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There is evidence for interbreeding between archaic and modern humans during the
Middle Paleolithic The Middle Paleolithic (or Middle Palaeolithic) is the second subdivision of the Paleolithic The Paleolithic or Palaeolithic or Palæolithic (), also called the Old Stone Age (from Greek palaios - old, lithos - stone), is a period in prehi ...
and early
Upper Paleolithic The Upper Paleolithic (or Upper Palaeolithic) also called the is the third and last subdivision of the or Old . Very broadly, it dates to between 50,000 and years ago (the beginning of the ), according to some theories coinciding with the ...
. The interbreeding happened in several independent events that included
Neanderthal Neanderthals (, also Neandertals, ''Homo neanderthalensis'' or ''Homo sapiens neanderthalensis'') are an extinct species In biology, a species is the basic unit of biological classification, classification and a taxonomic rank of an org ...
s and
Denisovan The Denisovans or Denisova hominins ) are an extinct species or subspecies of archaic human that ranged across Asia during the Lower Paleolithic, Lower and Middle Paleolithic. Denisovans are known from few remains, and, consequently, most of wh ...
s, as well as several unidentified
hominins The Hominini form a taxonomic tribe of the subfamily Homininae Homininae (), also called "African hominids" or "African apes", is a subfamily of Hominidae The Hominidae (), whose members are known as great apes or hominids (), are a t ...
. In Eurasia, interbreeding between Neanderthals and Denisovans with
modern humans Early modern human (EMH) or anatomically modern human (AMH) are terms used to distinguish ''Homo sapiens Humans (''Homo sapiens'') are the most abundant and widespread of , characterized by and large, complex brains. This has enabled ...
took place several times. The
introgression Introgression, also known as introgressive hybridization, in genetics Genetics is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, ch ...
events into modern humans are 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 has been found in the genomes of most or possibly all contemporary populations, varying noticeably by region. It accounts for 1–4% of modern genomes for people outside Sub-Saharan Africa, although estimates vary, and either none or possibly up to 0.3% — according to recent research — for those in Africa. It is highest in East Asians, intermediate in Europeans, and lower in Southeast Asians. According to some research, it is also lower in
Melanesians Melanesians are the predominant and Indigenous peoples of Oceania, indigenous inhabitants of Melanesia, in a wide area from the Maluku Islands, East Nusa Tenggara and New Guinea to as far east as the islands of Vanuatu and Fiji. Most speak eithe ...

Melanesians
compared to both East Asians and Europeans. However, other research finds higher Neanderthal admixture in
Australo-Melanesians Australo-Melanesians (also known as Australasians or Australomelanesoid race or Australoid race) is an outdated historical grouping of various people indigenous to Melanesia Melanesia (, ) is a subregion A subregion is a part of a larger r ...
, as well as in Native Americans, than in Europeans (though not higher than in East Asians). Denisovan-derived ancestry is largely absent from modern populations in Africa and Western Eurasia. The highest rates, by far, of Denisovan admixture have been found in
Oceanian Oceania (, , ) is a Region, geographic region that includes Australasia, Melanesia, Micronesia and Polynesia. Spanning the eastern hemisphere, Eastern and Western Hemispheres, Oceania has a land area of and a population of over 41 million. Wh ...
and some
Southeast Asian Southeast Asia or Southeastern Asia is the southeastern subregion of Asia Asia () is Earth's largest and most populous continent, located primarily in the Eastern Hemisphere, Eastern and Northern Hemisphere, Northern Hemisphere of the ...
populations. An estimated 4–6% of the genome of modern
Melanesians Melanesians are the predominant and Indigenous peoples of Oceania, indigenous inhabitants of Melanesia, in a wide area from the Maluku Islands, East Nusa Tenggara and New Guinea to as far east as the islands of Vanuatu and Fiji. Most speak eithe ...

Melanesians
is derived from Denisovans, but the highest amounts detected thus far are found in the
Negrito The term Negrito () refers to several diverse ethnic groups who inhabit isolated parts of Southeast Asia Southeast Asia, also spelled South East Asia and South-East Asia, and also known as Southeastern Asia or SEA, is the geographical U ...

