Submitted by Marlene Santos (marlene.bc.ufg@gmail.com) on 2016-08-30T17:12:19Z No. of bitstreams: 2 Tese - Jacqueline de Souza Lima - 2015.pdf: 3724963 bytes, checksum: 3dff51d6112fdaaa0cca812853de7c82 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2016-08-31T13:03:24Z (GMT) No. of bitstreams: 2 Tese - Jacqueline de Souza Lima - 2015.pdf: 3724963 bytes, checksum: 3dff51d6112fdaaa0cca812853de7c82 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2016-08-31T13:03:24Z (GMT). No. of bitstreams: 2 Tese - Jacqueline de Souza Lima - 2015.pdf: 3724963 bytes, checksum: 3dff51d6112fdaaa0cca812853de7c82 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2015-06-18 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Eugenia dysenterica is a plant species from Cerrado that is widely distributed throughout the biome. Previous studies showed that natural populations of species have a high genetic structure, suggesting that historical changes in the geographic distribution and habitat fragmentation may have affected its genetic differentiation. In this context, studies of phylogeographic and landscape genetics are needed to understand which factors influence the distribution of genetic diversity of the species. In the first chapter we used the statistical phylogeography integrated to modeling analysis to reconstruct the demographic history and dispersal routes of E. dysenterica lineages and investigated the Quaternary climate change effects on its spatial pattern of genetic diversity. In the second chapter, we evaluated if habitat loss and fragmentation affect genetic diversity and connectivity in the species. Our results suggest that the central region of the Cerrado biome is probably the center of distribution of E. dysenterica and the spatial pattern of its genetic diversity may be the outcome of population stability through periods of the Quaternary. Moreover, also indicate that habitat fragmentation may be related to the increase in differentiation and a decrease of genetic diversity in these populations. / Eugenia dysenterica é uma espécie de planta nativa do Cerrado que apresenta ampla distribuição ao longo do bioma. Estudos anteriores revelam que populações naturais da espécie apresentam alta estruturação genética, sugerindo que mudanças históricas na distribuição geográfica e a fragmentação do habitat podem ter afetado o padrão de diferenciação genética da espécie. Nesse contexto, estudos filogeográficos e de genética da paisagem se fazem necessários para entender os fatores responsáveis pela distribuição da diversidade genética da espécie. No primeiro capítulo foi utilizada a filogeografia estatística integrada às análises de paleomodelagem para acessar a história demográfica da espécie e compreender como as mudanças climáticas do Quaternário influenciaram sua distribuição geográfica e estrutura genética. No segundo capítulo, procura-se responder como a perda de habitat e fragmentação pode influenciar a diversidade genética e conectividade das populações da espécie no Cerrado. Os resultados apresentam evidências de que a origem de dispersão dos haplótipos analisados se deu na região central do bioma e que mudanças ocorridas durante o Pleistoceno, provavelmente, resultaram no padrão de distribuição da diversidade genética observado. Além disso, indicam que a fragmentação do habitat pode estar relacionada com o aumento da diferenciação e diminuição da diversidade genética nas populações estudadas.

