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Marsh birds (rallids, bitterns, and grebes) depend on emergent wetlands, and habitat loss and degradation are the primary suspected causes for population declines among many marsh bird species. We evaluated the effect of natural wetland characteristics, wetland management practices, and surrounding landscape characteristics on marsh bird occupancy in Illinois during late spring and early summer 2015-2017. We conducted call-back surveys following the North American Standardized Marsh Bird Survey Protocol three times annually at all sites (2015 n = 49, 2016 n = 57, 2017 n = 55). Across all species and groups, detection probability declined 7.1% ± 2.1 each week during the marsh bird survey period. Wetlands managed for waterfowl (ducks, geese, and swans) had greater occupancy than reference wetlands. Marsh bird occupancy increased with greater wetland complexity, intermediate levels of waterfowl management intensity, greater proportions of surface water inundation, and greater proportions of persistent emergent vegetation cover. Wetland management practices that retain surface water during the growing season, encourage perennial emergent plants (e.g., Typha sp.), and increase wetland complexity could be used to provide habitat suitable for waterfowl and marsh birds.

Increased understanding of the influence of habitat (e.g., composition, patch size) and intrinsic (e.g., age, birth mass) factors on survival of neonatal pronghorn (Antilocapra americana) is a prerequisite to successful management programs, particularly as they relate to population dynamics and the role of population models in adaptive species management. Nevertheless, few studies have presented empirical data quantifying the influence of habitat variables on survival of neonatal pronghorn. During 2002-2005, we captured and radiocollared 116 neonates across two sites in western South Dakota. We documented 31 deaths during our study, of which coyote (Canis latrans) predation (n = 15) was the leading cause of mortality. We used known fate analysis in Program MARK to investigate the influence of intrinsic and habitat variables on neonatal survival. We generated a priori models that we grouped into habitat and intrinsic effects. The highest-ranking model indicated that neonate mortality was best explained by site, percent grassland, and open water habitat; 90-day survival (0.80; 90% CI = 0.71-0.88) declined 23% when grassland and water increased from 80.1 to 92.3% and 0.36 to 0.40%, respectively, across 50% natal home ranges. Further, our results indicated that grassland patch size and shrub density were important predictors of neonate survival; neonate survival declined 17% when shrub density declined from 5.0 to 2.5 patches per 100 ha. Excluding the site covariates, intrinsic factors (i.e., sex, age, birth mass, year, parturition date) were not important predictors of survival of neonatal pronghorns. Further, neonatal survival may depend on available land cover and interspersion of habitats. We have demonstrated that maintaining minimum and maximum thresholds for habitat factors (e.g., percentages of grassland and open water patches, density of shrub patches) throughout natal home ranges will in turn, ensure relatively high (>0.50) neonatal survival rates, especially as they relate to coyote predation. Thus, landscape level variables (particularly percentages of open water, grassland habitats, and shrub density) should be incorporated into the development or implementation of pronghorn management plans across sagebrush steppe communities of the western Dakotas, and potentially elsewhere within the geographic range of pronghorn.

New-hoof growth is regarded as the most reliable metric for predicting age of newborn ungulates, but variation in estimated age among hoof-growth equations that have been developed may affect estimates of survival in staggered-entry models. We used known-age newborns to evaluate variation in age estimates among existing hoof-growth equations and to determine the consequences of that variation on survival estimates. During 2001-2009, we captured and radiocollared 174 newborn (≤24-hrs old) ungulates: 76 white-tailed deer (Odocoileus virginianus) in Minnesota and South Dakota, 61 mule deer (O. hemionus) in California, and 37 pronghorn (Antilocapra americana) in South Dakota. Estimated age of known-age newborns differed among hoof-growth models and varied by >15 days for white-tailed deer, >20 days for mule deer, and >10 days for pronghorn. Accuracy (i.e., the proportion of neonates assigned to the correct age) in aging newborns using published equations ranged from 0.0% to 39.4% in white-tailed deer, 0.0% to 3.3% in mule deer, and was 0.0% for pronghorns. Results of survival modeling indicated that variability in estimates of age-at-capture affected short-term estimates of survival (i.e., 30 days) for white-tailed deer and mule deer, and survival estimates over a longer time frame (i.e., 120 days) for mule deer. Conversely, survival estimates for pronghorn were not affected by estimates of age. Our analyses indicate that modeling survival in daily intervals is too fine a temporal scale when age-at-capture is unknown given the potential inaccuracies among equations used to estimate age of neonates. Instead, weekly survival intervals are more appropriate because most models accurately predicted ages within 1 week of the known age. Variation among results of neonatal-age models on short- and long-term estimates of survival for known-age young emphasizes the importance of selecting an appropriate hoof-growth equation and appropriately defining intervals (i.e., weekly versus daily) for estimating survival.

Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy (TSE) that affects cervid species throughout North America. We evaluated gene expression in white‐tailed deer collected by Illinois Department of Natural Resource wildlife managers during annual population reduction (e.g., sharpshooting) and disease monitoring efforts throughout the CWD‐endemic area of northcentral Illinois. We conducted comparative transcriptomic analysis of liver and retropharyngeal lymph node tissue samples between CWD‐positive (n = 5) and CWD‐not detected (n = 5) deer. A total of 74,479 transcripts were assembled, and 51,661 (69.36%) transcripts were found to have matched proteins in NCBI‐NR and UniProt. Our analysis of functional categories showed 40,308 transcripts were assigned to at least one Gene Ontology term and 37,853 transcripts were involved in at least one pathway. We identified a total of 59 differentially expressed genes (DEGs) in CWD‐positive deer, of which 36 and 23 were associated with liver and retropharyngeal lymph node tissues, respectively. Functions of DEGs lend support to previous relationships between misfolded PrP and cellular membranes (e.g., STXBP5), and internal cellular components. We identified several genes that suggest a link between CWD and retroviruses and identified the gene ADIPOQ that acts as a tumor necrosis factor (TNF) antagonist. This gene may lead to reduced production of TNF and impact disease progression and clinical symptoms associated with CWD (i.e., wasting syndrome). Use of candidate genes identified in this study suggests the activation of endogenous processes in CWD‐positive deer, which in turn may enable earlier detection of the disease. We evaluated gene expression in white‐tailed deer collected by the Illinois Department of Natural Resources during annual population reduction and disease monitoring efforts throughout the CWD‐endemic area of northcentral Illinois. We identified 59 differentially expressed genes (DEGs) in CWD–infected deer LV (n = 36) and RPLN (n = 23) tissues, of which 28 genes were up‐regulated and 31 down‐regulated. Use of candidate genes identified in this study suggests the activation of endogenous processes in CWD‐positive deer, which in turn may enable earlier detection of the disease.

The human-mediated spread of exotic and invasive species often leads to unintentional and harmful consequences. Invasive wild pigs ( Sus scrofa ) are one such species that have been repeatedly translocated throughout the United States and cause extensive damage to natural ecosystems, threatened and endangered species, agricultural resources, and private lands. In 2005, a newly established population of wild pigs was confirmed in Fulton County, Illinois, U.S. In 2011, a state-wide wild pig damage management program involving federal, state, and local government authorities directed a concerted effort to remove wild pigs from the county until the last wild pig (of 376 total) was successfully removed in 2016. We examined surveillance data from camera traps at bait sites and records of wild pig removals during this elimination program to identify environmental and anthropogenic factors that optimized removal of this population. Our results revealed that wild pigs used bait sites most during evening and nocturnal periods and on days with lower daily maximum temperatures. Increased removals of wild pigs coincided with periods of cold weather. We also identified that fidelity and time spent at bait sites by wild pigs was not influenced by increasing removals of wild pigs. Finally, the costs to remove wild pigs averaged $50 per wild pig (6.8 effort hours per wild pig) for removing the first 99% of the animals. Cost for removing the last 1% increased 84-fold, and averaged 122.8 effort hours per wild pig removed. Our results demonstrated that increased effort in removing wild pigs using bait sites should be focused during periods of environmental stress to maximize removal efficiency. These results inform elimination programs attempting to remove newly established populations of wild pigs, and ultimately prevent population and geographic expansion.

