Stepping stones to extirpation: Puma patch occupancy thresholds in an urban-wildland matrix

Habitat loss and fragmentation are the leading causes of species range contraction and extirpation, worldwide. Factors that predict sensitivity to fragmentation include high trophic level, large body size, and extensive spatial requirements. Pumas (Puma concolor) exemplify these qualities, making them particularly susceptible to fragmentation and subsequent reductions in demographic connectivity. The chaparral-dominated ecosystems surrounding the greater San Francisco Bay Area encompass over 10,000 km2 of suitable puma habitat, but inland waterways, croplands, urban land uses, and extensive transportation infrastructure have resulted in widespread habitat fragmentation. Pumas in this region now exist as a metapopulation marked by loss of genetic diversity, collisions with vehicles, and extensive human-puma conflict. Given these trends, we conducted a photo survey from 2017 to 2021 across 19 patches of predicted habitat and compiled a dataset of >6584 puma images. We used a logistic regression analytical framework to evaluate the hypothesis that puma patch occupancy would exhibit a threshold response explained by patch size, isolation, and habitat quality. Contrary to predictions, only variables related to patch size demonstrated any power to explain occupancy. On average, occupied patches were 18× larger than those where they were not detected (825 ± 1238 vs. 46 ± 101 km2). Although we observed pumas in patches as small as 1 km2, logistic regression models indicated a threshold occupancy probability between 300 and 400 km2, which is remarkably close to the mean male puma home range size in coastal California (~381 km2). Puma populations dependent on habitats below this value may be susceptible to inbreeding depression and human-wildlife conflict, and therefore vulnerable to extirpation. For species conservation, we suggest conflicts might be ameliorated by identifying the largest, isolated patches for public education campaigns with respect to management of domestic animals, and remaining connective parcels be identified, mapped, and prioritized for targeted mitigation.

Density-dependent habitat selection alters drivers of population distribution in northern Yellowstone elk

Although it is well established that density dependence drives changes in organismal abundance over time, relatively little is known about how density dependence affects variation in abundance over space. We tested the hypothesis that spatial trade-offs between food and safety can change the drivers of population distribution, caused by opposing patterns of density-dependent habitat selection (DDHS) that are predicted by the multidimensional ideal free distribution. We addressed this using winter aerial survey data of northern Yellowstone elk (Cervus canadensis) spanning four decades. Supporting our hypothesis, we found positive DDHS for food (herbaceous biomass) and negative DDHS for safety (openness and roughness), such that the primary driver of habitat selection switched from food to safety as elk density decreased from 9.3 to 2.0 elk/km² . Our results demonstrate how population density can drive landscape-level shifts in population distribution, confounding habitat selection inference and prediction and potentially affecting community-level interactions.

ABCG2 Polymorphisms and Predictive Fluoroquinolone Phototoxicity in Nondomestic Felids

Fluoroquinolones are a widely used class of chemotherapeutics within veterinary medicine, prized for their broad-spectrum bactericidal activity. These drugs present a known risk of retinal phototoxicity in domestic cats (Felis catus); therefore, using lower doses and alternative antibiotic classes is encouraged in this species. This adverse drug effect of fluoroquinolones, and enrofloxacin specifically, has been determined to be species-specific in domestic felids. Four feline-specific missense variants in ABCG2 result in four amino acid changes (E159M, S279L, H283Q, and T644I) that are unique to the domestic cat compared with multiple other nonfeline mammalian species. These changes alter the ABCG2 protein involved with the cellular transmembrane transport of drugs, including fluoroquinolones, making the protein functionally defective in domestic cats. The predisposition to fluoroquinolone-mediated phototoxicity in nondomestic felids was explored in this study. At least eight nondomestic felids share the four ABCG2 missense variants with domestic cats, and eleven other felids shared at least three of the four domestic cat variants. Taken together, these results suggest the genetic potential for nondomestic felids to also experience fluoroquinolone-induced retinal phototoxicity; therefore, cautions similar to those for domestic cats should be followed for these drugs in the entire feline taxon.