Por meio de uma amostragem padrozinada de longa duração, realizamos levantamentos de pequenos mamíferos com armadilhas de interceptação e queda em 68 sítios distribuídos em seis paisagens de 10.000 ha (três em mata contínua e três em paisagens fragmentadas) localizadas em três regiões do Planalto Atlântico Paulista. As paisagens fragmentadas compreendem diferentes quantidades de matas remanescentes, 50%, 30% e 10%, porcentagens acima e próximas dos limites superior e inferior do limiar teórico de fragmentação (10-30%). A presente tese de doutoramento foi dividida em quatro capítulos e duas abordagens principais. A primeira delas (Capítulo 2) teve por objetivo avaliar se os pequenos mamíferos listados como ameaçados de extinção são afetados pela fragmentação e pela qualidade dos remanescentes de Mata Atlântica do Planalto Atlântico Paulista. Para isso, utilizamos os dados coletados nos 68 sítios amostrados, os quais estavam distribuídos em oito categorias: nove em matas maduras contínuas, nove em matas secundárias contínuas, quatro em fragmentos grandes e 11 em fragmentos pequenos da paisagem com 50% de remanescentes, sete em fragmentos grandes e 13 em fragmentos pequenos da paisagem com 30% de remanescentes, e quatro em fragmentos grandes e 11 em fragmentos pequenos da paisagem com 10% de remanescentes. Avaliamos se 10 espécies de pequenos mamíferos listados como ameaçados de extinção e cinco espécies endêmicas comuns nas mata contínuas e ausentes das listas vermelhas são afetados igualmente pela fragmentação, na escala da paisagem e da mancha, e pela qualidade dos remanescentes de Mata Atlântica. Nenhuma das espécies analisadas, independentemente do grau de ameaça ou de raridade, respondeu a variação do estádio de regeneração das matas contínuas. Por outro lado, nossos dados mostraram que as espécies endêmicas comuns respondem de forma mais congruente e negativamente à perda e fragmentação da Mata Atlântica do que as ameaçadas, as quais tanto podem não ser afetadas quanto ser positivamente ou negativamente afetadas pela fragmentação. Assim, sugerimos a separação das espécies em dois grupos nas listas vermelhas (naturalmente raras versus afetadas pelas ações antrópicas) e a utilização de outros critérios para avaliar o status de ameaça das espécies mais comuns, como a resposta à perda e fragmentação do habitat e a especificidade ao habitat na forma de endemismos e de grau de tolerância a matriz. A segunda abordagem (Capítulo 3) teve como objetivo verificar a influência do contexto (paisagem) e do tamanho do fragmento em paisagens com quantidades diferentes de remanescentes sobre a riqueza e abundância de espécies endêmicas e não-endêmicas. Para isso, utilizamos dados de 50 dos 68 fragmentos amostrados, localizados nas três paisagens 114 fragmentadas com 50%, 30% e 10% de remanescentes. A partir da avaliação da plausibilidade de oito modelos de regressão, que expressam visões teóricas alternativas da importância do contexto e da área dos fragmentos, investigamos se a influência positiva da área das manchas de floresta é mais forte (1) para as espécies endêmicas e (2) na paisagem próxima ao limite superior do limiar de fragmentação (sensu Andrén, 1994), já que em contexto de muita mata remanescente, fragmentos pequenos e grandes poderiam abrigar populações viáveis, e em contexto de pouca mata remanescente, espécies sensíveis já teriam desaparecido. Com exceção da riqueza de espécies não-endêmicas, modelos que incluem o contexto foram as hipóteses mais plausíveis para descrever a variação da riqueza e abundância das espécies de pequenos mamíferos. Como esperado, a influência positiva da área do fragmento foi mais importante na paisagem com 30% de floresta para a maioria das espécies de pequenos mamíferos endêmicos, enquanto que os modelos que incluem a influência da área do fragmento não estiveram entre os mais plausíveis para as espécies não-endêmicas. Nossos resultados corroboram a existência de um limiar de fragmentação e indicam que, ainda que os limiares variem entre espécies, é possível identificar grupos com respostas semelhantes à perda e fragmentação do habitat, auxiliando as políticas de manejo e conservação. / A long-term standardized survey of the Atlantic Forest small mammals was conducted using pitfall traps in 68 sites distributed in six 10.000-ha landscapes (three in continuous forest and three in fragmented landscapes) located in three regions in the Atlantic Plateau of São Paulo. The fragmented landscapes harbored different amounts of remnants, 50%, 30% and 10%, percentages above or within the superior and inferior limits of the theoretical fragmentation threshold (10-30%). This thesis was divided in four chapters e two main approaches. The first approach (Chapter 2) aimed to evaluate if small mammals listed as threatened were affected by forest fragmentation and quality in the Atlantic Plateau of São Paulo state. For this, we used data from 68 sites distributed in eight categories: nine in mature continuous forests, nine in secondary continuous forests, four in large and 11 in small patches in the landscape with 50% of remnants, seven in large and 13 in small patches in the landscape with 30% of remnants and four in large and 11 in small patches in the landscape with 10% of remnants. We investigated if 10 threatened small mammals and five non-threatened endemic species commonly found in continuous forests were equally affected by fragmentation, at the landscape and patch scales, and by forest quality. Regardless of threat or rarity level, no analyzed species responded to differences in the regeneration stage in continuous forests. On the other hand, our data showed that common endemic species respond more strongly and negatively to the loss and fragmentation of the Atlantic Forest than threatened species, which either may not be affected by fragmentation, or be positively or negatively affected. we suggest separating species in two groups (naturally rare versus affected by human impact) in the Red Lists and including different criteria to evaluate common species such as response to habitat loss and fragmentation as well as habitat specificity in terms of endemism and level of matrix tolerance. The second approach (Chapter 3) aimed to evaluate the effects of context (landscape) and patch area in landscapes with different amounts of remnants on the richness and abundance of the endemic and non-endemic species. We used data from 50 sites located in the three fragmented landscapes. By analyzing the plausibility of eight regression models, which express alternative theoretical hypothesis about the importance of context and patch area, we investigate if the positive influence of patch area was stronger (1) for endemic species and (2) in the landscape within the superior limit of the fragmentation threshold (sensu Andrén, 1994), since in a context of high proportion of remnants, small and large patches could harbor viable populations and in a context of low proportion of remnants, sensitive species would have gone extinct. Except for the non116 endemic species richness, the models including context were the most plausible hypothesis to describe small mammal richness and abundance variations. As expected, the positive influence of patch area was more important in the landscape with 30% of remnants for the majority of the endemic small mammals, whereas the models including patch area were not among the most plausible ones for the non-endemic species. Our data corroborate the existence of a fragmentation threshold and point out that, although thresholds vary among species, it is possible to identify groups with similar response to habitat loss and fragmentation, directing management and conservation policies.

