Population dynamics of large ungulates are complex and vary with fluctuations in factors such as predation, resource availability, human disturbance, and weather (Gaillard et al. 1998, Forrester and Wittmer 2013). These regulating factors exhibit similar effects on ungulate populations by changing vital rates such as birthrate, death rate, emigration or immigration (Gaillard et al. 2000). To better understand the mechanisms influencing population change, it is useful to involve tools from multiple disciplines (Krausman et al. 2013). Here we explore population dynamics of mule deer (Odocoileus hemionus) through the lenses of two distinct fields: population ecology and genomics. In the first chapter we examine the influence of maternal effects on offspring fitness. In the second chapter we present a high-quality, chromosome-level reference genome for mule deer. We expect results from each of these studies to provide valuable resources for continued research and conservation of mule deer.

Mule deer (Odocoileus hemionus) populations are influenced by multiple factors, including interspecific competition and predation. Interspecific competition can affect resource acquisition and survival through altering space use and access to preferred habitat. Mule deer in some areas alter space use in the presence of competing species, including bison (Bison bison), cattle (Box taurus), elk (Cervus canadensis), and feral horses (Equus caballus), however the influence of competition on survival of mule deer during specific life history stages, such as birthing and rearing of neonates, is largely unknown. In addition to competition, predation can influence mule deer populations and even limit population growth by reducing recruitment of neonates into the adult population. The effects of predation may increase within a complex predator community, as predator species differ in hunting strategies, which may influence timing of predation events. We investigated the effects of interspecific competition on space use by mule deer during birthing and rearing of young (Chapter 1) and analyzed temporal patterns of predator kills of neonate mule deer in a complex predator community (Chapter 2). We hypothesized that mule deer would avoid competing ungulate species during birth and rearing of young, and that survival of neonate mule deer would decrease in areas of with increased likelihood of competition. We also hypothesized that timing of kills and habitat characteristics of kill sites would differ by predator species due to different hunting strategies. We captured 98 neonate mule deer and fit them with mortality-sensing radiocollars to test our hypotheses. We did not observe any evidence of competitive interactions between mule deer and other ungulate species. Further, we observed a positive association between space use by mule deer and elk following parturition. We also observed an increase in probability of survival for neonate mule deer in areas with higher probability of use by elk (Hazard ratio= 0.185, SE=0.497). We observed differences in timing of kills among predator species (p=0.026), however habitat characteristics of kill sites did not differ for those species. It appears that resource availability and climatic conditions influence space use by mule deer more strongly than space use by competing species. Further, timing of kills of neonate mule deer differ by predator species, which may lead to an additive effect of predation within a complex predator community.

Objectives were (1) to evaluate the seasonal and daily use by mule deer (Odocoileus hemionus) of adjoining converted and natural pinyon pine-Utah juniper woodland (P-J) winter range, and (2) to determine the major factors influencing mule deer use of converted P-J range to provide criteria for deer management. The study was conducted on 3 sites in central, eastern, ar.d southeastern Utah between 1969-72. Data for 1969-72 on physiographic, climatic, and vegetational attributes of the three Utah study areas were related to data from approximately 10,000 deer observations, 5,000 0.01-acre pellet-group count plots, feeding observations of 1,100 deer, 220 miles of track counts on trails, and 450 radio locations of nine adult female deer. Conclusions were: (1) In the initial 12 years post-treatment, no increase in deer numbers X was correlated with P-J conversion. (2) Increasing deer use during the study was concentrated on natural P-J. (3) The bulk of the use on chainings occurred in March and April. (4) Radio telemetry indicated that, from November to May, about 55 percent of the deer within 0.5-mile of the chaining edge used the chainings at night, and 5 percent in the day. (5) Deer fed and bedded in alternate 2-hour periods. Thus, the Mayfield chainings contributed 25 to 30 percent of the deer forage, but comprised over 50 percent of the land area. (6) The greatest overwinter deer use occurred in shallow valleys and on slopes of 10-20°. Least preferred by deer were flats and hilltops. Chaining decreased the relative deer use on hilltops, increased it on hillsides, and had no effect on the use of valleys. (7) Deer use was greatest on north exposures in the natural P-J and on south exposures on chainings. (8) No edge effect existed in the initial mile of P-J away from the chaining edge, whereas, deer use of chainings declined 50 percent in the initial 0.2-mile. (9) Radio telemetry showed a mean home range radius of 0.6- mile between November and May for nine adult female deer. (10) Moon phase effected deer use on the chainings but with reversed influence between November and May. (11) Snow cover over 10 inches and wind velocity greater than 20 miles-per-hour each decreased considerably deer use of chainings. (12) An increase in shrub density increased deer use of chainings more than any other variables measured. (13) Chaining of P-J apparently decreased Cercocarpus montanus, Quercus gambelii, and Pinus edulis shrub density but increased Juni£eru~ osteosperma and Artemisia spp. Forb cover did not markedly change post-chaining, while grass cover increased by 400 percent. (14) Total forage crown cover increased 25 percent 3-12 years post-treatment. However, total palatable browse cover was less on treated than untreated range. (15) Juniperus spp., Artemisia spp. and green grasses comprised 60 to 75 percent of the over-winter diet; the remainder was composed largely of Quercus gambelii and Cercocarpus montanus. (16) Optimum tree density for deer use of P-J appears to be 50 to 100 per acre, depending upon maturity of the stand. Management recommendations are that P-J chainings should: (1) be less than 0.4-mile wide, compose no more than 20 percent of the winter range 1n a 25 year period, (2) be single chained only, (3) be confined to small valleys and gentle slopes, (4) have 20 percent slash cover, 5-10 percent grass cover, and many of the pushed-over tree tops ~eft alive, (5) be confined largely to south and west exposures, (6) be grazed in a spring- fall rotation by cattle.

