How territoriality and sociality influence the habitat selection and movements of a large carnivore.

While territoriality is one of the key mechanisms influencing carnivore space use, most studies quantify resource selection and movement in the absence of conspecific influence or territorial structure. Our analysis incorporated social information in a resource selection framework to investigate mechanisms of territoriality and intra-specific competition on the habitat selection of a large, social carnivore. We fit integrated step selection functions to 3-h GPS data from 12 collared African wild dog packs in the Okavango Delta and estimated selection coefficients using a conditional Poisson likelihood with random effects. Packs selected for their neighbors' 30-day boundary (defined as their 95% kernel density estimate) and for their own 90-day core (defined as their 50% kernel density estimate). Neighbors' 30-day boundary had a greater influence on resource selection than any habitat feature. Habitat selection differed when they were within versus beyond their neighbors' 30-day boundary. Pack size, pack tenure, pup presence, and seasonality all mediated how packs responded to neighbors' space use, and seasonal dynamics altered the strength of residency. While newly-formed packs and packs with pups avoided their neighbors' boundary, older packs and those without pups selected for it. Packs also selected for the boundary of larger neighboring packs more strongly than that of smaller ones. Social structure within packs has implications for how they interact with conspecifics, and therefore how they are distributed across the landscape. Future research should continue to investigate how territorial processes are mediated by social dynamics and, in turn, how territorial structure mediates resource selection and movement. These results could inform the development of a human-wildlife conflict (HWC) mitigation tool by co-opting the mechanisms of conspecific interactions to manage space use of endangered carnivores.

Mesocarnivores vary in their spatiotemporal avoidance strategies at communications hubs of an apex carnivore.

Mesocarnivores face interspecific competition and risk intraguild predation when sharing resources with apex carnivores. Within a landscape, carnivores across trophic levels may use the same communication hubs, which provide a mix of risks (injury/death) and rewards (gaining information) for subordinate species. We predicted that mesocarnivores would employ different strategies to avoid apex carnivores at shared communication hubs, depending on their trophic position. To test our prediction, we examined how different subordinate carnivore species in the Santa Cruz Mountains of California, USA, manage spatial overlap with pumas (Puma concolor), both at communication hubs and across a landscape-level camera trap array. We estimated species-specific occurrence, visitation rates, temporal overlap, and Avoidance-Attraction Ratios from camera traps and tested for differences between the two types of sites. We found that mesocarnivores generally avoided pumas at communication hubs, and this became more pronounced when pumas scent-marked during their most recent visit. Coyotes (Canis latrans), the pumas' closest subordinate competitor in our system, exhibited the strongest avoidance at communication hubs. Gray foxes (Urocyon cinereoargenteus) avoided pumas the least, which may suggest possible benefits from pumas suppressing coyotes. Overall, mesocarnivores exhibited various spatiotemporal avoidance strategies at communication hubs rather than outright avoidance, likely because they benefit from information gained while 'eavesdropping' on puma activity. Variability in avoidance strategies may be due to differential predation risks, as apex carnivores often interact more aggressively with their closest competitors. Combined, our results show how apex carnivores trigger complex species interactions across the entire carnivore guild and how trophic position determines behavioral responses and subsequent space use of subordinate mesocarnivores across the landscape.

Season, prey availability, sex, and age explain prey size selection in a large solitary carnivore.

Prey selection is a fundamental aspect of ecology that drives evolution and community structure, yet the impact of intraspecific variation on the selection for prey size remains largely unaccounted for in ecological theory. Here, we explored puma (Puma concolor) prey selection across six study sites in North and South America. Our results highlighted the strong influence of season and prey availability on puma prey selection, and the smaller influence of puma age. Pumas in all sites selected smaller prey in warmer seasons following the ungulate birth pulse. Our top models included interaction terms between sex and age, suggesting that males more than females select larger prey as they age, which may reflect experiential learning. When accounting for variable sampling across pumas in our six sites, male and female pumas killed prey of equivalent size, even though males are larger than females, challenging assumptions about this species. Nevertheless, pumas in different study sites selected prey of different sizes, emphasizing that the optimal prey size for pumas is likely context-dependent and affected by prey availability. The mean prey weight across all sites averaged 1.18 times mean puma weight, which was less than predicted as the optimal prey size by energetics and ecological theory (optimal prey = 1.45 puma weight). Our results help refine our understanding of optimal prey for pumas and other solitary carnivores, as well as corroborate recent research emphasizing that carnivore prey selection is impacted not just by energetics but by the effects of diverse ecology.

