A busca de padrões consistentes na natureza tem sido a principal meta dos ecólogos. Essa dissertação teve como objetivo usar abordagens filogenéticas na tentativa de compreender melhor o processo ecológico da expansão florestal sobre áreas abertas. O uso da informação filogenética em análises ecológicas considera as espécies não independentes umas das outras, pois estas compartilham grande parte da história evolutiva. Essa hierarquia de organização das espécies é muito importante para determinar as regras que governam os processos de montagem das comunidades locais. Nesta dissertação foram avaliados padrões filogenéticos de estruturação da vegetação lenhosa florestal ocorrente em ecótonos de áreas abertas com vegetação florestal distribuídos em diferentes regiões do extremo sul do Brasil. Estes ecótonos são formados por diversas formações florestais, as quais tendem a expandir sobre as áreas abertas. Dados sobre composição de espécies provieram de estudos já realizados e de amostragens em alguns sítios. Duas métricas filogenéticas complementares foram usadas para avaliar a estrutura filogenética em cada categoria de habitat nos ecótonos: índice de parentesco líquido (NRI) e coordenadas principais da estrutura filogenética (PCPS). As análises dos valores de NRI não mostraram um padrão nítido de estruturação filogenética das comunidades. Já a análise dos PCPS mostrou padrões consistentes nas três escalas espaciais abordadas e independente da composição de espécies. Clados basais associaram-se às áreas florestais, enquanto clados de diversificação recente associaram-se às áreas abertas. Estes resultados indicam que áreas abertas atuam como um filtro filogenético de habitat para as espécies lenhosas florestais em todos os locais analisados, independentemente da escala e da composição de espécies de cada local. Os resultados sugerem que os clados de Rosanae e Asteranae estão na linha de frente do processo de expansão florestal sobre as áreas abertas, e o clado de Magnolianae restrito às áreas florestais. A busca por padrões gerais de organização das comunidades ecológicas a partir de sua estrutura filogenética parece consistir numa ferramenta útil para a exploração e entendimento sobre o funcionamento de sistemas ecológicos. Estas abordagens poderiam beneficiar estratégias de gerenciamento e conservação destes sistemas, por simplificarem sistemas ecológicos complexos e por mostrarem padrões gerais independentes da escala espacial analisada. / The search for consistent patterns in nature has been a major goal of ecologists. This study aimed to employ phylogenetic analyses to improve the understanding of an ecological process, the expansion of forest expansion over open areas. The use of evolutionary information considers species as not independent units in relation to each other, as they share their evolutionary history. Such hierarchical organization of species is very important to determine the rules governing assembly processes in local communities. Phylogenetic approaches were used to evaluate phylogenetic patterns in forest woody vegetation occurring in ecotones comprising open areas and forest vegetation, and distributed across different regions in the southernmost Brazilian region. Those ecotones are composed by different forest vegetation types, which tend to expand over open areas. Data on species composition were compiled from previous studies, and vegetation sampling was carried out in sites without available information on species composition in ecotones. Two complementary phylogenetic metrics were used to evaluate the phylogenetic structure in each habitat type occurring in ecotones: net relatedness index (NRI) and principal coordinates of phylogenetic structure (PCPS). Analyses of NRI values did not show any clear pattern of phylogenetic structuring of the communities. Nonetheless, PCPS analysis showed consistent patterns across the threes spatial scales evaluated, which were independent of the species composition of the sites. Basal clades were associated with forest areas, while late-divergence clades were associated with open areas. These findings indicate that open areas act as a phylogenetic habitat filtering to forest woody species throughout the region, independently of the spatial scale and of the species composition in each site. The results suggest that the clades Rosanae and Asteranae represent the vanguard in theforest expansion process over open areas, while the distribution of the basal clade Magnolianae is restricted to forest sites. The search for general organization patterns in ecological communities based on their phylogenetic structure seems to be a useful tool for exploring and understanding the functioning of ecological systems. Such approach might benefit ecosystem managing and conservation strategies, as it simplifies complex ecological systems, and shows general patterns independently of the scale analyzed.

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.

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.

