Die zu den Sirenia, oder Seekühen, zählende Gattung Halitherium ist mit Arten aus dem Obereozän bis Untermiozän bekannt. Obwohl Halitherium als monophyletisch angesehen wird, bestätigen alle bisherigen phylogenetischen Analysen die Paraphylie dieser Gruppe. Auch die auf Halitherium basierende nur fossil bekannte Unterfamilie Halitheriinae ist paraphyletisch und umfasst wiederum fast ausnahmslos paraphyletische Gattungen. Der Fokus liegt auf der Typusart H. schinzii. Deren Holotyp, ein Premolar, wird als undiagnostisch definiert und infolgedessen H. schinzii als nomen dubium eingestuft. Die Neubeschreibung sämtlicher dieser Art zugeordneter Skelettreste liefert neue morphologische Daten. So kann die Hypothese von zwei sympatrisch vorkommenden Morphospezies im Unteroligozän Zentraleuropas auf Basis mehrerer unterscheidender Merkmale gestützt werden. Für die Verwandtschaftsanalyse der „Halitherium“ traditionell zugeordneten Arten und die Ermittlung ihrer phylogenetischen Stellung innerhalb der Ordnung Sirenia finden strenge kladistische Prinzipien Berücksichtigung. Eine revidierte, ergänzte und erweiterte Merkmalsmatrix stellt dabei den bisher größten morphologischen Datensatz über Sirenia dar. Die phylogenetischen Analysen zeigen, dass die „Halitherium“ Arten keine monophyletische Gruppe bilden. Im Zuge dieser systematisch-taxonomischen Revision werden die „Halitheriinae“ eingezogen und vier neue Gattungen aufgestellt. Des Weiteren wird eine neue Klassifikation der Sirenia vorgeschlagen, in der eine konsequente Unterscheidung zwischen einer paraphyletischen Stammgruppe und einer monophyletischen Kronengruppe Anwendung findet. Diese Studie liefert neue Daten über die Diversität und Biogeographie von Sirenen. Die herausragendsten Ergebnisse sind zum einen die Revision einer der zweifelhaftesten Sirenia Gruppen, die „Halitheriinae“. Zum anderen wird für den Ursprung der Kronengruppensirenen ein eher unteroligozäner statt eozäner Zeitpunkt postuliert. / The genus Halitherium includes a number of fossil sirenian species, or sea cows, ranging from the late Eocene to early Miocene. Although Halitherium is assumed to be monophyletic, all previous phylogenetic analyses reveal this group to be paraphyletic. As such, the exclusively extinct subfamily Halitheriinae based on Halitherium is paraphyletic comprising mainly genera that are invariably paraphyletic as well. The focus lies on the type species H. schinzii and the morphological basis for its establishment. The holotype, a single premolar, is considered non-diagnostic, which resulted in the recognition of this taxon name as a nomen dubium. Abundant skeletal material originally assigned to “H. schinzii” is re-described providing new data on the morphology of this sirenian. In this process, the hypothesis of two sympatric morphospecies in the lower Oligocene of Central Europe is corroborated by a suite of distinguishing characters. For the analysis of the interrelationships of the species traditionally assigned to “Halitherium”, and the identification of their phylogenetic position within the order Sirenia, robust cladistic principles are applied. A revised, supplemented and extended data matrix represents the hitherto largest data set on Sirenia based on morphological characters. The phylogenetic analyses show that the “Halitherium” species do not form a monophyletic group. In the course of this systematic and taxonomic revision the “Halitheriinae” are refuted and four new genera are established. Furthermore, a new systematic framework is introduced for Sirenia primarily distinguishing between a paraphyletic stem group and a monophyletic crown group. This study provides new data on the past sirenian diversity and biogeography. The most important results are that one of the most disputed sirenian groups, the “Halitheriinae”, is revised, and that the divergence time of crown group sirenians is estimated as early Oligocene rather than Eocene.

