The forest refuge hypothesis (FRH) has long been a paradigm for explaining the extreme biological diversity of tropical forests. According to this hypothesis, forest retraction and fragmentation during glacial periods would have promoted reproductive isolation and consequently speciation in forest patches (ecological refuges) surrounded by open habitats. The recent use of paleoclimatic models of species and habitat distributions revitalized the FRH, not by considering refuges as the main drivers of allopatric speciation, but instead by suggesting that high contemporary diversity is associated with historically stable forest areas. However, the role of the emerged continental shelf on the Atlantic Forest biodiversity hotspot of eastern South America during glacial periods has been ignored in the literature. Here, we combined results of species distribution models with coalescent simulations based on DNA sequences to explore the congruence between scenarios of forest dynamics through time and the genetic structure of mammal species cooccurring in the central region of the Atlantic Forest. Contrary to the FRH predictions, we found more fragmentation of suitable habitats during the last interglacial (LIG) and the present than in the last glacial maximum (LGM), probably due to topography. We also detected expansion of suitable climatic conditions onto the emerged continental shelf during the LGM, which would have allowed forests and forest-adapted species to expand. The interplay of sea level and land distribution must have been crucial in the biogeographic history of the Atlantic Forest, and forest refuges played only a minor role, if any, in this biodiversity hotspot during glacial periods.T he extreme biological diversity of tropical forests has inspired and puzzled naturalists and scientists for centuries, and the forest refuge hypothesis (FRH) has long been one of the major paradigms to explain it. According to the FRH, forest retraction and fragmentation during glacial periods would have promoted isolation and consequently allopatric speciation in forest patches, or ecological refuges, surrounded by open habitats in the Amazon (1). Although originally based on climate fluctuations in the Pleistocene, the FRH was subsequently invoked for climate changes irrespective of the time period (2). The FRH was also applied to South America's Atlantic Forest (3), one of the topfive biodiversity hotspots on Earth (4). The FRH gained broad acceptance during the 1980s when empirical paleoecological data from neotropical rainforests were still lacking. Nevertheless, heavy criticism came upon the FRH because some paleobotanical data showed that forests had persisted throughout glacial cycles (5). As paleoclimatic models of species and habitats became widely used, recent studies revitalized the FRH, not by considering refuges as the main drivers of allopatric speciation, but instead by suggesting that high contemporary diversity and endemism are associated with historically stable Atlantic Forest areas (6).This hypothesis is ba...

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Brazil is the fifth largest country in the world and the first of the megadiversity countries, accounting for roughly 14% of the world's biota. It has the largest mammal diversity (more than 530 described species) with many yet to be discovered and cataloged. Very few sites have been adequately surveyed, and local lists are usually incomplete, which makes for knowledge gaps that hamper conservation and management initiatives and regional analyses. According to the Brazilian Institute for the Environment (IBAMA), 66 species are threatened, and the World Conservation Union lists 74. Primates, mostly Atlantic Forest endemics, are the most endangered group (40% of the threatened taxa). Carnivores and rodents are also notable members of the lists. Twenty-nine percent of listed species are marine, 18% occur in the Atlantic Forest, 13% in the Pampas, 12% in the Cerrado, 11% in the Pantanal, 7% in the Amazon, and 6% in the Caatinga. Human-induced habitat loss and fragmentation are major threats to land mammals in Brazil, and large-and medium-sized mammals are hunted. The major threat to small mammals is the scarcity of basic scientific knowledge-taxonomy, systematics, distribution, and natural history. Aquatic mammals are threatened by commercial hunting, accidental netting, long-line fisheries, chemical pollution, habitat degradation, tourism, and boat traffic. Mammal conservation has benefited from a number of recent initiatives by government and nongovernmental organizations, including legislation, nationwide initiatives to define priority areas for conservation, management plans for some threatened species, sustainable landscape planning, and new protected areas. Given the rate of habitat loss, a nationwide program of short-and long-term field surveys and increased support for natural history collections is of particularly urgency. Progress has been made toward conserving Brazilian mammals in recent years, but threats are growing fast, and conservation science must keep growing to provide the wherewithal to minimize and remove these threats. Conservación de Mamíferos en BrasilResumen: Brasil es el quinto país más grande del mundo y el primero de los países megadiversos, con casi 14% de la biota mundial. Tiene la mayor diversidad de mamíferos (más de 530 especies descritas) con aun mucho por descubrir y catalogar. Pocos sitios han sido muestreados adecuadamente, y las listas locales generalmente están incompletas, lo que constituye huecos de conocimiento que obstaculizan iniciativas de conservación y manejo y análisis regionales. De acuerdo con el Instituto Brasileño del Medio Ambiente (IBAMA), sesenta y seis especies están amenazadas, y la Unión de Conservación Mundial enlista 74. Los Primates, principalmente endémicos del bosque Atlántico, son el grupo en mayor peligro. Veintinueve porciento de las especies enlistadas son marinas, 18% ocurren en el bosque Atlántico, 13% en las Pampas, 12% en el Cerrado, 11% en el Pantanal, 7% en el Amazonas y 6% en la Caatinga. La pérdida y fragmentación de hábitat inducida por huma...

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for providing critical comments that improved the quality of this monograph. I would also like to thank the Brazilian Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brasília, for granting me a predoctoral fellowship and partial support for fieldwork. Collecting permits were provided by the Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis (IBAMA), Brasília, and the