The Phylogenetic reconstruction has seen great development in the last 30 years. Computers have become more powerful and more generally accessible, and computer algorithms more sophisticated. It comes the effort of scientists to reconstruct the entire tree of life from a large amount of phylogenetic data. Just for this purpose are formed phylogenetic supertrees that allow the combination of all information gathered so far. The aim of this work is to find a method to construct supertree that will give correct results.

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Explaining the origin and maintenance of biodiversity is a central goal in ecology and evolutionary biology. Some of the most important, theoretical explanations for this diversity centre on the evolution of life histories. Comparative studies on life history evolution, have received significant attention in the zoological literature, but have lagged in plants. Recent developments, however, have emphasised the value of comparative analysis of data for many species to test existing theories of life history evolution, as well as to provide the basis for developing additional or alternative theories. The primary goal of this study was to explore existing theories of life history evolution using a dataset of demographic information in the form of matrix population models for a large number of plant species. By projecting average matrix population models for 207 plant species, life tables and fecundity schedules were obtained and, in turn, were used to estimate relevant life history parameters. These parameters were then used to explore the i) lability of life history traits in plants ii) their continuum of life history variation, iii) the evolution of senescence and iv) the significance of demographic entropy in population ecology. Elasticities and sensitivities of life history traits showed significant phylogenetic signal compared to other life history traits, although, all the values of phylogenetic signal observed were < 1 indicating that life history traits are generally labile. Eighty one percent of species in the datset had mortality curves that increased with age compared to one hundred percent of species that showed a reproductive value curve that decreases with age at the end of life. In particular, the parameters that measured pace and duration were inversely related suggesting in general, the presence of senescence in our data set. Finally, the tenets of the directionality theory based on demographic entropy were generally not confirmed. This study provides an important contribution to the life history evolution of iteroparous perennial plants and confirms existing theories on life history evolution.

Phylogenetics is a field primarily concerned with the reconstruction of the evolutionary history of present day species. Evolutionary history is often modeled by a phylogenetic tree, similar to a family tree. To recreate a phylogenetic tree from information about current species, one needs to make assumptions about the evolutionary process. These assumptions can range from full parametrised models of evolution to simple observations. This thesis looks at the reconstruction of phylogenetic trees under two different assumptions. The first, known as the ordinal assumption, has been previously studied and asserts that as species evolve, they become more dissimilar. The second, the convex assumption, has not previously been studied in this context and asserts that changes species go through to become dissimilar are progressively larger than the current differences between those species. This thesis presents an overview of mathematical results in tree reconstruction from dissimilarity maps (also known as distance matrices) and develops techniques for reasoning about the ordinal and convex assumptions. In particular, three main results are presented: a complete classification of phylogenetic trees with four leaves under the ordinal assumption; a partial classification of phylogenetic trees with four leaves under the convex assumption; and, an independent proof of a result on the relationship between ultrametrics and the ordinal assumption.

Biological and molecular characteristics of the pathogenic mollicute, Spiroplasma penaei, isolated from the hemolymph of infected Pacific white shrimp, Penaeus vannamei, were investigated. The doubling times of a S. penaei were 6.13 h (2% NaCl) and 3.43 h (no salt) under aerobic conditions, and 6.63 h (2% NaCl) and 3.22 h (no salt) under anaerobic conditions. Small diffuse white colonies with granular centers, surrounded by small satellite colonies that appeared embedded in the agar matrix, were detected on solid M1D medium (2% Noble agar) under aerobic conditions at 28°C. The genome size of the S. penaei was 1778 Kb, as determined by pulsed-field gel electrophoresis using undigested DNA. Reduction of virulence of S. penaei was not detected in serial passage 24 and 76 isolates but passage 131 isolate was attenuated as indicated by the number of surviving shrimp and histological findings of challenged P. vannamei. Toxicity was not detected in supernatant fractions of M1D medium cultures of S. penaei isolates. The most predominant host responses to the S. penaei reference isolate and to serial passage isolates were hemocytic nodules and hemocytic infiltration observed in hematoxylin and eosin-stained histological sections. Transmission electron microscopy of the lymphoid organ of experimentally infected P. vannamei depicted S. penaei without cell wall and free in the cytoplasm of lymphoid organ cells. The lesions observed in histological sections were verified by in situ hybridization using a digoxigenin (DIG)-labeled probe specific to the spiralin gene of Spiroplasma spp. Evolutionary relationship trees, based on five partial DNA sequences of 16S rDNA, 23S rDNA, 5S rDNA, gyrB, rpoB genes and two complete DNA sequences of 16S-23S and 23S-5S ISR, were constructed using the distance-based Neighboring-Joining method with Kimura-2-parameter substitution model. The NJ trees based on all DNA sequences investigated in this study positioned S. penaei in the Citri-Poulsonii clade and corroborates the observations by other investigators using the 16S gene. Pairwise genetic distance calculation between sequences of spiroplasmas showed S. penaei to be closely related to S. insolitum and distantly related to Spiroplasma sp. SHRIMP from China.

