Interbreeding between early humans, such as Neanderthals and Denisovans, and anatomically modern humans (Homo sapiens) occurred during the Middle Paleolithic and early Upper Paleolithic periods. Genomic studies show that all modern human populations outside Africa today have approximately 1–4% Neanderthal DNA. This DNA came from genetic mixing that happened after modern humans left Africa. Denisovan DNA is most common in Oceania, where modern humans have about 4–6% Denisovan ancestry. People in Eurasia and the Americas have smaller amounts of Denisovan DNA.
In Africa, repeated migrations from Eurasia during the Neolithic period brought Neanderthal DNA to North African populations. Earlier, it was believed that sub-Saharan African populations had no Neanderthal DNA, but recent studies have found small amounts from these migrations.
The mixing of archaic human DNA with modern human DNA has affected human biology. Some genetic changes helped humans survive in new environments, such as genes related to the immune system, skin and hair traits, and high-altitude living. However, certain parts of the modern human genome, especially on the X chromosome and in genes active in testes, lack archaic DNA. This suggests that harmful genetic traits were removed through natural selection, which may have reduced fertility in male hybrids.
These discoveries have changed scientific understanding in paleoanthropology. Previously, the dominant theory was that modern humans replaced archaic populations without significant mixing. However, evidence from fossils like the Oase 1 mandible suggested otherwise. Since 2010, genomic data has shown that while most modern human ancestry comes from Africa, the genetic makeup of today’s populations was shaped by ancient interbreeding events with archaic humans in Africa and Eurasia.
Neanderthals
On May 7, 2010, scientists published a draft of the Neanderthal genome after studying the DNA of three Neanderthals from Vindija, Croatia. This study showed that Neanderthals shared more genetic traits with people from Europe and Asia than with people from sub-Saharan Africa. The researchers believed that this similarity was due to gene mixing between Neanderthals and modern humans after humans left Africa. They estimated that 1–4% of the DNA in people from Europe and Asia came from Neanderthals. Other studies later gave slightly different numbers, such as 1–6% or 1.5–2.1%. In 2017, a study revised the estimate to 1.8–2.6% for people outside of Oceania.
A 2020 study by Chen et al. found that people in Africa also have Neanderthal DNA. This DNA was estimated to cover about 0.3% of the genome in African populations. The researchers suggested that this Neanderthal DNA came from modern humans who had previously lived in Europe and later returned to Africa around 20,000 years ago. However, some scientists, like David Reich, questioned how much DNA could have returned to Africa, saying the evidence was weak.
Studies have shown that 50% of the Neanderthal genome is found in people from India, and 41% in Icelanders. Earlier research suggested that about 20% of the Neanderthal genome was present in modern Eurasians, though some estimates were higher. A 2023 study found that modern humans mixed with Neanderthals about 250,000 years ago, with about 6% of the Altai Neanderthal genome coming from modern humans.
East Asians have more Neanderthal DNA than Europeans, with estimates showing about 20% more mixing. Scientists have proposed several reasons for this, including additional mixing events after East Asians and Europeans separated, or differences in how Neanderthal genes were passed down. Studies suggest that East Asians may have had more Neanderthal DNA due to more mixing events, not because of weaker natural selection. Research also found small differences in Neanderthal DNA among European groups but not among East Asian groups. A 2017 study noted that East Asians have 2.3–2.6% Neanderthal DNA, compared to 1.8–2.4% in Western Eurasians.
A 2020 study corrected earlier estimates, showing that East Asians have 8% more Neanderthal DNA than Europeans, not 20% as previously thought. This change happened because earlier studies assumed Africans had no Neanderthal DNA, which led to underestimating Neanderthal DNA in other populations. The researchers believe the most likely explanation is a single mixing event after humans left Africa, though other factors like later migrations may also play a role.
Genomic analysis shows that Neanderthal DNA is more common in non-African populations than in sub-Saharan Africans. North African groups share similar levels of Neanderthal DNA with non-African populations, while sub-Saharan Africans generally have little to no Neanderthal DNA. The amount of Neanderthal DNA in North African populations depends on their mix of African, European, and Near Eastern ancestry. For example, Tunisian Berbers, who have more indigenous North African ancestry, have the highest levels of Neanderthal DNA, while populations with more sub-Saharan ancestry have the lowest. A 2012 study suggested that Neanderthal DNA in Africa is not from recent mixing with Europeans or Near Easterners but from older African populations. Small amounts of Neanderthal DNA have also been found in the Maasai of East Africa, likely from recent mixing with non-African populations.
