Neanderthal genetics

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Genetic studies on Neanderthal ancient DNA became possible in the late 1990s. [1] The Neanderthal genome project, established in 2006, presented the first fully sequenced Neanderthal genome in 2013.

Contents

Since 2005, evidence for substantial admixture of Neanderthal DNA in modern populations is accumulating. [2] [3] [4]

The divergence time between the Neanderthal and modern human lineages is estimated at between 750,000 and 400,000 years ago. The recent time is suggested by Endicott et al. (2010) [5] and Rieux et al. (2014). [6] A significantly deeper time of parallelism, combined with repeated early admixture events, was calculated by Rogers et al. (2017). [7]

Genome sequencing

In July 2006, the Max Planck Institute for Evolutionary Anthropology and 454 Life Sciences announced that they would sequence the Neanderthal genome over the next two years. It was hoped the comparison would expand understanding of Neanderthals, as well as the evolution of humans and human brains. [8]

In 2008 Richard E. Green et al. from Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, published the full sequence of Neanderthal mitochondrial DNA (mtDNA) and suggested "Neanderthals had a long-term effective population size smaller than that of modern humans." [9] In the same publication, it was disclosed by Svante Pääbo that in the previous work at the Max Planck Institute, "Contamination was indeed an issue," and they eventually realised that 11% of their sample was modern human DNA. [10] [11] Since then, more of the preparation work has been done in clean areas and 4-base pair 'tags' have been added to the DNA as soon as it is extracted so the Neanderthal DNA can be identified.

Geneticist at the Max Planck Institute for Evolutionary Anthropology extracting ancient DNA (2005 photograph) Neanderthal DNA extraction.jpg
Geneticist at the Max Planck Institute for Evolutionary Anthropology extracting ancient DNA (2005 photograph)

The project first sequenced the entire genome of a Neanderthal in 2013 by extracting it from the phalanx bone of a 50,000-year-old Siberian Neanderthal. [12]

Among the genes shown to differ between present-day humans and Neanderthals were RPTN , SPAG17 , CAN15 , TTF1 , and PCD16 . [13]

A visualisation map of the reference modern-human containing the genome regions with high degree of similarity or with novelty according to a Neanderthal of 50 ka [12] has been built by Pratas et al. [14]

Interbreeding with anatomically modern humans

Researchers addressed the question of possible interbreeding between Neanderthals and anatomically modern humans (AMH) from the early archaeogenetic studies of the 1990s. As late as 2006, no evidence for interbreeding was found. [15] As late as 2009, analysis of about one third of the full genome of the Altai individual showed "no sign of admixture". The variant of microcephalin common outside Africa, suggested [16] to be of Neanderthal origin and responsible for rapid brain growth in humans, was not found in Neanderthals; nor was a very old MAPT variant found primarily in Europeans. [10] However, more recent studies have concluded that gene flow between Neanderthals and AMH occurred multiple times over thousands of years. [17]

Positive evidence for admixture was first published in May 2010. [13] Neanderthal-inherited genetic material is found in all non- Sub Saharan African populations and was initially reported to comprise 1 to 4 percent of the genome. [13] This fraction was refined to 1.5 to 2.1 percent. [12] Further analyses have found that Neanderthal gene flow is even detectable in African populations, suggesting that some variants obtained from Neanderthals posed a survival advantage. [17]

Approximately 20 percent of Neanderthal DNA survives in modern humans; however, a single human has an average of around 2% Neanderthal DNA overall with some countries and backgrounds having a maximum of 3% per human. [18] Modern human genes involved in making keratin, a protein constituent of skin, hair, and nails, contain high levels of introgression. For example, the genes of approximately 66% of East Asians contain a POUF23L variant introgressed from Neanderthals,[ clarification needed ] while 70% of Europeans possess an introgressed allele of BNC2. Neanderthal variants affect the risk of developing several diseases, including lupus, biliary cirrhosis, Crohn's disease, type 2 diabetes, and SARS-CoV-2. [18] [19] [20] The Neanderthal allele of MC1R (a gene with mutations linked to red hair in modern populations) is found at a frequency of 5% in Europeans, but is present in Taiwanese Aborigines at a frequency of 70% and at 30% in other East Asian populations. [21] While interbreeding is the most parsimonious interpretation of these genetic findings, the 2010 research of five present-day humans from different parts of the world does not rule out an alternative scenario, in which the source population of several non-African modern humans was more closely related than other Africans to Neanderthals because of ancient genetic divisions within early Hominoids. [13] [22]

