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Roof rats (Rattus rattus) are common invasive pests in both urban and agricultural sites as well as a significant public health threat. The use of anticoagulant rodenticides to help control the rodent population poses a risk of developing resistance to these products. Several reports have associated the non-synonymous Single Nucleotide Polymorphism (nsSNP) Tyr25Phe (Y25F) of the vitamin K epoxide reductase subcomponent 1 (Vkorc1) gene to anticoagulant rodenticide resistance (Diaz et al. 2021). We conducted a nsSNP screen in the population of Rattus spp. in Orange County to determine the prevalence of the Y25F nsSNP in the sampled rodents. Thirty-seven live rat traps were set throughout the county and the species of each trapped rat was determined by sequencing the cytochrome oxide I (COI) gene using primers previously described in Goulois et al. (2015). Twenty specimens were identified as R. rattus and 12 as R. tanezumi (Asian house rat); the other five specimens were non-Rattus species. To further evaluate the rat species, we used tree-based methods using sequence alignments for three mitochondrial DNA regions, cytochrome b, COI, and non-coding displacement (D) loop using a different set of primers used by Robins et al. (2007). Sequences were aligned by Geneious Prime (v.2020.2.4), and maximum-likelihood phylogeny using 1,000 bootstrap replications was constructed using Mega (10.2.6). Sequences were compared to reference sequences in Robins et al. (2007) and Rattus norvegicus (Norway rat) was used to root the tree. Phylogenetic analysis confirmed the presence of R. tanezumi in our collected samples as well as two haplotypes of R. rattus. In addition to the concatenated data set, each gene was examined individually, and all phylogenetic trees generally agreed on topology. The Y25F nsSNP was present in both R. rattus (40%; 8 of 20) and R. tanezumi (16.67%; 2 of 12). Further genetic testing in Orange County and other areas of Southern California are needed to determine the extent of these Rattus populations and their hybridization as well as the presence of this adaptive trait.

Secondary exposure to anticoagulant rodenticides (ARs) remains a significant problem for wild carnivores living at the urban-wildland interface. Although direct mortality is the most obvious concern, AR exposure may also cause subtle, sub-lethal effects, such as reduced body condition and increased parasite loads, that ultimately contribute to poorer performance at the population level. However, relatively little is known about such effects on wild animals, or about the environmental factors that contribute to AR exposure. We examined relationships between levels of AR exposure, demographic factors, and landscape variables associated with urbanization, for coyotes (Canis latrans) from urban Los Angeles and Orange counties, California. AR exposure was estimated from residue assays of livers from 353 carcasses, collected opportunistically as road kills or euthanized nuisance animals from 2015 to 2018. We also conducted veterinary necropsies on a subset of 50 carcasses to investigate effects of AR exposure on body weight, overall condition, and parasite burdens. Nearly all coyotes (98%) contained residues of at least one AR, with second-generation ARs (SGARs) detected in 97%, first-generation ARs (FGARs) detected in 75%, and 66% exposed to both types. Individual coyotes had residues of 0-6 compounds (mode = 4), with three SGARs (bromadiolone, brodifacuom, difethialone) and one FGAR (diphacinone) detected often (≥65 coyotes). Adults were exposed to more ARs and had significantly higher residue concentrations than juveniles. Road-killed coyotes were over-represented among coyotes with high numbers of SGARs and had significantly higher SGAR residue levels than euthanized ones. Contrary to our expectations, landscape patterns suggested higher numbers and residue concentrations of SGARs in coyotes associated with less intensive urban development. Very few coyotes (6 of 353) showed any evidence of mange, and these animals had similar AR numbers and residue concentrations to those without mange. Of the 50 animals that we necropsied thoroughly, coyotes with obvious internal hemorrhage tended to have high residue concentrations of SGARs, while those exposed to multiple FGAR compounds and with high FGAR residue concentrations tended to be in poorer body condition. ARs are an important tool for managing rodent pests but given the ubiquitous exposure of coyotes to ARs and evidence of potential sub-lethal effects, notably from FGARs, we need more information on pathways of exposure and better strategies to reduce the total amount of ARs on the landscape.

