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Browsing by Author "Funk, W. Chris, committee member"

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    A noninvasive method using auditory predator calls and hair snares to detect and genetically sample cougars (Puma concolor)
    (Colorado State University. Libraries, 2016) Yeager, Kirstie L., author; Kendall, William L., advisor; Alldredge, Mathew W., committee member; Crooks, Kevin R., committee member; Funk, W. Chris, committee member
    A noninvasive method that will sample all individuals in a population over multiple occasions is a useful tool in assessing population demographics with little disturbance to the target animals; however, finding such a method for large carnivores, such as cougars, is challenging due to their elusive nature and large home-range sizes. Current methods to sample cougars usually involve a physical capture component, but obtaining reliable estimates can be difficult and cost prohibitive when using capture as the sole sampling method. Because cougars leave sign, and exhibit behaviors like territoriality and curiosity, a noninvasive-genetic-sampling (NGS) method may be a plausible alternative. Hair contains DNA, which can be genetically analyzed to yield the individual identification necessary for population assessments and can be obtained without handling the animal. I tested NGS techniques using attractants, specifically scent lures and auditory calls, and hair snares to sample cougars at lure sites on the Front Range, Colorado during February – April, 2012 and November, 2012 – April, 2013. First, I established 16 – 20 sites over four ≈ 30-day sampling periods. At sites with auditory calls, photographs documented 40 visits by ≥ 13 individual cougars, and I obtained 14 hair samples. Only two hair samples were collected using scented scratch pads and no samples were acquired via a novel hair snare. Because my initial results indicated calls were more effective attractants than scents, I narrowed my focus to the cubby hair-snare design and increased my effort by establishing 148 lure sites over three or four sampling periods in two study areas: the Front Range (FR; 1,270 km2) and the Uncompahgre Plateau (UP; 540 km2). Each site was active an average of 28.5 days (4,214 sampling nights). On the FR, I observed 98 detections by 13 independent marked cougars, two sibling groups, and ≥ 16 unique unmarked animals. On the UP, I documented 18 detections by seven independent marked cougars. Collectively, 14 of the 20 marked cougars detected were observed multiple times. I used the GPS location data of 27 previously marked cougars to determine availability and estimate detection probabilities. The probability of detecting via camera an independent marked cougar at least once during the study with no assumption of closure (superpopulation) was 0.65 ± 0.11 (FR) and 0.64 ± 0.15 (UP). I collected 59 hair samples. Thirty-two were genotyped at ≥ 8 loci identifying 26 unique cougars. I conclude that auditory calls and hair snares may be an effective way to collect the various biological data that are needed to inform management decisions.
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    A tail of two fish: an integrative approach to understand how trade-offs and salinity influence two closely related euryhaline fish
    (Colorado State University. Libraries, 2021) Mauro, Alexander Anthony, author; Ghalambor, Cameron K., advisor; Hoke, Kim L., committee member; Funk, W. Chris, committee member; Hufbauer, Ruth A., committee member
    It is well understood that adaptive evolution can occur rapidly in nature and that anthropogenic climate change is causing - and will continue to cause - mass extinctions of the planet's biodiversity. These facts represent somewhat of a paradox: rapid adaptation can and does occur in nature, yet many populations are failing to adapt to environmental change. This dissertation lies at the interface of this paradox as it investigates the adaptive process. However, instead of investigating a case of adaptive success, it explores the mechanisms and circumstances underlying a case when evolution appears to be constrained. More specifically, it investigates how a trade-off between salinity tolerance and competitive ability contributes to an evolutionary range limit in Poecilia reticulata. It also investigates how salinity influences genetic variation in a more widespread fish, Poecilia picta.In chapter 1, a conceptual framework of trade-offs as evolutionary constraints that utilizes network/pathway thinking is presented. In chapter 2, it is experimentally shown that P. reticulata experiences a trade-off between salinity tolerance and competition with P. picta, that the trade-off is genetically based, and that it is indeed range limiting. In chapter 3 why this trade-off occurs at the physiological network level is investigated. It is shown that a negative relationship between salinity tolerance and competition arises because salinity exposure in P. reticulata results in the activation of hormonally mediated pathways in the brain associated with ion regulation and a decrease in aggression. Chapter 4 shifts the focus from P. reticulata to P. picta. to investigate how salinity influences the distribution of both neutral and adaptive genetic variation in a species that is found both freshwater and brackish water unlike P. reticulata. It is found that salinity can drive differentiation at putatively adaptive loci despite high levels of population connectivity in populations of P. picta.