Tradeoffs between resources and risks shape the responses of a large carnivore to human disturbance.

Wide-ranging carnivores experience tradeoffs between dynamic resource availabilities and heterogeneous risks from humans, with consequences for their ecological function and conservation outcomes. Yet, research investigating these tradeoffs across large carnivore distributions is rare. We assessed how resource availability and anthropogenic risks influence the strength of lion (Panthera leo) responses to disturbance using data from 31 sites across lions' contemporary range. Lions avoided human disturbance at over two-thirds of sites, though their responses varied depending on site-level characteristics. Lions were more likely to exploit human-dominated landscapes where resources were limited, indicating that resource limitation can outweigh anthropogenic risks and might exacerbate human-carnivore conflict. Lions also avoided human impacts by increasing their nocturnal activity more often at sites with higher production of cattle. The combined effects of expanding human impacts and environmental change threaten to simultaneously downgrade the ecological function of carnivores and intensify human-carnivore conflicts, escalating extinction risks for many species.

Anthropogenic activities and age class mediate carnivore habitat selection in a human-dominated landscape.

Human activities increasingly challenge wild animal populations by disrupting ecological connectivity and population persistence. Yet, human-modified habitats can provide resources, resulting in selection of disturbed areas by generalist species. To investigate spatial and temporal responses of a generalist carnivore to human disturbance, we investigated habitat selection and diel activity patterns in caracals (Caracal caracal). We GPS-collared 25 adults and subadults in urban and wildland-dominated subregions in Cape Town, South Africa. Selection responses for landscape variables were dependent on subregion, animal age class, and diel period. Contrary to expectations, caracals did not become more nocturnal in urban areas. Caracals increased their selection for proximity to urban areas as the proportion of urban area increased. Differences in habitat selection between urban and wildland caracals suggest that individuals of this generalist species exhibit high behavioral flexibility in response to anthropogenic disturbances that emerge as a function of habitat context.

The ecology of human-caused mortality for a protected large carnivore.

Mitigating human-caused mortality for large carnivores is a pressing global challenge for wildlife conservation. However, mortality is almost exclusively studied at local (within-population) scales creating a mismatch between our understanding of risk and the spatial extent most relevant to conservation and management of wide-ranging species. Here, we quantified mortality for 590 radio-collared mountain lions statewide across their distribution in California to identify drivers of human-caused mortality and investigate whether human-caused mortality is additive or compensatory. Human-caused mortality, primarily from conflict management and vehicles, exceeded natural mortality despite mountain lions being protected from hunting. Our data indicate that human-caused mortality is additive to natural mortality as population-level survival decreased as a function of increasing human-caused mortality and natural mortality did not decrease with increased human-caused mortality. Mortality risk increased for mountain lions closer to rural development and decreased in areas with higher proportions of citizens voting to support environmental initiatives. Thus, the presence of human infrastructure and variation in the mindset of humans sharing landscapes with mountain lions appear to be primary drivers of risk. We show that human-caused mortality can reduce population-level survival of large carnivores across large spatial scales, even when they are protected from hunting.

Habitat fragmentation reduces survival and drives source-sink dynamics for a large carnivore.

