Interbreeding between archaic and modern humans

Interbreeding between archaic humans (such as Neanderthals and Denisovans) and anatomically modern humans (contemporaneous Homo sapiens) took place during the Middle Paleolithic and early Upper Paleolithic. It has been revealed via genomic sequencing that all modern human populations outside of Africa today carry approximately 1–4% Neanderthal DNA, which is a result of genetic admixture that occurred after modern humans migrated out of Africa. Denisovan admixture is most prominent in Oceania, where modern human populations derive approximately 4–6% of their genome from this archaic group, while those in Eurasia and the Americas have been found to be carrying lower levels.

Within Africa, successive Eurasian back-migrations that continued into the Neolithic introduced Neanderthal DNA to the modern human populations of North Africa, and while it was initially thought to be completely absent in the modern human populations of sub-Saharan Africa, low levels of Neanderthal DNA from these back-migrations have since been identified among them as well.

The introgression of archaic human DNA has influenced the biology of modern humans through both positive and negative selection. Adaptive introgression provided genetic variants that proved beneficial for survival in new environments, including genes related to the immune system (such as HLA alleles), skin and hair morphology, and high-altitude adaptation. Conversely, large regions of the modern human genome, particularly on the X chromosome and in genes expressed in the testes, are devoid of archaic ancestry. This suggests that purifying selection acted to remove deleterious alleles that likely caused reduced fertility in male hybrids.

These findings have resolved long-standing debates in paleoanthropology, shifting the scientific consensus from a strict "Out of Africa" replacement model to one of assimilation. For decades, the prevailing view was that modern humans replaced archaic populations without significant interbreeding, despite some morphological evidence from fossils like the Oase 1 mandible suggesting otherwise. The accumulation of genomic data since 2010 has confirmed that while the majority of modern human ancestry is African in origin, the gene pools of contemporary populations were significantly shaped by ancient hybridization events with archaic hominins across Eurasia and Africa.