La sous-famille des Dialioideae (Fabaceae/Leguminosae) regroupe 17 genres et 90 espèces réparties sur la majorité des continents. Bien que ce clade soit composé d’un nombre restreint d’espèces, une grande diversité de caractères morphologiques floraux est retrouvée au sein de ce groupe. Malgré les informations moléculaires et morphologiques apportées par plusieurs études, les relations évolutives entre les genres et les espèces demeurent peu résolues. En utilisant des données génomiques de 152 gènes nucléaires issues du séquençage ciblé, cette étude vise à établir une phylogénie bien supportée pour les Dialioideae. Nos résultats renforcent la position de plusieurs taxons, dont l’emplacement était mal défini dans les études précédentes, et fournissent de nouvelles perspectives sur l'histoire évolutive du clade. Nos analyses proposent que Koompassia forme un clade avec Apuleia, avec Distemonanthus comme groupefrère. Un placement pour le clade Martiodendron et Zenia est également suggéré, en tant que groupe-frère des Dialioideae excluant le groupement Baudouinia et Eligmocarpus ainsi que Poeppigia procera. De nouvelles relations au sein du clade qui regroupe Kalappia, Storckiella, Labichea et Petalostylis sont également présentées. De plus, cette étude propose une phylogénie basée sur des séquences du génome chloroplastique (matK-trnK, rps16 et trnL), présentant les relations évolutives entre les genres, mais également entre 38 espèces de Dialioideae. Étant donné le nombre réduit de gènes et de taxons utilisés dans les études actuelles, nous cherchions à obtenir une phylogénie présentant les relations évolutives à plusieurs niveaux taxonomiques. Nos résultats exposent des relations évolutives bien supportées et soulèvent le besoin d’échantillonnage des genres Dialium et Labichea. De plus, cette recherche fournit de nouvelles informations génomiques sur la conservation de copies paralogues de gènes fonctionnels associés à la morphologie florale et foliaire chez les végétaux (DICH, DIV, FLO/LFY-like, KNOX1, LEGCYC2, PALM1, PHAN, RAD, UFO). Nos résultats contribuent à la création de nouveau matériel pertinent pouvant être utilisé dans de futures études s’intéressant à la variabilité de caractères morphologiques existante entre les genres du clade. / Subfamily Dialioideae (Fabaceae/Leguminosae) comprises 17 genera and 90 species distributed over Central and South America, Africa, Asia and Oceania. Although this clade groups a small number of taxa, an important diversity of floral morphological characters is found within this group. Despite the molecular and morphological information provided by several studies, the evolutionary relationships amongst genera and species remain poorly resolved. Using genomic data from targeted sequencing of 152 nuclear genes, this study aims to establish a well-supported phylogeny for the Dialioideae. Our results strengthen the position of several taxa and provide new insights into the evolutionary history of the clade. Our analyses provide a resolution for Koompassia, whose position was not clearly defined in previous studies, suggesting it forms a clade with Apuleia, sister to which is the genus Distemonanthus. A placement for the Martiodendron and Zenia clade is also suggested, as a sister group to all Dialioideae except the Baudouinia and Eligmocarpus lineage, and Poeppigia procera, the sister group to all Dialioideae. New relationships within the clade including Kalappia, Storckiella, Labichea and Petalostylis are also presented. Furthermore, this study proposes a phylogeny based on chloroplast sequences (matK-trnK, rps16 and trnL), presenting the evolutionary relationships amongst genera, but also amongst 38 species of Dialioideae. Our results highlight well-supported evolutionary relationships and raise the need for increased sampling of the genera Dialium and Labichea. Furthermore, this research provides new genomic information on the conservation of paralogous copies of functional genes associated with floral and leaf morphology in plants (DICH, DIV, FLO/LFY-like, KNOX1, LEGCYC2, PALM1, PHAN, RAD, UFO). Our results contribute to the creation of new relevant material that can be used in future studies to investigate variability in morphology observed in Dialioideae.

