Temporally Dynamic Waves of Selection on Archaic Variation in Peruvians

Selection on archaic introgressed variation in Peruvians was temporally dynamic, with ARG-inferred onset windows for 21 loci and no robust evidence for a fixed number of discrete waves.

• Why it matters: Adaptive introgression in Indigenous Americans is hard to resolve because demographic history and recent admixture can mimic false positives in genome-wide scans.
• What they did: The study re-evaluated previously reported candidate loci in Peruvians, refining 150+ signals to 25 high-confidence loci with concordant Neanderthal- or Denisovan-like ancestry and positive selection, then used ARG methods to infer selection onset windows for 21 loci.
• The result: Pre-Columbian ancient DNA evidence supports inheritance through ancestral Native American populations rather than post-Columbian introduction, and functional analyses indicate polygenic selection in lipid metabolic and immune-related pathways, including regulatory effects across archaic haplotypes and a missense variant at CXCR4.

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