Through long-term laboratory selection (over 200 generations), we have generated Drosophila melanogaster populations that tolerate severe, normally lethal, levels of hypoxia. Because of initial experiments suspecting genetic mechanisms underlying this adaptation, we compared the genomes of the hypoxia-selected flies with those of controls using deep resequencing. By applying unique computing and analytical methods we identified a number of DNA regions under selection, mostly on the X chromosome. Several of the hypoxia-selected regions contained genes encoding or regulating the Notch pathway. In addition, previous expression profiling revealed an activation of the Notch pathway in the hypoxia-selected flies. We confirmed the contribution of Notch activation to hypoxia tolerance using a specific γ-secretase inhibitor, N-[N-(3,5-Difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT), which significantly reduced adult survival and life span in the hypoxiaselected flies. We also demonstrated that flies with loss-of-function Notch mutations or RNAi-mediated Notch knockdown had a significant reduction in hypoxia tolerance, but those with a gain-of-function had a dramatic opposite effect. Using the UAS-Gal4 system, we also showed that specific overexpression of the Notch intracellular domain in glial cells was critical for conferring hypoxia tolerance. Unique analytical tools and genetic and bioinformatic strategies allowed us to discover that Notch activation plays a major role in this hypoxia tolerance in Drosophila melanogaster.evolution | next-generation sequencing O xygen homoeostasis is essential for development, growth, and integrity of cells, tissues, and organisms. Limited oxygen supply to cells and tissues (hypoxia) has a wide range of physiologic and potentially pathologic consequences, ranging from ischemic/hypoxic heart disease, stroke, and pulmonary hypertension to a number of obstetrical/perinatal complications, to high-altitude illnesses, to organ transplantation, and finally to intratumor hypoxia and cancer progression. Despite the clinical importance and societal disease impact of such a wide range of disorders, the molecular underpinnings of susceptibility or tolerance of cells or tissues to lack of O 2 are not well understood. Many studies have investigated the mechanisms that lead to injury when cells are deprived of O 2 , but to potentially treat or prevent the consequences of hypoxia necessitates also the understanding of the inherent tissue mechanisms that are critical for tolerance and survival. To do so, we use a long-term laboratory selection strategy that unmasks mechanisms that play an important role in hypoxia tolerance in a genetic model, Drosophila melanogaster (1, 2). In this attempt, starting with 27 isofemale D. melanogaster strains, and applying decreasing levels of O 2 over >200 generations, we generated Drosophila populations that tolerate severe levels of hypoxia, which are lethal to the original parental lines. These hypoxia-adapted flies (AF) pass the tolerance trait ...