Des souris aux baleines en passant par les humains, la diversité écologique des mammifères placentaires est des plus fascinantes. Bien qu'il s'agisse là d'un des groupes les plus étudiés, leur origine fait pourtant l'objet de bien des mystères. Leurs relations de parenté les plus basales restent en effet incertaines, et l'on ignore encore beaucoup du mode de vie qu'avaient nos ancêtres du Crétacé, ces mammifères placentaires qui auraient côtoyé les dinosaures pendant plus de 30 millions d'années.Afin d'aborder ces questions, cette thèse a utilisé l'outil de la génomique comparative. L'une de ses principales originalités est la prise en compte d'un distorteur majeur de notre évolution moléculaire: la conversion génique biaisée. Truquant la loterie génétique, ce mécanisme associé à la recombinaison méiotique avantage les nucléotides G et C au détriment des nucléotides A et T. Façonnés par son influence, nos paysages nucléotidiques présentent ainsi ponctuellement des taux de GC anormalement élevés.Jusque là, ce phénomène n'avait été étudié que chez une poignée d'organismes modèles. Son analyse chez plus d'une trentaine de génomes mammaliens a mis en évidence une série de résultats clés. En particulier, l'évolution du contenu en GC des gènes s'est avéré dépendre de la masse corporelle et la longévité des espèces. E nreliant ainsi évolution moléculaire et traits d'histoire de vie, des reconstructions de séquences ancestrales ont permis d'estimer la durée de vie des premiers mammifères placentaires à plus de 25 ans. Cette longévité va bien au delà de ce que peuvent espérer atteindre les souris ou musaraignes actuelles, des animaux au mode de vie pourtant jusqu'ici supposé comme étant proche de celui de nos ancêtres.Parallèlement à ces résultats, une tendance à produire des phylogénies inexactes a été détectée chez les gènes les plus GC-riches. Moins soumis à la conversion génique biaisée, les gènes AT-riches se sont montrés plus fiables, tout en soutenant que les espèces originaires d'Afrique sont situés à la base de l'arbre des placentaires. Ce résultat suggère ainsi la possible résolution d'un des noeuds les plus controversés de notre histoire évolutive.Du simple nucléotide à la naissance d'une infraclasse de plus de 4000espèces, ce travail révèle comment l'évolution moléculaire peut porter un nouveau regard sur nos origines les plus profondes. / From mice to whales through humans, placental mammals present astunning diversity. Despite being one of the most studied group ever,mysteries persist about their origin. Indeed, their most basalrelationships still remain uncertain, and nothing is really knownabout the lifestyle of our cretaceous ancestors, these placentalmammals which lived side by side with non-avian dinosaurs during 30My.To answer these evolutionnary questions, comparative genomic studiesof placental mammals have been conducted. One of its originalities isto take into account biased gene conversion. Rigging the geneticlottery, this recombination-associated mechanism involves a reparationbias favouring the G and C nucleotides over the A and T ones, whichmark the mammalian genomic landscapes by inducing localized peaks ofGC-content.This phenomenon has been so far studied in few model species. Theexploration of biased gene conversion in more than 30 mammal genomesled to several key results. In particular, GC content evolution hasproved to be correlated to the longevity and the body mass of species.By linking together molecular evolution and life history traits, thereconstruction of ancestral sequences allowed us to estimate alife-span above 25 years for early placental mammals. This value ismarkedly different from that of mice or shrews, although our mammalianancestors have often been represented as such. In addition to these results, GC-rich genes were found to be prone toproduce false phylogenies. Less affected by recombination associatedartifacts, AT-rich genes are shown to be more reliable, and to supportspecies of African origin as the sister group of all other placentalmammals - perhaps resolving one of the most controversial nodes of themammalian tree.From nucleotide to the birth of a 4,000 species infraclass, this workreveals how molecular evolution can shed new light onour deepest origins.

This dissertation deals with alternative techniques for analysis of genetic information of organisms. The theoretical part presents two different approaches for evaluation of relationship between organisms based on mutual similarity of genetic information contained in their DNA sequences. The first approach is currently standardized phylogenetics analysis of character based records of DNA sequences. Although this approach is computationally expensive due to the need of multiple sequence alignment, it allows evaluation of global and local similarity of DNA sequences. The second approach is represented by techniques for classification of DNA sequences in a form of numerical vectors representing characteristic features of their genetic information. These methods known as „alignment free“ allow fast evaluation of global similarity but cannot evaluate local changes. The new method presented in this dissertation combines the advantages of both approaches. It utilizes numerical representation similar to 1D digital signal, i.e. representation that contains specific trend along x-axis. The experimental part of dissertation deals with design of a set of appropriate tools for genomic signal processing to allow evaluation mutual similarity of taxonomically specific trends. On the basis of the mutual similarity of genomic signals, the classification in the form of dendrogram is applied. It corresponds to phylogenetic trees used in standard phylogenetics.

