Abstract
This thesis focuses on understanding how environmental factors and biotic interactions influence the diversification of Neotropical groups. The Neotropics harbour a very high biological diversity that evolved in a unique geological and climatic context during the Cenozoic. Through an integrative phylogenetic approach combining diversification models and historical biogeography approaches, this thesis studies the factors of diversification of Neotropical biodiversity, mainly on mammalian and avian groups, and tries to contribute to the wider advancement of some major questions in macroevolution.In the first chapter, I pursued methodological developments that allow detecting diversification shift at clade level in order to better reconstruct the dynamics of paleodiversity from dated molecular phylogenies. The first developments of this approach have been particularly promising in detecting phases of palaeodiversity decline with phylogenies that are exclusively composed of extant species. This method is now more accessible and more user-friendly through its new implementation in the RPANDA package. I also exploited this method through simulations and empirical cases to show the arguably greater prevalence of decline phases within empirical phylogenies.In a second chapter, I studied the diversification factors of five groups of neotropical mammals. The work in the first chapter of this thesis investigated how the paleodiversity dynamics of one group could influence the diversification of other groups, while comparing to the effects of abiotic factors. The results of this approach show some effects of the Andean orogeny and global mean temperature evolution but more interestingly, it seems that biotic interactions played a more important role than climatic or geological changes. Among the competitive interactions, Marsupial palaeodiversity appears to have negatively affected the speciation of the Platyrrhini. More surprisingly, facilitative interactions, i.e. increasing the rate of speciation or decreasing the rate of extinction, seem to have contributed in the diversification of the Neotropical mammal groups studied. Contrary to hypotheses of faunal replacements, these results call for more studies on potential positive effects of competition on diversification, as it is already explored for species coexistence at the community level.In a third chapter, I tried to understand what factors had driven the geographical diversification of the largest clade of Neotropical birds. The Tyranni account for one third of Neotropical bird diversity. Through this study, we reconstructed the biogeographic history of the Tyranni and tried to better understand how and when the Great American Biotic Interchange (GABI) affected the history of the group. Indeed, the complete closure of the Isthmus of Panama dates from about 3.5 million years ago, but several studies, mainly on fossil mammals, have revealed earlier faunal passages. Overall, the Amazon region appears to be the region of origin of the group and the main source of diversity. However, the 1272 species of Tyranni show different patterns of diversification within their families. The Furnariidae, for example, have diversified southward and are not concern by GABI. Overall, few lineages colonised the North but several passages are estimated to have occurred during the late Miocene, well before the closure of the isthmus.In a fourth chapter, I collaborate with a team of Argentinian researchers to understand the diversification of Calyceraceae. This group of herbaceous plants, native to the southern Neotropics, has only 46 species compared to over 20,000 for its globally distributed sister group, the Asteraceae. By combining several models of diversification and historical biogeography, we demonstrated that this group has diversified steadily, at a low rate and without any diversification factor since the late Oligocene, illustrating an unexpected case in the Neotropics.