A busca de padrões consistentes na natureza tem sido a principal meta dos ecólogos. Essa dissertação teve como objetivo usar abordagens filogenéticas na tentativa de compreender melhor o processo ecológico da expansão florestal sobre áreas abertas. O uso da informação filogenética em análises ecológicas considera as espécies não independentes umas das outras, pois estas compartilham grande parte da história evolutiva. Essa hierarquia de organização das espécies é muito importante para determinar as regras que governam os processos de montagem das comunidades locais. Nesta dissertação foram avaliados padrões filogenéticos de estruturação da vegetação lenhosa florestal ocorrente em ecótonos de áreas abertas com vegetação florestal distribuídos em diferentes regiões do extremo sul do Brasil. Estes ecótonos são formados por diversas formações florestais, as quais tendem a expandir sobre as áreas abertas. Dados sobre composição de espécies provieram de estudos já realizados e de amostragens em alguns sítios. Duas métricas filogenéticas complementares foram usadas para avaliar a estrutura filogenética em cada categoria de habitat nos ecótonos: índice de parentesco líquido (NRI) e coordenadas principais da estrutura filogenética (PCPS). As análises dos valores de NRI não mostraram um padrão nítido de estruturação filogenética das comunidades. Já a análise dos PCPS mostrou padrões consistentes nas três escalas espaciais abordadas e independente da composição de espécies. Clados basais associaram-se às áreas florestais, enquanto clados de diversificação recente associaram-se às áreas abertas. Estes resultados indicam que áreas abertas atuam como um filtro filogenético de habitat para as espécies lenhosas florestais em todos os locais analisados, independentemente da escala e da composição de espécies de cada local. Os resultados sugerem que os clados de Rosanae e Asteranae estão na linha de frente do processo de expansão florestal sobre as áreas abertas, e o clado de Magnolianae restrito às áreas florestais. A busca por padrões gerais de organização das comunidades ecológicas a partir de sua estrutura filogenética parece consistir numa ferramenta útil para a exploração e entendimento sobre o funcionamento de sistemas ecológicos. Estas abordagens poderiam beneficiar estratégias de gerenciamento e conservação destes sistemas, por simplificarem sistemas ecológicos complexos e por mostrarem padrões gerais independentes da escala espacial analisada. / The search for consistent patterns in nature has been a major goal of ecologists. This study aimed to employ phylogenetic analyses to improve the understanding of an ecological process, the expansion of forest expansion over open areas. The use of evolutionary information considers species as not independent units in relation to each other, as they share their evolutionary history. Such hierarchical organization of species is very important to determine the rules governing assembly processes in local communities. Phylogenetic approaches were used to evaluate phylogenetic patterns in forest woody vegetation occurring in ecotones comprising open areas and forest vegetation, and distributed across different regions in the southernmost Brazilian region. Those ecotones are composed by different forest vegetation types, which tend to expand over open areas. Data on species composition were compiled from previous studies, and vegetation sampling was carried out in sites without available information on species composition in ecotones. Two complementary phylogenetic metrics were used to evaluate the phylogenetic structure in each habitat type occurring in ecotones: net relatedness index (NRI) and principal coordinates of phylogenetic structure (PCPS). Analyses of NRI values did not show any clear pattern of phylogenetic structuring of the communities. Nonetheless, PCPS analysis showed consistent patterns across the threes spatial scales evaluated, which were independent of the species composition of the sites. Basal clades were associated with forest areas, while late-divergence clades were associated with open areas. These findings indicate that open areas act as a phylogenetic habitat filtering to forest woody species throughout the region, independently of the spatial scale and of the species composition in each site. The results suggest that the clades Rosanae and Asteranae represent the vanguard in theforest expansion process over open areas, while the distribution of the basal clade Magnolianae is restricted to forest sites. The search for general organization patterns in ecological communities based on their phylogenetic structure seems to be a useful tool for exploring and understanding the functioning of ecological systems. Such approach might benefit ecosystem managing and conservation strategies, as it simplifies complex ecological systems, and shows general patterns independently of the scale analyzed.

