To understand present patterns of biodiversity, knowledge of a lineage’s past – both evolutionary and geographic – is required. Here I present the first comprehensive phylogenomic study of an Amazonian poison frog genus, Ameerega, as well as the introduction of a new method for characterizing ancestral distributions via phylogenetic niche modeling, which I use to investigate Ameerega’s biogeographic past. I sequenced thousands of ultraconserved elements from over 100 tissue samples, representing almost every described Ameerega species, as well as undescribed cryptic diversity. My phylogenetic inference diverged strongly from those of previous studies. I also introduce a new phylogenetic niche modeling method, which accounts for issues of bias in other methods by incorporating knowledge of evolutionary relationships into niche models. Given modern-day and paleoclimatic data, species occurrence data, and a time-calibrated phylogeny, my method constructs niche models for each extant taxon, uses ancestral character estimation to reconstruct ancestral niche models, and projects these models into paleoclimate data to provide a historical estimate of the geographic range of a lineage. I demonstrate my method on the Ameerega bassleri group. I also use simulations to show that my method can reliably reconstruct the niche of a known ancestor in both geographic and environmental space.

Verrucariaceae are a family including mostly lichenized species (Verrucariales, Ascomycota). Its current generic classification, which mainly relies on three morphological characters (spore septation, thallus structure, and hymenial algae), has never been subjected to molecular data. Because these characters were suspected to be homoplastic, the monophyly of the genera as currently delimited based on morphology need to be assessed. A three-gene phylogenetic analysis was carried out using three methods (Maximum Parsimony, Maximum Likelihood, and a Bayesian approach) on 83 taxa, selected from 15 genera in Verrucariaceae. Ancestral state reconstructions were undertaken for four characters (spore septation, thallus structure, hymenial algae, and upper cortex structure). The results confirmed that most of the genera were not monophyletic, and that the most recent common ancestor of Verrucariaceae was most likely crustose, lacking hymenial algae, and with simple spores and a pseudocortex. The use of symplesiomorphic traits to define Verrucaria, the largest and type genus for the Verrucariaceae, as well as the non monophyly of the genera Polyblastia, Staurothele and Thelidium, explain most of the discrepancies between the current classification and a classification using monophyly as a grouping criterion. In order to accommodate newly inferred monophyletic groups, existing genera were re-delimited and three new genera were proposed. Recent broad-scale phylogenetic analyses have shown that Verrucariales was sister to Chaetothyriales, an order first known as including mostly saprophytes and opportunistic animal and human parasites. Investigations of fungal communities colonizing rocks in extreme environments have shown that some slow-growing melanized fungi inhabiting bare rock surfaces belonged to the Chaetothyriales. Multigene phylogenetic analyses were carried out using Maximum Likelihood and a Bayesian approach in order to confirm the affiliation of 25 of these rock isolates. Ancestral state reconstructions were then undertaken on two different datasets to look at the evolutionary history of lichenization within Pezizomycotina, and the rock-inhabiting habit within Eurotiomycetes. Results suggest that the ancestor of the lineage including Verrucariales and Chaetothyriales was likely to be an extremotolerant non-lichenized, rock-inhabiting fungus. Virulence factors of opportunistic parasites within Chaetothyriales, such as melanization and meristematic growth, might have primary been adaptations for life in extreme habitats. / Dissertation

The morphologies and behaviors of animals evolve and diversify, filling ecological niches in their environments. In this study I examine how a morphological trait, body mass, and three ecological traits, namely diel activity patterns, diving/non-diving locomotion, and diet, evolve in the Anseriformes (waterfowl). Through ancestral state reconstructions using a maximum likelihood approach the evolution of these traits was compared to see if any patterns of trait coevolution emerged. Body mass was compared to each ecological trait using a phylogenetic ANOVA to test if there were body size differences between ecological groups. The pattern of male and female body mass evolution across the clade was found to be remarkably similar, indicating that selection effected body mass in similar ways between the sexes. Diving locomotion appears to be the ancestral state for Anseriformes with non-diving independently evolving probably five times. The ancestral state of diet appears to be either herbivory or omnivory, with carnivory secondarily evolving twice independently. For diel activity patterns, the ancestral state reconstruction showed little resolution at the internal nodes, indicating the high degree of plasticity in this trait among the species studied. Body mass in both males and females was not significantly correlated with any particular diet, diving locomotion, or diel activity pattern.

