Quantifying the contribution of Neanderthal introgression to the heritability of complex traits

Abstract Eurasians have ~2% Neanderthal ancestry, but we lack a comprehensive understanding of the genome-wide influence introgression on modern human diseases and traits. Here, quantify contribution introgressed alleles to heritability more than 400 diverse We show that genomic regions in which detectable ancestry remains are depleted for all traits considered, except those related skin hair. Introgressed variants themselves also contributions most However, shared across multiple populations enriched consistent directions effect several with potential relevance adaptation non-African environments, including hair traits, autoimmunity, chronotype, bone density, lung capacity, menopause age. Integrating our results, propose model selection against functional variation was dominant trend (especially cognitive traits); however, few provided beneficial via uni-directional (e.g., lightening color) or bi-directional modulating immune response) effects.