Durch vergleichende Analysen von morphologischen, anatomischen und molekulargenetischen Daten habe ich die Systematik zweier distinkter Taxa von Süßwasserschnecken innerhalb der Superfamilie Cerithioidea untersucht: Thiaridae Gill, 1871 und Pachychilidae Troschel, 1858. Die Familie Thiaridae wird durch eine endemische Art auf Jamaika (Hemisinus lineolatus) sowie zwei endemische Arten auf Kuba (H. cubanianus und Cubaedomus brevis) vertreten. Morphologisch unterscheidet sich Hemisinus von den anderen Thiaridae durch ein kurzes, anteriores Osphradium, einen Mitteldarm mit flach ausgeprägten Blinddarm sowie ein großes „accessory pad“. Phylogenetischen Analysen zeigen dass die jamaikanische H. lineolatus eng mit den Thiariden des nördlichen Südamerikas verwandt ist. Die anatomischen und morphologischen Ähnlichkeiten zwischen Hemisinus und afrikanischen Familien lassen vermuten, dass diese einen gemeinsamen Vorfahren haben. Die Geologischen und geographischen Daten deuten auf einen kontinentalen Ursprung von Hemisinus mit nachfolgender Kolonialisierung auf den Inseln hin. Bei den Pachychilidae beschränkte sich meine Arbeit auf die Karibischen und mittelamerikanischen Arten. Die geringen morphologischen Variationen der Schale und der Radula zwischen den meisten Arten, deuten auf Homoplasie hin, so dass diese Merkmale taxonomische wenig geeignete sind. Des weiteren scheint der Besitz von glatten Gehäusen ein konvergentes Merkmal ist, dass mindestens zweimal entstanden ist, während skulpturierte Schalen ehe Synapomorphie darstellen. Molekulare Untersuchungen zeigen dass die mittelamerikanischen und kubanischen Pachychilidae monophyletisch sind, während die Pachychiliden aus Zentral-Mexiko, Kuba sowie P. vallesensis nicht in die Gattung Pachychilus gehören. Die Analysierten Daten deuten auf einen vikarianten Ursprung der kubanischen und einen von Zentral-Guatemala ausgehenden, dispersiven Ursprung der kontinentalen Pachychilidae hin. / Through comparative analyses of morphological, anatomical and molecular genetic data, I reviewed the systematics of two distinct lineages of Neotropical freshwater snails within the superfamily Cerithioidea: Thiaridae Gill, 1871 and Pachychilidae Troschel, 1858. Concerning the Thiaridae, this family is represented by one endemic species in Jamaica (Hemisinus lineolatus), and two endemic species in Cuba (H. cubanianus and Cubaedomus brevis). The diagnostic characters that separate Hemisinus from the rest of the thiarid are a short and anterior osphradium and a midgut with shallow caecum and large accessory pad. Phylogenetic analysis showed the Jamaican H. lineolatus closely related to the northern South American Thiaridae. I also found Hemisinus sharing anatomical and morphological features with African families other than Thiaridae, indicating common ancestry with an Oriental freshwater lineage. Geological and geographical data point to a continental origin of Hemisinus with subsequent dispersal to the Caribbean Islands. About the Pachychilidae, I have carried out a critical systematic revision only on its Mesoamerican members. Anatomical studies of shell and radula characters as well as phylogenetic analyses based on two mitochondrial genes (COI, 16S), were performed. Due to the subtle morphological variations in shells and radulae found, I propose that both are homoplasic features generally unsuitable for distinguishing Neotropical pachychilids. Molecular analyses showed that the Cuban and Mesoamerican Pachychilidae are monophyletic, suggesting also that the species from central Mexico, Cuba and P. vallesensis belong to genera different than Pachychilus. Also, that in the group the possession of smooth shells is a convergent character which has evolved at least twice, while a sculptured shell is a synapomorphy. Analyzed data evidence a vicariant origin of the Cuban Pachychilidae, and a dispersal origin of the continental members from a central Guatemalan ancestor.

