Abstrakt: Jag har undersökt hur älvreglering påverkar mängden knott (Tvåvingar: Simuliidae) längs flera norrlandsälvar och vilka konsekvenser denna påverkan får för den landlevande fågelfaunan. Studien visar att utbyggnad av älvar har en negativ effekt på mängden knott. Det fanns sju gånger högre tätheter av knott längs "orörda älvar" jämfört med utbyggda älvar. Skillnaden i antal knott mellan älvtyperna var mycket större för knotthanar än för knotthonor, vilket förklaras av att honorna är rörligare eftersom de flyger och letar efter blod. Knott lever av blod från ett flertal däggdjur och fåglar och visar en stor variation i värd-specificitet mellan olika arter. Jag fann en högre frekvens av haemosporida blod parasiter (Leucocytozoon) i fåglar längs "orörda" Vindelälven jämfört med den reglerade Umeälven. Detta mönster stämmer väl överens med tätheten fågelparasiterande knott som är lägre längs Umeälven. Knott attackerade främst värdar som var stora och vanliga. Fågelsamhällets sammansättning skiljde sig mellan orörda och utbyggda älvdalar. Tätheten av icke insektsätande fåglar tenderade att minska, efter häcksäsongen, längs orörda älvar medan den ökade längs utbyggda älvar. Den insektsätande fågeln svartvit flugsnappare (Ficedula hypoleuca Pallas) uppvisade större häckningsframgång längs orörda älvar jämfört med utbyggda älvar. Detta är förmodligen en effekt av den större mängden insekter som finns längs orörda älvar. / The effects of river regulation on blackfly (Diptera: Simuliidae) abundances and consequences for the avifauna in terrestrial environments were studied along multiple rivers in northern Sweden. I found that impoundment of rivers has detrimental effect to blackfly abundances. The densities of large-river breeding blackfly species were several-fold higher along free-flowing than along regulated rivers. The difference in abundances was much larger in males than blood-seeking females. Blackflies attacked a variety of mammalian and avian hosts and showed different levels of host-specificity between species. I found higher prevalence of haemosporidian blood parasites (Leucocytozoon) in birds along the free-flowing Vindel River in comparison to the regulated Ume River, where the lower densities of ornithophilic blackflies were reduced. Blood-seeking blackflies predominantly attacked large and/abundant hosts. Assemblages of birds differed between valleys of regulated and free-flowing rivers. Densities of noninsectivorous birds tended to decrease along free-flowing rivers in the post-breeding season, but increased along regulated rivers at the same time. Insectivorous European pied flycatcher (Ficedula hypoleuca Pallas) showed greater fledging success along free-flowing than regulated rivers, which probably reflects the higher insect abundances found along freeflowing rivers.

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.

abstract: The Southwestern Willow Flycatcher (Empidonax traillii extimus) has been studied for over two decades and listed as endangered for most of that time. Though the flycatcher has been granted protected status since 1995, critical habitat designation for the flycatcher has not shared the same history. Critical habitat designation is essential for achieving the long-term goals defined in the flycatcher recovery plan where emphasis is on both the protection of this species and "the habitats supporting these flycatchers [that] must be protected from threats and loss" (U.S. Fish and Wildlife Service 2002). I used a long-term data set of habitat characteristics collected at three study areas along the Lower Colorado River to develop a method for quantifying habitat quality for flycatcher. The data set contained flycatcher nest observations (use) and habitat availability (random location) from 2003-2010 that I statistically analyzed for flycatcher selection preferences. Using both Pearson's Chi-square test and SPSS Principal Component Analysis (PCA) I determined that flycatchers were selecting 30 habitat traits significantly different among an initial list of 127 habitat characteristics. Using PCA, I calculated a weighted value of influence for each significant trait per study area and used those values to develop a habitat classification system to build predictive models for flycatcher habitat quality. I used ArcGIS® Model Builder to develop three habitat suitability models for each of the habitat types occurring in western riparian systems, native, mixed exotic and exotic dominated that are frequented by breeding flycatchers. I designed a fourth model, Topock Marsh, to test model accuracy on habitat quality for flycatchers using reserved accuracy assessment points of previous nest locations. The results of the fourth model accurately predicted a decline in habitat at Topock Marsh that was confirmed by SWCA survey reports released in 2011 and 2012 documenting a significant decline in flycatcher productivity in the Topock Marsh study area. / Dissertation/Thesis / M.S. Applied Biological Sciences 2013

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.

