Is evolution faster at ecotones? A test using rates and tempo of diet transitions in Neotropical Sigmodontinae (Rodentia, Cricetidae)

We evaluated whether evolution is faster at ecotones as niche shifts may be needed to persist under unstable environment. We mapped diet evolution along the evolutionary history of 350 sigmodontine species. Mapping was used in three new tipbased metrics of trait evolution – Transition Rates, Stasis Time, and Last Transition Time – which were spatialized at the assemblage level (aTR, aST, aTL). Assemblages were obtained by superimposing range maps on points located at core and ecotone of the 93 South American ecoregions. Using Linear Mixed Models, we tested whether ecotones have species with more changes from the ancestral diet (higher aTR), have maintained the current diet for a shorter time (lower aST), and have more recent transitions to the current diet (lower aLT) than cores. We found lower aTR, and higher aST and aLT at ecotones than at cores. Although ecotones are more heterogeneous, both environmentally and in relation to selection pressures they exert on organisms, ecotone species change little from the ancestral diet as generalist habits are necessary toward feeding in ephemeral environments. The need to incorporate phylogenetic uncertainty in tip-based metrics was evident from large uncertainty detected. Our study integrates ecology and evolution by analyzing how fast trait evolution is across space

Sinal filogenético e conservação filogenética de nicho : integrando métodos aos conceitos ecológicos

Compreender os fatores que afetam a distribuição das espécies tem sido um dos principais objetivos dos ecólogos. Atualmente, sabe-se que os processos ecológicos e evolutivos moldam a dinâmica de especiação e extinção de espécies, e determinam a distribuição e abundância das mesmas. Ao longo dos últimos anos, tem havido um aumento no número de estudos que utilizam informação filogenética para explicar as dinâmicas populacionais e as distribuições de espécies, e que buscam identificar os mecanismos responsáveis pela montagem das comunidades. Interações das espécies, sejam elas intraespecífica, interespecífica ou com o ambiente, ocorrem baseadas nas diferenças e semelhanças fenotípicas. Essas variações fenotípicas tem origem na evolução das espécies, e com isso espera-se que as espécies proximamente relacionadas tendam a ser ecologicamente mais semelhantes entre si do que as espécies distantemente relacionadas. Esta concepção tem dado origem a um conceito importante, com implicações para estudos tanto ecológicos quanto evolutivos: o conceito de conservação filogenética de nicho, isto é, quando as espécies relacionadas mantêm seus nichos ancestrais ao longo do tempo evolutivo. Esse padrão tem importância para diversas áreas de ecologia, permitindo a ligação das espécies aos processos ecológicos e auxiliando na maior compreensão da ecologia evolutiva das diferentes linhagens. Devido à sua importância, é fundamental o desenvolvimento de métodos estatísticos adequados para quantificar esses padrões e inferir os processos que o subjazem. Atualmente, os métodos utilizados para inferir conservação filogenética de nicho são, em sua maioria, incompatíveis com determinados conceitos ecológicos e não abrangem todos os tipos de dados e esse fato explica uma visão incompleta dos processos presentes nas comunidades e conflitante com o objetivo de muitos estudos ecológicos e conservacionistas que buscam vincular as espécies aos processos ecológicos e evolutivos. Desta forma, o principal objetivo desta tese é propor novos métodos para quantificar o sinal filogenético que integrem diferentes aspectos do conceito de nicho ecológico. Apresentamos aqui os novos métodos em detalhes e avaliamos suas propriedades estatísticas (erro tipo I e poder estatístico) por meio de dados simulados. No capítulo 1, nós propomos um método para medir sinal filogenético utilizando o teste de Mantel, incorporando modelos evolutivos para testar hipóteses específicas da evolução dos atributos. No capítulo 2, descrevemos um conjunto de funções e um novo pacote estatístico para explorar os padrões filogenéticos no nível de metacomunidade. Este pacote permite explorar a distribuição de linhagens filogenéticas através de gradientes ecológicos, a análise de sinal filogenético no nível da metacomunidade e explorar a associação entre clados e gradientes ecológicos. No capítulo 3, investigamos a relação entre sinal filogenético dos atributos com os padrões de coocorrência das espécies nos níveis da comunidade. Esta abordagem permite testar se espécies filogeneticamente relacionadas que coocorrem expressam as suas dimensões de nicho com maior semelhança do que seria esperado por modelos neutros de evolução. Por fim, testamos as propriedades estatísticas destes métodos em relação dois modelos nulos, que incorporam diferentes aspectos da estrutura da comunidade e evolução dos atributos das espécies. Os três capítulos representam diferentes trabalhos que se interconectam no sentido de elucidar o conceito de sinal filogenético e conservação filogenética de nicho.Understanding the factors that can affect species distributions has been a main goal of ecologists. Currently, it is known that evolutionary and ecological processes shape the speciation dynamics, species extinction and determine the distribution and abundance of species. Over the last years, there has been an increase in the number of studies using phylogenetic information to explain the dynamics of population, species distribution and identifying the mechanisms of community assembly. Species interactions – intraspecific, interspecific or with the environment – occur based on their phenotypic differences and similarities. As phenotypic variation has a basis in evolutionary history, it is expected that closely related species tend to be more ecologically similar to each other than distantly related ones. This notion has given rise to an important concept, with implications for both evolutionary and ecological studies: the concept of phylogenetic niche conservatism, that is, when related species maintain their ancestral niches over evolutionary time. This pattern is important for several areas of ecology, and allows to link species to ecological processes and to understand the evolutionary ecology of different lineages. Despite its importance, it is crucial the development of appropriate statistical method to measure this pattern and to infer the processes behind it. The methods currently available to infer phylogenetic niche conservatism are sometimes incompatible with some ecological concepts and do not cover all kind of data, this fact leads to an incomplete view of the process acting in the currents communities and conflict with the goal of many ecological and conservation studies that need to link species to ecological and evolutionary processes. The main goal of this dissertation is to propose novel methods to measure phylogenetic signal incorporating different aspects of ecological niche. We introduce novel methods in detail and evaluate its statistical properties (type I error and statistical power) by means of simulated data with known structure. In chapter 1 we propose a method to measure phylogenetic signal using the Mantel test, incorporating evolutionary model to test specific hypothesis of trait evolution. In chapter 2, we describe a set of function and a new statistical package for exploring the phylogenetic patterns at the metacommunity level. This package allows the exploration of distribution of phylogenetic lineages across ecological gradients, the analysis of phylogenetic signal at metacommunity level and to explore the association between clades and ecological gradients. In the chapter 3, we access the relationship between phylogenetic signal in traits and species co-occurrence patterns in the community levels. This approach allows one to test whether phylogenetic close related species cooccurring in metacommunities express their niche dimensions more similarly than would be expected by neutral expectation. We tested the statistical properties of these methods in relation to two null models, which incorporate these different aspects of the community structure and evolution of species traits. The three chapters represent different works that are interconnected in order to elucidate the concept of phylogenetic signal and phylogenetic niche conservatism

