites les plus riches, sans que cela ne soit relié à l’existence d’une relation aire-espèce significative. Enfin, l’étude de l’aménagement des parcs et de leur gestion a permis de souligner l’effet d’interactions plus locales sur l’organisation des communautés. Cependant, le contexte paysager semble fortement conditionner la composante végétale autour, mais aussi dans les parcs, notamment par le biais de sa gestion par les services municipauxGiven the wide range of issues (economic, social and environmental) that are concerned by natural environments under the impact of human development, it is a matter of urgency to understand the factors that determine their functioning. Even if they do not constitute priority areas for the conservation for rare and endangered species, urban areas are by no means devoid of biodiversity. This biodiversity and the ecological processes involved remain poorly known.The approach here is to use the communities of Rhopaloceres (butterflies) as a framework for reading the urban and outlying suburban landscapes. On the basis of a study of butterfly communities (and secondarily those of birds) in the PACA (Provence Alpes Côte d’Azur) region, the main aim of this study is to provide evidence of the patterns of organisation of these communities in order to understand the factors that control the assemblages of species in the urban and outlying suburban environment.Focused on the Mediterranean area, which constitutes an original site from the biogerographical point of view, this investigation has focused on two study sites in order to offer two different expressions of the process of urban development affecting the territory of Provence: (i) the village of Lauris (84), characteristic of a Mediterranean hinterland ‘in the process of metropolisation’; and (ii) the Marseille conurbation (13), the 2nd most populous city in France.On the basis of an analysis of the assemblages of species of four habitats (fallow land, private gardens, vineyards, forests), the investigations carried out in Lauris are focused on the response of the communities of Rhopaloceres in the face of rapid changes in land use. The results provide evidence of variations in terms of structure and functional composition, underlining the influence both of the landscape context and of the type of habitat on the organisation of these communities. This study also highlights the interest of the garden compartment as a reservoir of biodiversity.Then, the investigation has focused on the question of the biodiversity accommodated in the man-made areas of the city. To this end, 24 public parks in the city of Marseille have been studied. It has been possible to show how the functional traits of species (butterflies and birds) can be used to predict their distribution along a gradient of urban development. The various studies carried out on Marseille have also shown the importance of the landscape scale and of the regional spatial dynamic (dispersal and colonisation) with regard to the organisation of assemblages of species. The communities of Rhopaloceres appear to be strongly conditioned by the degree of isolation of parks with regard to the semi-natural massifs, raising the idea of the strengthening of the intra-urban assemblages by a regional pool of species situated around the outskirts. This hypothesis is further supported by the overlapping pattern of distribution of the species (nested subsets) between the parks, where the poorest sites in terms of species composition constitute sub-samples of the richest sites, without this being linked to the existence of a significant species-area relationship. Finally, the study of the development of parks and their management has enabled us to highlight the impact of more local interactions on the organisation of the communities. Nevertheless, the landscape context would appear to strongly condition the plant component in the surroundings, but also in the parks, in particular via the management practices of the municipal departments
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Tambosi, Leandro Reverberi. "Estratégias espaciais baseadas em ecologia de paisagens para a otimização dos esforços de restauração." Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/41/41134/tde-29052014-112453/.
