Modern humans expanded into Eurasia more than 40,000 years ago following their dispersal out of Africa. These Eurasians carried similar to 2-3% Neanderthal ancestry in their genomes, originating from admixture with Neanderthals that took place sometime between 50,000 and 60,000 years ago, probably in the Middle East.
In Europe, the modern human expansion preceded the disappearance of Neanderthals from the fossil record by 3,000-5,000 years. The genetic makeup of the first Europeans who colonized the continent more than 40,000 years ago remains poorly understood since few specimens have been studied.
Here, we analyse a genome generated from the skull of a female individual from Zlaty kun, Czechia. We found that she belonged to a population that appears to have contributed genetically neither to later Europeans nor to Asians.
Her genome carries similar to 3% Neanderthal ancestry, similar to those of other Upper Palaeolithic hunter-gatherers. However, the lengths of the Neanderthal segments are longer than those observed in the currently oldest modern human genome of the similar to 45,000-year-old Ust'-Ishim individual from Siberia, suggesting that this individual from Zlaty Uri is one of the earliest Eurasian inhabitants following the expansion out of Africa.