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The Pleistocene was characterized by worldwide shifts in community compositions. Some of these shifts were a result of changes in fire regimes, which influenced the distribution of species belonging to fire-dependent communities. We studied an endangered juniper-oak shrubland specialist, the black-capped vireo (Vireo atricapilla). This species was locally extirpated in parts of Texas and Oklahoma by the end of the 1980s as a result of habitat change and loss, predation, brood parasitism, and anthropogenic fire suppression. We sequenced multiple nuclear loci and used coalescence methods to obtain a deeper understanding of historical population trends than that typically available from microsatellites or mtDNA. We compared our estimated population history, a long-term history of the fire regime and ecological niche models representing the mid-Holocene, last glacial maximum, and last interglacial. Our Bayesian skyline plots showed a pattern of historical population fluctuation that was consistent with changing fire regimes. Genetic data suggest that the species is genetically unstructured, and that the current population should be orders of magnitude larger than it is at present. We suggest that fire suppression and habitat loss are primary factors contributing to the recent decline of the BCVI, although the role of climate change since the last glacial maximum is unclear at present. [ABSTRACT FROM AUTHOR]