Data from: Application of a novel haplotype-based scan for local adaptation to study high-altitude adaptation in rhesus macaques

When natural populations split and migrate to different environments, they
may experience different selection pressures that can lead to local
adaptation. To capture the genomic patterns of a local selective sweep, we
develop XP-nSL, a genomic scan for local adaptation that compares
haplotype patterns between two populations. We show that XP-nSL has power
to detect ongoing and recently completed hard and soft sweeps, and we then
apply this statistic to search for evidence of adaptation to high altitude
in rhesus macaques. We analyze the whole genomes of 23 wild rhesus
macaques captured at high altitude (mean altitude > 4000m above sea
level) to 22 wild rhesus macaques captured at low altitude (mean altitude
< 500m above sea level) and find evidence of local adaptation in
the high-altitude population at or near 303 known genes and several
unannotated regions. We find the strongest signal for adaptation at EGLN1,
a classic target for convergent evolution in several species living in low
oxygen environments. Furthermore, many of the 303 genes are involved in
processes related to hypoxia, regulation of ROS, DNA damage repair,
synaptic signaling, and metabolism. These results suggest that, beyond
adapting via a beneficial mutation in one single gene, adaptation to high
altitude in rhesus macaques is polygenic and spread across numerous
important biological systems.