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La recherche en bactériologie et virologie est à la fois de nature cognitive et appliquée. Elle consiste à fédérer et mettre en place une capacité de recherche multidisciplinaire et pouvoir l'intégrer sur un champ très vaste de microorganismes et de maladies. Les nouvelles avancées conceptuelles et technologiques dans le domaine de la génomique, notamment les avancées dans les techniques à haut débit (séquençage, PCR...) permettent actuellement d’avoir rapidement des génomes bactériens et viraux entiers, ou seulement sur quelques gènes d’une grande population. Les progrès dans ce domaine permettent l’accès à ces informations en évitant une combinaison de plusieurs méthodologies, et à moindre coûts. Dans notre travail de thèse, nous avons été porté à analyser et traiter les données de deux études genomiques et métagenomiques, mettant en évidence avantages, limites et attentes liés à ces techniques. La première étude porte sur l'analyse génomique de nouveaux virus géants et chlamydia infectant Vermamoeba vermiformis. La deuxième étude concerne le pyroséquençage 16S de microbiote intestinal de nouveau-nés atteint de l'entérocolite nécrosante. Pour le premier projet du travail de thèse, nous avons analysé les génomes de trois nouvelles espèces de Chlamydiae et onze virus giants (premiers membres de deux probables nouvelles familles) qui se multiplient naturellement dans Vermamoeba vermiformis. L'objectif étant de mettre en évidence les caractéristiques génétiques spécifiques à ces micro-organismes. La deuxième partie a été consacrée à l'analyse des données de pyroséquençage 16S des selles de nouveau-nés atteints de l'entérocolite nécrosante. / Research in bacteriology and virology is both cognitive and applied. It involves federating and developing a multidisciplinary research capacity and being able to integrate it into a very broad field of microorganisms and diseases. New genomic and conceptual advances in genomics, including advances in high-throughput techniques, now permit rapid bacterial and viral genomes, or only a few genes of a large population. Progress in this area allows access to this information by avoiding a combination of several methodologies and at lower costs. In our thesis work, we were led to analyze and process the data of two genomic and metagenomic studies, highlighting advantages, limitations and expectations related to these techniques. The first study focuses on the genomic analysis of new giant viruses and chlamydia infecting Vermamoeba vermiformis. The second study concerns the 16S pyrosequencing of intestinal microbiota of neonates with necrotizing enterocolitis. The first project of the thesis work analyzed the genomes of three new species of Chlamydiae and eleven giant viruses (first members of two probable new families) which naturally multiply in Vermamoeba vermiformis. The objective is to highlight the genetic characteristics specific to these microorganisms. The second part was devoted to the analysis of 16S pyrosequencing data from neonatal enterocolitis neonatal stools. The goal was to identify an agent responsible for this disease.

