Our goal is to investigate protein networks conserved between different organisms. Given the protein interaction networks for two species and a list of homologous pairs of protein in the two species, we propose a model for measuring whether two subnetworks, one in each protein interaction network, are conserved. Our model separately measures the degree of conservation of the two subnetworks and the quality of the edges in each subnetwork. We propose an algorithm for finding pairs of networks, one in each protein interaction network, with high conservation and high quality. When applied to publicly-available protein-protein interaction data and gene sequences for baker's yeast and fruit fly, our algorithm finds many conserved networks with a high degree of functional enrichment. Using our method, we find many conserved protein interaction networks involved in functions such as DNA replication, protein folding, response to heat, protein serine/threonine phosphatase activity, kinase activity, and ATPase activity. / Master of Science

Neurons have an extremely high rate of energy consumption and use mitochondrial-derived ATP as the primary energy source to drive biochemical processes involved in various functions. Consequently, neurons produce reactive oxygen species (ROS) as 'by-products' of oxidative phosphorylation. Excessive levels of ROS are highly detrimental to neurons as ROS can directly oxidize and induce damage to cellular macromolecules including lipids, DNA and proteins. Hence, the high-energy demands of neurons, together with their high levels of ROS production, place them at risk during conditions of stress, which occur during aging and in neurodegenerative disorders including Alzheimer's and Huntington's disease. Uncoupling proteins (UCPs) belong to a family of inner mitochondrial membrane proteins initially identified as regulators of thermogenesis in fat cells wherein they uncouple energy-substrate oxidation from mitochondrial ATP production, resulting in the production of heat. UCPs also regulate ROS production from mitochondria by physiologically lowering the mitochondrial membrane potential below the critical level for ROS production. Because of their important role in co-regulating energy metabolism and ROS production, there has been considerable interest in the functions of UCPs. Neurons express at least three UCPs including the widely expressed UCP2 and the brain- specific UCP4 and UCP5. Despite a great deal of interest, to date neither the molecular mechanism nor the biochemical and physiological functions of brain UCPs are well understood. Our previous studies showed that UCP4 is highly expressed in subpopulations of neurons with high energy demands. Knockdown ofUCP4 expression in cultured primary neurons markedly enhances neuronal death suggesting that endogenous UCP4 is critical for neuronal survival. Expression of UCP4 shifts cellular ATP synthesis from oxidative phosphorylation to anaerobic glycolysis, which might be beneficial to cell survival. In this study, we investigated the underlying mechanism of UCP4-mediated metabolic adaptation in response to mitochondrial inhibition. We found that UCP4 enhances glucose uptake and glycolysis which may compensate for the reduced supply of ATP from compromised mitochondria. In addition, the activation of mitogen activated protein kinases (MAPKs) and several transcription factors play a role in augmenting nonoxidative synthesis of ATP in response to metabolic stress possibly by acting downstream of UCP4. Elucidating the underlying mechanism(s) whereby this brain UCP mediates metabolic adaptation in response to mitochondrial inhibition will likely lead to the development of novel preventative and therapeutic strategies for neurodegenerative disorders.

The Caretta caretta, or Loggerhead sea turtle, is a protected species found across all temperate and subtropical oceans. Previous research has identified that the Caretta caretta has preferences for nesting sites based on beach width, beach slope, and vegetation coverage, which facilitated the development of a nesting site suitability index. In this thesis, these indices were integrated with standard coastal geomorphology metrics in the ESRI Suitability Modeler to pinpoint potential nesting locations for the C. caretta on various beach reaches. The results were then validated against observed nesting site data. The results of this study can inform critical decisions regarding beach use and maintenance as it pertains to sea turtle conservation. Overall, this study demonstrates the utility of geospatial analysis and suitability models in understanding and safeguarding sea turtle nesting habitats.

