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The gray fox (Urocyon cinereoargenteus) lineage diverged from all other extant canids at their most basal node and is restricted to the Americas. Previous mitochondrial analysis from coastal populations identified deeply divergent (up to 1 Mya) eastern and western lineages that predate most intraspecific splits in carnivores. We conducted genotyping by sequencing and mitochondrial analysis on gray foxes sampled across North America to determine geographic concordance between nuclear and mitochondrial contact zones and divergence times. We also estimated the admixture within the contact zone between eastern and western gray foxes based on nuclear DNA. Both datasets confirmed that eastern and western lineages met in the southern Great Plains (i.e. Texas and Oklahoma), where they maintained high differentiation. Admixture was generally low, with the majority of admixed individuals carrying

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.

Long-term studies of mountain lions (Puma concolor) in Southern California have documented persistent small population sizes and the lowest genetic variation of any mountain lion population, except for the Federally endangered mountain lion subspecies, the Florida panther (Puma concolor coryi). There is overwhelming molecular evidence supporting inbreeding and low genetic diversity in these Southern California populations but there is a lack of phenotypical evidence of inbreeding depression. The primary goal of this study was to assess male mountain lions, in Southern California, for teratospermia (>60% abnormal sperm production), one of the first signs of inbreeding depression in mountain lions that are associated with decreased reproduction and population decline. From December 2019 to December 2020, we surveyed mountain lions during live captures, after mortality events, and in images collected from camera traps in the following populations: Santa Monica Mountains, Santa Susana Mountains, Santa Ana Mountains, and the Eastern Peninsular Range. Mountain lions were sampled for known physical abnormalities associated with inbreeding depression such as teratospermia, cryptorchidism, and distal tail kinks. For teratospermia, we extracted testes from five males post-mortem to assess sperm morphology. Epididymal sperm evaluations revealed all males were teratospermic. Across all samples, on average, 93% of observed spermatozoa were abnormal. We physically examined 32 mountain lions (males and females) for distal tail kinks, and we observed one individual affected. We examined 15 male mountain lions for cryptorchidism, and we observed one unilaterally cryptorchid male and one male with testes that differed significantly in size, likely reflecting asynchronous migration of the testes during puberty. Further, we identified three other animals in camera-trap images that had distal tail kinks, for a total of four. In conclusion, from December 2019 to December 2020, we identified nine individuals exhibiting physical signs of inbreeding depression. These reproductive and physical signs of inbreeding depression in Southern California mountain lions increase the urgency of conservation efforts in the region.

Spatially heterogeneous landscape factors such as urbanisation can have substantial effects on the severity and spread of wildlife diseases. However, research linking patterns of pathogen transmission to landscape features remains rare. Using a combination of phylogeographic and machine learning approaches, we tested the influence of landscape and host factors on feline immunodeficiency virus (FIVLru) genetic variation and spread among bobcats (Lynx rufus) sampled from coastal southern California. We found evidence for increased rates of FIVLru lineage spread through areas of higher vegetation density. Furthermore, single-nucleotide polymorphism (SNP) variation among FIVLru sequences was associated with host genetic distances and geographic location, with FIVLru genetic discontinuities precisely correlating with known urban barriers to host dispersal. An effect of forest land cover on FIVLru SNP variation was likely attributable to host population structure and differences in forest land cover between different populations. Taken together, these results suggest that the spread of FIVLru is constrained by large-scale urban barriers to host movement. Although urbanisation at fine spatial scales did not appear to directly influence virus transmission or spread, we found evidence that viruses transmit and spread more quickly through areas containing higher proportions of natural habitat. These multiple lines of evidence demonstrate how urbanisation can change patterns of contact-dependent pathogen transmission and provide insights into how continued urban development may influence the incidence and management of wildlife disease.

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. ispartof: VIROLOGY vol:562 pages:176-189 ispartof: location:United States status: published

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

Polyomaviruses are oncogenic viruses that are generally thought to have co-evolved with their hosts. While primate and rodent polyomaviruses are increasingly well-studied, less is known about polyomaviruses that infect other mammals. In an effort to gain insight into polyomaviruses associated with carnivores, we surveyed fecal samples collected in the USA from bobcats (Lynx rufus), pumas (Puma concolor), Canada lynxes (Lynx canadensis), and grizzly bears (Ursus arctos). Using a viral metagenomic approach, we identified six novel polyomavirus genomes. Surprisingly, four of the six genomes showed a phylogenetic relationship to polyomaviruses found in prey animals. These included a putative rabbit polyomavirus from a bobcat fecal sample and two possible deer-trophic polyomaviruses from Canada lynx feces. One polyomavirus found in a grizzly bear sample was found to be phylogenetically distant from previously identified polyomaviruses. Further analysis of the grizzly bear fecal sample showed that it contained anelloviruses that are known to infect pigs, suggesting that the bear might have preyed on a wild or domestic pig. Interestingly, a polyomavirus genome identified in a puma fecal sample was found to be closely related both to raccoon polyomavirus 1 and to Lyon-IARC polyomavirus, the latter of which was originally identified in human saliva and skin swab specimens but has since been found in samples from domestic cats (Felis catus).

