The inference of species boundaries and phylogenetic relationships are fundamental for evolutionary, ecological, and conservation studies. The resolution of species boundaries and the inference of phylogenetic relationships among species are required to define the units of analysis and to find the most closely related units for evaluating alternative models of speciation. I highlight lizards as model organisms for ecological and evolutionary studies, emphasizing their contributions to advances in understanding linkages between phylogeography and speciation. In this dissertation, I focus on the phylogenetic relationships of the lizards in the Liolaemus darwinii group, and the species boundaries of a nested clade within the group, the L. darwinii complex, because of several advantages that make these taxa ideal for phylogeographic studies of speciation. I infer a phylogeny for the L. darwinii group based on DNA sequences of 20 loci (19 nuclear and 1 mitochondrial) using species trees methods that take into account the incongruence among gene trees. I found the minimum number of loci, number of sequences per species, and number of base pairs per locus that should be included in an analysis for an accurate and precise estimate of the species tree. The species tree based on all available data support a clade of closely related species (L. darwinii, L. grosseorum, and L. laurenti) known as the L. darwinii complex. A new method for species delimitation using Approximate Bayesian Computation is introduced and is shown to accurately delimit species given that limited or no gene flow has occurred after divergence and despite biased estimates of demographic parameters. ABC analyses supported the distinctness of two lineages within L. darwinii under a model of speciation with gene flow. Based on the species tree and the species limits obtained in this dissertation, phylogenetic comparative methods can be carried out to address the morphological and ecological evolution in the L. darwinii group and several sister species can be used for testing the alternative speciation models via correlation analyses of genetic, morphological, and ecological datasets. Future studies should assess the role speciation due to adaptive processes and its association the species' ecological niches and life histories.

No description available.

The amount of biological sequence data is increasing rapidly, a promising development that would transform biology if we can develop methods that can analyze large-scale data efficiently and accurately. A fundamental question in evolutionary biology is building the tree of life: a reconstruction of relationships between organisms in evolutionary time. Reconstructing phylogenetic trees from molecular data is an optimization problem that involves many steps. In this dissertation, we argue that to answer long-standing phylogenetic questions with large-scale data, several challenges need to be addressed in various steps of the pipeline. One challenges is aligning large number of sequences so that evolutionarily related positions in all sequences are put in the same column. Constructing alignments is necessary for phylogenetic reconstruction, but also for many other types of evolutionary analyses. In response to this challenge, we introduce PASTA, a scalable and accurate algorithm that can align datasets with up to a million sequences. A second challenge is related to the interesting fact that various parts of the genome can have different evolutionary histories. Reconstructing a species tree from genome-scale data needs to account for these differences. A main approach for species tree reconstruction is to first reconstruct a set of ``gene trees'' from different parts of the genome, and to then summarize these gene trees into a single species tree. We argue that this approach can suffer from two challenges: reconstruction of individual gene trees from limited data can be plagued by estimation error, which translates to errors in the species tree, and also, methods that summarize gene trees are not scalable or accurate enough under some conditions. To address the first challenge, we introduce statistical binning, a method that re-estimates gene trees by grouping them into bins. We show that binning improves gene tree accuracy, and consequently the species tree accuracy. To address the second challenge, we introduce ASTRAL, a new summary method that can run on a thousand genes and a thousand species in a day and has outstanding accuracy. We show that the development of these methods has enabled biological analyses that were otherwise not possible.

