Abstract
The contemporary European genetic makeup formed in the last 8,000 years when local Western Hunter-Gatherers (WHGs) mixed with incoming Anatolian Neolithic farmers and Pontic Steppe pastoralists.1–3 This encounter combined genetic variants with distinct evolutionary histories and, together with new environmental challenges faced by the post-Neolithic Europeans, unlocked novel adaptations.4 Previous studies inferred phenotypes in these source populations, using either a few single loci5–7 or polygenic scores based on genome-wide association studies,8–10 and investigated the strength and timing of natural selection on lactase persistence or height, among others.6,11,12 However, how ancient populations contributed to present-day phenotypic variation is poorly understood. Here, we investigate how the unique tiling of genetic variants inherited from different ancestral components drives the complex traits landscape of contemporary Europeans and quantify selection patterns associated with these components. Using matching individual-level genotype and phenotype data for 27 traits in the Estonian biobank13 and genotype data directly from the ancient source populations, we quantify the contributions from each ancestry to present-day phenotypic variation in each complex trait. We find substantial differences in ancestry for eye and hair color, body mass index, waist/hip circumferences, and their ratio, height, cholesterol levels, caffeine intake, heart rate, and age at menarche. Furthermore, we find evidence for recent positive selection linked to four of these traits and, in addition, sleep patterns and blood pressure. Our results show that these ancient components were differentiated enough to contribute ancestry-specific signatures to the complex trait variability displayed by contemporary Europeans.
•Ancient groups differentially contributed to complex traits in contemporary Europeans•In contemporary Estonians 11 out of 27 traits show association with some ancestry•Hunter-Gatherer and Yamnaya ancestries divergently influence cholesterol levels•Post-admixture selection is not necessary to have trait-ancestry associations
Marnetto e al. quantitatively analyze how ancient populations differentially contributed to the complex trait variability in contemporary Europeans. Using the Estonian biobank as case study, they find that 11 out of 27 traits show association with some ancestral European group, including anthropometric, pigmentation, and metabolic traits.