Interbreeding between archaic and modern humans

Genetics Proportion of admixture , Nobel Prize laureate and one of the researchers who published the first sequence of the Neanderthal genome. 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 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. 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, 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). 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, 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. Such models show a pulse to ancestral Eurasians, followed by separation and an additional pulse to ancestral East Asians. Prüfer et al. (2017) remarked that East Asians carry more Neanderthal DNA (2.3–2.6%) than Western Eurasians (1.8–2.4%). 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 (100–138%); high among North African populations carrying greater European or Near Eastern admixture, such as groups in North Morocco and Egypt (~60–70%); and lowest among North African populations with greater Sub-Saharan admixture, such as in South Morocco (20%). Quinto et al. (2012) 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 (post-Neanderthal) 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. Distance to lineages Neanderthal skull reconstitution, Neues Museum Berlin. 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 (North Caucasus) than to the Altai Neanderthal (Siberia) or the Vindija Neanderthals (Croatia). Mitochondrial DNA and Y chromosome No evidence of Neanderthal mitochondrial DNA has been found in modern humans. This suggests that successful Neanderthal admixture happened in pairings with Neanderthal males and modern human females. Possible hypotheses are that Neanderthal mitochondrial DNA had detrimental mutations that led to the extinction of carriers, that the hybrid offspring of Neanderthal mothers were raised in Neanderthal groups and became extinct with them, or that female Neanderthals and male Sapiens did not produce fertile offspring. Furthermore, the study concludes that the replacement of the Y chromosomes and mitochondrial DNA in Neanderthals after gene flow from modern humans is highly plausible given the increased genetic load in Neanderthals relative to modern humans. In 2026, a study published in the journal Science confirmed that interbreeding between Neanderthals and modern humans was predominantly between Neanderthal males and sapiens females. This conclusion was based on a comparative genomic analysis that revealed an excess of modern human DNA in the X chromosomes of Neanderthals and very little Neanderthal inheritance in the X chromosome of modern sapiens. The bias detected could reflect cultural or social differences between the two species. Although it could not be determined whether the encounters were consensual or forced, paleoanthropologist Steven E. Churchill stated that if males of one species monopolised females of the other, it would imply competitive and hostile interactions. Reduced contribution There are large genomic regions with strongly reduced Neanderthal contribution in modern humans due to negative selection, Rates of selection against Neanderthal sequences varied for European and Asian populations. There are signals of positive selection, as the result of adaptation to diverse habitats, in genes involved with variation in skin pigmentation and hair morphology. The introgressive haplotypes were positively selected in only East Asian populations, rising steadily from 45,000 years BP until a sudden increase of growth rate around 5,000 to 3,500 years BP. This distribution difference between Africa and Eurasia suggests that the D allele originated from Neanderthals according to Lari et al. (2010), but they found that a Neanderthal individual from the Mezzena Rockshelter (Monti Lessini, Italy) was homozygous for an ancestral allele of microcephalin, thus providing no support that Neanderthals contributed the D allele to modern humans and also not excluding the possibility of a Neanderthal origin of the D allele. Green et al. (2010), having analyzed the Vindija Neanderthals, also could not confirm a Neanderthal origin of haplogroup D of the microcephalin gene. Looking at heterozygous individuals (carrying both Neanderthal and modern human versions of a gene), the allele-specific expression of introgressed Neanderthal alleles was found to be significantly lower in the brain and testes relative to other tissues. Neanderthal admixture is also positively correlated with an increase in white and gray matter volume localized to the right parietal region adjacent to the right intraparietal sulcus. A Neanderthal allele inherited by modern humans, SNP rs3917862, is associated with hypercoagulability. This can be harmful, but women lacking the allele are 0.1% more likely to die in childbirth. In December 2023, scientists reported that genes inherited by modern humans from Neanderthals and Denisovans may biologically influence the daily routine of modern humans. Population substructure theory Although less parsimonious than recent gene flow, the observation may have been due to ancient population sub-structure in Africa, causing incomplete genetic homogenization within modern humans when Neanderthals diverged while early ancestors of Eurasians were still more closely related to Neanderthals than those of Africans were to Neanderthals. On the basis of allele frequency spectrum, it was shown that the recent admixture model had the best fit to the results while the ancient population sub-structure model had no fit—demonstrating that the best model was a recent admixture event that was preceded by a bottleneck event among modern humans – thus confirming recent admixture as the most parsimonious and plausible explanation for the observed excess of genetic similarities between modern non-African humans and Neanderthals. On the basis of linkage disequilibrium patterns, a recent admixture event is likewise confirmed by the data. In conjunction with archaeological and fossil evidence, the gene flow is thought likely to have occurred somewhere in Western Eurasia, possibly the Middle East. Morphology The early Upper Paleolithic burial remains of a modern human child from Abrigo do Lagar Velho (Portugal) features traits that indicate Neanderthal interbreeding with modern humans dispersing into Iberia. Considering the dating of the burial remains (24,500 years BP) and the persistence of Neanderthal traits long after the transitional period from a Neanderthal to a modern human population in Iberia (28,000–30,000 years BP), the child may have been a descendant of an already heavily admixed population. The early modern human Oase 1 mandible from Peștera cu Oase (Romania) of 34,000–36,000 14C years BP presents a mosaic of modern, archaic, and possible Neanderthal features. The skeleton had up to 9% Neanderthal DNA compared to today's 2% for non sub-Saharan descended humans, which has led David Reich to suggest that natural selection has been removing Neanderthal genes in the time since. Manot 1, a partial calvarium of a modern human that was recently discovered at the Manot Cave (Western Galilee, Israel) and dated to 54.7±5.5 kyr BP, represents the first fossil evidence from the period when modern humans successfully migrated out of Africa and colonized Eurasia. It also provides the first fossil evidence that modern humans inhabited the southern Levant during the Middle to Upper Palaeolithic interface, contemporaneously with the Neanderthals and close to the probable interbreeding event. Until the early 1950s, most scholars thought Neanderthals were not in the ancestry of living humans. Nevertheless, Hans Peder Steensby proposed interbreeding in 1907 in the article Race studies in Denmark. He strongly emphasised that all living humans are of mixed origins. He held that this would best fit observations, and challenged the widespread idea that Neanderthals were ape-like or inferior. Basing his argument primarily on cranial data, he noted that the Danes, like the Frisians and the Dutch, exhibit some Neanderthaloid characteristics, and felt it was reasonable to "assume something was inherited" and that Neanderthals "are among our ancestors". Carleton Stevens Coon in 1962 found it likely, based upon evidence from cranial data and material culture, that Neanderthal and Upper Paleolithic peoples either interbred or that the newcomers reworked Neanderthal implements "into their own kind of tools". By the early 2000s, the majority of scholars supported the Out of Africa hypothesis, according to which anatomically modern humans left Africa about 50,000 years ago and replaced Neanderthals with little or no interbreeding. Yet some scholars still argued for hybridisation with Neanderthals. The most vocal proponent of the hybridisation hypothesis was Erik Trinkaus of Washington University in St. Louis. Trinkaus claimed various fossils as products of hybridised populations, including the skeleton of a child found at Lagar Velho in Portugal and the Peștera Muierii skeletons from Romania. ==Denisovans==

