Wide-ranging species cannot persist in reserves alone. Consequently, there is growing interest in the conservation value of agricultural lands that separate or buffer natural areas. The value of agricultural lands for wildlife habitat and connectivity varies as a function of the crop type and landscape context, and quantifying these differences will improve our ability to manage these lands more effectively for animals. In southern California, many species are present in avocado orchards, including mammalian carnivores. We examined occupancy of avocado orchards by mammalian carnivores across agricultural-wildland gradients in southern California with motion-activated cameras. More carnivore species were detected with cameras in orchards than in wildland sites, and for bobcats and gray foxes, orchards were associated with higher occupancy rates. Our results demonstrate that agricultural lands have potential to contribute to conservation by providing habitat or facilitating landscape connectivity.

As natural habitats become fragmented by human activities, animals must increasingly move through human-dominated systems, particularly agricultural landscapes. Mapping areas important for animal movement has therefore become a key part of conservation planning. Models of landscape connectivity are often parameterized using expert opinion and seldom distinguish between the risks and barriers presented by different crop types. Recent research, however, suggests different crop types, such as row crops and orchards, differ in the degree to which they facilitate or impede species movements. Like many mammalian carnivores, bobcats (Lynx rufus) are sensitive to fragmentation and loss of connectivity between habitat patches. We investigated how distinguishing between different agricultural land covers might change conclusions about the relative conservation importance of different land uses in a Mediterranean ecosystem. Bobcats moved relatively quickly in row crops but relatively slowly in orchards, at rates similar to those in natural habitats of woodlands and scrub. We found that parameterizing a connectivity model using empirical data on bobcat movements in agricultural lands and other land covers, instead of parameterizing the model using habitat suitability indices based on expert opinion, altered locations of predicted animal movement routes. These results emphasize that differentiating between types of agriculture can alter conservation planning outcomes.

Mountain lions (Puma concolor) throughout North and South America are infected with puma lentivirus clade B (PLVB). A second, highly divergent lentiviral clade, PLVA, infects mountain lions in southern California and Florida. Bobcats (Lynx rufus) in these two geographic regions are also infected with PLVA, and to date, this is the only strain of lentivirus identified in bobcats. We sequenced full-length PLV genomes in order to characterize the molecular evolution of PLV in bobcats and mountain lions. Low sequence homology (88% average pairwise identity) and frequent recombination (1 recombination breakpoint per 3 isolates analyzed) were observed in both clades. Viral proteins have markedly different patterns of evolution; sequence homology and negative selection were highest in Gag and Pol and lowest in Vif and Env. A total of 1.7% of sites across the PLV genome evolve under positive selection, indicating that host-imposed selection pressure is an important force shaping PLV evolution. PLVA strains are highly spatially structured, reflecting the population dynamics of their primary host, the bobcat. In contrast, the phylogeography of PLVB reflects the highly mobile mountain lion, with diverse PLVB isolates cocirculating in some areas and genetically related viruses being present in populations separated by thousands of kilometers. We conclude that PLVA and PLVB are two different viral species with distinct feline hosts and evolutionary histories. Importance: An understanding of viral evolution in natural host populations is a fundamental goal of virology, molecular biology, and disease ecology. Here we provide a detailed analysis of puma lentivirus (PLV) evolution in two natural carnivore hosts, the bobcat and mountain lion. Our results illustrate that PLV evolution is a dynamic process that results from high rates of viral mutation/recombination and host-imposed selection pressure.