In human-dominated landscapes, habitat fragmentation and barriers to movement can interrupt gene flow. While often considered at a local extent, regional analyses are also needed to reveal broader landscape-mediated population processes. To explore the relationship between patterns of gene flow and fragmentation resulting from urbanization across southern California, we used the bobcat as an indicator species. We assembled data for a landscape level genetic analysis across southern California from both archived and new samples, including two northern Californian populations for comparison, to identify local and regional areas affected by isolation. Our regional analyses focused on a dataset of 19 microsatellite loci for 118 individuals and a dataset of 422 individuals genotyped at 11 loci. We examined population genetic structure and examined how pairwise genetic distance of all population clusters aligned with geographic distance. We employed a landscape genetic analysis based on resistance to determine which features of the landscape likely play a role in determining the patterns of genetic structure we observed. Study populations generally exhibited a pattern of isolation by distance and localized areas of genetic isolation. The landscape genetic analysis suggested that, in southern California, these patterns are driven by overall landscape permeability. Although local studies are key to examining the effects of urbanization and habitat fragmentation on populations, we demonstrate the importance of combining local and regional analyses for wide-ranging species to understand and maintain connectivity at local scales, while also improving and establishing sustainable linkages to habitats at the regional scale.

Urbanization is decreasing wildlife habitat and connectivity worldwide, including for apex predators, such as the puma (

Urbanization is decreasing wildlife habitat and connectivity worldwide, including for apex predators, such as the puma (Puma concolor). Puma populations along California’s central and southern coastal habitats have experienced rapid fragmentation from development, leading to calls for demographic and genetic management. To address urgent conservation genomic concerns, we used double-digest restriction-site associated DNA (ddRAD) sequencing to analyze 16,285 genome-wide single-nucleotide polymorphisms (SNPs) from 401 broadly sampled pumas. Our analyses indicated support for 4–10 geographically nested, broad- to fine-scale genetic clusters. At the broadest scale, the 4 genetic clusters had high genetic diversity and exhibited low linkage disequilibrium, indicating pumas have retained statewide genomic diversity. However, multiple lines of evidence indicated substructure, including 10 fine-scale genetic clusters, some of which exhibited allelic fixation and linkage disequilibrium. Fragmented populations along the Southern Coast and Central Coast had particularly low genetic diversity and strong linkage disequilibrium, indicating genetic drift and close inbreeding. Our results demonstrate that genetically at-risk populations are typically nested within a broader-scale group of interconnected populations that collectively retains high genetic diversity and heterogeneous fixations. Thus, extant variation at the broader scale has potential to restore diversity to local populations if management actions can enhance vital gene flow and recombine locally sequestered genetic diversity. These state- and genome-wide results are critically important for science-based conservation and management practices. Our broad- and fine-scale population genomic analysis highlights the information that can be gained from population genomic studies aiming to provide guidance for fragmented population conservation management.

Wildlife strongly alter behaviour in response to human disturbance; however, fundamental questions remain regarding the influence of human infrastructure and activity on animal movement. The Covid‐19 pandemic created a natural experiment providing an opportunity to evaluate wildlife movement during a period of greatly reduced human activity. Speculation in scientific reviews and the media suggested that wildlife might be increasing movement and colonizing urban landscapes during pandemic slowdowns. However, theory predicts that animals should move and use space as efficiently as possible, suggesting that movement might actually be reduced relative to decreased human activity. We quantified space use, movement, and resource‐selection of 12 GPS‐collared mountain lions (eight females, four males) occupying parklands in greater Los Angeles during the Spring 2020 California stay‐at‐home order when human activity was far below normal. We also tested the hypothesis that reduced traffic on Los Angeles area roadways increased permeability of these barriers to animal movement. Contrary to expectations that wildlife roamed more widely during pandemic shutdowns, resident mountain lions used smaller areas and moved shorter distances relative to their historical behaviour in greater Los Angeles. They also relaxed avoidance of anthropogenic landscape features such as trails and development, which likely facilitated increased travelling efficiency. However, there was no detectable change in road‐crossing, despite reduced traffic volume. Our results support the theoretical prediction that animals maximize movement efficiency and suggest that carnivores incur energetic costs while avoiding humans. While mountain lions may restrict movement at the landscape level relative to barriers, they appear to increase distances moved at finer scales when avoiding human activity – highlighting the scale‐dependent nature of animal responses to human disturbance. Avoiding humans can reduce direct mortality of large carnivores and is often suggested to be an important mechanism promoting coexistence in shared landscapes. However, energetic costs incurred by increased movement and space‐use while avoiding human activity may have important consequences for population viability, predator–prey interactions, community structure, and human–wildlife conflict. Management providing sufficient wild prey and education regarding best practices for protection of domestic animals are important for conserving large carnivores in human‐dominated landscapes.

