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]

Neanderthal genomes sequenced include those from Denisova Cave [8] [9] [10] including an offspring of a Neanderthal and a Denisovan, [11] from Chagyrskaya Cave, [12] from Vindija Cave, [13] [9] [14] Mezmaiskaya cave, Les Cottés cave, Goyet Caves and Spy Cave, [14] Hohlenstein-Stadel and Scladina caves [15] Galería de las Estatuas [16] and Gibraltar. [17]

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. [18]

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." [19] 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. [20] [21] 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. [8]

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 [8] has been built by Pratas et al. [22]

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. [23] 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 [24] 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. [20] However, more recent studies have concluded that gene flow between Neanderthals and AMH occurred multiple times over thousands of years. [25]

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. [8] 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. [25]

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. [26] 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. [26] [27] [28] The Val92Met variant of the MC1R gene, which has not been found in Neanderthal genomes but is putatively Neanderthal, and may be weakly associated with red hair and UV radiation sensitivity, [29] is found at a frequency of 5% in Europeans, 70% in Taiwanese and 30% in other East Asian populations. [30] 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] [31]

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. [33] 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. [33]

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." [34]

Khrameeva et al. (2014), a German-Russian-Chinese collaboration, compiled an elementary Neanderthal genome based on the Altai individual and three Vindija 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. [35]

Kuhlwilm et al. (2016) presented evidence for AMH admixture to Neanderthals at roughly 100,000 years ago. [36]

At minimum, research indicates three episodes of interbreeding. The first occurred with some modern humans. The second occurred after the ancestral Melanesians branched off; these people seem to have bred with Denisovans. The third involved Neanderthals and the ancestors of East Asians only. [37] [38] [39]

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. [40]

In October 2023, scientists reported that an anatomically-modern-human-to-Neanderthal admixture event occurred roughly 250,000 years ago, and also noted that roughly 6% of the Altai Neanderthal genome was inherited from anatomically modern humans. [41]

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. [42] Similar to Europeans, modern Indians derive around 1-2% genetic make-up from ancient hominins, Neanderthals and Denisovans, however, Indians carry a much larger variety of these ancient genes compared with other populations. [43] [44] It is unclear what, if any, advantage these genes may have provided.

Epigenetics

Complete DNA methylation maps for Neanderthal and Denisovan individuals were reconstructed in 2014. [45] 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. [45] [46]

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">Bacho Kiro cave</span> Archaeological site in Bulgaria

The Bacho Kiro cave is situated 5 km (3.1 mi) west of the town Dryanovo, Bulgaria, only 300 m (980 ft) away from the Dryanovo Monastery. It is embedded in the canyons of the Andaka and Dryanovo River. It was opened in 1890 and the first recreational visitors entered the cave in 1938, two years before it was renamed in honor of Bulgarian National Revival leader, teacher and revolutionary Bacho Kiro. The cave is a four-storey labyrinth of galleries and corridors with a total length of 3,600 m (11,800 ft), 700 m (2,300 ft) of which are maintained for public access and equipped with electrical lights since 1964. An underground river has over time carved out the many galleries that contain countless stalactone, stalactite, and stalagmite speleothem formations of great beauty. Galleries and caverns of a 1,200 m (3,900 ft) long section have been musingly named as a popular description of this fairy-tale underground world. The formations succession: Bacho Kiro’s Throne, The Dwarfs, The Sleeping Princess, The Throne Hall, The Reception Hall, The Haidouti Meeting-Ground, The Fountain and the Sacrificial Altar.

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

<span class="mw-page-title-main">Early human migrations</span> Spread of humans from Africa through the world

Early human migrations are the earliest migrations and expansions of archaic and modern humans across continents. They are believed to have begun approximately 2 million years ago with the early expansions out of Africa by Homo erectus. This initial migration was followed by other archaic humans including H. heidelbergensis, which lived around 500,000 years ago and was the likely ancestor of Denisovans and Neanderthals as well as modern humans. Early hominids had likely crossed land bridges that have now sunk.

The Sidrón Cave is a non-carboniferous limestone karst cave system located in the Piloña municipality of Asturias, northwestern Spain, where Paleolithic rock art and the fossils of more than a dozen Neanderthals were found. Declared a "Partial Natural Reserve" in 1995, the site also serves as a retreat for five species of bats and is the place of discovery of two species of Coleoptera (beetles).

<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.

<span class="mw-page-title-main">Recent African origin of modern humans</span> "Out of Africa" theory of the early migration of humans

In paleoanthropology, the recent African origin of modern humans or the "Out of Africa" theory (OOA) is the mainstream academic model of the geographic origin and early migration of anatomically modern humans. It follows the early expansions of hominins out of Africa, accomplished by Homo erectus and then Homo neanderthalensis.

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

The Denisovans or Denisova hominins 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 25 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 in Siberia, Russia.

<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

Interbreeding between archaic and modern humans occurred during the Middle Paleolithic and early Upper Paleolithic. The interbreeding happened in several independent events that included Neanderthals and Denisovans, as well as several unidentified hominins.

Mezmaiskaya Cave is a prehistoric cave site overlooking the right bank of the Sukhoi Kurdzhips in the southern Russian Republic of Adygea, located in the northwestern foothills of the North Caucasus in the Caucasus Mountains system.

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

Johannes Krause is a German biochemist with a research focus on historical infectious diseases and human evolution. Since 2010, he has been professor of archaeology and paleogenetics at the University of Tübingen. In 2014, Krause was named a founding co-director of the new Max Planck Institute for the Science of Human History in Jena.

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

Ust'-Ishim man is the term given to the 45,000-year-old remains of one of the early modern humans to inhabit western Siberia. The fossil is notable in that it had intact DNA which permitted the complete sequencing of its genome, one of the oldest modern human genomes to be so decoded.

<span class="mw-page-title-main">Goyet Caves</span> Caves and archaeological site in Belgium

The Goyet Caves are a series of connected caves located in Belgium in a limestone cliff about 15 m (50 ft) above the river Samson near the village of Mozet in the Gesves municipality of the Namur province. The site is a significant locality of regional Neanderthal and European early modern human occupation, as thousands of fossils and artifacts were discovered that are all attributed to a long and contiguous stratigraphic sequence from 120,000 years ago, the Middle Paleolithic to less than 5,000 years ago, the late Neolithic. A robust sequence of sediments was identified during extensive excavations by geologist Edouard Dupont, who undertook the first probings as early as 1867. The site was added to the Belgian National Heritage register in 1976.

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

Denny is an ~90,000 year old fossil specimen belonging to a ~13-year-old Neanderthal-Denisovan hybrid girl. To date, she is the only first-generation hybrid hominin ever discovered. Denny’s remains consist of a single fossilized fragment of a long bone discovered among over 2,000 visually unidentifiable fragments excavated at the Denisova Cave in the Altai Mountains, Russia in 2012.

Viviane Slon is a paleogeneticist at the Max Planck Institute for Evolutionary Anthropology. She identified that a teenage girl born 90,000 years ago had both Neanderthal and Denisovan parents. She was selected as one of Nature's 10 in 2018.

<span class="mw-page-title-main">Initial Upper Paleolithic</span> First stage of the Upper Paleolithic

The Initial Upper Paleolithic covers the first stage of the Upper Paleolithic, during which modern human populations expanded throughout Eurasia.

References

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