La dispersion, c’est-à-dire le déplacement d’un individu entre deux sites de reproduction, est un processus clé pour la dynamique des métapopulations et les flux de gènes. Son succès peut être modulé par des différences de phénotype ou syndromes de dispersion. Cependant, les contraintes environnementales (externes) et physiologiques (internes) qui sous-tendent ces syndromes restent mal connus. Ce projet vise à clarifier l’impact des variations environnementales et des contraintes oxydatives (liées aux espèces réactives de l’oxygène produites durant la respiration) sur les phénotypes associés à la dispersion chez un passereau, le gobemouche à collier Ficedula albicollis. La demande énergétique a été expérimentalement (i) augmentée en manipulant la surface alaire ou (ii) diminuée par une supplémentation en nourriture. L’équilibre oxydo-réducteur des gobemouches en reproduction est influencé par des interactions complexes entre facteurs intrinsèques (statut de dispersion) et extrinsèques (densité de couples reproducteurs, année, traitement expérimental). La capacité antioxydante dépend principalement des différences permanentes entre individus, alors que les pro-oxydants présentent de grandes variations intra-individu. Les variations environnementales et les contraintes énergétiques modulent aussi les différences de succès reproducteur et de comportement parental liées au statut de dispersion. Nos résultats confirment que les oiseaux dispersants et philopatriques diffèrent dans leur gestion de l’équilibre oxydo-réducteur lorsqu’il est en compétition avec l’investissement reproducteur. Ces différences pourraient avoir des conséquences à long terme sur la valeur sélective et compenser les différences de succès reproducteur entre individus dispersants et philopatriques dans les habitats de faible qualité. Ce travail souligne que les traits associés à la dispersion sont souvent déterminés par des normes de réaction à l’environnement et non des différences fixées entre individus, et améliore notre compréhension des syndromes de dispersion / Dispersal, i.e. individual movement between breeding sites, is a key process for metapopulation dynamics and gene flow. Its success can be modulated by phenotypic differences between dispersing and philopatric individuals, or dispersal syndromes. However, the environmental (external) and physiological (internal) constraints underlying such syndromes remain poorly known. This project aimed at clarifying the impact of environmental variation and oxidative constraints, linked to the reactive oxygen species produced during respiration, on phenotypes associated to dispersal in a passerine bird, the collared flycatcher Ficedulla albicollis. Energetic demand was experimentally (i) increased through a wing load manipulation or (ii) relieved through food supplementation. The oxidative balance of breeding flycatchers was influenced by complex interactions of dispersal status and extrinsic factors (breeding density, year, experimental treatments). Interestingly, antioxidant capacity was influenced both by permanent individual differences and by food availability, whereas measures of pro-oxidants were highly variables within individuals. Environmental variation and energetic constraints also modulated the differences in reproduction associated with dispersal: dispersing and philopatric birds differ in their management of the oxidative balance when it is competing with reproductive investment. This thesis highlights that reaction norms, rather than fixed differences, often shape traits associated to dispersal

L’évolution divergente est un processus clef générant de la biodiversité. Elle peut avoir lieu entre localités, via la réduction des flux de gènes, et au sein des localités via la spécialisation écologique. Dans le cas des systèmes parasitaires multi-hôtes, l’adaptation dépend des taux relatifs de flux de gènes des hôtes et des parasites entre différentes localités, ainsi que des échanges locaux de parasites entre différents types d’hôtes. En combinant génétique des populations et expérimentations sur le système composé de la puce Ceratophyllus gallinae et deux de ses hôtes, la mésange charbonnière Parus major et le gobe-mouche à collier Ficedula albicollis dans un habitat fragmenté, nous avons examiné comment l’adaptation et l’isolation génétique façonnent l’évolution des parasites. Nous avons aussi testé comment les choix d’habitat des hôtes pouvaient influencer la rencontre avec des populations de parasites spécialisées. Les analyses de microsatellites révèlent que les populations de puce sont différenciées à une échelle spatiale fine, et fréquemment entre espèces hôtes. De plus, des populations de parasites semblent adaptées à chaque type d’hôte. Cependant, aucune variation dans les choix d’habitats par rapport aux parasites n’a été observée chez les hôtes. Enfin, la réponse des hôtes aux parasites variait entre nos deux zones réplica ; l’histoire des populations d’hôtes pourrait donc influer sur la coevolution avec leurs parasites. Ce système semble donc localement façonné à la fois par une isolation génétique et une sélection par différents hôtes. L’étude de nouveaux sites permettraient d’évaluer si cette évolution divergente peut être génératrice de biodiversité / Divergent evolution is a key process generating biodiversity. This can occur between localities, through reduced gene flow followed by local adaptation or genetic drift, and within localities through ecological specialization. In the case of multi-host parasite systems, adaptation can be driven by the relative rate of host-parasite gene flow among spatially isolated populations, and the amount of parasite exchange among local host types. Combining population genetics and field experiments, we examined how adaptation and genetic isolation shape parasite evolution. Focusing on the hen flea Ceratophyllus gallinae, a presumed host generalist, and two of its hosts, the great tit Parus major and the collared flycatcher Ficedula albicollis, we investigated parasite population structure and adaptation within a fragmented landscape. Additionally, we tested how hosts can influence encounter rates with specialized flea populations through their habitat choice. Neutral markers analyses show that flea populations are genetically differentiated at fine spatial scales, and frequently between the two host species. Evidence for parasite adaptation to each host type were also observed. Host specialization may therefore be ongoing in hen fleas. However, birds did not show specific habitat choice strategies regarding flea-infested nests. Host responses differed between two replicate sites, indicating that local population history may impact parasite evolution. Both isolation and host-based selection are therefore acting on hen flea populations at a local scale. Investigations in new localities will help to assess to what extend this divergent evolution may generate biodiversity