Submitted by Marlene Santos (marlene.bc.ufg@gmail.com) on 2018-07-26T17:56:37Z No. of bitstreams: 2 Tese - Jesús Nazareno Pinto Ledezma - 2017.pdf: 8871426 bytes, checksum: 451cfc37da75487787cfc68ca57f9d82 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2018-07-27T15:03:35Z (GMT) No. of bitstreams: 2 Tese - Jesús Nazareno Pinto Ledezma - 2017.pdf: 8871426 bytes, checksum: 451cfc37da75487787cfc68ca57f9d82 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2018-07-27T15:03:35Z (GMT). No. of bitstreams: 2 Tese - Jesús Nazareno Pinto Ledezma - 2017.pdf: 8871426 bytes, checksum: 451cfc37da75487787cfc68ca57f9d82 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2017-06-07 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / One of the major challenges in biology is to understand the processes that originate and maintain of species diversity, and that in turn, determinate the observed patterns of biological diversity at different spatial and temporal scales. Here, we explore the historical processes that generate the species diversity and the assembly of local assemblages of Furnariides, the largest bird continental endemic radiation. In general, we used data of geographic distribution, local assemblages, life history (e.g., habitat preference) and molecular phylogenies. Furnariides diversified mainly during the Tertiary period, period in which South America was an island continent. Also, they are tightly related with the habitat that they occupy, where, the forest habitats represent the ancestral habitat for this clade. The Furnariides species richness pattern follows the same species richness pattern of birds in general, with a higher concentration of species at low latitudes and in forest habitats. Although the concentration of species is higher in these regions, the regions at higher latitudes and of open habitats, present rapid rates of speciation, extinction and colonization, suggesting that these habitats represent an effective arena for diversification in the Neotropics, and that are important for the maintenance of species diversity in forest habitats. Finally, the phylogenetic structure of assemblages of Furnariides, is influenced for the habitat preferences, and that the assembly of local assemblages is determined by the combined effect of historical colonisation and local extinction, as well as, the niche conservatism and environmental filtering. / Um dos principais desafios em biologia é entender os processos que dão origem e mantêm a diversidade de espécies, e que, por sua vez, determinam os padrões observados da diversidade biológica em diferentes escalas espaciais e temporais. Nesta tese, exploramos os processos históricos que geram a diversidade de espécies e a montagem de assembleias locais no infraorder dos Furnariides, a maior radiação continental endêmica de aves. De maneira geral se usaram dados de distribuição das espécies, de assembleias locais, historia de vida (e.g., preferência de habitat) e filogenias moleculares. Se demostra que os Furnariides principalmente diversificaram no período Terciário, período no qual América do Sul foi uma ilha continente. Além disso, estão estreitamente relacionadas com o habitat que elas ocupam, sendo que os habitats de floresta representam o habitat ancestral deste clado. O padrão de riqueza de espécies de Furnariides segue o mesmo padrão de riqueza de aves em geral, com uma maior concentração de espécies em latitudes menores e em habitats de floresta. Embora a concentração de espécies seja maior em estas regiões, as regiões de latitudes maiores e de habitats abertos, apresentaram taxas de especiação, extinção e dispersão mais rápidas, sugerindo que os habitats abertos representam areias efetivas de diversificação no Neotrópico e são importantes para o mantimento da diversidade de espécies em habitats de floresta. Finalmente, a estrutura filogenética das assembleias dos Furnariides e influenciada pela preferência de habitat, além disso, a montagem de assembleias locais depende do efeito combinado das taxas diferencias de colonização e extinção local, assim como a conservação de nicho e da filtragem ambiental.

