Meandering rivers provide fresh water and important aquatic ecosystem services, yet at the same time induce flood and erosion hazards. In the face of ongoing development pressure and changing climate, growing concern for meandering rivers has increased the demand to model accurately the flow and predict the sediment transport in a meandering river channel. Calibration and validation of these models based on comparable field-based data, as opposed to laboratory-scale experimental data, may decrease uncertainty and improve understanding of complex flow structures in natural meandering rivers. In this thesis, spatially intensive field data are utilized to develop appropriate calibration and validation methods for 3D meandering river models. Validated models are then applied to the study of morphodynamic processes and the influence of channel change on fish habitat availability in meandering rivers. This study presents a novel methodology for use of three-dimensional (3D) velocity for improved calibration of a 3D hydro-morphodynamic model. A natural tortuously meandering river was simulated using the Delft3D hydrodynamic model. A spatially intensive acoustic Doppler current profiler (ADCP) survey was conducted throughout the study river, providing fully 3D distributed velocities for model calibration. For accurate and realistic comparison of the fully 3D predicted and measured velocities, an algorithm was developed to match the location of each ADCP bin with 3D model grid points. The results suggest that different calibration approaches can result in different calibration parameterizations whose simulated results can differ significantly. It is shown that the model which was calibrated based on the proposed 3D calibration approach had the best model performance. Depending upon the nature and objectives of the numerical modelling exercise, the results demonstrate the importance of model calibration with spatially intensive field data. Given the importance of pressure gradients in driving secondary flow, it is worth studying how the modelled flow structures in a natural river bend can be impacted by the assumption of hydrodynamic pressure. Accordingly, the performance of hydrostatic versus non-hydrostatic pressure assumption in the Delft3D hydrodynamic modelling of a tortuously meandering river was studied. An Acoustic Doppler Velocimeter (ADV) was employed to measure the 3D flow field at a section in a sharp bend of the simulated river at two different flow stages. The field-based ADV data were employed to validate the simulated hydrodynamic models. The results indicate the surprisingly superior performance of the hydrostatic over non-hydrostatic Delft3D modelling of the secondary flow. It was determined that the non-hydrostatic routine employed in Delft3D was not mass conservative, which diminished model accuracy. Despite several decades of intensive study of the morphological changes in meandering rivers, less attention has been paid to confined meanders. This thesis includes a study of the meandering behavior of a semi-alluvial cohesive bed river over a 10-year period. We employed a paired sub-reach study approach, wherein one sub-reach is freely meandering and the second adjacent sub-reach is confined by a railway embankment. Channel migration and morphological changes of the channel banks along each of these sub-reaches were analyzed by comparing the historical aerial photography, light detection and ranging (LIDAR) data, bathymetric data obtained from a total station survey, and field examination. Moreover, two different spatially intensive ADCP surveys were conducted in the study area to find the linkage between the hydrodynamics and morphological changes in the two different sub-reaches. The unconfined sub-reach displayed a typical channel migration pattern with deposition on the inner bank and erosion on the outer bank of the meander bend. On the other hand, the confined sub-reach showed greater bank instabilities than the unconfined sub-reach. In the confined sub-reach, an irregular meandering pattern occurred by the evolution of a concave-bank bench, which was caused by reverse flow eddies. The results of this study could shed light on the potential impacts of channel confinement on bank retreat and river migration in comparable case studies. It is reasonable to expect that hydro-morphodynamic processes in rivers can affect fish habitat availability and quality, but the impact of river morphological changes on fish habitat is not well studied. Herein, we investigate the impact of morphological development of a cohesive meandering creek on the quality of fish habitat available for juvenile yellow perch (Perca flavescens) and white sucker (Catostomus commersonii). A 3D morphodynamic model was first developed to simulate the hydro-morphodynamics of the study creek over a 1-year period. Total station topographic surveys were conducted to provide bathymetric change data for calibration of the morphodynamic module. Successful calibration efforts indicated that the developed model could be reasonably employed to predict the hydro-morphodynamics of the study creek. Two fish sampling surveys were carried out at the beginning and the end of the study period to determine habitat utilization of each fish species in the study reach. ANOVA multiple comparison tests indicate that morphological development of the river was a significant factor for the habitat utilization of juvenile yellow perch, whereas juvenile white sucker habitat utilization was not significantly impacted by the changes in the creek morphology. It is shown that flow depth, depth-averaged velocity, and suspended sediment transport also significantly influenced presence of the juvenile yellow perch at the 5% significant level. As for the juvenile white sucker, the only significant factor was the depth-averaged velocity. The results of the developed 3D hydro-morphodynamic model were fed into a fish habitat model. Comparison of the predicted fish habitat map of the juvenile yellow perch with the results of fish sampling surveys confirms that the habitat quality was better predicted when the impact of morphological changes was taken into account in the fish habitat modelling. The results of the proposed methodology could provide some insights into the impact of sediment transport processes on the fish community. This has important implications for effective river management.