Negrito
populations of the Philippines. While some southeast Asian Negrito populations carry Denisovan admixture, others have none, such as the
Andamanese The Andamanese are the various indigenous peoples Indigenous peoples, also referred to as first peoples, first nations, aboriginal peoples, native peoples (with these terms often capitalized when referred to relating to specific countrie ...
. In addition, low traces of Denisovan-derived ancestry have been found in mainland Asia, with an elevated Denisovan ancestry in South Asian populations compared to other mainland populations. In Africa, archaic
allele An allele (, ; ; modern formation from Greek ἄλλος ''állos'', "other") is one of two, or more, forms of a given gene In biology, a gene (from ''genos'' "...Wilhelm Johannsen coined the word gene to describe the Mendelian_inheritance ...
s consistent with several independent admixture events in the subcontinent have been found. It is currently unknown who these archaic African hominins were. 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 Early modern human (EMH) or anatomically modern human (AMH) are terms used to distinguish ''Homo sapiens Humans (''Homo sapiens'') are the most abundant and widespread of , characterized by and large, complex brains. This has enabled ...
.


Neanderthals


Genetics


Proportion of admixture

On 7 May 2010, following the
genome sequencing Whole genome sequencing (WGS), also known as full genome sequencing, complete genome sequencing, or entire genome sequencing, is the process of determining the entirety, or nearly the entirety, of the DNA Deoxyribonucleic acid (; DNA) i ...
of three Vindija
Neanderthals Neanderthals (, also Neandertals, ''Homo neanderthalensis'' or ''Homo sapiens neanderthalensis'') are an extinct species In biology, a species is the basic unit of biological classification, classification and a taxonomic rank of an org ...
, 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 authors, the observed excess of genetic similarity is best explained by recent
gene flow In population genetics Population genetics is a subfield of that deals with genetic differences within and between s, and is a part of . Studies in this branch of examine such phenomena as , , and . Population genetics was a vital ingredient ...

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, Lohse and Frantz (2014) infer a higher rate of 3.4–7.3% in Eurasia. In 2017, Prüfer et al. revised their estimate to 1.8–2.6% for non-Africans outside Oceania. According to a later study by Chen et al. (2020), Africans (specifically, the African populations) also have Neanderthal admixture, with this Neanderthal admixture in African individuals accounting for 17 megabases, which is 0.3% of their genome. According to the authors, Africans gained their Neanderthal admixture predominantly from a back-migration by peoples (modern humans carrying Neanderthal admixture) that had diverged from ancestral Europeans (postdating the split between East Asians and Europeans). This back-migration is proposed to have happened about 20,000 years ago. However, some scientists, such as geneticist David Reich, dispute the study's conclusions suggesting Neanderthal admixture in sub-Saharan Africans.


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 In natural selection, negative selection or purifying selection is the selective removal of alleles that are Mutation#Harmful mutations, deleterious. This can result in stabilising selection through the purging of deleterious genetic polymorphism ...
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. Prüfer et al. (2017) remarked that
East Asians East Asian people (East Asians) are the people from East Asia East Asia is the eastern region of Asia, which is defined in both Geography, geographical and culture, ethno-cultural terms. The modern State (polity), states of East Asia incl ...
carry more Neanderthal DNA (2.3–2.6%) than
Western Eurasians The most significant recent dispersal of modern humans from Africa gave rise to an undifferentiated "recent African origin, non-African" lineage by some 70–50 ka (70-50,000 years ago). By about 50–40 ka a basal West Eurasian lineage had ...
(1.8–2.4%). It was later determined by Chen et al. (2020) that East Asians have 8% more Neanderthal ancestry, revised from the previous reports of 20% more Neanderthal ancestry, compared to Europeans. This stems from the fact that Neanderthal ancestry shared with Africans had been masked, because Africans were thought to have no Neanderthal admixture and were therefore used as reference samples. Thus, any overlap in Neanderthal admixture with Africans resulted in an underestimation of Neanderthal admixture in non-Africans and especially in Europeans. The authors give a single pulse of Neanderthal admixture after the out-of-Africa dispersal as the most parsimonious explanation for the enrichment in East Asians, but they add that variation in Neanderthal ancestry may also be attributed to dilution to account for the now-more-modest differences found. As a proportion of the total amount of Neanderthal sequence for each population, 7.2% of the sequence in Europeans is shared exclusively with Africans, while 2% of the sequence in East Asians is shared exclusively with Africans. 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 Berbers or ''Imazighen'' ( ber, translit=Imaziɣen, ⵉⵎⴰⵣⵉⵖⵏ, ⵎⵣⵗⵏ; singular: , ) are an ethnic group mostly concentrated in North Africa, specifically Morocco, Algeria, Tunisia, Libya, the Canary Islands, and to a lesser ...

