The well-known high species richness of the tropical forests is not uniform through its different regions; Africa is species-poor when compared to Southeast Asia and the Neotropical region. One of the hypotheses for differences between the richness in the Neotropics and Africa points to the importance of recent speciation in the Neotropics. This is considered in particular in Andean-centred taxa that probably diversified in response to the opportunities for speciation offered by the final uplift of the tropical Andes (during the past c. 25 million years [Ma] to the present, with higher rates on the past 10 Ma to the present). The aim of this thesis is to test this hypothesis in the genus Renealmia L.f. (Zingiberaceae), an Andean centred lineage (c. 64 Neotropical spp.) that also occurs in Africa (c. 17 spp.). A taxonomic account of the Colombian species (c. 32; the country with the most species) is presented, and three species new to science were discovered and are described in an updated revision. I designed a new approach for obtaining nuclear phylogenetic markers for estimating species-level phylogenies using transcriptomes for recent diversification that could be applied to samples from herbarium specimens. I generated de-novo transcriptomes for two Renealmia species and a relative in the subfamily Alpinioideae that were combined with data available in repositories to target low copy number and potentially orthologous genes with short introns. I obtained sequence data for eight introns (ranging from 219 to 924 bp) and an rRNA (ITS1 & ITS2) marker for 40 species and at least one marker for 64 species, comprising a total of 137 accessions of which 67.9%(93) were sampled from herbarium specimens. Gene and species-trees were estimated for the genus. I found that most of the subgroups based on morphological characters are supported by the molecular data but a possible combination of incomplete lineage sorting (related to recent radiations or large population sizes) and/or introgression through hybridisation makes difficult to solve the relationships among these subgroups. Finally I estimated and compared diversification rates of the Neotropical and African lineages using dated phylogenies based on the trees estimated. I used available and customized methods that take into account incomplete taxon sampling, the uncertainty in the phylogenetic relationships and the stochasticity inherent to diversifications processes. Differences in diversification rates between Africa and the Neotropics indicate increased speciation attributable to the Andean orogeny in the Neotropical lineages of Renealmia.

<p>Morphological characters from the gametophyte and sporophyte generations have been used in land plants to infer relationships and construct classifications, but sporophytes provide the vast majority of data for the systematics of vascular plants. In bryophytes both generations are well developed and characters from both are commonly used to classify these organisms. However, because morphological traits of gametophytes and sporophytes can have different genetic bases and experience different selective pressures, taxonomic emphasis on one generation or the other may yield incongruent classifications. The moss order Hookeriales has a controversial taxonomic history because previous classifications have focused almost exclusively on either gametophytes or sporophytes. The Hookeriales provide a model for comparing morphological evolution in gametophytes and sporophytes, and its impact on alternative classification systems. Sometimes, placement of certain groups within Hookeriales remains challenging even at the molecular level. That is the case of the genus <italic>Calyptrochaeta</italic>. We study diversification dynamics in this genus to elucidate possible mechanisms obscuring its placement and we address biogeographic questions using the Tropical Conservatism scenario as our null hypothesis. Furthermore, to better understand biogeographic patterns in the Southern Hemisphere, infraspecific molecular patterns are compared in two species of the genus <italic>Calyptrochaeta</italic> (i.e., <italic>C. apiculata</italic> and <italic>C. asplenioides</italic>) and vicariance and recent long distance dispersal are tested to explain the disjunct distributions observed in these species. </p><p>In this study we reconstruct relationships among pleurocarpous mosses in or associated to the Hookeriales, in <italic>Calyptrochaeta</italic>, and within <italic>Calyptrochaeta</italic>. Six molecular markers are explored in total from all three genome compartments to reconstruct the evolution of morphological characters and habitat preferences in our phylogenies. Divergence times are estimated in a Bayesian framework using a relaxed molecular clock, and diversification rates are calculated on the chronograms resulting from these estimations. </p><p>As a result, we found that the Hookeriales, as currently circumscribed, are monophyletic and that both sporophyte and gametophyte characters are labile. We documented parallel changes and reversals in traits from both generations. We show that diversification rates in <italic>Calyptrochaeta</italic> have changed through its history. Also, though we lack support to clearly reject the tropical conservatism hypothesis, our data point to a more complex scenario where both temperate and tropical species can be ancient and give rise to one another, since shifts between tropical and temperate regions seem to be possible in any direction. Finally, we have show that recent long distance dispersal best explains the distribution of both <italic>C. apiculata</italic> and <italic>C. asplenioides</italic> in the Southern Hemisphere.</p> / Dissertation