Rigorous understanding of how environmental conditions impact population dynamics is essential for species conservation, especially in mixed-use landscapes where source-sink dynamics may be at play. Conservation of large carnivore populations in fragmented, human-dominated landscapes is critical for their long-term persistence. However, living in human-dominated landscapes comes with myriad costs, including direct anthropogenic mortality and sublethal energetic costs. How these costs impact individual fitness and population dynamics are not fully understood, partly due to the difficulty in collecting long-term demographic data for these species. Here, we analyzed an 11-year dataset on puma (Puma concolor) space use, mortality, and reproduction in the Santa Cruz Mountains, California, USA, to quantify how living in a fragmented landscape impacts individual survival and population dynamics. Long-term exposure to housing density drove mortality risk for female pumas, resulting in an 18-percentage-point reduction in annual survival for females in exurban versus remote areas. While the overall population growth rate appeared stable, reduced female survival in more developed areas resulted in source-sink dynamics across the study area, with 42.1% of the Santa Cruz Mountains exhibiting estimated population growth rates <1. Since habitat selection is often used as a proxy for habitat quality, we also assessed whether puma habitat selection predicted source and sink areas. Patterns of daytime puma habitat selection predicted source areas, while time-of-day-independent habitat selection performed less well as a proxy. These results illuminate the individual- and population-level consequences of habitat fragmentation for large carnivores, illustrating that habitat fragmentation can produce source-sink dynamics that may not be apparent from other metrics of habitat quality. Locally, conserving high-quality source habitat within the Santa Cruz Mountains is necessary to support long-term puma population persistence. More broadly, source-sink dynamics may at play for other carnivore populations in similar fragmented systems, and linking landscape conditions to population dynamics is essential for effective conservation. Caution should be used in inferring habitat quality from habitat selection alone, but these results shed light on metrics of selection that may be better or worse proxies to identify source areas for large carnivores.

Standardizing protocols for determining the cause of mortality in wildlife studies.

Mortality site investigations of telemetered wildlife are important for cause-specific survival analyses and understanding underlying causes of observed population dynamics. Yet, eroding ecoliteracy and a lack of quality control in data collection can lead researchers to make incorrect conclusions, which may negatively impact management decisions for wildlife populations. We reviewed a random sample of 50 peer-reviewed studies published between 2000 and 2019 on survival and cause-specific mortality of ungulates monitored with telemetry devices. This concise review revealed extensive variation in reporting of field procedures, with many studies omitting critical information for the cause of mortality inference. Field protocols used to investigate mortality sites and ascertain the cause of mortality are often minimally described and frequently fail to address how investigators dealt with uncertainty. We outline a step-by-step procedure for mortality site investigations of telemetered ungulates, including evidence that should be documented in the field. Specifically, we highlight data that can be useful to differentiate predation from scavenging and more conclusively identify the predator species that killed the ungulate. We also outline how uncertainty in identifying the cause of mortality could be acknowledged and reported. We demonstrate the importance of rigorous protocols and prompt site investigations using data from our 5-year study on survival and cause-specific mortality of telemetered mule deer (Odocoileus hemionus) in northern California. Over the course of our study, we visited mortality sites of neonates (n = 91) and adults (n = 23) to ascertain the cause of mortality. Rapid site visitations significantly improved the successful identification of the cause of mortality and confidence levels for neonates. We discuss the need for rigorous and standardized protocols that include measures of confidence for mortality site investigations. We invite reviewers and journal editors to encourage authors to provide supportive information associated with the identification of causes of mortality, including uncertainty.

Temporal scale of habitat selection for large carnivores: Balancing energetics, risk and finding prey.

When navigating heterogeneous landscapes, large carnivores must balance trade-offs between multiple goals, including minimizing energetic expenditure, maintaining access to hunting opportunities and avoiding potential risk from humans. The relative importance of these goals in driving carnivore movement likely changes across temporal scales, but our understanding of these dynamics remains limited. Here we quantified how drivers of movement and habitat selection changed with temporal grain for two large carnivore species living in human-dominated landscapes, providing insights into commonalities in carnivore movement strategies across regions. We used high-resolution GPS collar data and integrated step selection analyses to model movement and habitat selection for African lions Panthera leo in Laikipia, Kenya and pumas Puma concolor in the Santa Cruz Mountains of California across eight temporal grains, ranging from 5 min to 12 hr. Analyses considered landscape covariates that are related to energetics, resource acquisition and anthropogenic risk. For both species, topographic slope, which strongly influences energetic expenditure, drove habitat selection and movement patterns over fine temporal grains but was less important at longer temporal grains. In contrast, avoiding anthropogenic risk during the day, when risk was highest, was consistently important across grains, but the degree to which carnivores relaxed this avoidance at night was strongest for longer term movements. Lions and pumas modified their movement behaviour differently in response to anthropogenic features: lions sped up while near humans at fine temporal grains, while pumas slowed down in more developed areas at coarse temporal grains. Finally, pumas experienced a trade-off between energetically efficient movement and avoiding anthropogenic risk. Temporal grain is an important methodological consideration in habitat selection analyses, as drivers of both movement and habitat selection changed across temporal grain. Additionally, grain-dependent patterns can reflect meaningful behavioural processes, including how fitness-relevant goals influence behaviour over different periods of time. In applying multi-scale analysis to fine-resolution data, we showed that two large carnivore species in very different human-dominated landscapes balanced competing energetic and safety demands in largely similar ways. These commonalities suggest general strategies of landscape use across large carnivore species.