The Sonorini is a diverse assemblage of cryptozoic to fossorial snakes. Molecular and morphological evidence is ambiguous as to whether the tribe is monophyletic or consists of two or more independent clades. Morphological analysis, using Coluber constrictor and Liochlorophis vernalis as outgroups, indicates that the genera Conopsis, Ficimia, Gyalopion, Pseudoficimia, Stenorrhina, and Sympholis form the sister group to Chilomeniscus, Chionactis, and Sonora. This clade, in turn, is sister to Scolecophis and Tantilla. The putative genera Geagras and Tantillita are nested within the Tantilla calamarina and T. taeniata species groups, respectively.Each of the three major clades contains one or more highly fossorial forms that appear to be independently derived. Morphometric and natural history data from museum specimens, field studies, and the literature indicate that taxa with highly fossorial morphologies specialize on buried prey. Sympholis is at least a part-time commensal of leaf-cutting ants that feeds on beetle grubs; Chilomeniscus is a soil burrower that feeds on burrowing roaches and vermiform beetle larvae, whereas other members of the Ficimia and Sonora clades feed on various combinations of arachnids, orthopterans, and beetle grubs. Geagras redimitus, presumably a detritus burrower, feeds on vermiform beetle larvae, whereas Scolecophis and most Tantilla feed on centipedes. At least three other Tantilla species, including T. gracilis, T. relicta, and T. vermiformis, show parallel trends towards miniaturization, fossorial morphology, and diet of insect larvae.

Le genre Quercus comprend plus de 500 espèces et est réparti sur l’ensemble de l’hémisphère nord. La phylogénie du genre, faite à ce jour à partir d’un nombre très limité de marqueurs nucléaires, n’était pas résolue. Des incertitudes demeuraient au niveau des nœuds profonds où ont divergé les principaux groupes taxonomiques aujourd’hui reconnus. L’objectif de cette thèse était d’explorer de manière plus exhaustive les ressources génomiques nucléaires et chloroplastiques pour affiner la phylogénie du genre. Les travaux sont basés sur les séquences de six gènes nucléaires et de l’ensemble du génome chloroplastique. Ces travaux confirment le caractère diffus du signal phylogénétique et le gain de résolution obtenu par l’adjonction de séquences nouvelles. Ils confirment également la subdivision du genre en six groupes infragénériques (Cyclobalanopsis, Ilex, Cerris, Lobatae, Quercus s.s. et Protobalanus), dont les relations phylogénétiques ont été précisées, même si certaines irrésolutions persistent. La thèse met très clairement en évidence l’empreinte phylogéographique dans le génome chloroplastique au niveau du genre et de sa distribution mondiale. Le signal phylogéographique chloroplastique ajouté à la phylogénie nucléaire permet d’échafauder un scénario biogéographique de diversification du genre. Ce scénario devra être corroboré par des apports d’autres disciplines (paléontologie et géologie historique). / The genus Quercus comprises more than 500 species, and is widely distributed across the Northern hemisphere. Phylogenetic reconstructions based on traditional molecular sequences were so far irresolutive at the deeper nodes where the major extant taxonomic groups have diverged. This thesis aims at improving the phylogeny of the genus by exploring the current nuclear and chloroplastic genomic resources. The phylogenetic investigations are based on sequences of six nuclear genes and the entire chloroplastic genome. The results confirm that the phylogenetic signal is rather diluted and that substantial improvements can be obtained by adding sequences from additional genes. They also confirm that the genus can be subdivided in six infrageneric groups (Cyclobalanopsis, Ilex, cerris, Lobatae, Quercus s.s. et Protobalanus). Phylogenetic relationships among these groups are refined, although not fully clarified. There is a very clear phylogeographic imprint in the chloroplast genome that extends at the macroevolutionary level at the whole genus across its entire distribution. The phylogeographic structure together with the phylogeny at the nuclear level allows to elaborate an historical scenario of the radiation of the genus. Additional elements coming from other disciplines (paleontology, historical geology) are however necessary to confirm this scenario.

