A genetic warning system for a hierarchically structured wildlife monitoring framework.

Genetic variation is a well-known indicator of population fitness yet is not typically included in monitoring programs for sensitive species. Additionally, most programs monitor populations at one scale, which can lead to potential mismatches with ecological processes critical to species' conservation. Recently developed methods generating hierarchically nested population units (i.e., clusters of varying scales) for greater sage-grouse (Centrocercus urophasianus) have identified population trend declines across spatiotemporal scales to help managers target areas for conservation. The same clusters used as a proxy for spatial scale can alert managers to local units (i.e., neighborhood-scale) with low genetic diversity, further facilitating identification of management targets. We developed a genetic warning system utilizing previously developed hierarchical population units to identify management-relevant areas with low genetic diversity within the greater sage-grouse range. Within this warning system we characterized conservation concern thresholds based on values of genetic diversity and developed a statistical model for microsatellite data to robustly estimate these values for hierarchically nested populations. We found that 41 of 224 neighborhood-scale clusters had low genetic diversity, 23 of which were coupled with documented local population trend decline. We also found evidence of cross-scale low genetic diversity in the small and isolated Washington population, unlikely to be reversed through typical local management actions alone. The combination of low genetic diversity and a declining population suggests relatively high conservation concern. Our findings could further facilitate conservation action prioritization in combination with population trend assessments and (or) local information, and act as a base-line of genetic diversity for future comparison. Importantly, the approach we used is broadly applicable across taxa.

Defining biologically relevant and hierarchically nested population units to inform wildlife management.

Wildlife populations are increasingly affected by natural and anthropogenic changes that negatively alter biotic and abiotic processes at multiple spatiotemporal scales and therefore require increased wildlife management and conservation efforts. However, wildlife management boundaries frequently lack biological context and mechanisms to assess demographic data across the multiple spatiotemporal scales influencing populations. To address these limitations, we developed a novel approach to define biologically relevant subpopulations of hierarchically nested population levels that could facilitate managing and conserving wildlife populations and habitats. Our approach relied on the Spatial "K"luster Analysis by Tree Edge Removal clustering algorithm, which we applied in an agglomerative manner (bottom-to-top). We modified the clustering algorithm using a workflow and population structure tiers from least-cost paths, which captured biological inferences of habitat conditions (functional connectivity), dispersal capabilities (potential connectivity), genetic information, and functional processes affecting movements. The approach uniquely included context of habitat resources (biotic and abiotic) summarized at multiple spatial scales surrounding locations with breeding site fidelity and constraint-based rules (number of sites grouped and population structure tiers). We applied our approach to greater sage-grouse (Centrocercus urophasianus), a species of conservation concern, across their range within the western United States. This case study produced 13 hierarchically nested population levels (akin to cluster levels, each representing a collection of subpopulations of an increasing number of breeding sites). These closely approximated population closure at finer ecological scales (smaller subpopulation extents with fewer breeding sites; cluster levels ≥2), where >92% of individual sage-grouse's time occurred within their home cluster. With available population monitoring data, our approaches can support the investigation of factors affecting population dynamics at multiple scales and assist managers with making informed, targeted, and cost-effective decisions within an adaptive management framework. Importantly, our approach provides the flexibility of including species-relevant context, thereby supporting other wildlife characterized by site fidelity.

Endemic chronic wasting disease causes mule deer population decline in Wyoming.

Chronic wasting disease (CWD) is a fatal transmissible spongiform encephalopathy affecting white-tailed deer (Odocoileus virginianus), mule deer (Odocoileus hemionus), Rocky Mountain elk (Cervus elaphus nelsoni), and moose (Alces alces shirasi) in North America. In southeastern Wyoming average annual CWD prevalence in mule deer exceeds 20% and appears to contribute to regional population declines. We determined the effect of CWD on mule deer demography using age-specific, female-only, CWD transition matrix models to estimate the population growth rate (λ). Mule deer were captured from 2010-2014 in southern Converse County Wyoming, USA. Captured adult (≥ 1.5 years old) deer were tested ante-mortem for CWD using tonsil biopsies and monitored using radio telemetry. Mean annual survival rates of CWD-negative and CWD-positive deer were 0.76 and 0.32, respectively. Pregnancy and fawn recruitment were not observed to be influenced by CWD. We estimated λ = 0.79, indicating an annual population decline of 21% under current CWD prevalence levels. A model derived from the demography of only CWD-negative individuals yielded; λ = 1.00, indicating a stable population if CWD were absent. These findings support CWD as a significant contributor to mule deer population decline. Chronic wasting disease is difficult or impossible to eradicate with current tools, given significant environmental contamination, and at present our best recommendation for control of this disease is to minimize spread to new areas and naïve cervid populations.

Chronic Wasting Disease Drives Population Decline of White-Tailed Deer.

Chronic wasting disease (CWD) is an invariably fatal transmissible spongiform encephalopathy of white-tailed deer, mule deer, elk, and moose. Despite a 100% fatality rate, areas of high prevalence, and increasingly expanding geographic endemic areas, little is known about the population-level effects of CWD in deer. To investigate these effects, we tested the null hypothesis that high prevalence CWD did not negatively impact white-tailed deer population sustainability. The specific objectives of the study were to monitor CWD-positive and CWD-negative white-tailed deer in a high-prevalence CWD area longitudinally via radio-telemetry and global positioning system (GPS) collars. For the two populations, we determined the following: a) demographic and disease indices, b) annual survival, and c) finite rate of population growth (λ). The CWD prevalence was higher in females (42%) than males (28.8%) and hunter harvest and clinical CWD were the most frequent causes of mortality, with CWD-positive deer over-represented in harvest and total mortalities. Survival was significantly lower for CWD-positive deer and separately by sex; CWD-positive deer were 4.5 times more likely to die annually than CWD-negative deer while bucks were 1.7 times more likely to die than does. Population λ was 0.896 (0.859-0.980), which indicated a 10.4% annual decline. We show that a chronic disease that becomes endemic in wildlife populations has the potential to be population-limiting and the strong population-level effects of CWD suggest affected populations are not sustainable at high disease prevalence under current harvest levels.

Ocular plague (Yersinia pestis) in mule deer (Odocoileus hemionus) from Wyoming and Oregon.

Although plague is relatively rare in wild ungulates, this report describes ocular lesions associated with Yersinia pestis infection in three free-ranging mule deer (Odocoileus hemionus) from Wyoming and Oregon, USA. All deer were observed antemortem and seemed to be blind. Post-mortem examination revealed gross lesions of bilateral keratoconjunctivitis and/or panophthalmitis in the first two deer, but only partial retinal detachment in the third deer. Microscopically, all deer had moderate-to-severe necrotizing and fibrinopurulent endophthalmitis and varying degrees of keratoconjunctivitis with abundant intralesional coccobacilli. The lesions in the first (D1) and third deer (D3) suggested an acute course, whereas those in the second deer (D2) were subacute to chronic. Yersinia pestis was isolated from ocular tissue swabs or ocular fluids of D1 and D2, and it was demonstrated by immunohistochemistry within ocular lesions of D1 and D3. Although plague does not seem to be a major cause of morbidity or mortality in free-ranging mule deer, keratoconjunctivitis or pinkeye is relatively common in these animals and plague should be considered as a differential diagnosis in such cases, with appropriate precautions taken to protect the human and animal health.