Das impedanzwandelnde Hören ist eine wichtige Verfeinerung des Gehörsystems der Tetrapoden indem es einen Energieverlust während der Schallübertragung vermeidet. Anatomisch ist es durch eine Unterteilung des Foramen Metoticum in eine vordere Fenestra Pseudorotunda und ein hinteres Vagus Foramen charakterisiert. Dieses System trat mehrmals unabhängig in Amniota auf, und obwohl schon vorher vermutet wurde, dass es eine Homoplasie für Archosauria darstellt, wurde diese Hypothese bisher noch nicht geprüft. Demnach wurden 17 Hirnschädel Merkmale für 111 Taxa kodiert und auf einem informellen Supertrees optimiert. Die Analyse ergab, dass die Fenestra Pseudorotunda unbhängig acht Mal in Archosauria auftrat, mit fünf Umkehrungen. Während dieses Merkmal plastisch für Dinosauria ist, es trat nur einmal in Pseudosuchia auf. Eine Tree Shape-Analyse ergab, dass sechs Verschiebungen in den Diversifizierungsraten in Pseudosuchia und sieben in Dinosauria zu finden sind, von denen nur die der Ornithischia mit der Fenestra Pseudorotunda in Beziehung stehen. Viele Zustandsveränderungen erfolgen an der Basis der Dinosauria aber bei Pseudosuchia sind diese vor der Entstehung der Crocodyliformes und an der Basis der Notosuchia und Thalattosuchia konzentriert. Die Korrelationen zwischen Zustandsveränderungen und Verschiebungen sind höher in Dinosauria, während bei Pseudosuchia nur Mesoeucrocodylia eine ähnliche Anzahl aufweist. Daraus folgt, dass das impedanzwandelnde Hören nicht homolog in Archosauria ist, und dass es nicht als Schlüsselinnovation zur Erklärung der Vielfalt betrachtet werden kann, obwohl es eine Rolle in der Diversifizierung der Ornithischia spielte. Insgesamt ist die Anatomie des Hirnschädels der Dinosauria plastischer als die der Pseudosuchia. Die Positionierung des Pterygoid-Quadratum-Komplexes an die Seitenwand des Hirnschädels in Crocodyliformes stellt eine anatomische Beschränkung dar, welche nur von Notosuchia und Thalattosuchia durchbrochen wurde. / Impedance-matching hearing is considered an important refinement of the auditory system of tetrapods because it reduces energy loss during sound transmission. Anatomically, it is characterized by the sub-division of the metotic foramen into a posterior vagus foramen and an anterior fenestra pseudorotunda. Impedance-matching hearing has evolved independently in several tetrapod groups including archosaurs and although it has been suggested that it represents a homoplasy, this hypothesis has never been tested. Therefore, 17 braincase characters were coded for 111 taxa and mapped on an informal supertree. Optimization of the characters revealed that the fenestra pseudorotunda appeared eight times independently in Archosauria, with five reversals. While this character is plastic in dinosaurs, it appeared only once in pseudosuchians. A tree-shape analysis revealed that pseudosuchians had six shifts in diversification rates, while dinosaurs had seven. Of these, only ornithischian ones are correlated to the appearance of impedance-matching hearing. Many of the overall state changes occur at the origin of major dinosaurian clades, but for pseudosuchians they are concentrated prior to the origin of Crocodyliformes and at the origin of Notosuchia and Thalattosuchia. The overall number of correspondences between character state changes and shifts in diversification rates is higher for dinosaurs, whereas in Pseudosuchia only Mesoeucrocodylia has a similar amount. It is thus possible to conclude that impedance-matching hearing is not homologous for archosaurs, and that it cannot be considered a key innovation triggering diversification. However, it may have played some role in ornithischian diversification. In general, the braincase anatomy of dinosaurs is more plastic than that of pseudosuchians. The abutting of the pterygo-quadrate complex against the lateral braincase wall was a strong anatomical constraint for crocodyliforms broken only by notosuchians and thalatosuchians.

Les Angiospermes forment un clade connu pour sa grande diversité d’espèces et une répartition inégale de cette diversité en son sein. Ce travail se concentre sur la reconstruction d’états ancestraux de caractères floraux sur les phylogénies dans le but d’étudier leur impact sur la diversification. En premier lieu, nous nous sommes focalisés sur deux innovations-clés potentielles chez les Proteaceae, la symétrie bilatérale du périanthe et la présence dans les hotspots à climat méditerranéen. L’utilisation sur une phylogénie de modèles de diversification dépendants des états de caractère a permis de montrer que le premier état caractère n’a pas d’impact significatif sur la diversification des espèces dans ce groupe, contrairement au second. Ensuite, nous avons reconstruit les états ancestraux de la symétrie du périanthe à l’échelle de toutes les Angiospermes, avec une stratégie d’échantillonnage permettant de refléter toutes les transitions de ce caractère. Nous avons mis en évidence un minimum de 130 origines de la symétrie bilatérale, suivies de 69 réversions vers la symétrie radiaire. Enfin, la même méthode a été étendue à l’étude de quatre autres caractères du périanthe. Différents modèles de reconstruction d’états ancestraux ont été utilisés sur une phylogénie de 1232 espèces pour examiner l’influence des changements de modèle sur les états ancestraux reconstruits. Nos résultats montrent que les changements de modèles de reconstruction ont une influence sur l’état de certains nœuds seulement, jamais sur l’ensemble. Les différents résultats trouvés pour la symétrie, caractère commun aux trois chapitres, révèlent que notre méthode d’échantillonnage présente l’inconvénient d’estimer des taux de transition trop élevés pour donner des résultats concluants avec la méthode du maximum de vraisemblance. Les résultats sont en revanche beaucoup moins biaisés lorsque l’on examine plusieurs caractères simultanément. / Angiosperms are a clade known for its great species diversity and the uneven distribution of this diversity among its lineages. This work focuses on the ancestral state reconstruction of floral characters on phylogenies in the purpose of studying their impact on diversification. We first focused on two potential key innovations in Proteaceae, bilateral perianth symmetry and presence in Mediterranean-climate hotspots. Using character state dependent diversification models, we found that the first character state did not have any significant impact on species diversification in this group, contrary to the second one. We then reconstructed ancestral states for perianth symmetry in angiosperms as a whole, using a sampling strategy aimed at capturing all of the transitions in this character. We found a minimum of 130 origins of bilateral symmetry, followed by 69 subsequent reversals to radial symmetry. Lastly, the same approach was extended to the study of four other perianth characters. Different ancestral state reconstruction models were used on a phylogenetic tree of 1232 species to test the influence of model changes on reconstructed ancestral states. Our results show that changes in reconstruction models have an impact on the inferred ancestral state of some nodes, but not all of them. The various results obtained for symmetry, a character shared among the three chapters, indicate that our sampling method has the drawback of estimating transition rates too high to give conclusive results with maximum likelihood. On the other hand, results are much less biased when several characters are examined simultaneously.