A família Rallidae é representada por aves cosmopolitas popularmente conhecidas como saracuras, sanãs, carquejas, galinhas-d`água e frangos-d`água. Compreende cerca de 135 espécies distribuídas em 33 gêneros, dos quais 13 são monotípicos. As relações filogenéticas baseadas em caracteres morfológicos e dados moleculares indicam diferentes afinidades entre os membros da família, principalmente na posição dos gêneros Rallus, Porphyrio, Gallinula e Fulica. Neste estudo, focado em espécies Neotropicais da família, uma nova análise filogenética baseada em caracteres osteológicos é proposta. Uma amostra de 100 esqueletos de 13 gêneros e 31 espécies foi analisada. No total 50 caracteres foram codificados, dos quais 17 são cranianos e 33 pós-cranianos para a construção de uma matriz e subseqüente análise filogenética de acordo com o princípio da parcimônia. Foram calculados árvores de consenso estrito e consenso de maioria. A primeira gerou 151 árvores igualmente parcimoniosas com 99 passos. A análise com método de pesagem sucessiva dos caracteres obteve melhores resoluções entre as espécies amostradas. A topologia do cladograma permite a validade de determinados gêneros como entidades monofiléticas, como Rallus, Porphyrio, Aramides, Gallinula e Fulica. O posicionamento de Porphyrio como um ramo basal dentro da subfamília Rallinae foi suportado e suas relações interespecíficas demonstram que as espécies do Novo mundo são mais proximamente relacionadas do que P. porphyrio, permitindo a inclusão taxonômica de Porphyrula. A relação próxima entre as espécies do gênero Gallinula e Fulica foi corroborada, no entanto, G. melanops é um ramo basal do clado que inclui as espécies de Fulica, indicando que uma mudança taxonômica é necessária. A relação entre as espécies de Rallus e Pardirallus é distante e não suporta a inclusão das espécies de Pardirallus em Rallus. As maiores discordâncias da filogenia proposta em comparação com estudos moleculares referem-se à posição interna dos membros de Porphyrio e suas relações com outros gêneros / The family Rallidae is represented by cosmopolitan birds commonly known as wood-rails, crakes, coots, gallinules and swamp hens. It comprises around 135 species, distributed in 33 genera, of which 13 are monotypics. The phylogenetic relationships based on morphological characters and molecular parameters indicate different affinities among family species, mainly the position of the genera Rallus, Porphyrio, Gallinula and Fulica. In this study, focused on the Neotropical species of the family, a new phylogenetic analysis based on osteological characters is proposed. A sample of 100 skeletons of 13 genera and 31 species was analyzed. A total of 50 characters was codified, of which 17 were cranial and 33 post-cranial to provide a matrix construction and a subsequent phylogenetic analysis according to the principle of parsimony. A strict consensus and a majority rule consensus tree were calculated. The former generated 151 equally parsimonious trees with 99 steps. The successive weighting approach analyses of characters obtained better resolutions around the sampled species. The cladogram topology allows the acceptance of some genera as valid monophyletic groups, such as Rallus, Porphyrio, Aramides, Gallinula and Fulica. The position of Porphyrio as a basal branch within the subfamily Rallinae was supported and the interspecific relationships show that New World species were more closely related than P. porphyrio, allowing the taxonomic inclusion of Porphyrula. The close relationship between the species of Gallinula and Fulica was corroborated, but G. melanops is a basal branch of a clade that includes Fulica species, indicating that a taxonomic change is needed. The relationship of Rallus and Pardirallus is distant and so does not support the inclusion of Pardirallus species in Rallus. The major discordances of the proposed phylogeny in comparison with molecular studies concern the internal position of the Porphyrio members and their relationships with other genera.

