  Living at high-altitude is one of the most difficult challenges that humans
had to cope with during their evolution. Whereas several genomic studies have
revealed some of the genetic bases of adaptations in Tibetan, Andean and
Ethiopian populations, relatively little evidence of convergent evolution to
altitude in different continents has accumulated. This lack of evidence can be
due to truly different evolutionary responses, but it can be also due to the
low power of former studies that have mainly focused on populations from a
single geographical region or performed separate analyses on multiple pairs of
populations to avoid problems linked to shared histories between some
populations. We introduce here a hierarchical Bayesian method to detect local
adaptation that can deal with complex demographic histories. Our method can
identify selection occurring at different scales, as well as convergent
adaptation in different regions. We apply our approach to the analysis of a
large SNP dataset from low- and high-altitude human populations from America
and Asia. The simultaneous analysis of these two geographic areas allows us to
identify several candidate genome regions for altitudinal selection, and we
show that convergent evolution among continents has been quite common. In
addition to identifying several genes and biological processes involved in high
altitude adaptation, we identify two specific biological pathways that could
have evolved in both continents to counter toxic effects induced by hypoxia.
