Primary data for: Use of secondary diversity data to improve diversity estimates at multiple geographic scales.

This dataset contains the primary and secondary biodiversity data supporting the study published in <i>Biodiversity and Conservation</i>. It provides the information necessary to evaluate amphibian diversity patterns across the Mexican Southern Altiplano. The dataset encompasses data from three distinct sources: presence-only datasets (POD), stacked species distribution models (stacked SDMs), and empirical species checklists from well-surveyed protected areas. These records facilitate the assessment of community emergent properties—including alpha diversity, beta diversity (such as Sørensen dissimilarity, turnover, and nestedness), per-site range size, and sample coverage completeness. Furthermore, the data are structured to allow systematic comparisons across five spatial scales: 1/2°, 1/4°, 1/8°, 1/16°, and 1/32°.