Tag: Denisovans

Wider traces of the elusive Denisovans

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We know that when anatomically modern humans (AMH) arrived in Asia they shared the landscape with ‘archaic’ humans that had a much longer pedigree. In 2010 an individual’s little-finger bone dated to around 30 to 49 ka old was found in the Denisova Cave in central Siberia (at 50°N). It yielded a full genome that was distinctly different from those of AMH and Neanderthals (see: Other rich hominin pickings; May 2010). Four other fossils found subsequently in the Denisova Cave contained similar DNA. Checking the DNA of living humans and fossil Neanderthal remains revealed that the newly discovered human group had interbred with both. In the case of AMH, segments of Denisovan DNA are found in the genomes of indigenous people living in East and South Asia, Australia, the Pacific Islands and the Americas, at levels of 0.2%, rising to 6% in Melanesian people of Papua-New Guinea. But such introgressions have not been found in Europeans (but see below), suggesting that the Denisovans were restricted to Asia.

There have been suggestions that at least some of the ‘archaic’ human remains found widely and abundantly in China may have been Denisovans; although they might equally be of Homo erectus. But none of the Chinese fossils have been subjected to gene sequencing – those found in caves outside tropical and sub-tropical climates might retain DNA just as well as Neanderthal and even older remains in temperate Europe. Yet a partial lower jaw discovered in a cave on the Tibetan Plateau (at 35°N) did yield proteins that had close affinities to those recovered from Siberian Denisovans. Now similar analyses have been performed on an abnormally large molar found in a cave in Northern Laos, showing that it too is most likely to be from a young (as suggested by its being little worn), possibly female (it lacks male-specific peptides), Denisovan. The locality lies at about 20°N, far to the south of the other two Denisovan sites (Demeter, F. et al. A Middle Pleistocene Denisovan molar from the Annamite Chain of northern Laos. Nature Communications, v. 13, article 2557; DOI: 10.1038/s41467-022-29923-z). Sparse as the evidence is, Denisovans were able to tolerate climate differences across 30 degrees of latitude.

A probable Denisovan molar from 164 to 131 ka old cave sediments in northern Laos. (credit: Demeter, et al.; Fig. 2)

The Wikipedia entry for Denisovans is a mine of additional information. For instance, detailed analysis of the roughly 5% of their genome that indigenous people of New Guinea carry suggests that the two groups may have interbred there as late as 30 ka. Since Both New Guinea and Australia were until 8 thousand years ago part of the Sahul landmass when sea level was low during the last ice age, these inferences add tropical occupancy to the Denisovan range. Does this suggest that Papuans and indigenous Australians migrated with Denisovans, or had the latter crossed the sea from Timor earlier and independently, after moving from Asia by ‘hopping’ from island to island through eastern Indonesia? There is a possibility that Denisovans could even have survived in Sahul until as late as 14.5 ka. Even more odd, modern Icelandic people are unique among Europeans in having detectable traces of Denisovan DNA. However, rather than having been directly shared between Denisovans and ancestral Scandinavians – a possibility – it may have been carried by Neanderthal-Denisovan hybrids migrating westwards from Siberia with whom the Icelanders’ ancestors interbred. There are other interesting points in the Wikipedia entry. One is that the consistently lower Denisovan ancestry in living East Asians compared with people of Oceania, may indicate two separate waves of eastward migration by AMH. The latter may have arrived first, had greater contact with Denisovans and then moved on across seaways to remain isolated from the later migrants.

Finally, something that puzzles me as a non-geneticist. If both Denisovans and Neanderthals died out as genetically distinct groups tens of millennia ago how could the genetic traces of interbreeding with AMH have been retained at such high levels until the present; i.e. through thousands of generations? Each of us carries a 50% deal of genes from our parents. Then with each subsequent generation the proportion is diluted, so that we inherit 25% from grandparents, 12.5 % from great-grandparents and so on. Yet Papuans still have 5 to 6 percent of Denisovan DNA: much the same holds for Europeans’ Neanderthal heritage. Does such a high level of retention of this ancestry suggest that a large proportion of the earliest migrating AMH individuals stemmed from generation to generation interbreeding on a massive scale? Did the ‘newcomers’ and ‘locals’ band eventually together almost completely to merge genetically, or am I missing something … ? Probably

