Critical Effects of Urbanization on a Charismatic Carnivore: Genetic Change, Disease and Toxicant Exposure, and Disease Susceptibility in Bobcat Populations in an Urban, Fragmented Landscape

Urbanization has profound ecological impacts that reach beyond city boundaries. Obvious ecological consequences of urbanization include habitat loss and fragmentation. Anthropogenic barriers reduce habitat connectivity, impede gene flow between populations and accelerate the loss of genetic diversity in populations due to drift. Urbanization may have also cryptic consequences such as the effects of human-introduced toxicants on wildlife populations. Toxicants are a leading cause of population decline for a variety of animal species worldwide and may directly threaten animal populations by causing direct mortalities, or indirectly through sublethal, chronic effects such as reproductive impairment, decreased immune competence, and increased disease susceptibility or emergence. If population-level impacts occur as a result of toxicant exposure, genetic consequences may also accompany reduced population sizes and connectivity. These include inbreeding depression that may increase the probability of population extinction and the loss of adaptive potential that reduces the ability of populations to respond to novel selection regimes. Overall, urbanization presents wildlife with many novel stressors to which they must adapt or perish. Urbanization is increasing at an unprecedented pace; understanding both the obvious and the cryptic threats to wild animal populations persisting near urban areas will be vital to promoting conservation and the maintenance of global biodiversity.To address the consequences of urbanization on wildlife populations, I focused on a well-studied population of bobcats (Lynx rufus) living in and around Santa Monica Mountains National Recreation Area (SMMNRA). This region comprises a collection of protected park areas near downtown Los Angeles. Bobcats inhabiting SMMNRA have been monitored by National Park Service (NPS) biologists since 1996. Within a localized region of SMMNRA, the NPS has demonstrated that a major freeway (US-101) acts not only as a barrier to movement for bobcat and coyote (Canis latrans) populations, but potentially also as a social barrier. Further, from 2002-2005, a notoedric mange epizootic associated with secondary anticoagulant rat poison exposure was the greatest source of mortality for bobcats. During this period, the annual survival rate for radio-collared animals fell by > 50% and in 2003 the mange mortality rate reached a high of 51%. Long-term samples were collected from this population from 1996-2012, allowing the rare opportunity to make direct comparisons before, during, and after the population decline. Using these data as a foundation, my research focused on three main objectives. First, I characterized neutral and adaptively relevant genetic diversity in bobcat populations across SMMNRA in both fragmented urban and protected natural areas. Second, I examined anticoagulant rodenticide exposure in bobcats across southern California, contrasting seasonal, demographic and spatial risk factors in both natural and urbanized areas. Third, I characterized physiological and immunological parameters in bobcats across SMMNRA to evaluate the effects of disease and toxicant exposure on bobcat health in an urban, fragmented landscape.I found that two freeways are significant barriers to gene flow. Further, the 3-year disease epizootic, associated with secondary anticoagulant rodenticide exposure, caused a population bottleneck that led to significant genetic differentiation pre- and post-disease populations that was greater than that between populations separated by major freeways for > 60 years. However, balancing selection acted on immune-linked loci during the epizootic, maintaining variation at functional regions. With respect to anticoagulant rodenticide exposure, I detected high prevalence of exposure (89%, liver; 39%, blood) and found that for individuals with paired liver and blood data (N = 64), 92% were exposed most frequently to greater than or equal to 3 compounds. Prevalence and the amounts of contaminants were associated with human activities that included commercial, residential, and agricultural development. I found a strong association between AR exposure to greater than and equal to 0.25 ppm or greater than and equal to 2 compounds and an ectoparasitic disease, notoedric mange. Finally, I observed that AR exposure has both immune stimulatory and suppressive effects that may explain increased bobcat susceptibility to notoedric mange as a result of chronic exposure to anticoagulant rodenticides. Bobcats exposed to ARs had elevated lymphocyte, and specifically B cell counts, and decreased percentages of neutrophils. Overall, these data highlight that even for free-ranging animals that are considered relatively adaptable to urbanization, habitat fragmentation and toxicant exposure can have profound population level effects that threaten the long-term stability of wildlife populations in an increasingly urbanized landscape

Population Genetics of California Gray Foxes Clarify Origins of the Island Fox

We used mitochondrial sequences and nuclear microsatellites to investigate population structure of gray foxes (Urocyon cinereoargenteus) and the evolutionary origins of the endemic island fox (Urocyon littoralis), which first appeared in the northern Channel Islands <13,000 years ago and in the southern Channel Islands <6000 years ago. It is unclear whether island foxes evolved directly from mainland gray foxes transported to the islands one or more times or from a now-extinct mainland population, already diverged from the gray fox. Our 345 mitochondrial sequences, combined with previous data, confirmed island foxes to be monophyletic, tracing to a most recent common ancestor approximately 85,000 years ago. Our rooted nuclear DNA tree additionally indicated genome-wide monophyly of island foxes relative to western gray foxes, although we detected admixture in northern island foxes from adjacent mainland gray foxes, consistent with some historical gene flow. Southern California gray foxes also bore a genetic signature of admixture and connectivity to a desert population, consistent with partial replacement by a late-Holocene range expansion. Using our outgroup analysis to root previous nuclear sequence-based trees indicated reciprocal monophyly of northern versus southern island foxes. Results were most consistent with island fox origins through multiple introductions from a now-extirpated mainland population

