Long non-protein coding RNAs (lncRNAs) represent a diverse and enigmatic classification of RNA. With roles associated with development and stress responses, these non-coding gene regulators are essential, and yet remain understudied in plants. Thus far, of just over 430 experimentally validated lncRNAs, only 13 are derived from plant systems and many of which do not meet the classic criteria of the RNA class. Without a solid definition of what makes a lncRNA, and few empirically validated transcripts, methods currently available for prediction fall short. To address this deficiency in lncRNA research, we constructed and applied a machine learning-based lncRNA prediction protocol that does not impose predefined rules, and utilises only experimentally confirmed lncRNAs in its training datasets. Through model evaluation, we found that our novel lncRNA prediction tool had an estimated accuracy of over 96%. In a study that predicted lncRNAs from transcriptomes of evolutionary diverse plant species, we determined that molecular features of lncRNAs display different phylogenetic signal patterns compared to protein-coding genes. Additionally, our analyses suggested that stress-resistant species express fewer lncRNAs than more stress sensitive species. To expand on these results, we used the prediction tool in concert with a transcriptomic study of two natural accessions of the drought tolerant species Eutrema salsugineum. Previously reported to show little physiological differences in a first drought, but differ significantly in a second, we instead demonstrated that the two ecotypes displayed vastly different transcriptomic responses, including the expression of lncRNAs, to a first and second drought treatment. In conclusion, the prediction tool can be applied to studies to further our knowledge of lncRNA evolution and as an additional tool in classic transcriptomic studies. The suggested importance of lncRNAs in drought resistance, and evidence of expression in two natural E. salsugineum accessions, merits further studies on the molecular and evolutionary mechanisms of these putatively regulatory transcripts. / Thesis / Doctor of Philosophy (PhD)

Projecting environmental niche models through time is a common goal when studying species response to climatic change. Species distribution models (SDMs) are commonly used to estimate a species' niche from observed patterns of occurrence and environmental predictors. However, a species niche is also shaped by non-environmental factors--including biotic interactions and dispersal barrier—truncating SDM estimates. Though truncated SDMs may accurately predict present-day species niche, projections through time are often biased by environmental condition change. Modeling niche in a phylogenetic framework leverages a clade's shared evolutionary history to pull species estimates closer towards phylogenetic conserved values and farther away from species specific biases. We propose a new Bayesian model of phylogenetic niche implemented in R. Under our model, species SDM parameters are transformed into biologically interpretable continuous parameters of environmental niche optimum, breadth, and tolerance evolving under multivariate Brownian motion random walk. Through simulation analyses, we demonstrated model accuracy and precision that improved as phylogeny size increased. We also demonstrated our model on a clade of eastern United States Plethodontid salamanders by accurately estimating species niche, even when no occurrence data is present. Our model demonstrates a novel framework where niche changes can be studied forwards and backwards through time to understand ancestral ranges, patterns of environmental specialization, and niche in data deficient species. / Master of Science / As many species face increasing pressure in a changing climate, it is crucial to understand the set of environmental conditions that shape species' ranges--known as the environmental niche--to guide conservation and land management practices. Species distribution models (SDMs) are common tools that are used to model species' environmental niche. These models treat a species' probability of occurrence as a function of environmental conditions. SDM niche estimates can predict a species' range given climate data, paleoclimate, or projections of future climate change to estimate species range shifts from the past to the future. However, SDM estimates are often biased by non-environmental factors shaping a species' range including competitive divergence or dispersal barriers. Biased SDM estimates can result in range predictions that get worse as we extrapolate beyond the observed climatic conditions. One way to overcome these biases is by leveraging the shared evolutionary history amongst related species to "fill in the gaps". Species that are more closely phylogenetically related often have more similar or "conserved" environmental niches. By estimating environmental niche over all species in a clade jointly, we can leverage niche conservatism to produce more biologically realistic estimates of niche. However, currently a methodological gap exists between SDMs estimates and macroevolutionary models, prohibiting them from being estimated jointly. We propose a novel model of evolutionary niche called PhyNE (Phylogenetic Niche Evolution), where biologically realistic environmental niches are fit across a set of species with occurrence data, while simultaneously fitting and leveraging a model of evolution across a portion of the tree of life. We evaluated model accuracy, bias, and precision through simulation analyses. Accuracy and precision increased with larger phylogeny size and effectively estimated model parameters. We then applied PhyNE to Plethodontid salamanders from Eastern North America. This ecologically-important and diverse group of lungless salamanders require cold and wet conditions and have distributions that are strongly affected by climatic conditions. Species within the family vary greatly in distribution, with some species being wide ranging generalists, while others are hyper-endemics that inhabit specific mountains in the Southern Appalachians with restricted thermal and hydric conditions. We fit PhyNE to occurrence data for these species and their associated average annual precipitation and temperature data. We identified no correlations between species environmental preference and specialization. Pattern of preference and specialization varied among Plethodontid species groups, with more aquatic species possessing a broader environmental niche, likely due to the aquatic microclimate facilitating occurrence in a wider range of conditions. We demonstrated the effectiveness of PhyNE's evolutionarily-informed estimates of environmental niche, even when species' occurrence data is limited or even absent. PhyNE establishes a proof-of-concept framework for a new class of approaches for studying niche evolution, including improved methods for estimating niche for data-deficient species, historical reconstructions, future predictions under climate change, and evaluation of niche evolutionary processes across the tree of life. Our approach establishes a framework for leveraging the rapidly growing availability of biodiversity data and molecular phylogenies to make robust eco-evolutionary predictions and assessments of species' niche and distributions in a rapidly changing world.