The understanding of diversification of intraspecific lineages can shed light on speciation processes and ultimately biogeographic patterns across multiple spatial and temporal scales. In this dissertation I investigated the geographical and ecological factors promoting diversification across the South American dry diagonal biomes (i.e. Cerrado, Chaco, and Seasonally Dry Tropical Forests - SDTFs), through a coupled approach between multilocus phylogeographic and geospatial methods, in the larger context of interpreting the consequences of the resulting patterns for the conservation of biodiversity and evolutionary processes. In Chapter 1 I evaluate biogeographic hypotheses previously proposed and emphasize that the dry diagonal biomes are particularly biodiverse and biogeographically complex, but poorly studied and under protected. I also propose testable predictions for the subsequent chapters and future diversification studies. In the subsequent chapters I adopt a biodiversity prediction approach based on estimating palaeodistributions and habitat stability surfaces to formulate and test spatially explicit diversification hypotheses based on squamate richness and phylogeography. In Chapter 2 I identify historically stable areas of SDTFs and in Chapter 3 I found that the historical climatic stability is a good predictor of Cerrado squamate richness. In Chapter 4 I use a multilocus dataset to estimate the phylogenetic relationships among described species of the lizard genus Phyllopezus (Phyllodactylidae), distributed across the ‘dry diagonal’ biomes. In Chapter 5 I used a dense sampling design focused in the species complex P. pollicaris (more individuals, localities, and markers), and coalescent phylogeographic methods to test the relative influences of Tertiary geomorphological vs. Quaternary climatic events on diversification in this lizard. I found unprecedented levels of cryptic genetic diversity, deep phylogeographic structure, and diversification dating back to at least the Neogene with persistence across Quaternary fluctuations. My dissertation emphasizes that patterns of diversification across the ‘dry diagonal’ biomes are much more complex than previously proposed and reflect the primary influence of geologically old processes. Evidence of allopatric and ecological speciation between lineages that coincide with genetic clusters associated with each of the biomes, contradicts early views that the biomes would have a shared diversification history. These patterns illustrate that low-vagility complexes, characterized by strong structure and pre-Pleistocene divergences, represent ideal radiations to investigate broad biogeography of associated biomes. Future studies should investigate patterns of temporal and spatial congruence across co-distributed taxa, and integrate morphological and further ecological data to refine species limits, taxonomy, and patterns of trait evolution across these radiations.

Section Restricti is one of the last sections of the genus Aspergillus that hasn't been revised in the modern taxonomic era. All species are osmophilic, have simple morphology and they are mainly important because of the food, feed and seed spoilage, some of them also have negative influence to the indoor air. The section consists of seven species according to the last taxonomic revision from 2008 based only on molecular data. It currently consists of six asexual and one homothalic species. 126 isolates from the section coming from four continents were studied in this thesis, including ex-type strains. Revision of the section was carried out combining molecular phylogenetic analysis and conventional taxonomic methods. Modern methods of species delimitation based on multispecies coalescent model were used for the phylogenetic reconstruction. From the conventional methods analysis of morphology (macro- and micromorphology including scanning electron microscopy) and physiology (ability of growing in osmotic gradient and several different temperatures) was performed. Apart from the seven known species, eight new undescribed species were discovered. Majority of the new species belongs to the Aspergillus penicillioides species complex. Key words: Aspergillus restrictus, osmophilic fungi, species...

Phylogenetics is the research of ancestor-descendant relationships among different groups of organisms, for example, species or populations of interest. The datasets involved are usually sequence alignments of various subsets of taxa for various genes. A major task of phylogenetics is often to combine estimated gene trees from many loci sampled from the genes into an overall estimate species tree topology. Eventually, one can construct the tree of life that depicts the ancestor-descendant relationships for all known species around the world. If there is missing data or incomplete sampling in the datasets, then supertree methods can be used to assemble gene trees with different subsets of taxa into an estimated overall species tree topology. In this study, we assume that gene tree discordance is solely due to incomplete lineage sorting under the multispecies coalescent model (Degnan and Rosenberg, 2009). If there is missing data or incomplete sampling in the datasets, then supertree methods can be used to assemble gene trees with different subsets of taxa into an estimated species tree topology. In addition, we examine the performance of the most commonly used supertree method (Wilkinson et al., 2009), namely matrix representation with parsimony (MRP), to explore its statistical properties in this setting. In particular, we show that MRP is not statistically consistent. That is, an estimated species tree topology other than the true species tree topology is more likely to be returned by MRP as the number of gene trees increases. For some situations, using longer branch lengths, randomly deleting taxa or even introducing mutation can improve the performance of MRP so that the matching species tree topology is recovered more often. In conclusion, MRP is a supertree method that is able to handle large amounts of conflict in the input gene trees. However, MRP is not statistically consistent, when using gene trees arise from the multispecies coalescent model to estimate species trees.