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Os efeitos deletérios da perda e fragmentação de habitat são considerados a maior ameaça à manutenção da biodiversidade do planeta. Uma das maneiras de evitar a perda de espécies em paisagens fragmentadas é a restauração ecológica, que propicia tanto o aumento da quantidade quanto a melhoria da qualidade do habitat remanescente. Além de influenciar a persistência de espécies, as condições da paisagem são reconhecidas como importantes para o sucesso das ações de restauração. Entretanto, as diretrizes para incorporação das características da paisagem no planejamento da restauração são ainda ambíguas, não facilitando o processo de tomada de decisão. O presente trabalho teve como objetivo contribuir para o avanço do uso de análises espacialmente explícitas da estrutura da paisagem para o planejamento de ações de restauração. Para isso, foram elaboradas propostas metodológicas embasadas no atual conhecimento da ecologia de paisagens e foram realizadas simulações para comparar os potenciais benefícios para a biodiversidade resultantes de diferentes estratégias para seleção de áreas para restauração. A primeira proposta, apresentada no capítulo 2, utiliza análises de paisagens em múltiplas escalas, baseadas na teoria dos grafos, para estimar a resiliência das paisagens, entendida neste trabalho como a capacidade das paisagens de reverterem extinções locais por processos de migração. Em seguida, as paisagens com condições ideais para restauração são classificadas segundo sua importância como corredores biológicos e gargalos de conectividade. Essa proposta metodológica é aplicada no caso da Mata Atlântica (capítulo 3), a fim de estabelecer diferentes níveis de prioridade para restauração no conjunto deste bioma. No quarto capítulo, é apresentada uma segunda proposta metodológica, também baseada em análises de conectividade com o uso da teoria dos grafos, mas desta vez voltada para a identificação de áreas prioritárias para restauração em escala local. Essa proposta permite ainda a comparação de prioridades entre áreas situadas em paisagens com diferentes condições de cobertura e conectividade de habitat. Por fim, no quinto capítulo, foi realizado um conjunto de simulações de restauração para comparar os efeitos das características da paisagem (e.g. a cobertura e configuração florestal), das espécies (e.g. a capacidade de dispersão) e da estratégia de restauração (e.g. o tamanho das áreas restauradas e a ordem temporal da restauração) no aumento da disponibilidade de habitat em três paisagens reais da Mata Atlântica. Os resultados desta tese permitiram estabelecer prioridades de restauração tanto em escala regional quanto em escala local, reduzindo as áreas a serem visitadas em campo e possibilitando a otimização dos esforços de restauração. Também foi possível concluir que a adoção de estratégias espaciais para a seleção de áreas para restauração deve ser feita considerando tanto as características das espécies quanto as características das paisagens e a forma de implementação da restauração. Na ausência de informações detalhadas sobre a capacidade de dispersão das espécies, abordagens baseadas em múltiplas capacidades de dispersão são recomendadas. O embasamento teórico da ecologia de paisagens e as ferramentas atuais de tratamento e integração de dados espacializados permitem a definição das melhores estratégias de restauração a partir de simulações em computador, reduzindo substancialmente os custos da restauração e aumentando a sua eficácia para a conservação das espécies em paisagens fragmentadasThe deleterious effects of habitat loss and fragmentation are considered the main threats to biodiversity. To avoid species loss due to these deleterious effects, there is an urgent need to conduct restoration actions to increase the quantity and quality of the remaining habitat. Besides influencing species persistence, the landscape structure also influences the results of restoration actions. However, guidelines to adopt a landscape approach during restoration planning are not always consistent, nor easy to apply. The objective of this study was to contribute to advances in the use of spatially explicit landscape analysis during restoration planning. To achieve this goal we developed methodological frameworks based on landscape ecology theory to set priority areas for restoration. We also adopted a simulation approach to analyze the potential benefits of different restoration strategies for biodiversity conservation. The methodological proposal presented in chapter 2 consists in multi-scale landscape analyses, based on graph theory, to estimate landscape resilience. We considered landscape resilience as the capacity to revert local species extinctions through recolonization processes. Then, those landscapes considered ideal targets to restoration actions were classified according to their importance as corridors or bottlenecks for biological flow. In chapter 3, the methodological proposal presented in chapter 2 was applied to the Atlantic Forest Biome to set restoration priorities. Chapter 4 consists in a methodological proposal, also based on graph theory, to set restoration priorities in local scale. This methodological proposal also allows the comparison of local restoration priority between landscapes with different amount and configuration of habitat cover. Finally, in the fith chapter we adopted a simulation approach to analyze the improvement of habitat availability, in three Atlantic Forest landscapes, due to different restoration strategies considering: (i) different species dispersal capabilities, (ii) initial habitat amount in the landscape, (iii) the dynamics of landscapes during restoration implementation, i.e., the changes in habitat availability as new areas were restored, and (iv) size of restored areas. The results of this study allowed us to establish local and regional restoration priorities, thus reducing field visits and optimizing restoration efforts. It was also possible to conclude that spatial strategies to set restoration priorities should be conceived based on species dispersal capacities, landscape structure and also considering the strategies to implement restoration actions. If data on species dispersal characteristics is not available, a multi species approach to set restoration priorities is also recommended. The theoretical background of landscape ecology and the available tools to manage spatial data allow identifying the best restoration strategies, reducing the costs and optimizing the benefits to conserve biodiversity in fragmented landscapes
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Auffret, Alistair G. "Seed mobility and connectivity in changing rural landscapes." Doctoral thesis, Stockholms universitet, Institutionen för naturgeografi och kvartärgeologi (INK), 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-89105.