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 ) , image_map = Morocco (orthographic projection, WS claimed).svg , map_caption = Location of Morocco in northwest Africa.Dark green: Undisputed territory of Morocco.Lighter green: Western Sahara, a United Nations lis ...

Morocco
and
Egypt Egypt ( ar, مِصر, Miṣr), officially the Arab Republic of Egypt, is a transcontinental country This is a list of countries located on more than one continent A continent is one of several large landmasses. Generally identi ...

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 Maasai may refer to: *Maasai people *Maasai language *Maasai mythology *MAASAI (band) See also

* Masai (disambiguation) * Massai {{disambiguation Language and nationality disambiguation pages Maasai People were a very old tribe in the sorther ...

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 (
North Caucasus The North Caucasus ( ady, Темыр Къафкъас, Temır Qafqas; kbd, Ишхъэрэ Къаукъаз, İṩxhərə Qauqaz; ce, Къилбаседа Кавказ, Q̇ilbaseda Kavkaz; rus, Северный Кавказ, r=Severnyy Ka ...
) than to the Altai Neanderthal (
Siberia Siberia (; rus, Сибирь, r=Sibir', p=sʲɪˈbʲirʲ, a=Ru-Сибирь.ogg) is an extensive geographical region, constituting all of North Asia, from the Ural Mountains in the west to the Pacific Ocean in the east. It has been a part of R ...

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 Neanderthal. 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 Early modern human (EMH) or anatomically modern human (AMH) are terms used to distinguish ''Homo sapiens Humans (''Homo sapiens'') are the most abundant and widespread species of primate, characterized by bipedality, bipedalism and larg ...
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 Mitochondrial DNA (mtDNA or mDNA) is the DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five car ...

mitochondrial DNA
has been found in modern humans. This suggests that successful Neanderthal admixture happened in pairings with Neanderthal males and modern human females. Possible hypotheses are that Neanderthal mitochondrial DNA had detrimental mutations that led to the extinction of carriers, that the hybrid offspring of Neanderthal mothers were raised in Neanderthal groups and became extinct with them, or that female Neanderthals and male Sapiens did not produce fertile offspring. However, the hypothesized incompatibility between Neanderthals and modern humans is contested by findings that suggest that the Y chromosome of Neanderthals was replaced by an extinct lineage of the modern human Y chromosome, which introgressed into Neanderthals between 100,000 and 370,000 years ago. Furthermore, the study concludes that the replacement of the Y chromosomes and mitochondrial DNA in Neanderthals after gene flow from modern humans is highly plausible given the increased genetic load in Neanderthals relative to modern humans. As shown in an interbreeding model produced by Neves and Serva (2012), the Neanderthal admixture in modern humans may have been caused by a very low rate of interbreeding between modern humans and Neanderthals, with the exchange of one pair of individuals between the two populations in about every 77 generations. This low rate of interbreeding would account for the absence of Neanderthal mitochondrial DNA from the modern human gene pool as found in earlier studies, as the model estimates a probability of only 7% for a Neanderthal origin of both mitochondrial DNA and Y chromosome in modern humans.


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 The X chromosome is one of the two sex-determining chromosome A chromosome is a long DNA molecule with part or all of the genome, genetic material of an organism. Most eukaryotic chromosomes include packaging proteins called histones whic ...