A difficulty in using diffusion models to predict large-scale animal population dispersal is that individuals move differently based on local information (as opposed to gradients) in differing habitat types. This can be accommodated by using ecological diffusion. However, real environments are often spatially complex, limiting application of a direct approach. Homogenization for partial differential equations has long been applied to Fickian diffusion (in which average individual movement is organized along gradients of habitat and population density). In this work, we derive a homogenization procedure for ecological diffusion, which allows us to determine the impact of small-scale (10-100 m) habitat variability on large-scale (10-100 km) movement, and apply it to models for chronic wasting disease (CWD) in mule deer. CWD is an infectious prion disease that affects members of the Cervidae family. It is a slow-developing, fatal disease, which is rare in the free-ranging deer population of Utah. We first present a simple spatial disease model to illustrate our homogenization procedure and the use of ecological diffusion as a way to connect animal movement with disease spread. Then we develop a more disease-specific sex-structured model for the spread of CWD, incorporating both horizontal and environmental transmission pathways. We apply our homogenization technique to greatly reduce the computational load for a simulation of disease spread from the La Sal Mountains to the Abajo Mountains of Southeast Utah. We use the averaged coefficients from the homogenized model to explore asymptotic invasion speed and critical population size for portions of our study area. Lastly, we describe the estimation of motilities for the disease-specific model from GPS location data, using a continuous-time correlated random walk model.

Mule deer (Odocoileus hemionus) reproduction and survival on the LaSal Mountains, Utah were studied from 1978-81. Reproductive rates were high, suggesting that summer and fall forage quality was adequate and was not responsible for low recruitment observed in recent years. The combined fetal rate, determined from laparotomies and carcasses, was 1.72 for all females older than 1 year (N = 114). Fetal rates were 1.15 for yearlings (N = 20), 1.80 for prime females (2-7 years, N = 78), and 1.75 for old females (8+ years, N = 16). No evidence of breeding was found among fawns (N = 18). Estimated intrauterine mortality was 3.9%. A compensatory response to inadequate winter nutrition was not identified as a factor in maintaining high reproductive potentials, although its role might have been obscured by the high predation rate on young fawns. During 1979 and 1980, an average of 67% of the total annual loss of radio-monitored fawns occurred within 54 days postpartum. Survival of transmittered fawns (N = 54) from capture to December averaged 42.7%. Direct causes of mortality during the summer included predation (73%}, primarily by coyotes (Canis latrans} and black bears (Ursus americanus}; starvation, accidents, and illegal kills (9%}; and unknown factors (18%}. Overwinter survival of fawns and does was inversely related to winter intensity. Fawn survival from January to June was 58.3% of the December population in 1980 and 88.9% in 1981. During this period, predation or probable predation, primarily by coyotes, accounted for 82% of the observed deaths and accidents for 18%. Substantial losses to malnutrition and domestic dogs occurred in Castle Valley during the severe winter of 1978-79. Total annual survival of transmittered fawns was similar both years, 28.9% for the 1979 cohort and 31.8% for the 1980 cohort. Application of a change-in-ratio estimator yielded estimates of fawn survival that were similar to survival rates from samples of radio-monitored fawns, except during summer 1979 when prenatal and immediate postpartum mortality may have been high following the severe 1978-79 winter. Annual survival rates of radio-monitored does were 68.9% in 1979 (N = 38) and 86.6% (N = 22) in 1980. Causes of death included malnutrition and predation by coyotes and domestic dogs. No mortality occurred among radio-monitored females (N = 32} between January and June 1981. Recruitment rates, estimated from spring fawn proportions were 15% in 1979, 18% in 1980, and 32% in 1981, suggesting herd declines in the first 2 years and herd growth in 1981.

