Tag: mtDNA

Chinese skull confirmed as Denisovan

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For over a century Chinese scientists have been puzzling over ancient human skulls that show pronounced brow ridges. Some assigned them to Homo, others to species that they believe were unique to China. A widely held view in China was that people now living there evolved directly from them, adhering to the ‘Multiregional Evolution’ hypothesis as opposed to that of ‘Out of Africa’. However, the issue might now have been resolved. In the last few years palaeoanthropologists have begun to suspect that these fossilised crania may have been Denisovans, but none had been subject to genetic and proteomic analysis. The few from Siberia and Tibet that initially proved the existence of Denisovans were very small: just a finger bone and teeth.  Out of the blue, teeth in a robust hominin mandible dredged from the Penghu Channel between Taiwan and China yielded protein sequences that matched proteomic data from Denisovan fossils in Denisova Cave and Baishiya Cave in Tibet, suggesting that Denisovans were big and roamed  widely in East Asia. In 2021 a near-complete robust cranium came to light that had been found in the 1930s near Harbin in China and hidden – at the time the area was under Japanese military occupation. It emerged only when its finder revealed its location in 2018, shortly before his death. It was provisionally called Homo longi or ‘Dragon Man’. Qiaomei Fu of the Institute of Vertebrate Paleontology and Paleoanthropology in Beijing and her colleagues have made a comprehensive study of the fossil.

The cranium found near Harbin, China belonged to a Denisovan. Credit: Hebei Geo University

It is at least 146 ka old, probably too young to have been H. erectus, but predates the earliest anatomically modern humans to have reached East Asia from Africa (~60 ka ago). The Chinese scientists have developed protein- and DNA extraction techniques akin to those pioneered at the Max Planck Institute for Evolutionary Anthropology in Leipzig. It proved impossible to extract sufficient ancient nuclear DNA from the cranium bone for definitive genomic data to be extracted, but dental plaque (calculus) adhering around the only surviving molar in the upper jaw did yield mitochondrial DNA. The mtDNA matched that found in Siberian Denisovan remains (Qiaomei Fu et al. 2025. Denisovan mitochondrial DNA from dental calculus of the >146,000-year-old Harbin cranium. Cell, v. 188, p. 1–8; DOI: 10.1016/j.cell.2025.05.040). The bone did yield 92 proteins and 122 single amino acid polymorphisms, as well as more than 20 thousand peptides (Qiaomei Fu and 8 others 2025. The proteome of the late Middle Pleistocene Harbin individual. Science, v. 388: DOI: 10.1126/science.adu9677). Again, these established a molecular link with the already known Denisovans, specifically with one of the Denisova Cave specimens. Without the painstaking research of the Chinese team, Denisovans would have been merely a genome and a proteome without much sign of a body! From the massive skull it is clear that they were indeed big people with brains much the same size as those of living people. Estimates based on the Harbin cranium suggest an individual weighing around 100 kg (220 lb or ~15 stone): a real heavyweight or rugby prop!

The work of Qiaomei Fu and her colleagues, plus the earlier, more limited studies by Tsutaya et al., opens a new phase in palaeoanthropology. Denisovans now have a genome and well-preserved parts of an entire head, which may allow the plethora of ancient skulls from China to be anatomically assigned to the species. Moreover, by extracting DNA from dental plaque for the first time they have opened a new route to obtaining genomic material: dental calculus is very much tougher and less porous than bone.

See also: Curry, A. ‘Dragon Man’ skull belongs to mysterious human relative. 2025. Science, v. 388; DOI: 10.1126/science.z8sb68w. Smith K. 2025. We’ve had a Denisovan skull since the 1930s – only nobody knew. Ars Technica, 18 June 2025. Marshall, M. 2025. We finally know what the face of a Denisovan looked like. New Scientist 18 June 2025.

How did African humans survive the 74 ka Toba volcanic supereruption?