Le Moustier Neanderthal skull reconstruction, Neues Museum Berlin Le Moustier skull in Berlin reconstitution.jpg
Le Moustier Neanderthal skull reconstruction, Neues Museum Berlin

Research since 2010 refined the picture of interbreeding between Neanderthals, Denisovans, and anatomically modern humans. Interbreeding appears asymmetrically among the ancestors of modern-day humans, and this may explain differing frequencies of Neanderthal-specific DNA in the genomes of modern humans. Vernot and Akey (2015) concluded the greater quantity of Neanderthal-specific DNA in the genomes of individuals of East Asian descent (compared with those of European descent) cannot be explained by differences in selection. [24] They suggest "two additional demographic models, involving either a second pulse of Neanderthal gene flow into the ancestors of East Asians or a dilution of Neanderthal lineages in Europeans by admixture with an unknown ancestral population" are parsimonious with their data. [24]

Kim and Lohmueller (2015) reached similar conclusions:

" According to some researchers, the greater proportion of Neanderthal ancestry in East Asians than in Europeans or West Asians is due to purifying selection is less effective at removing the so-called 'weakly-deleterious' Neanderthal alleles from East Asian populations. Computer simulations of a broad range of models of selection and demography indicate this hypothesis cannot account for the higher proportion of Neanderthal ancestry in East Asians than in Europeans. Instead, complex demographic scenarios, likely involving multiple pulses of Neanderthal admixture, are required to explain the data." [25]

Khrameeva et al. (2014), a German-Russian-Chinese collaboration, compiled an elementary Neanderthal genome based on the Altai individual and three Vindjia individuals. This was compared to a consensus chimpanzee genome as the out-group and to the genome of eleven modern populations (three African, three East Asian, three European). Beyond confirming a greater similarity to the Neanderthal genome in several non-Africans than in Africans, the study also found a difference in the distribution of Neanderthal-derived sites between Europeans and East Asians, suggesting recent evolutionary pressures. Asian populations showed clustering in functional groups related to immune and haematopoietic pathways, while Europeans showed clustering in functional groups related to the lipid catabolic process. [26]

Kuhlwilm et al. (2016) presented evidence for AMH admixture to Neanderthals at roughly 100,000 years ago. [27]

At minimum, research indicates three episodes of interbreeding. The first occurred with some modern humans. The second occurred after the ancestral Melanesians branched; these people seem to have bred with Denisovans. The third involved Neanderthals and the ancestors of East Asians only. [28] [29] [30]

2016 research indicates some Neanderthal males might not have viable male offspring with some AMH females. This could explain the reason why no modern man has a Neanderthal Y chromosome. [31]

2018 research indicates interbreeding between Neanderthals and modern humans led to the exposure of each species to unfamiliar viruses. Later on, the exchange of genes granted resistance to those viruses, too. [32]

On July 3, 2020, scientists reported finding a major genetic risk factor of the COVID-19 virus was inherited from archaic Neanderthals 60,000 years ago. [19] [20] [33] It is estimated that 16% of people in Europe and 50% of people in south Asia have the particular sequence on chromosome III, [34] with 63% of Bangladeshis having these gene sequences. North Africans sub Saharan Africans, West Asians and East Asians feature the presence of the chromosome in very negligible amounts. [35]

In December 2023, scientists reported that genes inherited by modern humans from Neanderthals and Denisovans may biologically influence the daily routine of modern humans, including the ability for some humans to wake earlier than others. [36]

It has been found that 50% of the Neanderthal genome is present among people in India, [37] and 41% has been found in Icelanders. [38]

Epigenetics

Complete DNA methylation maps for Neanderthal and Denisovan individuals were reconstructed in 2014. [39] Differential activity of HOX cluster genes lie behind many of the anatomical differences between Neanderthals and modern humans, especially in regards to limb morphology. In general, Neanderthals possessed shorter limbs with curved bones. [39] [40]