This dissertation consists of three essays, of which, two involve assessing the value of tree cover in urban communities and the other evaluates cooperative management of an invasive species by urban communities. The first chapter summarizes the three topics and briefly describes the motivation, methods applied and main conclusions in each study. Chapter 2 presents a meta-analysis of hedonic property value studies on the value of tree cover. A meta-regression was performed using implicit value estimates for tree cover at property-level from various locations in the U.S. along with auxiliary data of county-level tree cover to investigate the relationship between tree cover and implicit-price estimates for residential properties. The study found that on average 35 percent and 40 percent tree cover respectively at property-level and county-level optimize the benefits to the property owners in urban areas. These results provide insights to forward-looking communities to adapt their tree planting and protection efforts to lessen climate-induced impacts. Chapter 3 applies a first-stage Hedonic property price model to estimate preference for tree cover in urban communities using single-family house sales data from multiple property markets across the U.S. The study analyses how home owners' preference for tree cover vary across the landscape and across cities. Further, it identifies what factors affect these variations via the general inferences obtained from an internal meta-analysis. The study confirms the heterogeneity of preferences as affected by the differences in the abundance of tree cover in study locations, regional differences and household characteristics. These findings add to the hedonic literature and provide useful information for future urban planning. Chapter 4 focuses on cooperative management of invasive species in landscapes with mixed land ownerships. This study analyzes the effect of the land ownership on the management efforts between an infested municipality and an uninfested municipality when a transferable payment scheme is involved in the cooperative agreement. A dynamic optimization problem was set up to evaluate the case of Emerald ash borer (EAB) control in multiple jurisdictions in the Twin Cities, Minnesota. The results suggest that when the infested municipality has more public lands and when the transfer payments are efficiently used to implement greater control, the municipalities are more likely to commit to bargaining, and smaller transfer payments paid over a longer span of time are sufficient for optimal control of the spread of invasive species across the municipalities. The last chapter concludes the three studies and discusses the insights for future research. / Ph. D. / Mountain pine beetles (Dendroctonus ponderosae) are a native insect that has decimated millions of hectares of mature pine forests in western North America. The purpose of this study was to investigate, using GIS-derived variables, biophysical and climatic factors that have influenced past mountain pine beetle insect outbreaks, as evident by beetle-induced tree mortality in the Crown of the Continent Ecosystem (CCE) from 1962 to 2014. Specific objectives of this study were to determine how selected biophysical variables (slope, aspect, elevation, and latitude), regional climate variables (temperature, precipitation, and drought) and global climate oscillations (ENSO, PDO, NAO, AO, and PNA) relate to bark beetle infestations in the Crown of the Continent Ecosystem from 1962 through 2014, as measured by aerial surveyrecorded tree mortality. We sought to contextualize the results of the statistical models with historical data to further understand the relationship between increases and decreases of tree mortality by comparing these trends to geopotential height and sea-surface temperatures that may influence CCE climate. Our work revealed first, that while the aerial survey data has important limitations, overall it is a useful dataset for analyzing historical spatio-temporal patterns of insect infestations. Second, there appears to be a link between local biophysical factors, such as latitude, elevation, and winter precipitation (as opposed to global climate factors) and tree mortality within the CCE. Local climate analysis revealed the importance of winter precipitation to be the biggest influence of MPB decrease or increase along with lower geopotential heights during a decline in MPB spread over the CCE. Finally, a combination of a negative PDO and El Niño was important in forecasting a decline in MPB spread, as shown by damage, during a given year. This is the first study to use aerial survey data in a geospatial analysis incorporating biophysical variables for the US portion of the Crown of the Continent Ecosystem. Additionally, this study is unique to explore the potential relationship between global teleconnections and regional climate in the CCE area, and the spatio-temporal extent of mountain pine beetle infestations.Urban trees have become a key resource in building sustainable communities. Knowledge of preferences for trees, costs and benefits of trees, and how trees are managed by private and public landowners, is indispensable in making targeted planning that would fulfill the economic, social and environmental objectives of the urban communities This dissertation explores on these topics in three papers. Chapter 1 summarizes the three topics and briefly describes the motivation, methods applied and main conclusions in each study. Chapter 2 presents a meta-analysis that combines the non-market value estimates for tree cover from previous hedonic studies from various locations in the U.S. along with auxiliary data to investigate the relationship between the level of tree cover and value estimates. The study found that on average 35% and 40% tree cover respectively at property-level and county-level optimize the benefits to the property owners. Chapter 3 analyses how home owners’ preferences for trees vary across the landscape in multiple cities in the U.S., and the results are systematically summarized via an internal-meta analysis. The study confirms the preference heterogeneity across the landscape and found that the relative abundance of tree cover in study locations, regional differences and household characteristics affect the preferences. Chapter 4 develops a dynamic optimization model to study how private and public land ownership in local municipalities affects the cooperative management of urban trees to control the Emerald ash borer (EAB) infestation in Twin Cities, Minnesota. The results suggest that when an infested municipality has more public lands and when the transfer payments are efficiently used to implement greater control, the municipalities are more likely to commit to bargaining agreements that last for longer period of time. Results from the three studies provide insights to forward-looking communities to adapt their tree planting and protection efforts to lessen climate-induced impacts. The last chapter concludes the three studies and discusses the insights for future research.

