Landscape fragmentation poses a major threat to biodiversity world-wide. The goal of my dissertation research was to determine the effects of landscape fragmentation on a lizard community in the Mescalero-Monahans shinnery sands, New Mexico and the extent to which conservation efforts might protect biodiversity in this ecosystem. My research relied heavily on data collected from a large-scale spatially-replicated comparative study. The purpose of this study was to evaluate the impacts of landscape fragmentation as a result of oil and gas development on the dunes sagebrush lizard (Sceloporus arenicolus). Results from analysis of lizard community structure indicate that fragmented sites are less diverse than non-fragmented sites. In particular, two species are found in lower density and occupancy in the fragmented locations (Holbrookia maculata and Sceloporus arenicolus). Analysis of landscape configuration at the scale of a trapping grid indicated that sand dune blowout shape and size differed between fragmented and non-fragmented locations. Differences in landscape pattern were associated with reduced lizard diversity. Because of this association between lower diversity and altered landscape pattern, extensive alterations to landscape pattern may cause disassembly at the ecosystem level. The maintenance of existing landscape pattern may be important to the maintenance of diversity in this ecosystem. Evaluations of habitat use patterns of the lizards in this community demonstrate that a few species have narrow preferences for certain habitats. In particular, H. maculata, Phrynosoma cornutum, and S. arenicolus all demonstrated narrow habitat use patterns. Effect size of fragmentation for each species indicated that the same three species showed a large effect when comparing their average abundances between fragmented and non-fragmented locations. Thus species that are most likely to benefit or be harmed by landscape fragmentation are those with the most specific habitat requirements. Umbrella species represent one of many approaches to conservation using surrogate species. I used data on ants, beetles, small mammals, lizards, and endemic species to test the use of the dunes sagebrush lizard (Sceloporus arenicolus) as an umbrella for endemism and biodiversity of the Mescalero-Monahans shinnery sands ecosystem. I applied a comparative approach at three spatial scales to examine how conservation practices at different scales may affect biodiversity and endemism in this ecosystem. At the largest scale, the frequency of occurrence for endemic species increased though no other patterns emerged because S. arenicolus was present at all sites and there were no relationships between relative abundances of S. arenicolus and the other taxonomic groups. At the smallest scale, both beetle species richness, diversity, and endemic species richness were higher in the presence of S. arenicolus. To protect biodiversity in this ecosystem, conservation efforts should focus on protection at the scale of the species distribution rather than on the small-scale placement of individual well pads.