Multi‐population puma connectivity could restore genomic diversity to at‐risk coastal populations in California

Multi-generational benefits of genetic rescue

Genetic rescue-an increase in population fitness following the introduction of new alleles-has been proven to ameliorate inbreeding depression in small, isolated populations, yet is rarely applied as a conservation tool. A lingering question regarding genetic rescue in wildlife conservation is how long beneficial effects persist in admixed populations. Using data collected over 40 years from 1192 endangered Florida panthers (Puma concolor coryi) across nine generations, we show that the experimental genetic rescue implemented in 1995-via the release of eight female pumas from Texas-alleviated morphological, genetic, and demographic correlates of inbreeding depression, subsequently preventing extirpation of the population. We present unequivocal evidence, for the first time in any terrestrial vertebrate, that genetic and phenotypic benefits of genetic rescue remain in this population after five generations of admixture, which helped increase panther abundance (> fivefold) and genetic effective population size (> 20-fold). Additionally, even with extensive admixture, microsatellite allele frequencies in the population continue to support the distinctness of Florida panthers from other North American puma populations, including Texas. Although threats including habitat loss, human-wildlife conflict, and infectious diseases are challenges to many imperiled populations, our results suggest genetic rescue can serve as an effective, multi-generational tool for conservation of small, isolated populations facing extinction from inbreeding.

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.

Feline Leukemia Virus Frequently Spills Over from Domestic Cats to North American Pumas

Feline leukemia virus (FeLV) is a gammaretrovirus with horizontally transmitted and endogenous forms. Domestic cats are the primary reservoir species, but FeLV outbreaks in endangered Florida panthers and Iberian lynxes have resulted in mortalities. To assess prevalence and interspecific/intraspecific transmission, we conducted an extensive survey and phylogenetic analysis of FeLV infection in free-ranging pumas (n = 641) and bobcats (n = 212) and shelter domestic cats (n = 304). Samples were collected from coincident habitats across the United States between 1985 and 2018. FeLV infection was detected in 3.12% of the puma samples, 0.47% of the bobcat samples, and 6.25% of the domestic cat samples analyzed. Puma prevalence varied by location, with Florida having the highest rate of infection. FeLV env sequences revealed variation among isolates, and we identified two distinct clades. Both progressive and regressive infections were identified in cats and pumas. Based on the time and location of sampling and phylogenetic analysis, we inferred 3 spillover events between domestic cats and pumas; 3 puma-to-puma transmissions in Florida were inferred. An additional 14 infections in pumas likely represented spillover events following contact with reservoir host domestic cat populations. Our data provide evidence that FeLV transmission from domestic cats to pumas occurs widely across the United States, and puma-to-puma transmission may occur in genetically and geographically constrained populations. IMPORTANCE Feline leukemia virus (FeLV) is a retrovirus that primarily affects domestic cats. Close interactions with domestic cats, including predation, can lead to the interspecific transmission of the virus to pumas, bobcats, or other feline species. Some infected individuals develop progressive infections, which are associated with clinical signs of disease and can result in mortality. Therefore, outbreaks of FeLV in wildlife, including the North American puma and the endangered Florida panther, are of high conservation concern. This work provides a greater understanding of the dynamics of the transmission of FeLV between domestic cats and wild felids and presents evidence of multiple spillover events and infections in all sampled populations. These findings highlight the concern for pathogen spillover from domestic animals to wildlife but also identify an opportunity to understand viral evolution following cross-species transmissions more broadly.

Development of a 95 SNP panel to individually genotype mountain lions (Puma concolor) for microfluidic and other genotyping platforms

The mountain lion (Puma concolor) is one of the few remaining large predators in California, USA with density estimation from fecal genotypes becoming an essential component of conservation and management. In highly urbanized southern California, mountain lions are fragmented into small, inbred populations making proper marker selection critical for individual identification. We developed a panel of single nucleotide polymorphism (SNP) markers that can be used for consistent, routine mountain lion monitoring by different laboratories. We used a subset of existing Illumina HiSeq data for 104 individuals from throughout California to design a single, highly heterozygous multiplex of 95 SNPs for the Fluidigm platform. This panel confidently differentiates individual mountain lions, identifies sex, and discriminates mountain lions from bobcats. The panel performed well on fecal DNA extracts and based on design, had sufficient resolution to differentiate individual genotypes in even the population with lowest genetic diversity in southern California.