Aerial surveys flown at low altitudes allow detection, identification, and enumeration of waterfowl and other waterbirds, but few studies have assessed disturbance to these guilds during the nonbreeding period. Excessive disturbance can potentially increase energy expenditure and exposure to hunting mortality contrary to objectives of many waterfowl sanctuaries where surveys are conducted. We used concurrent ground and aerial surveys to estimate the proportion of waterfowl and other waterbirds that exhibited a noticeable reaction (i.e., disturbance) or left the survey area entirely (i.e., abandonment) during low-altitude (i.e., 60–90m above ground level) aerial surveys during September through January 2014–2017 in Illinois, USA. Overall, disturbance and abandonment probabilities of waterfowl (x̄= 14±2% [SE] and x̄= 3±1%, respectively) during aerial surveys were low. However, disturbance and abandonment probabilities varied considerably among taxa (e.g., American coot [Fulica americana] x̄= 2±1% and x̄= 0±0%, respectively; killdeer [Charadrius vociferus] x̄= 92±8% and x̄= 17±17%, respectively). Additionally, disturbance and abandonment probabilities of light geese (i.e., snow goose [Chen caerulescens] and Ross’s goose [C. rossii]) and greater white-fronted geese (Anser albifrons) were relatively high, and nearly all light geese abandoned a survey location as a result of the aerial survey. Among waterfowl taxa, the odds of disturbance from the survey aircraft were 2.2–6.2 times greater at locations closed to waterfowl hunting than locations open to waterfowl hunting. Temperature, wind speed, and cloud cover were not important predictors of disturbance for most guilds, except for a negative influence of temperature on disturbance of geese. Low-altitude aerial surveys were not a significant source of disturbance for many taxa and abandonment events were rare, except events involving light geese. Periodic low-altitude aerial surveys appear to be compatible with objectives of providing sanctuary conditions for most waterfowl and other waterbirds.

Response to infectious disease outbreaks and ongoing management actions can vary greatly across geopolitical units. Understanding relationships between management actions of governance systems within social ecological systems (SES) is important when resource units (e.g. wildlife) and users (e.g. humans) inextricably connect them. Surveillance efforts provide critical information to governance systems for diseases such as coronavirus, influenza, and ebola. However, diseases that spread rapidly across multiple SESs are coarsely managed and monitored over weeks, months, or years. Such time and spatial constraints can challenge evaluation of management actions. Assessing importance of disease management across SESs for slow-moving infectious diseases can provide rare insights about management actions. We investigated an exemplary outbreak of Chronic Wasting Disease (CWD) in white-tailed deer populations along the geopolitical border of Illinois and Wisconsin, USA. We illustrated challenges of disease management in wildlife populations along geopolitical borders, where differences in management actions of adjacent governance systems were stark and subject to sudden change. Our analysis provided evidence of abrupt change in outbreak progression following drastic changes in management actions. In addition, we showed evidence of inconsistent and highly variable outcomes of management actions along a geopolitical border when adjacent governance systems are unable to cooperatively manage across interconnected SESs. Total annual harvest in a county is a primary management action used to control CWD, where increasing harvest potentially reduces prevalence. We showed that the effects of increasing total county-level harvest on cumulative incidence of CWD were highly heterogeneous. In some counties, increasing harvest had the opposite of the intended effect.

Avian diet quality is typically measured using true metabolizable energy (TMEN), which is a measure of assimilable energy of food items accounting for innate endogenous losses. Originally developed for use in the poultry industry, TMEN methods have been adapted to determine the value of natural foods consumed by waterfowl to parameterize bioenergetics models for conservation planning. Because there is little knowledge of the variation in TMEN estimates among food items and waterfowl species, we investigated TMEN of 6 common species of submersed aquatic vegetation for mallards (Anas platyrhynchos; i.e., a diet generalist) and gadwall (Mareca strepera; i.e., a diet specialist) in the midwestern United States during autumn 2015–2017. We precision fed and collected excreta from ducks using standard bioassays to estimate TMEN. Mallards had slightly greater TMEN than gadwall, but there was considerable variation in TMEN among vegetation species, duck species, and individuals within each species. True metabolizable energy (±SE; kcal/g[dry]) for mallards was greatest for Canadian waterweed (Elodea canadensis; 1.66 ± 0.26), followed by coontail (Ceratophyllum demersum; 1.51 ± 0.28), southern naiad (Najas guadalupensis; 1.37 ± 0.39), sago pondweed (Stuckenia pectinata; 0.50 ± 0.22), wild celery (Vallisneria americana; 0.05 ± 0.42), and Eurasian watermilfoil (Myriophyllum spicatum; –0.13 ± 0.42). Mean TMEN for gadwall was greatest for Eurasian watermilfoil (0.77 ± 0.32), followed by Canadian waterweed (0.70 ± 0.31), coontail (0.55 ± 0.28), southern naiad (–0.61 ± 0.34), wild celery (–0.98 ± 0.39), and sago pondweed (–1.07 ± 0.33). Generally, TMEN for most vegetation species was less than agricultural grains, but it was similar to ranges reported for seeds of naturally occurring hydrophytic vegetation and aquatic macroinvertebrates. We recommend that conservation planners incorporate species-specific TMEN estimates in bioenergetics models and that future researchers improve TMEN assays for wild waterfowl following our recommendations.

