Interbreeding between early human groups, such as Neanderthals and Denisovans, and anatomically modern humans (Homo sapiens) happened during the Middle Paleolithic and early Upper Paleolithic periods. Genomic testing has shown that all modern human populations outside Africa today have about 1–4% Neanderthal DNA. This DNA came from genetic mixing that occurred after modern humans left Africa. Denisovan DNA is most common in Oceania, where modern humans have about 4–6% Denisovan DNA in their genomes. People in Eurasia and the Americas have smaller amounts of Denisovan DNA.
In Africa, later migrations from Eurasia during the Neolithic period brought Neanderthal DNA to modern human populations in North Africa. Earlier, it was believed that Neanderthal DNA was absent in sub-Saharan African populations, but recent studies have found small amounts of Neanderthal DNA in these groups as well, likely from these migrations.
The mixing of archaic human DNA with modern human DNA affected human biology through both helpful and harmful genetic changes. Helpful genetic traits, such as those related to the immune system (like HLA alleles), skin and hair features, and high-altitude survival, were passed on and helped humans adapt to new environments. However, large parts of the modern human genome, especially on the X chromosome and in genes linked to testes function, lack archaic DNA. This suggests that harmful genetic traits were removed over time through natural selection, which may have reduced fertility in male hybrids.
These discoveries have changed scientific views about human history. Previously, the "Out of Africa" model suggested that modern humans replaced archaic humans without much mixing. However, fossil evidence, such as the Oase 1 mandible, hinted at some interbreeding. Since 2010, genomic research has shown that while most modern human ancestry comes from Africa, populations today have been shaped by ancient hybridization events with archaic humans in Africa and Eurasia. This has shifted the scientific understanding from a strict replacement model to one that includes mixing between human groups.
Neanderthals
On May 7, 2010, scientists published a draft of the Neanderthal genome after studying the DNA of three Vindija Neanderthals. The study showed that Neanderthals shared more genetic material with people from Eurasia (Europe and Asia) than with people from sub-Saharan Africa. The researchers believed this similarity was due to Neanderthals sharing genes with modern humans after humans left Africa. They estimated that about 1–4% of the Eurasian genome came from Neanderthals. Later studies, such as those by Durand et al. (2011) and Prüfer et al. (2013), suggested similar or slightly different ranges, such as 1–6% or 1.5–2.1%. In 2017, Prüfer et al. revised their estimate to 1.8–2.6% for non-Africans outside Oceania.
A 2020 study by Chen et al. found that Africans also had some Neanderthal genes. This admixture was estimated to cover 17 megabases, or 0.3% of the genome. The researchers suggested that this occurred when people with Neanderthal genes (who had left Africa) returned to Africa about 20,000 years ago. However, some scientists, like David Reich, questioned how much DNA could have returned to Africa, noting the signal was weak.
Studies found that about 50% of the Neanderthal genome is present in people from India, and 41% in Icelanders. Earlier estimates suggested 20% of the Neanderthal genome was in modern Eurasians, though some studies said a third. A 2023 study found that modern humans contributed about 6% of the Altai Neanderthal genome around 250,000 years ago.
East Asians have more Neanderthal ancestry than Europeans, with estimates showing about 20% more introgression into East Asians. This could be due to additional mixing events after East Asians and Europeans separated, or because purifying selection (a process that removes harmful genes) was less effective in East Asian ancestors. Simulations suggested that additional mixing events, not just selection, explain the higher Neanderthal ancestry in East Asians. Prüfer et al. (2017) noted that East Asians have 2.3–2.6% Neanderthal DNA, while Western Eurasians have 1.8–2.4%.
Chen et al. (2020) revised earlier estimates, finding that East Asians have 8% more Neanderthal ancestry than Europeans, not 20% as previously thought. This change was due to a flawed assumption that Africans had no Neanderthal genes, which led to underestimating Neanderthal ancestry in non-Africans. The study suggested a single mixing event after humans left Africa as the most likely explanation for the higher Neanderthal ancestry in East Asians.
Genomic analysis shows that Neanderthal genes are more common in non-African populations than in sub-Saharan African groups. North African populations share similar levels of Neanderthal alleles with non-African groups, while sub-Saharan Africans generally lack Neanderthal admixture. The amount of Neanderthal DNA in North Africans depends on their ancestry mix, with higher levels in groups with more North African heritage, such as Tunisian Berbers (100–138% of Eurasian levels), and lower levels in groups with more sub-Saharan ancestry, such as in South Morocco (20%). Quinto et al. (2012) suggested that this signal in North Africa is not from recent gene flow but from ancient North African populations. Low but significant Neanderthal admixture was also found in the Maasai of East Africa, likely from non-African gene flow around 100 generations ago.