See also

Related Research Articles

<span class="mw-page-title-main">Svante Pääbo</span> Swedish geneticist (born 1955)

Svante Pääbo is a Swedish geneticist and Nobel Laureate who specialises in the field of evolutionary genetics. As one of the founders of paleogenetics, he has worked extensively on the Neanderthal genome. In 1997, he became founding director of the Department of Genetics at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. Since 1999, he has been an honorary professor at Leipzig University; he currently teaches molecular evolutionary biology at the university. He is also an adjunct professor at Okinawa Institute of Science and Technology, Japan.

<span class="mw-page-title-main">Early modern human</span> Old Stone Age Homo sapiens

Early modern human (EMH), or anatomically modern human (AMH), are terms used to distinguish Homo sapiens that are anatomically consistent with the range of phenotypes seen in contemporary humans, from extinct archaic human species. This distinction is useful especially for times and regions where anatomically modern and archaic humans co-existed, for example, in Paleolithic Europe. Among the oldest known remains of Homo sapiens are those found at the Omo-Kibish I archaeological site in south-western Ethiopia, dating to about 233,000 to 196,000 years ago, the Florisbad site in South Africa, dating to about 259,000 years ago, and the Jebel Irhoud site in Morocco, dated about 315,000 years ago.

<span class="mw-page-title-main">Neanderthal extinction</span> Prehistoric event

Neanderthals became extinct around 40,000 years ago. Hypotheses on the causes of the extinction include violence, transmission of diseases from modern humans which Neanderthals had no immunity to, competitive replacement, extinction by interbreeding with early modern human populations, natural catastrophes, climate change and inbreeding depression. It is likely that multiple factors caused the demise of an already low population.

<span class="mw-page-title-main">Human genetic variation</span> Genetic diversity in human populations

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The Neanderthal genome project is an effort of a group of scientists to sequence the Neanderthal genome, founded in July 2006.

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<span class="mw-page-title-main">Vindija Cave</span> Cave and archaeological site in Croatia

Vindija Cave is an archaeological site associated with Neanderthals and modern humans, located in the municipality of Donja Voća, northern Croatia. Remains of three Neanderthals were selected as the primary sources for the first draft sequence of the Neanderthal genome project in 2010. Additional research was done on the samples and published in 2017.

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<span class="mw-page-title-main">Denisovan</span> Asian archaic human

The Denisovans or Denisova hominins(di-NEE-sə-və) are an extinct species or subspecies of archaic human that ranged across Asia during the Lower and Middle Paleolithic, and lived, based on current evidence, from 285 to 52 thousand years ago. Denisovans are known from few physical remains; consequently, most of what is known about them comes from DNA evidence. No formal species name has been established pending more complete fossil material.

<span class="mw-page-title-main">Denisova Cave</span> Cave and archaeological site in Russia

Denisova Cave is a cave in the Bashelaksky Range of the Altai mountains, Siberian Federal District, Russia. The cave has provided items of great paleoarchaeological and paleontological interest. Bone fragments of the Denisova hominin originate from the cave, including artifacts dated to around 40,000 BP. Remains of a 32,000-year-old prehistoric species of horse have also been found in the cave.

<span class="mw-page-title-main">Neanderthal</span> Extinct Eurasian species or subspecies of archaic humans

Neanderthals are an extinct group of archaic humans who lived in Eurasia until about 40,000 years ago. The type specimen, Neanderthal 1, was found in 1856 in the Neander Valley in present-day Germany.

<span class="mw-page-title-main">Interbreeding between archaic and modern humans</span> Evidence of human hybridization during the Paleolithic

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<span class="mw-page-title-main">Johannes Krause</span> German biochemist, geneticist and paleontologist

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<span class="mw-page-title-main">Ust'-Ishim man</span> Hominin fossil found in Siberia

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<i>Denny</i> (hybrid hominin) Hominin fossil

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<span class="mw-page-title-main">Liran Carmel</span> Israeli scientist (born 1971)

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References

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