Estrutura filogenética de comunidades de plantas lenhosas em ecótonos vegetacionais

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

Estrutura filogenética de comunidades de plantas lenhosas em ecótonos vegetacionais

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

PCPS – an R-package for exploring phylogenetic eigenvectors across metacommunities

PCPS is an R package for exploring phylogenetic eigenvectors across metacommunities. It offers a set of functions for analyzing principal coordinates of phylogenetic structure (PCPS), allowing analysis of phylogenetic signal in ecological traits of species at the metacommunity level, and the association between each PCPS and environmental, spatial and historical factors. The package is a flexible solution for exploring the distribution of major phylogenetic lineages across ecological or biogeographic gradients. The package is freely available on the CRAN official web server for R.&nbsp

Land use explains the distribution of threatened new world amphibians better than climate

Background: We evaluated the direct and indirect influence of climate, land use, phylogenetic structure, species richness and endemism on the distribution of New World threatened amphibians. Methodology/Principal Findings: We used the WWF’s New World ecoregions, the WWFs amphibian distributional data and the IUCN Red List Categories to obtain the number of threatened species per ecoregion. We analyzed three different scenarios urgent, moderate, and the most inclusive scenario. Using path analysis we evaluated the direct and indirect effects of climate, type of land use, phylogenetic structure, richness and endemism on the number of threatened amphibians in New World ecoregions. In all scenarios we found strong support for direct influences of endemism, the cover of villages and species richness on the number of threatened species in each ecoregion. The proportion of wild area had indirect effects in the moderate and the most inclusive scenario. Phylogenetic composition was important in determining the species richness and endemism in each ecoregion. Climate variables had complex and indirect effects on the number of threatened species. Conclusion/Significance: Land use has a more direct influence than climate in determining the distribution of New World threatened amphibians. Independently of the scenario analyzed, the main variables influencing the distribution of threatened amphibians were consistent, with endemism having the largest magnitude path coefficient. The importance of phylogenetic composition could indicate that some clades may be more threatened than others, and their presence increases the number of threatened species. Our results highlight the importance of man-made land transformation, which is a local variable, as a critical factor underlying the distribution of threatened amphibians at a biogeographic scale

Land use explains the distribution of threatened new world amphibians better than climate

Background: We evaluated the direct and indirect influence of climate, land use, phylogenetic structure, species richness and endemism on the distribution of New World threatened amphibians. Methodology/Principal Findings: We used the WWF’s New World ecoregions, the WWFs amphibian distributional data and the IUCN Red List Categories to obtain the number of threatened species per ecoregion. We analyzed three different scenarios urgent, moderate, and the most inclusive scenario. Using path analysis we evaluated the direct and indirect effects of climate, type of land use, phylogenetic structure, richness and endemism on the number of threatened amphibians in New World ecoregions. In all scenarios we found strong support for direct influences of endemism, the cover of villages and species richness on the number of threatened species in each ecoregion. The proportion of wild area had indirect effects in the moderate and the most inclusive scenario. Phylogenetic composition was important in determining the species richness and endemism in each ecoregion. Climate variables had complex and indirect effects on the number of threatened species. Conclusion/Significance: Land use has a more direct influence than climate in determining the distribution of New World threatened amphibians. Independently of the scenario analyzed, the main variables influencing the distribution of threatened amphibians were consistent, with endemism having the largest magnitude path coefficient. The importance of phylogenetic composition could indicate that some clades may be more threatened than others, and their presence increases the number of threatened species. Our results highlight the importance of man-made land transformation, which is a local variable, as a critical factor underlying the distribution of threatened amphibians at a biogeographic scale