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Little is known about the cumulative effects of conservation practices on individual species and biodiversity. The Conservation Effects Assessment Project, a nationwide effort conducted by the National Resource Conservation Service, seeks to quantify these effects. A first step towards assessing the effects of conservation practices is to identify a set of biodiversity metrics and species that are of conservation interest. Models of conservation practice effects can then be developed for these conservation priorities. Additionally, species-level models can provide information regarding the potential effects a conservation practice can have on a group of species that share similar ecological requirements (e.g., grassland obligates). We present a general method for characterizing a site in a broader ecological context and identifying biodiversity, species, and land cover-based conservation priorities. We applied this method to the Bureau of Land Management's Las Cruces district in New Mexico, though the method can ultimately be applied to any area in the United States. Species and land cover data were obtained from the Southwest Regional Gap Analysis Project. The method for ecological site characterization was robust to consideration of ecological contexts (i.e., site surroundings) defined using different types of boundaries. We identified 46 natural land cover types, 22 biodiversity metrics, and 18 focal species as conservation priorities for the Las Cruces district. Of the species identified as conservation priorities,, scaled quail was selected for species-level modeling. STELLA was used to construct a dynamic systems model representing the effects of brush control, grazing, and precipitation on potential scaled quail habitat over time. We present results of this fine-scale modeling in relation to the larger biodiversity metrics.