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    Advancing conservation genomics of migratory species toward a full annual cycle approach
    (Colorado State University. Libraries, 2023) DeSaix, Matthew G., author; Ruegg, Kristen C., advisor; Funk, W. Chris, committee member; Koons, David N., committee member; Marra, Peter M., committee member
    Global biodiversity loss is one of the foremost concerns of conservation efforts in the 21st century. The maintenance of genetic diversity within species is a critical factor in a species' persistence and adaptive potential in the face of changing environmental conditions. Migratory species make up more than 12% of the global vertebrate biodiversity and pose distinct challenges to conservation efforts due to inhabiting different geographical regions at different times of the year. The field of conservation genomics provides a valuable toolkit to addressing and understanding global biodiversity loss but requires additional methodological developments to better address the conservation challenges posed by migratory species. In my dissertation, I demonstrate advancements in conservation genomics aimed toward better understanding migratory species. In my first study, I addressed the question of ecological and genomic vulnerability to climate change in the Brown-capped Rosy-Finch (Leucosticte australis), an elevational migratory songbird of conservation concern. Second, I addressed a methodological gap in population genomics and developed statistical genetics models for using genotype likelihood data from low-coverage whole genome sequencing data to implement population assignment. In my last study, I demonstrate the utility of low-coverage whole genome sequencing for population assignment with detailing migratory connectivity in the American Redstart (Setophaga ruticilla). Altogether, my doctoral research demonstrates how genomic tools can help unravel the complexities of migratory species conservation. Furthermore, the species-specific results are tied to knowledge gaps identified by wildlife managers and provide valuable information tied to conservation and management applications.
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    Body size, first year breeding, and extra-pair paternity in an island endemic, the Island Scrub-Jay
    (Colorado State University. Libraries, 2014) Desrosiers, Michelle A., author; Angeloni, Lisa M., advisor; Ghalambor, Cameron K., advisor; Funk, W. Chris, committee member; Sillett, T. Scott, committee member; Crooks, Kevin R., committee member
    Body size is a fundamental characteristic that shapes all aspects of an organism's biology. The advantages of large body size may include increased probability of territory acquisition, a critical component of fitness for species that require a territory to breed. Large body size, an indicator of quality, may also be advantageous to males in acquiring mates, including matings outside of a pair bond. Such advantages could be especially important in island systems because habitat saturation may result in strong intra-specific competition for territories, and females may be especially motivated to seek large extra-pair mates to increase the body size of their offspring. We tested the role of body size in determining the ability of an island-endemic bird, the Island Scrub-Jay, Aphelocoma insularis, to acquire a territory and breed in their first spring, as well as to sire extra-pair offspring. We compared the body size of individuals that obtained a territory and bred to those that did not, as well as the body size of social fathers to the extra-pair sires to whom they lost paternity. We found that large body size was important in the siring of extra-pair young. However, body size did not predict the ability of male or female Island Scrub-Jays to acquire a territory and breed in their first year. We suggest that year-to-year variation in environmental conditions and chance may be more important than a large body size or weapon performance in early territory acquisition. Our study provides evidence for a mechanism, specifically female preference for a large body size in males, that supports the observed rates of extra-pair paternity, and demonstrates the general difficulty, even for individuals with a relatively large body size, of acquiring a territory as a yearling in an island system with saturated habitat.