A busca de padrões consistentes na natureza tem sido a principal meta dos ecólogos. Essa dissertação teve como objetivo usar abordagens filogenéticas na tentativa de compreender melhor o processo ecológico da expansão florestal sobre áreas abertas. O uso da informação filogenética em análises ecológicas considera as espécies não independentes umas das outras, pois estas compartilham grande parte da história evolutiva. Essa hierarquia de organização das espécies é muito importante para determinar as regras que governam os processos de montagem das comunidades locais. Nesta dissertação foram avaliados padrões filogenéticos de estruturação da vegetação lenhosa florestal ocorrente em ecótonos de áreas abertas com vegetação florestal distribuídos em diferentes regiões do extremo sul do Brasil. Estes ecótonos são formados por diversas formações florestais, as quais tendem a expandir sobre as áreas abertas. Dados sobre composição de espécies provieram de estudos já realizados e de amostragens em alguns sítios. Duas métricas filogenéticas complementares foram usadas para avaliar a estrutura filogenética em cada categoria de habitat nos ecótonos: índice de parentesco líquido (NRI) e coordenadas principais da estrutura filogenética (PCPS). As análises dos valores de NRI não mostraram um padrão nítido de estruturação filogenética das comunidades. Já a análise dos PCPS mostrou padrões consistentes nas três escalas espaciais abordadas e independente da composição de espécies. Clados basais associaram-se às áreas florestais, enquanto clados de diversificação recente associaram-se às áreas abertas. Estes resultados indicam que áreas abertas atuam como um filtro filogenético de habitat para as espécies lenhosas florestais em todos os locais analisados, independentemente da escala e da composição de espécies de cada local. Os resultados sugerem que os clados de Rosanae e Asteranae estão na linha de frente do processo de expansão florestal sobre as áreas abertas, e o clado de Magnolianae restrito às áreas florestais. A busca por padrões gerais de organização das comunidades ecológicas a partir de sua estrutura filogenética parece consistir numa ferramenta útil para a exploração e entendimento sobre o funcionamento de sistemas ecológicos. Estas abordagens poderiam beneficiar estratégias de gerenciamento e conservação destes sistemas, por simplificarem sistemas ecológicos complexos e por mostrarem padrões gerais independentes da escala espacial analisada. / The search for consistent patterns in nature has been a major goal of ecologists. This study aimed to employ phylogenetic analyses to improve the understanding of an ecological process, the expansion of forest expansion over open areas. The use of evolutionary information considers species as not independent units in relation to each other, as they share their evolutionary history. Such hierarchical organization of species is very important to determine the rules governing assembly processes in local communities. Phylogenetic approaches were used to evaluate phylogenetic patterns in forest woody vegetation occurring in ecotones comprising open areas and forest vegetation, and distributed across different regions in the southernmost Brazilian region. Those ecotones are composed by different forest vegetation types, which tend to expand over open areas. Data on species composition were compiled from previous studies, and vegetation sampling was carried out in sites without available information on species composition in ecotones. Two complementary phylogenetic metrics were used to evaluate the phylogenetic structure in each habitat type occurring in ecotones: net relatedness index (NRI) and principal coordinates of phylogenetic structure (PCPS). Analyses of NRI values did not show any clear pattern of phylogenetic structuring of the communities. Nonetheless, PCPS analysis showed consistent patterns across the threes spatial scales evaluated, which were independent of the species composition of the sites. Basal clades were associated with forest areas, while late-divergence clades were associated with open areas. These findings indicate that open areas act as a phylogenetic habitat filtering to forest woody species throughout the region, independently of the spatial scale and of the species composition in each site. The results suggest that the clades Rosanae and Asteranae represent the vanguard in theforest expansion process over open areas, while the distribution of the basal clade Magnolianae is restricted to forest sites. The search for general organization patterns in ecological communities based on their phylogenetic structure seems to be a useful tool for exploring and understanding the functioning of ecological systems. Such approach might benefit ecosystem managing and conservation strategies, as it simplifies complex ecological systems, and shows general patterns independently of the scale analyzed.

Few studies have explored the relative strength of ecogeographic versus lineage-specific effects on a global scale, particularly for poikilotherms, those organisms whose internal temperature varies with their environment. Here, we compile a global dataset of life history traits in Daphnia, at the species-and population-level, and use those data to parse the relative influences of lineage-specific effects and climate. We also compare the thermal response (plasticity) of life history traits and their dependence on climate, temperature, precipitation, and latitude. We found that the mode of evolution for life history traits varies but that the thermal response of life history traits most often follows a random walk model of evolution. We conclude that life history trait evolution in Daphnia is not strongly species-specific but is ecogeographically distinct, suggesting that life history evolution should be understood at the population level for Daphnia and possibly for other poikilotherms.

