The developments of species distribution modeling techniques have brought new opportunities in the field of biological invasion management. In particular, statistical niche modeling for spatio-temporal predictions of species’ distribution is a widely spread tool that has proved its efficiency. The main purpose of this Master thesis is to study applicability of species distribution modeling to invasive alien species, with the aim of supporting efficient decision-making for their prevention. Some research questions are: how useful can species distribution modeling be for invasives’ prevention? Is distribution modeling technically feasible in the case of invasive species? What types of techniques are recommended to model distributions of IAS? What are the limits of such a tool? The methods employed to answer these questions are literature review and expert advice. I found that species distribution models can provide risk maps which are necessary to enable effective invasive alien species’ prevention. However intrinsic characteristics of invasives introduce uncertainties in the predictions made. Consequently several preliminary analyses should be conducted before applying the distribution model. Finally recommendations were made on the most appropriate distribution modeling technique to use depending on the urgency of the situation and the availability of data. / Utvecklingen av metoder för modelering av artdistribution har medfört nya möjligheter inom området hantering av biologiska invasioner. Statistisk nischmodelering för spatio-temporala förutsägelser av arters distribution är ett väl använt verktyg som har visat sig vara effektivt. Det övergripande målet med det här arbetet har varit att studera hur lämpad artmodelering är vid förebyggande av invasioner av främmande arter. Det har även undersökts huruvida metoden kan bidra till bättre och enklare beslutsfattande när det kommer till att förhindra sådana invasioner. Forskningsfrågorna lyder: hur användbart är fördelningsmodelering för förebyggande av spriding av invasiva arter? Är distributionsmodelering tekniskt genomförbar när det gäller invasiva arter? Vilka olika tekniker rekommenderas för att modelera spridningen av invasiva arter? Vilka begräsningar har modelerna? De metoder som används är litteraturöversikt och expertråd. Resultaten visar att artdistributionsmodelering kan bidra till att sammanställa riskkartor som är nödvändiga för att möjliggöra ett förebyggande arbete. Men speciella egenskaper hos de invasiva arterna som är svåra att förutse skapar osäkerheter i resultatet. Därför kan preliminära analyser med fördel genomföras innan modelering. I slutsatserna återfinns rekommendationer för vilken distributionsmodelteknik man bör använda, beroende av hur brådskande situationen är och om data finns tillgängligt.

Doctor of Philosophy / Department of Biology / Keith B. Gido / A fundamental goal of ecology is to understand environmental associations of species. These associations can provide a basis for predicting spatial distributions in contemporary habitats as well as how those distributions might change in response to anthropogenic environmental change. Developing species distribution models is limited by an incomplete understanding of functional traits, spatial scaling, and the mechanisms and generalities of correlations among abundance and environmental gradients. I address these four issues using observational and experimental approaches. First, I tested opposing mechanisms of community assembly by measuring the dispersion (i.e., diversity) of three types of functional strategies at three spatial scales and along environmental gradients. I found that communities are assembled via abiotic environmental filtering, but the strength of this filtering depends on the spatial scale of investigation, longitudinal network position, and type of functional strategy. Second, I quantified community-environment relationships across thirteen sub-basins, nested within the three major basins within Kansas to evaluate the consistency (i.e., generality) in predictive capability of environmental variables among sub-basins and across spatial extents. I found that longitudinal network position is consistently the strongest predictor of community composition among sub-basins, but in-stream and catchment predictors become stronger correlates of community composition with increasing spatial extent. Third, I used environmental niche models to quantify distributions of four pairs of congeneric cyprinids and found that species within each pair exhibited contrasting stream-size preferences. I then used field experiments to test for differences in individual-level performance between one pair of species (Pimephales notatus and P. vigilax) along a gradient of stream size. I found that adult spawn success and juvenile growth and condition increased with stream size for both species, indicating that these congeners respond similarly to abiotic gradients associated with the river continuum. I concluded that complementary distributions are a consequence of biotic interactions, differential environmental filtering evident in an unmeasured performance metric, or differential environmental filtering by an environmental factor operating at longer timescales. These studies demonstrate the context dependencies of characterizing habitat associations of stream fishes, but also reveal the general importance of stream size and associated environmental gradients in structuring stream fish communities.

