LANDSCAPE ECOLOGY AND POPULATION GENOMICS OF TWO SYMPATRIC PITVIPER SPECIES ACROSS A FRAGMENTED APPALACHIAN LANDSCAPE

Understanding the link between landscape patterns and ecological and evolutionary processes is an important prerequisite for informed wildlife conservation and management, especially in rapidly changing landscapes. Until recently, the inaccessibility of spatial and genomic data sets of sufficient resolution limited our ability to incorporate the impacts of landscape patterns into predictions of ecological and environmental outcomes. In this dissertation, I utilized several high-resolution spatial and genomic data sets to address ecological questions in a rapidly fragmenting landscape in southeastern Kentucky. Overall, my results indicate that large-scale surface coal mining is causing widespread homogenization of landforms, resulting in a uniquely permanent form of habitat loss. This is likely causing significant fragmentation of remain forested habitat in many portions of the Cumberland Plateau of Kentucky, as evidenced by reductions in suitable overwintering habitat for the timber rattlesnake (Crotalus horridus). At the level of the individual, the high resolution and three-dimensional imagery provided by lidar remote sensing systems allows for a much more accurate assessment of the drivers of individual movement in C. horridus than using coarse topographic data sets alone. While this fragmentation might be expected to limit migration and increase genetic differentiation among population, patterns of genomic diversity in another common pit viper, the copperhead (Agkistrodon contortrix), suggest that contemporary surface mining is not associated with spatial patterns of genomic diversity. However, using a 2,140 SNP data set, I did find significant associations between a historic highway path and divergent genomic patterns, suggesting a time lag may be responsible for contemporary genomic patterns associated with a historic barrier to movement. When examining the landscape at broad spatial scales, the topographic rearrangement of land after mining followed steady patterns until approximately 2011. At this point, coinciding with federal policy shifts aimed at reducing the frequency of valley fill operations, mining impacts in stream bottoms decreased markedly, but ridgetops and upper slopes continued to be impacted at rates equal to or greater than before 2011. I recommend topographic restoration be highlighted as a worthy goal of reclamation, on par with vegetation establishment and erosion control

Multi-Scale Threat Assessment of Riverine Ecosystems in the Colorado River Basin

Freshwater ecosystems are facing a deepening biodiversity crisis. Developing robust indicators to assess ecological integrity across large spatial scales and identifying the specific threats and pathways of impairment are thus critically needed if we are to inform freshwater conservation strategies. Here we present the first comprehensive threat assessment across the Colorado River Basin – one of the largest and most endangered river basins in North America – using a spatial framework accounting for the wide range of human activities (land uses, transportation infrastructure, exploitative activities, water withdrawals), pathways (local footprint, overland runoff, upstream cumulative effects), and spatial extent of influence (valley bottom, catchment and river network) known to affect the ecological integrity of riverine ecosystems. We quantified and mapped 69 individual threat indices with geospatial tools for each permanent, ephemeral, and intermittent stream segment within the Basin, encompassing a total of \u3e1,067,700 river kilometers. We further aggregated these indices into components of water quality (diffuse and point-source pollution), hydrology (flow regulation/uses and climate change), and physical system (connectivity and geomorphology). To demonstrate the potential of our framework to inform spatial planning decision processes, we examined the typical combinations of threats experienced by different hydrologic areas and stream segment types, identified candidate watersheds for habitat restoration and enhancement where hotspots of biodiversity and threat overlapped, and assessed the associations between threat indices and in situ measurements of ecological integrity describing a suite of biological (benthic macroinvertebrate, fish), chemical (total nitrogen load, water conductivity), hydrological (flow alteration) and physical indicators (streambed stability, instream habitat complexity). Our assessment highlights clear disparities in term of overall degree of threat that result from different combinations and contributions of individual stressors, with different priorities emerging for perennial versus intermittent or ephemeral stream segments, and between the upper and lower parts of the Basin. Importantly, we showed that our threat indices were generally correlated with biological, chemical, hydrological and physical indicators of ecological integrity they were intended to capture. In addition to its implications for the conservation and management of the highly imperiled Colorado River Basin, our case study illustrates how multi-faceted threat mapping can be used to assess the ecological integrity of riverine ecosystems in the absence of spatially extensive in situ measurements

Freshwater ecosystem services in mining regions : modelling options for policy development support