Delimitar espécies e reconstruir a história evolutiva em complexos de espécies pode demandar grandes esforços uma vez que grupos taxonomicamente problemáticos são muitas vezes consequência de eventos de especiação recente ou de rápida especiação. O complexo \'Cattleya coccinea\', da família Orchidaceae, é composto por orquídeas com alto valor ornamental, epifíticas e rupícolas de porte pequeno. Apesar de estarem descritas com caracteres morfológicos diagnósticos claros que permitem sua identificação, a delimitação das espécies atualmente reconhecidas é problemática. Portanto, os objetivos dessa pesquisa foram revisar a delimitação de espécies do complexo e a relação entre as espécies, além de avaliar a diversidade e estrutura genética, aliadas às análises filogeográficas para testar a ocorrência de eventos demográficos históricos. Para responder tais questões foram utilizadas regiões de sequência de cpDNA e nrDNA, 11 locos microssatélites, além de inferência bayesiana e modelo coalescente somadas às estatísticas tradicionais como metodologia. Os resultados suportam o monofiletismo para o clado para as regiões de cpDNA concatenadas. Indicam também quatro grandes eventos de reticulação das espécies do clado C. coccinea com outras espécies do gênero Cattleya. Adicionalmente, suportam o reconhecimento de sete diferentes espécies para o clado C. coccinea, composto por duas principais linhagens evolutivas mais ao norte da região Sudeste: C. brevipedunculata predominante da Serra do Espinhaço e C. wittigiana do norte da Serra do Mar. E cinco espécies distribuídas ao longo da Serra do Mar e Serra da Mantiqueira (C. coccinea, C. mantiqueirae, e mais três espécies correspondentes às populações de DMES; SJPSP e CSRS/JOSC/PMPR. As análises de diversidade mostraram de moderados a altos níveis de diversidade genética e apontam que as espécies C. coccinea e C. brevipedunculata apresentam os maiores níveis de diversidade comparadas a outras espécies do clado. A estruturação genética entre populações dentro de espécies mostrou variação entre níveis baixos a altos. A análise de atribuição de indivíduos a partir de inferência bayesiana mostrou a formação de oito grupos geneticamente distintos. A análise de taxa de dispersão de fluxo gênico pólen x semente mostrou que a dispersão via pólen é aproximadamente oito vezes mais eficiente que a dispersão via sementes somente para C. coccinea. Além disso, a rede de haplótipos indicou que as espécies raramente compartilham haplótipos e que C. coccinea e C. brevipedunculata apresentam maior diversidade com eventos de expansão. A análise de estimativa de tempo de divergência demonstrou que C. brevipedunculata e C. wittigiana provavelmente se originaram entre o Plioceno e o Pleistoceno. As outras espécies do clado se diversificaram no Pleistoceno. Eventos de expansão populacional foram observados para todas as espécies em eras glaciais do Pleistoceno. Por se tratarem de espécies ameaçadas, esse estudo recomenda a conservação \"in situ\" como também a conservação \"ex situ\" de todas as espécies do clado, com atenção especial às duas espécies do Espírito Santo: C. wittigiana e a espécie da localidade DMES, além da espécie da localidade SJPSP em São Paulo. / Species delimitation and reconstruction of the evolutionary history of species complexes may require great efforts since taxonomically problematic groups are often a result of recent speciation events or rapid speciation. The \'Cattleya coccinea\' complex, of the orchid family, consists of epiphytic and small rupicolous orchids with high ornamental value. Despite being described with clear diagnostic morphological characters that allow their identification, delimitation of the currently recognized species is problematic. Therefore, the objectives of this study were to review the species delimitation of the complex and the relationship between species, and to evaluate the genetic diversity and structure, combined with phylogeographic analyzes to test the occurrence of historical demographic events. To answer such questions, cpDNA and nrDNA sequence regions, 11 microsatellite loci, and Bayesian inference and coalescent model were used, combined with