Highway mortality of deer (Odocoileus sp.) is a nationwide concern. In 1991, 538,000 deer-vehicle collisions occurred nationwide. Property damage to vehicles, human injuries and fatalities, and potential impacts to local deer populations occur from deer-vehicle collisions. Techniques have been evaluated to reduce highway mortality of deer; however, an effective, cost-efficient solution does not exist for widespread use. If mitigative technologies are to be successful, we need to understand deer behavior and movement patterns associated with highway relationships. Most research about highway deer kills has focused on white-tailed deer (Odocoileus virginianus) in mixed hardwood habitat types. The following study pertains to mule deer (Odocoileus hemionus) in a mountain brush and sagebrush-grass zone. The study area was located at the site of the newly constructed Jordanelle Reservoir near Park City, Utah. Area roads were relocated due to inundation of existing highways. Preconstruction road-kill was docwnented to be 0.29 kills/km. Annual road-kill levels of 278 (5.9 kills/km) and 119 (2.5 kills/km) deer occurred along the new roads from October 1991 to October 1993. Even though there was a 64.2% reduction in observed deer density, second year mortality was still 9 times the pre-project kill. A study design of road-kill data collection and repetitive spotlight censuses was used to compare levels and composition of deer road-kills to that of the living population. Deer-vehicle collision levels tracked large population fluctuations. Deer behavior predisposed deer to mortality. Numbers of road-killed deer peaked in the fall of both years, coincident with breeding and hunting periods. Road-kill peaks also occurred in July and April of each year, respectively. Traffic characteristics, road alignment, and vegetative and topographic features were described relative to mule deer kill locations (recorded to the .10 mile). Traffic volume and percent vegetative cover were higher along US40 than either state route; road-kills were correspondingly higher along US40. Roads adjacent to agricultural areas along all routes sustained the fewest highway mortalities of deer. Deer approached roads along drainages; large drainages intersected highways in 79% of designated kill areas. Right-of-way vegetation and slope influenced kill locations.

Desert mule deer (Odocoileus hemionus crooki) abundance and distribution, deer activity and diet, fawn survival, and predation were studied in Big Bend National Park, Texas from 15 January 1980 to 9 December 1981. Deer abundance was correlated with total plant, forage, and succulent densities but was also related to perennial water abundance and bed site availability. Fawn production and survival were related to spring rainfall. Diurnal and annual deer activity were influenced by temperature where spring and winter had longer daily activity compared to summer. Daily activity by deer was highest during the morning and evening. Forage use varied seasonally with browse use decreasing from spring to winter with a corresponding increase in use of forbs. Diets of two deer herds were compared and during drought periods forb use decreased until summer rains occurred. Prior to the rains, deer relied on evergreen browse species. Additionally, deer within mesic areas had a higher use of forb species contrasted with deer within xeric areas. Predator diet significantly changed with a decline in the deer population determined from pellet-group transects. Mountain lions (Felis concolor) used smaller prey including javelina and lagomorphs. Coyotes (Canis latrans) fed opportunistically by increasing use of insects, birds, reptiles, and lagomorphs. Bobcats (Lynx rufus) increased use of lagomorphs with little change in other prey species. Given alternate prey species, predator populations remained relatively constant given the deer decline.

No description available.