X chromosome
—with fivefold lower Neanderthal ancestry compared to
autosome An autosome is any chromosome that is not a sex chromosome (an allosome). The members of an autosome pair in a diploid cell have the same morphology, unlike those in allosome pairs which may have different structures. The DNA in autosomes is coll ...
s. 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 Zygosity (the noun, zygote A zygote (from Greek ζυγωτός ''zygōtos'' "joined" or "yoked", from ζυγοῦν ''zygoun'' "to join" or "to yoke") is a eukaryotic cell formed by a fertilization event between two gamete A gamete ( /ˈɡ ...
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{{Short description, A phenomenon inducing a loss of genetic diversity Background selection describes the loss of genetic diversity Genetic diversity is the total number of genetic characteristics in the genetic makeup of a species, it ranges widel ...
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 have adaptive sequences introgressed from archaic humans, which provided a source of advantageous genetic variants that are adapted to local environments and a reservoir for additional genetic variation. Adaptive introgression from Neanderthals has targeted genes involved with keratin filaments, sugar metabolism, muscle contraction, body fat distribution, enamel thickness, and
oocyte An oocyte (, ), oöcyte, ovocyte, or rarely ocyte, is a female gametocyte A gametocyte is a eukaryotic germ cell that divides by mitosis into other gametocytes or by meiosis into gametids during gametogenesis. Male gametocytes are called ''sperm ...
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 Keratin () is one of a family of structural fibrous proteins also known as ''scleroproteins''. Alpha-keratin Alpha-keratin, or α-keratin, is a type of keratin Keratin () is one of a family of fibrous structural proteins known as Scleroprot ...

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 Lupus, technically known as systemic lupus erythematosus (SLE), is an autoimmune disease in which the body's immune system mistakenly attacks healthy tissue in many parts of the body. Symptoms vary between people and may be mild to severe. Co ...
,
primary biliary cirrhosis Primary biliary cholangitis (PBC), previously known as primary biliary cirrhosis, is an autoimmune disease of the liver. It results from a slow, progressive destruction of the small bile ducts of the liver, causing bile and other toxins to build ...
,
Crohn's disease Crohn's disease is a type of inflammatory bowel disease (IBD) that may affect any segment of the gastrointestinal tract. Symptoms often include abdominal pain, diarrhea (which may be bloody if inflammation is severe), fever, abdominal distension, ...

Crohn's disease
,
optic disk The optic disc or optic nerve head is the point of exit for Retinal ganglion cell, ganglion cell axons leaving the human eye, eye. Because there are no rod cell, rods or cone cell, cones overlying the optic disc, it corresponds to a small Blind s ...
size, smoking behavior,
interleukin 18 Interleukin-18 (IL18, also known as interferon-gamma inducing factor) is a protein Proteins are large biomolecule , showing alpha helices, represented by ribbons. This poten was the first to have its suckture solved by X-ray crystallogra ...
levels, and
diabetes mellitus type 2 Type 2 diabetes (T2D), formerly known as adult-onset diabetes, is a form of diabetes Diabetes mellitus, commonly known as just diabetes, is a group of metabolic disorders characterized by a hyperglycemia, high blood sugar level over a pro ...
. 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 Microcephalin (MCPH1) is a gene In biology, a gene (from ''genos'' "...Wilhelm Johannsen coined the word gene to describe the Mendelian_inheritance#History, Mendelian units of heredity..." (Greek language, Greek) meaning ''generation'' or ' ...

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 In genetics Genetics is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular inter ...

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 The cerebellum (Latin for "little brain") is a major feature of the hindbrain The hindbrain or rhombencephalon is a developmental Development of the human body is the process of growth to maturity. The process begins with fertilization ...

cerebellum
and
basal ganglia #REDIRECT Basal ganglia The basal ganglia (or basal nuclei) are a group of subcortical The cerebral cortex, also known as the cerebral mantle, is the outer layer of neural tissue Nervous tissue, also called neural tissue, is the main tissue ...

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 TLR 1 is a member of the toll-like receptor family Toll-like receptors (TLRs) are a class of proteins that play a key role in the innate immune system. They are Bitopic protein, single-pass membrane-spanning Receptor (biochemistry), receptors u ...