No description available.

Through pollination, bees are responsible for the persistence of many biological systems on our planet. Bees have also been used for thousands of years in agriculture to improve crop quality and yield. Recently, there have been declines in honeybees worldwide. This decline is concerning because it threatens food supplies and global biodiversity. An alternative to alleviating the effect of a honey bee shortage could be to use native bees. Problems with adoption of native bees in agriculture occur because of a lack of large scale analysis methods for native bees, regional species lists and management knowledge. This research explores the use of GIS in modeling native bee habitat to provide a landscape scale analysis method for native bees and develop a systematic sampling method for regional species list development. Raster GIS modeling, incorporating decision support and Poisson statistical methods were used to develop a native bee habitat model. The results show landscape composition is important to bee abundance and diversity. In addition, habitat fragmentation may not be as detrimental to bees as previously thought. Bees are most sensitive to landscape composition at a scale of 250 m, but require large patches of floral resources. GIS proved to be very useful in modeling bee habitat and provides an opportunity to conduct landscape scale bee population analysis. / Master of Science

<p>Effective conservation and management of top predators requires a comprehensive understanding of their distributions and of the underlying biological and physical processes that affect these distributions. The Mid-Atlantic Bight shelf break system is a dynamic and productive region where at least 32 species of cetaceans have been recorded through various systematic and opportunistic marine mammal surveys from the 1970s through 2012. My dissertation characterizes the spatial distribution and habitat of cetaceans in the Mid-Atlantic Bight shelf break system by utilizing marine mammal line-transect survey data, synoptic multi-frequency active acoustic data, and fine-scale hydrographic data collected during the 2011 summer Atlantic Marine Assessment Program for Protected Species (AMAPPS) survey. Although studies describing cetacean habitat and distributions have been previously conducted in the Mid-Atlantic Bight, my research specifically focuses on the shelf break region to elucidate both the physical and biological processes that influence cetacean distribution patterns within this cetacean hotspot. </p><p>In Chapter One I review biologically important areas for cetaceans in the Atlantic waters of the United States. I describe the study area, the shelf break region of the Mid-Atlantic Bight, in terms of the general oceanography, productivity and biodiversity. According to recent habitat-based cetacean density models, the shelf break region is an area of high cetacean abundance and density, yet little research is directed at understanding the mechanisms that establish this region as a cetacean hotspot. </p><p>In Chapter Two I present the basic physical principles of sound in water and describe the methodology used to categorize opportunistically collected multi-frequency active acoustic data using frequency responses techniques. Frequency response classification methods are usually employed in conjunction with net-tow data, but the logistics of the 2011 AMAPPS survey did not allow for appropriate net-tow data to be collected. Biologically meaningful information can be extracted from acoustic scattering regions by comparing the frequency response curves of acoustic regions to theoretical curves of known scattering models. Using the five frequencies on the EK60 system (18, 38, 70, 120, and 200 kHz), three categories of scatterers were defined: fish-like (with swim bladder), nekton-like (e.g., euphausiids), and plankton-like (e.g., copepods). I also employed a multi-frequency acoustic categorization method using three frequencies (18, 38, and 120 kHz) that has been used in the Gulf of Maine and Georges Bank which is based the presence or absence of volume backscatter above a threshold. This method is more objective than the comparison of frequency response curves because it uses an established backscatter value for the threshold. By removing all data below the threshold, only strong scattering information is retained.</p><p>In Chapter Three I analyze the distribution of the categorized acoustic regions of interest during the daytime cross shelf transects. Over all transects, plankton-like acoustic regions of interest were detected most frequently, followed by fish-like acoustic regions and then nekton-like acoustic regions. Plankton-like detections were the only significantly different acoustic detections per kilometer, although nekton-like detections were only slightly not significant. Using the threshold categorization method by Jech and Michaels (2006) provides a more conservative and discrete detection of acoustic scatterers and allows me to retrieve backscatter values along transects in areas that have been categorized. This provides continuous data values that can be integrated at discrete spatial increments for wavelet analysis. Wavelet analysis indicates significant spatial scales of interest for fish-like and nekton-like acoustic backscatter range from one to four kilometers and vary among transects. </p><p>In Chapter Four I analyze the fine scale distribution of cetaceans in the shelf break system of the Mid-Atlantic Bight using corrected sightings per trackline region, classification trees, multidimensional scaling, and random forest analysis. I describe habitat for common dolphins, Risso’s dolphins and sperm whales. From the distribution of cetacean sightings, patterns of habitat start to emerge: within the shelf break region of the Mid-Atlantic Bight, common dolphins were sighted more prevalently over the shelf while sperm whales were more frequently found in the deep waters offshore and Risso’s dolphins were most prevalent at the shelf break. Multidimensional scaling presents clear environmental separation among common dolphins and Risso’s dolphins and sperm whales. The sperm whale random forest habitat model had the lowest misclassification error (0.30) and the Risso’s dolphin random forest habitat model had the greatest misclassification error (0.37). Shallow water depth (less than 148 meters) was the primary variable selected in the classification model for common dolphin habitat. Distance to surface density fronts and surface temperature fronts were the primary variables selected in the classification models to describe Risso’s dolphin habitat and sperm whale habitat respectively. When mapped back into geographic space, these three cetacean species occupy different fine-scale habitats within the dynamic Mid-Atlantic Bight shelf break system. </p><p>In Chapter Five I present a summary of the previous chapters and present potential analytical steps to address ecological questions pertaining the dynamic shelf break region. Taken together, the results of my dissertation demonstrate the use of opportunistically collected data in ecosystem studies; emphasize the need to incorporate middle trophic level data and oceanographic features into cetacean habitat models; and emphasize the importance of developing more mechanistic understanding of dynamic ecosystems.</p> / Dissertation