Evaluating and integrating spatial capture-recapture models with data of variable individual identifiability

Spatial capture-recapture (SCR) models have become the preferred tool for estimating densities of carnivores. Within this family of models are variants requiring identification of all individuals in each encounter (SCR), a subset of individuals only (generalized spatial mark-resight, gSMR), or no individual identification (spatial count or spatial presence-absence). Although each technique has been shown through simulation to yield unbiased results, the consistency and relative precision of estimates across methods in real-world settings are seldom considered. We tested a suite of models ranging from those only requiring detections of unmarked individuals to others that integrate remote camera, physical capture, genetic, and global positioning system (GPS) data into a hybrid model, to estimate population densities of black bears, bobcats, cougars, and coyotes. For each species, we genotyped fecal DNA collected with detection dogs during a 20-d period. A subset of individuals from each species was affixed with GPS collars bearing unique markings and resighted by remote cameras over 140 d contemporaneous with scat collection. Camera-based gSMR models produced density estimates that differed by <10% from genetic SCR for bears, cougars, and coyotes once important sources of variation (sex or behavioral status) were controlled for. For bobcats, SCR estimates were 33% higher than gSMR. The cause of the discrepancies in estimates was likely attributable to challenges designing a study compatible for species with disparate home range sizes and the difficulty of collecting sufficient data in a timeframe in which demographic closure could be assumed. Unmarked models estimated densities that varied greatly from SCR, but estimates became more consistent in models wherein more individuals were identifiable. Hybrid models containing all data sources exhibited the most precise estimates for all species. For studies in which only sparse data can be obtained and the strictest model assumptions are unlikely to be met, we suggest researchers use caution making inference from models lacking individual identity. For best results, we further recommend the use of methods requiring at least a subset of the population is marked and that multiple data sets are incorporated when possible.

COVID-19 suppression of human mobility releases mountain lions from a landscape of fear

Humans have outsized effects on ecosystems, in part by initiating trophic cascades that impact all levels of the food chain.^1,2 Theory suggests that disease outbreaks can reverse these impacts by modifying human behavior,^3,4 but this has not yet been tested. The COVID-19 pandemic provided a natural experiment to test whether a virus could subordinate humans to an intermediate link in the trophic chain, releasing a top carnivore from a landscape of fear. Shelter-in-place orders in the Bay Area of California led to a 50% decline in human mobility, which resulted in a relaxation of mountain lion aversion to urban areas. Rapid changes in human mobility thus appear to act quickly on food web functions, suggesting an important pathway by which emerging infectious diseases will impact not only human health but ecosystems as well.

Species Distribution Model of Trichinella Species in Cougars (Puma concolor) for the Southwestern Region of Colorado, USA

Little information exists on the occurrence of Trichinella spp. in cougars (Puma concolor) throughout North and South America. However, species distribution models (SDM) can be used to predict suitable habitat for elusive species with limited occurrence data. In 2018, we used existing occurrence data to estimate the suitable habitat and ecological drivers of Trichinella species in cougars from the southwestern region of Colorado, US from winter months. Environmental layers were constructed and an SDM was then created for the southwestern region of Colorado. The final model (area under the curve=0.73) found areas of suitable habitat for Trichinella spp. to be associated with lower elevation, lower temperature, and higher proportions of evergreen needleleaf forests and grasslands. These results might indicate potential transmission hotspots for Trichinella spp. in the southwestern region of Colorado for where cougars are consuming infected hosts and where cougars can transmit to other hosts, including humans. However, due to limited occurrence data, more suitable habitat likely exists.

Feline immunodeficiency virus in puma: Estimation of force of infection reveals insights into transmission

