Interbreeding between archaic and modern humans

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A model of the phylogeny of H. sapiens over the last 600,000 years (vertical axis). The horizontal axis represents geographic location; the vertical axis represents time in thousands of years ago. Homo heidelbergensis is shown as diverging into Neanderthals, Denisovans and H. sapiens. With the expansion of H. sapiens after 200 kya, Neanderthals, Denisovans and unspecified archaic African hominins are displayed as again subsumed into the H. sapiens lineage. Possible admixture events involving certain modern populations in Africa are also shown.

 

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, Denisovans, as well as several unidentified hominins. 

In Eurasia, interbreeding between Neanderthals and Denisovans with modern humans took place several times. The introgression events into modern humans is estimated to have happened about 47,000–65,000 years ago with Neanderthals and about 44,000–54,000 years ago with Denisovans. Neanderthal-derived DNA was found in the genome of contemporary populations in Europe and Asia. It accounted for 1–4% of modern genomes, although estimates may vary. Neanderthal-derived ancestry is absent from most modern populations in sub-Saharan Africa, while Denisovan-derived ancestry is absent from modern populations in Western Eurasia and Africa. However, in Africa, archaic alleles consistent with several independent admixture events in the subcontinent have been found. It is currently unknown who these archaic African hominins were.

The highest rates of Denisovan admixture has been found in Oceanian and certain Southeast Asian populations, with an estimated 4–6% of the genome of modern Melanesians being derived from Denisovans for example. In addition, Denisovan-derived ancestry has been found in very low trace amounts in mainland Asia, with a relative elevated Denisovan ancestry in South Asian populations. Regarding Neanderthal admixture, it is found in all non-African groups but varies slightly between populations. It is highest in East Asians, intermediate in Europeans, and lower in Southeast Asians. According to some evidence, it is also lower in Melanesians compared to both East Asians and Europeans. However, some research finds higher Neanderthal admixture in Oceanians, as well as in Native American groups, than in Europeans (though not higher than in East Asians).

Although the narratives of human evolution are often contentious, DNA evidence shows that human evolution should not be seen as a simple linear or branched progression, but a mix of related species. In fact, genomic research has shown that hybridization between substantially diverged lineages is the rule, not the exception, in human evolution. Furthermore, it is argued that hybridization was an essential driving force in the emergence of modern humans.

Neanderthals

Genetics

Proportion of admixture

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 (e.g. French, Han Chinese, and Papua New Guinean) than with sub-Saharan African populations (e.g. Yoruba and San). According to 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. They estimated the proportion of Neanderthal-derived ancestry to be 1–4% of the Eurasian genome. Prüfer et al. (2013) estimated the proportion to be 1.5–2.1% for non-Africans, which was revised in 2017 to a higher 1.8–2.6% for non-Africans outside Oceania. Lohse and Frantz (2014) infer a higher rate of 3.4–7.3% in Eurasia. Prüfer et al. (2017) noted that East Asians carry more Neandertal DNA (2.3–2.6%) than Western Eurasians (1.8–2.4%).

Introgressed genome

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.

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. This could possibly be explained by the occurrence of further admixture events in the early ancestors of East Asians after the separation of Europeans and East Asians, dilution of Neanderthal ancestry in Europeans by populations with low Neanderthal ancestry from later migrations, or natural selection that may have been relatively lower in East Asians than in Europeans. Studies simulating admixture models indicate that a reduced efficacy of purifying selection against Neanderthal alleles in East Asians could not account for the greater proportion of Neanderthal ancestry of East Asians, thus favoring more-complex models involving additional pulses of Neanderthal introgression into East Asians. Such models show a pulse to ancestral Eurasians, followed by separation and an additional pulse to ancestral East Asians. It is observed that there is a small but significant variation of Neanderthal admixture rates within European populations, but no significant variation within East Asian populations.

Genomic analysis suggests that there is a global division in Neanderthal introgression between Sub-Saharan African populations and other modern human groups (including North Africans) rather than between African and non-African populations. 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 autochthonous 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 maximal autochthonous 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

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 (Caucasus) than to the Altai Neanderthal (Siberia) or the Vindija Neanderthals (Croatia). By high-coverage sequencing the genome of a 50,000-year-old female Vindija Neanderthal fragment, it was later found that the Vindija and Mezmaiskaya Neanderthals did not seem to differ in the extent of their allele-sharing with modern humans. In this case, it was also found that the Neanderthal component in non-African modern humans is more closely related to the Vindija and Mezmaiskaya Neanderthals than to the Altai Neandertal. These results suggest that a majority of the admixture into modern humans came from Neanderthal populations that had diverged (about 80–100kya) from the Vindija and Mezmaiskaya Neanderthal lineages before the latter two diverged from each other.

Analyzing chromosome 21 of the Altai (Siberia), El Sidrón (Spain), and Vindija (Croatia) Neanderthals, it is determined that—of these three lineages—only the El Sidrón and Vindija Neanderthals display significant rates of gene flow (0.3–2.6%) into modern humans, suggesting that the El Sidrón and Vindija Neanderthals are more closely related than the Altai Neanderthal to the Neanderthals that interbred with modern humans about 47,000–65,000 years ago. Conversely, it is also determined that significant rates of modern human gene flow into Neanderthals occurred—of the three examined lineages—for only the Altai Neanderthal (0.1–2.1%), suggesting that modern human gene flow into Neanderthals mainly took place after the separation of the Altai Neanderthals from the El Sidrón and Vindija Neanderthals that occurred roughly 110,000 years ago. The findings show that the source of modern human gene flow into Neanderthals originated from a population of early modern humans from about 100,000 years ago, predating the out-of-Africa migration of the modern human ancestors of present-day non-Africans.