David Reich noted that about 2% of the DNA in all non-sub-Saharan African populations comes from Neanderthals. A high-quality genome of a Neanderthal from Altai, Siberia, showed that the Neanderthal DNA in non-African humans is more similar to Neanderthals from the Caucasus (Mezmaiskaya) and Croatia (Vindija) than to the Altai Neanderthal. Later studies found that the Vindija and Mezmaiskaya Neanderthals shared similar levels of DNA with modern humans. These results suggest that most Neanderthal DNA in modern humans came from Neanderthals who lived before the Vindija and Mezmaiskaya groups split from each other.
Analysis of chromosome 21 in Neanderthals from Altai, Spain (El Sidrón), and Croatia (Vindija) showed that only the El Sidrón and Vindija Neanderthals had significant DNA mixing with modern humans. This suggests that the El Sidrón and Vindija Neanderthals were more closely related to the Neanderthals that mixed 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 genes with Denisovans than other groups like Eurasians and Africans. Scientists estimate that 4% to 6% of the DNA in Melanesians comes from Denisovans. However, no Denisovan genes have been found in Eurasians or Africans. Researchers have observed that Denisovans contributed genes to Melanesians but not to East Asians. This suggests that early ancestors of Melanesians interacted with Denisovans, but this interaction did not occur near southern Siberia, where Denisovan remains have been discovered. Aboriginal Australians also share more genes with Denisovans than Eurasians or Africans, which supports the idea that Denisovans and Melanesians interbred more frequently.
In 2011, Reich and others found that Oceanian populations, such as Aboriginal Australians 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 pattern suggests that Denisovans and early humans may have interbred in Southeast Asia rather than in mainland Eurasia. Scientists like Cooper and Stringer (2013) believe this interbreeding likely happened east of the Wallace Line, a boundary in Southeast Asia.
Skoglund and Jakobsson (2011) noted that Oceanians and Southeast Asians have the highest Denisovan gene mixing compared to other groups. They also found possible traces of Denisovan genes in East Asians but not in Native Americans. However, Prüfer and others (2013) found that mainland Asians and Native Americans might have a very small amount of Denisovan genes (about 0.2%), which is much less than in Oceanian populations. The way these genes spread is still unclear. Wall and others (2013) found no evidence of Denisovan genes in East Asians.
Research shows 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, suggesting interbreeding happened before their ancestors moved to Sahul (a region that included modern-day New Guinea and Australia) at least 44,000 years ago. In some groups, like those from Nusa Tenggara, Moluccas, Polynesia, and Fiji, the amount of Denisovan genes matches the amount of Near Oceanian ancestry. However, the Philippine Mamanwa and Manobo groups have more Denisovan genes than Near Oceanian ancestry. Reich and others (2011) proposed that early humans migrated eastward, some of whom interbred with Denisovans before splitting into different groups.
Browning and others (2018) found evidence of at least two separate times when Denisovan genes mixed with human populations. In East Asians, such as Japanese and Han Chinese, genes from two different Denisovan groups were found. In South Asians and Oceanians, like Papuans, genes from one Denisovan group were observed.
Sankararaman and others (2016) estimated that Denisovan genes mixed with humans between 44,000 and 54,000 years ago. Oceanians had the most Denisovan genes compared to other groups with Denisovan ancestry, such as those in America, Central Asia, and East Asia. Surprisingly, South Asians had more Denisovan genes than other non-Oceanian groups, though still much less than Oceanians. Scientists suggest this could mean one major mixing event that spread differently or multiple separate events.
A 2021 study found that Denisovan genes mixed with Philippine Negritos, with the Ayta Magbukon group having the highest Denisovan ancestry in the world. This suggests that Denisovans in the Philippines interbred with early humans after they arrived.
Eurasians have some Denisovan genes, but much less than other groups. This is because Denisovans are related to Neanderthals, who contributed genes to Eurasians, not because Denisovans interbred directly with Eurasian ancestors.
A 40,000-year-old human skeleton from China showed Neanderthal genes but no Denisovan genes. This 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 often infertile. This is supported by the lower presence of Denisovan genes on the X chromosome and in genes linked to male reproduction.