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 The occipital bone () is a neurocranium, cranial dermal bone and the main bone of the occiput (back and lower part of the skull). It is Trapezoid, trapezoidal in shape and curved on itself like a shallow dish. The occipital bone overlies the occi ...

occipital
and inferior
parietal bone The parietal bones () are two bones in the skull The skull is a bone A bone is a rigid tissue Tissue may refer to: Biology * Tissue (biology), an ensemble of similar cells that together carry out a specific function * ''Triphosa haesi ...

parietal bone
s to bilateral . In regards to modern human brain morphology, Neanderthal admixture is positively correlated with an increase in sulcal depth for the right
intraparietal sulcus The intraparietal sulcus (IPS) is located on the lateral surface of the parietal lobe The parietal lobe is one of the four major lobes of the cerebral cortex The cerebral cortex, also known as the cerebral mantle, is the outer layer of neura ...
and an increase in cortical complexity for the early
visual cortex The visual cortex of the brain is the area of the cerebral cortex that processes visual perception, visual information. It is located in the occipital lobe. Sensory input originating from the Eye, eyes travels through the lateral geniculate nucleu ...

visual cortex
of the left hemisphere. Neanderthal admixture is also positively correlated with an increase in
white White is the lightest color Color (American English American English (AmE, AE, AmEng, USEng, en-US), sometimes called United States English or U.S. English, is the set of varieties of the English language native to the Unite ...
and
gray matter Grey matter (or gray matter) is a major component of the central nervous system The central nervous system (CNS) is the part of the nervous system In biology Biology is the natural science that studies life and living organisms, ...
volume localized to the right parietal region adjacent to the right
intraparietal sulcus The intraparietal sulcus (IPS) is located on the lateral surface of the parietal lobe The parietal lobe is one of the four major lobes of the cerebral cortex The cerebral cortex, also known as the cerebral mantle, is the outer layer of neura ...
. In the area overlapping the
primary visual cortex The visual cortex of the brain A brain is an organ Organ may refer to: Biology * Organ (anatomy) An organ is a group of Tissue (biology), tissues with similar functions. Plant life and animal life rely on many organs that co-exist in org ...
gyrification Gyrification is the process of forming the characteristic folds of the cerebral cortex. The peak of such a fold is called a gyrus In neuroanatomy, a gyrus (pl. ''gyri'') is a ridge on the cerebral cortex. It is generally surrounded by one o ...
in the left hemisphere, Neanderthal admixture is positively correlated with gray matter volume. The results also show evidence for a negative correlation between Neanderthal admixture and white matter volume in the
orbitofrontal cortex The orbitofrontal cortex (OFC) is a prefrontal cortex In mammalian brain anatomy, the prefrontal cortex (PFC) is the cerebral cortex The cerebral cortex, also known as the cerebral mantle, is the outer layer of neural tissue of the cerebrum ...

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 Occam's razor, Ockham's razor, Ocham's razor ( la, novacula Occami), also known as the principle of parsimony or the law of parsimony ( la, lex parsimoniae), is the problem-solving principle that "entities should not be multiplied beyond necessi ...
than recent gene flow, the observation may have been due to ancient population sub-structure in Africa, causing incomplete genetic homogenization within modern humans when Neanderthals diverged while early ancestors of Eurasians were still more closely related to Neanderthals than those of Africans were to Neanderthals. On the basis of
allele frequency Allele frequency, or gene frequency, is the relative frequency of an allele An allele (, ; ; modern formation from Greek ἄλλος ''állos'', "other") is one of two, or more, forms of a given gene In biology, a gene (from ''genos'' "... ...
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 Bottleneck literally refers to the narrowed portion (neck) of a bottle A bottle is a narrow-necked container made of an impermeable material (clay, glass, plastic, aluminium etc.) in various shapes and sizes to store and transport liquids (w ...