Urbanization is a major contributor to habitat loss and fragmentation and is considered a global threat to biodiversity. We studied reptile and amphibian species diversity and abundance in a highly fragmented landscape adjacent to the second largest metropolitan area in the United States. Habitat patches in our study area were made up of remnant native vegetation surrounded by roads, housing, and other urban development. Species richness and diversity were positively associated with patch size, but patch age was not significantly associated with community characteristics. Four relatively common species were not detected in the small patches, indicating the possibility they had been extirpated by the time monitoring began, and six rarer species were not detected or detected only once in these patches. Although the patch size effect on species diversity was strong, we found that several of the small habitat patches had similar diversity to large patches, indicating potential value of these small habitat patches in protecting species as “microreserves.” In addition, one lizard species was found to be significantly more abundant in the smaller patches. To determine if abundance changed over time, we compared capture rates for four common lizards at the same sites ten years later. For three of the four species, abundance decreased over that period, specifically in the small patches. Although our long-term monitoring has confirmed that the full suite of herpetofauna is currently preserved in the study area overall, declines even in the common species over time hint at the potential severity of the threat of urbanization to rare species.

Smacoviruses are small circular single-stranded DNA viruses that appear to be prevalent in faeces of a range of animals and have also been found in a few insect species. In this study, we report the first viral genomes from faeces of free-roaming wild felids on two continents. Two smacoviruses were recovered from the faeces of two North American bobcats (Lynx rufus), and one was recovered from an African lion (Panthera leo). All three genomes are genetically different, sharing 59-69% genome-wide sequence identity to other smacoviruses. These are the first full smacovirus genome sequences associated with a large top-end feline predator, and their presence in these samples suggests that feline faeces are a natural niche for the organisms that these viruses infect. Electronic supplementary material The online version of this article (10.1007/s00705-019-04329-3) contains supplementary material, which is available to authorized users.

Mammals are known to vary in their sensitivity to urbanization. In heavily urbanized southern California, bobcats (Lynx rufus) prey on rabbits (Sylvilagus spp.) that forage for lush vegetation in developed areas. We collected data on the density of rabbits in adjacent urban and natural areas using visual line surveys. We also measured habitat use for seven GPS-collared female bobcats to determine if bobcats selected areas with higher rabbit densities. Estimated rabbit densities did not vary between urban, urban edge, and natural areas during wet or dry seasons, reflecting their consistent presence across the landscape. During daytime and crepuscular hours, bobcats used natural coastal sage scrub and grassland habitats more frequently (76–84% of the time) than urban areas. Conversely, at night, bobcats decreased their use of coastal sage scrub and doubled their time in urban areas. In summary, we found that rabbits were present across the landscape, and bobcats are likely selecting urban areas at night to prey on rabbits and avoid people.

Fragmentation of wildlife populations is increasing on a global scale and understanding current population genetic structure, genetic diversity, and genetic connectivity is key to informing wildlife management and conservation. We genotyped 992 pumas (Puma concolor) at 42 previously developed microsatellite loci and identified 10 genetic populations throughout the states of California and Nevada, USA. Although some genetic populations had large effective population sizes, others were small and inbred. Genetic diversity was extremely variable (heterozygosity, uHe = 0.33–0.53), with some populations nearly as low as an endangered subspecies, the Florida Panther (P. c. coryi, uHe = 0.24). Specifically, pumas in the Sierra Nevada were genetically diverse and formed the largest genetic source population in the region. In contrast, coastal and southern populations surrounded by urbanization had low genetic diversity, fragmented gene flow, and tended to be genetic sinks. The strong population genetic structuring of pumas across California (FST = 0.05–0.39) is vastly different than other genetic studies in less-urbanized states, including our analysis in Nevada, where pumas had few barriers to gene flow and weak population differentiation. Our results have far-reaching conservation and management implications for pumas and indicate large-scale fragmentation in one of North America’s most biodiverse and rapidly-urbanizing regions.

Fragmentation within urbanized environments often leads to a loss of native species diversity; however, variation exists in responses among-species and among-populations within species. We aimed to identify patterns in species biogeography in an urbanized landscape to understand anthropogenic effects on vertebrate communities and identify species that are more sensitive or resilient to landscape change. We investigated patterns in species richness and species responses to fragmentation in southern Californian small vertebrate communities using multispecies occupancy models and determined factors associated with overall commonness and sensitivity to patch size for 45 small vertebrate species both among and within remaining non-developed patches. In general, smaller patches had fewer species, with amphibian species richness being particularly sensitive to patch size effects. Mammals were generally more common, occurring both in a greater proportion of patches and a higher proportion of the sites within occupied patches. Alternatively, amphibians were generally restricted to larger patches but were more ubiquitous within smaller patches when occupied. Species range size was positively correlated with how common a species was across and within patches, even when controlling for only patches that fell within a species' range. We found sensitivity to patch size was greater for more fecund species and depended on where the patch occurred within a species' range. While all taxa were more likely to occur in patches in the warmer portions of their ranges, amphibians and mammals were more sensitive to fragmentation in these warmer areas as compared to the rest of their ranges. Similarly, amphibians occurred at a smaller proportion of sites within patches in drier portions of their ranges. Mammals occurred at a higher proportion of sites that were also in drier portions of their range while reptiles did not differ in their sensitivity to patch size by range position. We demonstrate that taxonomy, life history, range size and range position can predict commonness and sensitivity of species across this highly fragmented yet biodiverse landscape. The impacts of fragmentation on species communities within an urban landscape depend on scale, with differences emerging among and within species and populations.