Further back in the Eurasian human story

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About 800 to 950 thousand years (ka) ago the earliest human colonisers of northern Europe, both adults and children, left footprints and stone tools in sedimentary strata laid down by a river system that then drained central England and Wales. The fossil flora and fauna at the Happisburgh (pronounced ‘Haze-burra’) site in Norfolk suggest a climate that was somewhat warmer in summers than at present, with winter temperatures about 3°C lower than now: similar to the climate in today’s southern Norway. At that time the European landmass extended unbroken to the western UK, so any hunter-gatherers could easily follow migrating herds and take advantage of seasonal vegetation resources. These people don’t have a name because they left no body fossils. A group known from their fossils as Homo antecessor had occupied Spain, southern France and Italy in slightly earlier times (back to 1200 ka). Since the discovery of their unique mix of modern and primitive traits, they have been regarded as possible intermediaries between H. erectus and H. heidelbergensis – once supposed to be the predecessor of Neanderthals and possibly anatomically modern humans (AMH). Since the emergence about 10 years ago of ancient genomics as the prime tool in examining human ancestry the picture has been shown to be considerably more complex. Not only had AMH interbred with Neanderthals and Denisovans, those two groups were demonstrably interfertile too, and a complex web of such relationships had been pieced together by 2016. But there has been a new development.

700 ka Homo erectus from Java: a possible Eurasian ‘super-archaic’ human (credit: Gibbons 2020)

Population geneticists at the University of Utah, USA, have devised sophisticated means of making more of the detailed ATCG nucleotide sequences in ancient human DNA, despite there being very few full genomes of Neanderthals and Denisovans (Rogers, A.R. et al. 2020. Neanderthal-Denisovan ancestors interbred with a distantly related hominin. Science Advances, v. 6, article eaay5483; DOI: 10.1126/sciadv.aay5483). In Earth-logs you may already have come across the idea of the ancestral ‘ghosts’ that are represented by unusual sections of genomes from living West African people. Those sections seem likely to have resulted from interbreeding with an unknown archaic population – i.e. neither Neanderthal nor Denisovan. It now seems that both Neanderthal and Denisovan genomes also show traces of such introgression with ‘ghost’ populations during much earlier times. The ancestors of both these groups separated from the lineage that led to AMH perhaps 750 ka ago. Rogers et al. refer to the earliest as ‘neandersovans’ and consider that they split into the two groups after they entered Eurasia, at some time before 600 ka – perhaps around 740 ka. This division may well have occurred as a result of a population of ‘neandersovans’ having spread over the vastness of Eurasia and growing genetic isolation. The reanalysis of both sets of genomes show evidence of a ‘neandersovan’ population crash before the split. Thereafter, the early Neanderthal population may have risen to around 16 thousand then slowly declined to ~3400 individuals.

A ‘state-of-play’ view of human interbreeding in Eurasia since 2 Ma ago (credit: Gibbons 2020)

However, the ‘neandersovans’ did not enter a new continent devoid of hominins, for as long ago as 1.9 Ma archaic H. erectus had arrived from Africa.  Both Neanderthal and Denisovan genomes record the presence of sections of ‘super-archaic’ DNA, which reflect early  interbreeding with earlier Eurasian populations. Indeed, Denisovans seem to have repeated their ancestors’ sexual exploits, once they became a genetically distinct group.  From the ‘ghost’ DNA fragments Rogers et al. conclude that the ‘super-archaics’ separated from other humans about two million years ago. They were descended from the first ‘Out-of-Africa’ wave of humans, represented by the fossils humans from Dmanisi in Georgia (see First out of Africa, November 2003 and An iconic early human skull,  October 2013 in Earth-logs Human evolution and migrations). A measure of the potential of novel means of analysing available ancient human DNA is the authors’ ability even to estimate the approximate population size of the interbreeding ‘super-archaic’ group at 20 to 50 thousand. Long thought to be impossible, it now seems possible to penetrate back to the very earliest human genetics, and the more DNA that can be teased out of other Neanderthal and Denisovan fossils the more we will know of our origins.

See also: Gibbons, A. 2020. Strange bedfellows for human ancestors. Science, v. 367, p. 838–839; doi:10.1126/science.367.6480.838

The earliest humans in Tibet

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Modern Tibetans thrive in the rarefied air at altitudes above 4 km partly because they benefit from a genetic mutation of the gene EPAS1, which regulates haemoglobin production. Surprisingly, the segment of Tibetan’s DNA that contains the mutation matches that present in the genome of an undated Denisovan girl’s finger bone found in the eponymous Siberian cave. The geneticists who made this discovery were able to estimate that Tibetans inherited the entire segment sometime in the last 40 thousand years through interbreeding with Denisovans, who probably were able to live at high altitude too. Wherever and whenever this took place the inheritance was retained because it clearly helped those who carried it to thrive in Tibet. The same segment is present in a few percent of living Han Chinese people, which suggests their ancestors and those of the Tibetans were members of the same group some 40 ka ago, most of the Han having lost the mutation subsequently.