La chlamydiose aviaire, causée par la bactérie Chlamydia psittaci, représente un risque zoonotique important. L’infection chez l’animal est principalement asymptomatique, mais chez l’Homme elle peut entrainer des pneumopathies atypiques sévères et causer la mort dans les cas les plus graves. Les personnes infectées sont principalement celles exposées régulièrement à des oiseaux, particulièrement dans le cadre professionnel. En France, de nombreux cas humains sont liés à une exposition à des canards Mulard, espèce utilisée pour la production du foie gras. Afin d’évaluer la prévalence des Chlamydiaceae chez les volailles et de caractériser les souches circulantes, des suivis ont été réalisés à différents stades de l’élevage (couvoir, pré-gavage et gavage pour la filière canard, et abattoirs impliqués dans l’abattage de différentes espèces aviaires). Des prélèvements d’air et de poussières ainsi que des suivis sérologiques et biologiques de personnels volontaires ont été effectués en parallèle afin d’évaluer l’exposition des professionnels travaillant au contact des volailles. Des prélèvements environnementaux ainsi que des essais in vitro visant à étudier la survie de C. psittaci ont été réalisés afin de tenter de mieux caractériser les voies de contamination des oiseaux, ce qui pourrait, à terme, permettre de maitriser le risque de contamination par C. psittaci chez l’animal et donc de réduire l’exposition des professionnels. Les résultats ont démontré une prévalence importance de C. psittaci chez le canard Mulard, au contraire des autres volailles qui hébergent très majoritairement C. gallinacea. L’exposition des professionnels aux Chlamydia est réelle, tout au long du processus d’élevage des volailles, mais plus particulièrement en élevages de canards Mulard et à l’abattoir, aussi il convient pour les professionnels de se protéger à chaque contact avec les animaux. L’hypothèse d’une contamination environnementale des animaux se fait de plus en plus claire, avec notamment la mise en évidence d’un lien existant entre les procédures de nettoyage et désinfection et l’excrétion des canards, la description de la survie de C. psittaci en dehors de tout hôte vivant, ou encore la mise en évidence d’une possible survie de C. psittaci au sein d’A. castellanii. La mise au point de moyens de lutte efficaces permettant de réduire voire de supprimer l’excrétion chez les volailles est également nécessaire, dans le but de diminuer l’exposition des professionnels / Avian chlamydiosis is a factor of economic loss to the poultry industry as well as a risk for zoonotic transmission to human. Chlamydia psittaci is the primary avian chlamydial pathogen with zoonotic potential. Although being mainly asymptomatic in birds, it can cause a disease called “psittacosis” in humans, with severe atypical pneumonia that leads to death in the most severe cases. Persons affected are mainly those whose occupations put them at risk of exposure, and a number of recent reports in France have confirmed that most of the human cases seemed to be linked to poultry, especially mule ducks. Currently there is evidence suggesting that avian chlamydiosis in poultry involves a new chlamydial agent, namely C. gallinacea. In order to evaluate the presence of Chlamydiaceae in poultry and the exposure of workers, we conducted four studies in the poultry industries, in duck hatchery, breeding farms and slauhgterhouse, as well as a studie in two poultry slaughterhouses including samples from voluntary workers. Results showed an important asymptomatic carriage of C. psittaci by mule ducks and a real, invisible and unpredictable exposure of workers. The species C. gallinacea was really prevalent in poultry othe than ducks and we still ignore its impact on human. Contamination of animals on farm seems to be mainly made via the environment. In vitro studies have been done to examine the survival of C. psittaci as a function of temperature in a non-nutritiv middle and showed that viable bacteria were still detectable after two months. Finally, the possible interactions between C. psittaci and an amoeba, Acanthamoeba castellanii, were studied and seem to show that the bacteria was able to enter the amoeba but we still ignore if it can survive or not

<p>As human activity expands across the globe, disturbance of wildlife by anthropogenic activities such as fragmentation of habitat, and wildlife-human conflicts escalate. The Pueblo of Santa Ana is receiving pressure from road expansion and urban development and is concerned with the impacts of those activities upon wildlife populations. Specifically, mule deer is a species of concern for their Department of Natural Resources (DNR). Mule deer are important economically, culturally, and for recreational purposes. The DNR understands the need for better understanding mule deer ecology to manage for potential conflicts in their interactions with expanding human infrastructure. My objectives were first to model mule deer habitat use in and around the Pueblo of Santa Ana during the summer and winter at different times of the day. My second objective was to understand the relative impacts of different scenarios for road development in the Pueblo of Santa Ana upon the disturbance of mule deer using an Individual Based Modeling (IBM) framework.</p> <p> Using Geospatial Positioning System telemetry collar data collected on mule deer I used proximity based habitat predictors in a general linear mixed model to create resource selection functions. Generally I found that the season had a greater impact on mule deer habitat use than the time of day. Female and male mule deer select for similar habitat but sexually segregate in their summer distributions. My findings are consistent with results from other locations where mule deer studies have been conducted. In chapter two, I used the Simulation of Disturbance Activities (SODA) modeling framework to investigate the impact of vehicles on mule deer disturbance response behaviors, alert and fleeing. Using this framework I compared a baseline scenario to road expansion scenarios (DamRoad, ByPass, DeerCrossing) estimating the frequency of disturbance behavior of mule deer for each such scenario. My results show that mule deer were disturbed most in the baseline model. There were no significant differences in the frequency of disturbance for female mule deer across scenarios. Male mule deer did have some significant differences in alert and fleeing behavior across scenarios. My results may be a function of assumptions made in my modeling. Specifically, I assumed that mule deer would shift their areas of activity to new portions of the Pueblo of Santa Ana in response to altered habitat quality caused by new roads. If mule deer did not shift their areas of activity accordingly, my models may provide inaccurate assessments of disturbance patterns. </p> In conclusion my findings are similar to results from other locations. Specifically, the inferences that roads and road development are important to consider for mule deer management transcends variation associated with the unique characteristics of the Pueblo of Santa Ana mule deer population. Finally, my results suggest that the use of an IBM modeling framework has the potential to provide insights into the disturbance of mule deer by vehicular traffic even if my conclusions were constrained by study design.