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    Complex evolution of mitochondrial genomes: lessons from salamanders
    (Colorado State University. Libraries, 2014) Chong, Rebecca A., author; Mueller, Rachel L., advisor; Webb, Colleen T., committee member; Funk, W. Chris, committee member; McKay, John K., committee member
    This dissertation research on genome evolution focuses on understanding the mechanisms that drive the evolution of mitochondrial genome size, content, and organization in animals. This research uses a combination of empirical and computational approaches to examine the evolution of mitochondrial genomes in vertebrates, focusing on salamanders as an exemplar clade. Chapter One analyzes mitochondrial genome sequences of vertebrate lineages that differ in metabolic rates. Salamanders, which have the lowest metabolic requirements among tetrapods, experience weaker purifying selection on protein-coding sequences than do frogs, a comparable amphibian clade with higher metabolic rates. In contrast, there is no evidence for weaker selection against mitochondrial genome expansion in salamanders. Together, these results suggest that different aspects of mitochondrial genome evolution (i.e. nucleotide substitution, accumulation of non-coding sequences) are differently affected by metabolic variation across tetrapod lineages. Chapter Two describes the correlation between gene rearrangement/genome expansion and increased rates of substitution in salamander mitochondrial genomes. Most protein-coding genes maintain their position along the mutation gradient in rearranged/expanded mitochondrial genomes, and the genes that do move are unaffected by their new position because the mutation gradient in salamanders is weak. Additionally, genomic rearrangements/expansions occur independent of levels of selective constraint on genes. Together, these results demonstrate that large-scale changes to genome architecture impact mitochondrial gene evolution in predictable ways; however, despite these impacts, the same functional constraints act on mitochondrial protein-coding genes in both modified and normal genomes. Chapter Three reports the phylogenetic relationships among lineages of Aneides, sampling both within and among all six species, based on three nuclear markers and describes mitochondrial genome sequences for nine of the taxa represented in the phylogeny. Mitochondrial gene order and level of mitochondrial sequence divergence were estimated for these sequences and two previously published sequences. Two genome duplication events resulting in mitochondrial gene rearrangements were detected, the first rearrangement occurring in the common ancestor of Aneides and the second rearrangement existing across different populations of a single species, A. hardii. Comparisons of A. hardii genomes show that duplicated protein-coding and rRNA genes are lost more rapidly than other duplicated mitochondrial sequence (i.e. tRNAs, non-coding sequence) and suggests that these large scale changes can occur across very shallow levels of genetic divergence.
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    Determinants of geographic distribution in western North American monkeyflowers
    (Colorado State University. Libraries, 2014) Sheth, Seema Nayan, author; Angert, Amy L., advisor; Funk, W. Chris, committee member; McKay, John K., committee member; Mueller, Rachel L., committee member; Steingraeber, David, committee member
    The geographic range of a species represents the basic unit of biogeography. Despite ample evidence that properties of geographic ranges vary among species, we do not fully understand the ecological and evolutionary processes underlying these patterns, thereby hindering our ability to forecast changes in species' distributions in response to changing environments. Key hypotheses about variation in geographic range size among species emphasize the roles of ecological niche properties and the connectivity of suitable habitat. In the first study of my dissertation, I combined primary occurrence data with climate variables to test the relative importance of these hypotheses in 72 species of western North American monkeyflower (genus Mimulus). Climatic niche breadth, via its effect on the amount of suitable habitat, was a strong predictor of geographic range size, whereas climatic niche position (relative to regional climate) and connectivity of climatically suitable habitat were not. Given the role of climatic niche breadth in shaping geographic range sizes in Mimulus, the goal of the second study of my dissertation was to examine the relationship between thermal tolerance (an important axis of niche breadth) and range size experimentally using 5 pairs of closely related Mimulus species with differing range sizes. Within four species pairs, the more geographically widespread species had a broader thermal tolerance than the narrowly distributed species, providing further support for the hypothesis that species with broader niches are able to achieve larger geographic ranges. Further, within each species pair, the species with broader thermal tolerance encompassed greater variation in temperature across its geographic range and higher genetic variation for thermal tolerance than the species with narrower thermal tolerance, supporting the hypotheses that climatic variability and genetic variation in ecologically important traits can explain variation in environmental tolerance among species. Although species vary in range size, every species has a limited geographic range, leading to the question of what prevents a species from expanding its range via niche evolution. Thus, in the third study of my dissertation, I tested whether adaptation at geographic range margins is constrained by insufficient evolutionary potential. To do so, I used artificial selection experiments to quantify genetic variation in flowering time for populations from the northern edge, center, and southern edge of the geographic range of the scarlet monkeyflower (M. cardinalis). Contrary to prediction, southern populations exhibited significantly greater responses to selection (and thus evolutionary potential) than northern or central populations. Together, these results highlight an important role of niche breadth in explaining variation in geographic range size among species, and reveal variation in evolutionary potential that facilitates niche and range expansion within and among species.