That inheritance would have remained somewhat mysterious while the existing evidence for the colonisation of the Tibetan Plateau suggested sometime in the Holocene, possibly by migrating early farmers. A single archaeological site at 4600 m on the Plateau has changed all that (Zhang, X.L. and 15 others 2018. The earliest human occupation of the high-altitude Tibetan Plateau 40 thousand to 30 thousand years ago. Science, v.  362, p. 1049-1051; DOI: 10.1126/science.aat8824). The dig at Nwya Devu, which lies 250 km NW of Lhasa, has yielded a sequence of sediments (dated by optically stimulated luminescence at between 45 to 18 thousand years) that contains abundant stone tools made from locally occurring slate. The oldest coincides roughly with the age of the earliest anatomically modern human migrants into northern China, so the earliest Tibetans may well have been a branch of that same group of people, as suggested by the DNA of modern Tibetan and Han people. However, skeletal remains of both humans and their prey animals are yet to emerge from Nwya Devu, which leaves open the question of who they were. Anatomically modern humans or archaic humans, such as Denisovans?

The tools do not help to identify their likely makers. Slate is easy to work and typically yields flat blades with sharp, albeit not especially durable, edges; they are disposable perhaps explaining why so many were found at Nwya Devu. None show signs of pressure flaking that typify tools made from harder, more isotropic rock, such as flint. Yet they include a variety of use-types: scrapers; awls; burins and choppers as well as blades. The lack of associated remains of prey or hearths is suggested by the authors to signify that the site was a workshop; perhaps that will change with further excavation in the area. The age range suggests regular, if not permanent, occupancy for more than 20 ka

Related articles: Gibbons, A. 2014. Tibetans inherited high-altitude gene from ancient human. Science News,2 July 2014, Zhang J-F. & Dennell, R. 2018. The last of Asia conquered by Homo sapiens. Science, v. 362, p. 992-993; DOI: 10.1126/science.aav6863.

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Neanderthal Mum meets Denisovan Dad

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Two bone fragments from the Denisova Cave – the former abode of an 18th century Russian hermit called Denis – in the Altai region of Siberia yielded ancient  DNA. One matches that from previously analysed Neanderthal remains and the other a genome that could only be ascribed to a hitherto unknown ancient-human population, now known as the Denisovans. Since their discovery further analysis of both modern and ancient DNA has shown that modern humans living outside of Africa contain a few percent of DNA from both ancient-human groups. Soon after leaving Africa some of their ancestors interbred with both; indeed a 40 ka-old modern-human jaw from Romania revealed genetic evidence that the individual had a Neanderthal great-great grandparent. Their descendants spread far and wide to populate Eurasia, Australasia and the Americas. Using the ancient DNA to peer back in time suggests that Neanderthals and Denisovans diverged from a common ancestor between 470 and 380 ka, itself having split from modern-human ancestry between 770 to 550 ka. Denisovan DNA also contains evidence that its ancestry included segments that could only have come from a totally unknown hominin species. Interestingly, DNA from the Neanderthal bone fragment found at Denisova contains fragments from an anatomically modern-human.

Tourists at the entrance to Denisova Cave, Rus...
Tourists at the entrance to Denisova Cave, Russia (credit: Wikipedia)

With such riches from tiny fragments of human bones unearthed from the Denisova Cave, it is no surprise that the team led by Svante Pääbo at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, has subsequently analysed others that showed signs of human proteins. The latest ‘takes the biscuit’. A fragment of limb bone from someone who was at least 13 years old yielded DNA commensurate with their having been the child of a Neanderthal mother and a Denisovan father (Slon, V. and 18 others 2018. The genome of the offspring of a Neanderthal mother and a Denisovan father. Nature, v. 560, published on-line; doi: 10.1038/s41586-018-0455-x). Their child was a girl, who has been nicknamed ‘Denny’ by the team, though ‘Denise’ might seem more appropriate. The only clues to what her father, or any Denisovan, might have looked like stem from a few teeth and a skull fragment from the cave that have yielded Denisovan DNA. The teeth are much larger and the skull fragment is thicker than those of Neanderthals, suggesting that Denisovans were distinctly bigger and more robust than even the sturdy Neanderthals.