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The largest volcanic eruption during the 2.5 million year evolution of the genius Homo, about 74 thousand years (ka) ago, formed a huge caldera in Sumatra, now filled by Lake Toba. A series of explosions lasting just 9 to 14 days was forceful enough to blast between 2,800 to 6,000 km3 of rocky debris from the crust. An estimated 800 km3 was in the form of fine volcanic ash that blanketed South Asia to a depth of 15 cm. Thin ash layers containing shards of glass from Toba occur in marine sediments beneath the Indian Ocean, the Arabian and South China Seas. Some occur as far off as sediments on the floor of Lake Malawi in southern Africa. A ‘spike’ of sulfates is present at around 74 ka in a Greenland ice core too. Stratospheric fine dust and sulfate aerosols from Toba probably caused global cooling of up to 3.5 °C over a modelled 5 years following the eruption. To make matters worse, this severe ‘volcanic winter’ occurred during a climatic transition from warm to cold caused by changes in ocean circulation and falling atmospheric CO2 concentration, known as a Dansgaard-Oeschger event.

There had been short-lived migrations of modern humans out of Africa into the Levant since about 185 ka. However, studies of the mitochondrial DNA (mtDNA) of living humans in Eurasia and Australasia suggest that permanent migration began about 60 ka ago. Another outcome of the mtDNA analysis is that the genetic diversity of living humans is surprisingly low. This suggests that human genetic diversity may have been sharply reduced globally roughly around the time of the  Toba eruption. This implies a population bottleneck with the number of humans alive at the time to the order of a few tens of thousands (see also: Toba ash and calibrating the Pleistocene record; December 2012). Could such a major genetic ‘pruning’ have happened in Africa? Over six field seasons, a large team of geoscientists and archaeologists drawn from the USA, Ethiopia, China, France and South Africa have excavated a rich Palaeolithic site in the valley of the Shinfa River, a tributary of the Blue Nile in western Ethiopia. Microscopic studies of the sediments enclosing the site yielded glass shards whose chemistry closely matches those in Toba ash, thereby providing an extremely precise date for the human occupation of the site: during the Toba eruption itself (Kappelman, Y. and 63 others 2024. Adaptive foraging behaviours in the Horn of Africa during Toba supereruption. Nature, v. 627; DOI: 10.1038/s41586-024-07208-3).

Selection of possible arrowheads from the Shinfa River site (Credit: Kappelman et al.; Blue Nile Survey Project)

The artifacts and bones of what these modern humans ate suggest a remarkable scenario for how they lived. Stone tools are finely worked from local basalt lava, quartz and flint-like chalcedony found in cavities in lava flows. Many of them are small, sharp triangular points, some of which show features consistent with their use as projectile tips that fractured on impact; they may be arrowheads, indeed the earliest known. Bones found at the site are key pointers to their diet. They are from a wide variety of animal, roughly similar to those living in the area at present: from monkeys to giraffe, guinea fowl to ostrich, and even frogs. There are remains of many fish and freshwater molluscs. Although there are no traces of plant foods, clearly those people who loved through the distant effects of Toba were well fed. Although a period of global cooling may have increased aridity at tropical latitudes in Africa, the campers were able to devise efficient strategies to obtain victuals. During wet seasons they lived off terrestrial prey animals, and during the driest times ate fish from pools in the river valley. These are hardly conditions likely to devastate their numbers, and the people seem to have been technologically flexible. Similar observations were made at the Pinnacle Point site in far-off South Africa in 2018, where Toba ash is also present. Both sites refute any retardation of human cultural progress 74 ka ago. Rather the opposite: people may have been spurred to innovation, and the new strategies may have allowed them to migrate more efficiently, perhaps along seasonal drainages. In this case that would have led them or their descendants to the Nile and a direct route to Eurasia; along ‘blue highway’ corridors as Kappelman et al. suggest.

