Archaic human admixture with modern humans

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Model of the geographic distribution of species in the genus Homo over the last 2 million years. The horizontal axis represents geographic location; the vertical axis represents time in millions of years ago. Blue areas denote the presence of a certain species at a given time and place. Early modern humans spread from Africa across different regions of the globe and interbred with other descendants of Homo heidelbergensis, namely Neanderthals, Denisovans, and unknown archaic African hominins (top right).[1]

Archaic human admixture with modern humans is thought to have taken place through interbreeding between anatomically modern humans and Neanderthals, Denisovans, or possibly other archaic humans over the course of human history. Neanderthal-derived DNA accounts for an estimated 1–4% of the Eurasian genome, but it is significantly absent or uncommon in the genome of most groups in Sub-Saharan Africa. In Oceanian and Southeast Asian populations, there is a relative increase of Denisovan-derived DNA. An estimated 4–6% of the Melanesian genome is derived from Denisovans. Recent non-comparative DNA analyses—as no specimens have been discovered—suggest that modern West African populations have a genetic contribution from a now-extinct archaic African hominin lineage.

Some researchers have expressed doubts about the recent admixture events. Ancient subpopulation structure ancestral to modern humans, Neanderthals, Denisovans, and other possible archaic humans has been proposed as an alternative explanation for the observed genetic similarities.

Neanderthals

Genetics

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See also: Neanderthal genome project

Through whole-genome sequencing, a draft sequence of the Neanderthal genome 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).[2] 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.[2] The proportion of Neanderthal-derived ancestry was estimated to be 1–4% of the Eurasian genome.[2] Prüfer et al. (2013) revised the proportion to an estimated 1.5–2.1%,[3] but Lohse and Frantz (2014) infer an even higher rate of 3.4–7.3%.[4] Furthermore, 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).[3] About 20% of the Neanderthal genome has been found introgressed in the modern human population (by analyzing East Asians and Europeans),[5] but the figure has also been estimated at one-third.[6]

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.[2] 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.[7] On the basis of linkage disequilibrium patterns, a recent admixture event is likewise confirmed by the data.[8] 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.[8] In conjunction with archaeological and fossil evidence, the gene flow is thought likely to have occurred somewhere in Western Eurasia, possibly the Middle East.[8] 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 firmly ruled out and a Neanderthal admixture event was confirmed.[4]

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.[9] 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.[9] 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.[9]

Recent studies show a higher Neanderthal admixture in East Asians than in Europeans,[5][10][11][12][13] which is estimated to be about 20% more introgression into East Asians.[5][10][13] 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,[5][10][11][13] dilution of Neanderthal ancestry in Europeans by populations with low Neanderthal ancestry from later migrations,[10][13] or natural selection that may have been relatively lower in East Asians than in Europeans.[12][13] Studies 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.[14][15] It has also been observed that there's a small but significant variation of Neanderthal admixture rates within European populations, but no significant variation within East Asian populations.[5]

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.[16] 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.[17] 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%).[18] 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.[19] The Neanderthal-linked haplotype B006 of the dystrophin gene has also been found among nomad pastoralist groups in the Sahel and Horn of Africa, who are associated with northern populations. Consequently, the presence of this B006 haplotype on the northern and northeastern perimeter of Sub-Saharan Africa is attributed to gene flow from a non-African point of origin.[20] Low but significant rates of Neanderthal admixture has also been observed for the Maasai of East Africa.[21] 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.[11]

No evidence of Neanderthal mitochondrial DNA has been found in modern humans.[22][23][24] This would suggest that successful admixture with Neanderthals happened paternally rather than maternally on the side of Neanderthals.[25][26] Possible hypotheses are that Neanderthal mtDNA 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.[25] A 2012 study produced a model which demonstrated exponential growth is compatible with the survival of a single mtDNA or Y chromosome lineage only if the growth rate is in a narrow supercritical interval. Thus, even if Neanderthals and anatomically modern Africans belonged to the same interbreeding population and even if this population was allowed to grow exponentially with a small rate, the more probable outcome would still be all humans being descendants either of a single woman (mtDNA) or a single man (Y chromosome). The model estimated in only 7% the probability that humans could have either mtDNA or Y chromosome of a Neanderthal origin. Whereas there was a 93% probability for the lack of Neanderthal mtDNA in modern humans.[27]

It has been found that there's a presence of large genomic regions with strongly reduced Neanderthal contribution in modern humans due to negative selection,[5][12] partly caused by hybrid male infertility.[12] These large regions of low Neanderthal contribution were most-pronounced on the X chromosome—with fivefold lower Neanderthal ancestry compared to autosomes—and contained relatively high numbers of genes specific to testes, meaning that modern humans have relatively few Neanderthal genes that are located on the X chromosome or expressed in the testes, consistent with the fact that male infertility is affected by a disproportionately large amount of genes on X chromosomes.[12] It has also been shown that Neanderthal ancestry has been selected against in conserved biological pathways, such as RNA processing.[12]

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.[5][12] 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.[12]

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.[28] 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.[28] They occur at very high frequencies among East Asian populations in contrast to other Eurasian populations (e.g. European and South Asian populations).[28] The findings also suggests that this Neanderthal introgression occurred within the ancestral population shared by East Asians and Native Americans.[28]