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    Evolutionary and ecological processes in microparasite communities of bats
    (Colorado State University. Libraries, 2020) McKee, Clifton Dyer, author; Webb, Colleen T., advisor; Kosoy, Michael Y., committee member; Hayman, David T. S., committee member; Funk, W. Chris, committee member; Schountz, Tony, committee member
    The majority of parasites infecting humans come from animals, so it is necessary to study how parasites are maintained in nature to understand which human populations are at risk of spillover. Parasites are also highly diverse in their own right, with their own fascinating ecology, so studying parasite communities will give us a full perspective of Earth's biodiversity. Research has shown that bats are significant hosts of parasites globally, including important pathogens of humans. The unique evolution of flight in bats has influenced their ability to disperse parasites, and may have modified their immune systems to be more tolerant of infections compared to other mammals. Thus, studying bat parasite communities could deepen our knowledge of the evolutionary history of mammalian parasites and the importance of flight in the maintenance of parasite community diversity in bats. In this dissertation, I focus on the evolutionary history and ecological forces affecting diversity in blood-borne microparasite communities of bats. There is a particular focus in this dissertation on Bartonella bacteria, a common parasite in mammals. To determine the importance of bats in the historical diversification of Bartonella bacteria, I performed the most comprehensive phylogenetic analysis of the genus to date, including data from 121 strains cultured from bats globally. I discovered that Bartonella bacteria began infecting mammals 62 million years ago and likely originated from bats. In a review of other bat parasites, including eukaryotic trypanosomes and haemosporidian parasites, I find that bats have had a similarly deep influence on the evolution of these taxa, and their historical spread across continents and to other mammalian hosts. To examine the importance of dispersal on parasite community diversity at smaller ecological scales, I focused on Bartonella communities in African fruit bats. I investigated differences in the Bartonella communities in fruit bat populations across a West African island chain. In addition, I examined the population genetics of bat flies, the presumed vectors of Bartonella in bats, and bat fly symbionts to compare with the genetic population structure of the bat hosts. Bartonella communities differed across islands and showed a pattern of isolation by geographic distance, indicating that dispersal of parasite species is constrained by bat movement patterns. Population structure was reduced in bat flies and symbionts compared to that of the bat hosts, suggesting that bat movements between islands are going undetected from population genetics of the hosts alone. Finally, I investigated Bartonella community dynamics in a captive colony of fruit bats in Ghana over a sampling period of three years. In this study, the population density of bat flies declined over time and was then restored via reintroduction of flies from a wild source population, causing predictable changes in Bartonella prevalence within the bat colony. These results provide the first experimental confirmation of bat flies as vectors of Bartonella in bats. In addition, changes in Bartonella diversity within the colony that occurred in the absence of bat flies might be attributed to ecological drift and selection through interspecies competition mediated by the host immune system. These projects highlight the ecological and evolutionary processes affecting microparasite communities of bats, providing useful information for understanding how parasite biodiversity is created and maintained in natural populations.
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    Genetics, genomics, grouse, and conservation: use of genetic and genomic data to evaluate conservation actions and characterize populations of Gunnison sage-grouse
    (Colorado State University. Libraries, 2019) Zimmerman, Shawna Jean, author; Aldridge, Cameron L., advisor; Oyler-McCance, Sara J., advisor; Funk, W. Chris, committee member; Hooten, Mevin B., committee member
    To view the abstract, please see the full text of the document.
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    Informing the ecology and conservation of amphibians imperiled by chytridiomycosis
    (Colorado State University. Libraries, 2017) Mosher, Brittany Ann, author; Bailey, Larissa L., advisor; Huyvaert, Kathryn P., advisor; Funk, W. Chris, committee member; Muths, Erin, committee member
    To view the abstract, please see the full text of the document.
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    Managing vernal pool habitats on federal lands: maintaining obligate amphibian species
    (Colorado State University. Libraries, 2013) Green, Adam Wesley, author; Bailey, Larissa L., advisor; Funk, W. Chris, committee member; Nichols, James D., committee member; Noon, Barry, committee member
    To view the abstract, please see the full text of the document.