The flyingfishes (Teleostei: Exocoetidae) are a family of 53 epipelagic marine species distributed throughout tropical and subtropical surface waters. They form a key mid-trophic link between zooplankton and predators, and have evolved special adaptations to survive in the open ocean. However, little is known about their basic evolutionary history and ecology. Here, I apply a multidisciplinary approach to better understand the evolution and ecology of flyingfishes. I propose the first species-level phylogenetic hypothesis for the group, based on nuclear and mtDNA sequences, and show that the most speciose genus (Cheilopogon) is paraphyletic. Gliding evolved progressively from two- to four-wing strategies, and habitat preference is correlated with species range size. I also analyzed patterns of genetic diversity within the most abundant genus, Exocoetus, and found no evidence of cryptic species. Instead, I found that this genus likely consists of three genetically distinct species (in contrast to the five currently recognized) and two indistinct species that diverged very recently. Population genetic analysis of Exocoetus volitans (266 samples from 97 localities) indicates a single, circum-tropical population that is well connected; yet the Isthmus of Panama and an Equatorial barrier limit gene flow. Finally, I investigated species abundance, richness, diversity, and distributions within the eastern tropical Pacific Ocean (11,125 specimens). My results provide critical updates on species distributions and habitat preferences. Predictive modeling indicates that sea surface temperature is important for defining flyingfish habitat. This thesis addresses central issues concerning both evolution and ecology in the epipelagic zone, and highlights the need for better understanding remote marine regions and organisms.

Despite decades of protection, the endangered North Atlantic right whale (Eubalaena glacialis) has failed to recover, primarily due to interactions with fishing gear and ship strikes. Right whales range along the U.S. east coast, foraging year round in the Gulf of Maine while a subset of the population travels to the South Atlantic Bight each year to calve. The habitat requirements of the right whale are poorly understood. I investigated the relationship between the distribution of right whales and physical oceanographic conditions in an effort to create predictive models of essential right whale habitats. Additionally, the distribution of right and humpback whales (Megaptera novaeangliae) relative to fixed fishing gear was examined to assess spatio-temporal overlap. Habitat preferences were assessed using aerial survey data of whale locations and a range of topological and satellite derived physical parameters including bathymetry, sediment type, sea surface temperature, thermal gradients and surface roughness. A suite of non-parametric quantitative techniques including Mantel tests, log likelihood functions, Generalized Additive Models, Spearman Rank Correlations and the Williamson's spatial overlap index were used to assess relationships between whales and habitat variables. Our findings indicate that suitable calving habitat along the east coast may extend much farther to the north than is currently recognized. Our model correctly identified several well documented current and historic calving grounds in the eastern Atlantic but failed to fully identify a heavily used calving area off Argentina, which is characterized by lower surface water temperatures than the other calving regions. In the Gulf of Maine, right whale distribution was correlated primarily with sea surface temperature, sediment type and bathymetry. Predictive models offered insights into right whale habitat preferences for foraging but failed to wholly capture the physical factors underlying right whale distribution. I found the relative density of right and humpback whales and fixed fishing gear in the Gulf of Maine to be negatively correlated in most seasons and areas. These findings demonstrate that the regular co-occurrence of high densities of whales and gear is not a prerequisite for entanglement. Prohibiting entangling lines in areas where whales are known to forage could substantively reduce entanglement. / Dissertation

