Date of Award


Degree Name

MS in Biological Sciences


Biological Sciences


College of Science and Mathematics


Francis Villablanca

Advisor Department

Biological Sciences

Advisor College

College of Science and Mathematics


Chapter 1. Species’ occurrences are dependent on a variety of habitat characteristics, including physical landscape factors and anthropogenic land use and change. Understanding the influence of habitat attributes on species occurrence is essential to successful wildlife and habitat management, specifically in areas with active human use. We tested the influence of vegetation alliance, fragmentation, and human recreation in the form of off-highway vehicles (OHV) in an area of active land management in coastal California, with a focus on the occurrences of six small mammal species. The area is composed of sand dunes subject to natural habitat fragmentation. OHV recreation occurs around a portion of the habitat fragments, but not within the fragments. We used model selection and model averaging on single season occupancy models in program R to compare probability of occupancy across three habitat attributes: vegetation alliance (two states), fragmentation (present – absent), and recreation (present – absent). Vegetation alliance was the best predicter of occupancy for Dipodomys heermanni, Peromyscus maniculatus, Peromyscuscalifornicus, and Neotoma macrotis. Fragmentation influenced occupancy for three species, conferring a positive effect for N. macrotis and Microtus californicus, and a negative effect for Chaetodipus californicus. Only two species showed a response in occupancy to recreation, N. macrotis and M. californicus, but the responses showed an increase in occupancy in habitat surrounded by OHV use. Occupancy for the three remaining species (D. heermanni, P. maniculatus, P. californicus,) was not impacted by fragmentation or recreation. The response to fragmentation is larger than the response to OHV recreation. Taken together, these results indicate that direct management of dominant vegetation and habitat fragmentation will have more of an impact on occupancy than the direct management of OHV recreation, except where recreation contributes indirectly to fragmentation.

Chapter 2. Determining best methods to detect individuals and monitor populations that balance effort and efficiency can assist conservation and land management. This may be especially true for small, non-charismatic species, such as rodents (Rodentia), which comprise >40% of all mammal species. Given the importance of rodents to ecosystems, and the number of listed species, we tested two commonly used detection and monitoring methods, live traps and camera traps, to determine their efficiency in rodents. An artificial-intelligence machine-learning model was developed to process the camera trap images and identify the species within them which reduced camera trapping effort. We used occupancy models to compare probability of detection and occupancy estimates for six rodent species across the two methods. Camera traps yielded greater detection probability and occupancy estimates for all six species. Live trapping yielded biasedly low estimates of occupancy, required greater effort, and had a lower probability of detection. Camera traps, aimed at the ground to capture the dorsal view of an individual, combined with machine learning provided a practical, non-invasive, and low effort solution to detecting and monitoring rodents. Thus, camera trapping with A.I. is a more sustainable and practical solution for the conservation and land management of rodents.

Chapter 3. One third of missing mammal species thought to be extinct have been rediscovered as extant. Therefore, determining extinction correctly, without misinterpreting negative evidence, is difficult and takes a large amount of effort, especially for small, cryptic species. The Morro Bay kangaroo rat (MBKR), Dipodomys heermanni morroensis, is a small nocturnal rodent that has not been detected since 1986 and is suspected of being extinct. While numerous surveys have been done, additional work is still needed to determine if the subspecies is truly extinct. This work summarizes a survey of the Morro Bay sandspit, an area not previously considered part of its range but that has the potential to be occupied by the subspecies, given habitat characteristics of its closest subspecies. Inferences from the closest relative, Dipodomys heermanni arenae, were used to inform surveys and detection probability for D. h. morroensis. Visual surveys in areas with greatest probability of detecting sign (burrows, bipedal prints, tail drags, etc.) were carried out and yielded only a few occurrences of possible sign. Camera traps, which provide an efficient, accurate, and precise detection method, were deployed both in winter and summer at locations with possible sign but yielded no detection of MBKR. Combining our survey results with inference from Dipodomys heermanni arenae, the possibility that individuals are present on the sandspit but were undetected by cameras is extremely low. We conclude that the MBKR is not present on the Morro Bay sandspit, at least not in the habitat where its presence was most likely to be detected.

Available for download on Wednesday, December 06, 2023

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