Urbanization is increasing throughout the world, transforming natural habitats. Coyotes (Canis latrans) are found in highly urban, suburban, rural and undeveloped mountainous habitats, making them an exemplary model organism to investigate the effects of urbanization on animals. We hypothesized that coyotes in natural habitats are more genetically related to distant coyotes in similar natural habitats and less related to coyotes in urban areas due to natal habitat-biased dispersal. We also hypothesized that increasing urbanization would result in decreased genetic diversity due to habitat fragmentation, dispersal barriers and genetic drift. We analyzed 10 microsatellite genetic markers from 125 individual coyotes sampled across a spectrum of highly urban to highly natural areas in southern California. Most coyotes clustered into four distinct genetic populations, whereas others appeared to have admixed ancestry. Three genetic populations were associated primarily with urban habitats in Los Angeles and Orange Counties. In contrast, the remaining population was associated with more naturally vegetated land near the surrounding mountains. Coyotes living in natural areas formed a genetically distinct cluster despite long geographic distances separating them. Genetic diversity was negatively associated with urban/suburban land cover and local road density, and positively associated with the relative amount of natural vegetation. These results indicate that genetic differentiation and loss of genetic diversity coincided with the extremely rapid expansion of Greater Los Angeles throughout the 1900s. Thus, urbanization reduces gene flow and erodes genetic diversity even in a habitat generalist thought to be minimally impacted by land development.

Author(s): Saremi, Nedda F; Supple, Megan A; Byrne, Ashley; Cahill, James A; Coutinho, Luiz Lehmann; Dalen, Love; Figueiro, Henrique V; Johnson, Warren E; Milne, Heather J; O'Brien, Stephen J; O'Connell, Brendan; Onorato, David P; Riley, Seth PD; Sikich, Jeff A; Stahler, Daniel R; Villela, Priscilla Marqui Schmidt; Vollmers, Christopher; Wayne, Robert K; Eizirik, Eduardo; Corbett-Detig, Russell B; Green, Richard E; Wilmers, Christopher C; Shapiro, Beth | Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Understanding the environmental contributors to population structure is of paramount importance for conservation in urbanized environments. We used spatially explicit models to determine genetic population structure under current and future environmental conditions across a highly fragmented, human-dominated environment in Southern California to assess the effects of natural ecological variation and urbanization. We focused on 7 common species with diverse habitat requirements, home-range sizes, and dispersal abilities. We quantified the relative roles of potential barriers, including natural environmental characteristics and an anthropogenic barrier created by a major highway, in shaping genetic variation. The ability to predict genetic variation in our models differed among species: 11-81% of intraspecific genetic variation was explained by environmental variables. Although an anthropogenically induced barrier (a major highway) severely restricted gene flow and movement at broad scales for some species, genetic variation seemed to be primarily driven by natural environmental heterogeneity at a local level. Our results show how assessing environmentally associated variation for multiple species under current and future climate conditions can help identify priority regions for maximizing population persistence under environmental change in urbanized regions.

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., Pumas are experiencing increased isolation as human persecution and habitat loss fragment the populations of this once widespread species. Here, the authors estimate the genomic consequences of this isolation by analyzing the genomes of ten pumas from across North and South America.

Feline foamy virus (FFV) is a retrovirus that has been detected in multiple feline species, including domestic cats (Felis catus) and pumas (Puma concolor). FFV results in persistent infection but is generally thought to be apathogenic. Sero-prevalence in domestic cat populations has been documented in several countries, but the extent of viral infections in nondomestic felids has not been reported. In this study, we screened sera from 348 individual pumas from Colorado, Southern California and Florida for FFV exposure by assessing sero-reactivity using an FFV anti-Gag ELISA. We documented a sero-prevalence of 78.6% across all sampled subpopulations, representing 69.1% in Southern California, 77.3% in Colorado, and 83.5% in Florida. Age was a significant risk factor for FFV infection when analyzing the combined populations. This high prevalence in geographically distinct populations reveals widespread exposure of puma to FFV and suggests efficient shedding and transmission in wild populations.

Introduction paragraph/AbstractAcross the geographic range of mountain lions, which includes much of North and South America, populations have become increasingly isolated due to human persecution and habitat loss. To explore the genomic consequences of these processes, we assembled a high-quality mountain lion genome and analyzed a panel of resequenced individuals from across their geographic range. We found strong geographical structure and signatures of severe inbreeding in all North American populations. Tracts of homozygosity were rarely shared among populations, suggesting that assisted gene flow would restore local genetic diversity. However, the genome of an admixed Florida panther that descended from a translocated individual from Central America had surprisingly long tracts of homozygosity, indicating that genomic gains from translocation were quickly lost by local inbreeding. Thus, to sustain diversity, genetic rescue will need to occur at regular intervals, through repeated translocations or restoring landscape connectivity. Mountain lions provide a rare opportunity to examine the potential to restore diversity through genetic rescue, and to observe the long-term effects of translocation. Our methods and results provide a framework for genome-wide analyses that can be applied to the management of small and isolated populations.