<p>The construction of roads, either as an economic tool or as necessity for the implementation of other infrastructure projects is increasing in the tropical forest worldwide. However, roads are one of the main deforestation drivers in the tropics. In this study we analyzed the impact of road investments on both deforestation and jaguar habitat loss, in the Mayan Forest. As well we used these results to forecast the impact of two road investments planned in the region. Our results show that roads are the single deforestation driver in low developed areas, whether many other drivers play and important role in high developed areas. In the short term, the impact of a road in a low developed area is lower than in a road in a high developed area, which could be the result of the lag effect between road construction and forest colonization. This is consistent since roads resulted to be a significant deforestation driver for at least two decades. Roads significantly affect jaguar's habitat selection; however males showed a higher tolerance than females. From 1980 to 2000 female jaguars lost 36% of their habitat wile males lost 22%. Our forecasting of the impact of the proposed road, shows that it will promote the deforestation of approximately 16,851 has, and the jaguar habitat loss of 146,929, during the first decade; meanwhile the alternative route will have and impact of 2519 hectares and the habitat loss of 899 hectares.</p> / Dissertation

The flyingfishes (Teleostei: Exocoetidae) are a family of 53 epipelagic marine species distributed throughout tropical and subtropical surface waters. They form a key mid-trophic link between zooplankton and predators, and have evolved special adaptations to survive in the open ocean. However, little is known about their basic evolutionary history and ecology. Here, I apply a multidisciplinary approach to better understand the evolution and ecology of flyingfishes. I propose the first species-level phylogenetic hypothesis for the group, based on nuclear and mtDNA sequences, and show that the most speciose genus (Cheilopogon) is paraphyletic. Gliding evolved progressively from two- to four-wing strategies, and habitat preference is correlated with species range size. I also analyzed patterns of genetic diversity within the most abundant genus, Exocoetus, and found no evidence of cryptic species. Instead, I found that this genus likely consists of three genetically distinct species (in contrast to the five currently recognized) and two indistinct species that diverged very recently. Population genetic analysis of Exocoetus volitans (266 samples from 97 localities) indicates a single, circum-tropical population that is well connected; yet the Isthmus of Panama and an Equatorial barrier limit gene flow. Finally, I investigated species abundance, richness, diversity, and distributions within the eastern tropical Pacific Ocean (11,125 specimens). My results provide critical updates on species distributions and habitat preferences. Predictive modeling indicates that sea surface temperature is important for defining flyingfish habitat. This thesis addresses central issues concerning both evolution and ecology in the epipelagic zone, and highlights the need for better understanding remote marine regions and organisms.

This thesis deals with the landscape fragmentation in relation to the spatial and migration requirements of large carnivores in Western Carpathians region. Based on the data of the model species (Lynx Lynx) occurrence and selected environmental factors, the habitat suitability for Lynx Lynx is discussed using the Maxent habitat model. Employing the Effective Mesh Size method, the current landscape fragmentation caused by the transport infrastructure and urban development is studied in detail in terms of the fragmentation geometry. In addition to the analysis of measure of the current fragmentation, this thesis also includes a prediction of development of the landscape fragmentation in relation to the planned large transport constructions up to the year 2030. Comparing the habitat suitability model with the measure of current landscape fragmentation, the areas with the greatest potential of the Lynx Lynx permanent occurrence as well as the problematic areas in view of the dispersion and individuals migration are determined. Comparing the habitat suitability model with the prognosis of development of the landscape fragmentation, the impact of the planned road constructions on the suitable habitat is assessed.

