L'étude de la biodiversité passée, de sa dynamique et des paramètres déterminant son évolution, est un préalable nécessaire à la compréhension de l’érosion de la biodiversité actuelle. En étudiant les conditions environnementales et historiques associées aux assemblages taxinomiques, il est possible d'inférer les liens dynamiques qui unissent les variations de l'environnement et de la biodiversité. Pour cela, un Système d'Information Géographique (SIG) a été développé à partir des compilations du registre fossile des mammifères terrestres cénozoïques d'Amérique du Nord publiées par Janis et al. (1998, 2008). Ce registre, s'étendant de la crise Crétacé/Paléogène (66 Ma) au Pléistocène inférieur (�1,8 Ma) et couvrant les territoires actuels des Etats-Unis, du Canada et du Mexique, est l'un des registres fossiles les mieux connus et les plus complets au monde. Sur la base de ces données d'occurrences géoréférencées, il devient possible de caractériser les patrons de distributions et d'observer les fluctuations temporelles et spatiales de plusieurs dimensions de la biodiversité (diversité taxinomique, disparité, diversité fonctionnelle, diversité phylogénétique.). L'observation de ces variations spatio-temporelles de biodiversité peut être réalisée à différentes échelles (locale à continentale) et pour différents types d'assemblages écologiques ou taxinomiques (communautés, métacommunautés, guildes trophiques, groupes de taille, espèces, genres, familles.), permettant en retour de tester différentes hypothèses à l'interface entre macroévolution et macroécologie. Ainsi, deux axes de recherche principaux ont pu être développés dans le cadre de ce travail. Le premier s'enracine dans une problématique centrale en macroévolution : l'impact de l'organisation chronologique des informations paléontologiques dans un système biozonal discret sur la reconstruction de séries temporelles de diversité et de taux d'évolution (apparitions et extinctions). A partir de simulations, l'effet de la discrétisation temporelle est estimé en fonction du registre fossile étudié ; un algorithme est développé afin d'en corriger les distorsions. Le second axe de recherche s'enracine dans une problématique centrale en macroécologie : comment caractériser a posteriori, sur la base de données d’occurrences taxinomiques échantillonnées au sein d'assemblages, la part relative des processus d'assemblage par la niche et par la dispersion dans la construction et le maintien de communautés et métacommunautés ? Afin de répondre à cette question, un nouvel outil analytique appelé « PER-SIMPER » est développé à partir de la méthode SIMPER (Clarke 1993). Dans un premier temps, la précision et la consistance de cette nouvelle méthode sont évaluées à l'aide de simulations basées sur des automates cellulaires. Dans un second temps, l'analyse PER-SIMPER de l'ensemble des biozones enregistrées au sein du SIG est réalisée ; les résultats obtenus sont discutés au regard des changements climatiques et environnementaux associés à l’histoire évolutive des mammifères cénozoïques nord-américains. Finalement, les résultats obtenus permettent d’identifier différentes perspectives de recherche à court, moyen et long termes, tant sur leplan analytique que méthodologique / The study of past biodiversity, its evolutionary dynamics and related control parameters is a fundamental prerequisite for understanding the ongoing global biodiversity loss. Considering the environmental and historical conditions related to taxonomical assemblages, the dynamic links associating environmental changes and biodiversity can be inferred. To achieve this, a Geographic Information System (GIS) has been developed based on Janis et al.'s (1998, 2008) compilations of the north-American Cenozoic mammal fos- sil record. Ranging from the Cretaceous/Paleogene crisis (66 Ma) to the early Pleistocene (�1.8 Ma), this fossil record covers extant United States, Canada, and Mexico territories; it is one of the best known and most complete fossil record in the World. Based on these georeferenced data of fossil occurrences, it be- comes possible to characterize distribution patterns and to observe spatial and temporal variations of sev- eral aspects of biodiversity (taxonomical diversity, disparity, functional diversity, phylogenetic diversity.). The observation of spatial and temporal variations of biodiversity can be achieved at various geographical scales (local to continental) and for different types of ecological or taxonomical assemblages (communi- ties, metacommunities, trophic guilds, size groups, species, genera, families.); in turn, these observations make possible testing various hypotheses at the interface between macroevolution and macroecology. In this way, two main research axes have been developed in this work. The first research axis roots into a central issue of macroevolutionary studies: the impact of the chronological organization of paleontologi- cal data within a discrete biozonation on the reconstruction of biodiversity and evolutionary rate (origina- tion and extinction) time series. Based on simulations, the effect of time discretization is investigated; an algorithm is developed in order to correct the distorting effect