L'origine des eucaryotes est un problème important de la biologie évolutive, pour lequel de nombreuses hypothèses profondément différentes ont été proposées. L'une des stratégies majeures, pour discriminer ces hypothèses, est d'utiliser le fait qu'elles sont associées à des prédictions distinctes quant aux arbres phylogénétiques qui devraient être observés pour les gènes communs aux eucaryotes et aux archées ou aux eucaryotes et aux bactéries. C'est la problématique que j'ai étudiée au cours de ma thèse. J'ai réalisé des analyses phylogénétiques, à l'échelle génomique et à l'aide d'une approche semi-automatisée, pour tous les gènes présents chez les eucaryotes et les archées ou les bactéries. Mon analyse s'est appuyée sur une qualité méthodologique excellente en regard de la littérature existante sur le sujet. En particulier, j'ai développé de nouveaux principes et outils pour prendre en compte le remodelage constant des génomes procaryotes par les transferts horizontaux et les pertes de gènes. Ces innovations se sont révélées cruciales pour interpréter correctement les arbres de gènes à cette échelle évolutive, et mes résultats se distinguent nettement de ceux rapportés précédemment. Mon analyse a retrouvé, de façon très nette, les deux propriétés déjà connues du génome eucaryote : sa relation en apparence mosaïque aux archées et bactéries, et l'origine alphaproteobactérienne des mitochondries. Mon travail a ensuite permis de démontrer (i) que les gènes liant les eucaryotes aux alphaproteobactéries sont presque tous impliqués dans les fonctions de respiration et de synthèse protéique des mitochondries, et (ii) qu'il n'existe pas d'indices phylogénétiques pour une relation entre les eucaryotes et une lignée bactérienne autre que les alphaproteobactéries, contrairement à ce que prédisent une partie des hypothèses. De plus, mon travail montre clairement que les résultats obtenus par une approche phylogénomique large sur la question de la relation des eucaryotes et des archées dans l'arbre de la vie sont compatibles avec ceux obtenus par l'utilisation d'un jeu restreint de gènes universels. Mes données sont en effet favorables à ce que les eucaryotes branchent au voisinage du dernier ancêtre commun des archées. Mes résultats éclairent la problématique des origines des gènes eucaryotes avec une précision bien plus grande que celle qui avait été atteinte jusqu'alors. Ils montrent notamment l'absence de support phylogénétique pour les hypothèses basées sur une fusion impliquant une bactérie autre que l'ancêtre des mitochondries, et la relative rareté des gènes ayant une origine proto-mitochondriale avérée. Ces observations jouent en faveur des hypothèses se basant soit sur une origine précoce de la mitochondrie dans un hôte archéen, soit sur l'idée que les eucaryotes primitifs étaient fortement sujet aux transferts horizontaux de gènes / Pas de résumé en anglais

O gênero Porphyra (Rhodophyta) apresenta uma considerável importância econômica, sendo extensivamente cultivado e consumido como alimento. O gênero é representado por mais de 70 espécies e apresenta ampla distribuição geográfica, desde regiões tropicais até polares. Sua taxonomia, baseada em poucos caracteres da fase macroscópica do seu ciclo de vida, é ainda bastante problemática. Para tentar entender melhor a taxonomia e a história evolutiva de Porphyra foram utilizadas metodologias de biologia molecular e características da fase conchocelis do ciclo de vida. Verificou-se que caracteres da fase microscópica podem ser utilizados para complementar os conhecimentos taxonômicos tradicionais. Para tentar elucidar a posição filogenética do gênero Porphyra na divisão Rhodophyta e, dentro do gênero, entre espécies do Atlântico, o gene nuclear que codifica para o RNA ribossomal da subunidade pequena do ribossomo (rDNA 18S) foi amplificado através de PCR, clonado e completamente sequenciado. Foram utilizadas três espécies de Porphyra da Nova Escócia (Canadá) e duas de São Paulo (Brasil). As sequências obtidas foram alinhadas com as de alguns eucariontes e de outras algas vermelhas, incluindo uma sequência publicada de \"Porphyra umbilicalis\" da França. As árvores filogenéticas foram construídas através dos métodos de parcimônia, distancia e máxima verossimilhança. As analises mostraram que o gênero Porphyra é monofilético para as cinco espécies estudadas e constitui um dos ramos mais antigos dentro das algas vermelhas já analisados. O gênero Porphyra, subclasse Bangiophycidae, apresentou uma diferença substancial em relação aos gêneros da subclasse Florrideophycidae, sustentando assim, a divisão de Rhodophyta em duas subclasses pela taxonomia tradicional. Entre os eucariontes, Porphyra divergiu ao mesmo tempo que o nuclemorfo de Cryptomonas. O alto grau de divergência genética encontrada entre espécies de Porphyra, além de indicações