No description available.

The mainly tropical genus Lygodium differs from other ferns in that the fronds are indeterminate and are vine-like. A single species, L. palmatum is native in temperate North America. The temperate Asian L. japonicum is naturalized throughout much of the southeastern United States. About twenty years ago, L. microphyllum was introduced into South Florida and is now naturalized in several counties. The present study documents differences among spores and their generation, development of sporophytes from the fertilized egg, and in flavonoid chemistry. Hybridization experiments showed a strong possibility for cross fertility between species. Experiments with prothallial development and differentiation revealed that environment influenced variation and gametangium formation. Greater similarity in sporophyte developmental stages and in frond phytochemistry show that the native L. palmatum is phenetically closer to the tropical L. microphyllum than to L. japonicum. All three species are clearly distinct at all levels examined.

No description available.

In this dissertation, I explore the diversity of endophytic fungi associated with above-ground tissues of neotropical ferns, assess factors shaping their community structure in three forests, and explore the contributions of endophytes and related strains to our understanding of the diversity and ecology of a representative genus of Ascomycota. In Appendix A, I report a survey of endophytic fungi from seven species of ferns at La Selva, Costa Rica. Using both species-level and phylogenetic analyses, I compare culturable endophytes as a function of fern taxonomy, frond tissues (blades vs. stalks), habits (terrestrial vs. epiphytic), and vegetation types (arboretum vs. primary and secondary forest) during two consecutive years. Analysis of>500 strains provides a first taxonomic overview of fern endophytes at a community scale and reveals high diversity, host preference, and interannual variation in fungal assemblages. However, when variation due to host species is taken into account, community structure is similar among fern tissue types, habits, and sampling sites over a small spatial scale. In Appendix B, I expand my work to evaluate the abundance, species-level and phylogenetic diversity, and distributions of fern-affiliated endophytes in three neotropical forests (La Selva, Costa Rica; Barro Colorado Island, Panama; Los Tuxtlas, Mexico). My analysis of > 2000 isolates reveals that communities differ significantly among fern species within sites, and among ferns in different sites. Intersite differences in communities are correlated with geographic distance and environmental dissimilarity. My work suggests that extrapolative estimates of fungal diversity should take into account not just host species, but locality and environmental variation as well. In Appendix C I focus on a representative genus of Ascomycota (Lecythophora) to evaluate how multi-locus phylogenetic analyses of endophytes can detect new species. Lecythophora is a geographically widespread genus that includes opportunistic human pathogens, produces novel secondary metabolites, and consists presently of six described species. Multi-locus analysis of 33 newly collected strains suggested seven phylogenetic species that are new to science and highlighted their capacity to inhibit growth of two plant pathogenic fungi. This work shows how recognition of cryptic species even in well-characterized genera has major implications for estimating fungal biodiversity.

