abstract: The southwestern willow flycatcher (Empidonax traillii extimus) is listed as an endangered species throughout its range in the southwestern United States. Little is known about its sub-population spatial structure and how this impacts its population viability. In conjunction with being listed as endangered, a recovery plan was produced by the US Fish and Wildlife Service, with recovery units (sub-populations) roughly based on major river drainages. In the interest of examining this configuration of sub-populations and their impact on the measured population viability, I applied a multivariate auto-regressive state-space model to a spatially extensive time series of abundance data for the southwestern willow flycatcher over the period spanning 1995-2010 estimating critical growth parameters, correlation in environmental stochasticity or "synchronicity" between sub-populations (recovery units) and extinction risk of the sub-populations and the whole. The model estimates two parameters, the mean and variance of annual growth rate. Of the models I tested, I found the strongest support for a population model in which three of the recovery units were grouped (the Lower Colorado, Gila Basin, and Rio Grande recovery units) while keeping all others separate. This configuration has 6.6 times more support for the observed data than a configuration assigning each recovery unit to a separate sub-population, which is how they are circumscribed in the recovery plan. Given the best model, the mean growth rate is -0.0234 (CI95 -0.0939, 0.0412) with a variance of 0.0597 (CI95 0.0115, 0.1134). This growth rate is not significantly different from zero and this is reflected in the low potential for quasi-extinction. The cumulative probability of the population experiencing at least an 80% decline from current levels within 15 years for some sub-populations were much higher (range: 0.129-0.396 for an 80% decline). These results suggest that the rangewide population has a low risk of extinction in the next 15 years and that the formal recovery units specified by the original recovery plan do not correspond to proper sub-population units as defined by population synchrony. / Dissertation/Thesis / M.S. Biology 2012

Parental care can be important especially in passerine birds and can depend on environment, food availability and behaviour. A behaviour that can affect the food supply for the offspring is neophobia, the fear of novel objects. The more fear the bird exhibits the less it visits the nest with food. In my study I aimed to examine neophobia and how it differed based on sex and if offspring number and weight influenced the behaviour. Video recordings of collared flycatchers nest boxes were used to see how the behaviour differed by placing a novel object on the nest box. The behaviours tested were duration of perching, hovering and visit including latency and frequency of visit. The results showed that there was a significant difference between the sexes in duration, latency, and frequency of visit but also duration of perching before and after placing a novel object on the nest box. In addition, my results showed that nestling weight significantly influenced frequency of visit and nestling number influenced duration of visit. The study shows that the collared flycatchers do express neophobia differently based on the sex and the nestling’s weight and number. Future studies could investigate if neophobia is a plastic behaviour and the effects of prolonged exposure to novel objects whichcould change the offspring’s survival chances or even the nestling’s behaviour.

No description available.

Climate change is affecting the distribution of species, sometimes making previously separated species come into secondary contact. For closely related species, this often leads to competition and sometimes also hybridization, which can have negative effects on genetic bio? diversity. Collared flycatcher (Ficedula albicollis) and pied flycatcher (Ficedula hypoleuca) are two closely related species that hybridize where they meet on the Swedish islands Gotland and Öland. Studies from Gotland and the north of Öland have shown that the pied flycatcher is outcompeted and displaced from favourable, high-quality habitat by the collared flycatcher, leading to a decrease in the number of pied flycatchers in deciduous forest. However, this has not been shown for the ecologically important and one of the largest deciduous forests in Sweden, the Mittland forest located in central Öland. Here I use census data collected during two periods separated by 37 years from the Mittland forest to investigate habitat choice and competition between the two species. Although the number of collared flycatcher has greatly increased in the area, I show that the collared flycatcher has not outcompeted the pied flycatcher from favourable habitat. I also show that pied flycatcher does not have a preference for coniferous forest. Lastly, I show that the two species have a near complete overlap of habitat niches. These results indicate that they are in direct competition over the favourable habitat, that there is no equilibrium between the species and the collared flycatcher might still be expanding in the Mittland forest. Allowing more time to pass and further research will show if the pied flycatcher will be displaced from the high-quality habitats in this area or not.