Complex evolutionary history of felid anelloviruses.

Anellovirus infections are highly prevalent in mammals, however, prior to this study only a handful of anellovirus genomes had been identified in members of the Felidae family. Here we characterise anelloviruses in pumas (Puma concolor), bobcats (Lynx rufus), Canada lynx (Lynx canadensis), caracals (Caracal caracal) and domestic cats (Felis catus). The complete anellovirus genomes (n = 220) recovered from 149 individuals were diverse. ORF1 protein sequence similarity network analysis coupled with phylogenetic analysis, revealed two distinct clusters that are populated by felid-derived anellovirus sequences, a pattern mirroring that observed for the porcine anelloviruses. Of the two-felid dominant anellovirus groups, one includes sequences from bobcats, pumas, domestic cats and an ocelot, and the other includes sequences from caracals, Canada lynx, domestic cats and pumas. Coinfections of diverse anelloviruses appear to be common among the felids. Evidence of recombination, both within and between felid-specific anellovirus groups, supports a long coevolution history between host and virus.

Functional traits driving species role in the structure of terrestrial vertebrate scavenger networks.

Species assemblages often have a non-random nested organization, which in vertebrate scavenger (carrion-consuming) assemblages is thought to be driven by facilitation in competitive environments. However, not all scavenger species play the same role in maintaining assemblage structure, as some species are obligate scavengers (i.e., vultures) and others are facultative, scavenging opportunistically. We used a database with 177 vertebrate scavenger species from 53 assemblages in 22 countries across five continents to identify which functional traits of scavenger species are key to maintaining the scavenging network structure. We used network analyses to relate ten traits hypothesized to affect assemblage structure with the "role" of each species in the scavenging assemblage in which it appeared. We characterized the role of a species in terms of both the proportion of monitored carcasses on which that species scavenged, or scavenging breadth (i.e., the species "normalized degree"), and the role of that species in the nested structure of the assemblage (i.e., the species "paired nested degree"), therefore identifying possible facilitative interactions among species. We found that species with high olfactory acuity, social foragers, and obligate scavengers had the widest scavenging breadth. We also found that social foragers had a large paired nested degree in scavenger assemblages, probably because their presence is easier to detect by other species to signal carcass occurrence. Our study highlights differences in the functional roles of scavenger species and can be used to identify key species for targeted conservation to maintain the ecological function of scavenger assemblages.

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.

Disturbance type and species life history predict mammal responses to humans.

Human activity and land use change impact every landscape on Earth, driving declines in many animal species while benefiting others. Species ecological and life history traits may predict success in human-dominated landscapes such that only species with "winning" combinations of traits will persist in disturbed environments. However, this link between species traits and successful coexistence with humans remains obscured by the complexity of anthropogenic disturbances and variability among study systems. We compiled detection data for 24 mammal species from 61 populations across North America to quantify the effects of (1) the direct presence of people and (2) the human footprint (landscape modification) on mammal occurrence and activity levels. Thirty-three percent of mammal species exhibited a net negative response (i.e., reduced occurrence or activity) to increasing human presence and/or footprint across populations, whereas 58% of species were positively associated with increasing disturbance. However, apparent benefits of human presence and footprint tended to decrease or disappear at higher disturbance levels, indicative of thresholds in mammal species' capacity to tolerate disturbance or exploit human-dominated landscapes. Species ecological and life history traits were strong predictors of their responses to human footprint, with increasing footprint favoring smaller, less carnivorous, faster-reproducing species. The positive and negative effects of human presence were distributed more randomly with respect to species trait values, with apparent winners and losers across a range of body sizes and dietary guilds. Differential responses by some species to human presence and human footprint highlight the importance of considering these two forms of human disturbance separately when estimating anthropogenic impacts on wildlife. Our approach provides insights into the complex mechanisms through which human activities shape mammal communities globally, revealing the drivers of the loss of larger predators in human-modified landscapes.

Energetics and fear of humans constrain the spatial ecology of pumas.