traditional statistics and methodology. The results support the monophyly for the clade for concatenated cpDNA regions. They also indicate four major reticulation events of C. coccinea species clade with other species of the genus Cattleya. Additionally, results support the recognition of seven different species for C. coccinea clade, composed of two main evolutionary lineages further north in the Southeast: C. brevipedunculata predominant in the Serra do Espinhaço and C. wittigiana from northern Serra do Mar. And five species distributed along the Serra do Mar and Serra da Mantiqueira (C. coccinea, C. mantiqueirae, and three other species of the populations DMES; SJPSP and CSRS/JOSC/PMPR. The diversity analyzes showed moderate to high levels of genetic diversity and point out that the species C. coccinea and C. brevipedunculata have the highest levels of diversity compared to other species of the clade. The genetic structure of populations within species showed variation from low to high. Assigning individuals analysis from Bayesian inference showed the formation of eight genetically distinct groups. The dispersal rate analysis of pollen x seed gene flow showed that dispersal through pollen is approximately eight times more efficient than the dispersal through seeds only for C. coccinea. Furthermore, the haplotype network indicated that the species rarely share haplotypes and that C.coccinea and C. brevipedunculata present greater diversity with expansion events. The divergence time estimation analysis showed that C. brevipedunculata and C. wittigiana probably originated between the Pliocene and the Pleistocene. The other clade species have diversified in the Pleistocene. Population expansion events were observed for all species in the Pleistocene ice ages. Because they are endangered species, this study recommends the \"in situ\" conservation as well as \"ex situ\" conservation for all species of clade, with special attention for two species of Espírito Santo: C. wittigiana and the species of DMES locality, in addition to the species of SJPSP location in São Paulo.

Delimitar espécies e reconstruir a história evolutiva em complexos de espécies pode demandar grandes esforços uma vez que grupos taxonomicamente problemáticos são muitas vezes consequência de eventos de especiação recente ou de rápida especiação. O complexo \'Cattleya coccinea\', da família Orchidaceae, é composto por orquídeas com alto valor ornamental, epifíticas e rupícolas de porte pequeno. Apesar de estarem descritas com caracteres morfológicos diagnósticos claros que permitem sua identificação, a delimitação das espécies atualmente reconhecidas é problemática. Portanto, os objetivos dessa pesquisa foram revisar a delimitação de espécies do complexo e a relação entre as espécies, além de avaliar a diversidade e estrutura genética, aliadas às análises filogeográficas para testar a ocorrência de eventos demográficos históricos. Para responder tais questões foram utilizadas regiões de sequência de cpDNA e nrDNA, 11 locos microssatélites, além de inferência bayesiana e modelo coalescente somadas às estatísticas tradicionais como metodologia. Os resultados suportam o monofiletismo para o clado para as regiões de cpDNA concatenadas. Indicam também quatro grandes eventos de reticulação das espécies do clado C. coccinea com outras espécies do gênero Cattleya. Adicionalmente, suportam o reconhecimento de sete diferentes espécies para o clado C. coccinea, composto por duas principais linhagens evolutivas mais ao norte da região Sudeste: C. brevipedunculata predominante da Serra do Espinhaço e C. wittigiana do norte da Serra do Mar. E cinco espécies distribuídas ao longo da Serra do Mar e Serra da Mantiqueira (C. coccinea, C. mantiqueirae, e mais três espécies correspondentes às populações de DMES; SJPSP e CSRS/JOSC/PMPR. As análises de diversidade mostraram de moderados a altos níveis de diversidade genética e apontam que as espécies C. coccinea e C. brevipedunculata apresentam os maiores níveis de diversidade comparadas a outras espécies do clado. A estruturação genética entre populações dentro de espécies mostrou variação entre níveis baixos a altos. A análise de