To develop effective conservation planning and mitigate biodiversity loss, standardized metrics for monitoring and assessing biodiversity are needed. This information is particularly vital in Botswana, where knowledge of many of the diverse wildlife populations is lacking. To address this knowledge gap, my dissertation research evaluated the distributions, densities, and ecology of the wildlife community in northern Botswana, with a focus on terrestrial carnivore species given their importance both ecologically and economically. My objectives were threefold: 1) estimate the distributions of the mammal community (n = 44 species) and evaluate community, group, and species-specific responses to anthropogenic and environmental variables, 2) test whether the presence of intraguild species or resource availability had a larger influence on the seasonal distributions of carnivore species, and 3) simultaneously estimate the population densities of 7 carnivore species. To accomplish these objectives, I completed a multi-year camera trap survey in a 1,154-km2 study area and analyzed the data using occupancy models (single and multi- species) and spatially explicit capture-recapture models. Estimates of species richness ranged from 8 to 27 unique species, species had a mean occurrence probability of 0.32 (95% credible interval = 0.21–0.45), and estimated densities ranged from 1.8 aardwolves (Proteles cristata) to 12.7 spotted hyenas (Crocuta crocuta) per 100 km2. The occupancy and richness of terrestrial mammals was negatively associated with human disturbance and in general, positively associated with open grasslands/floodplains. Carnivore species, specifically, tended to have greater species richness and larger population densities in open habitats than in closed. I also found carnivore distributions were positively associated with the detection rate of intraguild competitors and predators, suggesting competitor/predator avoidance did not play a large role in shaping carnivore community structure. My research highlights the pivotal role protected areas and grasslands play in conserving wildlife populations in northern Botswana. Additionally, my research helps progress camera trap analyses from single to multi-species assessments. Broader application of this multi-species approach would likely result in a better understanding of wildlife and carnivore communities which in turn, may help inform management actions aimed at addressing the loss of wildlife populations globally. / Ph. D. / To conserve wildlife populations, information is needed on where species live, the resources (e.g., food, water, and shelter) they require, and how many there are. This information is particularly important in Botswana, where knowledge of many wildlife populations is lacking. To address this knowledge gap, my dissertation research evaluated the distributions, densities, and ecology of the wildlife community in northern Botswana, with a focus on carnivores given their importance both ecologically and economically. My objectives were threefold: 1) estimate the distributions of the mammal community (<i>n</i> = 44 species) and evaluate community, group, and species-specific responses to human and environmental variables, 2) test whether the presence of competitors/predators or resource availability had a larger influence on the seasonal distributions of carnivore species, and 3) estimate the population densities of 7 carnivore species. To accomplish these objectives, I completed a multi-year camera trap survey in a 1,154-km² study area and analyzed the data using advanced analytical techniques. I photographed 44 species of mammals and the estimated number of species per camera station ranged from 8 to 27. My estimated densities ranged from 1.8 aardwolves (<i>Proteles cristata</i>) to 12.7 spotted hyenas (<i>Crocuta crocuta</i>) per 100 km². Overall, mammal species were more likely to occupy grasslands and floodplains that were located further into protected areas (i.e., far from human disturbance). Open habitats seemed to be particularly important to carnivore species. In general, there were more carnivore species and these species had higher densities in open habitats than in closed. My results suggest carnivores did not avoid their competitors and predators by spatially separating themselves on the landscape, as has been found in the Serengeti. My research highlights the pivotal role protected areas and grasslands play in conserving wildlife populations, and advances camera trap analyses from assessments of a single species to assessments of entire wildlife communities. My research approach is applicable to camera trap studies worldwide and broader application would likely result in a better understanding of wildlife and carnivore communities. This information, in turn, can help inform management actions aimed at addressing the loss of wildlife populations around the globe.