Determining parameters that govern pathogen transmission (such as the force of infection, FOI), and pathogen impacts on morbidity and mortality, is exceptionally challenging for wildlife. Vital parameters can vary, for example across host populations, between sexes and within an individual's lifetime.Feline immunodeficiency virus (FIV) is a lentivirus affecting domestic and wild cat species, forming species-specific viral-host associations. FIV infection is common in populations of puma (Puma concolor), yet uncertainty remains over transmission parameters and the significance of FIV infection for puma mortality. In this study, the age-specific FOI of FIV in pumas was estimated from prevalence data, and the evidence for disease-associated mortality was assessed.We fitted candidate models to FIV prevalence data and adopted a maximum likelihood method to estimate parameter values in each model. The models with the best fit were determined to infer the most likely FOI curves. We applied this strategy for female and male pumas from California, Colorado, and Florida.When splitting the data by sex and area, our FOI modeling revealed no evidence of disease-associated mortality in any population. Both sex and location were found to influence the FOI, which was generally higher for male pumas than for females. For female pumas at all sites, and male pumas from California and Colorado, the FOI did not vary with puma age, implying FIV transmission can happen throughout life; this result supports the idea that transmission can occur from mothers to cubs and also throughout adult life. For Florida males, the FOI was a decreasing function of puma age, indicating an increased risk of infection in the early years, and a decreased risk at older ages.This research provides critical insight into pathogen transmission and impact in a secretive and solitary carnivore. Our findings shed light on the debate on whether FIV causes mortality in wild felids like puma, and our approach may be adopted for other diseases and species. The methodology we present can be used for identifying likely transmission routes of a pathogen and also estimating any disease-associated mortality, both of which can be difficult to establish for wildlife diseases in particular.

Do prey select for vacant hunting domains to minimize a multi-predator threat?

Many ecosystems contain sympatric predator species that hunt in different places and times. We tested whether this provides vacant hunting domains, places and times where and when predators are least active, that prey use to minimize threats from multiple predators simultaneously. We measured how northern Yellowstone elk (Cervus elaphus) responded to wolves (Canis lupus) and cougars (Puma concolor), and found that elk selected for areas outside the high-risk domains of both predators consistent with the vacant domain hypothesis. This enabled elk to avoid one predator without necessarily increasing its exposure to the other. Our results demonstrate how the diel cycle can serve as a key axis of the predator hunting domain that prey exploit to manage predation risk from multiple sources. We argue that a multi-predator, spatiotemporal framework is vital to understand the causes and consequences of prey spatial response to predation risk in environments with more than one predator.

Ecological effects of fear: How spatiotemporal heterogeneity in predation risk influences mule deer access to forage in a sky-island system

Forage availability and predation risk interact to affect habitat use of ungulates across many biomes. Within sky-island habitats of the Mojave Desert, increased availability of diverse forage and cover may provide ungulates with unique opportunities to extend nutrient uptake and/or to mitigate predation risk. We addressed whether habitat use and foraging patterns of female mule deer (Odocoileus hemionus) responded to normalized difference vegetation index (NDVI), NDVI rate of change (green-up), or the occurrence of cougars (Puma concolor). Female mule deer used available green-up primarily in spring, although growing vegetation was available during other seasons. Mule deer and cougar shared similar habitat all year, and our models indicated cougars had a consistent, negative effect on mule deer access to growing vegetation, particularly in summer when cougar occurrence became concentrated at higher elevations. A seemingly late parturition date coincided with diminishing NDVI during the lactation period. Sky-island populations, rarely studied, provide the opportunity to determine how mule deer respond to growing foliage along steep elevation and vegetation gradients when trapped with their predators and seasonally limited by aridity. Our findings indicate that fear of predation may restrict access to the forage resources found in sky islands.

Functional responses of cougars (Puma concolor) in a multiple prey-species system

The study of predator-prey interactions is commonly analyzed using functional responses to gain an understanding of predation patterns and the impact they have on prey populations. Despite this, little is known about predator-prey systems with multiple prey species in sites near the equator. Here we studied the functional response of cougars (Puma concolor) in relation to their main prey, armadillo (Dasypus novemcinctus), coati (Nasua narica) and white-tailed deer (Odocoileus virginianus). Between 2004 and 2010, cougar scats were collected along 5 transects to estimate the consumption of different prey species. A relative abundance index (RAI) was calculated for each prey species and cougar using 18 camera traps. We compared Holling type I, II and III functional response models to determine patterns in prey consumption based on the relative abundance and biomass of each prey species consumed. The 3 main prey species comprised 55% (armadillo), 17% (coati) and 8% (white-tailed deer) of the diet. Type I and II functional responses described consumption of the 2 most common prey species armadillos and coati similarly well, while a type I response best characterized consumption of white-tailed deer. A negative correlation between the proportions of armadillo versus coati and white-tailed deer biomass in cougar scats suggests switching to consume alternative prey, confirming high foraging plasticity of this carnivore. This work represents one of the few studies to compare functional responses across multiple prey species, combined with evidence for prey-switching at low densities of preferred prey.

