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Wildlife in an Anthropogenically-Driven World Graduate Theses, Dissertations, and Problem Reports 2017 Wildlife in an anthropogenically-driven world: how humans have shaped the distribution, genetic composition, and gene expression of North American forest hawks (Genus: Accipiter) Meghan K. Jensen Follow this and additional works at: https://researchrepository.wvu.edu/etd Recommended Citation Jensen, Meghan K., "Wildlife in an anthropogenically-driven world: how humans have shaped the distribution, genetic composition, and gene expression of North American forest hawks (Genus: Accipiter)" (2017). Graduate Theses, Dissertations, and Problem Reports. 5886. https://researchrepository.wvu.edu/etd/5886 This Dissertation is protected by copyright and/or related rights. It has been brought to you by the The Research Repository @ WVU with permission from the rights-holder(s). You are free to use this Dissertation in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you must obtain permission from the rights-holder(s) directly, unless additional rights are indicated by a Creative Commons license in the record and/ or on the work itself. This Dissertation has been accepted for inclusion in WVU Graduate Theses, Dissertations, and Problem Reports collection by an authorized administrator of The Research Repository @ WVU. For more information, please contact [email protected]. Wildlife in an anthropogenically-driven world: how humans have shaped the distribution, genetic composition, and gene expression of North American forest hawks (Genus: Accipiter) Meghan K. Jensen Dissertation submitted to the Davis College of Agriculture, Natural Resources and Design at West Virginia University in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Forest Resources Science Amy B. Welsh, Ph.D., Committee Chair Todd E. Katzner, Ph.D. Dana Huebert Lima, Ph.D. Michael P. Strager, Ph.D. Petra B. Wood, Ph.D. Division of Forestry and Natural Resources Morgantown, West Virginia 2017 Keywords: Accipiter, population genetics, microsatellites, RNA-seq, urbanization, lure owl, maximum entropy Copyright 2017 Meghan K. Jensen Abstract Wildlife in an anthropogenically-driven world: how humans have shaped the distribution, genetic composition, and gene expression of North American forest hawks (Genus: Accipiter) Meghan K. Jensen Humans are causing drastic environmental change on a global scale and this trend strongly influences the evolution of species. It is also becoming clear that tolerances to anthropogenic disturbance varies widely among organisms. Therefore, understanding the mechanisms by which wildlife cope with humans is a pressing question in modern ecology. North America’s forest raptors (Genus: Accipiter) are a useful model for investigating the effects of humans on wildlife species. All three Accipiter species experienced historic demographic declines as a result of anthropogenic activities, yet each species has rebounded differently since these declines. One species in particular is now exploiting urban areas, despite the fact that all of these species were traditionally considered highly dependent on large contiguous forests for survival. This dissertation consists of one introductory chapter, three chapters involving research to improve our current understanding of the impacts of anthropogenic activities on the raptors, and two chapters focused on the development of tools for improving future avian research. The first chapter provides background information on the history of Accipiter hawks in the eastern United States. There are also basic descriptions of some of the novel genetic tools that are becoming increasingly valuable in this and other wildlife studies. In addition, this chapter provides justification for the research and an outline of the project goals. For the second chapter, I developed a spatial habitat model using Maximum Entropy to locate nesting habitat for northern goshawks (Accipiter gentilis) in New York State, a potential stronghold for this species in the east. This species is the most secretive of the Accipiters, considered highly sensitive to human disturbance, and a species of concern in many eastern states. The model predicted nesting habitat with high success (AUC = 0.87), and ground-truthing efforts identified two previously unknown nest territories. In addition, my model provides some evidence of a shift in forest cover preference by goshawks nesting in New York, as coniferous land cover was the most important predictor in the model (67%). Future modeling efforts should include additional and more detailed environmental input layers. In the third chapter, I developed a new mechanical lure owl for trapping nesting raptors that exhibited both realistic head and wing movements. The mechanical owl was tested on six species of raptors and capture rates were similar or better than previously reported with a live lure owl for five of the six species. In addition, average time to capture was eight minutes faster with the mechanical owl as compared to a live owl when trapping northern goshawks (p < 0.01). A mechanical owl costs less and is ethically more appropriate to live lure owls and thus, the use of this type of owl may be warranted in future raptor research. For the fourth chapter, I investigated the genetic consequences of demographic declines in Accipiter hawks. I used microsatellite markers to test for evidence of significant genetic bottlenecks in northern goshawks and Cooper’s hawks (A. cooperii) in the northeastern United States. There was some evidence to suggest a bottleneck in goshawks using the heterozygosity excess method, while the M ratio method suggested a bottleneck in Cooper’s hawks. However, similar to previous studies, I found that the results of bottleneck testing are strongly dependent on mutation model parameters, which are not available for Accipiter hawks and numerous other non-model organisms. Still, by using the results from tests on both species, I was able to ascertain useful information about the relative impact of historic declines. The Cooper’s hawk likely experienced more drastic declines than goshawks, while the goshawk population has likely been small for a relatively long time. Finally, useful baseline information about the contemporary genetic structure of both species was gained from this research. There is no evidence of inbreeding in either population and both species have high levels of gene flow in the northeastern United States. In the fifth chapter, I compared two commercially available buffers for stabilization of RNA from avian blood for downstream RNA processing. Avian blood presents a particular challenge because it contains nucleated red blood cells and most buffers have been developed for blood with non-nucleated red blood cells (e.g. mammalian blood). Each buffer was subjected to a variety of room temperature incubation periods and freeze treatments, to simulate different field sampling scenarios. RNAlater outperformed RNAProtect; RNAlater reliably stabilized RNA regardless of treatment. However, RNA integrity numbers (RIN) varied widely between samples (1.7 – 7.5). RNA from Cooper’s hawk blood stored in RNAlater was sequenced and mapped to the golden eagle (Aquila chrysaetos) genome. Quality assessment suggested that reads were of high quality regardless of RIN value. However, reads that aligned to the reference genome had relatively low sensitivity (<14%) and a wide range of precision (10-61%). These results suggest that RNAlater can be used to obtain usable RNA for avian blood, but future research may be useful for improving stabilization buffers for species with nucleated red blood cells. The sixth and final chapter focuses on the Cooper’s hawk in urban environments. This species has recently been found nesting in high densities in urban centers and an extensive body of research has demonstrated differences between urban and exurban individuals. When colonizing urban areas, organisms can either adapt through heritable genetic mechanisms or acclimate through plastic mechanisms such as gene expression. Previous research suggested that highly mobile species may be more likely to acclimate since they are capable of moving away from potential stressors. Therefore, I used RNA-sequencing to compare gene expression patterns in the blood of urban and exurban adult and fledgling Cooper’s hawks in the Albuquerque, NM area. I also tested all individuals for the presence of an urban-associated parasite (Trichomonas gallinae). I found one and thirteen differentially expressed (DE) transcripts between urban and exurban adults and fledglings, respectively (q < 0.05). For fledglings, more abundant transcripts in the urban environment were mostly associated with nucleotide processing, while those in exurban environments were mostly associated with immune response. The single transcript identified as DE in the adults was more abundant in urban environments and is associated with nucleotide processing, metal ion binding, and platelet production in humans. The greater number of DE transcripts in the fledglings may suggest that changes in gene expression may be especially important for the sedentary offspring of a highly mobile avian urban exploiter. In addition, six fledglings tested positive for Trichomonas spp.; three in each environment. Yet, immune related transcripts were expressed in much higher levels in all exurban individuals, regardless of parasite presence. Future research is warranted to determine if toxin loading
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