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The success or failure of many organisms to respond to the challenges of habitat destruction and a warming climate lies in the ability of plant species to disperse between isolated habitats or to migrate to new ranges. European semi-natural grasslands represent one of the world's most species-rich habitats at small scales, but agricultural intensification during the 20th century has meant that many plant species are left only on small fragments of former habitat. It is important that these plants can disperse, both for the maintenance of existing populations, and for the colonisation of target species to restored grasslands. This thesis investigates the ecological, geographical and historical influences on seed dispersal and connectivity in semi-natural grasslands, and the mobility of plants through time and space. Seed dispersal by human activity has played a large role in the build-up of plant communities in rural landscapes, but patterns have shifted. Livestock are the most traditional, and probably the most capable seed dispersal vector in the landscape, but other dispersal methods may also be effective. Motor vehicles disperse seeds with similar traits to those dispersed by livestock, while 39% of valuable grasslands in southern Sweden are connected by the road network. Humans are found to disperse around one-third of available grassland species, including several protected and red-listed species, indicating that humans may have been valuable seed dispersers in the past when rural populations were larger. Past activities can also affect seed mobility in time through the seed bank, as seeds of grassland plant species are shown to remain in the soil even after the grassland had been abandoned. Today however, low seed rain in intensively grazed semi-natural grasslands indicates that seed production may be a limiting factor in allowing seeds to be dispersed in space through the landscape.At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Accepted. Paper 4: In press. Paper 5: Manuscript.
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Hidasi, Neto José. "Conservação de diversidade funcional e filogenética: identificando padrões e definindo prioridades." Universidade Federal de Goiás, 2014. http://repositorio.bc.ufg.br/tede/handle/tede/4048.
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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES
(Sem resumo em outra língua)
Listas Vermelhas de espécies ameaçadas categorizam os organismos vivos de acordo com a proximidade de serem extintos. Entretanto, essas listas ignoram diferenças ecológicas e evolutivas entre as espécies. Para determinar se ações conservacionistas baseadas em LV são efetivas para a proteção da diversidade funcional (FD, do inglês “functional diversity) e filogenética (PD, do inglês “phylogenetic diversity”) de comunidades naturais precisamos saber se categorias de ameaça das LV possuem espécies com atributos ecológicos e histórias evolutivas distintas. Além disso, como espécies normalmente interagem em escala local, essa escala seria a mais indicada para quantificar perdas consideráveis de FD e PD. Sendo assim, no Capítulo 1, utilizamos 21 características ecológicas e as relações filogenéticas para todas as aves do Brasil a fim de determinar se espécies em categorias de ameaça das Listas Vermelhas global da IUCN, brasileira, e de seis estados brasileiros representam perdas maiores de FD e PD do que seria esperado pela extinção aleatória de aves. Analisamos a eficiência das listas vermelhas em escala nacional, regional e local, esperando que a FD e PD de aves fosse melhor representada na escala local, pois é nela onde ocorrem as interações bióticas. Encontramos que, independente da escala, as categorias de ameaça das Listas Vermelhas capturaram, de maneira geral, perdas de FD e PD iguais ou menores ao esperado ao acaso. Portanto, ações conservacionistas baseadas somente nas categorias das Listas Vermelhas não protegem mais FD e PD das aves brasileiras do que se o mesmo número de espécies (em cada categoria) fosse preservado ao acaso. No capítulo 2, sugerimos uma forma de integrar o grau de ameaça, atributos ecológicos e história evolutiva para medir o nível de prioridade de conservação de espécies. Utilizamos esse protocolo para medir a prioridade de conservação dos mamíferos do mundo. De modo geral, espécies mais prioritárias tenderam a ser mais ameaçadas, além de estarem concentradas nas regiões de alguns hotspots de biodiversidade, como o Cerrado, Indo-Burma, Mata Atântica e Sundaland. Esses resultados possuem grandes consequências na conservação de espécies pois categorias de LV são normalmente utilizadas como ferramentas para a formulação de políticas relacionadas à conservação da biodiversidade
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Lechêne, Alain. "Trajectoire de restauration des marais intertidaux : réponse du necton à la dépoldérisation dans l’estuaire de la Gironde." Thesis, Bordeaux, 2017. http://www.theses.fr/2017BORD0883/document.
