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Application of island biogeography theory to prediction of species extinctions resulting from habitat loss is based on the assumption that the transformed landscape matrix is completely inhospitable to the taxa considered, despite evidence demonstrating the nontrivial influence of matrix on populations within habitat remnants. The island biogeography paradigm therefore needs refining to account for specific responses of taxa to the area of habitat "islands" and to the quality of the surrounding matrix. We incorporated matrix effects into island theory by partitioning the slope ( z value) of species-area relationships into two components: γ, a constant, and σ, a measure of taxon-specific responses to each component of a heterogeneous matrix. We used our matrix-calibrated model to predict extinction and endangerment of bird species resulting from land-use change in 20 biodiversity hotspots and compared these predictions with observed numbers of extinct and threatened bird species. We repeated this analysis with the conventional species-area model and the countryside species-area model, considering alternative z values of 0.35 (island) or 0.22 (continental). We evaluated the relative strength of support for each of the five candidate models with Akaike's information criterion (AIC). The matrix-calibrated model had the highest AIC weight (wi = 89.21%), which means the weight of evidence in support of this model was the optimal model given the set of candidate models and the data. In addition to being a valuable heuristic tool for assessing extinction risk, our matrix-calibrated model also allows quantitative assessment of biodiversity benefits (and trade-offs) of land-management options in human-dominated landscapes. Given that processes of secondary regeneration have become more widespread across tropical regions and are predicted to increase, our matrix-calibrated model will be increasingly appropriate for practical conservation in tropical landscapes.