Effect of Bungee-carcass enrichment on behavior and fecal glucocorticoid metabolites in two species of zoo-housed Felids

Enrichment can improve animal physiological and psychological well-being. This study sought to promote more natural felid behavior and prevent development or incidence of stereotypies through the use of a feeding enrichment. Our objectives are to use fecal glucocorticoid metabolites values and behavioral observations to quantify the effectiveness of the enrichment device for two species of large cats, Bengal tiger (Panthera tigris tigris; n = 2) and cougar (Felis concolor; n = 2). The feeding enrichment, a white-tailed deer carcass flank securely attached to an AussieDog Products(©) Felid 120-cm bungee, was implemented twice for each individual separated by 1 month. Fecal samples were obtained from each felid and analyzed for pre- and post-enrichment fecal glucocorticoid metabolites (FGM) concentrations using a cortisol enzyme immunoassay. An ethogram with 12 mutual exclusive behavioral categories was utilized to record behavioral responses to the enrichment. Results demonstrate that: 1) there were no differences (P > 0.05) in FGMs for either species between pre- and post-enrichment; 2) pacing decreased (P = 0.025) and walking increased (P = 0.017) after exposure to enrichment in both cougars; and 3) tigers reduced (P = 0.025) 'other' behavioral category after the first enrichment exposure and laid down more (P = 0.025) after the second enrichment exposure. The neutral hormonal impact on the animals coupled with the behavioral changes indicates that this enrichment is successful at altering the animals' behavior without adding physiological stress to their environments. These findings, combined with the low cost and versatility of the enrichment, promote the use of this enrichment to enhance large felid enclosures.

Cougars' key to survival through the Late Pleistocene extinction: insights from dental microwear texture analysis

Cougars (Puma concolor) are one of only two large cats in North America to have survived the Late Pleistocene extinction (LPE), yet the specific key(s) to their relative success remains unknown. Here, we compare the dental microwear textures of Pleistocene cougars with sympatric felids from the La Brea Tar Pits in southern California that went extinct at the LPE (Panthera atrox and Smilodon fatalis), to clarify potential dietary factors that led to the cougar's persistence through the LPE. We further assess whether the physical properties of food consumed have changed over time when compared with modern cougars in southern California. Using dental microwear texture analysis (DMTA), which quantifies surface features in three dimensions, we find that modern and Pleistocene cougars are not significantly different from modern African lions in any DMTA attributes, suggesting moderate durophagy (i.e. bone processing). Pleistocene cougars from La Brea have significantly greater complexity and textural fill volume than Panthera atrox (inferred to have primarily consumed flesh from fresh kills) and significantly greater variance in complexity values than S. fatalis. Ultimately, these results suggest that cougars already used or adopted a more generalized dietary strategy during the Pleistocene that may have been key to their subsequent success.

Genetic structure of mountain lion (Puma concolor) populations in California

Analysis of 12 microsatellite loci from431 mountain lions (Puma concolor)revealed distinct genetic subdivision that wasassociated with geographic barriers andisolation by distance in California. Levels ofgenetic variation differed among geographicregions, and mountain lions that inhabitedcoastal areas exhibited less heterozygositythan those sampled inland. The San FranciscoBay and Sacramento-San Joaquin River Delta, theCentral Valley, and the Los Angeles Basinappeared to be substantial barriers to geneflow, and allele frequencies of populationsseparated by those features differedsubstantially. A partial barrier to gene flowappeared to exist along the crest of the SierraNevada. Estimated gene flow was high amongmountain lions inhabiting the Modoc Plateau,the western Sierra Nevada, and northern sectionof the eastern Sierra Nevada. SouthernCalifornia mountain lion populations mayfunction as a metapopulation; however, humandevelopments threaten to eliminate habitat andmovement corridors. While north-south geneflow along the western Sierra Nevada wasestimated to be very high, projected loss andfragmentation of foothill habitat may reducegene flow and subdivide populations. Preservation of existing movement corridorsamong regions could prevent population declinesand loss of genetic variation. This studyshows that mountain lion management andconservation efforts should be individualizedaccording to region and incorporatelandscape-level considerations to protecthabitat connectivity.