do registo fóssil, na literatura, sugerem que o gênero é bastante primitivo dentro das algas vermelhas. Surpreendentemente, a sequência publicada para \"Porphyra umbilicalis\" apresentou mais de 99% de identidade com uma espécie de Palmaria que pertence à subclasse Florideophycidae; neste caso, a biologia molecular serviu para comprovar a identificação errônea do exemplar cuja sequência foi publicada. Durante a análise filogenética, verificou-se a ocorrência de um intron do grupo ICI nos genes rDNA 18S de Porphyra spiralis var. amplifolia. Esse intron ocorre na mesma posição que os introns do grupo IC1 nos rDNA 18S dos fungos Pneumocystis carinii, Protomyces inouyei e da alga verde Chlorella ellipsoidea, e apresenta identidade de sequências nos domínios P1 e P2, fora da região conservada, com o intron de Pn. Carinii. Três variantes, diferindo do tamanho da seqüencia do domínio P1, foram observados em três populações com distribuição geográfica diferente. O variante maior pode se auto-processar (\"self-splice\") in vitro. Quadros abertos de leitura estão presentes nos introns, mas não correspondem a nenhum gene conhecido. Introns estão presentes no rDNA 18S de outras espécies de Porphyra, que também podem apresentar variantes do rDNA 18S sem introns / The red algas genus Porphyra has considerable economic importance, and some species are extensively cultivated for human food. The genus is represented by more than 70 species, and occurs worldwide. Its taxonomy, based mainly on morphological characters of the macroscopic phase of its life-cycle is still unsettled. Alternatives to try to understand better the taxonomy and evolutive history of the genus were ascertained. It was verified that characters of the microscopic, filamentous phase, of the life-cycle of Porphyra may be used to complement the traditional taxonomic studies. To try to elucidate the phylogenetic position of Porphyra relative to the other red algae, and within the genus, among isolates from different locations, nuclear-encoded small-subunit ribosomal RNA genes (18S rDNAs) were PCR-amplified, cloned and completely sequenced. Three species of Porphyra from Nova Scotia and two species from Brasil were aligned with 18S sequences of other eukaryotes, including one published sequence of \"Porphyra umbilicalis\" from France. Phylogenetic trees were constructed by parsimony, distance and maximum-likelihood procedures. Analysis of our data revealed that these Porphyra species represented one of the deepest branches so far discovered within red algae. There was a great degree of primary sequence difference between Porphyra (subclass Bangiophycidae), and the other red algae belonging to the subclasses Florideophycidae. These results support the division of red algae into two subclasses by traditional taxonomy. Among eukaryotes Porphyra diverges at the same point as the Cryptomonas nucleomorph. The great among of sequence divergence, and the fossil record suggest that Porphyra, my indeed, be a very primitive red alga. Surprisingly, the 18S RNA sequence of the French \"Porphyra umbilicalis\" does not fit in our Porphyra category; instead, it has more than 99% identity with a species of Palmaria belonging to the subclass Florideophycidae. Therefore it was concluded that \"P. umbilicalis\" with the published sequence was actually a Palmaria palmate that was misidentified. During the phylogenetic analysis it was found that a group IC1 intron occurs in nuclear 18S rRNA genes of Porphyra spiralis var. amplifolia. This intron occurs at the same position of the group IC1 introns in 18S rDNAs of the fungus Pneumocystis carinii, Protomyces inouyei and the green alga Chlorella ellipsoidea, and shares primary-structural identity with the Pn. Carinii intron in domains P1 and P2, outside the conserved core. Three size-variants, differing in amount of optimal sequence in P1, exist and are differentially distributed in geographically distinct populations. The largest variant can self-splice in vitro. Open reading frames are present, but do correspond to known genes. Introns are present in the 18S rDNAs of several other Porphyra species, that may also have intronless rDNA copies