Ecótonos campo-floresta no sul do Brasil são originados pela expansão de ecossistemas florestais sobre os campestres, um processo natural gerado por mudanças climáticas de larga escala espacial e temporal. Este processo provoca mudanças vegetacionais que consequentemente modificam os padrões de distribuição, composição e riqueza faunística. Assim, ecótonos campo-floresta são sistemas adequados para inferir sobre a influência de processos históricos, biogeográficos e ecológicos na estruturação de comunidades. Para respondermos questões relacionadas a processos agindo em diferentes escalas espaciais, distribuímos as amostragens de modo a obtermos um panorama espacial da estrutura das assembléias. Assim, a proposta de estudo desenvolvido no Capítulo I foi avaliar o papel do ambiente e de dinâmicas espaciais sobre a composição, riqueza de espécies e número de indivíduos em metacomunidades de pequenos mamíferos não-voadores de ecótonos campo-floresta. Os resultados demonstram que os componentes ambiental, espacial e a estrutura espacial do ambiente contribuem igualmente na explicação da variância na composição de espécies, enquanto o ambiente foi mais importante em explicar mudanças na riqueza de espécies e número de indivíduos. Assim, concluímos que requerimentos de nicho das espécies e processos regionais como a limitação da dispersão, o distanciamento de centros de especiação e distribuição geográfica e o processo de expansão florestal conjuntamente explicam variações na estrutura de metacomunidades de pequenos mamíferos não-voadores em ecótonos campo-floresta no Sul do Brasil. No Capítulo II, inferimos sobre os processos gerando os padrões de coexistência de pequenos mamíferos não-voadores em assembléias baseando-se em afinidades filogenéticas e funcionais. Considerando estas similaridades, avaliamos se a diferenciação de nicho ou os filtros ambientais compõem processos importantes para explicar os padrões de coexistência em escalas de hábitat, paisagem e região. Os resultados apontam um padrão de agrupamento filogenético e funcional em todas as escalas avaliadas, embora um padrão de repulsão foi registrado no interior florestal, atestando a influência da diferenciação de nicho estruturando as assembléias de pequenos mamíferos não-voadores nesta porção do gradiente campo-floresta. A predominância do padrão de agrupamento filogenético e funcional afirma a ação de filtros ambientais como processos majoritariamente importantes em explicar os padrões de coexistência de espécies e indivíduos de pequenos mamíferos não-voadores nas escalas avaliadas. Desta forma, o estudo compõem uma das primeiras tentativas para definir os processos de estruturação de assembléias de pequenos mamíferos não-voadores neotropicais combinando aspectos taxonômicos, funcionais e filogenéticos, levantando também questões de conservação da biodiversidade nos sistemas ecológicos estudados. / Grassland-forest ecotones in southern Brazil are originated by forest expansion on grasslands, a natural process generated by climate shifts in large spatial and temporal scales, which causes vegetation changes and likely affects distribution, composition and faunal richness patterns. Thus, grassland-forest ecotones in southern Brazil are suitable systems to infer about influence of historical, biogeographical and ecological processes structuring communities. In order to make these inferences, we spatially sampled non-flying small mammals to characterize the spatial structure of species assemblages. The study proposal of Chapter I was to evaluate the role of environment and spatial dynamics on the composition, species richness and individuals number of nonflying small mammals metacommunities in grassland-forest ecotones. The results shows that environment, space and spatial structure of environment explained equally variations in species composition, while environment variables was the most important component explaining changes in species richness and number of individual. Thus, we conclude that niche requirements and regional processes like dispersal limitation, increase in distance of speciation cores and geographic distribution centers and the forest expansion process explain together variation in metacommunities structure of non-flying small mammals in grassland-forest ecotones at southern Brazil. In Chapter II, we inferred the coexistence patterns of non-flying small mammals based on phylogenetic and functional affinities. Considering these ecological similarities, we evaluate whether niche differentiation or environmental filters processes are responsible for patterns of species coexistence in habitat, landscape and regional scales. Results indicated a phylogenetic and functional cluster across all evaluated scales, although phylogenetic and functional repulsion was registered at forest interior, proving the importance of niche differentiation structuring non-flying small mammals assemblages in this grassland-forest gradient portion. Prevalence of phylogenetic and functional cluster across all scales attests environmental filters as important processes explaining species and individual coexistence patterns in habitat, landscape and regional scales. Therefore, this study comprises one of first attempts to define processes underlying the structure of neotropical non-flying small mammals assemblages combining taxonomic, functional and phylogenetic aspects, concurrently addressing important questions to biodiversity conservation in the ecological systems under study.