SUMMARYNotoedric mange, caused by obligately parasitic sarcoptiform Notoedres mites, is associated with potentially fatal dermatitis with secondary systemic disease in small mammals, felids and procyonids among others, as well as an occasional zoonosis. We describe clinical spectra in non-chiropteran hosts, review risk factors and summarize ecological and epidemiological studies. The genus is disproportionately represented on rodents. Disease in felids and procyonids ranges from very mild to death. Knowledge of the geographical distribution of the mites is highly inadequate, with focal hot spots known for Notoedres cati in domestic cats and bobcats. Predisposing genetic and immunological factors are not known, except that co-infection with other parasites and anticoagulant rodenticide toxicoses may contribute to severe disease. Treatment of individual animals is typically successful with macrocytic lactones such as selamectin, but herd or wildlife population treatment has not been undertaken. Transmission requires close contact and typically is within a host species. Notoedric mange can kill half all individuals in a population and regulate host population below non-diseased density for decades, consistent with frequency-dependent transmission or spillover from other hosts. Epidemics are increasingly identified in various hosts, suggesting global change in suitable environmental conditions or increased reporting bias.

Urban environments are unique because fragments of natural or semi-natural habitat are embedded within a potentially permeable matrix of human-dominated areas, creating increased landscape and, potentially, habitat heterogeneity. In addition, urban areas can provide diet subsidies for wildlife species in the form of fruiting ornamental plants, trash, and domestic animals. Ecological opportunity in the forms of habitat and food heterogeneity are thought to be important mechanisms in maintaining individual specialization. Identifying which contexts, traits, and mechanisms determine the success or failure of individuals within an urban wildlife population could potentially provide predictions about which populations may succeed in human-dominated landscapes and which may experience local extinction. We used both scat and stable isotope analysis of whiskers to investigate the degree to which coyotes (Canis latrans) utilized anthropogenic subsidies and exhibited individual diet specialization across the urban-rural gradient in southern California. Land use surrounding scat and isotope sample locations was also evaluated to determine the effect of land cover on diet. Human food constituted a significant portion of urban coyote diet (22% of scats, 38% of diet estimated by stable isotope analysis). Domestic cats (Felis catus) and ornamental fruit and seeds were also important items in urban coyote diets. Consumption of anthropogenic items decreased with decreasing urbanization. In suburban areas, seasonality influenced the frequency of occurrence of anthropogenic subsidies with increased consumption in the dry season. The amount of altered open space (areas such as golf courses, cemeteries, and landscaped parks) nearby had a negative effect on the consumption of anthropogenic items in both urban and suburban areas. Contrary to our hypothesis, urban coyotes displayed reduced between-individual variation compared to suburban and rural coyotes. It is possible that the core urban areas of cities are so densely developed and subsidized that wildlife inhabiting these areas actually have reduced ecological opportunity. Suburban animals had the broadest isotopic niches and maintained similar individual specialization to rural coyotes. Wildlife in suburban areas still have access to relatively undisturbed natural areas while being able to take advantage of anthropogenic subsidies in neighboring residential areas. Therefore, areas with intermediate urban development may be associated with increased ecological opportunity and specialization.

Understanding natural and human-caused mortality for top predators persisting in human-dominated landscapes is critical for conserving their populations. We estimated survival and cause-specific mortality rates and investigated factors influencing mortality risk of mountain lions by radio-tracking 58 individuals (33 males, 25 females) across the highly fragmented landscape in greater Los Angeles, California from 2002 to 2019. Mortality risk did not differ strongly between subadults (annual survival [ŝ] = 0.68, SE = 0.08) and adults (ŝ = 0.81, SE = 0.04). However, the different age-classes were subjected to mortality risks from different sources as subadults were more likely to be killed by conspecifics, whereas adults were more likely to die from human-caused mortality. Male subadults were frequently killed by territorial adult males in the isolated Santa Monica Mountains, mortality that may be exacerbated by substantial anthropogenic barriers to dispersal in this landscape. We also tracked kittens tagged at natal dens in the Santa Monica Mountains and estimated survival to independence to be 0.63 (SE = 0.13). Higher mortality from anthropogenic causes for adults, whose survival has the greatest influence on population growth and extinction probability for mountain lions, highlights the importance of mitigation strategies to reduce human-caused mortality. Our work provides novel information about patterns of survival and mortality of mountain lions from the most urbanized landscape occupied by large carnivores in North America.

