I focus on phylogenetic relationships of teiid lizards beginning with generic and species relationship within the family, followed by a detailed biogeographical examination of the Caribbean genus Pholidoscelis, and end by studying species boundaries and phylogeographic patterns of the widespread Giant Ameiva Ameiva ameiva. Genomic data (488,656 bp of aligned nuclear DNA) recovered a well-supported phylogeny for Teiidae, showing monophyly for 18 genera including those recently described using morphology and smaller molecular datasets. All three methods of phylogenetic estimation (two species tree, one concatenation) recovered identical topologies except for some relationships within the subfamily Tupinambinae (i.e. position of Salvator and Dracaena) and species relationships within Pholidoscelis, but these were unsupported in all analyses. Phylogenetic reconstruction focused on Caribbean Pholidoscelis recovered novel relationships not reported in previous studies that were based on significantly smaller datasets. Using fossil data, I improve upon divergence time estimates and hypotheses for the biogeographic history of the genus. It is proposed that Pholidoscelis colonized the Caribbean islands through the Lesser Antilles based on biogeographic analysis, the directionality of ocean currents, and evidence that most Caribbean taxa originally colonized from South America. Genetic relationships among populations within the Ameiva ameiva species complex have been poorly understood as a result of its continental-scale distribution and an absence of molecular data for the group. Mitochondrial ND2 data for 357 samples from 233 localities show that A. ameiva may consist of up to six species, with pairwise genetic distances among these six groups ranging from 4.7–12.8%. An examination of morphological characters supports the molecular findings with prediction accuracy of the six clades reaching 72.5% using the seven most diagnostic predictors.

Oenococcus oeni est la principale bactérie lactique retrouvée dans les fermentations malolactiques (FML) spontanées du vin. Pendant la FML, l’acide malique est converti en acide lactique, modulant l’acidité du vin et améliorant son goût. L’activité métabolique d’O. oeni produit aussi des changements dans la composition du vin, modifiant son profil aromatique. Des études précédentes ont suggéré que l’espèce est divisée en deux principaux groupes génétiques, désignés A et B. Nous avons examiné les souches d’O. oeni sous des approches de génomique comparative à l’aide d’outils bioinformatiques développés sur place, dévoilant l’existence de nouveaux de groupes et sous-groupes de souches. En outre, nos résultats suggèrent que certains groupes contiennent des souches qui sont adaptées à des produits spécifiques tels que le vin rouge, vin blanc, champagne et cidre. Ce phénomène est visible à différents niveaux des génomes des souches : l’identité de séquence, les signatures génomiques, et les caractéristiques génomiques spécifiques de groupes telles que la présence/absence de gènes et les mutations uniques. Afin de comprendre l’impact des caractéristiques génomiques dans l’adaptation de l’espèce à différents produits, nous avons sélectionné une collection de souches isolées de la même région, mais appartenant à deux groupes génétiques différents et adaptées soit au vin rouge, soit au vin blanc. Une analyse de données génomiques et métabolomiques intégrées révèle que les caractéristiques génomiques des souches de chaque groupe ont un impact sur l’adaptation des bactéries à leurs niches respectives et sur la composition de la fraction volatile du vin. / Oenococcus oeni is the main lactic acid bacteria found in spontaneous malolactic fermentation (MLF) of wine. During MLF, malic acid is converted into lactic acid, modulating wine’s acidity and improving its taste. The metabolic activity of O. oeni also produces changes in the composition of wine, modifying its aromatic profile. Previous studies have suggested that the species is divided in two major phylogenetic groups, namely A and B. We have examined O. oeni under comparative genomics approaches by the aid of bioinformatics tools developed in-place, unveiling the existence of more phylogenetic groups of O. oeni than previously thought. Moreover, our results suggest that certain groups are domesticated to specific products such as red wine, white wine, champagne and cider. This phenomenon is visible at different levels of the strains’ genomes: sequence identity, genomic signatures, and group-specific features such as presence/absence of genes and unique mutations. With the aim of understanding the impact of group-specific genomic features on the species adaptation to different products, we have selected a set of strains isolated from the same region, but belonging to two different genetic groups and adapted either to red wine, either to white wine. An integrated analysis of genomic and metabolomic data reveals that the genomic features of each genetic group have an impact on the strains adaptation to their respective niches, affecting the composition of the volatile fraction of wine.

