The Expectations and Challenges of Wildlife Disease Research in the Era of Genomics: Forecasting with a Horizon Scan-like Exercise.

The outbreak and transmission of disease-causing pathogens are contributing to the unprecedented rate of biodiversity decline. Recent advances in genomics have coalesced into powerful tools to monitor, detect, and reconstruct the role of pathogens impacting wildlife populations. Wildlife researchers are thus uniquely positioned to merge ecological and evolutionary studies with genomic technologies to exploit unprecedented "Big Data" tools in disease research; however, many researchers lack the training and expertise required to use these computationally intensive methodologies. To address this disparity, the inaugural "Genomics of Disease in Wildlife" workshop assembled early to mid-career professionals with expertise across scientific disciplines (e.g., genomics, wildlife biology, veterinary sciences, and conservation management) for training in the application of genomic tools to wildlife disease research. A horizon scanning-like exercise, an activity to identify forthcoming trends and challenges, performed by the workshop participants identified and discussed 5 themes considered to be the most pressing to the application of genomics in wildlife disease research: 1) "Improving communication," 2) "Methodological and analytical advancements," 3) "Translation into practice," 4) "Integrating landscape ecology and genomics," and 5) "Emerging new questions." Wide-ranging solutions from the horizon scan were international in scope, itemized both deficiencies and strengths in wildlife genomic initiatives, promoted the use of genomic technologies to unite wildlife and human disease research, and advocated best practices for optimal use of genomic tools in wildlife disease projects. The results offer a glimpse of the potential revolution in human and wildlife disease research possible through multi-disciplinary collaborations at local, regional, and global scales.

Sources of bias in applying close-kin mark-recapture to terrestrial game species with different life histories.

Close-kin mark-recapture (CKMR) is a method analogous to traditional mark-recapture but without requiring recapture of individuals. Instead, multilocus genotypes (genetic marks) are used to identify related individuals in one or more sampling occasions, which enables the opportunistic use of samples from harvested wildlife. To apply the method accurately, it is important to build appropriate CKMR models that do not violate assumptions linked to the species' and population's biology and sampling methods. In this study, we evaluated the implications of fitting overly simplistic CKMR models to populations with complex reproductive success dynamics or selective sampling. We used forward-in-time, individual-based simulations to evaluate the accuracy and precision of CKMR abundance and survival estimates in species with different longevities, mating systems, and sampling strategies. Simulated populations approximated a range of life histories among game species of North America with lethal sampling to evaluate the potential of using harvested samples to estimate population size. Our simulations show that CKMR can yield nontrivial biases in both survival and abundance estimates, unless influential life history traits and selective sampling are explicitly accounted for in the modeling framework. The number of kin pairs observed in the sample, in combination with the type of kinship used in the model (parent-offspring pairs and/or half-sibling pairs), can affect the precision and/or accuracy of the estimates. CKMR is a promising method that will likely see an increasing number of applications in the field as costs of genetic analysis continue to decline. Our work highlights the importance of applying population-specific CKMR models that consider relevant demographic parameters, individual covariates, and the protocol through which individuals were sampled.

FOOT INJURIES IN MICHIGAN, USA, GRAY WOLVES (CANIS LUPUS), 1992-2014.

The range of gray wolves (Canis lupus) in the contiguous US is expanding. Research and monitoring to support population recovery and management often involves capture via foothold traps. A population-level epidemiologic assessment of the effect of trap injuries on wolf survival remains needed to inform management. We describe the baseline rate, type, and severity of foot injuries of wolves born 1992-2013 in Michigan's Upper Peninsula, evaluate the reliability of field-scoring trap-related injuries, and the effect of injuries on wolf survival. We assessed foot injuries by physical and radiographic exam at postmortem and/or time of capture for 351 wolves using the International Organization for Standardization 10990-5 standard and the effects of injuries, sex, age, previous capture and body condition on survival using proportional hazards regression. We used ordinal regression to evaluate epidemiologic associations between sex, age, previous capture, body condition, cause of death and injury severity. Most wolves (53%) experienced no physically or radiographically discernable foot injuries over their lifetimes. Among those wolves that did experience injuries, 33% scored as mild. Foot injuries had little epidemiologically discernable effect on survival rates. Wolves with higher foot trauma scores did experience an increased risk of dying, but the magnitude of the increase was modest. Most limb injuries occurred below the carpus or tarsus, and scoring upper-limb injuries added little predictive information to population-level epidemiologic measures of survival and injury severity. There was little association between injury severity and cause of death. Based on necropsy exams, previous trap injuries likely contributed to death in only four wolves (1.1%). Our results suggest that injuries resulting from foothold traps are unlikely to be a limiting factor in recovery and ongoing survival of the Michigan gray wolf population.