Urbanization is a major factor driving habitat fragmentation and connectivity loss in wildlife. However, the impacts of urbanization on connectivity can vary among species and even populations due to differences in local landscape characteristics, and our ability to detect these relationships may depend on the spatial scale at which they are measured. Bobcats (Lynx rufus) are relatively sensitive to urbanization and the status of bobcat populations is an important indicator of connectivity in urban coastal southern California. We genotyped 271 bobcats at 13,520 SNP loci to conduct a replicated landscape resistance analysis in five genetically distinct populations. We tested urban and natural factors potentially influencing individual connectivity in each population separately, as well as study-wide. Overall, landscape genomic effects were most frequently detected at the study-wide spatial scale, with urban land cover (measured as impervious surface) having negative effects and topographic roughness having positive effects on gene flow. The negative effect of urban land cover on connectivity was also evident when populations were analyzed separately despite varying substantially in spatial area and the proportion of urban development, confirming a pervasive impact of urbanization largely independent of spatial scale. The effect of urban development was strongest in one population where stream habitat had been lost to development, suggesting that riparian corridors may help mitigate reduced connectivity in urbanizing areas. Our results demonstrate the importance of replicating landscape genetic analyses across populations and considering how landscape genetic effects may vary with spatial scale and local landscape structure.

Changing climate will impact species' ranges only when environmental variability directly impacts the demography of local populations. However, measurement of demographic responses to climate change has largely been limited to single species and locations. Here we show that amphibian communities are responsive to climatic variability, using >500,000 time-series observations for 81 species across 86 North American study areas. The effect of climate on local colonization and persistence probabilities varies among eco-regions and depends on local climate, species life-histories, and taxonomic classification. We found that local species richness is most sensitive to changes in water availability during breeding and changes in winter conditions. Based on the relationships we measure, recent changes in climate cannot explain why local species richness of North American amphibians has rapidly declined. However, changing climate does explain why some populations are declining faster than others. Our results provide important insights into how amphibians respond to climate and a general framework for measuring climate impacts on species richness. John Wesley Powell Center for Analysis and Synthesis - US Geological Survey U.S. Geological Survey-Amphibian Research and Monitoring Initiative (ARMI) U.S. Fish and Wildlife Service National Park Service U.S. Forest Service National Science Foundation [DEB-0841758, DEB-1149308] National Institutes of Health [R01GM109499] National Geographic Society Morris Animal Foundation David and Lucille Packard Foundation This work was conducted as part of the Amphibian Decline Working Group supported by the John Wesley Powell Center for Analysis and Synthesis, funded by the US Geological Survey. Funding and logistical support for field data collection came from a range of sources including the U.S. Geological Survey-Amphibian Research and Monitoring Initiative (ARMI), U.S. Fish and Wildlife Service, National Park Service, U.S. Forest Service, National Science Foundation (DEB-0841758, DEB-1149308), National Institutes of Health (R01GM109499), National Geographic Society, Morris Animal Foundation, and David and Lucille Packard Foundation. Data are deposited at the U.S. Geological Survey's John Wesley Powell Center for Analysis and Synthesis. This manuscript is contribution 654 of USGS ARMI. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

Extinction risk is elevated in small, isolated populations due to demographic and genetic interactions. Therefore, it is critical to model these processes realistically in population viability analyses (PVA) to inform local management and contribute to a greater understanding of mechanisms within the extinction vortex. We conducted PVA's for two small mountain lion populations isolated by urbanization in southern California to predict population growth, extinction probability, and loss of genetic diversity with empirical data. Specifically, we (1) provide the first PVA for isolated mountain lions in the Santa Ana Mountains (SAM) that considers both demographic and genetic risk factors and (2) test the hypothesis that variation in abundance and mortality between the SAM and Santa Monica Mountains (SMM) result in differences in population growth, loss of heterozygosity, and extinction probability. Our models predicted 16-21% probability of local extinction in the SAM due purely to demographic processes over 50 yr with current low levels or no immigration. Our models also predicted that genetic diversity will further erode in the SAM such that concern regarding inbreeding depression is warranted unless gene flow is increased, and that if inbreeding depression occurs, rapid local extinction will be highly likely. Dynamics of the two populations were broadly similar, but they also exhibited differences driven by larger population size and higher mortality in the SAM. Density-independent scenarios predicted a rapidly increasing population in the SMM, whereas growth potential did not differ from a stable trend in the SAM. Demographic extinction probability and loss of heterozygosity were greater in the SMM for density-dependent scenarios without immigration. However, higher levels of immigration had stronger, positive influences on both demographic viability and retention of genetic diversity in the SMM driven by lower abundance and higher adult survival. Our results elucidate demographic and genetic threats to small populations within the extinction vortex, and how these vary relative to demographic structure. Importantly, simulating seemingly attainable increases in connectivity was sufficient to greatly reduce extinction probability. Our work highlights that conservation of large carnivores is achievable within urbanized landscapes, but requires land protection, connectivity, and strategies to promote coexistence with humans.