induced by the time discretization process. The second research axis developed in this work roots into a central macroecological question: based on taxonomical occurrence data sampled within assemblages, how to characterize the relative contribution of niche- and dispersal-assembly processes in the building and conservation of communities and meta- communities? Building on Clarke's (1993) SIMPER method, a new analytical tool called "PER-SIMPER" has been developed in order to answer this question. First, the accuracy and consistency of this new method is evaluated through cellular automaton-like simulations. Then, the PER-SIMPER analysis of all biozones recorded within the GIS is achieved, and results are discussed with respect to the climate and environmen- tal changes related to the evolutionary history of north-American Cenozoic mammals. Finally, the results obtained from both research axes allow the identification of several short, middle and long-term analytical as well as methodological research perspectives

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Physical properties of the environment may shape signalling traits by determining how effective signals are in influencing the behaviour of other individuals. Evidence abounds of signalling environment driving the evolution of colours and sounds, yet little is known about its influence upon gestural displays. Here, we performed a continent-wide phylogenetic comparative analysis to test the hypothesis that habitat structure drives the evolution of aerial sexual displays in passerine birds. We found that aerial displays are seven times more likely to evolve in open-habitat passerines than in forest ones, likely as a result of physical properties that allow aerial displays to transmit more broadly in open habitats. Our results provide an emblematic example of how environmental factors may help predict the direction of evolution of otherwise unpredictable sexual traits. The broader range of aerial displays in open habitats may also mean that females can sample more males, potentially leading to more intense sexual selection in open-habitat, aerial-displaying males / Propriedades físicas do ambiente podem influenciar a evolução de sinais ao determinar quão efetivos eles são em influenciar o comportamento de outro indivíduo. Diversos estudos mostram a influência do ambiente sobre a evolução de cores e sons. Entretanto, pouco se sabe de sua influência sobre sinais motores (i.e., displays). Nesse trabalho, conduzimos uma análise comparativa filogenética para testar a hipótese de que a estrutura do hábitat influencia a evolução de displays sexuais aéreos em aves Passeriformes. Descobrimos que display aéreos têm uma probabilidade sete vezes maior de evoluir em passeriformes de ambiente aberto do que nos florestais, provavelmente decorrente de propriedades físicas que permitem que displays aéreos sejam transmitidos mais amplamente em ambientes abertos. Nossos resultados são um exemplo emblemático de como fatores ambientais podem ajudar a prever a direção de evolução de caracteres sexuais, frequentemente tidos como imprevisíveis. O raio mais amplo de displays aéreos em ambientes abertos também pode permitir que fêmeas consigam amostrar mais machos da população, potencialmente intensificado a seleção sexual sobre machos de ambiente aberto que exibem displays aéreos

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Phylogenetic trees capture the relationships between species and can be investigated by morphological and/or molecular data. When focusing on macroevolution, one considers the large-scale history of life with evolutionary changes affecting a single species of the entire clade leading to the enormous diversity of species obtained today. One major problem of biology is the explanation of this biodiversity. Therefore, one may ask which kind of macroevolutionary processes have given rise to observable tree shapes or patterns of species distribution which refers to the appearance of branching orders and time periods. Thus, with an increasing number of known species in the context of phylogenetic studies, testing hypotheses about evolution by analyzing the tree shape of the resulting phylogenetic trees became matter of particular interest. The attention of using those reconstructed phylogenies for studying evolutionary processes increased during the last decades. Many paleontologists (Raup et al., 1973; Gould et al., 1977; Gilinsky and Good, 1989; Nee, 2004) tried to describe such patterns of macroevolution by using models for growing trees. Those models describe stochastic processes to generate phylogenetic trees. Yule (1925) was the first who introduced such a model, the Equal Rate Markov (ERM) model, in the context of biological branching based on a continuous-time, uneven branching process. In the last decades, further dynamical models were proposed (Yule, 1925; Aldous, 1996; Nee, 2006; Rosen, 1978; Ford, 2005; Hernández-García et al., 2010) to address the investigation of tree shapes and hence, capture the rules of macroevolutionary forces. A common model, is the Aldous\\\'' Branching (AB) model, which is known for generating trees with a similar structure of \\\"real\\\" trees. To infer those