Global environmental change fundamentally affects plants and their interactions with other species, and this has profound impacts on communities and ultimately ecosystems. In order to understand the mechanisms involved, we need to elaborate on the combined effects of different global change drivers on multiple levels of plant organization, including the biochemical level (production of defence compounds), the whole organism, the population, and the plant-herbivore interaction level. This thesis investigates (1) the combined effects of factors related to climate change and habitat fragmentation on Brassica nigra and (2) the effects of Zn soil pollution on the heavy metal hyperaccumulator Noccaea caerulescens at these different levels. Common garden and greenhouse experiments with B. nigra applied drought stress and elevated CO₂ to examine climate change impacts, while crossing treatments (inbreeding and between-population outbreeding) were used to investigate habitat fragmentation effects. Heterosis was lost under drought stress, and there were several interactive effects of the experimental treatments that varied within and among populations. In a greenhouse experiment with N. caerulescens, plants were grown on soil with different amounts of zinc. Plants had greater herbivore resistance when grown on Zn-amended soil, and invested more in herbivore tolerance when grown on soil without added Zn. In general, the results indicate that factors related to global environmental change have complex and interactive effects on different levels of plant organization. The findings are discussed in terms of their implications for ecology, evolution and conservation.

This study sought to identify critical areas for puma (Puma concolor) movement across the state of Arizona in the American Southwest and to identify those most likely to be impacted by current and future human land uses, particularly expanding urban development and associated increases in traffic volume. Human populations in this region are expanding rapidly, with the potential for urban centers and busy roads to increasingly act as barriers to demographic and genetic connectivity of large-bodied, wide-ranging carnivores such as pumas, whose long-distance movements are likely to bring them into contact with human land uses and whose low tolerance both for and from humans may put them at risk unless opportunities for safe passage through or around human-modified landscapes are present. Brownian bridge movement models based on global positioning system collar data collected during bouts of active movement and linear mixed models were used to model habitat quality for puma movement; then, a wall-to-wall application of circuit theory models was used to produce a continuous statewide estimate of connectivity for puma movement and to identify pinch points, or bottlenecks, that may be most at risk of impacts from current and future traffic volume and expanding development. Rugged, shrub- and scrub-dominated regions were highlighted as those offering high quality movement habitat for pumas, and pinch points with the greatest potential impacts from expanding development and traffic, although widely distributed, were particularly prominent to the north and east of the city of Phoenix and along interstate highways in the western portion of the state. These pinch points likely constitute important conservation opportunities, where barriers to movement may cause disproportionate loss of connectivity, but also where actions such as placement of wildlife crossing structures or conservation easements could enhance connectivity and prevent detrimental impacts before they occur.