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    Microgeographic divergence in a single-island endemic: evolutionary patterns and conservation implications
    (Colorado State University. Libraries, 2014) Langin, Kathryn M., author; Ghalambor, Cameron K., advisor; Crooks, Kevin R., committee member; Funk, W. Chris, committee member; Morrison, Scott A., committee member; Sillett, T. Scott, committee member
    Understanding the processes that generate biological diversity is the central goal of evolutionary biology. Geographic isolation has traditionally been viewed as the primary scenario favoring evolutionary divergence. However, there is growing appreciation for the role of ecological variation and natural selection in driving adaptive differentiation, even in the absence of geographic barriers to gene flow. My dissertation tests for microgeographic patterns of local adaptation within one of the most range-restricted bird species in North America, the Island Scrub-Jay (Aphelocoma insularis). The species is restricted to Santa Cruz Island in southern California, USA, where it occurs in a diversity of habitat types within its narrow (250 km2) geographic range. Remarkably, I found that Island Scrub-Jays in three separate stands of pine habitat had longer, narrower bills than those in oak habitat, a pattern that mirrors adaptive differences between allopatric populations of the species' mainland congener (A. californica). Adaptive divergence was not constrained by genetic diversity, even though Island Scrub-Jays had much lower levels of neutral genetic diversity than A. californica. Genetic data indicate that Island Scrub-Jays in pine habitat were more closely related to individuals in adjacent oak habitat than to individuals in other pine stands, indicating that each pine stand can be considered an independent case where adaptive divergence has been maintained in the face of some gene flow with adjacent oak birds. Morphological differences were not abrupt across the pine-oak boundary, as bill length declined gradually with distance from pine habitat, a clinal pattern that is also consistent with a scenario of divergence-with-gene flow. Individuals mated non-randomly with respect to bill length within the population, which may be due to a combination of (1) isolation-by-distance (localized dispersal) across the landscape and spatial autocorrelation in bill morphology, and (2) assortative mating at a more local scale based on bill morphology or correlated acoustic signals. These findings provide strong support for the notion that microgeographic patterns of local adaptation may be more common than is currently appreciated, even in mobile taxonomic groups like birds. They also underscore the importance of conserving Island Scrub-Jays across the entire island in order to preserve the species' full range of biological diversity and to facilitate adaptive responses to future environmental changes.
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    Risk of gene introgression from transgenic wheat to jointed goatgrass
    (Colorado State University. Libraries, 2010) Econopouly, Bethany F., author; Byrne, Patrick F., 1948-, advisor; McKay, John K., advisor; Funk, W. Chris, committee member; Lapitan, Nora Lyssa V., committee member
    To view the abstract, please see the full text of the document.
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    Role of endogenous retrovirus in control of feline leukemia virus infection and implications for cross species transmission
    (Colorado State University. Libraries, 2019) Chiu, Elliott S., author; VandeWoude, Sue, advisor; Hoover, Edward A., committee member; Ebel, Gregory D., committee member; Funk, W. Chris, committee member
    Endogenous retroviruses (ERV) are markers of ancient retroviral infections, though evolutionary forces have limited the capacity for ERV replication and virulence. While they are seldom considered infectious alone, they maintain the ability to interact with their exogenous retroviral (XRV) progenitors. In Chapter One, we review the interactions that exist between ERV and XRV dyads. One such couplet includes feline leukemia virus (FeLV), a common domestic cat pathogen. In Chapter Two, we review FeLV subgroup taxonomy and the methods used from which they were originally characterized. Though the domestic cat is regarded as the natural host for the virus, recent reports have documented FeLV infections in wild felids with pathogenic consequences. Chapter Three examines the root of a contemporary FeLV outbreak in Florida panthers (Puma concolor coryi), a species that lacks endogenous FeLV. Our phylogenetic analysis of the contemporary FeLV outbreak has further implicated domestic cats (Felis catus) as the origin of FeLV infections in wild felids. Furthermore, we detected a recombinant oncogenic variant in Florida panthers that is believed to be non-horizontally transmissible. These field studies have prompted us to examine the cellular basis of infection and intrinsic resistance to the virus. In Chapter Four, we interrogate the cellular basis of FeLV infections between puma (P. concolor) and domestic cat cells using in vitro approaches. We demonstrated that puma cells support greater infection and replication. Additionally, we documented enFeLV long terminal repeats (LTR) in domestic cats are negatively correlated to FeLV infection outcomes in vitro. Natural FeLV infections in both Florida panther and domestic cat tissues offered us the opportunity to examine end stage disease dynamics, which demonstrate that Florida panthers have the ability to produce more virus despite having lower proviral loads than domestic cats. The results of both in vivo and in vitro experiments prompted us to further investigate enFeLV-LTRs and their role in FeLV infection. Chapter Five took advantage of the publicly available data in the NCBI Sequence Read Archive (SRA) to evaluate enFeLV-LTR basal transcription levels. Data-mining the domestic cat transcriptome showed that lymphoid cells, which are relatively resistant to in vitro FeLV infection, transcribe more enFeLV elements than relatively susceptible cells (i.e., fibroblasts). We also identified microRNA transcripts are produced that have the potential ability to down-regulate FeLV RNA transcripts. In Chapter Six, we innovated a new methodology to characterize the enFeLV-LTR integration sites across the entire genome of 20 related and unrelated domestic cats in an attempt to uncover genes that may be influenced by LTR enhancement of gene expression. We found one LTR integration site in a limited number of cats that is within 1MB of APOBEC1, an antiviral gene, and that the most common gene found in close proximity to LTR integration sites are zinc fingers, a broad-acting class of regulatory proteins. Collectively, this groundwork provides future directions to uncover direct and indirect mechanisms of enFeLV-mediated restriction of FeLV infection. We conclude that because wild felids lack enFeLV, they may be more vulnerable to FeLV infection. As urbanization forces niche overlap and contact between wild and domestic felids, the risk of infection of these species is likely to increase, and thus it will be important to consider contacts between FeLV-infected domestic cats and wild felid populations during development of conservation action plans.