Urban coyotes are commonly exposed to rodenticides used to control non-native commensal rodents, but these rodents are rare in published accounts of their diets. An alternative source of rodenticide exposure is through the consumption of mesocarnivores that have themselves eaten either toxic bait directly or poisoned rodents or invertebrates. Carcasses of 311 nuisance and road-killed coyotes from suburban and urban areas of southern California were collected from 2016-2018. Stomachs were dissected and prey items were identified visually. Stomach contents containing tissue from suspected mammalian prey (N = 178) were homogenized and DNA was extracted. Genus-specific primers (123-366 bp) were designed for Virginia opossums, raccoons, and striped skunks, regionally common species that are known to be consumed by coyotes. PCR was performed for each primer pair, and presence of PCR products of particular amplicon lengths were determined by gel electrophoresis. Coyote stomachs containing a PCR product of the appropriate size were considered to contain that prey item. Land use data were used to assess landscape factors that are associated with the consumption of mesocarnivores. Combining both techniques, mesocarnivores were detected at low frequencies: opossums (8%) were more common than raccoons (2%) and skunks (2%). Some 72% of meso-carnivores present in stomachs were detected by molecular methods, while 66% were identified by morphological methods. Opossums were associated with increased development and anthropogenic land use, while skunks were associated with large natural areas, and raccoons used all habitat types. The extent to which mesocarnivores themselves eat poisoned prey remains unknown, although they may be a potential source of exposure for coyotes. Additionally, landscape factors do not appear to be related to raccoon consumption but may influence presence, and therefore consumption, of skunks and opossums.

Non-native, commensal rodents damage property and represent a significant public health hazard through the spread of diseases. Pest management professionals commonly use second-generation anticoagulant rodenticides, usually placed in tamper-proof bait stations, to control commensal rodents in urban areas; however, there are significant concerns about poisoning of native wildlife, especially through secondary exposure of predators and scavengers that consume prey killed by rodenticides. Behavioral responses of commensal and native rodents to bait stations are not well understood, especially at the urban-wildland interface. The goals of this project were to 1) determine temporal patterns of bait station use by commensal rodents; 2) identify factors that may influence bait station visitation by native species; and 3) devise simple mitigation techniques to reduce wildlife exposure to rodenticides. We deployed Reconyx™ PC800 digital cameras to monitor bait stations placed in 90 residential yards across Orange County, California. Two bait stations, armed with non-toxic bait, were monitored continuously in each yard for approximately 30 consecutive days from December 2017 to August 2018 (Session 1). A subset of 64 of these yards were surveyed again from September 2018 to March 2019 (Session 2). One bait station was placed on the ground, whereas the other was elevated 1-1.5 m in a tree or along a fence to determine if non-target exposure to rodenticides could be reduced by elevating bait stations. Roof rats (Rattus rattus) were the only commensal rodents detected in Orange County yards, and were present at 80% of sites, with average activity ranging from 0 to 9 hours each night. Bait stations were discovered quickly in yards with a lot of rat activity, especially at boxes placed directly on the ground, where rats were recorded in nearly 90% of yards within 10 days of placement. Time to discovery did not differ significantly, however, between ground and elevated stations, with mean times ranging from 7 to 10 days across both sampling sessions. Mean time to enter the bait station also did not differ between elevated and ground stations, varying from 10 days in Session 1 and 11-12 days in Session 2. Rats entered only 59-70% of the bait stations they visited, suggesting some degree of neophobia. Native rodents, including California ground squirrels (Otospermophilus beecheyi), woodrats (Neotoma sp.), and deer mice (Peromyscus sp.) were relatively rare among our 90 sites (13% of yards), and were recorded at elevated stations much less frequently than ground stations. Woodrats, deer mice, and, in one instance, a juvenile Virginia opossum (Didelphis virginiana), were photographed entering bait stations, and non-native fox squirrels (Sciurus niger) were able to access bait by chewing through the top and walls of the bait stations. Yards visited by native rodents tended to be closer to areas of natural vegetation and to have no significant barriers to entry (e.g., solid fences or walls) from nearby open spaces. We identified several ways that our results may help improve the management of commensal rodents at the urban-wildland interface in southern California, where reducing non-target exposure is a critical concern. First, the high level of rat activity in some yards suggests that bait may be rapidly depleted, which could reduce effectiveness. Rats had a behavioral response to bait depletion and replenishment, so it may be useful to monitor bait consumption frequently during the first week of bait application and adjust levels accordingly. We caution, however, that our stations contained bait but lacked rodenticides, so we do not know how the presence of toxicant or the deaths of other rats might alter behavioral responses to bait stations. Second, the fact that rats were photographed entering only a fraction of the bait stations suggests either that cameras missed some of these events or that rats showed some reluctance to enter bait stations, even in the absence of rodenticide. Even in yards where rats eventually entered bait stations, it was 7 or 8 days until their first direct exposure to bait. Because the first mortalities from rodenticide might not occur for more several days, pest management professionals should be prepared to communicate the possibility of delays to customers to prevent them from becoming impatient and taking more drastic (and potentially illegal) measures if results are not immediate. Lastly, given the mobility of many wild predators and scavengers in southern California, if rodenticides are the only option available for effective pest control, special efforts should be made to search for and remove rat carcasses quickly, especially in yards that are accessible to native wildlife or adjacent to natural areas. In open, accessible yards close to natural areas, integrated pest control approaches should first be attempted to minimize risk to non-target wildlife species. If rodenticides must be used to control roof rats, bait stations should be elevated to try to prevent native rodents from consuming bait; this approach may also reduce exposure to children and pets.