David Reich noted that all non-sub-Saharan Africans have about 2% Neanderthal ancestry. A high-quality genome sequence of a female Altai Neanderthal showed that the Neanderthal DNA in non-African modern humans is more closely related to the Mezmaiskaya Neanderthal (from the North Caucasus) than to the Altai or Vindija Neanderthals. Later studies of a 50,000-year-old Vindija Neanderthal found that the Vindija and Mezmaiskaya Neanderthals shared similar levels of allele-sharing with modern humans. This suggests that most Neanderthal DNA in modern humans came from populations that split from the Vindija and Mezmaiskaya lineages about 80,000–100,000 years ago.
Analysis of chromosome 21 from Altai, El Sidrón (Spain), and Vindija Neanderthals showed that only El Sidrón and Vindija Neanderthals had significant gene flow into modern humans (0.3–2.6%). This suggests El Sidrón and Vindija Neanderthals are more closely related to the Neanderthals that interbred with modern humans about 47,000–65,000 years ago than the Altai Neanderthal.
Denisovans
Studies show that Melanesians, such as people from Papua New Guinea and Bougainville Island, share more genetic traits with Denisovans compared to other groups like Eurasians and Africans. It is estimated that 4% to 6% of the genes in Melanesians came from Denisovans, while no Eurasians or Africans have Denisovan genes. Evidence suggests that Denisovans shared genes with Melanesians but not with East Asians, meaning early Melanesian ancestors interacted with Denisovans, but this interaction did not occur in southern Siberia, where Denisovan remains have been found. Aboriginal Australians also share more genetic traits with Denisovans than Eurasians or Africans, supporting the idea that Denisovans and Melanesians interbred more frequently.
Research by Reich et al. (2011) found that Oceanian populations, such as Aboriginal Australians, Near Oceanians, and Polynesians, have the highest levels of Denisovan genes. Some eastern Southeast Asian groups also show Denisovan genes, but mainland East Asian populations do not. This suggests that Denisovans may have interbred with early humans in Southeast Asia, not in mainland Eurasia. Cooper and Stringer (2013) noted that the high Denisovan genes in Oceania and low levels in mainland Asia indicate that interbreeding between Denisovans and early humans likely happened east of the Wallace Line, which separates Southeast Asia from other regions.
Skoglund and Jakobsson (2011) found that Oceanians and some Southeast Asian groups have the most Denisovan genes, while East Asians and Native Americans have very little or none. Prüfer et al. (2013) reported that mainland Asians and Native Americans may have 0.2% Denisovan genes, which is much lower than in Oceanian populations. Wall et al. (2013) found no evidence of Denisovan genes in East Asians.
Studies suggest that Denisovan genes were passed to the ancestors of Aboriginal Filipinos, Aboriginal Australians, and New Guineans. New Guineans and Australians have similar levels of Denisovan genes, showing interbreeding occurred before their ancestors moved to Sahul (Pleistocene New Guinea and Australia) about 44,000 years ago. Populations in Nusa Tenggara, Moluccas, Polynesia, and Fiji have Denisovan genes in amounts similar to their Near Oceanian ancestry, except for the Philippine Mamanwa and Manobo, who have higher Denisovan ancestry than Near Oceanian ancestry. Reich et al. (2011) proposed that early humans migrated eastward, with some interbreeding with Denisovans before splitting into different groups.
Browning et al. (2018) found evidence of at least two separate times when Denisovan genes mixed with modern humans. East Asians, such as Japanese and Han Chinese, show genes from two different Denisovan groups, while South Asians and Oceanians, like Papuans, show genes from one Denisovan group.
Sankararaman et al. (2016) estimated Denisovan genes entered modern humans 44,000–54,000 years ago. Oceanians had the most Denisovan genes compared to other groups. South Asians also had more Denisovan genes than other non-Oceanian groups, though still much less than Oceanians. Researchers suggested this could mean one Denisovan mixing event spread differently or multiple events occurred.
A 2021 study found Denisovan genes in Philippine Negritos, with the Ayta Magbukon having the highest Denisovan ancestry in the world, even more than Australians and Papuans. This suggests Denisovans in the Philippines interbred with early humans after they arrived.
Eurasians have some genetic material from Denisovans, but much less than other groups. This is because Denisovans are related to Neanderthals, who contributed genes to Eurasians, not from direct Denisovan-Eurasian interbreeding.