Ecótonos campo-floresta no sul do Brasil são originados pela expansão de ecossistemas florestais sobre os campestres, um processo natural gerado por mudanças climáticas de larga escala espacial e temporal. Este processo provoca mudanças vegetacionais que consequentemente modificam os padrões de distribuição, composição e riqueza faunística. Assim, ecótonos campo-floresta são sistemas adequados para inferir sobre a influência de processos históricos, biogeográficos e ecológicos na estruturação de comunidades. Para respondermos questões relacionadas a processos agindo em diferentes escalas espaciais, distribuímos as amostragens de modo a obtermos um panorama espacial da estrutura das assembléias. Assim, a proposta de estudo desenvolvido no Capítulo I foi avaliar o papel do ambiente e de dinâmicas espaciais sobre a composição, riqueza de espécies e número de indivíduos em metacomunidades de pequenos mamíferos não-voadores de ecótonos campo-floresta. Os resultados demonstram que os componentes ambiental, espacial e a estrutura espacial do ambiente contribuem igualmente na explicação da variância na composição de espécies, enquanto o ambiente foi mais importante em explicar mudanças na riqueza de espécies e número de indivíduos. Assim, concluímos que requerimentos de nicho das espécies e processos regionais como a limitação da dispersão, o distanciamento de centros de especiação e distribuição geográfica e o processo de expansão florestal conjuntamente explicam variações na estrutura de metacomunidades de pequenos mamíferos não-voadores em ecótonos campo-floresta no Sul do Brasil. No Capítulo II, inferimos sobre os processos gerando os padrões de coexistência de pequenos mamíferos não-voadores em assembléias baseando-se em afinidades filogenéticas e funcionais. Considerando estas similaridades, avaliamos se a diferenciação de nicho ou os filtros ambientais compõem processos importantes para explicar os padrões de coexistência em escalas de hábitat, paisagem e região. Os resultados apontam um padrão de agrupamento filogenético e funcional em todas as escalas avaliadas, embora um padrão de repulsão foi registrado no interior florestal, atestando a influência da diferenciação de nicho estruturando as assembléias de pequenos mamíferos não-voadores nesta porção do gradiente campo-floresta. A predominância do padrão de agrupamento filogenético e funcional afirma a ação de filtros ambientais como processos majoritariamente importantes em explicar os padrões de coexistência de espécies e indivíduos de pequenos mamíferos não-voadores nas escalas avaliadas. Desta forma, o estudo compõem uma das primeiras tentativas para definir os processos de estruturação de assembléias de pequenos mamíferos não-voadores neotropicais combinando aspectos taxonômicos, funcionais e filogenéticos, levantando também questões de conservação da biodiversidade nos sistemas ecológicos estudados. / Grassland-forest ecotones in southern Brazil are originated by forest expansion on grasslands, a natural process generated by climate shifts in large spatial and temporal scales, which causes vegetation changes and likely affects distribution, composition and faunal richness patterns. Thus, grassland-forest ecotones in southern Brazil are suitable systems to infer about influence of historical, biogeographical and ecological processes structuring communities. In order to make these inferences, we spatially sampled non-flying small mammals to characterize the spatial structure of species assemblages. The study proposal of Chapter I was to evaluate the role of environment and spatial dynamics on the composition, species richness and individuals number of nonflying small mammals metacommunities in grassland-forest ecotones. The results shows that environment, space and spatial structure of environment explained equally variations in species composition, while environment variables was the most important component explaining changes in species richness and number of individual. Thus, we conclude that niche requirements and regional processes like dispersal limitation, increase in distance of speciation cores and geographic distribution centers and the forest expansion process