Energetic demands and fear of predators are considered primary factors shaping animal behavior, and both are likely drivers of movement decisions that ultimately determine the spatial ecology of wildlife. Yet energetic constraints on movement imposed by the physical landscape have only been considered separately from those imposed by risk avoidance, limiting our understanding of how short-term movement decisions scale up to affect long-term space use. Here, we integrate the costs of both physical terrain and predation risk into a common currency, energy, and then quantify their effects on the short-term movement and long-term spatial ecology of a large carnivore living in a human-dominated landscape. Using high-resolution GPS and accelerometer data from collared pumas (Puma concolor), we calculated the short-term (i.e., 5-min) energetic costs of navigating both rugged physical terrain and a landscape of risk from humans (major sources of both mortality and fear for our study population). Both the physical and risk landscapes affected puma short-term movement costs, with risk having a relatively greater impact by inducing high-energy but low-efficiency movement behavior. The cumulative effects of short-term movement costs led to reductions of 29% to 68% in daily travel distances and total home range area. For male pumas, long-term patterns of space use were predominantly driven by the energetic costs of human-induced risk. This work demonstrates that, along with physical terrain, predation risk plays a primary role in shaping an animal's "energy landscape" and suggests that fear of humans may be a major factor affecting wildlife movements worldwide.

Surviving in steep terrain: a lab-to-field assessment of locomotor costs for wild mountain lions (Puma concolor).

BACKGROUND: Under current scenarios of climate change and habitat loss, many wild animals, especially large predators, are moving into novel energetically challenging environments. Consequently, changes in terrain associated with such moves may heighten energetic costs and effect the decline of populations in new localities. METHODS: To examine locomotor costs of a large carnivorous mammal moving in mountainous habitats, the oxygen consumption of captive pumas (Puma concolor) was measured during treadmill locomotion on level and incline (6.8°) surfaces. These data were used to predict energetic costs of locomotor behaviours of free-ranging pumas equipped with GPS/accelerometer collars in California's Santa Cruz Mountains. RESULTS: Incline walking resulted in a 42.0% ± 7.2 SEM increase in the costs of transport compared to level performance. Pumas negotiated steep terrain by traversing across hillsides (mean hill incline 17.2° ± 0.3 SEM; mean path incline 7.3° ± 0.1 SEM). Pumas also walked more slowly up steeper paths, thereby minimizing the energetic impact of vertical terrains. Estimated daily energy expenditure (DEE) based on GPS-derived speeds of free-ranging pumas was 18.3 MJ day- 1 ± 0.2 SEM. Calculations show that a 20 degree increase in mean steepness of the terrain would increase puma DEE by less than 1% as they only spend a small proportion (10%) of their day travelling. They also avoided elevated costs by utilizing slower speeds and shallower path angles. CONCLUSIONS: While many factors influence survival in novel habitats, we illustrate the importance of behaviours which reduce locomotor costs when traversing new, energetically challenging environments, and demonstrate that these behaviours are utilised by pumas in the wild.

Mixed-species herding levels the landscape of fear.

Prey anti-predator behaviours are influenced by perceived predation risk in a landscape and social information gleaned from herd mates regarding predation risk. It is well documented that high-quality social information about risk can come from heterospecific herd mates. Here, we integrate social information with the landscape of fear to quantify how these landscapes are modified by mixed-species herding. To do this, we investigated zebra vigilance in single- and mixed-species herds across different levels of predation risk (lion versus no lion), and assessed how they manage herd size and the competition-information trade-off associated with grouping behaviour. Overall, zebra performed higher vigilance in high-risk areas. However, mixed-species herding reduced vigilance levels. We estimate that zebra in single-species herds would have to feed for approximately 35 min more per day in low-risk areas and approximately 51 min more in high-risk areas to compensate for the cost of higher vigilance. Furthermore, zebra benefitted from the competition-information trade-off by increasing the number of heterospecifics while keeping the number of zebra in a herd constant. Ultimately, we show that mixed-species herding reduces the effects of predation risk, whereby zebra in mixed-species herds, under high predation risk, perform similar levels of vigilance compared with zebra in low-risk scenarios.

How climate impacts the composition of wolf-killed elk in northern Yellowstone National Park.