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.

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.

Reduced contribution

There is a presence of large genomic regions with strongly reduced Neanderthal contribution in modern humans due to negative selection, partly caused by hybrid male infertility. These large regions of low Neanderthal contribution 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.

It has also been shown that Neanderthal ancestry has been selected against in conserved biological pathways, such as RNA processing.

Consistent with the hypothesis that purifying selection has reduced Neanderthal contribution in present-day modern human genomes, Upper Paleolithic Eurasian modern humans (such as the Tianyuan modern human) carry more Neanderthal DNA (about 4–5%) than present-day Eurasian modern humans (about 1–2%).

Rates of selection against Neanderthal sequences varied for European and Asian populations.

Changes in modern humans

In Eurasia, modern humans acquired adaptive introgression 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 have targeted genes involved with keratin filaments, sugar metabolism, muscle contraction, body fat distribution, enamel thickness, 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.

Researchers found Neanderthal introgression of 18 genes—several of which are related to UV-light adaptation—within the chromosome 3p21.31 region (HYAL region) of East Asians. 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. They occur at very high frequencies among East Asian populations in contrast to other Eurasian populations (e.g. European and South Asian populations). The findings also suggests that this Neanderthal introgression occurred within the ancestral population shared by East Asians and Native Americans.

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.

Furthermore, correlating the genotypes of introgressed Neanderthal alleles with the expression of nearby genes, it is found that archaic alleles contribute proportionally more to variation in expression than nonarchaic alleles. Neanderthal alleles affect expression of the immunologically genes OAS1/2/3 and TLR1/6/10, which can be specific to cell-type and is influenced by environmental stimuli.

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 has influence on eating disorders, visceral fat accumulation, rheumatoid arthritis, schizophrenia, as well as the response to antipsychotic drugs.

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.

In Papuans, assimilated Neanderthal inheritance is found in highest frequency in genes expressed in the brain, whereas Denisovan DNA has the highest frequency in genes expressed in bones and other tissues.

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 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. 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. In conjunction with archaeological and fossil evidence, the gene flow is thought likely to have occurred somewhere in Western Eurasia, possibly the Middle East. Through another approach—using one genome each of a Neanderthal, Eurasian, African, and chimpanzee (outgroup), and dividing it into non-recombining short sequence blocks—to estimate genome-wide maximum-likelihood under different models, an ancient population sub-structure in Africa was ruled out and a Neanderthal admixture event was confirmed.

Morphology

The early Upper Paleolithic burial remains of a modern human child from Abrigo do Lagar Velho (Portugal) features traits that indicates 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 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.

The modern human Oase 2 skull (cast depicted), found in Peştera cu Oase, displays archaic traits due to possible hybridization with Neanderthals.

 

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. It displays a lingual bridging of the mandibular foramen, not present in earlier humans except Neanderthals of the late Middle and Late Pleistocene, thus suggesting affinity with Neanderthals. 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.

The earliest (before about 33 ka BP) European modern humans and the subsequent (Middle Upper Paleolithic) Gravettians, falling anatomically largely inline with the earliest (Middle Paleolithic) African modern humans, also show traits that are distinctively Neanderthal, suggesting that a solely Middle Paleolithic modern human ancestry was unlikely for European early modern humans.

A late-Neanderthal jaw (more specifically, a corpus mandibulae remnant) from the Mezzena rockshelter (Monti Lessini, Italy) shows indications of a possible interbreeding in late Italian Neanderthals. The jaw falls within the morphological range of modern humans, but also displayed strong similarities with some of the other Neanderthal specimens, indicating a change in late Neanderthal morphology due to possible interbreeding with modern humans.

The Manot 1, a partial calvaria 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. The morphological features suggest that the Manot population may be closely related or given rise to the first modern humans who later successfully colonized Europe to establish early Upper Palaeolithic populations.

History

The interbreeding has been discussed ever since the discovery of Neanderthal remains in the 19th century, though earlier writers believed that Neanderthals were a direct ancestor of modern humans. Thomas Huxley suggested that many Europeans bore traces of Neanderthal ancestry, but associated Neanderthal characteristics with primitivism, writing that since they "belong to a stage in the development of the human species, antecedent to the differentiation of any of the existing races, we may expect to find them in the lowest of these races, all over the world, and in the early stages of all races".

Hans Peder Steensby in the 1907 article Racestudier i Danmark ("Race studies in Denmark") rejected that Neanderthals were ape-like or inferior, and, while emphasizing that all modern humans are of mixed origins, suggested interbreeding as the best available explanation of a significant number of observations which by then were available.

In the early twentieth century, Carleton Coon argued that the Caucasoid race is of dual origin consisting of Upper Paleolithic (mixture of H. sapiens and H. neanderthalensis) types and Mediterranean (purely H. sapiens) types. He repeated his theory in his 1962 book The Origin of Races.