Orientador: Maria das Graças Sajo / Resumo: Esta tese está organizada em dois Capítulos que tiveram como objetivos: a. descrever e revisar a anatomia radicular na subtribo Pleurothallidinae, b. apontar caracteres anatômicos radiculares que possam identificar táxons, c. reconstruir a história dos caracteres radiculares usando dados genéticos da região ITS disponíveis no GenBank, e por fim, d. mostrar a ontogenia dos tilossomos em Anathallis sclerophylla. No primeiro Capítulo foi analisada a anatomia radicular de 82 espécies distribuídas em 29 gêneros, abrangendo oito das nove Afinidades dentro da subtribo Pleurothallidinae. Concluímos que o velame biestratificado é comum na subtribo, ocorrendo nas oito Afinidades e em mais de 75% das espécies amostradas. Ainda ocorre velame uniestratificado em Lepanthes calodictyon, e velames com três, quatro e cinco camadas em espécies das Afinidades Restrepia e Masdevallia. Reafirmamos a importância taxonômica dos espessamentos parietais do velame apresentando-os de forma detalhada na organografia do complexo velame-exoderme, sendo os padrões morfológicos e sua distribuição entre as camadas do velame uma rica fonte de informação para o reconhecimento dos gêneros na subtribo. Mostramos os tilossomos de 39 espécies e notamos que morfologias mais simples ocorrem nas Afinidades mais basais e morfologias mais complexas ocorrem nas Afinidades mais derivadas. Na exoderme, espessamentos em “O” ou em “∩” ocorrem principalmente nos gêneros mais basais, a exoderme de paredes finas pode ser inter... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: This thesis is organized in two Chapters that aimed: a. describe and review the root anatomy in the Pleurothallidinae subtribe, b. point out radicular anatomical characters that can identify taxa, c. reconstruct the history of root characters using GenBank genetic data from ITS region, and finally d. to show the ontogeny of tilosomes in Anathallis sclerophylla. In the first Chapter we analyzed the root anatomy of 82 species distributed in 29 genera, covering eight of the nine Affinities within the Pleurothallidinae. We conclude that bistratified velamen is common, occurring in the eight Affinities and in more than 75% of the sampled species. Single layered velamen still occur in Lepanthes calodictyon, in the same way three, four, and five layer occurs in Restrepia and Masdevallia Affinities. We reinforce the taxonomic importance of the velamen parietal thickening, presenting them in detail such a velamen-exodermis complex organogram. The morphological patterns and their distribution between the velamen layers are a rich information source for the genera recognition in the subtribe. We show the tilosomes of 39 species and note that simpler morphologies occur at the early divergent Affinities, and more complex morphologies occur in late divergent ones. In exodermis, “O” or “∩” thickening occurs mainly in basal genera, thin-walled exodermis can be interpreted as a derived apomorphic feature, and “U” thickened exodermis in Barbosella is the only synapomorphy found in the subtribe... (Complete abstract click electronic access below) / Doutor

Vertebrate evolution has resulted in a diversity of feeding mechanisms. Cetaceans are secondarily derived tetrapods that have returned to a marine habitat. As a result, they display feeding modes that have converged with more basal aquatic vertebrates, but display a diversity of new solutions and adaptations. To begin to explore the diversity of feeding adaptations among odontocetes, kinematics of feeding modes and feeding adaptations for belugas (Delphinapterus leucas), Pacific white-sided dolphins (Lagenorhynchus obliquidens), and long-finned pilot whales (Globicephala melas) were characterized. In addition, direct measurements of intraoral pressure were collected to determine maximum suction performance. Characters from these analyses were combined with data for other odontocetes, and were mapped onto a phylogeny of Odontoceti to begin to explore where changes in feeding modes took place. Feeding modes were diverse in belugas, Pacific white-sided dolphins, and pilot whales and included suction, ram, and a combination of both. In general, four phases were observed: (I) preparatory, (II) jaw opening, (III) gular depression, and (IV) jaw closing. Suction was a