Genetics genome was sequenced from a fragment of the distal phalanx of the fifth finger (replica depicted) found in the Denisova cave. Reich et al. (2011) observed that Oceanian populations have the highest rates of Denisovan admixture, followed by certain eastern Southeast Asian populations, and none in mainland East Asian populations. The observation of high Denisovan admixture in Oceania and the lack thereof in mainland Asia suggests that early modern humans and Denisovans had interbred east of the Wallace Line that divides Southeast Asia, according to Cooper and Stringer (2013). Skoglund and Jakobsson (2011) observed that particularly Oceanians, followed by Southeast Asians populations, have a high Denisovans admixture relative to other populations. Furthermore, they found possible low traces of Denisovan admixture in East Asians and no Denisovan admixture in Native Americans. New Guineans and Australians have similar rates of Denisovan admixture, indicating that interbreeding took place prior to their common ancestors' entry into Sahul (Pleistocene New Guinea and Australia), at least 44,000 years ago. Exploring derived alleles from Denisovans, Sankararaman et al. (2016) estimated that the date of Denisovan admixture was 44,000–54,000 years ago. They also determined that the Denisovan admixture was the greatest in Oceanian populations compared to other populations with observed Denisovan ancestry (i.e. America, Central Asia, East Asia, and South Asia). It has been shown that Eurasians have some but significantly lesser archaic-derived genetic material that overlaps with Denisovans, stemming from the fact that Denisovans are related to Neanderthals—who contributed to the Eurasian gene pool—rather than from interbreeding of Denisovans with the early ancestors of those Eurasians. The skeletal remains of an early modern human from the Tianyuan cave (near Zhoukoudian, China) of 40,000 years BP showed a Neanderthal contribution within the range of today's Eurasian modern humans, but it had no discernible Denisovan contribution. It is a distant relative to the ancestors of many Asian and Native American populations, but post-dated the divergence between Asians and Europeans. Tibetan people received an advantageous EGLN1 and EPAS1 gene variant, associated with hemoglobin concentration and response to hypoxia, for life at high altitudes from the Denisovans. The Denisovan-derived variant on the other hand limits this increase of hemoglobin levels, thus resulting in a better altitude adaption. The Denisovan-derived EPAS1 gene variant is common in Tibetans and was positively selected in their ancestors after they colonized the Tibetan plateau. == Archaic African hominins ==

