An early East Asian lineage with unexpectedly low Denisovan ancestry

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Abstract: Denisovan ancestry in present-day humans is heterogeneously distributed and comes from genetically distinct Denisovan groups. Understanding the origin of this heterogeneity could provide insights into the early population history of modern humans in Eurasia. However, population movements and admixture after the initial dispersals of modern humans have obscured the origin of this heterogeneity. To address this, we investigated how Denisovan ancestry in early modern humans relates to that in present-day humans. We found that varying levels of Denisovan ancestry in Eurasians were shaped by admixture between diverse early modern human lineages. In particular, ancient Japanese individuals from the Jomon period have the least Denisovan ancestry among individuals from Eastern Eurasia, providing evidence for an ancient East Asian lineage with little to no Denisovan ancestry. By contrast, the earliest mainland East Asians harbor the most Denisovan ancestry in Eastern Eurasia, including ancestry from multiple divergent Denisovan groups, already before the last glacial maximum. Together with evidence of Denisovan ancestry sharing among ancient and present-day genomes, these patterns show how Denisovan ancestry in Eurasia spread through gene flow from early East Asians. Our study provides the first systematic investigation of Denisovan admixture across time and extends our understanding of human population history in Eurasia.