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 In population genetics Population genetics is a subfield of that deals with genetic differences within and between s, and is a part of . Studies in this branch of examine such phenomena as , , and . Population genetics was a vital ingredien ...
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 indicate Neanderthal interbreeding with modern humans dispersing into Iberia. Considering the dating of the burial remains (24,500 years BP) and the persistence of Neanderthal traits long after the transitional period from a Neanderthal to a modern human population in Iberia (28,000–30,000 years BP), the child may have been a descendant of an already heavily admixed population. The 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 The brow ridge, or supraorbital ridge known as superciliary arch in medicine, refers to a bony ridge located above the eye sockets of all primates. In ''Homo sapiens sapiens'' (modern humans) the eyebrows are located on their lower margin. Struc ...
, a prominent
occipital bun An occipital bun, also called occipital spurs, occipital knob, chignon hooks or inion hooks, is a prominent bulge or projection of the occipital bone The occipital bone () is a neurocranium, cranial dermal bone and the main bone of the occiput ...
, an asymmetrical and shallow
mandibular notch The upper border of the ramus of mandible is thin, and is surmounted by two processes, the coronoid process anteriorly and the condyloid process The condyloid process or condylar process is the process on the human mandible In anatomy Anato ...
shape, a high mandibular coronoid processus, the relative perpendicular mandibular
condyle A condyle ( or ;Entry "condyle"
in
glenoid fossa. The early modern human Oase 1 mandible from
Peștera cu Oase Peștera cu Oase (, meaning "The Cave with Bones") is a system of 12 karstic galleries and chambers located near the city Anina, in the Caraș-Severin county, southwestern Romania Romania ( ; ro, România ) is a country located at the cr ...
(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 The mandibular foramen is an opening on the internal surface of the ramus of the mandible In anatomy Anatomy (Greek ''anatomē'', 'dissection') is the branch of biology concerned with the study of the structure of organism In biolo ...
, 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)
Gravettian The Gravettian was an archaeological industry of the European Upper Paleolithic The Upper Paleolithic (or Upper Palaeolithic) also called the Late Stone Age is the third and last subdivision of the Paleolithic or Old Stone Age. Very broad ...
s, falling anatomically largely in line 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. The morphology of a late Neanderthal mandible from the Mezzena rockshelter ( Monti Lessini, Italy) shows evidence of possible interbreeding with modern humans. 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. However, a more recent aDNA analysis of this jaw has shown that it does not belong to a Neanderthal, but to a fully modern human of the Holocene. Previous reports of a Mezzena "Neanderthal hybrid" were based on a faulty DNA analysis. Manot 1, a partial calvarium of a modern human that was recently discovered at the Manot Cave (Western Galilee, Israel) and dated to 54.7±5.5 kyr BP, represents the first fossil evidence from the period when modern humans successfully migrated out of Africa and colonized Eurasia. It also provides the first fossil evidence that modern humans inhabited the southern Levant during the Middle to Upper Palaeolithic interface, contemporaneously with the Neanderthals and close to the probable interbreeding event. The morphological features suggest that the Manot population may be closely related to or may have 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 Thomas Henry Huxley (4 May 1825 – 29 June 1895) was an English biologist and anthropologist specialising in comparative anatomy. He has become known as "Darwin's Bulldog" for his advocacy of Charles Darwin's theory of evolution. The stori ...
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". Until the early 1950s, most scholars thought Neanderthals were not in the ancestry of living humans. Nevertheless, proposed interbreeding in 1907 in the article ''Race studies in Denmark''. He strongly emphasised that all living humans are of mixed origins. He held that this would best fit observations, and challenged the widespread idea that Neanderthals were ape-like or inferior. Basing his argument primarily on cranial data, he noted that the Danes, like the Frisians and the Dutch, exhibit some Neanderthaloid characteristics, and felt it was reasonable to "assume something was inherited" and that Neanderthals "are among our ancestors." Carleton Stevens Coon in 1962 found it likely, based upon evidence from cranial data and material culture, that Neanderthal and Upper Paleolithic peoples either interbred or that the newcomers reworked Neanderthal implements "into their own kind of tools." By the early 2000s, the majority of scholars supported the
Out of Africa hypothesis upright=1.5, Expansion of early modern humans from Africa through the Near East In paleoanthropology Paleoanthropology or paleo-anthropology is a branch of paleontology and biological anthropology, anthropology which seeks to understand t ...
,. "Currently available genetic and archaeological evidence is supportive of a recent single origin of modern humans in East Africa. However, this is where the consensus on human settlement history ends, and considerable uncertainty clouds any more detailed aspect of human colonization history." according to which anatomically modern humans left Africa about 50,000 years ago and replaced Neanderthals with little or no interbreeding. Yet some scholars still argued for hybridisation with Neanderthals. The most vocal proponent of the hybridisation hypothesis was Erik Trinkaus of
Washington University Washington University in St. Louis (WashU, or WUSTL) is a private Private or privates may refer to: Music * "In Private "In Private" was the third single in a row to be a charting success for United Kingdom, British singer Dusty Springfiel ...
. Trinkaus claimed various fossils as products of hybridised populations, including the skeleton of a child found at Lagar Velho in
Portugal Portugal, officially the Portuguese Republic ( pt, República Portuguesa, links=yes ), is a country A country is a distinct territorial body or political entity A polity is an identifiable political entity—any group of people who ...