Submitted by Renata Lopes (renatasil82@gmail.com) on 2015-12-04T13:46:44Z No. of bitstreams: 1 viviangemilianopinto.pdf: 15850259 bytes, checksum: 65455db19a02c670e8a88c96f7e3c1aa (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2015-12-07T03:20:18Z (GMT) No. of bitstreams: 1 viviangemilianopinto.pdf: 15850259 bytes, checksum: 65455db19a02c670e8a88c96f7e3c1aa (MD5) / Made available in DSpace on 2015-12-07T03:20:18Z (GMT). No. of bitstreams: 1 viviangemilianopinto.pdf: 15850259 bytes, checksum: 65455db19a02c670e8a88c96f7e3c1aa (MD5) Previous issue date: 2015-06-10 / FAPEMIG - Fundação de Amparo à Pesquisa do Estado de Minas Gerais / Diante da escassez hídrica que se impõe como uma ameaça global, torna-se premente que as relações do homem com os recursos hídricos sejam repensadas e as formas de gestão reconstruídas. Sabendo-se que os subsídios para a gestão das grandes bacias hidrográficas se fundamentam na dinâmica das pequenas bacias e suas inter-relações, esta tese tem como objetivo buscar um olhar holístico da bacia hidrográfica do Ribeirão Espirito Santo (BHRES), situada em Juiz de Fora, Minas Gerais, identificando suas características bióticas e abióticas, pesquisando-se, de forma mais detalhada, as vazões ecológicas. Dada as dificuldades de se aprofundar a investigação ecohidrológica em toda a BHRES, determinaram-se dois trechos a serem estudados, um de cabeceira e outro de foz. Nesses dois trechos, buscou-se conhecer sua topobatimetria, sedimentos, características hidrodinâmicas, qualidade da água, ictiofauna e a relação com a vazão ecológica. Os resultados indicaram que os dois trechos estudados apresentam características bióticas e abióticas de ambientes moderadamente poluídos. Porém as particularidades das áreas marginais dos dois trechos implicam características de inundação bastante distintas, já que o primeiro trecho possui algumas depressões marginais, formando pequenas lagoas, ambientes amplamente reconhecidos pela sua importância na manutenção e integridade da biodiversidade aquática. Os dois trechos estudados, apesar de se situarem em posições bastante distintas na BHRES, não apresentam diferenças significativas com relação à granulometria dos sedimentos, parâmetros de qualidade da água, abundância, riqueza, diversidade e composição da ictiofauna. Essas caracteristicas permitiram a construção de curvas de adequação de habitat univariadas da ictiofauna investigada para a bacia hidrográfica como um todo. A metodologia de habitat, associada a uma ferramenta de reconhecimento do fluxo natural de cursos de água permitiu identificar o excedente hídrico nos dois trechos estudados, sinalizando para uma maior cautela na concessão de outorga de direito do uso da água em trechos de cabeceira, uma vez que, nos meses mais secos do ano não se identificou excedente hídrico; ao contrário, os fluxos naturais já impõem condição estressante às espécies analisadas. Por outro lado, o trecho de foz possui excedente hídrico superior à vazão de referência de outorga do estado de Minas Gerais nos meses mais úmidos e ainda é capaz de suportá-la nos meses mais secos. Note-se que as vazões mínimas remanescentes determinadas pelas legislações brasileiras se mostram incompatíveis com as necessidades para manutenção do ecossistema. / Under tre framework of the water scarcity that is imposed as a global threat, it is urgent that we rethink man's relationship with water resources and the reconstruction of approaches management. Given that subsidies for the management of large river basins are based on the dynamics of small basins and their interrelations, this thesis aims to pursue a holistic view for the Espírito Santo Stream Basin (ESSB), located in Juiz de Fora, Minas Gerais, Brazil, identifying their biotic and abiotic characteristics, researching up in more detail the ecological flow. Due to the difficulties of deepening ecohydrological research across ESSB, we determined two river stretches to be studied, one bedside and the other near the mouth. In these two stretches, we sought to know its topobathymetry, sediment, hydrodynamic characteristics, water quality, fish populations and the relationship with the ecological flow. The results indicated that the two stretches studied have biotic and abiotic characteristics of moderately polluted environments. However, the particularities of the marginal areas of the two stretches imply very different flood characteristics. The first stretch has some marginal depressions, forming small ponds, with such an environment widely recognized for its importance in the maintenance and integrity of aquatic biodiversity. The two sites studied, though situate themselves in very different positions in ESSB, do not differ significantly with respect to the grain size of the sediment, water quality parameters, abundance, richness, diversity and composition of fish populations. These characteristics allowed the construction of univariate habitat suitability curves of fish populations investigated for the river basin as a whole. The habitat methodology associated to a river natural flow recognition tool identified the water surplus in the two stretches studied, signaling greater caution with respect to granting right of water use in bedside stretches since it did not identify up water surplus; in the driest months of the year. In contrast, natural streams already impose stressful condition to the analyzed species. On the other side, the mouth stretch has a water surplus flow superior than Minas Gerais State flow reference for granting in the wettest months and is still able to support it in the driest months. It should be noted, that the remaining minimum flows determined by the Brazilian legislation appears to be incompatible with the needs for ecosystem maintenance.