La dispersion est un trait d'histoire de vie clé pour les processus écologiques et évolutifs dans les populations naturelles. Les dernières recherches se sont notamment focalisées sur les corrélations entre traits comportementaux et la dispersion, ceci afin de mettre en évidence des syndromes comportementaux de dispersion, tout en démontrant la base génétique de la dispersion. Les dispersants ne seraient donc pas une part aléatoire d'une population, mais des individus montrant des stratégies particulières qui augmenteraient leur chances de succès. Cette thèse s'est orientée vers trois objectifs de recherche majeurs. Le premier est la mise en évidence d'une base génétique de la probabilité de disperser dans une population fragmentée de gobe-mouches à collier Ficedula albicollis. Les résultats nous ont montré, au-delà de l'estimation de la base génétique de la dispersion, une distribution spatiale non aléatoire de l'apparentement dans cette population, qui pourrait être dû à des effets génétiques sur les règles de décision de choix de l'habitat. Le deuxième s'intéresse à la corrélation phénotypique et génétique entre le comportement de dispersion natale et le comportement de défense du nid, chez le martinet alpin Tachymarpis melba. Nous avons montré que la dispersion natale et le comportement de défense du nid sont négativement corrélés au niveau phénotypique mais aussi génétique dans ces populations. Enfin, le troisième nous à conduit à tester l'existence de syndromes comportementaux de dispersion, c'est-à-dire si les dispersants présentent un profil comportemental particulier, leur permettant en particulier de coloniser de nouveaux sites, chez le gobe-mouche à collier / Dispersal is a key like history trait for ecological and evolutionary processes in wild population. The last researching particularly focused on the correlation between behavioural trait and dispersal, in order to emphasize the existence of behavioural syndromes of dispersal, and on the estimation of the genetic basis of the dispersal behaviour. Dispersant individuals could not be a random part of the population, but individuals showing particular strategies, that help them to succeed in their dispersal attempt. This thesis has three main aims of research. The first is to show a genetic basis of the dispersal propensity in a fragmented population of collared flycatchers (Ficedulla albicollis). We shown not only the genetic bases of the dispersal, but also a non-random spatial distribution of relationship between individuals in this population, that might be due to genetic effects on the decision rules of habitat choice in this population. The second aim concerns phenotypic and genetic correlation between the natal dispersal and a behavioural trait, the nest-defense behaviour, in the alpin swift (Tachymarpis melba). We shown that natal dispersal and nest-defense behaviour are negatively correlated at a phenotypic level, but also at a genetic level in theses populations. Finally, the third aim attempt to test the existence of behavioural syndrome of dispersal, that is if dispersant individuals have a particular behavioural profile, which enable them to colonize new sites, in the collared flycatcher