large component of the prey capture method in belugas and subambient pressures in excess of 100 kPa were generated. Belugas were also capable of lateral lip gape occlusion and anterior lip pursing to form a small anterior aperture. Pacific whitesided dolphins relied on ram to capture prey. However, some degree of pursing and resultant subambient pressure was observed that was likely used to compensate for high ram speeds or for prey manipulation and transport to the esophagus. Pilot whales were more similar to belugas in kinematics, but maintained high approach velocities and did not generate significant suction pressures; suction and ram were used in combination. Belugas and pilot whales appeared to employ hyolingual depression as a primary suction generation mechanism, whereas Pacific white-sided dolphins relied on fast jaw opening. Ancestral state reconstructions indicated that suction feeding capability evolved independently at least six times within Odontoceti. These results indicate the diversity of feeding behaviors in odontocetes and provide directives for future studies on the diversity of feeding in secondarily aquatic mammals.

Les Angiospermes sont le clade le plus diversifié des plantes actuelles et sont exceptionnellement riches en espèces dans les régions tropicales. Dans cette thèse, j’ai étudié l’évolution des systèmes sexuels et l’histoire biogéographique de la famille des Moraceae, clade modèle utilisé pour comprendre l’origine et l’évolution de la diversité chez les Angiospermes. Dans le Chapitre I, j’ai reconstruit et calibré un nouvel arbre phylogénétique daté pour les Moraceae. J’ai ensuite utilisé cet arbre pour reconstruire les états ancestraux des systèmes sexuels chez les Moraceae et Ficus. Les âges des groupes-couronne des Moraceae et du genre Ficus sont estimés au Crétacé et à l’Eocène, respectivement. La dioécie est inférée comme l’état ancestral des systèmes sexuels chez les Moraceae, avec plusieurs transitions ultérieures vers la monoécie, y compris chez Ficus. Ce résultat suggère que la dioécie ne représente pas nécessairement un cul-de-sac évolutif. Dans le Chapitre II, j’ai reconstruit un arbre phylogénétique daté pour la tribu des Dorstenieae, distribuée principalement dans les régions tropicales, à partir d’un nouveau jeu de données génomiques nucléaires produit avec une approche Hyb-Seq. L’histoire biogéographique du groupe a ensuite été reconstruite en utilisant les modèles de dispersion-extinction-cladogenèse. Les âges des groupes-couronne des Dorstenieae et du genre Dorstenia sont estimés au Crétacé et dans la période du Crétacé au Paléocène, respectivement. Deux évènements de dispersion à longue distance depuis l’Afrique continentale vers l’Amérique du Sud ont eu lieu au Cénozoïque (Dorstenia et Brosimum s.l.). Dans le Chapitre III, j’ai testé les différences de niche climatique (température et précipitation) entre les deux systèmes sexuels (monoécie et gynodioécie) chez Ficus avec un nouveau jeu de données fiables d’occurrences spatiales et de systèmes sexuels chez 183 espèces. À cette fin, j’ai utilisé deux approches comparatives : équations d’estimation généralisées (GEE) et modèles linéaires généralisés (GLM). Une relation positive entre précipitation et gynodioécie est soutenue par les analyses GLM, et aucune méthode ne soutient une relation entre température et système sexuel. Une meilleure capacité à se disperser et le potentiel d’autopollinisation sont deux explications possibles pour la colonisation et la survie des espèces monoïques dans des environnements plus secs. Cette thèse démontre le potentiel des méthodes phylogénétiques comparatives et des données phylogénomiques pour répondre aux questions d’évolution des systèmes sexuels et de biogéographie chez les Moraceae et ouvre plusieurs nouvelles perspectives importantes méritant d’être approfondies chez d’autres clades de plantes, telles que la relation entre système sexuel et niche climatique. / Angiosperms are the most diversified clade of extant plants and are exceptionally species-rich in tropical regions. In this thesis, I investigated breeding system evolution and biogeographic history in the family Moraceae, which I used as a model clade to understand the origin and evolution of diversity of angiosperms. In Chapter I, I reconstructed and calibrated a new