Mammalian hibernators experience dramatic reductions in body temperature, metabolic rate, respiratory rate, and heart rate during hibernation. These changes are precisely controlled and reversible with only internally driven mechanisms, suggesting specific biochemical regulation. We present a model that integrates our observations of differential liver gene expression during preparation for, and maintenance of, the hibernating state, with the known phylogenetic interspersion of hibernating species in several major mammalian lineages. This model predicts a major role for the differential expression of existing mammalian genes in the biochemical regulation of hibernation.Hibernation is an adaptive strategy that is used by species in several mammalian orders to conserve energy in cold or inhospitable environments. During hibernation, these mammals dramatically lower their metabolic, heart, and respiratory rates as well as their body temperature in a precisely controlled manner. This strategy helps some, particularly small, mammals to survive cold winter conditions in temperate climates when food and water are scarce yet the demand for metabolic heat generation is high. Hibernating species are frequently closely related to nonhibernating species and are found in five orders of eutherian mammals as well as in a few species of marsupials and monotremes (ref. 1 and Fig. 1). The adaptive significance of hibernation, coupled with the interspersed phylogenetic distribution of hibernating species among mammals, makes hibernation an ideal model system to test the hypothesis that the molecular basis of important adaptive events during evolution involves mechanisms that lead to the differential regulation of existing genes and not the invention of new genes (reviewed in ref.3).The evolutionary origin of hibernation is unknown; either of two hypotheses can explain the interspersed nature of the distribution of extant hibernating species throughout Mammalia. One postulates that the common ancestor of all mammals was a hibernator, but the ability to hibernate was lost independently along multiple lineages. The alternative proposes that the common ancestor of all mammals was not a hibernator, and the ability to hibernate has been gained independently along multiple lineages (Fig. 1). With either scenario, we predict that a small number of regulatory changes determine the phenotype of hibernation, rather than the de novo creation or loss of numerous hibernation-specific biochemical functions, encoded by a collection of hibernation-specific genes. Thus, hibernation must be the result of a reprogramming of existing mammalian biochemical capabilities through the differential expression of existing genes.There is little evidence in the literature for differential gene expression during hibernation, although there are a few reports that demonstrate increases or decreases (4) in the amount of specific proteins relative to the active state. Mitochondrial uncoupling protein (thermogenin) is an example of a protein that increases i...