BACKGROUND:A multi-labeled tree, or MUL-tree, is a phylogenetic tree where two or more leaves share a label, e.g., a species name. A MUL-tree can imply multiple conflicting phylogenetic relationships for the same set of taxa, but can also contain conflict-free information that is of interest and yet is not obvious.RESULTS:We define the information content of a MUL-tree T as the set of all conflict-free quartet topologies implied by T, and define the maximal reduced form of T as the smallest tree that can be obtained from T by pruning leaves and contracting edges while retaining the same information content. We show that any two MUL-trees with the same information content exhibit the same reduced form. This introduces an equivalence relation among MUL-trees with potential applications to comparing MUL-trees. We present an efficient algorithm to reduce a MUL-tree to its maximally reduced form and evaluate its performance on empirical datasets in terms of both quality of the reduced tree and the degree of data reduction achieved.CONCLUSIONS:Our measure of conflict-free information content based on quartets is simple and topologically appealing. In the experiments, the maximally reduced form is often much smaller than the original tree, yet retains most of the taxa. The reduction algorithm is quadratic in the number of leaves and its complexity is unaffected by the multiplicity of leaf labels or the degree of the nodes.

Thesis (PhD) - Stellenbosch University, 2011. / ENGLISH ABSTRACT: The Albertine Rift is characterized by a heterogeneous landscape which may, at least in part, drive the exceptional biodiversity found across all taxonomic levels. Notwithstanding the biodiversity and beauty of the region, large areas are poorly understood because of political instability with the inaccessibility of most of the region as a contributing factor. The majority of studies in the Albertine Rift have focussed on charismatic mega fauna, with other taxa receiving less attention. One of the taxonomically and numerically more abundant small mammal genera is the genus Praomys, an African endemic with a wide distribution range spanning most of west, central and east Africa. Four species are typically recognized from the Albertine Rift namely P. degraaffi, P. jacksoni, P. misonnei and P. verschureni. In this study I used a combination of DNA sequence data (mitochondrial control region, mitochondrial cytochrome b and 7th intron of the nuclear ß-fibrinogen gene) as well as morphometric data (traditional and geometric) to investigate the systematics of the Praomys taxa occurring in the Albertine Rift. To allow meaningful DNA assessments and in an attempt to identify potential drivers of diversifications, other Praomys species were also included from public sequence data bases for comparisons. The main focus was on P. jacksoni (the numerically most abundant taxon; also, up to 2005, all Praomys in the Albertine Rift were mostly collected as “jacksoni”) and P. degraaffi (an Albertine Rift endemic). A surprising finding was the presence of P. mutoni; this represents a range extension for this species into the Albertine Rift. Distinct evolutionary lineages were found in both P. jacksoni (confirmed by sequence data as well as morphometrics) as well as P. degraaffi (based only on sequence data; insufficient samples precluded a full morphometric investigation). These lineages (in both P. jacksoni as well as P. degraaffi) appear to be separated along a north – south gradient; however, further investigations should confirm this. To further investigate the genetic patterns at local scales across the Albertine Rift, as well as introgression between species as revealed by sequence data, a species-specific microsatellite library was developed for P. jacksoni. Twelve polymorphic markers were identified of which nine also amplified in P. degraaffi. Introgression was confirmed between the two focal species with almost 20% of the individuals analysed being jacksoni-degraaffi hybrids. This is perhaps not so surprising given that there is considerable overlap in their ranges (between ~ 1500 m a.s.l. to 2450 m a.s.l.) as well as the relative ages of the species (the divergence time between these two species were estimated at 3.8 Mya). The presence of distinct lineages