Les montagnes sont des hotspots de biodiversité dont les réseaux plantes-pollinisateurs constituent un élément central, et où les conséquences du réchauffement climatique sont déjà avérées. Malgré le nombre colossal d’espèces potentiellement affectées par la destructuration du mutualisme entre les angiospermes et leurs pollinisateurs dans ces écosystèmes, les patrons spatio-temporels des communautés de pollinisateurs le long des gradients altitudinaux sont toujours méconnus. La première partie de ce travail propose une analyse des effets de l’altitude et de la phénologie sur l’abondance et la diversité des insectes anthophiles le long d’un gradient altitudinal de 1700 m. Nous montrons qu’il existe une structuration altitudinale et trophique entre les principaux ordres de pollinisateurs (hyménoptères, diptères, coléoptères), avec une nette prédominance des diptères dès 1500 m d’altitude qui s’amplifie jusqu’à la limite supérieure du gradient (2700 m). Ces diptères appartiennent principalement à trois familles (Anthomyiidae, Empididae, Muscidae) qui se structurent également le long du gradient par l’altitude, la phénologie et le choix des plantes visitées. Leur biologie, efficacité pollinisatrice comprise, est encore largement méconnue. Dans un second temps, nous étudions l’écologie de la pollinisation et les causes évolutives du succès d’un groupe central de ces communautés anthophiles, les Empidinae. Nous avons mesuré 1) leur importance relative dans un réseau plantes-visiteurs à l’étage subalpin et 2) leur efficacité pollinisatrice par rapport à celles des autres visiteurs pour une plante de ce réseau (Geranium sylvaticum L.). Nous montrons que les visites d’une grosse espèce d’Empis produisent le même nombre de graines que celles de l’abeille domestique (Apis mellifera L.), pollinisatrice réputée très efficace. Ces résultats suggèrent un rôle majeur des gros Empidinae dans la pollinisation des plantes alpines. Pour comprendre le rôle de la floricolie dans la diversification des Empidinae et l’origine de leur abondance en altitude, nous avons construit une phylogénie moléculaire mondiale sur la base de 4 marqueurs et pour plus de 210 espèces. La plupart des clades d’Empidinae contiennent des espèces qui occupent diverses altitudes, indiquant qu’il n’y a pas de conservatisme de niche impliqué dans leur distribution le long du gradient. L’association angiospermes-Empidinae remonte à la période de fin de radiation des angiospermes et semble, par l’intermédiaire de l’allongement de la trompe, avoir favorisé la radiation évolutive de certains clades en parallèle avec celles des plantes à fleurs. Leur large distribution altitudinale et leur capacité à visiter des morphotypes floraux inaccessibles à d’autres floricoles pourraient leur conférer une importante résistance aux changements globaux. / Mountains are biodiversity hotspots, where the effects of global warming have already been demonstrated in numerous studies. Plant-pollinator networks are a central element of these ecosystems, but, despite the tremendous number of species potentially affected by the disruption of this mutualism, spatial and temporal patterns of pollinator communities along altitudinal gradients are still poorly known. The first part of this work analyses the effects of elevation and phenology on the abundance and diversity of anthophilous insects along a 1700 m altitudinal gradient. I show that the main orders of pollinators (Diptera, Hymenoptera, Coleoptera) are structured by elevation and foraging preferences, with an increasing predominance of flies from 1500 m altitude up to 2700 m, the upper limit of the gradient. Most of these fly species belong to four families (Anthomyiidae, Empididae, Muscidae and Syrphidae) which also segregate along the gradient according to altitude, phenology and the choice of flowering plants they visit. The systematics and biology of these taxa, including their pollination efficiency, are still largely under-investigated. Second, I studied the pollination ecology and the evolutionary causes of the success of empidine dance flies (Empidinae), a central group in these anthophilous communities. I measured 1) their relative importance in the plant-visitor network of a subalpine meadow; and 2) the pollinating effectiveness of their visits to Geranium sylvaticum L. relative to the other visitors. Visits by large species of Empis produced the same number of seeds as those by the domestic bee (Apis mellifera L.), a highly effective pollinator. Such results suggest a major role of large empidines in the pollination of alpine plants. To understand the role of anthophily in Empidinae diversification and the origins of their abundance at altitude, I built a worldwide molecular phylogeny for the subfamily. The resulting cladogram includes 212 species for which four molecular markers were sequenced (28S D1-D2, D4-D5, 16S mtDNA, COI). Most clades of Empidinae contain species occupying various altitudes, indicating that there is no phylogenetic niche conservatism involved in their distribution along the gradient. The association between Empidinae and Angiosperms dates back to the end of the angiosperm radiation and seems, through the lengthening of the proboscis, to have favoured the evolutionary radiation of several clades in parallel with flowering plants. Their wide altitudinal distribution, combined with their ability to visit floral morphotypes inaccessible to other anthophilous insects, could confer them a strong resistance to global changes.