The world's islands are of singular importance from a conservation perspective because they hold a disproportionate share of global biodiversity. However, island ecosystems are fragile, and the introduction of invasive species poses an especially grave threat to their species. My research took place on the island of Guam, which has been particularly hard hit by invasive species in recent history. The introduction of the invasive Brown Treesnake (BTS; Boiga irregularis) to Guam in the mid-20th century caused the extinction of the vast majority of its avifauna. Of the remaining bird species, the native Såli (Aplonis opaca) is a forest starling now limited to breeding and roosting in certain urbanized areas on the island. Previous research has shown that although Såli adults appear to have high survival, their fledglings are highly vulnerable to predators. My research focused on refining our understanding of how BTS are impacting Såli ecology and survival, and how BTS management can benefit Såli conservation. In my first chapter, I conducted the first field study to investigate the influence of both prey and predator sizes on the frequency of ingestion success by snakes. I found that nearly half of ingestion attempts by BTS on fledgling Såli were unsuccessful, and that BTS routinely pushed the upper limits of their capacity to swallow prey. These results suggest that relatively small BTS pose a greater predation risk to birds than previously recognized, and broaden the size range of BTS that should be targeted in management efforts for avian conservation. In my second chapter, I investigated a potential life-history trade-off for Såli between the proximity of nest sites to foraging areas and the risk of fledgling predation by BTS. I found that Såli nesting closer to the forest make more yearly nesting attempts, but that fledgling survival was higher the farther their nest site was from the forest. Såli therefore balance potential fecundity with predation risk to fledglings in their selection of nest sites. In my third chapter, I examined the survival response of fledgling Såli to the suppression of BTS. I found that snake control did not lead to a change in fledgling survival from the pre-treatment baseline or in comparison to areas where snakes were not controlled, and that there was no shift from snake predation to other causes of mortality. Changes to the strategies or tools employed will therefore be required in order for future BTS control efforts within similar habitats to effectively improve avian survival. This body of work demonstrates that BTS are affecting Såli in unexpected ways, and offers new guidance on how to manage damaging invasive species for native species conservation. / Doctor of Philosophy / Islands are of high value important for conservation because they hold a more than their share of the world's animal and plant species. However, island ecosystems are fragile, and the introduction of damaging exotic species is especially threatening to species that live there. My research took place on the island of Guam, which has been particularly hard hit by damaging non-native species in recent history. The introduction of the Brown Treesnake (BTS; Boiga irregularis) to Guam in the mid-20th century caused the extinction of the vast majority of its bird species. Of the remaining bird species, the native Såli (Aplonis opaca) is now limited to breeding and roosting in certain developed areas on the island. Previous research has shown that although Såli adults appear to have high survival, their fledglings (young birds that recently left the nest) are highly vulnerable to predators. My research focused on refining our understanding of how BTS are impacting Såli life cycles, and how BTS management can benefit Såli conservation. In my first chapter, I conducted the first field study to investigate the influence of both prey and predator sizes on the capacity for snakes to swallow their prey. I found that nearly half of attempts by BTS to swallow fledgling Såli were unsuccessful, and that BTS routinely pushed the upper limits of their capacity to swallow prey. These results suggest that relatively small BTS pose a greater predation risk to birds than previously recognized, and broaden the size range of BTS that should be targeted in management efforts for avian conservation. In my second chapter, I investigated a potential life-history trade-off for Såli between how close their nest sites are to foraging areas and the risk of fledglings being killed by BTS. I found that Såli nesting closer to the forest make more nesting attempts per year, but that fledgling survival was higher the farther their nest site was from the forest. Såli therefore balance the potential number of young they can raise with the predation risk to those same young in their choice of nest sites. In my third chapter, I examined whether the suppression of BTS led to a change in the survival of fledgling Såli. I found that snake control did not lead to a change in fledgling survival from the period before the treatment or in comparison to areas where snakes were not controlled, and that there was no shift from snake predation to other causes of death. Changes to the strategies or tools employed will therefore be required in order for future BTS control efforts within similar habitats to effectively improve avian survival. This body of work demonstrates that BTS are affecting Såli in unexpected ways, and offers new guidance on how to manage damaging invasive species for native species conservation.

