Interbreeding between archaic and modern humans
[3] Cushitic and Semitic speaking populations from the Horn of Africa (such as Ethiopians), who derive a large portion of their ancestry from West Eurasians, have ~1% Neanderthal-derived DNA.
[5] A 2020 paper found that "despite their very low levels or absence of archaic ancestry, African populations share many Neanderthal and Denisovan variants that are absent from Eurasia, reflecting how a larger proportion of the ancestral human variation has been maintained in Africa.
[11] According to the authors Green et al. (2010), the observed excess of genetic similarity is best explained by recent gene flow from Neanderthals to modern humans after the migration out of Africa.
[3] 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".
[42] There are large genomic regions with strongly reduced Neanderthal contribution in modern humans due to negative selection,[20][25] partly caused by hybrid male infertility.
[25] This means that modern humans have relatively few Neanderthal genes that are located on the X chromosome or expressed in the testes, suggesting male infertility as a probable cause.
[5] The overlap of many deserts of Neanderthal and Denisovan sequences suggests that repeated loss of archaic DNA occur at specific loci.
[5] Adaptive introgression from Neanderthals has targeted genes involved with keratin filaments, sugar metabolism, muscle contraction, body fat distribution, enamel thickness, and oocyte meiosis, as well as brain size and functioning.
[44] 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.
[20][25] This is likewise for several genes involved in medical-relevant phenotypes, such as those affecting systemic lupus erythematosus, primary biliary cirrhosis, Crohn's disease, optic disk size, smoking behavior, interleukin 18 levels, and diabetes mellitus type 2.
[45] Evans et al. (2006) had previously suggested that a group of alleles collectively known as haplogroup D of microcephalin, a critical regulatory gene for brain volume, originated from an archaic human population.
[49] This downregulation suggests that modern humans and Neanderthals possibly experienced a relative higher rate of divergence in these specific tissues.
[5] Studying the high-coverage female Vindija Neanderthal genome, Prüfer et al. (2017) identified several Neanderthal-derived gene variants, including those that affect levels of LDL cholesterol and vitamin D, and that influence eating disorders, visceral fat accumulation, rheumatoid arthritis, schizophrenia, as well as responses to antipsychotic drugs.
[50] Neanderthal admixture is associated with an expansion of the posterolateral area of the modern human skull, extending from the occipital and inferior parietal bones to bilateral temporal locales.
[50] 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.
[50] In the area overlapping the primary visual cortex gyrification in the left hemisphere, Neanderthal admixture is positively correlated with gray matter volume.
[54] From the extent of linkage disequilibrium, it was estimated that the last Neanderthal gene flow into early ancestors of Europeans occurred 47,000–65,000 years BP.
[58] Concluding from the Oase 1 mandible, there was apparently a significant craniofacial change of early modern humans from at least Europe, possibly due to some degree of admixture with Neanderthals.
[60] 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.
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".
[56] It has been shown that Melanesians (e.g. Papua New Guinean and Bougainville Islander) share relatively more alleles with Denisovans when compared to other Eurasian-derived populations and Africans.
[74][77] 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.
[48] It is thought that these must have been contributed from Denisovans to modern humans, because it is unlikely to have been preserved independently in both for so long due to HLA alleles' high mutation rate.
[48] 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.
[44] The ancestral variant of EPAS1 upregulates hemoglobin levels to compensate for low oxygen levels—such as at high altitudes—but this also has the maladaption of increasing blood viscosity.
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.
[84][85] 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),[82] Hammer et al., 2011,[86] and Plagnol and Wall (2006).
[88] 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.
[89] 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.
[93] 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.