The eight southern African King Cricket genera, namely Bochus, Borborothis, Henicus, Libanasa, Libanasidus, Nasidius, Onosandridus, and Onosandrus are redescribed from type and museum material and a key to the genera is provided. Additionally, the status of Libanasidus impicta is investigated and species characteristics confirmed. A key to the two Libanasidus species is also provided. No morphological support for these eight southern African anostostomatid genera was attained with cladistic analysis, despite the incorporation of taxonomically important characters. High levels of homoplasy and possible incorrect species placement, resulting in character ambiguity within genera, renders many of the diagnostic characters of this group ineffective for resolving generic relationships. Genetic data based on the large ribosomal subunit (16S) did provide phylogenetic resolution between six of the genera with good bootstrap support. This confirmed speculation by previous authors as to the ancestral nature of Bochus and Borborothis to other genera within the Anostostomatini tribe, as well as the placement of Libanasa within a separate tribe, the Lutosini. The recent merge of the genus Platysiagon with Libanasa is also provisionally supported. Close association was obtained between Libanasidus and Nasidius with Onosandrus being more related to Bochus and Borborothis, supported by the lack of sexual dimorphism in Onosandrus and Borborothis. The phylogenetic position of the genera Henicus and Onosandridus remains unresolved. It is suggested that the designation of the eight anostostomatid genera in southern Africa are valid, but that species placement within these genera need to be revised to resolve character conflict. Focusing on the genetic and morphometric structuring within the famous Parktown Prawn, Libanasidus vittatus from southern Africa consistently suggests two main population assemblages. These correspond to a large North-South ranging population including individuals west of the prominent escarpment, and a smaller population including individuals from the eastern side of the escarpment. COI sequence data recovers two clades representing these two populations with good bootstrap support in likelihood, parsimony, Bayesian and distance analyses. Genetic divergence between the two clades averaged 3.3%, while population parameters estimated using maximum likelihood methods show low migration rates corresponding to less that one female migration per generation. A priori morphometric analyses including PCA&clustering methods show no biologically meaningful variation, suggesting that the two clades recovered represent cryptic sibling species. Inferring a molecular clock of 2% divergence per million years used for sister taxa, signifies isolation of the eastern population at 1.65 mya. A posteriori morphometric analyses confirmed the genetic results, based on 11 size-related measurements. This study provides a starting point for further work on the taxonomy, behaviour and ecology of these fascinating insects. Cytogenetics, multiple genetic loci and geometric morphometrics will provide useful insight into the taxonomic status of the 51 anostostomatid species in southern Africa and is promoted for further studies. / Dissertation (MSc Entomology)--University of Pretoria, 2006. / Zoology and Entomology / unrestricted

No description available.

Les Loricariinae appartiennent à la famille des poissons-chats néotropicaux cuirassés Loricariidae, la famille de poissons-chats la plus riche en espèce au monde, et se caractérisent par un pédoncule caudal long et aplati et par l’absence de nageoire adipeuse. Préalablement aux études évolutives réalisées, une phylogénie exhaustive et robuste a été établie sur la base de données mitochondriales et nucléaires. Cette phylogénie a ensuite été utilisée dans des analyses multivariées et multi-tableaux afin de révéler les principales tendances évolutives de la sous-famille. La phylogénie obtenue indique que la tribu Harttiini forme un groupe paraphylétique et est restreinte à trois genres, et que dans la tribu Loricariini, deux sous-tribus soeurs se distinguent, les Farlowellina et les Loricariina, chacune présentant des patterns évolutifs complexes. Plusieurs nouveaux taxa ont aussi été mis en évidence et décrits. En utilisant la phylogénie comme outil exploratoire, nous avons démontré : (1) avec l’analyse de co-inertie que les caractères diagnostiques fournis pour définir les différents genres étaient sous dépendance phylogénétique ; (2) avec l’analyse de co-inertie multiple que les forces évolutives sous-jacentes dirigeant leur diversification incluaient des composantes intraphénotypiques (morphologie et génétique) et extraphénotypique (écologie et distribution) ; (3) avec l’analyse RLQ que des évènements de co-dispersion entre espèces codistribuées avaient