La dispersion est définie comme le mouvement d'un individu entre le site de naissance et le premier site de reproduction ou entre deux sites de reproduction. La dispersion se traduit par des échanges d'individus et des flux de gènes entre les populations et est donc reconnue comme un trait d'histoire de vie clé de part son rôle déterminant sur de nombreux processus écologiques et évolutifs comme la dynamique ou la génétique des population, la répartition spatiale des espèces ou encore la capacité des espèces à faire face aux changements brutaux induits par les activités humaines. Pourtant les conséquences de la dispersion en terme de valeur sélective individuelle restent mal connues malgré leur importance dans l'évolution de la dispersion. Le but de cette thèse est d'identifier plus précisément les conséquences de la dispersion en terme de valeur sélective individuelle en utilisant à la fois des approches corrélative et expérimentale dans une population sauvage de passereaux migrateurs, le gobe mouche à collier (Ficedula albicollis). Grâce à des données à long terme comprenant plus de 20 ans de suivi, des différences entre les individus dispersants et philopatriques ont pu être mises en évidence à la fois à l'échelle de la vie des individus et à l'échelle annuelle, celle de l'événement de reproduction. Les résultats mettent en évidence des effets de la dispersion dépendant à la fois des conditions et du phénotype des individus et soulignent donc le fait que la balance entre les coûts et les bénéfices est le résultat d'interactions subtiles entre l'environnement et les caractéristiques de l'individu. D'autre part, l'expérience de dispersion forcée a permis de démontrer clairement l'existence de coûts liés à l'établissement dans un environnement non familier que seuls certains individus sont capables de surmonter. Enfin, l'absence de différence dans les décisions majeures de reproduction une fois les individus établis, suggère que la dispersion doit majoritairement être adaptative, une fois les coûts de l'installation surmontés / Dispersal is commonly defined as the movement of an individual from its natal or previous breeding site to a new breeding site. Because dispersal involves movements of individuals and genes among populations, it is widely recognized as a key life history trait with strong effects on many ecological and evolutionary processes, such as population dynamics and genetics but also species spatial distribution or response to brutal environmental variations induced by human activities. Yet, the consequences of dispersal in terms of individual fitness remain poorly understood despite their crucial importance in the understanding of the evolution of dispersal. The aim of this PhD is to get better insights in the fitness consequences of dispersal using both correlative and experimental approaches at different scales, i.e. annual and lifetime scales, in a wild patchy population of migratory passerine bird, the collared flycatcher (Ficedula albicollis). Using a long term data set encompasses more than 20 years of data, differences between dispersing and philopatric individuals were showed both at a lifetime and annual scale. The results highlighted strong phenotypic- and condition-dependent effects of dispersal and underline that the balance between the costs and benefits of dispersal is likely to be the result of subtle interactions between environmental factors and individuals’ phenotype. Moreover, the experiment of forced dispersal demonstrated that dispersal might entail costs linked with settlement in a new habitat, which only some individuals may overcome. Nevertheless, the absence of difference in major fitness related decisions after settlement suggests that dispersal is mostly adaptive for individuals overcome such costs

No description available.

Dispersal is a key life history trait for ecological and evolutionary processes in wild populations. The latest research has particularly focused on the correlation between behavioural traits and dispersal, in order to emphasize the existence of behavioural syndromes of dispersal, and on the estimation of the genetic basis of the dispersal behaviour. Dispersing individuals are not a random part of the population, but are individuals showing particular strategies, that help them to succeed in their dispersal attempt. This thesis has three main aims of research. The first is to show a genetic basis of the dispersal propensity in a fragmented population of collared flycatchers (Ficedulla albicollis). We show, not only, the genetic bases of the dispersal, but also a non-random spatial distribution of relationship between individuals in this population, that might be due to genetic effects on the decision rules of habitat choice in this population. The second aim concerns phenotypic and a genetic correlation between the natal dispersal and a behavioural trait, the nest-defense behaviour, in the alpin swift (Tachymarptis melba). We showed that natal dispersal and nest-defense behaviour were negatively correlated at a phenotypic level, but also at a genetic level in these populations. Finally, the third aim attempts to test the existence of a behavioural syndrome of dispersal, that is if dispersing individuals have a particular behavioural profile, which enable them to colonize new sites, in the collared flycatcher. / <p>The exmination will be videolinked to seminar room 1003 Evolutionary Biology Centre, EBC, Uppsala University.</p>