Change in gene expression is a powerful tool for evolution, because seemingly small expression changes can contribute important steps towards adaptation without necessarily affecting the whole organism. There is still much to learn about how gene expression evolves on genome- and population-wide levels, especially in non-model organisms. This thesis addresses some important questions in gene expression evolution via the quantitative measurement of RNA and protein levels in birds. First, I confirmed the state of incomplete dosage compensation in birds by sequencing the transcriptome of collared flycatchers (Ficedula albicollis). I showed that pleiotropy governs the evolution of expression male-bias from the Z chromosome. Sex-linked genes in females were more highly expressed than half the male expression level, indicative of a partial up-regulation. A comparison with data from ostrich (Struthio camelus), a bird with non-degenerated sex chromosomes, showed that sex-linked expression male-bias evolved following sex chromosome degradation. Second, using a combination of RNA sequencing and proteome mass spectrometry in chicken (Gallus gallus), I asked whether complete dosage compensation was achieved through regulation at translation. I showed that this was not the case and that incomplete dosage compensation extends to the protein level in birds. In addition, sex-linked genes showed more often an increased amount of regulation at translational level than autosomal genes. Third, I investigated gene expression divergence between collared and pied flycatchers (Ficedula hypoleuca) using RNA sequencing in multiple tissues and individuals. Tissues differed in the degree of expression variance and in the number of divergent genes, which I identified using expression QST. Variance within species was negatively correlated with expression breadth and protein interactivity, indicating that evolutionary constraints act predominantly within interbreeding populations. Among genes unique to one of the species, I identified one gene, DPP7, falling into a large genomic deletion fixed in pied flycatchers. Fourth, I investigated allele-specific expression (ASE) in the two flycatcher populations. ASE was identified from genetic variants within transcripts using RNA sequencing reads. We developed a Bayesian negative binomial approach that gained statistical power by estimating expression variance from combined SNPs within a transcript and overdispersion from the whole dataset.

Individuals vary from each other in their genetic content. Genetic diversity is at the core of the evolutionary theory. Rooted in a solid theoretical framework developed as early as the 1930s, current empirical observations of genomic diversity became possible due to technological advances. These measurements, originally based on a few gene sequences from several individuals, are becoming possible at the genome scale for entire populations. We can now explore how evolutionary forces shape diversity levels along different parts of the genome. In this thesis, I focus on the variation in levels of diversity within genomes using avian systems and in particular that of the collared flycatcher (Ficedula albicollis). First, I describe the variation in genetic diversity along the genome of the collared flycatcher and compare it to the amount of variation in diversity across individuals within the population. I provide guidelines on how a small number of makers can capture the extent of variability in a population. Second, I investigate the stability of the local levels of diversity in the genome across evolutionary time scales by comparing collared flycatcher to the hooded crow (Corvus (corone) corone). Third, I study how selection can maintain variation through pervasive evolutionary conflict between sexes. Lastly, I explore how shifts in genome-wide variant frequencies across few generations can be utilised to estimate the effective size of population.

<p>This thesis examines parental condition, how it is traded off against reproduction and how it is displayed in a secondary sexual trait. The studies were performed on nest-box breeding collared flycatchers Ficedula albicollis on the island of Gotland, in the Baltic Sea. Early breeding and high fitness were found to be associated with high levels of glycosylated haemoglobin possibly governed by migratory exertion and infectious disease. In order to test if immune function is expressed in secondary sexual traits and how it is traded off against reproductive effort a series of experiments were performed, in which birds were challenged with an antigen, via a vaccine containing neutralised paramyxovirus. The forehead patch of the male collared flycatcher serves as a badge of status and is under sexual selection. Good condition, as reflected in strong immune response and low levels of blood parasites was found to be associated with bigger patch size. Patch size was also found to vary in size within the same breeding season in a pattern predictable from immune response data. Immune response, in itself, was found to be costly in terms of reduced survival, confirming that trade-offs involving suppression of immune response may increase fitness. Mating effort was found to be traded off against immune function and moult. Experimental brood size manipulations revealed a trade-off females between number of offspring and immune function. Thus I suggest a set of parameters useful for condition estimation. I also show that immune response is costly and, second, that pathogen resistance probably plays an important role in the shaping of secondary sexual traits and life-history decisions.</p>

