-Andean highaltitude (HA) natives have a low (blunted) hypoxic ventilatory response (HVR), lower effective alveolar ventilation, and lower ventilation (VE) at rest and during exercise compared with acclimatized newcomers to HA. Despite blunted chemosensitivity and hypoventilation, Andeans maintain comparable arterial O 2 saturation (SaO 2 ). This study was designed to evaluate the influence of ancestry on these trait differences. At sea level, we measured the HVR in both acute (HVR-A) and sustained (HVR-S) hypoxia in a sample of 32 male Peruvians of mainly Quechua and Spanish origins who were born and raised at sea level. We also measured resting and exercise VE after 10 -12 h of exposure to altitude at 4,338 m. Native American ancestry proportion (NAAP) was assessed for each individual using a panel of 80 ancestry-informative molecular markers (AIMs). NAAP was inversely related to HVR-S after 10 min of isocapnic hypoxia (r ϭ Ϫ0.36, P ϭ 0.04) but was not associated with HVR-A. In addition, NAAP was inversely related to exercise VE (r ϭ Ϫ0.50, P ϭ 0.005) and ventilatory equivalent (VE/V O2, r ϭ Ϫ0.51, P ϭ 0.004) measured at 4,338 m. Thus Quechua ancestry may partly explain the wellknown blunted HVR (10,35,36,57,62) at least to sustained hypoxia, and the relative exercise hypoventilation at altitude of Andeans compared with European controls. Lower HVR-S and exercise VE could reflect improved gas exchange and/or attenuated chemoreflex sensitivity with increasing NAAP. On the basis of these ancestry associations and on the fact that developmental effects were completely controlled by study design, we suggest both a genetic basis and an evolutionary origin for these traits in Quechua. genetic markers; admixture; arterial saturation; Andes THE HYPOXIC VENTILATORY RESPONSE (HVR) is the increase in ventilation (VE) that occurs when arterial blood oxygen partial pressure PO 2 decreases (60). Typically, on acute exposure to hypoxia, VE increases to a peak in the first few minutes and thereafter declines somewhat to a level higher than control depending on the level of hypoxia (13,49). This attenuation of VE has been termed the hypoxic ventilatory decline (HVD), and it is usually assessed by protocols that give a sustained hypoxic exposure greater than ϳ10 min. The sustained vs. acute response has not been systematically evaluated in Andean highland natives, but groups from this region appear to have a lower or "blunted" acute HVR and a lower effective alveolar ventilation compared with high altitude (HA)-acclimatized control groups from the lowlands (10,35,36,43,57,61,62). Andeans also have lower VE during exercise at HA compared with acclimatized lowland controls (7,32,55,66). These traits may be unique to Andeans, as many studies show normal HVR and higher VE in natives of the Himalayan plateau (2,21,25,29,75). However, little is known about the underlying genetic and/or environmental basis for ventilatory trait differences between populations. One possibility is that there are genes at which allele frequencies differ ...