Denisovans

Genetics

The Denisovan genome was sequenced from the distal manual phalanx fragment (replica depicted) found in the Denisova cave.

Proportion of admixture

It has been shown that Melanesians (e.g. Papua New Guinean and Bougainville Islander) share relatively more alleles with Denisovans when compared to other Eurasians and Africans. It estimated that 4% to 6% of the genome in Melanesians derives from Denisovans, while no other Eurasians or Africans displayed contributions of the Denisovan genes. It has been observed that Denisovans contributed genes to Melanesians but not to East Asians, indicating that there was interaction between the early ancestors of Melanesians with Denisovans but that this interaction did not take place in the regions near southern Siberia, where as-of-yet the only Denisovan remains have been found. In addition, Aboriginal Australians also show a relative increased allele sharing with Denisovans, compared to other Eurasians and African populations, consistent with the hypothesis of increased admixture between Denisovans and Melanesians.

Reich et al. (2011) produced evidence that the highest presence of Denisovan admixture is in Oceanian populations, followed by many Southeast Asian populations, and none in East Asian populations. There is significant Denisovan genetic material in eastern Southeast Asian and Oceanian populations (e.g. Aboriginal Australians, Near Oceanians, Polynesians, Fijians, eastern Indonesians, Philippine Mamanwa and Manobo), but not in certain western and continental Southeast Asian populations (e.g. western Indonesians, Malaysian Jehai, Andaman Onge, and mainland Asians), indicating that the Denisovan admixture event happened in Southeast Asia itself rather than mainland Eurasia. 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. In contrast, Prüfer et al. (2013) found that mainland Asian and Native American populations may have a 0.2% Denisovan contribution, which is about twenty-five times lower than Oceanian populations. The manner of gene flow to these populations remains unknown. However, Wall et al. (2013) stated that they found no evidence for Denisovan admixture in East Asians.

Findings indicate that the Denisovan gene flow event happened to the common ancestors of Aboriginal Filipinos, Aboriginal Australians, and New Guineans. 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. It has also been observed that the fraction of Near Oceanian ancestry in Southeast Asians is proportional to the Denisovan admixture, except in the Philippines where there is a higher proportional Denisovan admixture to Near Oceanian ancestry. Reich et al. (2011) suggested a possible model of an early eastward migration wave of modern humans, some who were Philippine/New Guinean/Australian common ancestors that interbred with Denisovans, respectively followed by divergence of the Philippine early ancestors, interbreeding between the New Guinean and Australian early ancestors with a part of the same early-migration population that did not experience Denisovan gene flow, and interbreeding between the Philippine early ancestors with a part of the population from a much-later eastward migration wave (the other part of the migrating population would become East Asians).

Finding components of Denisovan introgression with differing relatedness to the sequenced Denisovan, Browning et al. (2018) suggested that at least two separate episodes of Denisovan admixture has occurred. Specifically, introgression from two distinct Denisovan populations is observed in East Asians (e.g. Japanese and Han Chinese), whereas South Asians (e.g. Telugu and Punjabi) and Oceanians (e.g. Papuans) display introgression from one Denisovan population.

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). The researchers also made the surprising finding that South Asian populations display an elevated Denisovan admixture (when compared to other non-Oceanian populations with Denisovan ancestry), albeit the highest estimate (which are found in Sherpas) is still ten times lower than in Papuans. They suggest two possible explanations: There was a single Denisovan introgression event that was followed by dilution to different extents or at least three distinct pulses of Denisovan introgressions must have occurred.

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. The lack of a Denisovan component in the Tianyuan individual suggests that the genetic contribution had been always scarce in the mainland.

Reduced contribution

There are large genomic regions devoid of Denisovan-derived ancestry, partly explained by infertility of male hybrids, as suggested by the lower proportion of Denisovan-derived ancestry on X chromosomes and in genes that are expressed in the testes of modern humans.

Changes in modern humans

Exploring the immune system's HLA alleles, it has been suggested that HLA-B*73 introgressed from Denisovans into modern humans in western Asia due to the distribution pattern and divergence of HLA-B*73 from other HLA alleles. Even though HLA-B*73 is not present in the sequenced Denisovan genome, HLA-B*73 was shown to be closely associated to the Denisovan-derived HLA-C*15:05 from the linkage disequilibrium. From phylogenetic analysis, however, it has been concluded that it is highly likely that HLA-B*73 was ancestral.

The Denisovan's two HLA-A (A*02 and A*11) and two HLA-C (C*15 and C*12:02) allotypes correspond to common alleles in modern humans, whereas one of the Denisovan's HLA-B allotype corresponds to a rare recombinant allele and the other is absent in modern humans. 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.

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 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 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.

From three candidate regions with introgression found by searching for unusual patterns of variations (showing deep haplotype divergence, unusual patterns of linkage disequilibrium, and small basal clade size) in 61 non-coding regions from two hunter-gatherer groups (Biaka Pygmies and San who have significant admixture) and one West African agricultural group (Mandinka, who don't have significant admixture), it is concluded that roughly 2% of the genetic material found in the Biaka Pygmies and San was inserted into the human genome approximately 35,000 years ago from archaic hominins that separated from the ancestors of the modern human lineage around 700,000 years ago. A survey for the introgressive haplotypes across many Sub-Saharan populations suggest that this admixture event happened with archaic hominins who once inhabited Central Africa.