eu lieu et étaient responsables de la distribution actuelle des espèces ; et (4) avec l’analyse de patterns multi-échelles que la co-évolution des traits liés aux caractéristiques de la bouche était liée à des fonctions reproductrices responsables d’une évolution tertiaire de cet organe. / The Loricariinae belong to the Neotropical mailed catfish family Loricariidae, the mostspeciose catfish family in the world, and are united by a long and flattened caudal peduncle and the absence of an adipose fin. Despite numerous works conducted on this group, no phylogeny is presently available. Prior to conduct evolutionary studies, an exhaustive and robust phylogeny was reconstructed using mitochondrial and nuclear data. Then, this phylogeny was used in multivariate and multi-table analyses to reveal the main evolutionary trends of the subfamily. The resulting phylogeny indicated that the Harttiini tribe, as classically defined, formed a paraphyletic assemblage and was restricted to three genera, and within the Loricariini tribe, two sister subtribes were distinguished, Farlowellina and Loricariina, both displaying complex evolutionary patterns. In addition several new taxa were highlighted and described. Subsequently using this phylogeny as exploratory tool, we demonstrated: (1) using co-inertia analysis that the diagnostic features provided to define the different genera were phylogenetically dependent; (2) using multiple co-inertia analysis that the underlying evolutionary forces shaping their diversification included intraphenotypic (morphology and genetics) and extraphenotypic (ecology and distribution) components; (3) using the RLQ analysis that co-dispersion events occurred between co-distributed species responsible for the current fish distribution; and (4) using the multi-scale pattern analysis that the co-evolution in traits related to the mouth characteristics was linked to reproductive functions responsible for a tertiary evolution of this organ.

Lithophylloideae é uma subfamília de algas calcárias que inclui tanto gêneros articulados quanto os não articulados, que por sua vez compreende gêneros incrustantes e um moniliforme. Pela primeira vez a diversidade específica de Amphiroa, Lithophyllum, Paulsilvella e Titanoderma para o Brasil é investigada de maneira somatória e comparativa, quanto a uma variedade de aspectos que incluíram os morfológicos/anatômicos, ecológicos e moleculares (incluindo a própria avaliação das ferramentas moleculares e das características taxonomicamente importantes). Encontramos 26 espécies, sendo quinze Amphiroa, oito Lithophyllum, uma Paulsilvella e duas Titanoderma: Amphiroa rigida, A. vanbosseae, Amphiroa sp. 1, Amphiroa sp. 2, Amphiroa sp. 3, Amphiroa sp. 4, seis espécies para o Complexo A. fragilíssima, três espécies para o Complexo A. beauvoisii, Lithophyllum atlanticum, L. corallinae, Lithophyllum cf. depressum, Lithophyllum sp. 1, Lithophyllum sp. 2, Lithophyllum sp. 3, Lithophyllum sp. 4, Lithophyllum cf. margaritae, Paulsilvella huveorum, Titanoderma pustulatum e T. Prototypum. Para a caracterização molecular utilizamos quatro marcadores principais: UPA, COI-5P, psbA e rbcL-3P, atendendo a dois objetivos: a delimitação de espécies e a avaliação destes diferentes marcadores como DNA Barcodes para as espécies de Lithophylloideae dentro do contexto da variabilidade encontrada na costa brasileira. Para isto utilizamos cinco métodos de agrupamento: Taxas de Divergência, ABGD, MDS, PTP e SPN. A decisão final quanto à quantidade de espécies presentes é um consenso dos resultados encontrados para todos os marcadores e para todos os métodos de análise. Os casos conflitantes também foram observados quanto aos valores de divergência e de barcoding gap. Os quatro marcadores testados são confiáveis para a delimitação de espécies em Lithophylloideae, proporcionando ótimos valores de suporte para as espécies e valores significativos de barcoding gap. Apesar disto, dada a possibilidade de usar o rbcL-3P também para para fins filogenéticos, ressaltamos a aplicabilidade deste marcador, sendo o indicado caso exista a necessidade de se indicar um único marcador como DNA Barcode para este grupo de algas. A inferência das relações filogenéticas dentro de Lithophylloideae inclui os primeiros dados moleculares para Paulsilvella, através do psbA, do rbcL -3P e também do SSU rDNA. As análises indicam que Amphiroa é monofilético, enquanto que Lithophyllum e Titanoderma provavelmente são polifiléticos. Adicionalmente, é possível que Paulsilvella represente a primeira forma morfológica da subfamília. A distribuição de Amphiroa, Lithophyllum e Titanoderma ao longo da costa brasileira embasou a discussão quanto à distribuição das macroalgas marinhas bentônicas na costa, adicionando ao cenário o papel das correntes costeiras e do Giro do Atlântico Sul. Os dados moleculares