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Dégradés par plusieurs siècles d’endiguement et menacés par les effets du changement climatique, les marais intertidaux européens font aujourd’hui l’objet d’un nombre croissant de restaurations par rétablissement des marées sur d’anciennes zones endiguées, suivant une tendance générale appelée dépoldérisation. Cette thèse décrit la trajectoire de restauration des marais intertidaux à partir des communautés de necton (i.e., poissons et crustacés décapodes), sur la base de deux sites dépoldérisés accidentellement dans l’estuaire de la Gironde : le marais de Mortagne et l’île Nouvelle. L’évolution du necton dans les marais dépoldérisés est caractérisée à travers une approche synchronique à l’échelle de la mosaïque des habitats estuariens. La composition du necton dans les marais dépoldérisés est en grande partie similaire à celles des milieux intertidaux naturels et se différencie nette-ment des marais endigués, où les espèces exotiques d’eau douce prospèrent. Les marais restaurés apparaissent particulièrement attractifs pour le mulet porc, Liza ramada. La distribution des traits fonctionnels au sein des communautés de poissons révèle un changement de structure fonctionnelle au cours de la dépoldérisation, le temps de restauration étant inféré à partir d’un gradient de naturalité des habitats estuariens. En particulier, la spécialisation, la dispersion et la richesse fonctionnelle augmentent au cours de la restauration. Concernant l’évolution des règles d’assemblage, aucune tendance claire ne se dégage : les patrons diffèrent selon les traits fonctionnels.La dynamique temporelle de la composition des communautés de necton dans l’un des sites dépoldérisés montre une succession de trois phases au cours des quatre années suivant la restauration. Un changement plus abrupt concernant l’abondance de certaines espèces et la structure fonctionnelle des communautés est identifié au milieude la seconde phase, moins de deux ans après la dépoldérisation. La cinétique de transformation des communautés est probablement ralentie par le drainage incomplet du site dans les premiers temps de la dépoldérisation. Les résultats de cette thèse permettent de mieux comprendre la trajectoire de restauration des marais intertidaux, sans intervention humaine, tout en soulignant les atouts et les limites de certains modèles théoriques utilisés en écologie de la restaurationEuropean intertidal marshes have greatly declined during the past centuries because of land claim andhave recently been threatened by the effects of climate change. In recent years, an increasing number of tidal resto-ration projects have been implemented, following a global trend termed de-embankment. This thesis describes therestoration trajectory of tidally restored marshes from the response of nekton (i.e., fish and decapod crustaceans)based on two storm-breached study sites in the Gironde estuary : the Mortagne marsh and the Nouvelle island.Nekton assemblage composition of tidally restored marshes was described through a whole-estuary approach en-compassing natural, restored and dyked habitats. Nekton assemblages of tidally restored marshes showed highcompositional similarity with natural intertidal habitats and greatly departed from dyked marshes. Dyked marsheswere characterized by high occurrence of freshwater exotic taxa. Tidally restored marshes seemed particularly at-tractive for the thin-lipped grey mullet, Liza ramada. The functional traits’ distribution within fish communities revealeda change in functional structure in the course of restoration using the naturalness state of habitats as a proxy forrestoration time. Most notably, functional specialization, dispersion and richness increased with restoration time.No clear pattern of change was observed in community assembly over time ; trends chiefly varied with respect totraits. Temporal trends in one of the restored sites revealed three phases in the first four years of tide restoration.The abundance of several species and the community functional structure changed more steeply in the midst ofthe second phase, less than two years following tide restoration. Community turnover was probably delayed dueto incomplete drainage of the site in the early stages of restoration. The results of this thesis lead to a better un-derstanding of the restoration trajectory of tidal marshes without human intervention and highlight the strengths andweaknesses of some theoretical models used in restoration ecology