No description available.

Bien que les champignons soient régulièrement utilisés comme modèle d'étude des systèmes eucaryotes, leurs relations phylogénétiques soulèvent encore des questions controversées. Parmi celles-ci, la classification des zygomycètes reste inconsistante. Ils sont potentiellement paraphylétiques, i.e. regroupent de lignées fongiques non directement affiliées. La position phylogénétique du genre Schizosaccharomyces est aussi controversée: appartient-il aux Taphrinomycotina (précédemment connus comme archiascomycetes) comme prédit par l'analyse de gènes nucléaires, ou est-il plutôt relié aux Saccharomycotina (levures bourgeonnantes) tel que le suggère la phylogénie mitochondriale? Une autre question concerne la position phylogénétique des nucléariides, un groupe d'eucaryotes amiboïdes que l'on suppose étroitement relié aux champignons. Des analyses multi-gènes réalisées antérieurement n'ont pu conclure, étant donné le choix d'un nombre réduit de taxons et l'utilisation de six gènes nucléaires seulement. Nous avons abordé ces questions par le biais d'inférences phylogénétiques et tests statistiques appliqués à des assemblages de données phylogénomiques nucléaires et mitochondriales. D'après nos résultats, les zygomycètes sont paraphylétiques (Chapitre 2) bien que le signal phylogénétique issu du jeu de données mitochondriales disponibles est insuffisant pour résoudre l'ordre de cet embranchement avec une confiance statistique significative. Dans le Chapitre 3, nous montrons à l'aide d'un jeu de données nucléaires important (plus de cent protéines) et avec supports statistiques concluants, que le genre Schizosaccharomyces appartient aux Taphrinomycotina. De plus, nous démontrons que le regroupement conflictuel des Schizosaccharomyces avec les Saccharomycotina, venant des données mitochondriales, est le résultat d'un type d'erreur phylogénétique connu: l'attraction des longues branches (ALB), un artéfact menant au regroupement d'espèces dont le taux d'évolution rapide n'est pas représentatif de leur véritable position dans l'arbre phylogénétique. Dans le Chapitre 4, en utilisant encore un important jeu de données nucléaires, nous démontrons avec support statistique significatif que les nucleariides constituent le groupe lié de plus près aux champignons. Nous confirmons aussi la paraphylie des zygomycètes traditionnels tel que suggéré précédemment, avec support statistique significatif, bien que ne pouvant placer tous les membres du groupe avec confiance. Nos résultats remettent en cause des aspects d'une récente reclassification taxonomique des zygomycètes et de leurs voisins, les chytridiomycètes. Contrer ou minimiser les artéfacts phylogénétiques telle l'attraction des longues branches (ALB) constitue une question récurrente majeure. Dans ce sens, nous avons développé une nouvelle méthode (Chapitre 5) qui identifie et élimine dans une séquence les sites présentant une grande variation du taux d'évolution (sites fortement hétérotaches - sites HH); ces sites sont connus comme contribuant significativement au phénomène d'ALB. Notre méthode est basée sur un test de rapport de vraisemblance (likelihood ratio test, LRT). Deux jeux de données publiés précédemment sont utilisés pour démontrer que le retrait graduel des sites HH chez les espèces à évolution accélérée (sensibles à l'ALB) augmente significativement le support pour la topologie « vraie » attendue, et ce, de façon plus efficace comparée à d'autres méthodes publiées de retrait de sites de séquences. Néanmoins, et de façon générale, la manipulation de données préalable à l'analyse est loin d’être idéale. Les développements futurs devront viser l'intégration de l'identification et la pondération des sites HH au processus d'inférence phylogénétique lui-même. / Despite the popularity of fungi as eukaryotic model systems, several questions on their phylogenetic relationships continue to be controversial. These include the classification of zygomycetes that are potentially paraphyletic, i.e. a combination of several not directly related fungal lineages. The phylogenetic position of Schizosaccharomyces species has also been controversial: do they belong to Taphrinomycotina (previously known as archiascomycetes) as predicted by analyses with nuclear genes, or are they instead related to Saccharomycotina (budding yeast) as in mitochondrial phylogenies? Another question concerns the precise phylogenetic position of nucleariids, a group of amoeboid eukaryotes that are believed to be close relatives of Fungi. Previously conducted multi-gene analyses have been inconclusive, because of limited taxon sampling and the use of only six nuclear genes. We have addressed these issues by assembling phylogenomic nuclear and mitochondrial datasets for phylogenetic inference and statistical testing. According to our results zygomycetes appear to be paraphyletic (Chapter 2), but the phylogenetic signal in the available mitochondrial dataset is insufficient for resolving their branching order with statistical confidence. In Chapter 3 we show with a large nuclear dataset (more than 100 proteins) and conclusive supports that Schizosaccharomyces species are part of Taphrinomycotina. We further demonstrate that the conflicting grouping of Schizosaccharomyces with budding yeasts, obtained with mitochondrial sequences, results from a phylogenetic error known as long-branch attraction (LBA, a common artifact that leads to the regrouping of species with high evolutionary rates irrespective of their true phylogenetic positions). In Chapter 4, using again a large nuclear dataset we demonstrate with significant statistical support that nucleariids are the closest known relatives of Fungi. We also confirm paraphyly of traditional zygomycetes as previously suggested, with significant support, but without placing all members of this group with confidence. Our results question aspects of a recent taxonomical reclassification of zygomycetes and their chytridiomycete neighbors (a group of zoospore-producing Fungi). Overcoming or minimizing phylogenetic artifacts such as LBA has been among our most recurring questions. We have therefore developed a new method (Chapter 5) that identifies and eliminates sequence sites with highly uneven evolutionary rates (highly heterotachous sites, or HH sites) that are known to contribute significantly to LBA. Our method is based on a likelihood ratio test (LRT). Two previously published datasets are used to demonstrate that gradual removal of HH sites in fast-evolving species (suspected for LBA) significantly increases the support for the expected ‘true’ topology, in a more effective way than comparable, published methods of sequence site removal. Yet in general, data manipulation prior to analysis is far from ideal. Future development should aim at integration of HH site identification and weighting into the phylogenetic inference process itself.

