DNA methylation patterns are sex and tissue specific in many species, yet many studies useblood samples, due to its accessibility, to establish links between the DNA methylation anddifferent phenotypes. This raises the question of whether DNA methylation in blood samplesreflect the DNA methylation pattern in other tissues that are more relevant to the phenotypebeing studied. In this research, samples were collected from the brain, blood, liver and gonadof 16 house sparrow (Passer domesticus), half of them were female, while the others weremale. Reduced representation bisulfite sequencing (RRBS) was performed to get themethylation profile in each sample. The result showed a tissue specific methylation profile inthe four investigated tissues, a strong and positive correlation between 0.74 – 0.85 was foundbetween tissues, in which a weaker correlation was found between blood and other tissue. Indifferential methylation analysis, most of the differently methylated sites between sexes werefound in gonads, while the fewest was found in blood, and Z chromosome wasoverrepresented place in all four tissues where the majority of the differently methylated sitesbetween sexes were found. Comparison with the house sparrow genome annotation foundabout half of the differentially methylated sites between sexes were within genes and about 20 % of them were in the exon or coding region of a gene. The result suggested that bloodcould be useful in reflecting the general DNA methylation level in other tissues, but it was nota reliable bioindicator for further detailed study in DNA methylation pattern or in geneontology enrichment pathway analysis.

Changes in shrubsteppe passerine bird habitat associations in response to disturbance were investigated at multiple temporal and spatial scales. Spatial measures incorporated the effects of area at different ecological scales (nest site, territory, and landscape) to include ecologically meaningful extents. Temporal measures included seasonal and annual effects, and were designed to detect lagged responses should they occur. Local-to-landscape scale effects of mechanical restoration treatments on local extirpation and abundances of nine species indicated most were insensitive to changes in habitat quality, while abundance models showed only broad declines. Changing the availability of nesting habitat on both the attractiveness and quality of an area at multiple extents confirmed the need for long-term study effects due to lagged responses in expressed preference and changes to nesting habitat quality. Time since treatment affected nest success in two of the four species, yet the changes in habitat quality did not forecast changes in habitat preference as expected. Non-adaptive mismatches seemingly occurred as habitat preferences indicated treatments may create benign-appearing 'sink' habitat for species that remained in the area. The umbrella species concept is misapplied at this scale: each species' response was consistent, but responses varied in scale, timing, and direction among species. Patterns of nest density and nest site descriptions demonstrated population-level movement in response to treatments, suggesting half the focal species moved nest sites to remaining habitat areas. Larger scale responsive movements were observed in the remaining species, both out of and into the nest plot. Descriptions of nesting habitat characteristics for the focal species tested if the selected nesting habitat was consistent between pre- and post-treatment, and determined which habitat characteristics, including distance to disturbance, were related to nest success. Descriptions of nesting habitat characteristics support previous work in terms of structural characteristics. Habitat selection was consistent even when the available habitat was not, implying these species choose sites and are not merely settling randomly. However, selected nesting habitat was not strongly tied to nest success at local scales and nest success was negatively related to landscape qualities that treatments were designed to enhance.

Identifying species occurrence in ecosystems of high conservation concern is especially important in the context of modern landscapes. This study investigated how stand-scale and landscape-scale factors affect priority birds associated with longleaf pine (Pinus palutris) ecosystems. Herein, I compared priority bird occupancy among 12 stand types throughout the historic range of longleaf pine. I found open pine stands positively influenced red-cockaded woodpecker (Picoides borealis) and Bachman’s sparrow (Peucaea aestivalis) occupancy, but were not significantly linked to northern bobwhite (Colinus virginianus) and brown-headed nuthatch (Sitta pusilla) occurrence. Landscape- and stand-scale factors affected red-cockaded woodpecker, Bachman’s sparrow, and brown-headed nuthatch occupancy. Northern bobwhite occupancy was influenced solely by landscape-scale factors. Red-cockaded woodpecker and Bachman’s sparrow were positively influenced by metrics associated with longleaf pine ecosystems suggesting they are effective indicator species. My analysis indicates that using this multi-scale approach is valuable to identifying areas on the landscape of conservation and restoration priority.

No description available.

No description available.

The early environment impacts many aspects of an individual’s developing phenotype. In particular, early environmental conditions are important for shaping the hypothalamic-pituitary-adrenal (HPA) axis, which coordinates an individual’s stress response. These developmental changes are likely mediated by epigenetic modifications, functional changes to the genome that can alter gene expression in response to environmental variation, resulting in significant phenotypic differences (Kundakovic and Champagne 2015; Richards 2006). Determining how early life variation alters epigenetic modifications (such as DNA methylation) of genes throughout the HPA axis, and how these marks change over time, in wild organisms is important for understanding their potential long-term fitness consequences. Here, I examine DNA methylation modifications in the HPA axis in relation to early environmental variation in free-living house sparrows (Passer domesticus). In Chapter 1, I show a relationship between natural variation in the early environment and DNA methylation marks of numerous genes related to HPA axis function, which in turn predict growth trajectories. In Chapter 2, I show that early life stress in particular impacts DNA methylation in genes critical to HPA axis function, but does so differently depending on the life history stage in which stress is encountered. Finally, in Chapter 3, I find that these early life marks have long-term effects past the developmental period, predicting longevity as well as lifetime reproductive output in a sex-specific manner. Overall, my dissertation adds to a growing understanding of the dynamic role of epigenetic modifications in mediating phenotypic responses to the early life environment in wild birds, and demonstrates the potential long-term fitness outcomes of these changes.