explain together variation in metacommunities structure of non-flying small mammals in grassland-forest ecotones at southern Brazil. In Chapter II, we inferred the coexistence patterns of non-flying small mammals based on phylogenetic and functional affinities. Considering these ecological similarities, we evaluate whether niche differentiation or environmental filters processes are responsible for patterns of species coexistence in habitat, landscape and regional scales. Results indicated a phylogenetic and functional cluster across all evaluated scales, although phylogenetic and functional repulsion was registered at forest interior, proving the importance of niche differentiation structuring non-flying small mammals assemblages in this grassland-forest gradient portion. Prevalence of phylogenetic and functional cluster across all scales attests environmental filters as important processes explaining species and individual coexistence patterns in habitat, landscape and regional scales. Therefore, this study comprises one of first attempts to define processes underlying the structure of neotropical non-flying small mammals assemblages combining taxonomic, functional and phylogenetic aspects, concurrently addressing important questions to biodiversity conservation in the ecological systems under study.

Ecótonos campo-floresta no sul do Brasil são originados pela expansão de ecossistemas florestais sobre os campestres, um processo natural gerado por mudanças climáticas de larga escala espacial e temporal. Este processo provoca mudanças vegetacionais que consequentemente modificam os padrões de distribuição, composição e riqueza faunística. Assim, ecótonos campo-floresta são sistemas adequados para inferir sobre a influência de processos históricos, biogeográficos e ecológicos na estruturação de comunidades. Para respondermos questões relacionadas a processos agindo em diferentes escalas espaciais, distribuímos as amostragens de modo a obtermos um panorama espacial da estrutura das assembléias. Assim, a proposta de estudo desenvolvido no Capítulo I foi avaliar o papel do ambiente e de dinâmicas espaciais sobre a composição, riqueza de espécies e número de indivíduos em metacomunidades de pequenos mamíferos não-voadores de ecótonos campo-floresta. Os resultados demonstram que os componentes ambiental, espacial e a estrutura espacial do ambiente contribuem igualmente na explicação da variância na composição de espécies, enquanto o ambiente foi mais importante em explicar mudanças na riqueza de espécies e número de indivíduos. Assim, concluímos que requerimentos de nicho das espécies e processos regionais como a limitação da dispersão, o distanciamento de centros de especiação e distribuição geográfica e o processo de expansão florestal conjuntamente explicam variações na estrutura de metacomunidades de pequenos mamíferos não-voadores em ecótonos campo-floresta no Sul do Brasil. No Capítulo II, inferimos sobre os processos gerando os padrões de coexistência de pequenos mamíferos não-voadores em assembléias baseando-se em afinidades filogenéticas e funcionais. Considerando estas similaridades, avaliamos se a diferenciação de nicho ou os filtros ambientais compõem processos importantes para explicar os padrões de coexistência em escalas de hábitat, paisagem e região. Os resultados apontam um padrão de agrupamento filogenético e funcional em todas as escalas avaliadas, embora um padrão de repulsão foi registrado no interior florestal, atestando a influência da diferenciação de nicho estruturando as assembléias de pequenos mamíferos não-voadores nesta porção do gradiente campo-floresta. A predominância do padrão de agrupamento filogenético e funcional afirma a ação de filtros ambientais como processos majoritariamente importantes em explicar os padrões de coexistência de espécies e indivíduos de pequenos mamíferos não-voadores nas escalas avaliadas. Desta forma, o estudo compõem uma das primeiras tentativas para definir os processos de estruturação de assembléias de pequenos mamíferos não-voadores neotropicais combinando aspectos taxonômicos, funcionais e filogenéticos, levantando também questões de conservação da biodiversidade nos sistemas ecológicos estudados. / Grassland-forest ecotones in southern Brazil are originated by forest expansion on grasslands, a natural process generated by climate shifts in large spatial and temporal scales, which causes vegetation changes and likely affects distribution, composition and faunal richness patterns. Thus, grassland-forest ecotones in southern Brazil are suitable systems to infer about influence of historical, biogeographical and ecological processes structuring communities. In order to make these inferences, we spatially sampled non-flying small mammals to characterize the spatial structure of species assemblages. The study proposal of