Researching high-coverage whole-genome sequences of fifteen Sub-Saharan hunter-gatherer males from three groups—five Pygmies (three Baka, a Bedzan, and a Bakola) from Cameroon, five Hadza from Tanzania, and five Sandawe from Tanzania—there are signs that the ancestors of the hunter-gatherers interbred with one or more archaic human populations, probably over 40,000 years ago. Analysis of putative introgressive haplotypes in the fifteen hunter-gatherer samples suggests that the archaic African population and modern humans diverged around 1.2 to 1.3 million years ago.

Xu et al. (2017) analyzed the evolution of the Mucin 7 protein in the saliva of modern humans and found evidence that an unidentified ghost population of archaic African humans may have contributed DNA, with an estimated coalescence time to modern humans of about 4.5 million years BP, into the gene pool of modern Africans (e.g. African-American, African-Caribbean, Esan, Gambian, Luhya, Mende, and Yoruba people).

Related studies

In February 2019, scientists discovered evidence, based on genetics studies using artificial intelligence (AI), that suggest the existence of an unknown human ancestor species, not Neanderthal, Denisovan or human hybrid (like Denny), in the genome of modern humans.

Campanian Ignimbrite eruption

From Wikipedia, the free encyclopedia

Campanian Ignimbrite Eruption
Volcano	Phlegraean Fields
Date	around 39,000 years ago
Type	Plinian eruption
Location	Naples, Campania, Italy 40.827°N 14.139°ECoordinates: 40.827°N 14.139°E
VEI	7
Phlegraean Fields Location of eruption

The Campanian Ignimbrite eruption (CI, also CI Super-eruption) was a major volcanic eruption in the Mediterranean during the late Quaternary, classified at 7 on the Volcanic Explosivity Index (VEI). The event has been attributed to the Archiflegreo volcano, the 13-kilometre-wide (8.1 mi) caldera of the Phlegraean Fields, located 20 km (12 mi) west of Mount Vesuvius under the western outskirts of the city of Naples and the Gulf of Pozzuoli, Italy. Estimates of the date, magnitude and the amount of ejected material have varied considerably during several centuries of investigation. This applies to most significant volcanic events that originated in the Campanian Plain, as it is one of the most complex volcanic structures in the world. However, continued research, advancing methods and accumulation of volcanological, geochronological, and geochemical data has amounted to ever more precise dating.

The most recent dating determines the eruption event at 39,280±110 years BP and results of 3D Ash Dispersion Modelling published in 2012 concluded a dense-rock equivalent (DRE) of 300 km³ (72 cu mi) and emissions dispersed over an area of around 3,700,000 km² (1,400,000 sq mi). The accuracy of these numbers is of significance for marine geologists, climatologists, palaeontologists, paleo-anthropologists and researchers of related fields as the event coincides with a number of global and local phenomena, such as widespread discontinuities in archaeological sequences, climatic oscillations and biocultural modifications.

Etymology

The term Campanian refers to the Campanian volcanic arc located mostly but not exclusively in the region of Campania in southern Italy that stretches over a subduction zone created by the convergence of the African and Eurasian plates. It should not be confused with the Late Cretaceous stage Campanian. 

The word ignimbrite was made by New Zealand geologist Patrick Marshall from Latin ignis (fire) and imber (shower)) and -ite. It means the deposits that form as a result of a pyroclastic eruption.

Background

Solfatara Pozzuoli

 

The Phlegraean Fields (Italian: Campi Flegrei "burning fields") caldera is a nested structure with a diameter of around 13 km (8.1 mi). It is composed of the older Campanian Ignimbrite caldera, the younger Neapolitan Yellow Tuff caldera and widely scattered sub-aerial and submarine vents from which the most recent eruptions have originated. The Fields sit upon a Pliocene - Quaternary Extensional domain with faults, that run North-East to South-West and North-West to South-East from the margin of the Apennine thrust belt. The sequence of deformation has been subdivided into three periods.

Phlegraean Periods

• The First Period, which includes the Campanian Ignimbrite Eruption was the most decisive era in the Phlegraean Fields' geologic history. Beginning more than 40,000 years ago as the external caldera formed, subsequent caldera collapses and repeated volcanic activity took place within a limited area.
• During the Second Period, the smaller Neapolitan Yellow Tuff eruption (Neapolitan Yellow Tuff or NYT) took place around 15,000 years ago.
• Eruptions of the Third Period occurred during three intervals between 15,000 and 9500 years ago, 8600 and 8200 years ago and from 4800 to 3800 years ago.

The structure's magma chamber remains active as there apparently are solfataras, hot springs, gas emissions and frequent episodes of large-scale up- and downlift ground deformation (Bradyseism) do occur.

In 2008 it was discovered that the Phlegraean Fields and Mount Vesuvius have a common magma chamber at a depth of 10 km (6.2 mi).

The region's volcanic nature has been recognized since Antiquity, investigated and studied for many centuries. Methodical scientific research began in the late 19th century. The yellow tuff stone was extensively quarried for centuries, which left large underground cavities that served as aqueducts and cisterns for the collection of rain water.