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    Spatial, demographic, and phylogenetic patterns of Bartonella diversity in bats
    (Colorado State University. Libraries, 2015) McKee, Clifton Dyer, author; Webb, Colleen T., advisor; Kosoy, Michael Y., committee member; Funk, W. Chris, committee member; Schountz, Tony, committee member; Hayman, David T. S., committee member
    Much recent attention has focused on bats as potentially exceptional reservoirs of pathogens. Bats are known to carry zoonotic viruses deadly to humans with no apparent signs of pathology, however the evolutionary and physiological processes that are behind this ability remain largely unknown. Despite this uncertainty, bats’ long lifespans, deep evolutionary history, sociality, and migratory behavior make them a fascinating system in which to study patterns of diversity in viruses, bacteria, and other infectious organisms. This thesis explores ecological and evolutionary processes that structure the diversity of infectious bacteria in bats. I focus on Bartonella, a genus of vector-borne intracellular bacteria, because of its high prevalence and genetic diversity within bats. I examined the structure of Bartonella species assemblages in Eidolon spp. fruit bats across Africa and Madagascar using newly developed molecular and statistical tools. The results from this examination indicate that fruit bats from distant geographic locations host similar communities of Bartonella; I attribute this to widespread dispersal and communal roosting behavior in Eidolon spp. bats. To understand how Bartonella diversity has evolved and is structured geographically, I assembled a global dataset of Bartonella genotypes from bats and their ectoparasites. Using this dataset, I analyzed the contributions of cospeciation and sympatry among host species to the diversity of Bartonella in bats. Continued development of this research could provide a model system for the study of ecological and evolutionary processes contributing to pathogen diversification and infection dynamics in natural systems.
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    The molecular ecology and evolution of puma letivirus in bobcats and mountain lions in North America
    (Colorado State University. Libraries, 2013) Lee, Justin S., author; VandeWoude, Sue, advisor; Crooks, Kevin R., advisor; Funk, W. Chris, committee member; Troyer, Jennifer L., committee member
    Host-pathogen dynamics are influenced by ecological and evolutionary processes at all levels of biological organization. Within individuals, viruses that cause chronic infection must either avoid or escape the pressures of the host immune system. Furthermore, viruses adapted to one host environment may have low fitness when transmitted to different individuals, populations, and species. At the landscape level, the movement and distribution of directly transmitted obligate pathogens are inextricably associated with their hosts. We used molecular analyses to investigate the ecology and evolution of feline immunodeficiency virus (FIV) in bobcats and mountain lions within individuals, among populations, and between species of hosts. In Chapter One we investigated the effects of urban development on the movement of bobcats and feline immunodeficiency virus (FIV) among a fragmented landscape in southern California. Our results demonstrate that bobcat movement and gene flow are restricted across a major freeway that bisects the study area, resulting in two genetically and physically distinct subpopulations connected by a low level of migration. However, the FIV population is not similarly structured, suggesting that movements and contacts sufficient for disease transmission continue despite the low level of host migration observed. Chapter Two investigates the causes and effects of FIV evolution among bobcats and mountain lions across North America. Our results illustrate a dynamic host-pathogen relationship characterized by host-immune pressures and a rapidly evolving virus with a highly plastic genome. Finally, in Chapter Three we describe a pilot project aimed at improving the efficiency with which pathogen genetic data can be collected by combining the use of two modern technologies - targeted genome capture and next-generation sequencing. The results suggest this is a promising approach to detecting and sequencing multiple pathogens from biological samples. Collectively, the work described in this dissertation combines new and existing methodologies to generate, analyze, and interpret molecular data to answer complex questions about the ecological and evolutionary determinants of host-pathogen dynamics.