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.[29] 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.[29] The high frequency of the D haplogroup (70%) suggest that it was positively selected for in modern humans.[29] 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.[29] 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.[30] Green et al. (2010), having analyzed the Vindija Neanderthals, also could not confirm a Neanderthal origin of haplogroup D of the microcephalin gene.[2]

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.[31] 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.[31]

It has been found that introgressed Neanderthal genes exhibit cis-regulatory effects in modern humans, contributing to the genomic complexity and phenotype variation of modern humans.[32] 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.[32] In the brain, this was most pronounced at the cerebellum and basal ganglia.[32] This downregulation suggests that modern humans and Neanderthals possibly experienced a relative higher rate of divergence in these specific tissues.[32]

Morphology

The early Upper Paleolithic burial remains of a modern human child from Abrigo do Lagar Velho (Portugal) features traits that indicates Neanderthal admixtures with modern humans dispersing into Iberia.[33] 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.[33]

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' admixture with Neanderthals rather than a full replacement of Neanderthals.[34] 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.[34]

Oase 2 skull, Peștera cu Oase, Romania

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.[35] 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.[35] 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.[35]

File:Comparison of hybrid human skulls.png
Skulls of modern human, Neanderthal, and two possible hybrids

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.[36]

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.[37] 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.[37]

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.[38] 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.[38] 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.[38]

History

The hypothesis, variously under the names of interbreeding, hybridization, admixture or hybrid-origin theory, 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".[39]

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.[40]

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.[41]

Denisovans

Denisovan DNA has been found in modern humans, and it has been estimated that 90% of the Denisovan genome is still present.[6] 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.[42] 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.[42] 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.[42] 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.[43]

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.[44] 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.[44] 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).[45]

Skoglund and Jakobsson (2011) observed that particularly Oceanians, followed by Southeast Asians populations, have a high Denisovans admixture relative to other populations.[46] Furthermore, they found possible low traces of Denisovan admixture in East Asians and no Denisovan admixture in Native Americans.[46] 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.[3] The manner of gene flow to these populations remains unknown.[3] However, Wall et al. (2013) stated that they found no evidence for Denisovan admixture in East Asians.[11]

Findings indicate that the Denisovan gene flow event happened to the common ancestors of Aboriginal Filipinos, Aboriginal Australians, and New Guineans.[44][47] 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.[44] 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.[44] 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).[44]

It has been shown that Eurasians have some but significant 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.[10][42]

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.[48] It is ancestral to many Asian and Native American populations, but post-dated the divergence between Asians and Europeans.[48] The lack of a Denisovan component in the Tianyuan individual suggests that the genetic contribution had been always scarce in the mainland.[3]

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.[31] In modern humans, HLA-B*73 is concentrated in western Asia, but it is rare or absent elsewhere.[31] Even though HLA-B*73 is not present in the sequenced Denisovan genome, the study noted that it was associated to the Denisovan-derived HLA-C*15:05 from the linkage disequilibrium, consistent with the estimated 98% of those modern humans who carried B*73 also carried C*15:05.[31]

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.[31] 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.[31]

It has been found that a EPAS1 gene variant was introduced from Denisovans to modern humans.[49] The ancestral variant upregulates hemoglobin levels to compensate for low oxygen levels—such as at high altitudes—but this also has the maladaption of increasing blood viscosity.[49] The Denisovan-derived variant on the other hand limits this increase of hemoglobin levels, thus resulting in a better altitude adaption.[49] The Denisovan-derived EPAS1 gene variant is common in Tibetans and was positively selected in their ancestors after they colonized the Tibetan plateau.[49]

Archaic African hominins

Rapid decay of fossils in African environments makes it currently unfeasible to compare modern human admixture with reference samples of archaic African hominins.[50]

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 are significant for admixture) and one West African agricultural group (Mandinka who are not significant for admixture), it's concluded that roughly 2% of the genetic material found in some Sub-Saharan African populations was inserted into the human genome approximately 35,000 years ago from archaic hominins that broke away from the modern human lineage around 700,000 years ago.[51] 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.[51]

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,[50] probably over 40,000 years ago.[52] The median time of the most recent common ancestor of the fifteen test subjects with the putative introgressive haplotypes was 1.2–1.3 mya.[50]

Indirect evidence

Human papillomavirus type 58 causes cervical cancer in 10–20% of cases in East Asia. It is rarely found elsewhere. An estimate of the date of evolution of the most recent common ancestor places it at 478,600 years ago (95% HPD 391,000–569,600).[53] As this date is before the generally accepted date of the evolution of anatomically modern humans, this suggests that this virus was transmitted to humans from a now extinct hominin. As this virus is usually transmitted sexually this furthermore suggests that mating occurred in this area between modern humans and a now extinct hominin species.[53]

See also

References

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  2. ↑ 2.0 2.1 2.2 2.3 2.4 Lua error in package.lua at line 80: module 'strict' not found.
  3. ↑ 3.0 3.1 3.2 3.3 3.4 Lua error in package.lua at line 80: module 'strict' not found.
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