macroevolutionary forces structures, estimated trees are analyzed and compared to simulated trees generated by models. There are a few drawbacks on recent models such as a missing biological motivation or the generated tree shape does not fit well to one observed in empirical trees. The central aim of this thesis is the development and study of new biologically motivated approaches which might help to better understand or even discover biological forces which lead to the huge diversity of organisms. The first approach, called age model, can be defined as a stochastic procedure which describes the growth of binary trees by an iterative stochastic attachment of leaves, similar to the ERM model. At difference with the latter, the branching rate at each clade is no longer constant, but decreasing in time, i.e., with the age. Thus, species involved in recent speciation events have a tendency to speciate again. The second introduced model, is a branching process which mimics the evolution of species driven by innovations. The process involves a separation of time scales. Rare innovation events trigger rapid cascades of diversification where a feature combines with previously existing features. The model is called innovation model. Three data sets of estimated phylogenetic trees are used to analyze and compare the produced tree shape of the new growth models. A tree shape statistic considering a variety of imbalance measurements is performed. Results show that simulated trees of both growth models fit well to the tree shape observed in real trees. In a further study, a likelihood analysis is performed in order to rank models with respect to their ability to explain observed tree shapes. Results show that the likelihoods of the age model and the AB model are clearly correlated under the trees in the databases when considering small and medium-sized trees with up to 19 leaves. For a data set, representing of phylogenetic trees of protein families, the age model outperforms the AB model. But for another data set, representing phylogenetic trees of species, the AB model performs slightly better. To support this observation a further analysis using larger trees is necessary. But an exact computation of likelihoods for large trees implies a huge computational effort. Therefore, an efficient method for likelihood estimation is proposed and compared to the estimation using a naive sampling strategy. Nevertheless, both models describe the tree generation process in a way which is easy to interpret biologically. Another interesting field of research in biology is the coevolution between species. This is the interaction of species across groups such that the evolution of a species from one group can be triggered by a species from another group. Most prominent examples are systems of host species and their associated parasites. One problem is the reconciliation of the common history of both groups of species and to predict the associations between ancestral hosts and their parasites. To solve this problem some algorithmic methods have been developed in recent years. But only a few host parasite systems have been analyzed in sufficient detail which makes an evaluation of these methods complex. Within the scope of coevolution, the proposed age model is applied to the generation of cophylogenies to evaluate such host parasite reconciliation methods. The presented age model as well as the innovation model produce tree shapes which are similar to obtained tree structures of estimated trees. Both models describe an evolutionary dynamics and might provide a further opportunity to infer macroevolutionary processes which lead to the biodiversity which can be obtained today. Furthermore with the application of the age model in the context of coevolution by generating a useful benchmark set of cophylogenies is a first step towards systematic studies on evaluating reconciliation methods.

This thesis investigates the molecular evolutionary and macroevolutionary consequences of flight loss in insects. Chapter 2 tests the hypothesis that flightless groups have smaller effective population sizes than related flighted groups, expected to result in a consistent pattern of increased non-synonymous to synonymous ratios in flightless lineages due to the greater effect of genetic drift in smaller populations. Chapter 3 tests the hypothesis that reduced dispersal and species-level traits such as range size associated with flightlessness increase extinction rates, which over the long term will counteract increased speciation rates in flightless lineages, leading to lower net diversification. The wide-spread loss of flight in insects has led to increased molecular evolutionary rates and is associated with decreased long-term net diversification. I demonstrate that the fundamental trait of dispersal ability has shaped two forms of diversity—molecular and species—in the largest group of animals, and that microevolutionary and macroevolutionary patterns do not necessarily mirror each other. / Generously funded by NSERC with a Canada Graduate Scholarship and the Government of Ontario with an Ontario Graduate Scholarship to T. Fatima Mitterboeck; NSERC with a Discovery Grant to Dr. Sarah J. Adamowicz