Entender como comunidades são estruturadas a partir de um pool de espécies é uma questão central em Ecologia de Comunidades. Diversas abordagens foram propostas para estabelecer a ligação entre os padrões de estrutura de comunidades e os processos que os geram. As regras de assembleia e a abordagem filogenética em ecologia de comunidades são alguns exemplos. Entretanto, o que estas abordagens não levam em conta é o efeito de processos neutros na estruturação de comunidades. Há um consenso de que tanto nicho como neutralidade afetam a estrutura de comunidades e que se deve avaliar a importância relativa de cada um destes processos. A ideia desta tese foi usar modelos estatísticos para representar como processos neutros e de nicho geram padrões em comunidades. No Capítulo 2 propus uma abordagem baseada em modelos hierárquicos através da qual é possível expressar processos neutros e de nicho. A partir disso, foi possível representar hipóteses em que apenas processos neutros afetam a estrutura da comunidade, apenas processos de nicho ou diferentes combinações entre ambos. Usando seleção de modelos, identifiquei qual a combinação de processos melhor explica as abundâncias observadas das espécies. Com isso, mostrei que as comunidades de samambaias em gradientes altitudinais na Serra do Mar no Paraná, Brasil são estruturadas por uma mistura de filtro ambiental, deriva ecológica e limitação de dispersão. O filtro ambiental define as abundâncias das espécies selecionando as melhores estratégias ecológicas das espécies dependendo da altitude. A variação de abundância entre as espécies que compartilham as mesmas estratégias ecológicas é explicada em parte por deriva ecológica e limitação de dispersão e, em parte, por filtro de habitat independente dos atributos das espécies incorporados no modelo. Com isso, delimitei como processos baseados em nicho e neutralidade afetam a abundância das espécies de samambaias ao longo de gradientes altitudinais. No Capítulo 3 usei um estudo de caso para explorar a ideia central da abordagem filogenética em ecologia de comunidades de que é possível inferir os processos que afetam as comunidades com base em padrões locais de estrutura filogenética. Usei a abordagem de modelos proposta no Capítulo 2 para simular comunidades geradas por processos puramente neutros, puramente de nicho e uma combinação hierárquica entre os dois. Encontrei que comunidades geradas apenas por processos de nicho geram estruturas filogenéticas aleatórias na maioria dos casos. A detecção de estruturas filogenéticas aleatórias foi ainda mais frequente nas comunidades geradas por processos puramente neutros e pela combinação de processos neutros e de nicho, não sendo possível a distinção entre estes dois cenários. Desse modo, o estudo de caso mostrou que estruturas filogenéticas não aleatórias são muito pouco plausíveis e que os processos neutros geram uma forte assinatura nos padrões de estrutura filogenética. Com a abordagem proposta nesta tese foi possível delimitar a influência de processos de nicho e neutralidade em comunidades e entender suas consequências em termos dos padrões por eles gerados. A tradução dos diferentes processos em modelos mistos mostrou-se uma ferramenta poderosa para quantificar padrões e construir explicações de como os processos operam juntos / Understanding how communities are assembled from a species pool is a central question in community ecology. Different approaches to link pattern and processes in community ecology were proposed. Some examples are assembly rules and the community phylogenetic approach. However, one aspect not accounted in those approaches is how neutral processes affect community patterns. There is a consensus that both niche and neutral processes affect community assembly and that the goal should be assess the relative importance of each process. The general idea if this thesis was to use statistical models to represent how niche and neutral generate community patterns. In Chapter 3, I proposed a framework based on hierarchical models to express niche and neutral processes. I used this approach to represent hypothesis in which only niche processes affect community structure, only neutral processes or a hierarchical combination of both explains species abundance. By using model selection, I identifyied which combination of processes better predicts observed abundances on local communities. I showed that fern communities across altitudinal gradients at Serra do Mar in Paraná, Brazil are structured by a mixture of environmental filtering, ecological drift and limited dispersal. Environmental filtering defines species abundance, selecting the best ecological strategies of species depending on altitude. Variation on species abundance sharing the same ecological strategies is explained in part by drift and limited dispersal, and in part by habitat filtering independent of species traits considered in the models. Hence, I refined how niche and neutral processes affect fern abundance on altitudinal gradients. In Chapter 3, I used a case study to explore the idea from community phylogenetics of inferring processes affecting communities based on patterns of phylogenetic structure. I used the modeling framework from Chapter 3 to simulate communities built by niche, neutral and combination of both processes. I found that communities based on niche processes are likely to generate a random phylogenetic structure. The detection of random phylogenetic strucure was even more common on communities built solely by neutral processes and combination of both niche and neutral processes. Therefore, the case study showed that a non random phylogenetic strucure is unlikely and that neutral processes strongly affect the outcome of phylogenetic patterns. Based on the framework proposed on this thesis it is possible to delimit the influence of niche and neutral processes on community assembly and to understand what are the consequences in terms of community patterns. Translating different processes into mixed models can be a powerful tool to quantify patterns and built explanations on how the processes operate together

Apomixis is an evolutionarily important phenomenon across plant lineages. The interaction of apomixis with hybridization and polyploidy can lead to complex patterns of reticulation, complicating efforts to reconstruct evolutionary history in groups where apomixis is common. Ferns, in particular, are rich in apomictic species, notably in centers of species diversity like East Asia. Eastern North America too is home to a number of apomictic species. We investigated the East Asian ferns in Polystichum sections Xiphopolystichum and Duropolystichum (Dryopteridaceae) in order to elucidate the evolutionary and biogeraphic history of seven apomictic species in the group: Polystichum tsus-simense, P. xiphophyllum, P. sinotsus-simense, P. pseudoxiphophyllum, P. mayebarae. P. rigens, and P. neolobatum. In addition, we examined the evolutionary origin of an undescribed apomictic cytotype of North American genus Phegopteris (Thelypteridaceae). The datasets comprised phylogenetic inference based on three nuclear and three plastid markers, analysis of mixed nucleotide signals from chromatograms generated from Sanger sequencing of nuclear markers, ploidy estimates based on flow cytometry data and spore length measurements, morphometric analysis of representative specimens collected in southwest China and nearby regions, and climatic niche models. By interpreting these multiple lines of evidence synthetically, we have discerned multiple highly reticulate complexes of polyploid lineages derived largely from diploid sexual progenitors. Our findings highlight the importance of understanding the role of apomictic reproduction in the context of species diversity, an understanding central to similar future inquiry into the diversity of East Asian and North American ferns.