Mining is a widespread industrial activity that in many cases, via mining wastes, leads to altered concentrations of metals in close vicinity to the mining activities. Metals in mining waste can have high toxicity and may persist in environments for long time periods. The presence of metals, such as lead (Pb), is known to contaminate and cause damage to nearby organisms and ecosystems. Birds are at risk of metal contamination and, since they are predators high up in the food chain, may face accumulation of metal in tissue over time, via consumption of contaminated prey. Small passerine species, such as the pied flycatcher (Ficedula hypoleuca), are suitable for studying metal contamination as they are ubiqutious, and high up in the food chain. Pied flycatchers feed exclusively on invertebrates, making the abundance, quality, and potential contamination of invertebrates interesting to study with regard to the health of the birds. Studies have shown that hemoglobin (Hb) levels in young pied flycatchers are reduced by high background levels of Pb.  This may be linked to prey availability and quality, as invertebrates are known to alter their composition, and contain higher Pb concentrations in Pb contaminated areas. Here, I investigated how invertebrate abundance and community composition, and pied flycatcher Hb concentrations (i.e. health), in reference and Pb contaminated areas, were related to each other. Invertebrate traps were set and sampled twice during the summer of 2018 to provide invertebrate data to the study. Bird Hb levels was acquired by taking blood samples from nearly fledged chicks in birdhouses placed in the different areas. I found a potential trend towards higher Hb levels in reference areas (p=0.110), suggesting that bird health is reduced by the presence of Pb, but this could not be explained by differences in invertebrate community composition or abundance (p>0.05). Hence, based on this study, high Pb concentrations in the soil does not directly, or indirectly via potential impacts on the prey community composition, influence the health of pied flycatchers.

Life-history is the study of all the different stages of life that affect reproductive success and survival between the birth and death of an organism. The reproductive output of an organism is constrained by many things including time, resource, disease agents and environmental conditions. In addition, lineage-specific traits and the limitations of the physiological systems can limit how an organism responds to ecological processes, and thus constrains the variation of life histories represented in nature. Central to the theory of life history are the trade-offs that organisms make during their lifetime to maximise their reproductive potential. In this thesis, I focus on the effect of haemosporidian blood parasites on host life history, in relation to the glucocorticoid response and environmental conditions. The host study species is a population of collared flycatchers (Ficedula albicollis), a species that provides bi-parental care, located in the south of Gotland. We show that nestling condition predicts parasite infection and that parasite-mediated selection can start early on in the birds’ life. We also found a link between Lower levels of glucocorticoids and parasite infection, which might indicate a trade-off between immunity and reproductive effort. Adult birds’ upregulated glucocorticoids in response to an increase in reproductive effort and a predictable change in energy demand during reproduction. I also show that glucocorticoids respond to changing environmental conditions. These results together accentuate the importance of the plasticity of the glucocorticoid response to reproductive success. Moreover, higher levels of hormone during reproduction predicted survival to the next breeding season. In nestlings, glucocorticoid levels increased as a consequence of parent infection status and an increase in reproductive effort. Overall, our results indicate that the glucocorticoid response is context dependent. Finally, female collared flycatchers might pay a fitness cost as a consequence of parasite infection, but can still reproduce successfully suggesting that they can tolerate the parasite. To further our understanding of costs related to parasite infection, we must understand better the mechanisms that enable the host to tolerate infection. This study indicates that glucocorticoids provide a useful tool to detect how wild birds respond to predictable and unpredictable challenges.