<p dir="ltr">Small populations often fail to thrive, as the low levels of variation that are frequently present in small populations hinder the ability to acclimate and adapt to future environmental challenges. Despite this well-known phenomenon, many small populations persist but the factors that mediate the success of these populations are often poorly understood. In this dissertation, I conduct three studies that vary in scope and scale to better contextualize the ecological and evolutionary contexts that may lead to small population persistence. The first chapter synthesizes the theoretical and empirical evidence that allelic dominance can exert a strong influence on genetic diversity after a sharp population reduction. My findings demonstrate that dominance of one allele over another can increase additive genetic variation after a population reduction. However, maintaining the maximum amount of additive variation possible with allelic dominance may require more individuals than if two alleles have only additive effects. The second chapter focuses on elucidating the patterns of establishment and spread of three invasive anuran species that underwent sharp population declines upon their introduction to novel environments. The results from my study highlight different introduction and establishment histories that have all led to the success of each invasive species. The third and final chapter evaluates the maintenance of genomic variation in a small population with strong sexual selection, a process expected to erode variation. I tested the fit of empirical genomic and phenotypic variability data to theoretical models and found little support for the hypothesis of genic capture to maintain genetic variation. I thus discuss alternative mechanisms that may be responsible for maintaining diversity in this system. The maintenance of variation in small populations involves a complex interplay of ecological, environmental, and evolutionary forces but understanding how variation is sustained in small and imperiled populations is crucial for addressing challenges in conservation biology and the management of invasive species.</p>

The aim of this thesis is to analyse offered meaning, that is, what and how subject content is communicated to the recipients. In this case the subject content is biological diversity and the communicative artefacts are biology books for the latter grades in the Swedish compulsory school. The four papers cover aspects of biodiversity in biology books (I), connections between biology books and the world outside school (II), the definition of the species concept and the use of the concept species in textbooks and in pupils' assertions (III), and finally how instances of modes are connected in a multimodal text and how the design of texts may affect the possibilities of meaning making (IV). The biology books used for data collection are multimodal texts with different types of written text and a rich amount of illustrations. The collected data was primarily used for content analysis but also to explore the design of the books. In paper III and IV data was also obtained by two questionnaires to students. Data is analysed and the results are discussed on the basis of a social semiotic theory of communication and meaning making. The books contain many facts about biological diversity, but the concept is not defined explicitly in several of them. In relation to human beings and human activities are beneficial aspects of biological diversity given precedence over ethical, aesthetic and economic aspects. The results also show that the books contain inaccuracies and questionable formulations regarding biodiversity, as well as simplifications and colloquial expressions rather than scientifically accurate terminology. Direct address, anthropomorphism, analogies and connections to life outside school are also found in the books. To recognize themselves in many of the connections to everyday life, pupils need to have visited many habitats in different seasons. The use of concepts is an area where there is a great potential for change. The species concept can be seen as an example of how a concept is introduced early and that understanding is taken for granted in the remaining text. Responses from the questionnaires suggest that more time needs to be given to basic biological concepts and that a big amount of instances of modes may impede meaning making. Textbooks are compromise products created to suit a diverse audience. There