Yet the population bottleneck implied by mtDNA analyses is only vaguely dated: it may have been well before or well after Toba. Moreover, there is a 10 ka gap between Toba and the earliest accurately dated migrants who left Africa – the first Australians at about 65 ka. However, note that there is inconclusive evidence that modern humans may have occupied Sumatra by the time of the eruption.  Much closer to the site of the eruption in southeast India, stone artifacts have been found below and above the 74 ka datum marked by the thick Toba Ash. Whether these were discarded by anatomically modern humans or earlier migrants such as Homo erectus remains unresolved. Either way, at that site there is no evidence for any mass die-off, even though conditions must have been pretty dreadful while the ash fell. But that probably only lasted for little more than a month. If the migrants did suffer very high losses to decrease the genetic diversity of the survivors, it seems just as likely to have been due to attrition on an extremely lengthy trek, with little likelihood of tangible evidence surviving. Alternatively, the out-of-Africa migrants may have been small in number and not fully representative of the genetic richness of the Africans who stayed put: a few tens of thousand migrants may not have been very diverse from the outset.

Family links among the Neanderthals of Siberia

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Caves used by the Neanderthals of southern Siberia: A – location map; B – Chagyrskaya Cave; C – Okladnikov Cave. (Credit: adapted from Skov et al.; Extended Data Fig. 1)

The early focus on Neanderthals was on remains found in Western Europe from the 19th century onwards. That has shifted in recent years to southern Siberia in the foothills of the Altai mountains, despite the fossils’ fragmentary nature: a few teeth and bits of mandible. The Denisova Cave became famous not just because it contained the easternmost evidence of Neanderthal occupation but through the genetic analysis of a tiny finger-tip bone. It proved not to be from a Neanderthal but a distinctly different hominin species, dubbed Denisovan (see: Other rich hominin pickings; May 2010). What Denisovans looked like remains unknown but genetic traces of them are rife among living humans of the western Pacific islands and Australia, whose ancestors interbred with Denisovans, presumably in East Asia. Modern people indigenous to Europe and the Middle East have Neanderthal genes in their genomes. Other bone fragments from Denisova Cave also yielded Neanderthal genomes, and the cave sediments yielded traces of both groups (see: Detecting the presence of hominins in ancient soil samples; April 2017). Then in 2018 DNA extracted from a limb bone from the cave clearly showed that it was from a female teenager who had had a Neanderthal mother and a Denisovan father (see: Neanderthal Mum meets Denisovan Dad; August 2018). These astonishing and unexpected finds spurred further excavations and genetic analysis in other caves within 100 km of Denisova Cave. This was largely led by current and former co-workers of Svanti Pääbo, of the Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany: Pääbo was awarded the 2022 Nobel Prize in Physiology or Medicine for his coordination of research and discoveries concerning ancient human genomes. Their enormous field and laboratory efforts have paid astonishingly valuable dividends (Skov, L. and 34 others 2022. Genetic insights into the social organization of Neanderthals. Nature v. 610, p. 519–525; DOI: 10.1038/s41586-022-05283-y).

To the previously analysed 18 Neanderthal genomes from 14 archaeological sites across Eurasia (including Denisova Cave) Skov et al. have added 13 more from just two sites in Siberia (the Chagyrskaya and Okladnikov caves). Each site overlooks valleys along which game still migrates, so they may have been seasonal hunting camps rather than permanent dwellings: they are littered with bison and horse bones. Tools in the two 59-51 ka old human occupation levels are different from those at the older (130 to 91 Ka) Denisova Cave about 100 km to the east. As at the much older site, human fossils include several teeth and fragments of bones from jaws, hands, limbs and vertebrae. The detailed genomes recovered from 17 finds shows them to be from 14 individuals (12 from Chagyrskaya, 2 from Okladnikov).