Unmanaged cottontail rabbit populations can cause significant damage to drip irrigation tubing. Common integrated pest management strategies to reduce damage include trapping, exclusion, and repellent use. Trapping and exclusion, while effective at managing cottontail rabbits, are impractical when applied to large scale habitat restoration projects. To evaluate repellent use under these conditions, we conducted a preliminary conditioned avoidance field trial using anthraquinone applied to drip irrigation tubing installed in a riparian habitat undergoing restoration in Silverado, CA. The postingestive repellent, anthraquinone, was selected due to prior laboratory research indicating its effectiveness in inducing conditioned avoidance feeding behaviors in cottontail rabbits. Following a complete repair of the irrigation system, alternating sections of the irrigation tubing were treated. After the first treatment, there was an estimated 50% reduction in damaged tubing between the treated and control sections. An estimated 0.18% of the total tubing surveyed was damaged after the second treatment. Between the first and second treatments, we observed an estimated 99.5% decrease in total damaged tubing. Our results suggest that anthraquinone may be successful in reducing cottontail rabbit damage by inducing conditioned avoidance to drip irrigation line. As a preliminary study, these findings are promising and warrant future field trials to validate the use of anthraquinone as a repellant to reduce damage by cottontail rabbits.

Coyotes are among the most successful carnivores in urban and suburban environments, which has increasingly led to conflicts with pets and people in southern California. One possible contributor to high coyote population densities and human-coyote conflicts is an abundance of free-roaming domestic cats subsidized by backyard feeding and trap-neuter-release (TNR) programs. To determine if coyotes regularly eat free-roaming cats, we identified prey items in the stomachs of 311 coyotes between 2015 and 2018; specimens were either road-killed coyotes or coyotes taken as nuisance animals. We used two methods to estimate coyote diet: visual identification of stomach contents and molecular polymerase-chain reaction (PCR) analysis of prey remains in stomachs. A total of 245 coyotes stomachs contained identifiable food items, including 200 (43%) that contained mammalian prey (based on hair, bones, and tissue); 178 of these had sufficient tissue from which DNA could be extracted. Combining the two methods, we found cat remains in 35% (n = 86) of stomachs with identifiable mammalian remains. This makes cats the most common mammalian prey item identified, surpassing rabbits and small rodents, and means cats are likely a more common prey than has been reported previously, including in other areas of southern California. We used a GIS approach to compare landscape characteristics associated with known locations of coyotes that ate cats to the same characteristics around locations determined to be TNR cat colonies based on public shelter records. These characteristics included amount and intensity of urban development, coverage of grassland and shrubland, building density, and the distance to the nearest natural vegetation; these were entered into a principal component analysis (PCA) to create composite variables that described the degree of urbanization around coyote and TNR colony locations. Logistic regression of PCA variables revealed that cat-eating coyotes were significantly associated with landscapes that were more intensively developed, had little natural or altered green space, and a higher building density than coyotes that did not have cats in their stomachs. Locations of TNR cat colonies had similar landscape characteristics, with colonies often located in intensively developed areas such as apartment complexes or industrial or commercial zones that are relatively far from natural areas. The subset of coyotes associated with TNR colonies were also highly likely to have consumed cats. Coyotes that had been removed (vs. roadkill) tended to be cat-eaters, suggesting that consumption of pets may have led to targeting these coyotes for lethal removal. The high frequency of cats in coyote diets, combined with the concordance of landscape characteristics associated with TNR colonies and cat-eating coyotes, support the argument that high cat densities and supplemental feeding attract coyotes. Effective mitigation of human-coyote conflicts in southern California may require a ban on outdoor feeding of cats and wildlife, and the removal of TNR colonies that coyotes apparently exploit as an abundant source of food.

Although coyotes are a natural component of southern California ecosystems, they are sometimes considered a nuisance because their opportunistic habits and tolerance for urban and suburban environments bring them into conflict with people. Recent attacks on people and pets have increasingly led to lethal control of nuisance animals, yet it is unclear whether the demographic distribution of nuisance individuals is representative of the coyote population as a whole. We used two methods, cementum annuli analysis and tooth wear, to estimate the age of coyotes collected as nuisance or road-killed animals in southern California. Age estimates based on tooth wear, a non-lethal method, were broadly similar to those from cementum annuli analysis, although tooth-wear estimates were highly variable and tended to overestimate age, especially for younger individuals. The demographic structure of coyotes collected as nuisance animals was biased toward young adults and males, which suggests that this demographic class may be more likely to killed by control efforts, possibly because their behavior creates greater opportunities for conflict with people.