Os loricariíneos são Siluriformes altamente derivados e contabilizam cerca de 210 espécies, apresentando uma irradiação adaptativa bem sucedida, tendo representantes na Costa Rica, no Panamá e em toda a América do Sul, e ocorrendo também em ambos os lados dos Andes. Discussões taxonômicas conflituosas são encontradas sobre esta subfamília, envolvendo muitos de seus gêneros, principalmente os mais numerosos, como é o caso de Rineloricaria. O elevado número de espécies (64), a ampla distribuição geográfica e a presença de características diagnósticas válidas para todos os gêneros da subfamília, levam à discussão a proposta de uma subdivisão no gênero Rineloricaria, além de indicar as dificuldades de identificação apresentadas pelo gênero. Em relação às características citogenéticas, Loricariinae apresenta-se como uma subfamília heterogênea e diversificada, com o número diplóide variando de 2n=36 cromossomos a 2n=74 cromossomos. O gênero Rineloricaria contribui intensamente para essa variação, com números cromossômicos variando de 2n=36 a 2n=70 cromossomos. A participação de rearranjos Robertsonianos na evolução cariotípica de Rineloricaria é algo claro, mas evidências que confirmem a ordenação desses eventos não existem. No presente trabalho, técnicas citogenéticas e moleculares foram utilizadas com a finalidade de estabelecer relações evolutivas entre os integrantes da subfamília Loricariinae, em especial do gênero Rineloricaria, entender a evolução cariotípica dessa subfamília e identificar marcadores citogenéticos e moleculares úteis na identificação e descrição de espécies de Rineloricaria. Foram analisados os cromossomos de doze espécies de Loricariinae, pertencentes aos gêneros Harttia, Loricariia, Loricariichthys e Rineloricaria, coletadas na Bacia do Alto Paraná e nas drenagens do Leste brasileiro. Três regiões do genoma mitocondrial (ATPase 6 e 8, Citocromo b e Citocromo c Oxidase I) foram investigadas nessas espécies no presente trabalho. As análises filogenéticas recuperaram o gênero Rineloricaria como um grupo monofilético. Os dados citogenéticos permitiram o estabelecimento de tendências de evolução cromossômica em Loricariinae e no gênero Rineloricaria. O presente trabalho reforça a importância da utilização de diferentes abordagens na realização de estudos taxonômicos e evolutivos, sugerindo uma nova revisão do gênero Rineloricaria que leve em consideração os dados genéticos obtidos. / Loricariinae are Siluriformes highly derivative and account for about 210 species, with a successful adaptive radiation and representatives can be seen in Costa Rica, Panama and throughout South America, and also occurring on both sides of the Andes. Conflicting taxonomic discussions are found on this subfamily, involving many of its genera, especially the most numerous, as Rineloricaria. The high number of species (64), the wide geographic distribution and the presence of valid diagnostic features for all genera of the subfamily, leads to a discussion of a proposed subdivision in the genus Rineloricaria, besides indicating the difficulties of identification presented by the genus. With respect to cytogenetic characteristics, Loricariinae is presented as a heterogeneous and diverse subfamily, varying diploid number of 2n = 36 chromosomes to 2n = 74 chromosomes. The genus Rineloricaria contributes strongly to this variation, with chromosome numbers ranging from 2n = 36 to 2n = 70 chromosomes. The involvement of Robertsonian rearrangements in the karyotype evolution of Rineloricaria is something unclear, but evidences that confirm the ordination of these events does not exist. In this study, cytogenetic and molecular techniques were used in order to establish evolutionary relationships among members of the subfamily Loricariinae, especially the genus Rineloricaria, and also to understand the karyotype evolution of this subfamily and to identify cytogenetic and molecular markers useful in identifying and describing species of Rineloricaria. We analyzed the chromosomes of twelve species of Loricariinae from genera Harttia, Loricariia, Loricariichthys Rineloricaria from the Upper Paraná Basin and the drainages of eastern Brazil. Three regions of the mitochondrial genome (ATPase 6 and 8, Cytochrome b and Cytochrome c Oxidase I) were investigated in these species of this study. The phylogenetic analysis recovered the genus Rineloricaria as a monophyletic group. The cytogenetic data allowed us to establish trends in chromosomal evolution in Loricariinae and in the genus Rineloricaria. The present study underscores the importance of using different approaches in carrying out taxonomic and evolutionary studies, suggesting a further revision of the genus Rineloricaria that takes into account the genetic data obtained.