is a risk that the offered meaning of the books is not consistent with the perceived meaning of the students. The results of the thesis may contribute to reduce the gap between offered and perceived meaning. If awareness is raised about the problems pupils may face when using textbooks, the teachers' and the authors' ability to support meaning making may increase. / <p>Akademisk avhandling för filosofie doktorsexamen i Naturvetenskap, inriktning utbildningsvetenskap, som med tillstånd från Naturvetenskapliga fakulteten kommer att offentligt försvaras fredag den 7 november, 2014 kl. 10.00 i Föreläsningssalen, Institutionen för biologi och miljövetenskap, Medicinaregatan 18, Göteborg.</p><p>I. Ferlin, M. (2011). Biologisk mångfald i svenska läroböcker för skolår 6–9. NorDiNa, 7(1), 71–84</p><p>II. Ferlin, M. (2013). Vardagsanknytning i biologiböcker. Paideia 5, 52–61</p><p>III. Ferlin, M. &amp; Sundberg, P. (Accepterat manuskript). Grundskoleelevers uppfattningar om begreppet art relaterade till formuleringar i läroböcker i biologi. Publiceras i NorDiNa våren 2015.</p><p>IV. Ferlin, M. (Manuskript). Connections between instances of modes in multimodal texts.</p>

Today's arid and semi-arid zones of the Mediterranean are affected by desertification, resulting from various factors, including climatic variations and human activities such as overcultivation, overgrazing and deforestation. Afforestation programs are one of the most effective means in preventing desertification. For many years Libya has had afforestation programs in order to restore degraded land and in response to rapid desert encroachment in the north east of Libya, in the area called the Jabal Akhdar (Green Mountain), which has been investigated in this study. The purpose of this research was to investigate the relative roles of exotic compared to native tree species in preventing desertification and enhancing degraded land restoration in the Jabal Akhdar. The effect of environmental factors on exotic compared to native tree species have been assessed by observations on growth and reproductive success of the species, including variables of stocking rate, trunk diameter, tree height, crown diameter, tree coverage, natural mortality, felling and seedling regeneration, as well as calculated variables, derived from these measurements. The effects of methods and age of afforestation on the promotion of biological diversity have been investigated using the Shannon-Wiener diversity index. The effects of tree species on soil depth have also been investigated. Multivariate statistical analyses of site, species and environmental data, using both cluster analyses and factor analyses have been performed, with the aim of determining what is influencing the species, crops or differentiating between the sites, based on soil depth, angle of slope, altitude, rainfall and air temperature values. Pinus halepensis showed success in its growth and regeneration, particularly at higher altitudes and steeper slopes. Cupressus sempervirens was successful in growth and regeneration in the mountains. The exotic Eucalyptus gomphocephala was very successful in its growth, but did not regenerate well, while the exotic Acacia cyanophylla trees had a failure of both growth and regeneration. E. gomphocephala species appeared to favour relativley the flatter (non-mountain) sites, while A. Cyanophylla appeared to favour relativly the mountain sites. All the species responded positively to greater rainfall and deep soil, but they differed in where they were most likely to be successful. Environmental factors such as climate, terrain and soil are the main determinants of species distribution in the study area, in addition to their impact on the growth of the main trees. There appeared not to be any relationship between biodiversity and whether the main trees were native or exotic, and only P. halepensis showed any negative effect on the abundance of shrubs. There was greater diversity of trees and shrubs generally at the younger sites than the old sites. The present study emphasises the current mismanagement of planted forests, particularly with overgrazing contributing to desertification, through preventing tree growth and eliminating most sapling regeneration. This study concludes by making recommendations for more effective choice of tree species to plant, and for subsequent management to improve afforestation programmes in the Jabal Akhdar area.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.