Portugal
and the Peștera Muierii skeletons from Romania.


Denisovans


Genetics


Proportion of admixture

It has been shown that
Melanesians Melanesians are the predominant and Indigenous peoples of Oceania, indigenous inhabitants of Melanesia, in a wide area from the Maluku Islands, East Nusa Tenggara and New Guinea to as far east as the islands of Vanuatu and Fiji. Most speak eithe ...

Melanesians
(e.g. Papua New Guinean and Bougainville Islander) share relatively more alleles with
Denisovan The Denisovans or Denisova hominins ) are an extinct species or subspecies of archaic human that ranged across Asia during the Lower Paleolithic, Lower and Middle Paleolithic. Denisovans are known from few remains, and, consequently, most of wh ...
s when compared to other Eurasians and Africans. It is 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 East Asian people (East Asians) are the people from East Asia East Asia is the eastern region of Asia, which is defined in both Geography, geographical and culture, ethno-cultural terms. The modern State (polity), states of East Asia incl ...
, 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 The Wallace Line or Wallace's Line is a faunal boundary line drawn in 1859 by the British naturalist Alfred Russel Wallace Alfred Russel Wallace (8 January 18237 November 1913) was a British natural history, naturalist, explorer, geo ...
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. A study in 2021 analyzing archaic ancestry in 118 Philippine ethnic groups discovered an independent admixture event into Philippine
Negritos The term Negrito () refers to several diverse ethnic groups who inhabit isolated parts of Southeast Asia Southeast Asia, also spelled South East Asia and South-East Asia, and also known as Southeastern Asia or SEA, is the geographical U ...

Negritos
from
Denisovans The Denisovans or Denisova hominins ) are an extinct species or subspecies of archaic human that ranged across Asia during the Lower Paleolithic, Lower and Middle Paleolithic. Denisovans are known from few remains, and, consequently, most of wh ...
. The Ayta Magbukon in particular were found to possess the highest level of Denisovan ancestry in the world, with ∼30%–40% more than even that found in Australians and Papuans (
Australo-Melanesians Australo-Melanesians (also known as Australasians or Australomelanesoid race or Australoid race) is an outdated historical grouping of various people indigenous to Melanesia Melanesia (, ) is a subregion A subregion is a part of a larger r ...
), suggesting that distinct Islander Denisovan populations existed in the Philippines which admixed with modern humans after their arrival. 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 Zhoukoudian Peking Man Site (), also romanized as Choukoutien, is a cave, cave system in suburban Fangshan District, Beijing. It has yielded many archaeology, archaeological discoveries, including one of the first specimens of ''Homo erectus'' (' ...
, 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 Hypoxia-inducible factor prolyl hydroxylase 2 (HIF-PH2), or prolyl hydroxylase domain-containing protein 2 (PHD2), is an enzyme encoded by the ''EGLN1'' gene In biology, a gene (from ''genos'' "...Wilhelm Johannsen coined the word gene to d ...
and
EPAS1 Endothelial PAS domain-containing protein 1 (EPAS1, also known as hypoxia-inducible factor-2alpha (HIF-2alpha)) is a protein Proteins are large biomolecule , showing alpha helices, represented by ribbons. This poten was the first to have i ...
gene variant, associated with hemoglobin concentration and response to hypoxia, for life at high altitudes from the Denisovans. The ancestral variant of
EPAS1 Endothelial PAS domain-containing protein 1 (EPAS1, also known as hypoxia-inducible factor-2alpha (HIF-2alpha)) is a protein Proteins are large biomolecule , showing alpha helices, represented by ribbons. This poten was the first to have i ...
upregulates
hemoglobin Hemoglobin or haemoglobin (spelling differences Despite the various English dialects Dialect The term dialect (from Latin , , from the Ancient Greek word , , "discourse", from , , "through" and , , "I speak") is used in two distinct wa ...