North American Giant Salamanders (Cryptobranchus alleganiensis), commonly known as hellbenders, have been experiencing a population decline for decades due to human influences, such as pollution and habitat destruction. Many efforts are underway to save the hellbender but their entire potential geographical range has not been well-studied. Currently, hellbender populations are delineated by county boundaries and are on the International Union for Conservation of Nature Red List. The Genetic Algorithm for Rule-set Production, an Ecological Niche Model, was used to model the current hellbender potential distribution at a macro-scale under two different environmental scenarios. Additionally, future potential distributions were projected under two different climate change scenarios (Representative Concentration Pathways) to predict where possible habitat loss and expansion may occur in coming decades. Niche modeling was also used to evaluate the influence of environmental parameters across geography and between two sub-species of hellbender, the Eastern hellbender and the Ozark hellbender. Results showed that vegetation indices had some influence on current distribution predictions, while future models revealed that potentially large areas of currently suitable habitat may be lost, especially in the Ozark Mountains and the Southern Appalachian Mountains. Habitat expansion was predicted for several areas in the New England region of the northern Appalachian Mountains. The most influential variables were the maximum temperature of the warmest month, temperature annual range, and annual precipitation, while slope and elevation were less influential. However, areas of very high slope and elevation were not suitable for hellbenders, confirming previous descriptive habitat analyses. Current and future modeled distributions will provide conservationists with a more specific, and quantified, geographical and ecological description of where environmentally suitable areas exist for hellbenders. Micro-scale, stream-based studies provide areas of future research.

To understand present patterns of biodiversity, knowledge of a lineage’s past – both evolutionary and geographic – is required. Here I present the first comprehensive phylogenomic study of an Amazonian poison frog genus, Ameerega, as well as the introduction of a new method for characterizing ancestral distributions via phylogenetic niche modeling, which I use to investigate Ameerega’s biogeographic past. I sequenced thousands of ultraconserved elements from over 100 tissue samples, representing almost every described Ameerega species, as well as undescribed cryptic diversity. My phylogenetic inference diverged strongly from those of previous studies. I also introduce a new phylogenetic niche modeling method, which accounts for issues of bias in other methods by incorporating knowledge of evolutionary relationships into niche models. Given modern-day and paleoclimatic data, species occurrence data, and a time-calibrated phylogeny, my method constructs niche models for each extant taxon, uses ancestral character estimation to reconstruct ancestral niche models, and projects these models into paleoclimate data to provide a historical estimate of the geographic range of a lineage. I demonstrate my method on the Ameerega bassleri group. I also use simulations to show that my method can reliably reconstruct the niche of a known ancestor in both geographic and environmental space.

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Doctor of Philosophy / Department of Biology / Samantha Wisely / Habitat fragmentation and destruction are the most ubiquitous and serious environmental threats confronting the long-term survival of plant and animal species worldwide. However, some native or exotic species can take advantages of these alterations and expand their range, placing endemic species at risk of extinction by changing the composition of biotic communities and altering ecosystem. Capybara (Hydrochoerus hydrochaeris) are a widely distributed rodent throughout most of South and Central America, but restricted to areas of standing water. As the Gran Chaco ecosystem of Paraguay has been converted from dry tropical forest to pastureland, I hypothesized that this habitat alteration created potential for invasion by capybara into newly fragmented areas. I used ecological niche modeling to generate hypotheses about how the distribution of capybara has been affected by land use change, and tested those hypotheses with phylogeographic analyses. To understand the mechanisms that have allowed the invasion, I investigated home range, habitat use and thermoregulation of capybara via radiotelemetry in a deforested area in which capybara had recently invaded. Genetic analyses confirm a rapid range expansion scenario with evidence of secondary contact between two distinct phylogroups which had previously been disjunct. Modeling results indicated that conversion of forest to pastureland allowed the expansion to occur. Capybara selected water significantly more than it was available to them, and avoided shrub forest. I found a significant positive correlation between body temperature and distance from water, and a significant negative correlation between distance from water and Chaco ambient temperature. Capybara proximity to water appeared to be tightly linked to body thermoregulation. These results suggest that although capybara have expanded into the Chaco forest as it is converted to pastureland, the presence of permanent water sources in those pastures are the mechanism that allow capybara to persist in this habitat. This is the first study to characterize capybara in a xeric habitat without a year round water source, and scarce natural grasslands. My results show how anthropogenic habitat modification has allowed capybara to thrive. Understanding how capybara invade and utilize the deforested Central Dry Chaco will provide valuable information for the future management of the species and the Chaco ecosystem.