Life history traits affect the timing and pattern of maturation, reproduction, and survival during an organism’s lifecycle and are the major components influencing Darwinian fitness. Co-evolved patterns of these traits are known as life history strategies (LHS) and variation occurs between individuals, populations, and species. The polymorphisms underlying LHS are important targets of natural selection, yet the underlying genes and physiological mechanisms remain largely unknown. Mapping the genetic basis of a LHS and subsequently unraveling the associated physiological mechanisms is a challenging task, as complex phenotypes are often polygenic. However, in several systems discrete LHS are maintained within the population and are inherited as a single locus with pleiotropic effects. These systems provide a promising starting point for investigation into LHS mechanisms and this thesis focuses on one such strategy - the Alba polymorphism in Colias butterflies. Alba is inherited as a single autosomal locus, expressed only in females, and simultaneously affects development rate, reproductive potential, and wing color. Alba females are white, while the alternative morph is yellow/orange. About 28 of 90 species exhibit polymorphic females, though whether the Alba mechanism and associated tradeoffs are conserved across the genus remains to be determined. In this thesis I primarily focus on the species Colias croceus and integrate results from lipidomics, transcriptomics, microscopy, and genomics to gain insights to the proximate mechanisms underlying Alba and Alba’s evolution within the genus. Lipidomics confirm that, consistent with findings in New World species, C. croceus Alba females have larger abdominal lipid stores than orange, an advantage which is temperature dependent and arises primarily due to mobilized lipids. Gene expression data suggests differences in resource allocation, with Alba females investing in reproduction rather than wing color, consistent with previous findings in other Colias species. Additionally, I identify a morphological basis for Alba’s white wing color. Alba females from C. croceus, an Old World species, and Colias eurytheme, a New World species both exhibit a significant reduction in pigment granules, the structures within the wing scale that contain pigment. This is a trait that seems to be unique to Colias as other white Pierid butterflies have an abundance of pigment granules, similar to orange females. I also map the genetic basis of Alba to a single genomic region containing an Alba specific, Jockey-like transposable element insertion. Interestingly this transposable element​ is located downstream of BarH-1, a gene known to affect pigment granule formation in Drosophila. Finally, I construct a phylogeny using a global distribution of 20 Colias species to facilitate investigations of Alba’s evolution within the genus. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript. Paper 4: Manuscript.</p>