The presented study comprises a complete morphological and phylotaxonomic revision of basal Sphenacodontia, designated as the paraphyletic ‘haptodontines’. Ianthodon from the Kasimovian is known from newly identified elements, including most of the skull and particular postcrania. This species is determined as the best model for the initial morphology of the Sphenacomorpha (Edaphosauridae and Sphenacodontia). Remarkably older sphenacodontian remains from the Moscovian indicate a derived, though fragmentarily known form, possibly basal Sphenacodontoidea. The genus Haptodus is conclusively revised, including the revalidation of the type species H. baylei from the Artinskian. Haptodus grandis is renamed as Hypselohaptodus, gen. nov. “Haptodus” garnettensis is not monophyletic with Haptodus, moreover the material assigned to it yielded a greater diversity. Thus, its renaming includes Eohaptodus garnettensis, gen. nov., Tenuacaptor reiszi, gen. et spec. nov., and Kenomagnathus scotti, gen. et spec. nov. Along with Ianthodon and the basal edaphosaurid Ianthasaurus, these taxa from a single assemblage are differentiated by dentition and skull proportions, providing a case study of annidation. Since Ianthodon can be excluded from Sphenacomorpha, the larger, stem-based taxon Haptodontiformes is introduced. More derived ‘haptodontines’ apparently form another radiation, named as Pantherapsida. This new taxon includes Cutleria, Tetraceratops, Hypselohaptodus, the Palaeohatteriidae (Pantelosaurus and Palaeohatteria), and the Sphenacodontoidea. The ‘pelycosaur’-therapsid transition is affirmed as a long-term development. An integrative evolutionary hypothesis of basal sphenacodontians is provided, within which the ghost lineage of Early Permian therapsids can be explained by biome shift.:Chapter 1 ‘Haptodontines’ re-examined – An Introduction Chapter 2 New information on the cranial and postcranial anatomy of the early synapsid Ianthodon schultzei (Sphenacomorpha: Sphenacodontia), and its evolutionary significance Chapter 3 Reviewing the question of the oldest therapsid Chapter 4 Revision of the genus Haptodus (Synapsida: Haptodontiformes) and evolutionary implications from the Garnett fossil site Chapter 5 Morphological description and taxonomic status of Palaeohatteria and Pantelosaurus (Synapsida: Sphenacodontia) Chapter 6 Re-description of Cutleria and Tetraceratops (Synapsida, Sphenacodontia), with implications on the radiation of Sphenacodontoidea Chapter 7 Callibrachion and Datheosaurus, two historical and previously mistaken basal Caseasauria (Synapsida) from Europe Chapter 8 Synthesis and perspective

Soil nematodes play an important role in indication for assessing soil environments and ecosystems. Previous studies of nematode community analyses based on molecular identification have shown to be useful for assessing soil environments. Here we applied PCR-DGGE method for molecular analysis of five soil nematode communities (designed as S1 to S5) collected from four provinces in Southeastern Vietnam (Binh Duong, Ba Ria Vung Tau, Binh Phuoc and Dong Nai) based on SSU gene. By sequencing DNA bands derived from S5 community sample, our data show 15 species containing soil nematode, other nematode and non-nematode (fungi) species. Genus Meloidogyne was found as abundant one. The genetic relationship of soil nematode species in S5 community were determined by Maximum Likelihood tree re-construction based on SSU gene. This molecular approach is applied for the first time in Vietnam for identification of soil nematode communities. / Tuyến trùng đất đóng vai trò chỉ thị quan trọng trong công tác đánh giá môi trường và hệ sinh thái đất. Các nghiên cứu trước đây đã cho thấy lợi ích của việc phân tích cộng đồng tuyến trùng đất bằng định danh sinh học phân tử đối với việc đánh giá môi trường đất. Ở đây, chúng tôi ứng dụng phương pháp PCR-DGGE dựa trên gene SSU để phân tích năm (ký hiệu từ S1 đến S5) cộng đồng tuyến trùng đất thuộc các vùng trồng chuyên canh cây hồ tiêu ở miền nam Việt Nam (Bình Dương, Bà Rịa Vũng Tàu, Bình Phước và Đồng Nai). Bằng cách giải trình tự các vạch của mẫu tuyến trùng S5, kết quả cho thấy cộng đồng tuyến trùng này có 15 loài gồm nhóm tuyến trùng đất, nhóm các loại tuyến trùng khác và nhóm không phải tuyến trùng (nấm) và trong đó Meloidogyne là giống ưu thế. Mối quan hệ di truyền của các các loài tuyến trùng đất thuộc cộng đồng S5 được xác định bằng việc thiết lập cây phát sinh loài Maximum Likelihood dựa trên gene SSU. Đây là nghiên cứu đầu tiên ở Việt Nam sử dụng kỹ thuật PCR-DGGE để phân tích các cộng đồng tuyến trùng đất trồng hồ tiêu.

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