Environmentally related selective pressures and community interactions are well-documented drivers for niche differentiation, as natural selection acts on adaptive traits best fit for survival. Here, we investigated niche evolution between and within Pinus taeda, Pinus rigida, and Pinus pungens and sought to identify which climate variables contributed to species divergence. We also sought to describe niche differentiation across genetic groupings previously identified for P. taeda and P. rigida. Ecological niche models were produced using Maximum Entropy followed by statistical testing based on a measure of niche overlap, Schoener’s D. Both niche conservatism and niche divergence were detected, thus leading us to conclude that directional or disruptive selection drove divergence of the P. taeda lineage from its ancestor with P. rigida and P. pungens, while stabilizing selection was associated with the divergence of P. rigida and P. pungens. The latter implies that factors beyond climate are important drivers of speciation within Pinus.

Orientador: Ananda Virginia de Aguiar / Resumo: Myracrodruon urundeuva é uma espécie madeireira natural com grande potencial de uso comercial no Brasil, principalmente nas regiões do Pantanal, do Cerrado e da Caatinga, onde ocorre a exploração de espécies nativas. A exploração intensiva tem causado grande perda de indivíduos e o isolamento de populações em ilhas, devido à fragmentação do habitat da espécie. Assim, a adoção de estratégias para conservação ex situ de espécie nativas torna-se indispensável. Duas propostas foram idealizadas neste trabalho. A primeira foi estimar a variabilidade genética e ganho genético com a seleção de um teste de progênies. O teste de progênie consorciado com as espécies Myracrodruon urundeuva, Terminalia argentea e Astronium fraxinifolium, foi instalado em 12 de julho de 1994 na Fazenda de Ensino, Pesquisa e Extensão (FEPE), do campus de Ilha Solteira (FEIS/UNESP) na cidade Selvíria – MS. O delineamento utilizado foi o de blocos completos casualizados, contendo 28 progênies, seis plantas por parcela e quatro repetições para as espécies instaladas. Os caracteres altura e diâmetro a altura do peito (DAP) foram mensurados aos 24 anos após o plantio. Verificou-se a existência de variação genética significativa entre as progênies para os caracteres analisados. A alta taxa de sobrevivência indica boa adaptação da espécie em testes consorciados. As estimativas do coeficiente de variação genética tiveram resultados de 19,41% e 17,26% para DAP e altura, em nível de indivíduo, e de 9,7% e 8,63%, entr... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Myracrodruon urundeuva is a natural timber species with great potential for commercial use in Brazil, especially in the Pantanal, Cerrado and Caatinga regions, where native species are exploited. Intensive exploitation has caused great loss of individuals and the isolation of populations on islands due to the fragmentation of the species' habitat. Thus, the adoption of strategies for ex situ conservation of native species becomes indispensable. Two proposals were conceived in this work. The first was to estimate the genetic variability and genetic gain with the selection of a progeny test. The progeny test consortium with the species Myracrodruon urundeuva, Terminalia argentea and Astronium fraxinifolium, was installed on July 12, 1994 at the Fazenda de Ensino, Pesquisa e Extensão (FEPE), at the campus of Ilha Solteira (FEIS / UNESP) in the city Selvíria MS. The design was a randomized complete block, containing 28 progenies, six plants per plot and four replications for the species installed. The height and diameter of the chest height (dch) were measured at 24 years after planting. There was significant genetic variation between the progenies for the characters analyzed. The high survival rate indicates good adaptation of the species in intercropping tests. Estimates of the coefficient of genetic variation showed results of 19.41% and 17.26% for DBH and height, at the individual level, and of 9.7% and 8.63% among progenies. The individual heritabilities ranged from moderate... (Complete abstract click electronic access below) / Mestre

