Satellite DNA (satDNA) is among the fastest evolving elements in the genome and is highly abundant in some eukaryotic genomes. Its highly repetitive nature means it is challenging to assemble, and thus underrepresented in most assemblies and often understudied as a result. Birds are an ideal model organism for the study of satDNA and its evolution, since the large amount of available sequenced genomes of this clade allows for dense sampling across various evolutionary timescales, and the low number of satDNA families within their satellitomes facilitates their study and comparison between species. Here, we characterize satDNA and its evolution across Passeriformes, an avian clade containing two-thirds of all bird species spanning ~50 million years of evolution. With this goal we use both short-read data and long-read assemblies of species representative of over 30 passerine families in this clade to shed light on the evolution of its satellitome. We focus on examining the phylogenetic relationships between satellites common to most species as well as characterizing satellite array structure and location in genome assemblies. We also analyse satellite abundance in each genome, focusing on differences in the satellite content between male and female individuals to look for satellites present in the female-specific W sex chromosome and the germline-restricted chromosome. Seven satDNA families shared by a quarter of the species were found, that were likely present in an ancestral species shared by most, if not all the species of Passeriformes. We observed that satDNA evolution is complex and does not follow species phylogeny and that satellite arrays generally have a simple head-to-tail conformation, with evidence in four of the sampled species of satDNA arrays with higher-order repeats. We also found two satDNA families with fairly consistent monomer length and conserved regions that we hypothesise to might be functional.

L'un des plus grands défis posés par la communication est que l'information codée par l'émetteur est toujours modifiée avant d'atteindre le récepteur, et que celui-ci doit traiter cette information altérée afin de recouvrer le message. Ceci est particulièrement vrai pour la communication acoustique, où la transmission du son dans l'environnement est une source majeure de dégradation du signal, ce qui diminue l'intensité du signal relatif au bruit. La question de savoir comment les animaux transmettent l'information malgré ces conditions contraignantes a été l'objet de nombreuses études, portant soit sur l'émetteur soit sur le récepteur. Cependant, une recherche plus intégrée sur l'analyse de scènes auditives est nécessaire pour aborder cette tâche dans toute sa complexité. Le but de ma recherche était d'utiliser une approche transversale afin d'étudier comment les oiseaux s'adaptent aux contraintes de la communication à longue distance, en examinant le codage de l'information au niveau de l'émetteur, les dégradations du signal acoustiques dues à la propagation, et la discrimination de cette information dégradée par le récepteur, au niveau comportemental comme au niveau neuronal. J'ai basé mon travail sur l'idée de prendre en compte les problèmes réellement rencontrés par les animaux dans leur environnement naturel, et d'utiliser des stimuli reflétant la pertinence biologique des problèmes posés à ces animaux. J'ai choisi de me focaliser sur l'information d'identité individuelle contenue dans le cri de distance des diamants mandarins (Taeniopygia guttata) et d'examiner comment la signature vocale individuelle est codée, dégradée, puis discriminée et décodée, depuis l'émetteur jusqu'au récepteur. Cette étude montre que la signature individuelle des diamants mandarins est très résistante à la propagation, et que les paramètres acoustiques les plus individualisés varient selon la distance considérée. En testant des femelles dans les expériences de conditionnement opérant, j'ai pu montrer que celles-ci sont expertes pour discriminer entre les signature vocales dégradées de deux mâles, et qu'elles peuvent s'améliorer en s'entraînant. Enfin, j'ai montré que cette capacité de discrimination impressionnante existe aussi au niveau neuronal : nous avons montré l'existence d'une population de neurones pouvant discriminer des voix individuelles à différent degrés de dégradation, sans entrainement préalable. Ce niveau de traitement évolué, dans le cortex auditif primaire, ouvre la voie à de nouvelles recherches, à l'interface entre le traitement neuronal de l'information et le comportement / In communication systems, one of the biggest challenges is that the information encoded by the emitter is always modified before reaching the receiver, who has to process this altered information in order to recover the intended message. In acoustic communication particularly, the transmission of sound through the environment is a major source of signal degradation, caused by attenuation, absorption and reflections, all of which lead to decreases in the signal relative to the background noise. How animals deal with the need for exchanging information in spite of constraining conditions has been the subject of many studies either at the emitter or at the receiver's levels. However, a more integrated research about auditory scene analysis has seldom been used, and is needed to address the complexity of this process. The goal of my research was to use a transversal approach to study how birds adapt to the constraints of long distance communication by investigating the information coding at the emitter's level, the propagation-induced degradation of the acoustic signal, and the discrimination of this degraded information by the receiver at both the behavioral and neural levels. Taking into account the everyday issues faced by animals in their natural environment, and using stimuli and paradigms that reflected the behavioral relevance of these challenges, has been the cornerstone of my approach. Focusing on the information about individual identity in the distance calls of zebra finches Taeniopygia guttata, I investigated how the individual vocal signature is encoded, degraded, and finally discriminated, from the emitter to the receiver. This study shows that the individual signature of zebra finches is very resistant to propagation-induced degradation, and that the most individualized acoustic parameters vary depending on distance. Testing female birds in operant conditioning experiments, I showed that they are experts at discriminating between the degraded vocal signatures of two males, and that they can improve their ability substantially when they can train over increasing distances. Finally, I showed that this impressive discrimination ability also occurs at the neural level: we found a population of neurons in the avian auditory forebrain that discriminate individual voices with various degrees of propagation-induced degradation without prior familiarization or training. The finding of such a high-level auditory processing, in the primary auditory cortex, opens a new range of investigations, at the interface of neural processing and behavior

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