possibilitaram ainda a observação do panorama de ocorrência das 26 espécies de Lithophylloideae quanto a sua ocorrência na coluna d\'água (profundidade). Para Amphiroa a maior diversidade está no mesolitoral, enquanto que para Lithophyllum e Titanoderma a maior diversidade se encontra no infralitoral. Oito espécies são restritas ao mesolitoral, enquanto que dez (incluindo P. huveorum) são restritas ao infralitoral. Estes fatos chamam a atenção da necessidade de se incluir diferentes técnicas de coleta nos trabalhos de diversidade em Florideophycideae, do contrário podemos negligenciar uma diversidade inexplorada / Lithophylloideae is a subfamily within Corallinaceae including both articulated and non-articulated genera. This work is the first effort to access the specific diversity for Amphiroa, Lithophyllum, Paulsilvella and Titanoderma for Brazil based on a sum of morphological anatomical, ecological and molecular data, including also the tools applicability evaluation. From the 26 species found, are Amphiroa, eight are Lithophyllum, two are Titanoderma and one is the first register for Paulsilvella for Atlantic waters: Amphiroa rigida, A. vanbosseae, Amphiroa sp. 1, Amphiroa sp. 2, Amphiroa sp. 3, Amphiroa sp. 4, six criptic species for the A. fragilissima Complex, three cryptic species for the A. beauvoisii Complex, Lithophyllum atlanticum, L. corallinae, Lithophyllum cf. depressum, Lithophyllum sp. 1, Lithophyllum sp. 2, Lithophyllum sp. 3, Lithophyllum sp. 4, Lithophyllum cf. margaritae, Titanoderma pustulatum, T. prototypum and Paulsilvella huveorum. For the molecular characterization four markers were used: UPA, COI-5P, psbA and rbcL-3P, which have attended to two the delimitation of species and also to the evaluation of these markers as DNA Barcodes for the species of Lithophylloideae within the context of variability found on the Brazilian coast. For these two purposes we have applied five clustering methods, based on the Divergence Rates, ABGD, MDS, PTP and SPN. Conflicting cases were also observed for values of barcoding gap. The four molecular markers are reliable for species delimitation within the Lithophylloideae, providing good support values for the species and significant amounts of barcoding gap. Nevertheless, given the possibility of using the rbcL marker also for phylogenetic purposes, we emphasize the applicability of rbcL-3P as the most appropriate marker, in case there is a need to indicate a single marker as DNA Barcode for this group alga. A phylogenetic inference for the Lithophylloideae included the first sequences for Paulsilvella and used psbA, rbcL-3P and SSU rDNA. We found that Amphiroa is monophyletic while Lithophyllum and Titanoderma are probably polyphyletic. Additionally, Paulsilvella may represent the first morphological form of the subfamily. Amphiroa, Lithophyllum and Titanoderma distribution along the Brazilian coast have allowed a new discussion concerning the benthic macroalgae distribution to the country, adding two new factors to this scenario: the coastal currents movement and the South Atlantic Gyre. The molecular data have also allowed accessing the preferences according to the depth on the water column for the 26 species. The major diversity for Amphiroa grows at the intertidal, while Lithophyllum and Titanoderma diversity is higher at the subtidal and Paulsilvella is restricted to the subtidal. There are eight species restricted to the intertidal and ten restricted to the subtidal (including P. huveorum), what addresses to a need to include these both environments on diversity studies for the Florideophycideae otherwise it will imply the existence of an unexplored diversity

L'objectif principal de ma thèse a été la caractérisation de l'histoire évolutive des voies de signalisation au travers d'une double approche: (i) l'analyse phylogénétique de leurs composés; et (ii) l'identification et la caractérisation de leurs interactions par l'analyse des interactomes d'organismes modèles. Or, bien que de nombreux outils soient disponibles pour la reconstruction d'arbres de gènes individuels, peu de méthodes ont été développées pour l'étude d'un ensemble de protéines impliquées dans un même processus cellulaire. Pourtant, au sein de la cellule, la plupart des protéines agissent en interaction avec d'autres protéines. Dans un premier temps, j'ai étudié l'histoire évolutive de la famille des PI3K (Phosphatidylinositol 3-kinases). Cette première analyse phylogénétique détaillée m'a permis de mettre en place une méthodologie applicable aux voies de signalisation. Un problème important rencontré dans cette étude a consisté en la sélection de transcrits alternatifs et ceci m'a conduit à développer un logiciel dédié nommé BATfinder (\Best Aligned Transcript finder). Dans le but d'étudier la voie de signalisation AKT/mTOR, j'ai effectué l'implémentation