Abstract
The influence of positive selection sweeps in human evolution is increasingly debated, although our ability to detect them is hampered by inherent uncertainties in the timing of past events. Ancient genomes provide snapshots of allele frequencies in the past and can help address this question. We combine modern and ancient genomic data in a simple statistic (DAnc) to time allele frequency changes, and investigate the role of drift and adaptation in population differentiation. Only 30% of the most strongly differentiated alleles between Africans and Eurasians changed in frequency during the colonization of Eurasia, but in Europe these alleles are enriched in genic and putatively functional alleles to an extent only compatible with local adaptation. Adaptive alleles—especially those associated with pigmentation—are mostly of hunter-gatherer origin, although lactose persistence arose in a haplotype present in farmers. These results provide evidence for a role of local adaptation in human population differentiation.
Highlights
The influence of positive selection sweeps in human evolution is increasingly debated, our ability to detect them is hampered by inherent uncertainties in the timing of past events
A number of recent studies have used DNA of ancient Europeans to explore the evidence that positive selection raised the frequency of pre-ascertained single nucleotide polymorphisms (SNPs)[15,16,17,18,19], showing that ancient DNA can enhance the identification of individual selective sweeps
Ancient genomes contain valuable information on the genetic make-up of ancestral populations, and combined with modern genomes hold the potential to improve the resolution of inferences on the timing of past allele frequency changes
Summary
The influence of positive selection sweeps in human evolution is increasingly debated, our ability to detect them is hampered by inherent uncertainties in the timing of past events. An important problem of existing approaches is that they are limited by the imperfect and indirect information that present-day genomes provide about the time of allele frequency changes In humans it is, for example, difficult to precisely distinguish changes that happened during strong bottlenecks (for example, the out-of-Africa migration that substantially increased drift14) or in other periods (for example, during the subsequent colonization of territories outside of Africa, when populations likely adapted to novel environments). We integrate modern and ancient genetic information in a new statistic that helps disentangle the effects of drift and adaptation on rapid, geographically localized allele frequency changes Incorporating this information provides clear evidence for positive selection raising the frequency of advantageous genic SNPs in Europe and contributing to strong population differentiation. We show that these alleles were mostly contributed by ancient hunter gatherers, who resided in Europe thousands of years before the arrival of southern farmer groups
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