The role of divergent climate adaptation in speciation has received surprisingly little scientific attention. My dissertation research focused on how resting metabolic rate (RMR) relates to the build up of prezygotic and postzygotic isolation in a natural Ficedula flycatcher hybrid zone. RMR is the amount of energy an organism needs to run its internal organs. Since RMR is related to life history traits and thermoregulation in other systems, it is likely to affect speciation processes at secondary contact. I found that adult collared flycatchers displace pied flycatchers into increasingly poor habitats (Paper I). Pied nestlings exhibit lower RMR in poor environments (Paper II), which may promote regional coexistence and habitat isolation by making it possible for pied flycatchers to escape competition from collared flycatchers and reduce the risk of hybridization by breeding in the poorer habitats. Further, I found that while collared flycatcher nestling RMR was not environmentally-dependent (Paper II, Paper III), those collared flycatcher nestlings that had a lower RMR in poor environments tended to have higher condition (Paper III). Further, RMR was genetically linked to a sexual ornament in collared males that has previously been shown to be beneficial in poor environments. Lastly, I found that by seven days old, nestlings increase their metabolic rate when listening to song, indicating that they are listening, and by 9 days they can discriminate between songs (Paper IV). Taken together, RMR could affect pre-zygotic isolation via correlations with life history strategies, song and sexual ornaments. RMR is also related to post zygotic isolation in Ficedula flycatchers. I found that flycatcher hybrids tended to have a higher RMR than the parental species (Paper V), and that there were many differentially expressed genes in energetically expensive organs in hybrids that were related to metabolic function (Paper VI). Thus, metabolic dysfunction, possibly caused by genetic incompatibilities, in Ficedula flycatcher hybrids could be a factor leading to infertility and postzygotic isolation between the parental species. Overall, I find that RMR could be a general physiological trait that affects both pre- and postzygotic isolation in hybridizing species at secondary contact, and ought to be more thoroughly considered in speciation research.

Between closely related species there are genomic regions with a higher level of differentiation compared to the rest of the genome. For a time it was believed that these regions harbored loci important for speciation but it has now been shown that these patterns can arise from other mechanisms, like recombination. The aim of this project was to estimate the recombination landscape for red-breasted flycatcher (Ficedula parva) and taiga flycatcher (F. albicilla) using patterns of linkage disequilibrium. For the analysis, 15 red-breasted and 65 taiga individuals were used. Scaffolds on autosomes were phased using fastPHASE and the population recombination rate was estimated using LDhelmet. To investigate the accuracy of the phasing, two re-phasings were done for one scaffold. The correlation between the rephases were weak on the fine-scale, and strong between means in 200 kb windows. 2,176 recombination hotspots were detected in red-breasted flycatcher and 2,187 in taiga flycatcher. Of those 175 hotspots were shared, more than what was expected by chance if the species were completely independent (31 hotspots). Both species showed a small increase in the rate at hotspots unique to the other species. The low number of shared hotspots might indicate that the recombination landscape is less conserved between red-breasted and taiga flycatchers than found between collared and pied flycatcher. However, the investigation of the phasing step indicate that the fine-scale estimation, on which hotspots are found, might not be reliable. For future analysis, it is important to use high-quality data and carefully chose methods.

No description available.

The southwestern willow flycatcher (Empidonax traillii extimus) is a federally-endangered neotropical migrant that breeds in the southwestern United States. The population of southwestern willow flycatchers on the South Fork Kern River in California was once thought to be one of the largest E. t. extimus populations. It declined from 38 pairs in 1997 to 12 pairs in 2000. My goals were to examine E. t. extimus habitat selection on the South Fork Kern River, to determine how habitat characteristics and food availability affect E. t. extimus demographics, and to make inferences about possible reasons for the decline. My first objective was to determine southwestern willow flycatcher habitat selection on the Kern on two spatial scales: territory and nest site. Southwestern willow flycathers selected habitat characteristics that appeared to be related to food availability, foraging ecology, or nest cover. Territories within the riparian forest were closer to water and the edge of forest and had fewer cottonwoods than unused areas. Nest sites had denser and more uniform canopy cover and a denser understory than randomly selected sites within territories. My second objective was to determine a relationship between measures of fitness (reproductive success and occupancy frequency) and territory categories (occupied 2 years, occupied 1 year, abandoned). Also, I examined the relationship between indirect measures of fitness, habitat characteristics and food availability, and territory categories. Compared to other territories, territories occupied more frequently had higher reproductive success, higher insect abundance indices, greater habitat heterogeneity, denser understories, and more stems 30-50 cm dbh. All of the habitat characteristics important in habitat selection and habitat quality on the South Fork Kern River were similar to other recent studies on E. t. extimus habitat selection and reproductive success. On the Kern, both suitable and optimal habitat appear to be limited and this limitation appears to be contributing to the population decline. Habitat quality may affect E. t. extimus demographics, particularly when the number of high quality territories in a population is limited as in site-dependent population regulation. Since the amount of suitable habitat is likely to continue to decline across the range of southwestern willow flycatchers, managers should consider manipulating habitat for high quality E. t. extimus habitat to aid conservation of this endangered species. / Master of Science