Anthropogenic disturbances are ubiquitous in coastal marine ecosystems. As such, more intensive monitoring efforts are necessary to conserve these valuable habitats. Bioindicators, organisms that predictably respond to changes in environmental variables, may be utilized in monitoring efforts to assess ecosystem functioning. To incorporate organisms into monitoring programs as bioindicators managers need to first understand the difference between the natural phenology of the focal organisms and their responses to different forms of anthropogenic disturbance. To determine if gammaridean amphipods could be used as indicators of changes in environmental quality in sub-tropical seagrass ecosystems, I conducted spatial and temporal surveys of amphipod communities in south Florida. Amphipod community structure varied significantly across sites and seasons. Variation in community structure was largely driven by macrophyte biomass, food availability, seasonally variable factors (epiphyte abundance, dissolved oxygen, salinity, and temperature), water-column nitrogen concentration, and factors related to freshwater input, including low Thalassia testudinum and high Halodule wrightii densities, and salinity. Amphipods are also susceptible to mechanical damage in seagrass habitats and could be used as indicators of ecological functioning of a region. A major source of mechanical damage in seagrass ecosystems is caused by boat propellers. I simulated propeller scars in continuous seagrass beds to investigate the effects of scarring on seagrass ecosystem functioning. Seagrasses located adjacent to propeller scars experienced a shift in the limiting resource from light to phosphorus. Amphipod community structure, however, was not impacted by scarring, but amphipod density was reduced in fragmented patches. To determine if plant-herbivore interactions were impacted by propeller scarring, we removed amphipods from half of the experimental plots and measured epiphyte biomass and community composition. Top-down control on epiphyte biomass or community composition by amphipods was not affected by fragmentation, despite reduced amphipod densities. My dissertation research demonstrates that amphipods could be incorporated into existing management programs in sub-tropical seagrass ecosystems as environmental indicators. Reduced amphipod densities in fragmented seagrass beds suggests that amphipods could also be used as ecological indicators, but more research is needed to determine the extent of the impacts of fragmentation on higher trophic levels.

This study analyzes the remaining suitable habitat of the one-horned rhinoceros, Rhinoceros unicornis, in Royal Chitwan National Park of Nepal. An April 2003 Landsat image was classified into eight land cover types: wetland, sand, water, mixed forest, sal forest, agriculture, settlement, and grassland. This image was converted into habitat suitability maps using cover, food, and water. The rhinoceros prefers grassland habitat with oxbow lakes and closed canopy during the monsoon season. Nominal values of five parameters were used to create a map of habitat suitability index. The map was categorized into four habitat classes: highly unsuitable, unsuitable, moderately suitable habitat, and suitable. Landscape metrics, patch metrics and class metrics associated with habitat were determined through the use of FRAGSTATS.

Greater sage-grouse (Centrocercus urophasianus) currently inhabit about 56% of pre-settlement distribution of potential habitat. In 2005, the Castle Country Adaptive Resources Management Local Working Group (CaCoARM) was formed to address concerns regarding local sage-grouse populations in Carbon and Emery counties. In 2006-2007, CaCoARM identified the Wildcat Knolls and Horn Mountain as areas of special concern for greater sage-grouse conservation. Both sites selected by the group were inhabited by what appeared to be small isolated sage-grouse populations. Factors limiting small isolated greater sage-grouse populations throughout its range are diverse and largely site-specific. During 2008-2009, I captured, radio-collared, and monitored 43 sage-grouse between the two populations to document their ecology and seasonal habitat use patterns. The sites are only 24 km apart, but the populations appear to be isolated from each other. Sage-grouse on Horn Mountain and Wildcat Knolls are one-stage migratory and non-migratory, respectively. Although nesting and brooding success varied between sites, my results were comparable to those published in studies throughout the species' range. Overall male survival was lower on the Wildcat Knolls than Horn Mountain (P = 0.003). Hens that selected brood sites exhibiting increased shrub cover and grass height were more successful than hens that selected sites with lower shrub cover and lower grass height. Potential nesting habitat on the Wildcat Knolls and Horn Mountain were estimated at 2,329 and 5,493 ha, respectively. Hens that selected nest sites farther from non-habitat edge were more successful than hens that selected nest sites that were closer to non-habitat edge on the Wildcat Knolls. Higher nest success observed on the Wildcat Knolls was attributed to less habitat fragmentation. Isolated populations of greater sage-grouse are more susceptible to lower amounts of genetic diversity that may lead to inbreeding depression and increased rates of disease and parasites. I collected mitochondrial DNA samples from both the Wildcat Knolls and Horn Mountain populations. Although the haplotype frequencies recorded in the Wildcat Knolls and Horn Mountain populations were low, one was shared with several Utah populations. The documented low genetic diversity (especially on Horn Mountain) confirmed the isolation suspected by the local working group. Microsatellite tests may provide insights to enhance understanding of genetic differences among sites, and assist managers in determining whether or not translocations are necessary to maintain population genetic diversity. Biologists should not only continue to take samples for genetic comparison, but also record morphometric and behavior data.

