Leveraging ancient DNA to uncover signals of natural selection in Europe lost due to admixture or drift.

Large ancient DNA (aDNA) studies offer the chance to examine genomic changes over time, providing direct insights into human evolution. While recent studies have used time-stratified aDNA for selection scans, most focus on single-locus methods. We conducted a multi-locus genotype scan on 708 samples spanning 7000 years of European history. We show that the G12 statistic, originally designed for unphased diploid data, can effectively detect selection in aDNA processed to create 'pseudo-haplotypes'. In simulations and at known positive control loci (e.g., lactase persistence), G12 outperforms the allele frequency-based selection statistic, SweepFinder2, previously used on aDNA. Applying our approach, we identified 14 candidate regions of selection across four time periods, with half the signals detectable only in the earliest period. Our findings suggest that selective events in European prehistory, including from the onset of animal domestication, have been obscured by neutral processes like genetic drift and demographic shifts such as admixture. Large-scale ancient DNA (aDNA) studies offer the chance to examine genomic changes over time, providing direct insights into human evolution. Here the authors use aDNA from 708 European samples to identify 14 regions of natural selection over 7,000 years. They find that many early signals of selection are lost in later periods due to neutral processes like genetic drift and admixture. [ABSTRACT FROM AUTHOR]