In 2016 Italian Volcanologists announced plans to drill a probe 1.9 mi (3.1 km) deep into the Phlegraean Fields several years after the 2008 Campi Flegrei Deep Drilling Project which had aimed to drill a 3.5 km (2.2 mi) diagonal borehole in order to bring up rock samples and install seismic equipment. The project was suspended in 2010 due to safety problems.

Eruptive sequence

Diagram of a Plinian eruption. (key: 1. Ash plume 2. Magma conduit 3. Volcanic ash rain 4. Layers of lava and ash 5. Stratum 6. Magma chamber)

 

The CI eruption has been interpreted as the largest volcanic eruption of the past 200,000 years in Europe. Tephra deposits indicate two distinct plume forming phases, a Plinian and a co-ignimbrite, characterized by multiple caldera-forming eruptions.

Plinian phase

Evidence shows that the eruption was a single event lasting 2 to 4 days. It was triggered by abrupt changes in composition, properties and physical state in the melt or overpressure in the magma chamber. The eruption started with phreatomagmatic explosions, followed by a Plinian eruption column, fed by simultaneous extraction of two magma layers. The resulting ash plume is estimated to have been 70 km (43 mi) high. As gradually an unstable pulsating column formed, fed only by the most evolved magma due to upward migration of the fragmentation surface, reduced magma eruption rate, and/or activation of fractures, the Plinian phase ended. Emissions consisted of pumice and dark colored volcanic rock (scoria). The mafic minerals cover smaller areas than the more acidic members, also indicating a decrease of explosivity over the course of the eruption. The eruption column caused a large pumice-fall deposit to the east of the source area.

Pyroclastic density currents

Pyroclastic flow

 

The initial eruption was followed by a caldera collapse and a large pyroclastic flow, fed by the upper magma layer, a single flow unit with lateral variations in both pumice and lithic fragments, that covered an area of 30,000 km² (12,000 sq mi). Currents that moved toward the North and the South overflowed 1,000-metre-high (3,300 ft) mountain ranges and crossed the Gulf of Naples over the sea, extinguishing all life within a radius of about 100 km (62 mi). Textural and morphological features of the deposits, and areal distribution suggests that the eruption was of the type of highly expanded low-temperature pyroclastic cloud. 

The pyroclastic sequence from base to top:

• densely welded ignimbrite and lithic-rich breccias
• sintered ignimbrite, low-grade ignimbrite and lithic-rich breccia
• lithic-rich breccia and spatter agglutinate
• low-grade ignimbrite

Ignimbrite deposit

Ignimbrite

The ignimbrite is a gray, poorly to moderately welded, nearly saturated potassic trachyte, similar to many other trachytes of the Quaternary volcanic province of Campania. It consists of pumice and lithic fragments in a devitrified matrix that contains sanidine, lesser plagioclase rimmed by sanidine, two clinopyroxenes, biotite, and magnetite. The column collapse that generated the widespread ignimbrite deposit most likely occurred due to an increase of the Mass Eruption Rate (MER).

The immediate area was completely buried by thick layers of pyroclastic fragments, volcanic blocks, lapilli and ash. Two thirds of Campania sank under an up to 100 m (330 ft) thick layer of tuff. The greater ignimbrite deposit, mostly trachytic ash and pumice, covered an area of at least 7,000 km² (2,700 sq mi), encompassing most of the southern Italian peninsula and the eastern Mediterranean region.

Calculations of ash thickness measurements collected at 115 sites and a three dimensional ash dispersal model add up to a total amount of fallout material of 300 km³ of tephra across an area of 3,700,000 km² (1,400,000 sq mi). Considering volume estimations of up to 300 km³ (72 cu mi) for the proximal pyroclastic density current deposits, the total bulk volume of the CI eruption is 680 km³ (160 cu mi) covering most of the eastern Mediterranean and ash clouds reaching as far as central Russia.

Global impact

Graphic of deposit dispersal during the eruption

 

The event's recent dating at 39,280±110 years ago draws considerable scholarly attention as it marks a time interval characterized by biocultural modifications in western Eurasia and widespread discontinuities in archaeological sequences, such as the Middle to Upper Palaeolithic transition. At several archaeological sites of South-eastern Europe, the ash separates the cultural layers containing Middle Palaeolithic and/or Earliest Upper Palaeolithic assemblages from the layers in which Upper Palaeolithic industries occur. At some sites the CI tephra deposit coincides with a long interruption of paleo-human occupation.

Effect on climate

The climatic importance of the eruption was tested in a three-dimensional sectional aerosol model that simulated the global aerosol cloud under glacial conditions. Authors calculate that up to 450 million kilograms (990 million pounds) of sulphur dioxide would have been accumulated into the atmosphere, driving down temperatures at least by 1 to 2 degrees Celsius (1.8-3.6 degrees Fahrenheit) for a period of 2 to 3 years. The Heinrich event 4 (H4), the name given to a cooling period, characterized by a break off of unusual large sections of ice from polar glaciers occurred around 40,000 years ago being well documented in the North Atlantic Ocean, although its impact on terrestrial areas is a matter of ongoing debate.

Effect on living organisms

Sulphur dioxide and chloride emissions caused acidic rains, fluorine-laden particles become incorporated into plant matter, potentially inducing dental fluorosis, replete with eye, lung and organ damage in animal populations.