Duas espécies de cetáceos apresentam padrões de distribuição peculiares ao longo da costa brasileira, muito provavelmente em resposta às condições hidrográficas e topográficas que ocorrem entre 20 e 33°S. A primeira espécie, a franciscana ou toninha (Pontoporia blainvillei), é um golfinho de distribuição restrita do Brasil até a Argentina, que ocorre primariamente na plataforma continental interna, raramente ultrapassando os 50 m de profundidade. Já a segunda espécie, o golfinho-pintado-do-Atlântico (Stenella frontalis), é um golfinho de distribuição restrita ao Oceano Atlântico, que ocupa principalmente a plataforma continental. Estas duas espécies apresentam hiatos ao longo da sua distribuição no Brasil que tem consequências na morfologia e estrutura genética das espécies. Através da aplicação de diferentes métodos, o principal objetivo deste estudo foi investigar a influência do ambiente marinho no padrão de distribuição e na estrutura genética destas duas espécies com ênfase na costa brasileira. No primeiro capítulo, investigou-se a relação do ambiente marinho com o padrão de distribuição da franciscana. Para tanto, uma revisão e atualização da distribuição das áreas de manejo da franciscana (FMA), e dos limites dos hiatos, ao longo do Brasil foram realizadas. Análises de nicho ecológico sugerem que os hiatos fazem parte do nicho fundamental da franciscana que seriam, portanto, relativamente adequados para a espécie.No entanto, o estreitamento da plataforma continental parece ser o principal fator que explica a ausência da espécie nos hiatos e, inclusive poderia explicar a diferenciação genética entre algumas FMAs No segundo e terceiro capítulos, a relação entre similaridade genética e distâncias geográficas e ambientais foram investigadas para o golfinho-pintado-do- Atlântico em duas escalas: ao longo de praticamente toda distribuição e em uma escala mais restrita com ênfase no Brasil. Populações geneticamente distintas ao longo de toda distribuição da espécie foram identificadas com base em um marcador mitocondrial, que podem ser resultado Isolamento por Distância e Isolamento por Resistência, relacionados tanto com condições ambientais contemporâneas quanto do passado (Último Glacial Máximo). As análises de estrutura populacional do golfinho-pintado-do-Atlântico no Brasil, investigada mais profundamente com marcadores genômicos, indicam ao menos a existência de três populações (Brasil, Colômbia e Oceânica) suportanto, portanto, a hipótese de uma população isolada no sudeste do Brasil. De forma geral, conclui-se que o ambiente marinho e, principalmente, fatores como extensão da plataforma continental, batimetria e temperatura tem um papel fundamental para explicar o padrão de distribuição destas espécies no Brasil. Além disso, outros processos podem estar envolvidos na estruturação genética do golfinho-pintado-do-Atlântico e também da franciscana como, por exemplo, estrutura social, filopatria e a história evolutiva destas espécies. O maior desafio para conservação da franciscana é seu status de Criticamente Ameaçada no Brasil e, em relação ao golfinho-pintado-do-Atlântico é a deficiência de dados. Uma vez que ambas espécies ocorrem na porção mais desenvolvida do país, os resultados aqui obtidos têm impacto direto na conservação destas espécies, porque trazem informações que podem ser utilizadas em planos futuros de conservação e manejo. / Along Brazilian coastal waters, either franciscana and Atlantic spotted dolphins exhibited distributional gaps, which is most likely resulting from changes in the environmental features between 20 and 33°S. The former species, franciscana (Pontoporia blainvillei), is a river dolphin with restricted distribution from Brazil to Argentina, recorded mainly up to 50 m deep over the inner shelf. The second species, Atlantic spotted dolphin (Stenella frontalis), is a delphinine dolphin distributed across the Atlantic Ocean, being mainly recorded over the continental shelf. The distribution patterns that these species showed in Brazil have a direct influence on the morphology/ecology and genetic struture of both species. Different approaches were applied to address the main goal of this study, which was investigating the influence of marine environment in shaping the distribution pattern, as well as genetic strcuture of franciscana and Atlantic spotted dolphin with emphasis in the Brazilian coastal waters. In the first chapter, I investigated the franciscana distribution in Brazil using an ecological niche modeling approach. In order to do that, I performed a review of records of the species along Brazial and, updated the limits of franciscana management areas (FMAs) and distributional gaps. The results suggested that gaps are within franciscana fundamental niche and, therefore, both gaps would be suitable for franciscana. However, the narrow of continental shelf seems to be the main factor inhibiting the presence of franciscana in these areas. Furthermore, the narrowing of continental shelf play a role to explain the genetic differentiation among FMAs. In the second and third chapters, the relationship between genetic distances and geographic and environmental distances were investigated both in a restrict and a broad scale. I found genetically distinct populations 12 across Atlantic spotted dolphin distribution based on mtDNA, that are probably resulting of Isolation-by-Distance and Isolation-by-Resistance related both with contemporary and past conditions (e.g. Last Glacial Maximum). Furthermore, I investigated population struture using genomic markers (Single Nucleotide Polymorphisms, SNPs) across Western South Atlantic, Caribbean and Eastern Atlantic. The results suggested at least three different populations, and therefore, confirmed previous hypothesis of an isolated population in the southeastern Brazil. Overall, I concluded that marine envinronment, especially the extension of continental shelf, bathymetry and sea surface temperature, are the main factors that explaning the distribution pattern of franciscana and Atlantic spotted dolphin in Brazil. Besides that, other process such as, social structure and phylopatry, as well as biogeographical process might be investigated in further studies. Franciscana is considered “Critically endangered” in Brazil, and Atlantic spotted dolphin has not enough data to determine its conservation status. Since both species are recorded in the most developed region of the country with high anthropic pressure, my results could help in future management and conservation plans for both species in a regional scale.