The Neanderthal genome sequence used as a reference was primarily from the high-quality genome sequenced from the Vindija Cave Neanderthal — also a product of the Max Planck Institute for Evolutionary Anthropology, where Prüfer works.

The quality of this reference genome contributed directly to the confidence of the Zlatý kůň analysis.

The Vindobona Moment: Modern Humans Meet Neanderthals

The fact that Zlatý kůň’s Neanderthal admixture was relatively recent in her lineage — perhaps six to nine generations before her birth, as estimated from segment lengths — places the actual interbreeding event at roughly 50,000 to 52,000 years ago, shortly after the initial modern human dispersal from Africa through the Levant and into western and central Asia.

This timing is consistent with what is now understood, from multiple ancient genomes and from modern population genetics, about when and where the main pulse of Neanderthal admixture into the ancestors of all non-African modern humans occurred.