Neanderthal ancestry remains across modern Eurasian genomes and introgressed sequences influence diverse phenotypes. Here, we demonstrate that introgressed sequences reintroduced thousands of ancestral alleles that were lost in Eurasian populations before introgression. Our simulations and variant effect predictions argue that these reintroduced alleles (RAs) are more likely to be tolerated by modern humans than are introgressed Neanderthal-derived alleles (NDAs) due to their distinct evolutionary histories. Consistent with this, we show enrichment for RAs and depletion for NDAs on introgressed haplotypes with expression quantitative trait loci (eQTL) and phenotype associations. Analysis of available cross-population eQTLs and massively parallel reporter assay data show that RAs commonly influence gene expression independent of linked NDAs. We further validate these independent effects for one RA in vitro. Finally, we demonstrate that NDAs are depleted for regulatory activity compared to RAs, while RAs have activity levels similar to non-introgressed variants. In summary, our study reveals that Neanderthal introgression reintroduced thousands of lost ancestral variants with gene regulatory activity and that these RAs were more tolerated than NDAs. Thus, RAs and their distinct evolutionary histories must be considered when evaluating the effects of introgression.

现代欧亚基因组中仍然保留着尼安德特人的血统，渗入序列影响着不同的表型。在这里，我们证明基因渗入序列重新引入了基因渗入之前在欧亚人群中丢失的数千个祖先等位基因。我们的模拟和变异效应预测表明，由于其独特的进化历史，这些重新引入的等位基因（RA）比渐渗的尼安德特人衍生等位基因（NDAs）更容易被现代人类容忍。与此一致，我们显示在具有表达数量性状基因座（eQTL）和表型关联的渐渗单倍型上RA富集和NDAs耗尽。对可用的跨群体 eQTL 和大规模平行报告分析数据的分析表明，RA 通常独立于连锁的 NDA 影响基因表达。我们进一步在体外验证了一种 RA 的这些独立效应。最后，我们证明，与 RA 相比，NDA 的调节活性较低，而 RA 的活性水平与非基因渗入变体相似。总之，我们的研究表明，尼安德特人基因渗入重新引入了数千种丢失的具有基因调控活性的祖先变异，并且这些 RA 比 NDA 更具耐受性。因此，在评估基因渗入的影响时，必须考虑 RA 及其独特的进化历史。