In response to hypoxic stress, many animals compensate for a reduced cellular O 2 supply by suppressing total metabolism, thereby reducing O 2 demand. For small endotherms that are native to high-altitude environments, this is not always a viable strategy, as the capacity for sustained aerobic thermogenesis is critical for survival during periods of prolonged cold stress. For example, survivorship studies of deer mice (Peromyscus maniculatus) have demonstrated that thermogenic capacity is under strong directional selection at high altitude. Here, we integrate measures of whole-organism thermogenic performance with measures of metabolic enzyme activities and genomic transcriptional profiles to examine the mechanistic underpinnings of adaptive variation in this complex trait in deer mice that are native to different elevations. We demonstrate that highland deer mice have an enhanced thermogenic capacity under hypoxia compared with lowland conspecifics and a closely related lowland species, Peromyscus leucopus. Our findings suggest that the enhanced thermogenic performance of highland deer mice is largely attributable to an increased capacity to oxidize lipids as a primary metabolic fuel source. This enhanced capacity for aerobic thermogenesis is associated with elevated activities of muscle metabolic enzymes that influence flux through fatty-acid oxidation and oxidative phosphorylation pathways in high-altitude deer mice and by concomitant changes in the expression of genes in these same pathways. Contrary to predictions derived from studies of humans at high altitude, our results suggest that selection to sustain prolonged thermogenesis under hypoxia promotes a shift in metabolic fuel use in favor of lipids over carbohydrates.functional genomics | RNA-seq | thermoregulation | transcriptomics D uring cold stress, homeothermic endotherms maintain a constant body temperature by increasing metabolic heat production. In small endotherms like mice that have high thermoregulatory demands, thermogenic capacity influences survival in cold environments and therefore has a clear connection to Darwinian fitness (1, 2). Indeed, thermogenic capacity in freeranging deer mice (Peromyscus maniculatus) is subject to strong directional selection at high altitude (3).Sustaining maximal thermogenic capacities during prolonged periods of cold stress requires a high rate of O 2 flux through oxidative pathways, and this requirement presents a unique challenge for endothermic animals that live under conditions of chronic O 2 deprivation at high altitude. The reduced partial pressure of O 2 (PO 2 ) at high altitude imposes well-documented constraints on aerobic metabolism (4-8), thereby exacerbating the increased thermoregulatory demands faced by endothermic animals that are native to cold, alpine environments.In rodents, aerobic thermogenesis is accomplished through both shivering and nonshivering mechanisms, and in deer mice, shivering accounts for roughly 35-50% of total thermogenic capacity (9). As with other forms of strenuous exerci...