Camera-trapping data analyzed with spatially explicit capture–recapture (SCR) models can provide a rigorous method for estimating density of small populations of elusive carnivore species. We sought to develop and evaluate the efficacy of SCR models for estimating density of a presumed low-density bobcat (Lynx rufus) population in fragmented landscapes of west-central Illinois, USA. We analyzed camera-trapping data from 49 camera stations in a 1,458-km² area deployed over a 77-day period from 1 February to 18 April 2017. Mean operational time of cameras was 52 days (range = 32–67 days). We captured 23 uniquely identifiable bobcats 113 times and recaptured these same individuals 90 times; 15 of 23 (65.2%) individuals were recaptured at ≥2 camera traps. Total number of bobcat capture events was 139, of which 26 (18.7%) were discarded from analyses because of poor image quality or capture of only a part of an animal in photographs. Of 113 capture events used in analyses, 106 (93.8%) and 7 (6.2%) were classified as positive and tentative identifications, respectively; agreement on tentative identifications of bobcats was high (71.4%) among 3 observers. We photographed bobcats at 36 of 49 (73.5%) camera stations, of which 34 stations were used in analyses. We estimated bobcat density at 1.40 individuals (range = 1.00–2.02)/100 km². Our modeled bobcat density estimates are considerably below previously reported densities (30.5 individuals/100 km²) within the state, and among the lowest yet recorded for the species. Nevertheless, use of remote cameras and SCR models was a viable technique for reliably estimating bobcat density across west-central Illinois. Our research establishes ecological benchmarks for understanding potential effects of colonization, habitat fragmentation, and exploitation on future assessments of bobcat density using standardized methodologies that can be compared directly over time. Further application of SCR models that quantify specific costs of animal movements (i.e., least-cost path models) while accounting for landscape connectivity has great utility and relevance for conservation and management of bobcat populations across fragmentedMidwestern landscapes.

We studied home range use, spatial activity patterns, and annual survival of southern flying squirrels (SFS; Glaucomys volans) across fragmented landscapes of west-central Illinois. We calculated seasonal home range sizes and annual survival from 67 animals (36 males, 31 females) captured during 2014–2016. Home range and core area sizes were similar (P ≥ 0.46) among males and females across summer (April–September) and winter (October–March) seasons. Average distance between consecutive animal locations did not vary by sex, season, or year. Similarly, cumulative distance between consecutive locations did not vary by sex, season, or year and ranged from 1,189 to 1,661 m between summer and winter seasons. Mean annual composite home range and core area sizes were 10.39 and 1.25 ha, respectively; estimated home ranges (10.3 ha) of females are the largest documented for this species. We documented 8 deaths, all attributed to predation, the majority (63%) of which occurred during winter; annual survival was 71%. Our results underscore effects of habitat productivity on seasonal home range dynamics and space use patterns of SFS in fragmented landscapes. SFS may compensate for reduced availability of overstory mast-producing trees that characterize unproductive habitats and low-density populations by exhibiting similar movement patterns and use of available habitat by both sexes throughout the year. Winter communal nesting appears to be influenced by availability of cavity trees, thereby confirming the importance of standing snags in contributing essential habitat to flying squirrel populations in fragmented forests.