de la méthodologie validée avec les PI3K. Cette implémentation a pris la forme d'un pipeline automatique nommé EPINe (Easy Phylogenetics for Interaction Networks). Ce pipeline est théoriquement utilisable pour l'analyse phylogénétique de tout réseau métabolique eucaryote / The main goal of my thesis was the characterization of the evolutionary history of signalling pathways through a twofold approach: (i) the phylogenetic analysis of their components; and (ii) the identification and characterization of their interactions by the analysis of model organisms interactomes. While many tools are available for single genes tree reconstruction, only a few methods have been developed for the study of a set of proteins involved in the same cellular process. However, inside the cell, most of proteins interact with others.Initially, I studied the evolutionary history of the PI3K family (Phosphati-dylinositol 3-kinases). This first detailed phylogenetic analysis allowed me to set up a methodology suitable for signalling pathways. One of the important problems encountered in this study was the selection of alternative transcripts and this led me to develop a software called BATfinder (Best Aligned Transcript finder ). In order to study the AKT/mTOR signalling pathway, I have implemented the methodology previously validated with PI3Ks. This implementation was carried out as an automated pipeline called EPINe (Easy Phylogenetics for Interaction Networks). This pipeline is theoretically usable for the phylogenetic analysis of any eukaryotic metabolic network

Mesoclemmys vanderhaegei Bour, 1973 pertence à família Chelidae, que apresenta maior riqueza de espécies de Testudines no Brasil. Apesar de não se suspeitar do monofiletismo da família, há muitas dúvidas sobre as relações entre os táxons de Chelidae, com a possibilidade de vários grupos se revelarem parafiléticos. Mesoclemmys vanderhaegei tem uma ampla distribuição no centro-sul do continente sul-americano, havendo sido estudada mais especificamente sob uma temática ecológica. Seus aspectos taxonômicos e filogenéticos, porém, ainda necessitam de uma investigação mais detalhada, visto que o grupo pode representar um complexo de espécies. O presente trabalho visa, portanto, estudar as populações de M. vanderhaegei sob um ponto de vista taxonômico e filogenético, buscando identificar e caracterizar as populações através das divergências evolutivas que venham a ser reveladas, justificando assim um eventual desmembramento da espécie. Sendo assim, as populações de M. vanderhaegei foram investigadas por meio de técnicas de morfometria tradicional, morfometria geométrica, e uma filogenia molecular foi proposta para o gênero. Para a morfometria tradicional foram analisadas medidas lineares do plastrão, carapaça e cabeça; enquanto que para a morfometria geométria foram selecionados landmarks nos vértices dos escudos do casco e na linha média dorsal e ventral de cada espécime. Para o estudo de filogenia molecular, foram sequenciados três genes nucleares (RAG-2, R35 e c-mos), e dois mitocondriais (12S e NADH) de representantes da maioria das populações da espécie, e de todas as espécies do gênero. A análise discriminante tanto para os dados de medidas lineares quanto para os de landmarks separa a população do sul da Bacia do Paraguai (próxima à localidade tipo da espécie) das demais populações brasileiras. As análises morfométricas diferenciam outras duas populações: uma população composta por espécimes da Chapada dos Guimarães (MT), região de Cuiabá e um exemplar de Bonito (MS); enquanto a outra população é representada por espécimes de São João da Ponte (MG), na Bacia do São Francisco. A topologia resultante da análise de máxima verossimilhança aponta M. vanderhaegei como um grupo polifilético, com a possibilidade de ser dividida em quatro espécies: uma com os espécimes do sul da Bacia Amazônica; outra com os espécimes de Montes Claros (MG), na Bacia do São Francisco; uma terceira com os espécimes de São João da Lagoa e do interior de São Paulo (Bacia do Paraná, sub Bacia do Tietê); além daquela formada pelos espécimes próximos à localidade tipo. Sugere-se, portanto, (1) que a distribuição de Mesoclemmys vanderhaegei seja restringida ao norte da Argentina, Paraguai, e oeste do Mato Grosso do Sul até que novos estudos venham a elucidar o quanto a espécie adentra o território brasileiro; (2) que as populações da região da Chapada dos Guimarães e do interior de Minas Gerais sejam elevadas ao nível de espécie; (3) e que se façam novos estudos para elucidar a relação das populações da Bacia do Tocantins-Araguaia e Paraná com os outros grupos do complexo.! / Mesoclemmys vanderhaegei Bour, 1973 belongs to the family Chelidae, which presents the greatest variety of species of Testudines in Brazil. In spite of theories that suggest that the family might be