dated phylogenetic tree for Moraceae as a whole. I then used this tree to reconstruct ancestral states of breeding systems in Moraceae and Ficus. The crown group ages of Moraceae and Ficus were estimated in the Cretaceous and in the Eocene, respectively. Dioecy was inferred as the ancestral breeding systems of Moraceae, with several subsequent transitions to monoecy, including in Ficus. This result suggests that dioecy is not necessarily an evolutionary dead end. In Chapter II, I reconstructed a dated phylogenetic tree for tribe Dorstenieae, mainly distributed in tropical regions, with a new data set of nuclear genomic data generated with a Hyb-Seq approach. Biogeographic history was then reconstructed using dispersal-extinction-cladogenesis models. The crown group ages of Dorstenieae and Dorstenia were estimated in the Cretaceous and in the Cretaceous/Paleocene period, respectively. Two long-distance dispersal events from continental Africa to South America occurred in the Cenozoic (Dorstenia and Brosimum s.l.). In Chapter III, I tested the climatic niche difference (temperature and precipitation) between the two breeding systems (monoecy and gynodioecy) in Ficus using a new dataset of cleaned spatial occurrence records and breeding systems for 183 species. I used two comparative approaches: generalized estimating equations (GEE) and generalized linear models (GLM). A positive relationship between precipitation and gynodioecy was supported by GLM, but not GEE analyses, and no relationship between temperature and breeding systems was supported by either method. Higher dispersal ability and the potential for self-fertilization may explain why monoecious species of Ficus have been able to colonize and survive in drier environments. This thesis highlights the potential of phylogenetic comparative methods and phylogenomic data to address questions of breeding system evolution and biogeography in Moraceae, and opens up several important new perspectives worth investigating in other plant clades, such as a relationship between breeding system and climatic niche.

Pseudomonas syringae is a common foliar plant pathogenic bacterium that causes diseases on many crop plants. We hypothesized that today's highly virulent P. syringae crop pathogens with narrow host range might have evolved after the advent of agriculture from ancestral P. syringae strains with wide host range that were adapted to mixed plant communities. The model tomato and Arabidopsis pathogen P. syringae pv. tomato (Pto) DC3000 and its close relatives isolated from crop plants were thus selected to unravel basic principles of host range evolution by applying molecular evolutionary analysis and comparative genomics approaches. Phylogenetic analysis was combined with host range tests to reconstruct the host range of the most recent common ancestor of all analyzed strains isolated from crop plants. Even though reconstruction of host range of the most recent common ancestor of all analyzed strains was not conclusive, support for this hypothesis was found in some sub-groups of strains. The focus of my studies then turned to Pto T1, which was found to represent the most common P. syringae lineage causing bacterial speck disease on tomato world-wide. Five genomes were sequenced and compared to each other. Identical genotypes were found in North America and Europe suggesting frequent pathogen movement between these continents. Moreover, the type III-secreted effector gene hopM1 was found to be under strong selection for loss of function and non-synonymous mutations in the fliC gene allowed to identify a region that triggers plant immunity. Finally, Pto T1 was compared to closely related bacteria isolated from snow pack and surface water in the French Alps. Recombination between alpine strains and crop strains was inferred and virulence gene repertoires of alpine strains and crop strains were found to overlap. Alpine strains cause disease on tomato and have relatively wider host ranges than Pto T1. The conclusion from these studies is that Pto T1 and other crop pathogens may have evolved from ancestors similar to the characterized environmental strains isolated in the French Alps by adapting their effector repertoire to individual crops becoming more virulent on these crops but losing virulence on other plants. / Ph. D.