Chagyrskaya yielded evidence for 5 females (3 adults and 2 children) and 7 males (3 children and 4 adults). One female estimated to have lost a premolar tooth when a teenager was the daughter of a Chagyrskaya adult male. He, in turn, was brother or father to another male, so the girl seems to have had an uncle as well. Another male and female proved to be second-degree relations (includes uncles, aunts, nephews, nieces, grandparents, grandchildren, half-siblings, and double cousins). The two people from Okladnikov were an adult female and an unrelated male child. The boy was not related to the Chagyrskaya group, but the woman was, her former presence at that cave lingering in its cave-sediment DNA. None of the newly discovered individuals were closely related to six of the seven much older Denisova Cave Neanderthals, but the Okladnikov boy had similar mtDNA to one individual from Denisova.

Further information about the Chagyrskaya group came from comparison of DNA in Y-chromosomes and mitochondria. The father of the teenage girl had two types of mtDNA – the unusual characteristic of heteroplasmy – that he shared with two other males. This suggests that three of the males shared the same maternal lineage – not necessarily a mother – and also indicates that they lived at roughly the same time. The mtDNA recovered from all Chagyrskaya individuals was much more varied than was their Y-chromosome DNA (passed only down male lineage). One way of explaining that would be females from different Neanderthal communities having migrated into the Chagyrskaya group and mated with its males, who largely remained in the group: a ‘tradition’ known as patrilocality, which is practised in traditional Hindu communities, for instance.

So, what has emerged is clear evidence for a closely related community of Neanderthals at Chagyrskaya, although it cannot be shown that all were present there at the same time, apart from the five who show first- or second-degree relatedness or mitochondrial heteroplasmy. Those represented only by individual teeth didn’t necessarily die there: adult teeth can be lost through trauma and deciduous teeth fall out naturally. There was also some individual physical connection between the two caves: The Okladnikov woman’s DNA being in the sediment at Chagyrskaya. Looking for DNA similarities more widely, it appears that all individuals at Chagyrskaya may have had some ancestral connection with Croatian Neanderthals, as did the previously mentioned mother of the Denisovan-Neanderthal hybrid girl. Four of the Chagyrskaya individuals can also be linked genetically to Neanderthals from Spain, more so than to much closer individuals found in the Caucasus Mountains. So, by around 59-51 ka the results of a wave of eastward migration of Neanderthals had reached southern Siberia. Yet the apparent matrilineal relatedness of the Okladnikov boy to the much older Neanderthals of Denisova Cave suggests that the earlier group continued to exist.

The new results are just as fascinating as the 2021 discovery that ancient DNA from Neolithic tomb burials in the Cotswolds of SW England suggests that the individual skeletons represent five continuous generations of one extended family. The difference is that they were farmers tied to the locality, whereas the Siberian Neanderthals were probably hunter gatherers with a very wide geographic range.  Laurits Skov and his colleagues have analysed less than one-quarter of the Neanderthal remains already discovered in Chagyrskaya and Okladnikov caves and only a third of the cave deposits have been excavated. Extracting and analysing ancient DNA is now far quicker, more detailed and cheaper than it was in 2010 when news of the first Neanderthal genome broke. So more Neanderthal surprises may yet come from Siberia. Progress on the genetics of their anatomically-modern contemporaries in NE Asia has not been so swift.

See also:  Callaway, E. 2022. First known Neanderthal family discovered in Siberian cave.  Nature online 19 October 2022.