Habitat fragmentation, and the resulting increase in edge habitat, has important effects on birds, including the increased probability of nest predation, changes in habitat structure, and the increased presence of non-native plant species. It is critical to understand the effects of fragmentation at all stages of the avian life cycle, including the often overlooked postfledging period. Because much of juvenile mortality occurs during the immediate postfledging period, and juvenile mortality contributes substantially to population dynamics, it is necessary to understand if fledgling survival is reduced in edge habitats and if fledglings' survival is influenced by their habitat use. During 2008 and 2009 I radio-tracked 52 fledgling Spotted Towhees (Pipilo maculatus) during the 30-day postfledging period in a 24-ha urban park near Portland, Oregon. Thirty-six fledglings (69%) survived the 27-day tracking period (an estimated 62.1% survived the entire 30-day postfledging period). At least 9 of 16 predation events were attributable to domestic cats (Felis domesticus) or Western Screech-owls (Megascops kennicottii). Although fledglings were more likely to be found near edges than the park interior, fledglings located closer to park edges had a higher probability of dying. However, I found that towhee nests were more likely to be found near edges, nests near edges produced more fledglings, and nestlings near edges were heavier. I used a STELLA-based stochastic model of nest success and fledgling survival to show that the benefits initially gained by nesting near edges were reversed during the postfledging period. The number of fledglings per nest that survived to the end of the 30-day postfledging period was significantly lower near edges than in the park interior. This apparent preference for nesting near edges, paired with higher fledgling mortality near edges, is consistent with the idea that edges are ecological traps. Fledgling habitat was significantly more structurally dense and had a greater abundance of non-native plant species, particularly Himalayan Blackberry (Rubus armeniacus), than nest habitat. Towhees avoided English Ivy (Hedera helix) for both nesting and care of fledglings. However, fledgling survival was not related to vegetation characteristics, which suggests that increased fledgling mortality near edges was a direct result of increased predator abundance or predation near edges, and was not an artifact of changes in habitat near edges. My results help to establish that fledgling survival and the unique habitat requirements of fledglings should be considered along with nest success and nest habitat when examining the effects of habitat fragmentation on bird populations. More broadly, this study has important implications for conservation, as it exemplifies how phenomena such as ecological traps created by anthropogenic changes in the environment can be overlooked if only one life history stage is studied.

Mozambique is to fifty percent covered by forest, most of which belongs to the biodiverse miombo woodlands. The last decades, Mozambique has been suffering from rapid deforestation. The once continuous forest cover has turned into a mosaic of forest patches, farmland, settlements etc. The remaining forest patches are in many cases very isolated. These forests have distinct edges towards the neighbouring land, which means that the edge zones have different environmental conditions (more light, higher temperatures etc.) and tree species composition than the interior. In order to examine how the forests of Mozambique are affected by edge effects, the highly isolated Nhamacoa forest was studied. An additional aim of the project was to make a floristic inventory of the forest in order to further assess its conservation status. Specimens were collected, pressed and photographed for identification. Edge effects were studied in plots at the edge and in the interior of the forest in a paired design. Trees inside the plots were identified, counted and measured (dbh (diameter at breast height) and height) to search for differences in species richness, diversity, biomass and height-to-dbh ratios. Environmental parameters (air temp., soil temp., light and slope) were also measured. In total, 76 species of trees were sampled and 44 (35 in the interior and 32 at the edge) of these were found inside the plots. The interior plots harboured significantly more individuals and species of trees than their paired edge plots. Additionally, biomass and height-to-dbh ratios were higher in the interior plots than in the edge plots. These differences strongly suggest that the Nhamacoa forest is affected by edge effects, although none of the measured environmental parameters could explain why. That the Nhamacoa forest is affected by edge effects goes in line with the research hypothesis and shows that it is important to maintain large and intact pieces of forest in order to preserve the Mozambican miombo forests. For future studies, additional environmental parameters (wind speed, humidity etc.) could be examined in order to better explain the presence of edge effects in the Nhamacoa forest.

In December 2019, the Danish government finished building a fence on the border with Germany. Although the fence was nominally intended to prevent wild boar entering Denmark, the government had recently acquired enough barbed wire to reinforce it against human migrants. I tell the story of the wild boar fence in the context of a global trend for escalating border enforcement and environmental change. I explore how border fences shape human and wild animal worlds, drawing on ecological data and using theory from environmental history, border and animal studies. In order to understand how humans and wild animals interact with the German-Danish border fence, I journeyed along it on foot in August 2022. My methodology is autobiographical – by walking the route myself and interviewing local experts and activists in the field, I explored how far humans and wild animals are free to move on the German-Danish border and what habitat fragmentation means for them. Without the ability to move, species worldwide, including humans, could be trapped as regions become uninhabitable due to climate change. A barbed wire border fence on the German-Danish border could prevent people, deer, wolves and other species from adapting to dramatic sea level rise and flooding. I argue that migration is the adaptation, rather than the crisis, and that mobility is something to be protected rather than supressed.