within each of these species was confirmed by microsatellite analyses (these lineages diverged approcimately at same time at ca. 3.4 Mya). As suggested by sequence and morphometric data, these lineages had a largely north – south distribution but with considerable overlap in the central Albertine Rift in the vicinity of Lake Kivu. The phylogeographic patterns obtained for both focal species were not consistent with the physical barriers such as the rivers, lakes or mountains, nor were they exclusively associated with Pleistocene phenomena such as the change of the course of the rivers or uplift; rather, the lineages predate the Pleistocene and fall firmly in the Pliocene (>3 Mya). Biogeographically, the north - south location of lineages with a centrally - located contact zone could be a result of parapatric speciation due to habitat fragmentation or past climate change, followed by secondary contact. Barcoding using genetic information provides a useful tool to identify unknown taxa, cryptic diversity or where different life stages are difficult to identify. From an invasion biology perspective, it allows for the rapid identification of problem taxa against a known data base. By adopting such a barcoding approach (senso lato), the presence of three invasive rodents was confirmed in the Democratic Republic of the Congo (DRC); these are Rattus rattus (black rat), R. norvegicus (Norway rat) and Mus musculus domesticus (house mouse). A comparison with global data available for these species revealed two possible introduction pathways namely via the shipping port at Kinshasa/Matadi (with strong links to Europe) and via the slave trade routes in the east (strong links to the Arab world and the east). Of these three taxa, only R. rattus is currently documented from the DRC although the others have received mention in the gray literature. These findings draw attention to the lack of any official policy regarding biosecurity in the DRC, and argue for the development of strict control measures to prevent further introductions. / AFRIKAANSE OPSOMMING: Die Albertine Rift word gekenmerk deur 'n heterogene landskap wat kan, ten minste gedeeltelik, die uitsonderlike biodiversiteit wat oor al die taksonomiese vlakke gevind word teweeg bring. Nieteenstaande die biodiversiteit en die skoonheid van die streek, is groot gebiede onbekend as gevolg van politieke onstabiliteit met die ontoeganklikheid van meeste van die streek as 'n bydraende faktor. Die meerderheid van studies in die Albertine Rift het gefokus op die charismatiese mega fauna, met ander taxa wat minder aandag ontvang. Een van die taksonomies en numeries meer volop klein soogdier genera is die genus Praomys, 'n Afrika endemiese groep met 'n wye verspreiding wat strek oor die grootste deel van van wes-, sentraal en oos-Afrika. Vier spesies word tipies erken van die Albertine Rift naamlik P. degraaffi, P. jacksoni, P. misonnei en P. verschureni. In hierdie studie het ek 'n kombinasie van DNA volgorde data (mitochondriale beheer streek, mitochondriale sitochroom b en 7de intron van die kern ß-fibrinogeen geen) sowel as morfometriese data (tradisioneel en meetkundig) gebruik om die sistematiek van die Praomys taxa te ondersoek. Om betekenisvolle DNA aanslae toe te laat en in 'n poging om potensiële aandrywers van diversiteit te identifiseer, is ander Praomys spesies van openbare volgorde data basisse vir vergelykings ingesluit. Die hooffokus is op P. jacksoni (die numeries volopste takson, ook, tot en met 2005 is alle Praomys in die Albertine Rift meestal as "jacksoni" versamel) en P. degraaffi ('n Albertine Rift endemiese spesie). 'n Verrassende bevinding was die teenwoordigheid van P. mutoni, dit verteenwoordig' n verspreidingsuitbreiding vir hierdie spesie in die Albertine Rift. Bepaalde evolusionêre ontwikkelingslyne was in beide P. jacksoni (bevestig deur die volgorde data sowel as morfometrie) sowel as P. degraaffi (wat slegs gebaseer is op die volgorde data, onvoldoende monsters verhinder 'n volledige morfometriese ondersoek). Hierdie lyne (in beide P. jacksoni sowel as P. degraaffi) word geskei langs 'n noord - suid gradiënt, maar verdere ondersoeke moet dit bevestig. Om die genetiese patrone op plaaslike skaal oor die Albertina Rift verder te ondersoek, sowel as introgressie