monophyletic, there are still areas of doubt over the relationships between the taxa that belong to the Chelidae, and the possibility that various groups might prove to be paraphyletic. Mesoclemmys vanderhaegei has a large distribution range along the central and southern regions of the South American continent, and has been most specifically studied through an ecological perspective. A more detailed investigation of its taxonomic and phylogenetic characteristics is still both relevant and necessary, since the complex might represent multiple species. The present work aims, therefore, to study the populations of M. vanderhaegei from a phylogenetic and taxonomic perspective, looking to identify and characterize the populations in accordance with the evolutionary divergences that may be observed, thus justifying the subdivision of the complex into mutiple species. With this in mind, the populations of M. vanderhaegei were investigated using techniques of traditional and geometric morphometry, and a molecular phylogeny was proposed for the genus. The traditional morphometric data accounted for linear measurements of the plastron, carapace and head whilegeometric morphometric data were chosen as landmarks on the vertices of the scutes of the shells and on the dorsal and ventral midline of each specimen. Using samples of the majority of the populations of the species, and of all the species of the genus, three nuclear (RAG-2, R35 and c-mos) and two mitochondrial genes (12S and NADH) were sequenced for the study of the molecular phylogeny. Both the discriminant analysis of the linear measurements data and that of the landmarks separate the population found in the South of the Paraguay Basin (near the type locality of the species) from other Brazilian populations. The morphometric analyses show two other distinct populations: a population composed of specimens from Chapada dos Guimarães (MT), in the region of Cuiabá and one specimen from Bonito (MS); while the other population is represented by specimens taken from São João da Lagoa (MG), in the Basin of São Francisco. The resulting tree topology of theMaximum-Likelihood analysis derived from the molecular data suggests that M. vanderhaegei should be considered a polyphyletic group, that can be divided into four species: one species represented by the specimens from the South of the Amazonian Basin; another represented by the specimens from Montes Claros (MG), in the Basin of São Francisco; a third represented by the specimens from São João da Lagoa and the interior of São Paulo (Paraná Basin, sub Basin of the river Tietê); in addition to the one formed of the specimens close to the type locality. This would suggest, therefore, (1) that the distribution of Mesoclemmys vanderhaegei is restricted to the North of Argentina, Paraguay, and the West of Mato Grosso do Sul, until further studies are made to elucidate the extent to which the species has spread into Brazilian territory; (2) that the population of the Chapada dos Guimarães region and of the interior of Minas Gerais should be elevated to the category of species; (3) and that new studies must be carried out to determine the relationship between the populations of the Basin of Tocantins-Araguaia and Paraná with the other groups of the complex.!

Three new species of cichlid fishes of the genus Geophagus, part of the Neotropical subfamily Geophaginae, are described from the Orinoco and Casiquiare drainages in Venezuela. Phylogenetic relationships among 16 genera and 30 species of Geophaginae are investigated using 136 morphological characters combined with DNA sequences coding for the mitochondrial gene NADH dehydrogenase subunit 4 (ND4) and the nuclear Recombination Activating Gene 2 (RAG2). Data from previous studies are integrated with the new dataset by incorporating published DNA sequences from the mitochondrial genes cytochrome b and 16S and the microsatellite flanking regions Tmo-M27 and Tmo-4C4. Total-evidence analysis revealed that Geophaginae is monophyletic and includes eighteen genera grouped into two major clades. In the first clade, the tribe Acarichthyini (genera Acarichthys and Guianacara) is sister-group to a clade in which Gymnogeophagus, 'Geophagus' steindachneri, and Geophagus sensu stricto are sister to 'Geophagus' brasiliensis and Mikrogeophagus; all these are in turn sister-group to Biotodoma, Dicrossus and Crenicara. In the second clade, Satanoperca, Apistogramma (including Apistogrammoides), and Taeniacara are sister to Crenicichla and Biotoecus. Monophyly and significantly short branches at the base of the phylogeny indicate that genera within Geophaginae differentiated rapidly within a relatively short period. High morphological, ecological, and behavioral diversity within the subfamily suggest that geophagine divergence may be the result of adaptive radiation.