A 40,000-year-old human skeleton from China showed Neanderthal genes but no Denisovan genes. This individual is related to many Asian and Native American populations but came after Asians and Europeans split. The lack of Denisovan genes in this skeleton suggests Denisovan genes were rare in mainland Asia.
Some parts of the human genome lack Denisovan genes, possibly because male hybrids between Denisovans and humans were less likely to survive, leading to fewer Denisovan genes on X chromosomes and in testes-related genes.
Studies of immune system genes (HLA) suggest that a specific HLA-B73 gene may have come from Denisovans in western Asia. Though HLA-B73 is not in the Denisovan genome, it is closely linked to another Denisovan gene, HLA-C15:05. Genetic analysis suggests HLA-B73 is an ancient trait.
Denisovans had HLA-A (A02 and A11) and HLA-C (C15 and C12:02) genes that are common in modern humans. One Denisovan HLA-B gene is rare in modern humans, and another is missing. These genes likely came from Denisovans to modern humans, as it is unlikely they developed independently due to the high mutation rate of HLA genes.
Tibetans have genetic traits from Denisovans, such as EGLN1 and EPAS1, which help them live at high altitudes.
Archaic African hominins
Fossils in Sub-Saharan Africa decay quickly, making it difficult to compare modern human DNA with ancient DNA from early humans in that region.
Ancient DNA from a person in Ethiopia who lived about 4,500 years ago, and from people in southern and eastern Africa who lived between 1,300 and 8,100 years ago, shows that some West African groups have small amounts of DNA that do not match DNA from other ancient African groups, such as early hunter-gatherers in eastern or southern Africa. This suggests that these West African groups, like the Yoruba in Nigeria and the Mende in Sierra Leone, inherited this DNA long before agriculture spread and possibly before the Holocene era (which began about 11,600 years ago). This ancient DNA likely came from a group that separated from the ancestors of the San people (a group in southern Africa) around 200,000 to 300,000 years ago.
Studies by scientists like Lachance, Hammer, and others support the idea that some modern African populations have DNA from an ancient group that split from the ancestors of humans and Neanderthals between 360,000 and 1.02 million years ago. This DNA is found in some West African groups but not in the San, Pygmies (from central Africa), or other hunter-gatherer groups.
A study of DNA from four fossils found in Cameroon, dating from 8,000 to 3,000 years ago, showed that these individuals had DNA similar to Central African hunter-gatherers (like the ancestors of the Pygmies) but did not share the ancient DNA found in the Yoruba or Mende. This confirmed earlier findings that West African groups differ genetically from eastern, central, and southern hunter-gatherers. Another study by Lipson in 2020 analyzed DNA from six fossils in eastern and southern Africa from the last 18,000 years and found that their DNA came from hunter-gatherer groups in those regions but not from the ancient DNA found in the Yoruba.
A 2020 study suggests that 2% to 19% of DNA in some West African groups may come from an unknown ancient human group that split from the ancestors of humans and Neanderthals between 360,000 and 1.02 million years ago. This study also found that some of this ancient DNA may be present in non-African populations, such as people in Eurasia. The mixing of this ancient DNA with modern human DNA likely happened between 0 and 124,000 years ago, a time that includes the period before humans migrated out of Africa and before the split between African and non-African populations. Another study found genetic differences in African populations that are older than modern humans and are not found in most non-African populations.
Archaic hominins in Eurasia
Hominins were present in Eurasia at least 2 million years before present. Genetic research shows that later, when Neanderthal and Denisovan lineages began to spread into Eurasia, the continent was already home to descendants of earlier hominins. These early hominins shared genetic material with Neanderthals and Denisovans, and this genetic mixing later influenced the genes of modern humans.
Studies of DNA reveal two major events where genetic material from superarchaic hominins mixed with others. This suggests that during the late middle Pleistocene, Eurasia was inhabited by at least two distinct groups of ancient hominins.
Roger et al. (2020) describes a mixing event that happened soon after Neanderthals and Denisovans (the common ancestors of these groups) began expanding into Eurasia. They encountered a lineage of superarchaic hominins that had separated from African hominin groups at least 2 million years ago.
Earlier research identified a more recent mixing event. Around 350,000 years ago, the genome of a hominid similar to Homo erectus was added to the Denisovan lineage. Since these two groups had separated about 2 million years ago and interbred 350,000 years ago, they were more distantly related than any other known human populations that interbred.
Related studies
In 2019, scientists used artificial intelligence to study human genetics. They said they found signs of a new type of human ancestor in the DNA of modern humans. This ancestor was not Neanderthal or Denisovan.