tussen spesies soos geopenbaar deur die volgorde data, is 'n spesie-spesifieke mikrosatelliet biblioteek ontwikkel vir P. jacksoni. Twaalf polimorfiese merkers is geïdentifiseer waarvan nege ook amplifiseer in P. degraaffi. Introgressie is bevestig tussen die twee brandpunt spesies met byna 20% van die individue wat ontleed is as jacksoni-degraaffi basters. Dit is miskien nie so verbasend gegee dat daar aansienlike oorvleueling is in hul gebiede (tussen ~ 1500 m bo seespieel tot 2450 m bo seespieel), sowel as die relatiewe ouderdomme van die spesies (die divergensie tussen hierdie twee spesies is geskat op 3,8 Mya). Die teenwoordigheid van verskillende lyne in elk van hierdie spesies is bevestig deur mikrosatelliet ontleding (hierdie lyne het gedivergeer ongeveer 3,4 Mya). Soos voorgestel deur die DNA volgorde en morfometriese data, het hierdie lyne 'n grootliks noorde – suid verspreiding, maar met 'n aansienlike oorvleueling in die sentrale Albertine Rift in die omgewing van die Kivumeer. Die filogeografiese patrone wat vir beide die brandpunt spesies gevind is nie in ooreenstemming met die fisiese struikelblokke soos die riviere, mere of berge nie, en hou ook nie uitsluitlik verband met die Pleistoseen verskynsels soos die verandering van die loop van die riviere nie; die afstammelinge is eerder veel ouer as die Pleistoseen en val binne die Plioseen (> 3 Mya). Biogeografies, die noorde – suid plasing van die lyne met 'n sentraal geleë kontak sone kan die gevolg wees van parapatriese spesiasie te danke aan habitatfragmentasie as gevolg van verandering in die klimaat, gevolg deur 'n sekondêre kontak. Strepieskodering met behulp van genetiese inligting verskaf 'n nuttige instrument om onbekend taxa, kriptiese diversiteit of waar verskillende lewensfases moeilik is om te identifiseer, te identifiseer. Vanuit 'n indringerbiologie perspektief, maak hierdie benadering dit moontlik om vinnige identifikasies van die probleem taksa teen' n bekende data basis te bekom. Deur gebruik te maak van so 'n strepieskoderingsbenadering (senso lato), is die teenwoordigheid van drie indringende knaagdiere bevestig in die Demokratiese Republiek van die Kongo (DRK), naamlik Rattus rattus (swart rot), R. norvegicus (Noorweë rot) en Mus musculus domesticus (huis muis). 'n Vergelyking met die globale data wat beskikbaar is vir hierdie spesies het aan die lig gebring dat twee moontlike betree-roetes bestaan, naamlik via die skeepshawe by Kinshasa / Matadi (met sterk skakels na Europa), en via die slawehandel roetes in die ooste (sterk skakels na die Arabiese wêreld en die ooste) . Van hierdie drie taxa, is tans slegs R. rattus van die Demokratiese Republiek van die Kongo gedokumenteer, hoewel die ander melding ontvang in die grys literatuur. Hierdie bevindinge vestig die aandag op die gebrek aan enige amptelike beleid ten opsigte van biosekuriteit in die Demokratiese Republiek van die Kongo, en argumenteer vir die ontwikkeling van streng beheermaatreëls om verdere indringerspesies te voorkom.

Thesis (MSc)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: The Afroedura nivaria complex is one of the six recognized species complexes within a southern African endemic genus, Afroedura. The A. nivaria complex is a morphologically conservative group of medium-sized geckos endemic to South Africa though they are unevenly distributed in the Eastern Cape, Free State and KwaZulu-Natal provinces. The complex comprises the following five species: A. nivaria (Boulenger 1894), A. amatolica (Hewitt 1925), A. karroica (Hewitt 1925), A. tembulica (Hewitt 1926) and A. halli (Hewitt 1935). These nocturnal and rupicolous geckos shelter in narrow rock crevices on outcrops. It is currently unknown whether a) the described species are valid and b) if additional lineages are present on isolated outcrops. I investigated the hypothesis that endemics with a narrow distribution, that is, A. amatolica and A. tembulica are valid species but that isolated populations in the widespread species (A. nivaria, A. karroica and A. halli) demonstrate genetic variation at the species level. Fragments of two mitochondrial genes (16S rRNA and ND4) and a single nuclear marker (KIAA) were sequenced and analysed using Bayesian inference, maximum parsimony and maximum likelihood. All analyses