Author(s): Serieys, Laurel E. K.; Lea, Amanda; Epeldegui, Marta; Foley, Janet; Moriarty, Joanne Gale; Riley, Seth P. D.; Uittenbogaart, Christel H.; Fraser, Devaughn; Mouton, Alice; Wayne, Robert K. | Abstract: Human activities threaten wildlife with a variety of novel stressors such as exposure to toxicants. Anticoagulant rodenticides (ARs) are toxicants applied worldwide and through bioaccumulation, threaten species that prey on poisoned rodents or their predators. We studied a population of urban bobcats in southern California that declined rapidly from 2002-2005 due to notoedric mange. We first assessed prevalence of AR exposure using blood and liver samples across the population and found widespread exposure (g90%). Death associated with mange was strongly correlated with cumulative first- and second-generation AR exposure. These findings suggested that exposure to both first- and second-generation ARs were an underlying cause of the disease. We next aimed to understand the sublethal immunological and physiological effects of AR exposure in this natural population. We used two approaches: 1) we used a comprehensive suite of health assays (complete blood counts, blood chemistry assessment, and immunological profiling), and 2) we quantified AR-induced differential gene expression in blood for a subset of individuals. We found that sublethal AR exposure, primarily measured as exposure to diphacinone, is associated with hallmark indicators of generalized systemic inflammation that in persistence could promote immune dysfunction. Further, differential gene expression findings supported the results of immunological profiling. Further, a decrease in the expression of genes associated with epithelial maintenance simultaneous to a decrease in gene expression linked with ectoparasitic immune response may explain the link between AR exposure and mange vulnerability. Such indirect effects of sublethal exposure exemplify the challenge of protecting wild populations from common toxicants in human-dominated environments.

Human development near protected areas may pose challenges for carnivore conservation. In southern California, residential use of anticoagulant rodenticides is linked to non-target impacts on wild felids. We use an interdisciplinary policy sciences meta-framework and mixed methods to investigate landscape, social and policy factors affecting secondary rodenticide impacts on bobcats (Lynx rufus). Results suggest that landscape features, such as fruit trees and irrigation ditches are common locations for deploying anticoagulants. Residents construct a wildland-urban interface discourse that influences residential rodent control behaviour. Interviews with pest control operators and wildlife managers reveal a “scientized” management paradigm masking third-party residential anticoagulant use, which may have greater impacts on wild felids than residential use alone. The US Environmental Protection Agency may have reason to refocus anticoagulant use regulations to increase effectiveness in mitigating impacts on ...

Urbanization profoundly impacts animal populations by causing isolation, increased susceptibility to disease, and exposure to toxicants. Genetic effects include reduced effective population size, increased population substructure, and decreased adaptive potential. We investigated the influence that urbanization and a disease epizootic had on the population genetics of bobcats (Lynx rufus) distributed across a highly fragmented urban landscape. We genotyped more than 300 bobcats, sampled from 1996 to 2012, for variation at nine neutral and seven immune gene-linked microsatellite loci. We found that two freeways are significant barriers to gene flow. Further, a 3-year disease epizootic, associated with secondary anticoagulant rodenticide exposure, caused a population bottleneck that led to significant genetic differentiation between 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. Conservation assessments need to assay loci that are potentially under selection to better preserve the adaptive potential of populations at the urban–wildland interface. Further, interconnected regions that contain appropriate habitat for wildlife will be critical to the long-term viability of animal populations in urban landscapes.

Anticoagulant rodenticides (ARs) are indiscriminate toxicants that threaten nontarget predatory and scavenger species through secondary poisoning. Accumulating evidence suggests that AR exposure may have disruptive sublethal consequences on individuals that can affect fitness. We evaluated AR-related effects on genome-wide expression patterns in a population of bobcats in southern California. We identify differential expression of genes involved in xenobiotic metabolism, endoplasmic reticulum stress response, epithelial integrity and both adaptive and innate immune function. Further, we find that differential expression of immune-related genes may be attributable to AR-related effects on leucocyte differentiation. Collectively, our results provide an unprecedented understanding of the sublethal effects of AR exposure on a wild carnivore. These findings highlight potential detrimental effects of ARs on a wide variety of species worldwide that may consume poisoned rodents and indicate the need to investigate gene expression effects of other toxicants added to natural environments by humans.

Owing to a complex history of host-parasite coevolution, lentiviruses exhibit a high degree of species specificity. Given the well-documented viral archeology of human immunodeficiency virus (HIV) emergence following human exposures to simian immunodeficiency virus (SIV), an understanding of processes that promote successful cross-species lentiviral transmissions is highly relevant. We previously reported natural cross-species transmission of a subtype of feline immunodeficiency virus, puma lentivirus A (PLVA), between bobcats ( Lynx rufus ) and mountain lions ( Puma concolor ) for a small number of animals in California and Florida. In this study, we investigate host-specific selection pressures, within-host viral fitness, and inter- versus intraspecies transmission patterns among a larger collection of PLV isolates from free-ranging bobcats and mountain lions. Analyses of proviral and viral RNA levels demonstrate that PLVA fitness is severely restricted in mountain lions compared to that in bobcats. We document evidence of diversifying selection in three of six PLVA genomes from mountain lions, but we did not detect selection among 20 PLVA isolates from bobcats. These findings support the hypothesis that PLVA is a bobcat-adapted virus which is less fit in mountain lions and under intense selection pressure in the novel host. Ancestral reconstruction of transmission events reveals that intraspecific PLVA transmission has occurred among panthers ( Puma concolor coryi ) in Florida following the initial cross-species infection from bobcats. In contrast, interspecific transmission from bobcats to mountain lions predominates in California. These findings document outcomes of cross-species lentiviral transmission events among felids that compare to the emergence of HIV from nonhuman primates. IMPORTANCE Cross-species transmission episodes can be singular, dead-end events or can result in viral replication and spread in the new species. The factors that determine which outcome will occur are complex, and the risk of new virus emergence is therefore difficult to predict. We used molecular techniques to evaluate the transmission, fitness, and adaptation of puma lentivirus A (PLVA) between bobcats and mountain lions in two geographic regions. Our findings illustrate that mountain lion exposure to PLVA is relatively common but does not routinely result in communicable infections in the new host. This is attributed to efficient species barriers that largely prevent lentiviral adaptation. However, the evolutionary capacity for lentiviruses to adapt to novel environments may ultimately overcome host restriction mechanisms over time and under certain ecological circumstances. This phenomenon provides a unique opportunity to examine cross-species transmission events leading to new lentiviral emergence.

