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.

Neanderthals

Genetics

Proportion of admixture

On 7 May 2010, following the genome sequencing of three Vindija Neanderthals, a draft sequence of the Neanderthal genome was published and revealed that Neanderthals shared more alleles with Eurasian populations than with sub-Saharan African populations According to the authors the observed excess of genetic similarity is best explained by recent gene flow from Neanderthals to modern humans after the migration out of Africa. They estimated the proportion of Neanderthal-derived ancestry to be 1–4% of the Eurasian genome. Durand et al. (2011) estimated 1–6% Neanderthal ancestry in non-Africans. Prüfer et al. (2013) estimated the proportion to be 1.5–2.1% for non-Africans. Lohse and Frantz (2014) infer a higher rate of 3.4–7.3% in Eurasia. In 2017, Prüfer et al. revised their estimate to 1.8–2.6% for non-Africans outside Oceania. According to a later study by Chen et al. (2020), Africans (specifically, the 1000 Genomes African populations) also have Neanderthal admixture, with this Neanderthal admixture in African individuals accounting for 17 megabases, which is 0.3% of their genome. According to the authors, Africans gained their Neanderthal admixture predominantly from a back-migration by peoples (modern humans carrying Neanderthal admixture) that had diverged from ancestral Europeans (postdating the split between East Asians and Europeans). This back-migration is proposed to have happened about 20,000 years ago. However, some scientists, such as geneticist David Reich, have doubts about how extensive the flow of DNA back to Africa would have been, finding the signal of Neanderthal admixture "really weak".

Introgressed genome It has been found that 50% of the Neanderthal genome is present among people in India, and 41% has been found in Icelanders. Previously it was found that about 20% of the Neanderthal genome was found in modern Eurasians, but the figure was also estimated at a third. A 2023 study found an introgression from modern humans to Neanderthals around 250,000 years ago, and estimated that roughly 6% of the Altai Neanderthal genome was inherited from modern humans.

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