The ecosystem services (ES) approach offers an integrated perspective of social-ecological systems, suitable for holistic assessments of mining impacts. Yet for ES models to be policy-relevant, methodological consensus in mining contexts is needed. We review articles assessing ES in mining areas focusing on freshwater components and policy support potential. Twenty-six articles were analysed concerning (i) methodological complexity (data types, number of parameters, processes and ecosystem-human integration level) and (ii) potential applicability for policy development (communication of uncertainties, scenario simulation, stakeholder participation and management recommendations). Articles illustrate mining impacts on ES through valuation exercises mostly. However, the lack of ground-and surface-water measurements, as well as insufficient representation of the connectivity among soil, water and humans, leave room for improvements. Inclusion of mining-specific environmental stressors models, increasing resolution of topographies, determination of baseline ES patterns and inclusion of multi-stakeholder perspectives are advantageous for policy support. We argue that achieving more holistic assessments exhorts practitioners to aim for high social-ecological connectivity using mechanistic models where possible and using inductive methods only where necessary. Due to data constraints, cause-effect networks might be the most feasible and best solution. Thus, a policy-oriented framework is proposed, in which data science is directed to environmental modelling for analysis of mining impacts on water ES

Spatial epidemiology of cancer : data types, spatial aggregation and geographical patterns at mainland Portugal