A combination of factors including land use change and fire suppression has resulted in the loss of pine savanna habitats across the southeastern U.S., affecting many avian species dependent on these habitats. However, due to the ephemeral nature of the habitat requirements of many pine savanna species (e.g., habitat is only present for a couple of years after a fire), targeted management of such habitats can be challenging. Moreover, the growing numbers of imperiled pine savanna species can make prioritizing management difficult. One potential tool to better inform management of pine savanna species is satellite imagery. Sentinel-2 satellite imagery data provides an instantaneous snapshot of habitat quality at a high resolution and across a large geographic area, which may make it more efficient than traditional, ground-based vegetation surveying. Thus, the objectives of my research were to 1) evaluate the use of remote sensing technology to predict habitat occupancy for pine savanna species, and 2) use satellite imagery-based models to inform multispecies management in a pine savanna habitat. To meet my objectives, I conducted point count surveys and built predictive models for three pine savanna bird species: Bachman's Sparrow (BACS; Peuacea aestivalis), Northern Bobwhite (NOBO; Colinus virginianus), and Red-Cockaded Woodpecker (RCW; Dryobates borealis) across Georgia. I assessed the performance of satellite imagery in predicting habitat occupancy of these pine savanna species and its potential for multispecies management. I found that models created using satellite imagery habitat metric data performed well at predicting the occupancy of all three species as measured by the Area Under the Receiver Operating Characteristic Curve: BACS=0.84, NOBO=0.87, RCW=0.76 (with values between 0.7-1 defined as acceptable or good predictive capacity). For BACS and NOBO, I was able to compare these satellite imagery models to field-based models, and satellite models performed better than those using traditional vegetation survey data (BACS=0.80, NOBO=0.79). Moreover, I found that satellite imagery data provided useful insights into the potential for multispecies management within the pine savanna habitats of Georgia. Finally, I found differences in the habitat selected by BACS, NOBO, and RCW, and that BACS may exhibit spatial variations in habitat use. The results of this study have significant implications for the conservation of pine savanna species, demonstrating that satellite imagery can allow users to build reliable occupancy models and inform multispecies management without intensive vegetation surveying. / Master of Science / Land-use changes have resulted in the disruption of natural disturbances such as fires, resulting in the loss of pine savanna habitats throughout the southeastern U.S. Although many of the species that occupy these habitats are experiencing rapid population declines, habitat for pine savanna species can be challenging to manage. Without reoccurring fire, pine savanna habitat can become unsuitable for obligate species within short periods of time, forcing these species to disperse to newly disturbed habitats. The transient nature of the preferred habitat of pine savanna species makes targeting management for these species difficult, as it can be challenging to locate exactly where occupied habitats exist. Furthermore, as the number of pine savanna species that are declining is large, prioritizing management of these species can be difficult especially given limited conservation funding. One potential tool to better inform the management of pine savanna species is satellite imagery. Satellite imagery can capture habitat information across broad areas, at fine resolutions, and at frequent intervals, potentially making satellite imagery more efficient than conducting field vegetation surveys on the ground for gaining information on habitat suitability. Thus, the objectives of my research were to 1) determine if satellite imagery can effectively predict the habitats occupied by pine savanna species (habitat occupancy), and 2) use satellite imagery-based models to inform the simultaneous management of multiple species (multispecies management) in a pine savanna habitat. To meet these objectives, I conducted surveys and built predictive models for three pine savanna bird species: Bachman's sparrow (BACS; Peuacea aestivalis), Northern Bobwhite (NOBO; Colinus virginianus), and Red-Cockaded Woodpecker (RCW; Dryobates borealis) in Georgia. I found models informed by satellite imagery performed well at predicting habitats occupied for all three species. Furthermore, models developed using satellite imagery performed better at predicting the habitats occupied by pine savanna species than models developed using on the ground vegetation surveys. I also found that satellite imagery data provided useful insights into strategies to manage pine savanna species simultaneously. I found evidence that BACS, NOBO, and RCW may have contrasting habitat needs and that BACS may use habitat differently between sites in Georgia. The results of this study demonstrate that satellite imagery can be used to predict the habitats occupied by pine savanna species and inform multispecies management without surveying vegetation on the ground, which is a more efficient use of time and funding.

No description available.

No description available.

Aim of this study was to assess distribution and abundance of common synanthropic species of birds (House sparrow, Tree sparrow, Eurasian collared dove and Blackbird) in area of the city České Budějovice in the Czech Republic in autumn and winter. Habitat preferences of these species were analysed. Study also determined influence of the certain characteristics of urban vegetation on their occupation by both species of sparrows.