Interbreeding between archaic and modern humans
Interbreeding between archaic and modern humans occurred during the Middle and early Upper Paleolithic, involving anatomically modern humans and archaic groups such as Neanderthals and Denisovans. Genomic sequencing has revealed that non-African populations carry approximately 1–4% Neanderthal DNA, a result of admixture events that took place after modern humans migrated out of Africa. While initially thought to be absent in sub-Saharan Africans, low levels of Neanderthal ancestry have been identified in these populations, attributed to back-migration from Eurasia. Denisovan admixture is most prominent in Oceanian populations, who derive 4–6% of their genome from this archaic group, with lower levels found in Southeast Asia and the Americas.
The introgression of archaic DNA has influenced the biology of modern humans through both positive and negative selection. Adaptive introgression provided genetic variants beneficial for survival in new environments, including genes related to the immune system, skin and hair morphology, and high-altitude adaptation in Tibetans. 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. estimated 1–6% Neanderthal ancestry in non-Africans. Prüfer et al. estimated the proportion to be 1.5–2.1% for non-Africans. Lohse and Frantz 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., Africans 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 that had diverged from ancestral 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.
Subpopulation admixture rate
A higher Neanderthal admixture was found in East Asians than in Europeans, which is estimated to be about 20% more introgression into East Asians. This could possibly be explained by the occurrence of further admixture events in the early ancestors of East Asians after the separation of Europeans and East Asians, dilution of Neanderthal ancestry in Europeans by populations with low Neanderthal ancestry from later migrations, or reduced efficacy of purifying selection in the ancestors of East Asians, due to smaller effective population sizes as they migrated to East Asia. Studies simulating admixture models indicate that a reduced efficacy of purifying selection against Neanderthal alleles in East Asians could not account for the greater proportion of Neanderthal ancestry of East Asians, thus favoring more-complex models involving additional pulses of admixture between Neanderthals and the ancestors of East Asians. Such models show a pulse to ancestral Eurasians, followed by separation and an additional pulse to ancestral East Asians. It is observed that there is a small but significant variation of Neanderthal admixture rates within European populations, but no significant variation within East Asian populations. Prüfer et al. remarked that East Asians carry more Neanderthal DNA than Western Eurasians.It was later determined by Chen et al. that East Asians have 8% more Neanderthal ancestry, revised from the previous reports of 20% more Neanderthal ancestry, compared to Europeans. This stems from the fact that Neanderthal ancestry shared with Africans had been masked, because Africans were thought to have no Neanderthal admixture and were therefore used as reference samples. Thus, any overlap in Neanderthal admixture with Africans resulted in an underestimation of Neanderthal admixture in non-Africans and especially in Europeans. The authors give a single pulse of Neanderthal admixture after the out-of-Africa dispersal as the most parsimonious explanation for the enrichment in East Asians, but they add that variation in Neanderthal ancestry may also be attributed to dilution to account for the now-more-modest differences found. As a proportion of the total amount of Neanderthal sequence for each population, 7.2% of the sequence in Europeans is shared exclusively with Africans, while 2% of the sequence in East Asians is shared exclusively with Africans.
Genomic analysis suggests that there is a global division in Neanderthal introgression between sub-Saharan African populations and other modern human groups rather than between African and non-African populations. North African groups share a similar excess of derived alleles with Neanderthals as do non-African populations, whereas sub-Saharan African groups are the only modern human populations that generally did not experience Neanderthal admixture. The Neanderthal genetic signal among North African populations was found to vary depending on the relative quantity of North African, European, Near Eastern and sub-Saharan ancestry. Using F4 ancestry ratio statistical analysis, the Neanderthal inferred admixture was observed to be highest among the North African populations with highest North African ancestry such as Tunisian Berbers, where it was at the same level or even higher than that of Eurasian populations ; high among North African populations carrying greater European or Near Eastern admixture, such as groups in North Morocco and Egypt ; and lowest among North African populations with greater Sub-Saharan admixture, such as in South Morocco. Quinto et al. therefore postulate that the presence of this Neanderthal genetic signal in Africa is not due to recent gene flow from Near Eastern or European populations since it is higher among populations bearing indigenous pre-Neolithic North African ancestry. Low but significant rates of Neanderthal admixture has also been observed for the Maasai of East Africa. After identifying African and non-African ancestry among the Maasai, it can be concluded that recent non-African modern human gene flow was the source of the contribution since around an estimated 30% of the Maasai genome can be traced to non-African introgression from about 100 generations ago.
Reich states that all present-day non Sub-Saharan Africans have around 2% of Neanderthal ancestry.
Distance to lineages
Presenting a high-quality genome sequence of a female Altai Neanderthal, it has been found that the Neanderthal component in non-African modern humans is more related to the Mezmaiskaya Neanderthal than to the Altai Neanderthal or the Vindija Neanderthals. By high-coverage sequencing the genome of a 50,000-year-old female Vindija Neanderthal fragment, it was later found that the Vindija and Mezmaiskaya Neanderthals did not seem to differ in the extent of their allele-sharing with modern humans. In this case, it was also found that the Neanderthal component in non-African modern humans is more closely related to the Vindija and Mezmaiskaya Neanderthals than to the Altai Neanderthal. These results suggest that a majority of the admixture into modern humans came from Neanderthal populations that had diverged from the Vindija and Mezmaiskaya Neanderthal lineages before the latter two diverged from each other.Analysis of chromosome 21 of the Altai, El Sidrón, and Vindija Neanderthals indicates that of these three lineages, only the El Sidrón and Vindija Neanderthals display significant rates of gene flow into modern humans, suggesting that the El Sidrón and Vindija Neanderthals are more closely related than the Altai Neanderthal to the Neanderthals that interbred with modern humans about 47,000–65,000 years ago. Conversely, significant rates of modern human gene flow into Neanderthals occurred—of the three examined lineages—for only the Altai Neanderthal, suggesting that modern human gene flow into Neanderthals mainly took place after the separation of the Altai Neanderthals from the El Sidrón and Vindija Neanderthals that occurred roughly 110,000 years ago. The findings show that the source of modern human gene flow into Neanderthals originated from a population of early modern humans from about 100,000 years ago, predating the out-of-Africa migration of the modern human ancestors of present-day non-Africans.