In 2016, the Wildlife Investigations Lab initiated a statewide mountain lion health surveillance study to understand population health and anticoagulant rodenticide (AR) exposure. Exposure to first-generation (FGARs) and second-generation (SGARs) anticoagulant rodenticides are common in predators such as raptors, wild canids (i.e., foxes and coyotes) and bobcats. However, statewide data regarding rodenticide exposure in these species, including mountain lions, have been limited. Our objectives were to determine the statewide prevalence and geographic distribution of AR exposure in necropsied mountain lions. We used liquid chromatography/mass spectroscopy to detect rodenticides in liver samples from 111 (77 male: 34 female) mountain lion carcasses from 37 counties that died between Feb 2016 and Feb 2017. Necropsied carcasses were lions taken on depredation permits, vehicular strike, public safety, or other reasons. Overall, we detected ARs from the liver tissue of mountain lions from 35 counties with 105 of the 111 (94.5%) lions having exposure. We detected FGARs in 81 individuals (73%) from 33 counties and SGARs in 102 individuals (92%) from 35 counties. Seventy-eight individuals (70%) were exposed to both SGARs and FGARs while 6 (5%) individuals had no detectable AR concentration. Of the FGARs detected, diphacinone was the most common and was observed in 67% of sampled individuals. Brodifacoum was the most common SGAR, detected in 90% of sampled individuals. Exposure to FGARs was correlated with exposure to SGARs (χ2 = 5.8, p = 0.01). Exposure to ARs was not associated with lower body condition score. Although our study represents only one year of data, we demonstrate that exposure to both FGARs and SGARs is widespread in California’s mountain lions. We recommend continued AR screening of livers from mountain lion carcasses to further enhance our understanding about the relative contributions they may have on population health. Continued monitoring would also measure the effectiveness of regulatory changes intended to reduce non-target wildlife exposure to rodenticides

A robust population of endangered San Joaquin kit foxes occurs in the city of Bakersfield, CA. In March 2013, sarcoptic mange was detected in this population and the disease quickly spread. In January 2019, mange also appeared in a smaller kit fox population in the neighboring town of Taft, CA. To date there have been more than 430 confirmed cases in and 100 confirmed deaths of kit foxes. An additional 118 unrecovered individuals are presumed deceased because there is no indication that kit foxes survive without medical intervention. These numbers are also presumed underestimations of the actual number of kit foxes that have contracted and died from mange. In addition to capturing and treating kit foxes, the Endangered Species Recovery Program has conducted a yearly citywide camera survey in Bakersfield since 2015 and Taft since 2019 to assess the occurrence of mange among kit foxes and the spatial pattern of spread. Based on the Bakersfield survey, the urban kit fox population has declined by 67% since 2015. This annual camera survey also provides information on co-occurring species that could contract or transmit mange. Of the total number of cameras that have detected kit foxes with mange, 88% of those also detected at least one secondary species including raccoons, opossums, striped skunks, California ground squirrels, and domestic cats and dogs. The annual camera surveys have also detected coyotes, red foxes, gray foxes, and opossums with active mange infestations. Transmission routes for all of these species remain uncertain and the potential for transmitting mites to new areas or new individuals of multiple species is possible. Overall, mange presents a risk to multiple species in the urban environment, including domestics, for as long as it continues to circulate.

Background

In 2013, sarcoptic mange, caused by Sarcoptes scabiei mites, precipitated a catastrophic decline of the formerly stable urban population of endangered San Joaquin kit foxes (Vulpes macrotis mutica) in Bakersfield, California, USA. In 2019, a smaller sarcoptic mange outbreak affected kit foxes 58 km southwest of Bakersfield in the town of Taft, California. To determine whether the Taft outbreak could have occurred as spillover from the Bakersfield outbreak and whether epidemic control efforts must involve not only kit foxes but also sympatric dogs (Canis lupus familiaris), coyotes (Canis latrans), and red foxes (Vulpes vulpes), we evaluated genotypes and gene flow among mites collected from each host species.

Methods

We used 10 Sarcoptes microsatellite markers (SARM) to perform molecular typing of 445 S. scabiei mites collected from skin scrapings from twenty-two infested kit foxes, two dogs, five coyotes, and five red foxes from Bakersfield, Taft, and other nearby cities.

Results

We identified 60 alleles across all SARM loci; kit fox- and red fox-derived mites were relatively monomorphic, while genetic variability was greatest in Bakersfield coyote- and dog-derived mites. AMOVA analysis documented distinct mite populations unique to hosts, with an overall F_ST of 0.467. The lowest F_ST (i.e. closest genetic relationship, F_ST = 0.038) was between Bakersfield and Taft kit fox-derived mites while the largest genetic difference was between Ventura coyote- and Taft kit fox-derived mites (F_ST = 0.843).

Conclusions

These results confirm the close relationship between the Taft and Bakersfield outbreaks. Although a spillover event likely initiated the kit fox mange outbreak, mite transmission is now primarily kit fox-to-kit fox. Therefore, any large-scale population level intervention should focus on treating kit foxes within the city.

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 pumas sampled broadly across the state. Our analyses indicated support for 4-10 geographically nested, broad- to fine-scale genetic clusters. At the broadest scale, the four genetic clusters had high genetic diversity and exhibited low linkage disequilibrium, indicating that pumas have retained genomic diversity statewide. However, multiple lines of evidence indicated substructure, including 10 finer-scale genetic clusters, some of which exhibited fixed alleles 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 retain high genetic diversity and heterogenous 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 nested population genomic analysis highlights the information that can be gained from population genomic studies aiming to provide guidance for the conservation of fragmented populations.