Estimates of population abundance and survival are critical for effective wildlife management. Obtaining estimates of these kind using traditional wildlife monitoring techniques (i.e. ground and aerial surveys) has proven to be difficult, especially for species that are wide ranging and exist in small, patchily distributed populations. My objective was to implement fecal DNA-based capture-recapture surveys to estimate abundance and survival of two different ungulate populations that inhabit the deserts of southeastern California. I also compared fecal DNA-based capture-recapture techniques to traditional methods by evaluating the costs and precision associated with both methods. Using artificial water sources as focal sampling sites, I performed sampling during the summers of 2015, 2016, and 2017 in the Mojave and Sonoran Deserts of California. I was able to obtain reasonably precise estimates of abundance and survival for both species. To my knowledge, my study provides the first abundance and survival estimates of desert mule deer in California in over 13 years. Additionally, my study shows that when compared to traditional methods, fecal DNA-based capture recapture techniques can achieve much higher precision at a fraction of the cost.

About 1,600,000 ha of desert mule deer range in Mexico are currently altered with vegetation clear-cutting and establishment of buffelgrass pastures. Consequently, the availability of resources as cover and forage from scrub vegetation has been reduced for mule deer. No previous research has been conducted to investigate how desert mule deer respond to those alterations. Therefore, the purpose of this research was to examine movements of mule deer, evaluate their home range sizes and determine habitat use, and analyze their diets in areas of central and western Sonora, Mexico. The approach involved the use of radiotelemetry techniques and GIS programs to calculate home range sizes, examine selection of vegetation associations, and identify the specific components of habitat that distinguished the characteristics of selected sites by desert mule deer. I used the microhistological technique to determine botanical components of desert mule deer diets, and compare diets of desert mule deer and cattle in habitat with buffelgrass pastures. Diet analyses included spatial and temporal comparisons of diversity and similarity indices. Sizes of home ranges were larger in the more arid environments of western Sonora (27.3 km2) than in central Sonora (14.5 km2). Desert mule deer used altered habitat differently than use areas without buffelgrass, however, there was no difference in the size of home ranges of mule deer from inside buffelgrass areas and the size of home ranges of deer in native scrub vegetation. Thermal cover, ground cover, and percent of gravel in the ground were the variables that distinguished locations selected by desert mule deer. Desert mule deer selected xeroriparian vegetation and sites closer to water sources. Water sources may have influenced mule deer to stay in buffelgrass areas despite the lack of cover and forage from shrubs and trees. For diets of mule deer, I identified 96 plant species, 69 of which have not previously been reported as forage for this herbivore. Desert mule deer and cattle shared 45 forage species from central Sonora. However, biological overlap of diets occurred only for spring. Results from these studies provide information to understand ecological relationships of desert mule deer on altered habitats.