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 who have significant admixture) and one West African agricultural group (
MandinkaMandinka, Mandika, Mandinkha, Mandinko, or Mandingo may refer to: * Mandingo (film), ''Mandingo'' (film), a 1975 film based on the eponymous 1957 novel * Mandingo (novel), ''Mandingo'' (novel), a bestselling novel published in 1957 * ''Mandingo (pla ...
, 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 In anthropology Anthropology is the of ity, concerned with , , , and , in both the present and past, including . studies patterns of behaviour, while studies cultural meaning, including norms and values. studies how language influence ...
(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. According to a study published in 2020, there are indications that 2% to 19% (or about ≃6.6 and ≃7.0%) of the DNA of four West African populations may have come from an unknown archaic hominin which split from the ancestor of humans and Neanderthals between 360 kya to 1.02 mya. However, the study also finds that at least part of this proposed archaic admixture is also present in Eurasians/non-Africans, and that the admixture event or events range from 0 to 124 ka B.P, which includes the period before the Out-of-Africa migration and prior to the African/Eurasian split (thus affecting in part the common ancestors of both Africans and Eurasians/non-Africans).https://advances.sciencemag.org/content/advances/suppl/2020/02/10/6.7.eaax5097.DC1/aax5097_SM.pdf Another recent study, which discovered substantial amounts of previously undescribed human genetic variation, also found ancestral genetic variation in Africans that predates modern humans and was lost in most non-Africans. "An analysis of archaic sequences in modern populations identifies ancestral genetic variation in African populations that likely predates modern humans and has been lost in most non-African populations...We found small amounts of Neanderthal ancestry in West African genomes, most likely reflecting Eurasian admixture. Despite their very low levels or absence of archaic ancestry, African populations share many Neanderthal and Denisovan variants that are absent from Eurasia, reflecting how a larger proportion of the ancestral human variation has been maintained in Africa."


Related studies

In 2019, scientists discovered evidence, based on using
artificial intelligence Artificial intelligence (AI) is intelligence Intelligence has been defined in many ways: the capacity for abstraction Abstraction in its main sense is a conceptual process where general rules and concept Concepts are defined as abstra ...

artificial intelligence
(AI), that suggests the existence of an unknown human ancestor species, not
Neanderthal Neanderthals (, also Neandertals, ''Homo neanderthalensis'' or ''Homo sapiens neanderthalensis'') are an extinct species In biology, a species is the basic unit of biological classification, classification and a taxonomic rank of an org ...
or
Denisovan The Denisovans or Denisova hominins ) are an extinct species or subspecies of archaic human that ranged across Asia during the Lower Paleolithic, Lower and Middle Paleolithic. Denisovans are known from few remains, and, consequently, most of wh ...
, in the genome of
modern humans Early modern human (EMH) or anatomically modern human (AMH) are terms used to distinguish ''Homo sapiens Humans (''Homo sapiens'') are the most abundant and widespread of , characterized by and large, complex brains. This has enabled ...
.


See also

*
Multiregional origin of modern humans The multiregional hypothesis, multiregional evolution (MRE), or polycentric hypothesis is a scientific model that provides an alternative explanation to the more widely accepted "Out of Africa" model of monogenesis for the pattern of human evolu ...
*
Neanderthal extinction Neanderthals Neanderthals (, also Neandertals, ''Homo neanderthalensis'' or ''Homo sapiens neanderthalensis'') are an extinct species or subspecies of archaic humans who lived in Eurasia until about 40,000 years ago. They most likely went ex ...
*
Red Deer Cave people The Red Deer Cave people are a prehistoric archaic human A number of varieties of ''Homo ''Homo'' () is the that emerged in the (otherwise extinct) genus ' that encompasses the extant species ' (), plus several extinct species classified ...


References

{{Human evolution Hominid hybrids Ancient human genetic history Middle Stone Age Anatomically modern humans