Notoedric mange was responsible for a population decline of bobcats ( Lynx rufus ) in 2 Southern California counties from 2002-2006 and is now reported to affect bobcats in Northern and Southern California. With this study we document clinical laboratory and necropsy findings for bobcats with mange. Bobcats in this study included free-ranging bobcats with mange (n = 34), a control group of free-ranging bobcats without mange (n = 11), and a captive control group of bobcats without mange (n = 19). We used 2 control groups to evaluate potential anomalies due to capture stress or diet. Free-ranging healthy and mange-infected bobcats were trapped or salvaged. Animals were tested by serum biochemistry, complete blood count, urine protein and creatinine, body weight, necropsy, and assessment for anticoagulant rodenticide residues in liver tissue. Bobcats with severe mange were emaciated, dehydrated, and anemic with low serum creatinine, hyperphosphatemia, hypoglycemia, hypernatremia, and hyperchloremia, and sometimes septicemic when compared to control groups. Liver enzymes and leukocyte counts were elevated in free-ranging, recently captured bobcats whether or not they were infested with mange, suggesting capture stress. Bobcats with mange had lower levels of serum cholesterol, albumin, globulin, and total protein due to protein loss likely secondary to severe dermatopathy. Renal insufficiency was unlikely in most cases, as urine protein:creatinine ratios were within normal limits. A primary gastrointestinal loss of protein or blood was possible in a few cases, as evidenced by elevated blood urea nitrogen, anemia, intestinal parasitism, colitis, gastric hemorrhage, and melena. The prevalence of exposure to anticoagulant rodenticides was 100% (n = 15) in bobcats with mange. These findings paint a picture of debilitating, multisystemic disease with infectious and toxic contributing factors that can progress to death in individuals and potential decline in populations.

Aquatic amphibians are known to be vulnerable to a myriad of invasive predators. Invasive crayfish are thought to have eliminated native populations of amphibians in some streams in the semi-arid Santa Monica Mountains of southern California. Despite their toxic skin secretions that defend them from native predators, newts are vulnerable to crayfish attacks, and crayfish have been observed attacking adult newts, and eating newt egg masses and larvae. For 15 years, we have observed invasive crayfish and native California newts coexisting in one stream in the Santa Monica Mountains. During that period, we monitored the densities of both crayfish and newt egg mass densities and compared these to annual rainfall totals. After three seasons of below average rainfall, we reduced crayfish numbers by manual trapping. Our long-term data indicated that crayfish did not fare well in years when rainfall is above the historic average. This invasive predator did not evolve with high velocity streams, and observations indicated that southern California storm events washed crayfish downstream, killing many of them. Newts exhibit increased reproduction in years when crayfish numbers were reduced. A comparison with a nearby stream that does not contain crayfish indicated that newt reproduction positively responded to increased rainfall, but that fluctuations were much greater in the stream that contains crayfish. We suggest that rainfall patterns help explain invasive crayfish/newt coexistence and that management for future coexistence may benefit from manual trapping.

The extinction vortex is a theoretical model describing the process by which extinction risk is elevated in small, isolated populations owing to interactions between environmental, demographic, and genetic factors. However, empirical demonstrations of these interactions have been elusive. We modelled the dynamics of a small mountain lion population isolated by anthropogenic barriers in greater Los Angeles, California, to evaluate the influence of demographic, genetic, and landscape factors on extinction probability. The population exhibited strong survival and reproduction, and the model predicted stable median population growth and a 15% probability of extinction over 50 years in the absence of inbreeding depression. However, our model also predicted the population will lose 40–57% of its heterozygosity in 50 years. When we reduced demographic parameters proportional to reductions documented in another wild population of mountain lions that experienced inbreeding depression, extinction probability rose to 99.7%. Simulating greater landscape connectivity by increasing immigration to greater than or equal to one migrant per generation appears sufficient to largely maintain genetic diversity and reduce extinction probability. We provide empirical support for the central tenet of the extinction vortex as interactions between genetics and demography greatly increased extinction probability relative to the risk from demographic and environmental stochasticity alone. Our modelling approach realistically integrates demographic and genetic data to provide a comprehensive assessment of factors threatening small populations.