Chapter I was to evaluate the role of environment and spatial dynamics on the composition, species richness and individuals number of nonflying small mammals metacommunities in grassland-forest ecotones. The results shows that environment, space and spatial structure of environment explained equally variations in species composition, while environment variables was the most important component explaining changes in species richness and number of individual. Thus, we conclude that niche requirements and regional processes like dispersal limitation, increase in distance of speciation cores and geographic distribution centers and the forest expansion process explain together variation in metacommunities structure of non-flying small mammals in grassland-forest ecotones at southern Brazil. In Chapter II, we inferred the coexistence patterns of non-flying small mammals based on phylogenetic and functional affinities. Considering these ecological similarities, we evaluate whether niche differentiation or environmental filters processes are responsible for patterns of species coexistence in habitat, landscape and regional scales. Results indicated a phylogenetic and functional cluster across all evaluated scales, although phylogenetic and functional repulsion was registered at forest interior, proving the importance of niche differentiation structuring non-flying small mammals assemblages in this grassland-forest gradient portion. Prevalence of phylogenetic and functional cluster across all scales attests environmental filters as important processes explaining species and individual coexistence patterns in habitat, landscape and regional scales. Therefore, this study comprises one of first attempts to define processes underlying the structure of neotropical non-flying small mammals assemblages combining taxonomic, functional and phylogenetic aspects, concurrently addressing important questions to biodiversity conservation in the ecological systems under study.

Phylogenetic Community Structure (PCS) metrics are becoming more common in community ecology. PCS metrics estimate the phylogenetic relatedness among members of an ecological community or assemblage. If ecological traits are conserved, then phylogenetic clustering (i.e., taxa are more closely related than expected by chance) indicates habitat filtering as the key process in community assembly. On the other hand, a pattern of phylogenetic overdispersion (i.e., taxa are more distantly related than expected by chance) suggests competition is dominant. Most studies to date have used PCS of unmanipulated ecosystems, but the value of PCS metrics will be best revealed in experiments. This project used PCS for aquatic beetle (Coleoptera) assemblages in experimentally manipulated seasonal wetlands on a cattle ranch in south-central Florida, and compared PCS metrics to standard ecological metrics. Wetlands were experimentally treated with all combinations of pasture management, fencing to exclude cattle, and controlled burning during 2006-2009. Beetle assemblages in fenced wetlands were significantly more overdispersed compared to non-fenced wetlands, suggesting that this treatment decreases habitat filtering, causing competition to become the dominant process in community formation. There was also a significant pasture x fence x burn interaction effect, with assemblages in wetlands differing in PCS depending on what combination of the three treatments were applied. Phylogenetic Diversity (PD – a measure of branch length of a community or assemblage on a phylogenetic tree) was highly correlated with genera richness (number of genera), and these metrics along with the expected number of genera (D – an ecological diversity index) found significant differences among burn treatments and a pasture x iii burn interaction. The results of this study indicate that PCS metrics complement classical ecological methods and should be widely applied.

Phylogenetics explores the evolutionary relationships among species and one of the main approaches is to construct phylogenetic trees through inference-based methods. Beyond the evolutionary insights these trees provide, the underlying tree structure can also be used to study geographical migration of species. These geographical models, reminiscent of models of DNA sequence evolution, have predominantly been discrete in their nature. However, this poses a multitude of challenges, especially with high-dimensional state-spaces. Previous work has explored the possibility of using continuous diffusion models for geographical migration, however these were not aiming to model non-local migration and large state-spaces. This paper presents and evaluates a scalable continuous phylogenetic migration model which aims to approximate conventional discrete migration models in the case of local and non-local migration.