Understanding others is a deeply human urge basic in our existential quest. It requires knowing where someone has come from and where they sit amongst peers. Phylogenetic analysis and genome wide association studies seek to tell us where we’ve come from and where we are relative to one another through evolutionary history and genetic makeup. Current methods do not address the computational complexity caused by new forms of genomic data, namely long-read DNA sequencing and increased abundances of assembled genomes, that are becoming evermore abundant. To address this, we explore specialized data structures for storing and comparing genomic information. This work resulted in the creation of novel data structures for storing multiple genomes that can be used for identifying structural variations and other types of polymorphisms. Using these methods we illuminate the genetic history of organisms in our efforts to understand the world around us.

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.

Both insect parasitic/entomopathogenic nematodes and plant parasitic nematodes are of great economic importance. Insect parasitic/entomopathogenic nematodes provide an environmentally safe and effective method to control numerous insect pests worldwide. Alternatively, plant parasitic nematodes cause billions of dollars in crop loss worldwide. Because of these impacts, it is important to understand how these nematodes evolve, and, in the case of entomopathogenic nematodes, how their bacterial symbionts evolve. This dissertation contains six chapters. Chapter one is a review of DNA markers and their use in the phylogenetic systematics of entomopathogenic and insect-parasitic nematodes as well as a review of phylogenetic, co-phylogenetic, and population genetic methodologies. Chapter two characterizes positive destabilizing selection on the luxA gene of bioluminescent bacteria. Our data suggests that bacterial ecology and environmental osmolarity are likely driving the evolution of the luxA gene in bioluminescent bacteria. Chapter 3 examines relationships among bacteria within the genus Photorhabdus. Our analyses produced the most robust phylogenetic hypothesis to date for the genus Photorhabdus. Additionally, we show that glnA is particularly useful in resolving specific and intra-specific relationships poorly resolved in other studies. We conclude that P. asymbiotica is the sister group to P. luminescens and that the new strains HIT and JUN should be given a new group designation within P. asymbiotica. Chapter 4 characterizes the morphology of the head and feeding apparatus of fungal feeding and insect infective female morphs of the nematode Deladenus siricidicola using scanning electron microscopy. Results showed dramatic differences in head, face, and stylet morphology between the two D. siricidicola female morphs that were not detected in previous studies using only light microscopy. Chapter five utilizes comparative transciptomics to identify putative plant and insect parasitism genes in the nematode Deladenus siricidicola. Results from this study provide the first transcriptomic characterization for the nematode Deladenus siricidicola and for an insect parasitic member of the nematode infraorder Tylenchomorpha. Additionally, numerous plant parasitism gene homologues were discovered in both D. siricidicola libraries suggesting that this nematode has co-opted these plant parasitism genes for other functions. Chapter six utilizes a phylogenomic approach to estimate the phylogeny of the nematode infraorder Tylenchomorpha.