Rapid decay of fossils in Sub-Saharan African environments makes it currently unfeasible to compare modern human admixture with reference samples of archaic Sub-Saharan African hominins. and from Southern (~2,300–1,300 BP), and Eastern and South-Central Africa (~8,100–400 BP) has clarified that some West Africa populations have small amounts of excess alleles best explained by an archaic source in West Africans that is not included in the pre-agricultural Eastern African hunter-gatherers, Southern African hunter-gatherer populations, or the genetic gradation between them. The West African groups carrying the archaic DNA include Yoruba from coastal Nigeria and Mende from Sierra Leone indicating that the ancient DNA was acquired long before the spread of agriculture and likely well before the Holocene (starting 11,600 BP), Such an archaic lineage must have separated before the divergence of San ancestors, which is estimated to have begun on the order of 200–300 thousand years ago. The hypothesis that there has been archaic line in the ancestry of present-day Africans that originated before the San, Pygmies and East African hunter gatherers (and the Eurasians) is supported by a line of evidence independent from the Skoglund findings based on long haplotypes with deep divergences from other human haplotypes including Lachance et al.(2012), Hammer et al., 2011, and Plagnol and Wall (2006). In the archaic DNA differences found by Hammer, et al., the pygmies (of Central Africa) are grouped with the San (of Southern Africa) in contrast to the Yoruba (of West Africa). Further clarification of the presence of archaic DNA in current West African populations with the extraction and sequencing of DNA from 4 fossils found at Shum Laka in Cameroon dating from 8,000 to 3,000 BP. These individuals were found to derive most of their DNA from Central African hunter gatherers (Pygmy ancestors) and did not share the archaic DNA found in the Yoruba and Mande. The pattern of differences between Eastern, Central and Southern hunter gatherers when compared to the West African groups which had been found by Hammer was confirmed. In a second study Lipson et al. (2020) studied DNA extracted from 6 additional Eastern and Southcentral African fossils from the last 18,000 years. It was determined that their genetic origins could be accounted for by DNA contributions from Southern, Central and Eastern hunter gatherers, and that none of them had the archaic DNA found in the Yoruba. According to a study published in 2020, there are indications that 2% to 19% (or about ≃6.6 and ≃7.0%) of the DNA of four West African populations may have come from an unknown archaic hominin which split from the ancestor of humans and Neanderthals between 360 kya to 1.02 mya. However, in contrast to the studies of Skoglund and Lipson with ancient African DNA, the study also finds that at least part of this proposed archaic admixture is also present in Eurasians/non-Africans, and that the admixture event or events range from 0 to 124 ka B.P, which includes the period before the Out-of-Africa migration and prior to the African/Eurasian split (thus affecting in part the common ancestors of both Africans and Eurasians/non-Africans). Another recent study, which discovered substantial amounts of previously undescribed human genetic variation, also found ancestral genetic variation in Africans that predates modern humans and was lost in most non-Africans. == Archaic hominins in Eurasia ==

Hominins' presence in Eurasia began at least 2 million years BP. Genetic evidence shows that thousands of years later when lineages of Neandertals and Denisovans started to expand into Eurasia, the continent was still inhabited by descendants of these archaic hominins, and their genetic admixture made its way into genome of Neanderthals and Denisovans and later indirectly into modern humans. Genetic studies show two major events of genetic admixture from superarchaics, suggesting that in the late middle Pleistocene, Eurasia was inhabited by at least two separate populations of ancient hominins. Roger et al. (2020) describes an event of admixture that occurred soon after Neandersovans (common ancestor of Neanderthals and Denisovans) started to expand into Eurasia. They met a lineage of superarchaic hominins that had been separated from African homo lineages since at least 2 Ma ago. Previous studies identified more recent event of admixture. About 350,000 years ago a genome of an "erectus-like" hominid was injected into the Denisovan lineage. With the separation time of about 2 Ma ago and interbreeding that happened 350 ka ago, the two populations involved were more distantly related than any pair of human populations previously known to interbreed. ==Related studies==

In 2019, scientists analyzing genetics using artificial intelligence claimed to find indications of an unknown human ancestor species – not Neanderthal or Denisovan – in the genome of modern humans. ==See also==