Os gaviões buteoninos são aves pertencentes à família Accipitridae de distribuição cosmopolita, mas predominante na região Neotropical. Nas classificações mais tradicionais, os buteoninos incluem os gêneros Buteo, Busarellus, Buteogallus, Geranoaetus, Geranospiza, Harpyhaliaetus, Leucopternis e Parabuteo. Recentemente, dados moleculares agregaram a este subgrupo os gêneros Ictinia e Rosthramus, historicamente considerados como pertencentes a outro subgrupo da família, popularmente conhecido como kites. Neste trabalho, foi realizado um estudo da anatomia comparada do esqueleto craniano de representantes da família Accipitridae e, entre eles, amostrados os táxons historicamente relacionados aos buteoninos. Para tanto, foram analisados 98 esqueletos cranianos, totalizando 45 espécies de representantes da ordem Falconiformes, sendo selecionadas 34 como espécies terminais para as análises filogenéticas. Foram codificados 59 caracteres do esqueleto craniano para a construção da matriz, sendo esta posteriormente submetida à análise filogenética e otimização dos caracteres, de acordo com o princípio da parcimônia. Foram calculados diagramas de consenso estrito e de maioria e, em uma análise adicional, foram realizados procedimentos de ponderação sucessiva dos caracteres. Os resultados permitem o reconhecimento da subfamília Buteoninae sustentada por quatro sinapomorfias e composta pelos gêneros: Buteo, Geranoaetus, Buteogallus, Harpyhaliaetus Leucopternis e Parabuteo. Dessa maneira, o resultado aqui obtido é parcialmente discordante da maioria dos estudos moleculares sobre o grupo, uma vez que os gêneros Ictinia, Rosthramus e Geranospiza não aparecem como componentes deste clado, enquanto o gênero Busarellus mostra-se como o táxon mais basal do componente irmão de Buteoninae. / The buteonine hawks are members of the family Accipitridae with a worldwide distribution but mainly restricted to the Neotropics. Traditionally, the buteonine group has included the genera Buteo, Busarellus, Buteogallus, Geranoaetus, Geranospiza, Harpyhaliaetus, Leucopternis and Parabuteo. Recently, molecular data has indicated that two other genera, Ictinia and Rosthramus, should be incorporated in this subgroup, although historically these have been treated as representative of another family subgroup, commonly known as kites. A comparative anatomical study was made on the cranial skeleton of representatives of the family Accipitridae, including those taxa historically related to the buteonine hawks. A sample of 98 cranial skeletons of 45 species representative of the order Falconiformes was analysed, and 34 of these were selected as terminal species in the phylogenetic analyses. A total of 59 characters were used to construct a data matrix which was submitted to a phylogenetic analysis and character optimization according to the principle of parsimony. Strict and majority rule consensus trees were calculated, and in an additional analysis, successive weighting approaches were conducted. The results permit the recognition of the subfamily Buteoninae supported by four synapomorphies and comprising the genera: Buteo, Geranoaetus, Buteogallus, Harpyhaliaetus Leucopternis and Parabuteo. However, the analysis does not fully support the relationships indicated by the molecular data for the group, since the genera Ictinia, Rosthramus and also Geranospiza are excluded from this clade, while the genus Busarellus appears as the most basal taxon of the sister group to the Buteoninae.