Neanderthal demise

The eruption coincided also with the final decline of the Neanderthal in Europe. Environmental stress caused by the eruption has been invoked as a potential explanation for the extinction as well as discontinuities in Palaeolithic societies, although the climatic effects of the eruption alone are considered insufficient to account for the demise of the Neanderthals in Europe. The notion remains contested; nonetheless, some studies suggest that significant volcanic cooling during the period immediately after the eruption might have severely disturbed these already precarious populations.

Island biodiversity

Ice age Earth

 

A joint study on the influence of the Late Quaternary climate change on island biodiversity has been published in 2016 in the Nature journal. This investigation on the consequences of abrupt climate changes for island biodiversity is apparently unprecedented. Established "island biogeographical models consider islands either as geologically static with biodiversity resulting from ecologically neutral immigration–extinction dynamics, or as geologically dynamic with biodiversity resulting from immigration–speciation–extinction dynamics influenced by changes in island characteristics over millions of years." Researchers argue that "climatic oscillations over short geological periods are likely to affect sea levels and cause huge changes in island size, isolation and connectivity, orders of magnitude faster than the geological processes of island formation..." Results suggest that "post-Last Glacial Maximum (LGM) changes in island characteristics, especially in area, have left a strong imprint on the present diversity of endemic species."

Laschamp event

In 2012 the GFZ German Research Centre for Geosciences has published a study on likely causal connections between the Laschamp magnetic reversal and the eruption as "sediment cores from the Black Sea show that during this period, a compass at the Black Sea would have pointed to the south instead of north." Evidence seems to be limited and the publication is no longer publicly available.

Denisovan (updated)

From Wikipedia, the free encyclopedia

The evolution and geographic spread of Denisovans as compared with Neanderthals, Homo heidelbergensis and Homo erectus.

 

The Denisovans or Denisova hominins ( /dɪˈniːsəvə/ di-NEE-sə-və) are an extinct species or subspecies of archaic humans in the genus Homo. Pending its taxonomic status, it currently carries temporary species or subspecies names Homo denisova, Homo altaiensis, Homo sapiens denisova, or Homo sp. Altai. In 2010, scientists announced the discovery of an undated finger bone fragment of a juvenile female found in the Denisova Cave in the Altai Mountains in Siberia, a cave that has also been inhabited by Neanderthals and modern humans. The mitochondrial DNA (mtDNA) of the finger bone showed it to be genetically distinct from Neanderthals and modern humans. The nuclear genome from this specimen suggested that Denisovans shared a common origin with Neanderthals, that they ranged from Siberia to Southeast Asia, and that they lived among and interbred with the ancestors of some modern humans, with about 3% to 5% of the DNA of Melanesians and Aboriginal Australians and around 6% in Papuans deriving from Denisovans. Several additional specimens were subsequently discovered and characterized.

A comparison with the genome of another Neanderthal from the Denisova cave revealed local interbreeding with local Neanderthal DNA representing 17% of the Denisovan genome, and evidence of interbreeding with an as yet unidentified ancient human lineage, while an unexpected degree of mtDNA divergence among Denisovans was detected.

The lineage that developed into Denisovans and Neanderthals is estimated to have separated from the lineage that developed into "anatomically modern" Homo sapiens approximately 600,000 to 744,000 years ago. Denisovans and Neanderthals then significantly diverged from each other genetically a mere 300 generations after that. Several types of humans, including Denisovans, Neanderthals and related hybrids, may have each dwelt in the Denisova Cave in Siberia over thousands of years, but it is unclear whether they ever co-habitated in the cave.

Discovery

Denisova Cave

Location of Denisova Cave in the Altai Mountains of Siberia

 

The Denisova Cave, where the "X woman" was found

 

The Denisova Cave is in south-western Siberia, Russia in the Altai Mountains near the border with Kazakhstan, China and Mongolia. It is named after Denis, a Russian hermit who lived there in the 18th century. The cave was originally explored in the 1970s by Russian paleontologist Nikolai Ovodov, who was looking for remains of canids. In 2008, Michael Shunkov from the Russian Academy of Sciences and other Russian archaeologists from the Institute of Archaeology and Ethnology of Novosibirsk investigated the cave. They found the finger bone of a juvenile hominin, originally referred to as the "X woman" (referring to the maternal descent of mtDNA), or the Denisova hominin. Artifacts (including a bracelet) excavated in the cave at the same level were dated using radiocarbon and oxygen isotopes to around 40,000 BP. Excavations have since revealed human artifacts showing an intermittent presence going back 125,000 years.

A team of scientists led by Johannes Krause and Svante Pääbo from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, sequenced mtDNA extracted from the fragment. The cool climate of the Denisova Cave preserved the DNA. The average annual temperature of the cave is 0 °C, which has contributed to the preservation of archaic DNA among the remains discovered. The analysis indicated that the Denisova hominin "diverged from a common ancestor well before Neanderthals and modern humans did"—around 1 million years ago.

The mtDNA analysis further suggested that this new hominin species was the result of an earlier migration out of Africa, distinct from the later out-of-Africa migrations associated with modern humans, but also distinct from the even earlier African exodus of Homo erectus. Pääbo noted that the existence of this distant branch creates a much more complex picture of humankind during the Late Pleistocene. This work shows that the Denisovans were actually a sister group to the Neanderthals, branching off from the human lineage 550,000 years ago, and diverging from Neanderthals, probably in the Middle East, 300,000 years ago.