While the functional response of predators is commonly measured, recent work has revealed that the age and sex composition of prey killed is often a better predictor of prey population dynamics because the reproductive value of adult females is usually higher than that of males or juveniles. Climate is often an important mediating factor in determining the composition of predator kills, but we currently lack a mechanistic understanding of how the multiple facets of climate interact with prey abundance and demography to influence the composition of predator kills. Over 20 winters, we monitored 17 wolf packs in Yellowstone National Park and recorded the sex, age and nutritional condition of kills of their dominant prey-elk-in both early and late winter periods when elk are in relatively good and relatively poor condition, respectively. Nutritional condition (as indicated by per cent marrow fat) of wolf-killed elk varied markedly with summer plant productivity, snow water equivalent (SWE) and winter period. Moreover, marrow was poorer for wolf-killed bulls and especially for calves than it was for cows. Wolf prey composition was influenced by a complex set of climatic and endogenous variables. In early winter, poor plant growth in either year t or t - 1, or relatively low elk abundance, increased the odds of wolves killing bulls relative to cows. Calves were most likely to get killed when elk abundance was high and when the forage productivity they experienced in utero was poor. In late winter, low SWE and a relatively large elk population increased the odds of wolves killing calves relative to cows, whereas low SWE and poor vegetation productivity 1 year prior together increased the likelihood of wolves killing a bull instead of a cow. Since climate has a strong influence on whether wolves prey on cows (who, depending on their age, are the key reproductive components of the population) or lower reproductive value of calves and bulls, our results suggest that climate can drive wolf predation to be more or less additive from year to year.

Author Correction: Puma genomes from North and South America provide insights into the genomic consequences of inbreeding.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Marine fog inputs appear to increase methylmercury bioaccumulation in a coastal terrestrial food web.

Coastal marine atmospheric fog has recently been implicated as a potential source of ocean-derived monomethylmercury (MMHg) to coastal terrestrial ecosystems through the process of sea-to-land advection of foggy air masses followed by wet deposition. This study examined whether pumas (Puma concolor) in coastal central California, USA, and their associated food web, have elevated concentrations of MMHg, which could be indicative of their habitat being in a region that is regularly inundated with marine fog. We found that adult puma fur and fur-normalized whiskers in our marine fog-influenced study region had a mean (±SE) total Hg (THg) (a convenient surrogate for MMHg) concentration of 1544 ± 151 ng g-1 (N = 94), which was three times higher (P < 0.01) than mean THg in comparable samples from inland areas of California (492 ± 119 ng g-1, N = 18). Pumas in California eat primarily black-tailed and/or mule deer (Odocoileus hemionus), and THg in deer fur from the two regions was also significantly different (coastal 28.1 ± 2.9, N = 55, vs. inland 15.5 ± 1.5 ng g-1, N = 40). We suggest that atmospheric deposition of MMHg through fog may be contributing to this pattern, as we also observed significantly higher MMHg concentrations in lace lichen (Ramalina menziesii), a deer food and a bioindicator of atmospheric deposition, at sites with the highest fog frequencies. At these ocean-facing sites, deer samples had significantly higher THg concentrations compared to those from more inland bay-facing sites. Our results suggest that fog-borne MMHg, while likely a small fraction of Hg in all atmospheric deposition, may contribute, disproportionately, to the bioaccumulation of Hg to levels that approach toxicological thresholds in at least one apex predator. As global mercury levels increase, coastal food webs may be at risk to the toxicological effects of increased methylmercury burdens.

Puma genomes from North and South America provide insights into the genomic consequences of inbreeding.

Pumas are the most widely distributed felid in the Western Hemisphere. Increasingly, however, human persecution and habitat loss are isolating puma populations. To explore the genomic consequences of this isolation, we assemble a draft puma genome and a geographically broad panel of resequenced individuals. We estimate that the lineage leading to present-day North American pumas diverged from South American lineages 300-100 thousand years ago. We find signatures of close inbreeding in geographically isolated North American populations, but also that tracts of homozygosity are rarely shared among these populations, suggesting that assisted gene flow would restore local genetic diversity. The genome of a Florida panther descended from translocated Central American individuals has long tracts of homozygosity despite recent outbreeding. This suggests that while translocations may introduce diversity, sustaining diversity in small and isolated populations will require either repeated translocations or restoration of landscape connectivity. Our approach provides a framework for genome-wide analyses that can be applied to the management of similarly small and isolated populations.