<p>Studies of hybrid zones offer important insights into the process of speciation. Much of the knowledge to be gained is dependent on an accurate estimation of the strength of pre- and post-zygotic isolation between hybridizing taxa. My results demonstrate that hybridization can variously affect different components of fitness. In Ficedula flycatchers, late-breeding females may directly benefit from pairing with a heterospecific male by gaining access to superior territories. The hybrid offspring possess an immune system that is as equally well functioning as in the parental species (the collared, F. albicollis, and pied flycatcher, F. hypoleuca). However, I found that a severe reduction in fertility persists for at least three generations after the actual hybridization event. Combining all information about the reproductive success of hybridizing individuals and their descendents revealed that postzygotic isolation between flycatchers is very strong; hybridizing individuals leave almost no descendents. This thesis presents one of few comprehensive summaries of the selection for/against assortative mating in a natural hybrid zone. These findings suggest a central role for intrinsic postzygotic isolation as a reproductive barrier separating newly evolved bird species, and contrast previous suggestions that postmating isolation is the slowest of the reproductive barriers to evolve in birds.</p><p>Despite this strong selection against hybridization, pre-mating isolation is incomplete. Hybridization often results from females lacking conspecific partners, but appears to be also caused by errors in species recognition. Much of this error probably reflects the short period of time that pied flycatchers on Gotland and Öland have been in sympatry. Compared to collared flycatchers, pied flycatchers are poorer able to discriminate between conspecific and heterospecific song, and male pied flycatchers more often falsely signal their own identity through heterospecific song copying. However, despite colonising the study site from other sympatric populations and having very little gene flow from allopatry, collared flycatchers also possess traits (e.g. delayed plumage maturation) that increase their hybridization risk. Once pre-mating isolation is strong, the rarity of hybridization probably inhibits further selection against traits promoting interspecific mating, especially when such traits may be beneficial in other contexts. This thesis highlights complex interactions between factors affecting hybridization rate that would not be detected if such a study were not field-based. Furthermore, it showcases likely examples in nature of a number of theoretical objections to the evolution of pre-mating barriers between populations living in sympatry.</p>

Studies of hybrid zones offer important insights into the process of speciation. Much of the knowledge to be gained is dependent on an accurate estimation of the strength of pre- and post-zygotic isolation between hybridizing taxa. My results demonstrate that hybridization can variously affect different components of fitness. In Ficedula flycatchers, late-breeding females may directly benefit from pairing with a heterospecific male by gaining access to superior territories. The hybrid offspring possess an immune system that is as equally well functioning as in the parental species (the collared, F. albicollis, and pied flycatcher, F. hypoleuca). However, I found that a severe reduction in fertility persists for at least three generations after the actual hybridization event. Combining all information about the reproductive success of hybridizing individuals and their descendents revealed that postzygotic isolation between flycatchers is very strong; hybridizing individuals leave almost no descendents. This thesis presents one of few comprehensive summaries of the selection for/against assortative mating in a natural hybrid zone. These findings suggest a central role for intrinsic postzygotic isolation as a reproductive barrier separating newly evolved bird species, and contrast previous suggestions that postmating isolation is the slowest of the reproductive barriers to evolve in birds. Despite this strong selection against hybridization, pre-mating isolation is incomplete. Hybridization often results from females lacking conspecific partners, but appears to be also caused by errors in species recognition. Much of this error probably reflects the short period of time that pied flycatchers on Gotland and Öland have been in sympatry. Compared to collared flycatchers, pied flycatchers are poorer able to discriminate between conspecific and heterospecific song, and male pied flycatchers more often falsely signal their own identity through heterospecific song copying. However, despite colonising the study site from other sympatric populations and having very little gene flow from allopatry, collared flycatchers also possess traits (e.g. delayed plumage maturation) that increase their hybridization risk. Once pre-mating isolation is strong, the rarity of hybridization probably inhibits further selection against traits promoting interspecific mating, especially when such traits may be beneficial in other contexts. This thesis highlights complex interactions between factors affecting hybridization rate that would not be detected if such a study were not field-based. Furthermore, it showcases likely examples in nature of a number of theoretical objections to the evolution of pre-mating barriers between populations living in sympatry.