A second paper from the Svante Pääbo group reported the prior discovery of a third upper molar from a young adult, dating from about the same time (the finger was from level 11 in the cave sequence, the tooth from level 11.1). The tooth differed in several aspects from those of Neanderthals, while having archaic characteristics similar to the teeth of Homo erectus. They performed mtDNA analysis on the tooth and found it to have a sequence somewhat similar to that of the finger bone, indicating a divergence time about 7,500 years before, and suggesting that it belonged to a different individual from the same population.

Fossils

So far, the fossils of four distinct Denisovans from Denisova Cave have been identified through their DNA: Denisova 2, Denisova 3, Denisova 4, and Denisova 8. Analysis of a fifth specimen, Denisova 11, proved it to have belonged to an F1 Denisovan-Neanderthal hybrid. Denisova 2 and Denisova 3 are prepubescent or adolescent females, while Denisova 4 and Denisova 8 are adult males. mtDNA analysis of the Denisovan individuals suggests the Denisova 2 fossil is the oldest, followed by Denisova 8, while Denisova 3 and Denisova 4 are roughly contemporaneous.

During DNA sequencing, a low proportion of the Denisova 2, Denisova 4 and Denisova 8 genomes were found to have survived, but a high proportion of the Denisova 3 genome had survived.

Anatomy

Little is known of the precise anatomical features of the Denisovans, since the only physical remains discovered thus far are the finger bone, two teeth from which genetic material has been gathered, and a toe bone. The single finger bone is unusually broad and robust, well outside the variation seen in modern people. It belonged to a female, indicating that the Denisovans were extremely robust, perhaps similar in build to the Neanderthals. The tooth does not share the derived morphological features seen in Neanderthal or modern human teeth. An initial morphological characterization of the toe bone led to the suggestion that it may have belonged to a Neanderthal-Denisovan hybrid individual, although a critic suggested that the morphology was inconclusive. This toe bone's DNA was analyzed by Pääbo. After looking at the full genome, Pääbo and others confirmed that humans produced hybrids with Denisovans.

Some older findings may or may not belong to the Denisovan line. These include the skulls from Dali and Maba, and a number of more fragmentary remains from Asia. Asia is not well mapped with regard to human evolution, and the above finds may represent a group of "Asian Neanderthals".

Mitochondrial DNA analysis

The mitochondrial DNA (mtDNA) from the finger bone discovered in Denisova Cave differs from that of modern humans by 385 bases (nucleotides) out of approximately 16,500, whereas the difference between modern humans and Neanderthals is around 202 bases. In contrast, the difference between chimpanzees and modern humans is approximately 1,462 mtDNA base pairs. This suggested a divergence time around one million years ago. The more divergent Denisovan mtDNA has been interpreted as evidence of admixture between Denisovans and an unknown archaic population. Studies suggest that a population related to modern humans contributed mtDNA to the Neanderthal lineage, but not to the Denisovan mitochondrial genomes yet sequenced. It has suggested the species could be Homo heidelbergensis, but that species is now generally considered to be too closely related to the Neanderthals. That it could have been a Homo erectus-like introgression into the Denisovans about 53,000 years ago that is responsible for the anomalously-divergent mtDNA has also been proposed.

The mtDNA from a tooth bore a high similarity to that of the finger bone, indicating that they belonged to the same population. From a second tooth, an mtDNA sequence was recovered that showed an unexpectedly large number of genetic differences compared to that found in the other tooth and the finger, suggesting a high degree of mtDNA diversity. These two individuals from the same cave showed more diversity than seen among sampled Neanderthals from all of Eurasia, and were as different as modern-day humans from different continents.

Nuclear genome analysis

The isolation and sequencing of nuclear DNA from the Denisova finger bone revealed an unusual degree of DNA preservation with only low-level contamination, allowing near-complete genomic sequencing and detailed comparison with the genomes of Neanderthals and modern humans. Despite the apparent divergence of their mitochondrial sequence, the Denisova population share a common branch with Neanderthals, with a more distant split from the lineage leading to modern African humans. The Denisovan and Neanderthal sequences were estimated to have diverged about 640,000 years ago, with divergence of the branch leading to these groups from modern Africans dating to about 800,000 years ago. The authors of the study speculated that the anomalous more-divergent Denisovan mtDNA resulted either from the persistence of an ancient mtDNA lineage purged from the other branches of humanity through genetic drift or else an introgression from an older hominin lineage.

The mtDNA sequence from the femur of a 400,000-year-old Homo heidelbergensis from the Sima de los Huesos cave in Spain was found to be related to those of Neanderthals and Denisovans, but closer to the latter. Analysis of nuclear DNA sequences from two specimens showed they were more closely related to Neanderthals rather than to Denisovans, yet one of these samples also had the Denisovan-related mtDNA. The studies' authors posited that the mtDNA found in these specimens represents an archaic sequence indicative of Neanderthal's kinship with Denisovans that was subsequently lost in Neanderthals due to replacement by modern-human-related sequence.