atribuição de indivíduos a partir de inferência bayesiana mostrou a formação de oito grupos geneticamente distintos. A análise de taxa de dispersão de fluxo gênico pólen x semente mostrou que a dispersão via pólen é aproximadamente oito vezes mais eficiente que a dispersão via sementes somente para C. coccinea. Além disso, a rede de haplótipos indicou que as espécies raramente compartilham haplótipos e que C. coccinea e C. brevipedunculata apresentam maior diversidade com eventos de expansão. A análise de estimativa de tempo de divergência demonstrou que C. brevipedunculata e C. wittigiana provavelmente se originaram entre o Plioceno e o Pleistoceno. As outras espécies do clado se diversificaram no Pleistoceno. Eventos de expansão populacional foram observados para todas as espécies em eras glaciais do Pleistoceno. Por se tratarem de espécies ameaçadas, esse estudo recomenda a conservação \"in situ\" como também a conservação \"ex situ\" de todas as espécies do clado, com atenção especial às duas espécies do Espírito Santo: C. wittigiana e a espécie da localidade DMES, além da espécie da localidade SJPSP em São Paulo. / Species delimitation and reconstruction of the evolutionary history of species complexes may require great efforts since taxonomically problematic groups are often a result of recent speciation events or rapid speciation. The \'Cattleya coccinea\' complex, of the orchid family, consists of epiphytic and small rupicolous orchids with high ornamental value. Despite being described with clear diagnostic morphological characters that allow their identification, delimitation of the currently recognized species is problematic. Therefore, the objectives of this study were to review the species delimitation of the complex and the relationship between species, and to evaluate the genetic diversity and structure, combined with phylogeographic analyzes to test the occurrence of historical demographic events. To answer such questions, cpDNA and nrDNA sequence regions, 11 microsatellite loci, and Bayesian inference and coalescent model were used, combined with traditional statistics and methodology. The results support the monophyly for the clade for concatenated cpDNA regions. They also indicate four major reticulation events of C. coccinea species clade with other species of the genus Cattleya. Additionally, results support the recognition of seven different species for C. coccinea clade, composed of two main evolutionary lineages further north in the Southeast: C. brevipedunculata predominant in the Serra do Espinhaço and C. wittigiana from northern Serra do Mar. And five species distributed along the Serra do Mar and Serra da Mantiqueira (C. coccinea, C. mantiqueirae, and three other species of the populations DMES; SJPSP and CSRS/JOSC/PMPR. The diversity analyzes showed moderate to high levels of genetic diversity and point out that the species C. coccinea and C. brevipedunculata have the highest levels of diversity compared to other species of the clade. The genetic structure of populations within species showed variation from low to high. Assigning individuals analysis from Bayesian inference showed the formation of eight genetically distinct groups. The dispersal rate analysis of pollen x seed gene flow showed that dispersal through pollen is approximately eight times more efficient than the dispersal through seeds only for C. coccinea. Furthermore, the haplotype network indicated that the species rarely share haplotypes and that C.coccinea and C. brevipedunculata present greater diversity with expansion events. The divergence time estimation analysis showed that C. brevipedunculata and C. wittigiana probably originated between the Pliocene and the Pleistocene. The other clade species have diversified in the Pleistocene. Population expansion events were observed for all species in the Pleistocene ice ages. Because they are endangered species, this study recommends the \"in situ\" conservation as well as \"ex situ\" conservation for all species of clade, with special attention for two species of Espírito Santo: C. wittigiana and the species of DMES locality, in addition to the species of SJPSP location in São Paulo.