Molecular dating (or molecular clock) is a powerful technique that uses the mutation rate of biomolecules to estimate divergence times among organisms. In the last two decades, the theory behind the molecular clock has been intensively developed, and it is now possible to employ sophisticated evolutionary models on genome-scaled datasets in a Bayesian framework. The molecular clock has been successfully applied to virtually all types of organisms and molecules to estimate timing of speciation, timing of gene duplications, and generation times: this knowledge allows contextualizing past and present events in the light of (paleo)ecological scenarios. Molecular clock studies are routinely used in evolutionary and ecological studies, but their use in applied fields such as agricultural and medical entomology is still scarce in particular because of a paucity of genome data. Genome-scaled clocks have been successfully applied, for example, to various model organisms such as Anopheles and Drosophila, as well as to invasive mosquitoes Aedes aegypti and Aedes albopictus. Many other invasive pests are emerging worldwide aided by global trade, increased connectivity among countries, lack of prevention, and flawed invasive species management. Among them, there is Aedes koreicus and Aedes japonicus, two invasive mosquito species which are monitored for public health concerns because of their harboured human pathogenic viruses. For these, as well as for other insects of societal relevance, such as the parasitoid Trissolcus japonicus, there is a paucity of gene markers and no genome data for large scale molecular clock studies. Invasive pests are typically studied using microevolutionary approaches that tackle events at an intraspecific level: these approaches provide important information for the pest management, for example, by revealing invasion routes and insecticide resistances. Approaches that tackle the deep-time evolution of the pest, such as the molecular clock, are instead less used in pest science. Many important traits associated with invasiveness have evolved by speciation over a long time frame: the molecular clock can reveal the paleo-ecological conditions that favoured these traits helping a better understanding of pest biology. Molecular clock, when coupled with phylogenomics, can further identify genes and patterns that characterize the pest: this knowledge can be used to enhance management practices. Although this is a data-driven thesis, its major aim is to provide new results to demonstrate the utility of the molecular clock in pest science. This has been done by systematically apply the molecular clock to various neglected organisms of medical and agricultural relevance. To this aim, I generated new genome data and/or assembled the largest genome-scaled data to date. I studied the molecular clock in mosquitoes, focusing on the Aedini radiation (Chapter 2) and identified a strong incongruence between the mitochondrial and nuclear phylogeny for what concerns their molecular clock. This result highlighted the importance of employing genome scaled data for these species to exclude stochastic effects due to poor/inaccurate sampling in clock studies. To tackle the absence of data, I further assembled the whole mitogenome of emerging invasive species Aedes koreicus and Aedes japonicus with the aim of producing useful data for molecular typing and of inferring divergence estimates using whole mitogenomes (Chapter 3). Dated phylogenies point toward more recent diversification of Aedini and Culicini compared to estimates from previous works, addressing the issue of taxon sampling sensitivity in dated phylogeny. Although it is possible to perform molecular clock studies on single/few gene markers, the current trend is to couple this methodology with genome-scaled datasets to reduce the stochastic effect of using few genes. For this reason, I sequenced the draft genome of A. koreicus and A. japonicus (Chapter 4). The assemblies were extremely fragmented, highlighting the problem of sequencing large genomes using short reads. The assemblies provided, however enough information for genome skimming allowing extraction of BUSCO genes for downstream analyses, whole mitogenome assemblies (used in Chapter 3), and characterisation of the associated metagenome. These data need to be integrated by long reads; it provides, however a first framework to investigate the genome evolution of these species. I further sequenced and assembled the genome of Trissolcus japonicus, the parasitoid wasp of the invasive pest Halyomorpha halys. To elucidate its divergence, estimate and define an intraspecific typing system to differentiate strains for biocontrol strategies, I reconstructed the mitochondrial genomes of two populations: the mitogenomes were surprisingly identical, suggesting that they belong to the same de facto population. I further provide a detailed clock investigation of Zika, a virus harboured and transmitted by some Aedes species (Chapter 5). Using the largest set of genomes to date, I could set the origin of ZIKV in the middle age and its first diversification in the mid-19th century. From a methodological point of view, the clocking of this virus highlighted the importance of checking for recombination and for cell-passages to obtain correct divergence estimates. I finally show my contributions to molecular clock studies of three other invasive species (Chapter 6): I helped disentangle the divergence times of Bactrocera, a genus of invasive fruit files pest of agriculture; I contributed in performing a phylogenomics study of opsin genes in Diptera; I used chloroplast and nuclear genome data to reconstruct the divergences of the invasive reed Arundo. In the various Chapters of my thesis, I highlighted the limits and the problems of current molecular clock methodologies and identified the best practices for different types of organisms in order to develop a cross-discipline understanding of the molecular clock techniques. The various results presented in this thesis further demonstrate the utility of the molecular clock approach in pest studies.

No description available.