Urbanization and anticoagulant poisons promote immune dysfunction in bobcats

Understanding how human activities influence immune response to environmental stressors can support biodiversity conservation across increasingly urbanizing landscapes. We studied a bobcat (Lynx rufus) population in urban southern California that experienced a rapid population decline from 2002-2005 due to notoedric mange. Because anticoagulant rodenticide (AR) exposure was an underlying complication in mange deaths, we aimed to understand sublethal contributions of urbanization and ARs on 65 biochemical markers of immune and organ function. Variance in immunological variables was primarily associated with AR exposure and secondarily with urbanization. Use of urban habitat and AR exposure has pervasive, complex and predictable effects on biochemical markers of immune and organ function in free-ranging bobcats that include impacts on neutrophil, lymphocyte and cytokine populations, total bilirubin and phosphorus. We find evidence of both inflammatory response and immune suppression associated with urban land use and rat poison exposure that could influence susceptibility to opportunistic infections. Consequently, AR exposure may influence mortality and has population-level effects, as previous work in the focal population has revealed substantial mortality caused by mange infection. The secondary effects of anticoagulant exposure may be a worldwide, largely unrecognized problem affecting a variety of vertebrate species in human-dominated environments

Evolution of Puma Lentivirus in Bobcats (Lynx rufus) and Mountain Lions (Puma concolor) in North America

Mountain lions (Puma concolor) throughout North and South America are infected with puma lentivirus clade B (PLVB). A second, highly divergent lentiviral clade, PLVA, infects mountain lions in southern California and Florida. Bobcats (Lynx rufus) in these two geographic regions are also infected with PLVA, and to date, this is the only strain of lentivirus identified in bobcats. We sequenced full-length PLV genomes in order to characterize the molecular evolution of PLV in bobcats and mountain lions. Low sequence homology (88% average pairwise identity) and frequent recombination (1 recombination breakpoint per 3 isolates analyzed) were observed in both clades. Viral proteins have markedly different patterns of evolution; sequence homology and negative selection were highest in Gag and Pol and lowest in Vif and Env. A total of 1.7% of sites across the PLV genome evolve under positive selection, indicating that host-imposed selection pressure is an important force shaping PLV evolution. PLVA strains are highly spatially structured, reflecting the population dynamics of their primary host, the bobcat. In contrast, the phylogeography of PLVB reflects the highly mobile mountain lion, with diverse PLVB isolates cocirculating in some areas and genetically related viruses being present in populations separated by thousands of kilometers. We conclude that PLVA and PLVB are two different viral species with distinct feline hosts and evolutionary histories. Importance: An understanding of viral evolution in natural host populations is a fundamental goal of virology, molecular biology, and disease ecology. Here we provide a detailed analysis of puma lentivirus (PLV) evolution in two natural carnivore hosts, the bobcat and mountain lion. Our results illustrate that PLV evolution is a dynamic process that results from high rates of viral mutation/recombination and host-imposed selection pressure

Novel Gammaherpesviruses in North American Domestic Cats, Bobcats, and Pumas: Identification, Prevalence, and Risk Factors

UnlabelledGammaherpesviruses (GHVs) are a diverse and rapidly expanding group of viruses associated with a variety of disease conditions in humans and animals. To identify felid GHVs, we screened domestic cat (Felis catus), bobcat (Lynx rufus), and puma (Puma concolor) blood cell DNA samples from California, Colorado, and Florida using a degenerate pan-GHV PCR. Additional pan-GHV and long-distance PCRs were used to sequence a contiguous 3.4-kb region of each putative virus species, including partial glycoprotein B and DNA polymerase genes. We identified three novel GHVs, each present predominantly in one felid species: Felis catus GHV 1 (FcaGHV1) in domestic cats, Lynx rufus GHV 1 (LruGHV1) in bobcats, and Puma concolor GHV 1 (PcoGHV1) in pumas. To estimate infection prevalence, we developed real-time quantitative PCR assays for each virus and screened additional DNA samples from all three species (n = 282). FcaGHV1 was detected in 16% of domestic cats across all study sites. LruGHV1 was detected in 47% of bobcats and 13% of pumas across all study sites, suggesting relatively common interspecific transmission. PcoGHV1 was detected in 6% of pumas, all from a specific region of Southern California. The risk of infection for each host varied with geographic location. Age was a positive risk factor for bobcat LruGHV1 infection, and age and being male were risk factors for domestic cat FcaGHV1 infection. Further characterization of these viruses may have significant health implications for domestic cats and may aid studies of free-ranging felid ecology.ImportanceGammaherpesviruses (GHVs) establish lifelong infection in many animal species and can cause cancer and other diseases in humans and animals. In this study, we identified the DNA sequences of three GHVs present in the blood of domestic cats (Felis catus), bobcats (Lynx rufus), and pumas (Puma concolor; also known as mountain lions, cougars, and panthers). We found that these viruses were closely related to, but distinct from, other known GHVs of animals and represent the first GHVs identified to be native to these feline species. We developed techniques to rapidly and specifically detect the DNA of these viruses in feline blood and found that the domestic cat and bobcat viruses were widespread across the United States. In contrast, puma virus was found only in a specific region of Southern California. Surprisingly, the bobcat virus was also detected in some pumas, suggesting relatively common virus transmission between these species. Adult domestic cats and bobcats were at greater risk for infection than juveniles. Male domestic cats were at greater risk for infection than females. This study identifies three new viruses that are widespread in three feline species, indicates risk factors for infection that may relate to the route of infection, and demonstrates cross-species transmission between bobcats and pumas. These newly identified viruses may have important effects on feline health and ecology