Studies of immune system genes called HLA alleles suggest that a specific HLA-B73 allele was introduced to humans in western Asia from Denisovans. Though HLA-B73 is not in the Denisovan genome, it is closely related to a Denisovan HLA-C15:05 allele. Scientists believe HLA-B73 is an ancient allele that likely existed before Denisovans.
Denisovans had HLA-A (A02 and A11) and HLA-C (C15 and C12:02) alleles that are common in modern humans. One HLA-B allele is rare, and another is missing in modern humans. Scientists think these genes were passed from Denisovans to humans because it is unlikely they developed independently due to the high mutation rate of HLA alleles.
Tibetan people have a gene variant (EGLN1 and EPAS1) that helps them live at high altitudes. This variant is believed to have come from Denisovans.
Archaic African hominins
Fossils in Sub-Saharan Africa decay quickly, making it difficult to compare DNA from modern humans with ancient human remains from that region.
Ancient DNA from a person in Ethiopia (about 4,500 years old), and from individuals in Southern Africa (about 2,300 to 1,300 years old), and in Eastern and South-Central Africa (about 8,100 to 400 years old), shows that some West African populations have small amounts of DNA that likely came from an ancient group not found in pre-agricultural Eastern African hunter-gatherers, Southern African hunter-gatherers, or the genetic differences between them. These West African groups include the Yoruba from coastal Nigeria and the Mende from Sierra Leone. This ancient DNA was likely acquired long before agriculture spread and possibly before the Holocene period (which began about 11,600 years ago). This ancient group must have separated from the ancestors of the San people (a group in Southern Africa) before the San’s ancestors began to diverge, which is estimated to have happened about 200,000 to 300,000 years ago.
Evidence supports the idea that some present-day Africans have genetic material from an ancient group that existed before the San, Pygmies, East African hunter-gatherers, and Eurasians. This evidence comes from studies that found long genetic patterns with deep differences from other human DNA, including research by Lachance et al. (2012), Hammer et al. (2011), and Plagnol and Wall (2006).
In one study, Hammer and others found that Central African Pygmies are genetically similar to Southern African San people, but different from West African Yoruba. Further analysis of DNA from four fossils in Cameroon (8,000 to 3,000 years old) showed that these individuals had DNA mostly from Central African hunter-gatherers (like Pygmies) and did not share the ancient DNA found in the Yoruba and Mende. This confirmed differences between Eastern, Central, and Southern hunter-gatherers compared to West African groups. A second study by Lipson et al. (2020) analyzed DNA from six more fossils in Eastern and South-Central Africa (from the last 18,000 years) and found that their DNA came from Southern, Central, and Eastern hunter-gatherers, but not from the ancient DNA found in the Yoruba.
A 2020 study suggests that 2% to 19% (or about 6.6% to 7.0%) of DNA in four West African populations may have come from an unknown ancient human group that split from the ancestor of modern humans and Neanderthals between 360,000 and 1.02 million years ago. However, unlike earlier studies, this research also found that some of this ancient DNA is present in non-African populations (Eurasians), and the mixing of DNA occurred between 0 and 124,000 years ago. This includes a time before humans left Africa and before the split between Africans and non-Africans, affecting the shared ancestors of both groups. Another recent study found genetic differences in Africans that existed before modern humans and were later lost in most non-African populations.
Archaic hominins in Eurasia
Hominins were present in Eurasia at least 2 million years before present. Genetic evidence shows that later, when Neandertals and Denisovans began expanding into Eurasia, the continent was already home to descendants of earlier hominins. These early groups shared genes with Neandertals and Denisovans, and some of these genes later passed into modern humans.
Genetic studies suggest two major events where genes from superarchaic hominins mixed with other groups. This happened during the late middle Pleistocene, a time when at least two separate populations of ancient hominins lived in Eurasia.
A study by Roger et al. (2020) describes an event where Neandertals and Denisovans (a group that includes both Neandertals and Denisovans) met a lineage of superarchaic hominins. This lineage had been separated from African Homo lineages for at least 2 million years.
Earlier research found another event when a genome similar to that of Homo erectus was introduced into the Denisovan lineage about 350,000 years ago. These two groups had been separated for about 2 million years, and their interbreeding occurred much later. This makes them the most distantly related populations known to have interbred.
Related studies
In 2019, scientists used artificial intelligence to study human genetics. They found signs of a new human ancestor species. This ancestor was different from Neanderthals or Denisovans. They discovered these signs in the genetic material of modern humans.