Radiações evolutivas estão entre os eventos mais fascinantes da evolução. Grande parte da diversidade da vida, tanto de espécies como ecológica, surgiu nos breves intervalos temporais de rápida especiação que configuram as radiações. As causas ecológicas e não-ecológicas do surgimento da diversidade em radiações evolutivas, em especial nas radiações adaptativas, são tema de pesquisa há muito tempo, pelo menos desde que Darwin observou a imensa diversidade de um grupo de pássaros nas ilhas Galápagos. Desde então, as ilhas têm sido os ambientes ideais para o estudo desse fenômeno, e foi a partir das observações e experimentos em ilhas que toda a teoria ecológica das radiações evolutivas surgiu. Contudo, as causas ecológicas das radiações explosivas ocorridas em amplas escalas continentais permanecem tema de constante debate. Nesta tese, foram investigados os determinantes ecológicos e não-ecológicos (e.g., geografia, contingências históricas, efeitos filogenéticos) da evolução morfológica dos roedores sigmodontíneos durante sua radiação na região Neotropical, em especial no continente sul-americano. Para isso, foi quantificada a morfologia do crânio e mandíbula de mais de dois mil exemplares do grupo, e foram investigadas variações ecomorfológicas nos níveis interespecífico (I), intraespecífico (II), e entre assembleias de sigmodontíneos (III). Na Parte I da tese, foram investigadas duas predições da teoria da radiação adaptativa, a correlação-fenótipo ambiente (capítulo 1) e a funcionalidade do fenótipo através da força da mordida (capítulo 2), permitindo determinar o papel da divergência ecológica na evolução morfológica das espécies. Na Parte II (capítulo 3), foram investigadas as contribuições relativas de processos determinísticos e neutros sobre a variação morfológica entre populações de uma espécie de roedor sigmodontíneo amplamente distribuída, Akodon cursor. Na Parte III, a influência da variação ambiental e da distribuição espacial das linhagens filogenéticas de sigmodontíneos sobre o tamanho corporal (capítulo 4) e forma do crânio e mandíbula (capítulo 5), foram investigados no contexto biogeográfico da variação no tamanho e forma média entre assembleias de sigmodontíneos. As contribuições originais desta tese foram: (i) mostrar que a radiação evolutiva dos roedores sigmodontíneos foi guiada principalmente por fatores históricos e geográficos ao invés de fatores ecológicos; (ii) sugerir que radiações evolutivas ocorridas em escalas continentais, especialmente de roedores, têm um componente geográfico e histórico mais determinante do que o componente ecológico; (iii) revelar que a força da mordida varia pouco entre roedores sigmodontíneos herbívoros e granívoros, o que provavelmente é resultado do fenótipo generalista desses roedores; (iv) apontar que sigmodontíneos com dieta insetívora têm uma taxa de evolução mais rápida, e parecem estar evoluindo sua forma do crânio/mandíbula e sua força da mordida em uma direção diferente das demais espécies; (v) demonstrar que, dentro de uma espécie de sigmodontíneo (Akodon cursor), fluxo gênico e deriva genética explicam melhor a forma do crânio entre populações, enquanto a variação ambiental explica melhor o tamanho do crânio, indicando que o tamanho é uma característica mais lábil e mais sujeita a pressões ambientais do que a forma do crânio; (vi) mostrar que a variação biogeográfica, tanto do tamanho quanto da forma média do crânio/mandíbula entre assembleias de sigmodontíneos, está sob influência da distribuição diferencial das linhagens filogenéticas ao longo do espaço geográfico, bem como de variáveis ambientais; o que indica conservação filogenética de nicho à nível de metacomunidades. De modo geral, ao investigar as contribuições relativas dos componentes adaptativo e não-adaptativo da evolução morfológica, foram obtidas informações importantes para conhecer as causas da diversificação morfológica em Sigmodontinae, aumentando nosso conhecimento sobre as origens de toda a diversidade biológica. / Evolutionary radiations are among the most fascinating phenomena of evolution. Most of the biological diversity on the planet, both in terms of species and ecological diversity, appeared during these brief intervals of rapid speciation. The ecological and non-ecological causes of the emergence of diversity in evolutionary radiations, especially in adaptive radiations, have long been the subject of research, beginning with Darwin and his notice of the astonishing diversity of bird forms in the Galapagos Islands. Islands have since been ideal environments in which to study evolutionary and adaptive radiations, and indeed it was from observations and experiments on islands that all ecological theory of evolutionary radiations arose. However, the ecological causes of explosive radiations occurring on large continental scales are still a matter of debate. In this dissertation, I investigated the ecological and non-ecological (e.g., geography, historical contingencies, phylogenetic effects) determinants of morphological evolution in sigmodontine rodents during their radiation in the Neotropical region, particularly on the South-American continent. The skull and