This thesis examines parental condition, how it is traded off against reproduction and how it is displayed in a secondary sexual trait. The studies were performed on nest-box breeding collared flycatchers Ficedula albicollis on the island of Gotland, in the Baltic Sea. Early breeding and high fitness were found to be associated with high levels of glycosylated haemoglobin possibly governed by migratory exertion and infectious disease. In order to test if immune function is expressed in secondary sexual traits and how it is traded off against reproductive effort a series of experiments were performed, in which birds were challenged with an antigen, via a vaccine containing neutralised paramyxovirus. The forehead patch of the male collared flycatcher serves as a badge of status and is under sexual selection. Good condition, as reflected in strong immune response and low levels of blood parasites was found to be associated with bigger patch size. Patch size was also found to vary in size within the same breeding season in a pattern predictable from immune response data. Immune response, in itself, was found to be costly in terms of reduced survival, confirming that trade-offs involving suppression of immune response may increase fitness. Mating effort was found to be traded off against immune function and moult. Experimental brood size manipulations revealed a trade-off females between number of offspring and immune function. Thus I suggest a set of parameters useful for condition estimation. I also show that immune response is costly and, second, that pathogen resistance probably plays an important role in the shaping of secondary sexual traits and life-history decisions.

In nature, environments are often variable and heterogeneous influencing ecological and evolutionary processes. This thesis focus on how animals interact with their environment and how that affects the reproductive decisions they make. Using empirical data collected from wild collared flycatcher populations, experiments and molecular approaches I try to unveil some of these relationships and the evolutionary, ecological and conservation implications of these findings are discussed. Firstly, collared flycatchers were shown to use breeding densities of their own and other species using similar resources when assessing costs and benefits associated to breeding in specific habitats. However, species will vary in how informative they are, and the worst competitor – with whom you overlap most in resources needs – also provides the best source of information. Collared flycatcher parents will also benefit differentially from investments in sons and daughters due to habitat characteristics and dispersal differences between the sexes. Here, I show that they will produce more of the sex that will give the highest expected fitness return given the environment they are in. These results also provide a reciprocal scenario to Clark's (1978) classical study of sex ratio adjustment in relation to local resource competition (LRC), as more of the natal philopatric sex is produced when LRC is low. Secondly, the effect of elaborated ornaments on paternity in the socially monogamous collared flycatcher was shown to be of more importance in areas where the intensity of intra- and intersexual conflicts are expected to be elevated. Hence, ornamentation by environmental interactions determines paternity, illustrating that sexual selection through extra-pair paternity is context dependent. Finally, even though the collared flycatcher populations that this thesis is based on have been studied on their breeding grounds for more then 25 years, we know little of where they are when they are not breeding. Here, stable isotope signatures in winter-grown feathers suggests that they may spend their winter with their breeding ground neighbours and do so repeatedly over years. Differences between breeding populations at this small scale should have many impactions for evolutionary and ecological processes as it will, for example, determine with whom individuals interact throughout their life.

Age is often a neglected factor in ecological studies. However, age-related changes in reproduction and survival of organisms may strongly influence population dynamics. The Gotlandic population of collared flycatchers is a perfect system for studying age-related changes in the wild, as the exact age and reproductive history of most individuals is known. Collared flycatchers (Ficedula albicollis) on Gotland show the typical pattern of age-related changes in survival and reproductive success; both factors show an increase early in life and a decrease late in life. This thesis presents a broad study not only of age-related patterns of reproduction and immunity, but also proposes the mechanisms driving these patterns. My results show that in addition to survival probability and reproductive performance, reproductive costs and life-history trade-offs also change with progressing age. There is a significant increase in reproductive performance at the population level during first years of life which result from selection against low quality phenotypes. On the individual level this pattern is best explained by an optimization of reproductive effort. However, high quality individuals have higher reproductive success as early as their first breeding event and are long-lived. Thus, they seem to adopt a different strategy than lower quality, short-lived individuals. Differences in individual quality seem to be shaped by the developmental conditions experienced as nestlings. Fledglings with longer tarsi, but lower body mass become long-lived, high quality adults. Young individuals breeding for first time pay higher costs of reproduction. They also express a limited ability to reduce these costs by breeding in high quality territories when compared to middle-aged individuals. Young individuals seem to invest more into self-maintenance, whereas old individuals reduce the level of self-maintenance (measured as immune response) and redistribute their investment towards reproduction. Thus, old individuals are limited in their ability to reduce reproductive costs under favorable conditions, especially as they also senesce, which pattern is also shaped by individual quality. Variation in individual quality appears to have an strong effect on age-related survival probability, reproductive performance, reproductive costs, and even life-history decisions. Therefore, taking this factor into account in studies of life-history patterns is necessary to obtain reliable results.