Abstract¡G Athyrioid ferns¡]Athyrioideae, Dryopteridaceae¡^consist of about 700 species with a distribution range from tropical to temperate zone in the world. In Taiwan, the subfamily includes 50 species commonly found from lowland to around 3000 meters in elevation. Phylogenetic relationships and the generic circumscription of athyrioid genera are confused and controversial. In this study, trnL-trnF spacer, which is a nucleotide sequence between genes in the chloroplast, was used to analyze and infer the phylogenetic relationships and evolutionary status of 35 species. Phylogenetic trees produced by neighbor-joining and maximum-parsimony methods are similar in topology. Athyrium and Cornopteris form a clade, and this indicates Cornopteris is more closely related to Athyrium than to Diplazium. Anisogonium nests within Diplazium clade, and it implies these two genera congeneric. Anisocampium is distinct from Athyrium sensu stricto and forms a clade with Athyrium nipponicum. Deparia clade includes Athyriopsis, Lunathyrium, Dryoathyrium, Dictyodroma, Diplazium subsinuatum and Matteuccia. These four clades may be seen as the core part of athyrioid ferns. Woodsia and Thelypteridaceae cluster next to these four clades. Cystopteris and Gymnocarpium occupy a position between Thelypteridaceae and Dryopteridaceae. Rhachidosorus is neither closely related to Athyrium nor Diplazium. Hypodematium is distantly related to athyrioid ferns and forms a clade with Dryopteridaceae. Therefore, Hypodematium may be isolated from athyrioid ferns. Based on the evidences mentioned above, athyrioid ferns are suggested to be closely related to Thelypteriaceae, and are probably members of Woodsiaceae¡]including Thelypteridaceae¡^instead of Dryopteridaceae. In addition, Cystopteris and Gymnocarpium are the most basal lineage of Woodsiaceae sensu lato. The core group of athyrioid ferns probably better treated as a monophyletic tribe or subfamily of Woodsiaceae at current stage.

Spore abortion rate was studied for a total of 109 samples belonging to 23 fern taxa. The resulting abortion rate was compared within several reproductive and phylogenetic groups. The method of spore abortion estimation was optimized by analyzing the amount of spores needed as well as the potential differences within frond.

Entender como comunidades são estruturadas a partir de um pool de espécies é uma questão central em Ecologia de Comunidades. Diversas abordagens foram propostas para estabelecer a ligação entre os padrões de estrutura de comunidades e os processos que os geram. As regras de assembleia e a abordagem filogenética em ecologia de comunidades são alguns exemplos. Entretanto, o que estas abordagens não levam em conta é o efeito de processos neutros na estruturação de comunidades. Há um consenso de que tanto nicho como neutralidade afetam a estrutura de comunidades e que se deve avaliar a importância relativa de cada um destes processos. A ideia desta tese foi usar modelos estatísticos para representar como processos neutros e de nicho geram padrões em comunidades. No Capítulo 2 propus uma abordagem baseada em modelos hierárquicos através da qual é possível expressar processos neutros e de nicho. A partir disso, foi possível representar hipóteses em que apenas processos neutros afetam a estrutura da comunidade, apenas processos de nicho ou diferentes combinações entre ambos. Usando seleção de modelos, identifiquei qual a combinação de processos melhor explica as abundâncias observadas das espécies. Com isso, mostrei que as comunidades de samambaias em gradientes altitudinais na Serra do Mar no Paraná, Brasil são estruturadas por uma mistura de filtro ambiental, deriva ecológica e limitação de dispersão. O filtro ambiental define as abundâncias das espécies selecionando as melhores estratégias ecológicas das espécies dependendo da altitude. A variação de abundância entre as espécies que compartilham as mesmas estratégias ecológicas é explicada em parte por deriva ecológica e limitação de dispersão e, em parte, por filtro de habitat independente dos atributos das espécies incorporados no modelo. Com isso, delimitei como processos baseados em nicho e neutralidade afetam a abundância das espécies de samambaias ao longo de gradientes altitudinais. No Capítulo 3 usei um estudo de caso para explorar a ideia central da abordagem filogenética em ecologia de comunidades de que é possível inferir os processos que afetam as comunidades com base em padrões locais de estrutura filogenética. Usei a abordagem de modelos proposta no Capítulo 2 para simular comunidades geradas por processos puramente neutros, puramente de nicho e uma combinação hierárquica entre os dois. Encontrei que comunidades geradas apenas por processos de nicho geram estruturas filogenéticas aleatórias na maioria dos casos. A detecção de estruturas filogenéticas aleatórias foi ainda mais frequente nas comunidades geradas por processos puramente neutros e pela combinação de processos neutros e de nicho, não sendo possível a distinção entre estes dois cenários. Desse modo, o estudo de caso mostrou que estruturas filogenéticas não aleatórias são muito pouco plausíveis e que os processos neutros geram uma forte assinatura nos padrões de estrutura filogenética. Com a abordagem proposta nesta tese foi possível delimitar a influência de processos de nicho e neutralidade em comunidades e entender suas consequências em termos dos padrões por eles gerados. A tradução dos diferentes processos em modelos mistos mostrou-se uma ferramenta poderosa para quantificar padrões e construir explicações de como os processos operam juntos / Understanding how communities are assembled from a species pool is a central question in community ecology. Different approaches to link pattern and processes in community ecology were proposed. Some examples are assembly rules and the community phylogenetic approach. However, one aspect not accounted in those approaches is how neutral processes affect community patterns. There is a consensus that both niche and neutral processes affect community assembly and that the goal should be assess the relative importance of each process. The general idea if this thesis was to use statistical models to represent how niche and neutral generate community patterns. In Chapter 3, I proposed a framework based on hierarchical models to express niche and neutral processes. I used this approach to represent hypothesis in which only niche processes affect community structure, only neutral processes or a hierarchical combination of both explains species abundance. By using model selection, I identifyied which combination of processes better predicts observed abundances on local communities. I showed that fern communities across altitudinal gradients at Serra do Mar in Paraná, Brazil are structured by a mixture of environmental filtering, ecological drift and limited dispersal. Environmental filtering defines species abundance, selecting the best ecological strategies of species depending on altitude. Variation on species abundance sharing the same ecological strategies is explained in part by drift and limited dispersal, and in part by habitat filtering independent of species traits considered in the models. Hence, I refined how niche and neutral processes affect fern abundance on altitudinal gradients. In Chapter 3, I used a case study to explore the idea from community phylogenetics of inferring processes affecting communities based on patterns of phylogenetic structure. I used the modeling framework from Chapter 3 to simulate communities built by niche, neutral and combination of both processes. I found that communities based on niche processes are likely to generate a random phylogenetic structure. The detection of random phylogenetic strucure was even more common on communities built solely by neutral processes and combination of both niche and neutral processes. Therefore, the case study showed that a non random phylogenetic strucure is unlikely and that neutral processes strongly affect the outcome of phylogenetic patterns. Based on the framework proposed on this thesis it is possible to delimit the influence of niche and neutral processes on community assembly and to understand what are the consequences in terms of community patterns. Translating different processes into mixed models can be a powerful tool to quantify patterns and built explanations on how the processes operate together