A thesis submitted in partial fulfillment of the requirements for the degree of Doctor in Information Management Specialization in Geographical Information SystemsThe importance of research on the spatial epidemiology of cancer has been progressively recognized and the number of studies in this field has been increasing steadily, having experienced significant growth over the last decade. Overall, spatial epidemiology is a comprehensive research area that covers a variety of subjects. Among those subjects, and particularly in the case of spatial epidemiology of cancer, one important topic is the level of spatial data aggregation. The analysis of individual data may present ethical data protection issues, so geographically-aggregated data are often used in epidemiological research. Conversely, the analysis of aggregated data also raises certain methodological issues, such as: a) the importance of calculating standardized rates (usually by sex and age) to allow for the comparison of different geographical units; b) the need to take into account the fact that the results obtained at a given level of geographical aggregation cannot be extrapolated as true for other levels of aggregation; and c) the possible existence of the “small numbers problem” and the relevance of using smoothed rates to try to solve it. This thesis takes a first look at this subject through a systematic review of the literature on the spatial epidemiology of cancer. The findings show that the questions which are considered most frequently in the literature consist of: a) the methodology used; b) the spatial distribution of cancer and its temporal evolution; and c) risk factors. The thesis then seeks to address these three aspects. In order to do that, several methodological issues related to the research of the spatial epidemiology of cancer are evaluated and the mortality distribution of all types of cancer is analyzed. Given the high rates of incidence and mortality due to colorectal cancer among the Portuguese population, this cancer type is taken as a case-study, and the distribution of its incidence and mortality is studied and compared with the distribution of the prevalence of the main risk factors. With regard to methodology, it is find that data aggregation at the municipality level makes it possible to obtain detailed information on the geographical distribution of cancer in mainland Portugal, and simultaneously address the small numbers problem. The use of statistical methods to calculate smoothed rates based on the spatial vicinity of the units under analysis also contributes to solving this latter problem. As far as cancer’s spatial distribution patterns are concerned, it is find significant heterogeneity across the municipalities of mainland Portugal, both when examining overall cancer mortality and when specifically looking at colorectal cancer incidence and mortality. Regarding the mortality distribution of all cancer types, it is find that the highest mortality rates tend to cluster around Oporto (on the north coast), Lisbon (on the west coast) and in the municipalities of southeast mainland Portugal. With respect to colorectal cancer, it are detected different patterns of incidence and mortality. The distribution of colorectal cancer incidence is more heterogeneous than that of colorectal cancer mortality. In addition, both colorectal cancer incidence and mortality exhibit especially high values for men in two municipalities in the center of mainland Portugal, which seems to call for a more detailed analysis of this area. In terms of risk factors, the following main risks, which have been identified as having a possible association with colorectal cancer, were considered: tobacco smoking; alcohol intake; and dietary behavior. Screening, as a secondary prevention measure aimed at the early detection of cancer and mortality reduction, was also considered in the analysis. However, data on these risk factors are representative only at much more aggregated geographic units, such as NUTS II. Therefore, a detailed analysis of association could not be performed. Finally, the natural background radiation in mainland Portugal was also analyzed, computing a mean by municipalities, and the conclusion is that its association with colorectal cancer is generally weak. This work points to a variety of interesting topics to study in future research, such as: a) to apply the same methodologies to other cancer types; b) to study the geographical association of risk factors, like socio-demographic and environmental risk factors, with cancer incidence and mortality; c) to test other spatial methods in the research of spatial epidemiology of cancer in Portugal, like, for an instance, kriging or multilevel models; and d) to establish suitable methodologies to study spatial epidemiology of cancer in the Portuguese islands.A importância da pesquisa sobre a epidemiologia espacial do cancro tem sido progressivamente reconhecida e o número de estudos nesse campo tem aumentado constantemente, tendo registado um crescimento significativo na última década. Em geral, a epidemiologia espacial é uma área de pesquisa abrangente que inclui uma variedade de assuntos. Entre esses assuntos, e particularmente no caso da epidemiologia espacial do câncer, um tópico importante é o nível de agregação dos dados espaciais. A análise de dados individuais pode apresentar problemas éticos de proteção de dados, pelo que é frequente utilizar dados agregados geograficamente em pesquisas epidemiológicas. Por outro lado, a análise de dados agregados também levanta certas questões metodológicas, tais como: a) a importância de calcular taxas padronizadas (geralmente por sexo e idade) para permitir a comparação de diferentes unidades geográficas; b) a necessidade de levar em conta o fato de que os resultados obtidos em um dado nível de agregação geográfica não podem ser extrapolados como verdadeiros para outros níveis de agregação; e c) a possível existência do “problema dos pequenos números” e a relevância do uso de taxas suavizadas para tentar resolvê-lo. Esta tese faz uma primeira abordagem ao tema através de uma revisão sistemática da literatura sobre a epidemiologia espacial do cancro. Os resultados mostram que as questões consideradas mais frequentemente na literatura estão relacionadas com: a) a metodologia utilizada; b) a distribuição espacial do cancro e a sua evolução temporal; e c) os fatores de risco. A tese procura então abordar esses três aspetos. Para isso, são avaliadas várias questões metodológicas relacionadas com a investigação em epidemiologia espacial do cancro e é analisada a distribuição da mortalidade por todos os tipos de cancro. considerando as elevadas taxas de incidência e mortalidade do cancro colorrectal na população portuguesa, este tipo de cancro é utilizado como caso de estudo, e a distribuição da sua incidência e mortalidade é estudada e comparada com a distribuição da prevalência dos principais fatores de risco. Em termos metodológicos, verifica-se que a agregação de dados ao nível do concelho permite obter informação detalhada sobre a distribuição geográfica do cancro em Portugal continental, e simultaneamente abordar o problema dos pequenos números. A utilização de métodos estatísticos para calcular taxas suavizadas com base na vizinhança espacial das unidades geográficas analisadas também contribui para a resolução deste último problema. No que diz respeito aos padrões de distribuição espacial do cancro, verifica-se uma heterogeneidade significativa entre os concelhos de Portugal continental, tanto na análise da mortalidade por todos os tipos de cancro como quando se analisa especificamente a incidência e mortalidade do cancro colorretal. No que diz respeito à distribuição da mortalidade de todos os tipos de cancro, verifica-se que as taxas de mortalidade mais elevadas tendem a agrupar-se em torno do Porto (na costa norte), Lisboa (na costa oeste) e nos concelhos do sudeste do continente. Em relação ao cancro colorretal, são detetados diferentes padrões de incidência e mortalidade. A distribuição da incidência de cancro colorretal é mais heterogênea que a mortalidade por por este tipo de cancro. Além disso, tanto a incidência como a mortalidade por cancro colorrectal registam valores particularmente elevados para os homens em dois concelhos do centro de Portugal continental, o que parece exigir uma análise mais detalhada dessa área. Em termos de fatores de risco, foram considerados os seguintes factores, que foram identificados como tendo possível associação com o câncer colorretal: tabagismo; ingestão de álcool; e comportamento alimentar. O rastreio, como medida secundária de prevenção que visa a deteção precoce do cancro e a redução da mortalidade, também foi considerado na análise. No entanto, os dados relativos a estes fatores de risco são representativos apenas em unidades geográficas muito agregadas, como as NUTS II. Assim, não foi possível realizar uma análise detalhada desta associação. Para além disto, analisou-se a radiação natural em Portugal Continental, calculando uma média por concelho, e concluiu-se que a sua associação com o cancro colorretal é geralmente fraca. Este trabalho aponta para uma variedade de tópicos interessantes para estudar em pesquisas futuras, tais como: a) aplicar as mesmas metodologias a outros tipos de cancro; b) estudar a associação geográfica de fatores de risco, tais como fatores sócio demográficos e ambientais, com a incidência e a mortalidade por cancro; c) testar outros métodos espaciais na análise da epidemiologia espacial do cancro em Portugal, como, por exemplo, modelos de krigagem ou multiníveis; e d) estabelecer metodologias adequadas para o estudo da epidemiologia espacial do cancro nas ilhas portuguesas