Early human migrations in southern Africa

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Comparing the DNA profiles of living people who are indigenous to different parts of the world has achieved a lot as regards tracing the migrations of their ancestors and amalgamations between and separations from different genetic groups along the way. Most such analyses have centred on alleles in DNA from mitochondria (maternal) and Y chromosomes (paternal), and depend on the assumption that rates of mutation (specifically those that have neither negative nor positive outcomes) in both remain constant over tens of thousand years and genetic intermixing through reproduction. Both provide plausible hypotheses of where migrations began, the approximate route that they took and the timing of both departures from and arrival at different locations en route. Most studies have focused on the ‘Out of Africa’ migration, which began, according to the latest data, around 80 ka ago. Arrival times at various locations differ considerably, from around 60 ka for the indigenous populations of Australia and New Guinea, roughly 40 ka for Europe and ~12 ka for the Americas. Yet an often overlooked factor is that not all migrating groups have descendants that are alive today. For instance, remains of anatomically modern humans (AMH)have been found in sediments in the Levant as old as 177 ka (see: Earliest departure of modern humans from Africa, January 2018), and between 170 to 210 ka in southern Greece (See: Out of Africa: The earliest modern human to leave). Neither have yielded ancient DNA, yet nor are their arrival times compatible with the ‘route mapping’ provided by genetic studies of living people. Such groups became extinct and left no traceable descendants, and there were probably many more awaiting discovery. Maybe these mysteries will be penetrated by DNA from the ancient bones, should that prove possible.

The recorded history of AMH within Africa began around 286 to 315 ka in Morocco (see: Origin of anatomically modern humans, June 2017) and their evolutionary development may have spanned much of the continent, judging by previously discovered fossils in Ethiopia and South Africa that are older than 200 ka. Again, ancient DNA has not been extracted from the oldest fossils; nor is that likely to be possible because the double helix breaks down quickly in hot and humid climates. Genetic data from living Africans are growing quickly. An additional 198 African mtDNA genomes reported recently have pushed up the total available for analysis, the bulk of them being from eastern and southern Africa (Chan, E.K.F. and 11 others 2019. Human origins in a southern African palaeo-wetland and first migrations. Nature, v. 575, p. 185-189; DOI: 10.1038/s41586-019-1714-1). The study focuses on data from the KhoeSan ethnic group, restricted to areas south of the Zambezi River, who speak a language with distinctive  click consonants. Some KhoeSan still practice a hunter-gatherer lifestyle. Previous genetic studies showed the KhoeSan to differ markedly from other inhabitants of southern Africa, and they are widely regarded as having inhabited the area for far longer than any other groups. A sign of this emerges from their mtDNA in a genetic lineage signified as L0. Comparing KhoeSan mtDNA with the wider genetic database allowed the researchers to plot a ‘family tree’. Measures of the degree of difference between samples push back the origin of L0 and the KhoeSan themselves to roughly 200 ka.

okavango
The Okavango Delta today during the wet season (Credit: Wikimedia Commons)

It turns out that the LO lineage has several variants, whose geographic distributions allow the approximate place of origin for the lineage and directions of later migration from it to be mapped. It seems that LO was originally indigenous to the modern Okavango Delta and Makgadikgadi salt flats of Botswana. People carrying the original (L0k) variant are estimated to have remained in the broad area for about 70 thousand years. During that time it was all lush, low-lying wetland around a huge, now vanished lake. The hydrology of the area was dramatically split by regional tectonic activity at around 60 ka. The lake simply evaporated to form the salt pan of the Makgadikgadi, leaving only the seasonal Okavango Delta as a destination for flood water. People carrying Lok stayed in the original homeland whereas other shifted. Migration routes to the northeast and towards the southwest and south are crudely mapped by the distribution of the other L0 variants among modern populations. They followed ‘green corridors’ between 130 and 110 ka, the collapse of the ecosystem leaving a small group of the founding population isolated from its descendants.

The paper claims that the former Botswana wetlands were the cradle of the first modern humans. Perhaps in southern Africa, but other, older AMH remains found far off and perhaps undiscovered elsewhere are more likely. But that can only be reconciled with the KhoeSan study by ancient DNA from fossils. Criticism of the sweeping claims in the paper has already been voiced, on these grounds and the study’s lack of data on paternal DNA or whole genomes from the sampled population.

See also: Gibbons, A. 2019. Experts question study claiming to pinpoint birthplace of all humans. Science (online); DOI: 10.1126/science.aba0155