Orientador: Ana Paula Fortuna Perez / Resumo: A família Lygodiaceae sempre teve uma taxonomia contraditória, o número de espécies aceitas no Brasil variando de duas a doze ao longo das décadas. Sendo Lygodiaceae uma família antiga, acredita-se que essas contradições possam ser causadas por híbridos. Os híbridos surgem pelo cruzamento de duas ou mais espécies e, geralmente, são primeiro identificados por suas características morfológicas intermediárias entre as espécies parentais. Normalmente, os híbridos recentes de samambaia são detectados ocorrendo junto com suas espécies parentais. Os esporos de indivíduos híbridos geralmente são mal formados e / ou abortados, portanto, inviáveis, mas os poucos esporos viáveis poderiam iniciar o processo de especiação de uma nova espécie. Considerando a sobreposição de características morfológicas, a hibridação poderia ter ocorrido entre duas espécies de Lygodium no Brasil, L. venustum e L. volubile gerando o hipotético híbrido L. × fayae. Devido à difícil identificação desses táxons, nossos estudos analisaram dois caracteres diferentes (tamanho e morfologia dos esporos e estômatos) por microscopia eletrônica de varredura, estudamos a germinação dos esporos e criamos novas descrições e uma chave de identificação às espécies aceitas para ajudar na delimitação taxonômica dos dois táxons de Lygodium e seu híbrido putativo. De acordo com nossos resultados, as espécies classificadas como L. × fayae na região sudeste do Brasil não são híbridas, mas uma variação morfológica de Lygodium venus... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The family Lygodiaceae has always had a contradictory taxonomy, the number of accepted species in Brazil varying from two to twelve through the decades. Lygodiaceae being an old family, this contradictions are believed to be caused by hybrids. Hybrids arise by the crossing of two or more species, and, usually, they are first identified by its intermediate morphological characteristics among the parental species. Normally, early fern hybrids are detected occurring along with its parental species. The spores of hybrid individuals generally are badly formed and/or aborted, thus, not viable, but the few balanced spores could starts the speciation process of a new species. Considering the overlapping of morphological characteristics, it could have occurred in two species of Lygodium in Brazil, L. venustum and L. volubile and the hypothetical hybrid L. ×fayae. Due to the difficult in identification of these taxa, our studies herein analysed two different characters (spore and stomata size and morphology) through scanning electronic microscopy, we studies the spore germination and new descriptions and an identification key were done to the accepted species to help clearing the taxonomic delimitation of the two taxa of Lygodium and their putative hybrid. According to our results, the species herein classified as L. ×fayae on the Brazilian south-east region is not a hybrid, but a morphological variation of Lygodium venustum. Additional studies on morphometric analysis with the measure... (Complete abstract click electronic access below) / Mestre