Epigenetics

An analysis of the natural degradation processes of ancient DNA, which differs between methylated and unmethylated cytosines, has provided insight into Denisovan and Neanderthal epigenetics. Because changes in cytosine methylation are correlated with gene regulation, the full DNA methylation maps allowed an assessment of gene activity throughout the Denisovan genome, as compared to that of modern humans and Neanderthals. About 200 genes were identified that show distinct regulatory patterns in Denisovans.

Interbreeding

A detailed comparison of the Denisovan, Neanderthal, and modern human genomes has revealed evidence for a complex web of interbreeding among the lineages. Through such interbreeding, 17% of the Denisova genome represents DNA from the local Neanderthal population, while evidence was also found of a contribution to the nuclear genome from an ancient hominin lineage yet to be identified, perhaps the source of the anomalously ancient mtDNA. DNA from this unidentified but highly archaic species that diverged from other populations over a million years ago represents as much as 8% of the Altai Denisovan genome. The only widespread remains of archaic humans in the Late Pleistocene Asian region are from Homo Erectus, although East Asian variants such as Dali Man have Neanderthal characteristics. The Denisovan genome shared more derived alleles with the Altai Neanderthal genome from Siberia than with the Vindija cave Neanderthal genome from Croatia and the Mezmaiskaya cave Neanderthal genome from the Caucasus, suggesting that the gene flow came from a population that was more closely related to the Altai Neanderthal. The web of archaic human intermixing is highlighted by the genome from a 90,000-year-old bone fragment from the Denisova cave, found to have belonged to a Denisovan-Neanderthal hybrid female. Her Denisovan father had the typical Altai Neanderthal introgression, while her Neanderthal mother represented a population more closely related to Vindija Neanderthals than to those of Altai.

Analysis of genomes of modern humans show that they mated with at least two groups of archaic humans: Neanderthals (more similar to those found in the Caucasus than those from the Altai region) and Denisovans, and that such interbreedings occurred on multiple occasions. Approximately 1–4% of the DNA of non-African modern humans is shared with Neanderthals as a result of interbreeding. Tests comparing the Denisova hominin genome with those of six modern humans – a ǃKung from South Africa, a Nigerian, a Frenchman, a Papua New Guinean, a Bougainville Islander and a Han Chinese – showed that between 4 and 6% of the genome of Melanesians (represented by the Papua New Guinean and Bougainville Islander) derives from a Denisovan population; a later study puts the amount at 1.11% (with an additional contribution from some different and yet unknown ancestor). This DNA was possibly introduced during the early migration to Melanesia. These findings are in concordance with the results of other comparison tests which show a relative increase in allele sharing between the Denisovan and the Aboriginal Australian genome, compared to other Eurasians and African populations; however, Papuans, the population of Papua New Guinea, have more allele sharing than Aboriginal Australians.

Melanesians are not the only modern-day descendants of Denisovans. David Reich of Harvard University and Mark Stoneking of the Planck Institute team found genetic evidence that Denisovan ancestry is shared also by Australian Aborigines, and smaller scattered groups of people in Southeast Asia, such as the Mamanwa, a Negrito people in the Philippines, though not all Negritos were found to possess Denisovan genes; Onge Andaman Islanders and Malaysian Jehai, for example, were found to have no significant Denisovan inheritance. This suggests that interbreeding occurred in mainland South-East Asia, and that Denisovans once ranged widely over eastern Asia. Based on the modern distribution of Denisova DNA, Denisovans may have crossed the Wallace Line, with Wallacea serving as their last refugium. Small amounts of Denisovan DNA, representing around 0.2% Denisovan ancestry, are also found in mainland Asians and Native Americans.

Statistical analysis of genomic DNA sequences from different Asian populations indicates that at least two distinct populations of Denisovans existed, and that a second introgression event from Denisovans into humans occurred. A study of Han Chinese, Japanese and Dai genomes revealed that modern East Asian populations include two Denisovan DNA components: one similar to the Denisovan DNA found in Papuan genomes, and a second that is closer to the Denisovan genome from the Altai cave. These components were interpreted as representing separate introgression events involving two divergent Denisovan populations. South Asians were found to have levels of Denisovan admixture similar to that seen in East Asians, but this DNA only came from the same single Denisovan introgression seen in Papuans. Though there is no genomic evidence to support the hypothesis, the Red Deer Cave people of China have been suggested to have been the result of interbreeding between Homo sapiens and Denisovans within a few thousands years of the end of the last glacial period.

The immune system's HLA alleles have drawn particular attention in the attempt to identify genes that may derive from archaic human populations. Although not present in the sequenced Denisova genome, the distribution pattern and divergence of HLA-B*73 from other HLA alleles has led to the suggestion that it introgressed from Denisovans into humans in west Asia. As of 2011, half of the HLA alleles of modern Eurasians represent archaic HLA haplotypes, and have been inferred to be of Denisovan or Neanderthal origin. The apparent over-representation of these alleles suggests a positive selective pressure for their retention in the human population. A higher-quality Denisovan genome published in 2012 reveals variants of genes in humans that are associated with dark skin, brown hair, and brown eyes – consistent with features found with Melanesians today. The Denisovan genome also contains a variant region around the EPAS1 gene that in Tibetans assists with adaptation to low oxygen levels at high altitude. In Papuans, introgressed Neanderthal alleles have highest frequency in genes expressed in the brain, whereas Denisovan alleles have highest frequency in genes expressed in bones and other tissues.