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

BackgroundNearly all Eurasians have [~]2% Neanderthal ancestry due to several events of inbreeding between anatomically modern humans and archaic hominins. Previous studies characterizing the legacy of Neanderthal ancestry in modern Eurasians have identified examples of both adaptive and deleterious effects of admixture. However, we lack a comprehensive understanding of the genome-wide influence of Neanderthal introgression on modern human diseases and traits. ResultsWe integrate recent maps of Neanderthal ancestry with well-powered association studies for more than 400 diverse traits to estimate heritability enrichment patterns in regions of the human genome tolerant of Neanderthal ancestry and in introgressed Neanderthal variants themselves. First, we find that variants in regions tolerant of Neanderthal ancestry are depleted of heritability for all traits considered, except skin and hair-related traits. Second, the introgressed variants remaining in modern Europeans are depleted of heritability for most traits; however, we discover that they are enriched for heritability of several traits with potential relevance to human adaptation to non-African environments, including hair and skin traits, autoimmunity, chronotype, bone density, lung capacity, and menopause age. To better understand the phenotypic consequences of these enrichments, we adapt recent methods to test for consistent directional effects of introgressed alleles, and we find directionality for several traits. Finally, we use a direction-of-effect-aware approach to highlight novel candidate introgressed variants that influence risk for disease. ConclusionOur results demonstrate that genomic regions retaining Neanderthal ancestry are not only less functional at the molecular-level, but are also depleted for variation influencing a diverse array of complex traits in modern humans. In spite of this depletion, we identify traits where introgression has an outsized effect. Integrating our results, we propose a framework for using quantification of trait heritability and direction of effect in introgressed regions to understand how Neanderthals were different from modern humans, how selection acted on different traits, and how introgression may have facilitated adaptation to non-African environments.