The father came from a population related to a later Denisovan found in the cave – the first to be sequenced. This suggests long-term occupancy of the area by Denisovans. But his genome also carries traces of Neanderthal ancestry. Surprisingly, the mother is more closely related to Croatian Neanderthals, rather than to an earlier Neanderthal found in the cave. Neanderthals were clearly capable of migrating between Europe and eastern Eurasia; more than 5000 km in this case. Even though very few archaic humans have been genetically sequenced it is beginning to look as if genetic mixing between diverse hominin groups in the last half million years was common, when they actually met. A custom of marrying outside a closely related group (exogamy) has been popular throughout recorded history; indeed it makes sound genetic sense. With the tiny human population density during the Late Pleistocene, it may then have been cause for mutual celebration.  As documented in Chapters 2 and 3 of David Reich’s Who We Are and How We Got Here (Oxford University Press, 2018) human origins since about 470 ka until the present chart a history of episodic migrations and genetic mixing that certainly makes nonsense of earlier ideas of ‘racial purity’ and casts doubt even on the term ‘species’ as regards members of the genus Homo.

If we are ever to discover who the Denisovans were and what they looked like, the evidence is likely to come from East Asia at latitudes where climate favours preservation of DNA. Advanced sequencing equipment and techniques are now operational in China, where suspected Denisovan remains have been found

See also: Warren, M. 2018. First ancient-human hybrid. Nature, v. 560, p. 417-418; doi: 10.1038/d41586-018-06004-0); Sample, I. 2018. Offspring of Neanderthal and Denisovan identified for first time. The Guardian (22 August 2918).

A revised and updated edition of Steve Drury’s book Stepping Stones: The Making of Our Home World can now be downloaded as a free eBook

Neanderthals and Denisovans at it more often

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Palaeogeneticists certainly have the bit between their teeth as DNA sequencing methods become faster and more productive and statistical methods of sequence analysis and comparison are made more powerful. Only last month I reported on the two-way breeding unearthed from the data on single-chromosome DNA extracted from Croatian and Spanish Neanderthals, as well as some of the tangible inheritance from Neanderthals found in living non-African people. Now a team of statisticians, anthropologists and genetic sequencers have applied the new approaches to the genomes of over 1500 non-Africans, including 35 living Melanesian people from Papua-New Guinea (Vernot, B. and 16 others 2016.  Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals. Science, v. 351 doi:10.1126/science.aad9416).  Melanesians had previously shown evidence of hybridization with both Neanderthals and Denisovans. The most interesting outcome is that the analyses pointed towards yet more instances of interbreeding between ancestors of modern non-Africans and Neanderthals. Many East Asians have 3 Neanderthals in their family trees, for Europeans and South Asians the score is 2, while Melanesians show descent from one Neanderthal and one Denisovan. Moreover, it emerges that interbreeding episodes were at different times among different populations since anatomically modern humans migrated from Africa, beginning perhaps as long ago as 130 ka and recurring later, after different regional groups of AMH had proceeded on their separate ways.

English: Melanesia, a cultural and geographica...
Melanesia, a cultural and geographical area in the Pacific. (credit: Wikipedia)

A second study (Sankararaman, S. et al. 2016. The combined landscape of Denisovan and Neanderthal ancestry in modern humans. Current Biology, v. 26, p. 1-7) has teased out evidence for Denisovan ancestry among South Asians, their admixture with Melanesians after that group acquired Neanderthal forebears, and significant signs  of dwindling fertility among hybrid males.

Early 2016 has been very fertile as regards palaeoanthropology. Katherine Zink and Daniel Lieberman of Harvard University focus on the small teeth of Homo erectus and later humans, wondering if they arose following a major shift in culinary practices (Zink, K.D. & Lieberman, D.E. 2016. Impact of meat and lower Palaeolithic food processing techniques on chewing in humans. Nature, v. 531, p. 500-503). Their work is based  on experiments to discover how much chewing is needed to make it possible to swallow different uncooked foodstuffs (assuming that cooking did not arise until after 500 ka). It seems that simply introducing meat to the diet would have reduced mastication by around 13% (2 million chews) per year, with a 15% reduction in applied chewing force. Simply slicing and pounding takes out another 750 thousand annual chews and gives a 12% fall in average biting force. So, here’s a link between tools and human gnashers as well as with development of the hand. Fascinating, perhaps, but every hominin species since 7 Ma old Sahelanthropus tchadensis had far smaller canine teeth than are the norm among non-hominin living and fossil apes. Something else was going on with dentition during our evolution, which may have been a loss of the need for threatening teeth. From ‘Do that again and I’ll bite you’, to ‘Let’s chew this over’…

More on Neanderthals, Denisovans and anatomically modern humans

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