strongly supported the genetic distinctiveness of the described species. The A. nivaria complex is not monophyletic, A. karroica appeared to be outside the species complex and A. pondolia (thought to be outside the A. nivaria complex) consistently nested within A. nivaria complex. Additional clades recovered in the phylogeny within A. halli and A. nivaria had large genetic divergences and no spatial overlap. Narrowly distributed A. amatolica showed to have two highly diverged clades. Clades recovered in the phylogeny highlight geographical structuring. These findings suggest the existence of up to four additional cryptic lineages within the complex. I used morphometric data (ecologically relevant morphological traits) to investigate whether the genetic lineages would present morphological conservatism. Multivariate analyses of 19 variables showed variation within the A. nivaria species complex was accounted for mostly by differences in locomotor apparatus (limbs and feet) and head dimensions. These traits are mostly related to microhabitat usage and/or dietary specialization in lizards. There were no significant differences for body dimensions between species within the complex, indicative of morphological conservatism. It appears genetic divergence has been achieved among the different clades within A. nivaria complex, but with much similarity in phenotype being retained because of fragmented but similar habitats occupied. / AFRIKAANSE OPSOMMING: Die Afroedura nivaria kompleks is een van ses herkende spesies komplekse binne die endemiese suidelike Afrika genus, Afroedura. Die A. nivaria kompleks is ‘n morfologiese konserwatiewe groep bestaande uit medium grootte geitjies endemies tot Suid Afrika, alhoewel hulle oneweredig verspreid is in die Oos Kaap, Vrystaat en Kwazulu-Natal provinsies. Die kompleks bestaan uit die volgende vyf spesies: A. nivaria (Boulenger 1894), A. amatolica (Hewitt 1925), A. karroica (Hewitt 1925), A. tembulica (Hewitt 1926) and A. halli (Hewitt 1935). Hierdie geitjies kom snags voor en skuil tussen nou skeure op klip koppies. Dit is tans onbekend of a) die beskryfde spesies geldig is en b) of die addisionele afstammelinge voorkom op geisoleerde koppies. Met die studie het ek die hipotese ondersoek dat endemiese spesies met ‘n noue verspreiding (A. amatolica en A. tembulica) geldige spesies is, maar dat spesies met ‘n wye verspreiding (A. nivaria, A. karroica and A. halli) genetiese variasie op spesie vlak wys. Fragmente van twee mitochondriale gene (16S rRNA and ND4) en ‘n enkele nuklêre merker (KIAA) se basispaaropeenvolgingsdata was verkry en geanaliseer deur Bayesian inferensie, maksimum parsimonie en maksimum waarskynlikheid. Alle analise het die genetiese kenmerkendheid van die beskryfde spesies sterk ondersteun. Die A. nivaria kompleks is monofileties, A. karroica het geblyk om buite die spesies kompleks voor te kom en A. pondolia (voorheen beskryf as buite die A. nivaria kompleks) het voortdurend binne die A. nivaria kompleks voorgekom. Addisionele klades afkomstig vanaf die filogenië van A. halli en A. nivaria het vir beide spesies groot genetiese divergensie met geen ruimtelike oorvleuling gewys. Afroedura amatolica, met sy noue verspreiding, het twee hoogs divergente klades getoon. Die klades onthul deur die filogenie beklemtoon ‘n geografiese struktuur. Hierdie bevindings blyk die bestaan van tot vier ekstra kriptiese afstammelinge binne die kompleks. Ek het morfometriese data (ekologiese relevante morfologiese eienskappe) gebruik om vas te stel of die genetiese afstammelinge morphologies konserwatief sal wees. Meerveranderlike analises op 19 veranderlikes het variasie binne die A. nivaria spesies kompleks getoon. Hierdie veranderinge was meestal gevind in die beweeglikheidsapparatuur (ledemate en voete) en kop dimensies. Die verskeie eienskappe hou meestal verband met die mikrohabitatte wat gebruik word en/of dieët spesialisering in akkedisse. Daar was geen noemenswaardige verskille in liggaamsdimensies tussen spesies in die kompleks nie, beduidend op ‘n konserwatiewe morfologie. Dit wil blyk of genetiese divergensie tussen die verskeie klades van die A. nivaria kompleks bewerkstellig is met ooreenstemming in die fenotipes as gevolg van gefragmenteerde maar soortgelyke habitat verbruik.