mandible morphology of more than two thousand specimens was quantified, and ecomorphological variation was investigated on three levels: interspecific (I), intraspecific (II), and among sigmodontine assemblages (III). In part I, two predictions from the ecological theory of adaptive radiation were investigated: the phenotype-environment correlation (chapter 1), and the trait utility through the bite force (chapter 2). This approach enabled determination of the role of ecological divergence in species morphological evolution. In part II (chapter 3), I investigated the relative contributions of deterministic and neutral processes to morphological variation among populations of one widely distributed sigmodontine species, Akodon cursor. In part III, I investigated the influence of environmental variation and spatial distribution of phylogenetic lineages on body size (chapter 4) and on shape of the skull and mandible (chapter 5), in the context of biogeographical variation of mean size and shape in sigmodontine assemblages. The original contributions of this dissertation are as follows: (i) to demonstrate that the evolutionary radiation of sigmodontines was driven mainly by historical and geographical factors instead of ecological factors; (ii) to suggest that evolutionary radiations on continental scales, especially rodent radiations, have a more determinant historical and geographical component than an ecological one; (iii) to show small variation in bite force between sigmodontine herbivores and granivores, which is likely a consequence of the generalist phenotype of these rodents; (iv) to highlight that insectivorous sigmodontines have a faster rate of morphological evolution than other diet groups, and that skull and mandible morphology and bite force are evolving in different directions than in other species; (v) to demonstrate that within a sigmodontine species (Akodon cursor), gene flow and genetic drift better explain variation in skull shape among populations, while environmental variation better explains variation in skull size, which suggests that size is more labile feature than shape and thus more prone to change with environmental pressures; and (vi) to show that biogeographical variation in mean body size, mean skull shape, and mean mandible shape across sigmodontine assemblages is influenced by the different distributions of phylogenetic lineages over geographical space, as well by environmental variables, which indicates phylogenetic niche conservatism at the metacommunity level. These results shed light on some of the factors driving morphological diversification in Sigmodontinae. Further, the analytical approach(es) utilized may be useful for general investigations of the relative contributions of adaptive and non-adaptive components of morphological evolution, thereby potentially increasing our knowledge of the origins of all biological diversity.

The epidemiology of blastomycosis remains poorly understood in part due to the lack of a robust and discriminatory strain typing method for Blastomyces dermatitidis. Here we describe the development of a multilocus sequence (MLST) method to study the genetic variation and population structure of B. dermatitidis. Eighty geographically diverse clinical and environmental isolates were examined. Thirty-six unique sequence types were identified. With a discriminatory index of 91.4%, MLST identifies significant genetic diversity for the characterization of local and global B. dermatitidis isolates. To test whether this fungus represented a single species throughout its geographic range we performed phylogenetic analyses, applying Genealogical Concordance Phylogenetic Species Recognition (GCPSR). Phylogenetic analysis revealed two distinct clades, with five of the eight gene phylogenies studied supporting the separation of these lineages, which were also geographically partitioned. Based on fulfillment of GCPSR, we propose the current species B. dermatitidis harbors two genetically distinct non-interbreeding phylogenetic species.

The epidemiology of blastomycosis remains poorly understood in part due to the lack of a robust and discriminatory strain typing method for Blastomyces dermatitidis. Here we describe the development of a multilocus sequence (MLST) method to study the genetic variation and population structure of B. dermatitidis. Eighty geographically diverse clinical and environmental isolates were examined. Thirty-six unique sequence types were identified. With a discriminatory index of 91.4%, MLST identifies significant genetic diversity for the characterization of local and global B. dermatitidis isolates. To test whether this fungus represented a single species throughout its geographic range we performed phylogenetic analyses, applying Genealogical Concordance Phylogenetic Species Recognition (GCPSR). Phylogenetic analysis revealed two distinct clades, with five of the eight gene phylogenies studied supporting the separation of these lineages, which were also geographically partitioned. Based on fulfillment of GCPSR, we propose the current species B. dermatitidis harbors two genetically distinct non-interbreeding phylogenetic species.