There is evidence for interbreeding between archaic and modern humans during the Middle Paleolithic and early Upper Paleolithic. The interbreeding happened in several independent events that included Neanderthals and Denisovans, as well as several unidentified hominins.
Introgression of DNA from other lineages has enabled humanity "to migrate to, and succeed in, numerous new environments". Therefore, a strong case can be made that hybridization was an essential driving force in the emergence of modern humans.
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, which is 0.3% of their genome. 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). 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".
About 20% of the Neanderthal genome has been found introgressed or assimilated in the modern human population (by analyzing East Asians and Europeans), but the figure has also been estimated at about a third.
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. However, the hypothesized incompatibility between Neanderthals and modern humans is contested by findings that suggest that the Y chromosome of Neanderthals was replaced by an extinct lineage of the modern human Y chromosome, which introgressed into Neanderthals between 100,000 and 370,000 years ago. 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.
As shown in an interbreeding model produced by Neves and Serva (2012), the Neanderthal admixture in modern humans may have been caused by a very low rate of interbreeding between modern humans and Neanderthals, with the exchange of one pair of individuals between the two populations in about every 77 generations. This low rate of interbreeding would account for the absence of Neanderthal mitochondrial DNA from the modern human gene pool as found in earlier studies, as the model estimates a probability of only 7% for a Neanderthal origin of both mitochondrial DNA and Y chromosome in modern humans.
There are large genomic regions with strongly reduced Neanderthal contribution in modern humans due to negative selection, partly caused by hybrid male infertility. These regions were most-pronounced on the X chromosome, with fivefold lower Neanderthal ancestry compared to autosomes. They also contained relatively high numbers of genes specific to testes. 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. It may be partly affected by hemizygosity of X chromosome genes in males.
Deserts of Neanderthal sequences may also be caused by genetic drift involving intense bottlenecks in the modern human population and background selection as a result of strong selection against deleterious Neanderthal alleles. The overlap of many deserts of Neanderthal and Denisovan sequences suggests that repeated loss of archaic DNA occur at specific loci.
In Eurasia, modern humans have adaptive sequences introgressed from archaic humans, which provided a source of advantageous genetic variants that are adapted to local environments and a reservoir for additional genetic variation. 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. 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. In the immune system, introgressed variants have heavily contributed to the diversity of immune genes, of which there's an enrichment of introgressed alleles that suggest a strong positive selection.
Genes affecting keratin were found to have been introgressed from Neanderthals into modern humans (shown in East Asians and Europeans), suggesting that these genes gave a morphological adaptation in skin and hair to modern humans to cope with non-African environments. 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.
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. The results show that haplogroup D introgressed 37,000 years ago (based on the coalescence age of derived D alleles) into modern humans from an archaic human population that separated 1.1 million years ago (based on the separation time between D and non-D alleles), consistent with the period when Neanderthals and modern humans co-existed and diverged respectively. The high frequency of the D haplogroup (70%) suggest that it was positively selected for in modern humans. The distribution of the D allele of microcephalin is high outside Africa but low in sub-Saharan Africa, which further suggest that the admixture event happened in archaic Eurasian populations. 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.
It has been found that HLA-A*02, A*26/*66, B*07, B*51, C*07:02, and C*16:02 of the immune system were contributed from Neanderthals to modern humans. After migrating out of Africa, modern humans encountered and interbred with archaic humans, which was advantageous for modern humans in rapidly restoring HLA diversity and acquiring new HLA variants that are better adapted to local pathogens.
It is found that introgressed Neanderthal genes exhibit cis-regulatory effects in modern humans, contributing to the genomic complexity and phenotype variation of modern humans. 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. In the brain, this was most pronounced at the cerebellum and basal ganglia. This downregulation suggests that modern humans and Neanderthals possibly experienced a relative higher rate of divergence in these specific tissues.
Examining European modern humans in regards to the Altai Neanderthal genome in high-coverage, results show that Neanderthal admixture is associated with several changes in cranium and underlying brain morphology, suggesting changes in neurological function through Neanderthal-derived genetic variation. 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. In regards to modern human brain morphology, Neanderthal admixture is positively correlated with an increase in sulcal depth for the right intraparietal sulcus and an increase in cortical complexity for the early visual cortex of the left hemisphere. 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. In the area overlapping the primary visual cortex gyrification in the left hemisphere, Neanderthal admixture is positively correlated with gray matter volume. The results also show evidence for a negative correlation between Neanderthal admixture and white matter volume in the orbitofrontal cortex.
The remains of an early Upper Paleolithic modern human from Peștera Muierilor (Romania) of 35,000 years BP shows a morphological pattern of European early modern humans, but possesses archaic or Neanderthal features, suggesting European early modern humans interbreeding with Neanderthals. These features include a large interorbital breadth, a relatively flat superciliary arches, a prominent occipital bun, an asymmetrical and shallow mandibular notch shape, a high mandibular coronoid processus, the relative perpendicular mandibular condyle to notch crest position, and a narrow scapular glenoid fossa. 2b1af7f3a8