The evolutionary origin and the phylogeny of higher metazoan taxa is still under debate although considerable progress has been made in the past 20 years. Metazoa represents a monophyletic group of highly diverse animals including Bilateria, Cnidaria, Porifera, Ctenophores, and Placozoa. Bilateria comprises the majority of metazoans and consists of three major clades: Deuterostomia, Spiralia (= Lophotrochozoa sensu lato), and Ecdysozoa, whereas the sister group taxa Spiralia and Ecdyzozoa form the monophyletic clade Protostomia. Molecular data have profoundly changed the view of the bilaterian tree of life. One of the main questions concerning bilaterian phylogeny is the on-going debate about the evolution of complexity in Bilateria. It was assumed that the last common ancestor of Deuterostomia, Ecdysozoa and Spiralia had a segmented and coelomate body organization resembling that of an annelid. On the contrary, the traditional view is the evolution of Bilateria from a simple body organization towards more complex forms, assuming that the last common ancestor of Bilateria resembles a platyhelminth-like animal without coelomic cavities and segmentation. To resolve this question, it is necessary to unravel the phylogenetic relationships within Bilateria. By using mitogenomic and phylogenomic data, this thesis had a major contribution to clarify phylogenetic relationships within problematic metazoan taxa: (1) the phylogeny of Deuterostomia, (2) the questionable monophyly of Platyzoa, and first assumptions concerning the phylogeny of Gnathostomulida, Gastrotricha and Polycladida, (3) phylogenetic relationships within annelid taxa, especially Terebelliformia, Diurodrilidae, and Syllidae, with new insights into the evolution of mitochondrial gene order, and (4) new insights into the evolution of annelids, especially the interstitial ones, as well as the colonization of the interstitial realm.

In this thesis, phylogenomic and comparative structural analyses of several widespread energy converting enzymes were performed. The focus was on the major subfamilies of the enzymes that process nucleoside triphosphates (ATP and GTP) and on some key enzymes of the electron transfer chains. First, we analyzed the P-loop GTPases, RadA/RecA recombinases, chaperone GroEL, branched-chain α-ketoacid dehydrogenase kinases, chaperone Hsc70, actins, and membrane pyrophosphatases. In the each inspected family we could identify (1) members which were potassium-dependent and/or contained K+ ions in the active site, and (2) potassium-independent enzymes with lysine or arginine residues as catalytic groups that occupy the positions of potassium ions in the homologous, K+-dependent enzymes. Based on the results of our analyses, we suggest that the appearance of the K+-binding sites could precede in evolution the recruitment of positively charged residues (lysine or arginine "fingers") with the latter providing more possibilities to control the enzyme reactions. Second, we have described the distinctive features of a phylogenetically separated subfamily of rotary membrane ATPases which we named N-ATPases. The N-ATPases have a specific operon organization with two additional subunits, absent in other rotary ATPases, and a complete set of Na+-binding ligands in the membrane c-subunits. We made a prediction, which was later confirmed, that these enzymes are capable of Na+ translocation across the membrane and may confer salt tolerance on marine prokaryotes. Third, phylogenomic analysis of the cytochrome bc complexes suggests that these enzyme complexes initially emerged within the bacteria and were then transferred to archaea via lateral gene transfer on several independent occasions. Our analysis indicates that the ancestral form of the cytochrome bc complex was a b6f-type complex; the fusion of the cytochrome b6 and the subunit IV to a "long" cytochrome b of the cytochrome bc1 complexes could have happened in different lineages independently. Fourth, our phylogenomic and comparative structural analyses of the cytochrome bc1 complex and of cytochrome c allowed us to trace how these enzymes became involved in triggering of apoptosis in Metazoa. We could trace the emergence of a specific cardiolipin-binding site within the cytochrome bc complex and the evolution of structural traits that account for the involvement of the cytochrome c as a trigger of apoptosis in vertebrates.