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The lack of long-term baseline data restricts the ability to measure changes in biological diversity directly and to determine its cause. This hampers conservation efforts and limits testing of basic tenets of ecology and conservation biology. We used a historical baseline survey to track shifts in the abundance and distribution of 296 native understory species across 82 sites over 55 years in the fragmented forests of southern Wisconsin. We resurveyed stands first surveyed in the early 1950s to evaluate the influence of patch size and surrounding land cover on shifts in native plant richness and heterogeneity and to evaluate changes in the relative importance of local site conditions versus the surrounding landscape context as drivers of community composition and structure. Larger forests and those with more surrounding forest cover lost fewer species, were more likely to recruit new species, and had lower rates of homogenization than smaller forests in more fragmented landscapes. Nearby urbanization further reduced both alpha and beta understory diversity. Similarly, understory composition depended strongly on local site conditions in the original survey but only weakly reflected the surrounding landscape composition. By 2005, however, the relative importance of these factors had reversed such that the surrounding landscape structure is now a much better predictor of understory composition than are local site conditions. Collectively, these results strongly support the idea that larger intact habitat patches and landscapes better sustain native species diversity and demonstrate that humans play an increasingly important role in driving patterns of native species diversity and community composition. [ABSTRACT FROM AUTHOR]