Prion protein polymorphisms in Michigan white-tailed deer (Odocoileus virginianus).

Chronic Wasting Disease (CWD), a well-described transmissible spongiform encephalopathy of the Cervidae family, is associated with the aggregation of an abnormal isoform (PrPCWD) of the naturally occurring host prion protein (PrPC). Variations in the PrP gene (PRNP) have been associated with CWD rate of infection and disease progression. We analysed 568 free-ranging white-tailed deer (Odocoileus virginianus) from 9 CWD-positive Michigan counties for PRNP polymorphisms. Sampling included 185 CWD-positive, 332 CWD non-detected, and an additional 51 CWD non-detected paired to CWD-positives by sex, age, and harvest location. We found 12 polymorphic sites of which 5 were non-synonymous and resulted in a change in amino acid composition. Thirteen haplotypes were predicted, of which 11 have previously been described. Using logistic regression, consistent with other studies, we found haplotypes C (OR = 0.488, 95% CI = 0.321-0.730, P < 0.001) and F (OR = 0.122, 95% CI = 0.007-0.612, P < 0.05) and diplotype BC (OR = 0.340, 95% CI = 0.154-0.709, P < 0.01) were less likely to be found in deer infected with CWD. As has also been documented in other studies, the presence of a serine at amino acid 96 was less likely to be found in deer infected with CWD (P < 0.001, OR = 0.360 and 95% CI = 0.227-0.556). Identification of PRNP polymorphisms associated with reduced vulnerability to CWD in Michigan deer and their spatial distribution can help managers design surveillance programmesand identify and prioritize areas for CWD management.

HISTOPATHOLOGY AND RISK FACTORS ASSOCIATED WITH NEOTROMBICULA MICROTI INFESTATION IN THE ENDANGERED AMARGOSA VOLE (MICROTUS CALIFORNICUS SCIRPENSIS).

The Amargosa vole (Microtus californicus scirpensis) is a profoundly endangered rodent found only in the Central Mojave Desert, Inyo County, California, US. In 2010, severe cases of trombiculiasis, caused by larval Neotrombicula microti mites, were discovered among voles and sympatric small mammals. We evaluated Amargosa voles and sympatric rodents for infestation with N. microti December 2011-November 2012 and evaluated histopathology of ear tissue from 13 actively N. microti-infested Amargosa voles and 10 Amargosa voles with no gross evidence of current or past infestation. Rodents with current infestation had mites visible on tissue, typically ear pinnae, whereas mites were not seen on rodents with presumptive past infestation, but some of these animals had gross tissue scarring and loss consistent with healing from infestation. Ears from infested voles had severe granulocytic and necrotizing dermatitis, most associated with stylostome fragments, whereas few lesions were present in grossly uninfested voles. There was no association between body condition and infestation or severity of lesions. Significantly more voles were infested (37%) with N. microti than sympatric rodents (3%), suggesting that sympatric rodents do not serve as an important source of N. microti exposure to voles. Although this chigger infestation was common and induced severe localized pathology, we did not detect a fitness cost to infestation and recommend further evaluation of the disease to discern its significance in this conservation context.

Pathogen infection and exposure, and ectoparasites of the federally endangered Amargosa vole (Microtus californicus scirpensis), California, USA.

Abstract We surveyed pathogens and ectoparasites among federally endangered Amargosa voles (Microtus californicus scirpensis) and sympatric rodents in Tecopa Hot Springs, Inyo County, California, December 2011-November 2012. We aimed to assess disease and detect possible spillover from or connectivity with other hosts within and outside the Amargosa ecosystem. We assessed 71 individual voles and 38 individual sympatric rodents for current infection with seven vector-borne zoonotic pathogens and past exposure to five pathogens. Thirteen percent of Amargosa voles were PCR positive for Toxoplasma gondii, a zoonotic protozoan that may alter host behavior or cause mortality. Additionally, we found antibodies against Borrelia burgdorferi sensu lato (SL) spp. in 21% of voles, against Anaplasma phagocytophilum in 2.6%, Rickettsia spp. in 13%, relapsing fever Borrelia (3.9%), and T. gondii (7.9%). Sympatric rodents also had active infections with Borrelia SL spp. (15%). Of the ectoparasites collected, the tick Ixodes minor is of particular interest because the study area is well outside of the species' reported range and because I. minor ticks infest migratory birds as well as rodents, showing a potential mechanism for pathogens to be imported from outside the Amargosa ecosystem.