Tag: Interbreeding

Seven thousand years of cultural sharing in Europe between Neanderthals and modern humans

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Two years ago material excavated from the Bacho Kiro cave in Bulgaria revealed that anatomically modern humans (AMH) had lived there between 44 and 47 ka ago: the earliest known migrants into Europe. Bacho Kiro contains evidence of occupancy by both Neanderthals and AMH. This discovery expanded the time over which Europe was co-occupied by ourselves and Neanderthals. The latter probably faded from the scene as an anatomically distinct group around 41 to 39 ka, although some evidence suggests that they lingered in Spain until ~37 ka and perhaps as late as 34 to 31 ka in the northern Ural mountains at the modern boundary of Europe and Asia. For most of Europe both groups were therefore capable of meeting over a period of seven to eight thousand years.

Aside from interbreeding, which they certainly did, palaeoanthropologists have long pondered on a range of tools that define an early Upper Palaeolithic culture known as the Châtelperronian, which also spans the same lengthy episode. But there have been sharp disagreements about whether it was a shared culture and, if so, which group inspired it. Evidence from the Grotte du Renne in eastern France suggests that the Neanderthals did abandon their earlier Mousterian culture to use the Châtelperronian approach early in the period of dual occupancy of Europe.

Dated appearances in France and NE Spain of Neanderthal fossils (black skulls), Châtelperronian artefacts (grey circles) and proto-Aurignacian artefacts (white squares) in different time ‘slots’ between 43.4 and 39.4 ka. (Credit: Djakovic et al., Fig. 3)

Igor Djakovic of Leiden University in the Netherlands , Alastair Key of Cambridge University, UK, and Marie Soressi, also of Leiden University have undertaken a statistical analysis of the geochronological and stratigraphic context of artefacts at Neanderthal and AMH sites in France and NW Spain during the co-occupancy period (Djakovic, I., Key, A. & Soressi, M. 2022. Optimal linear estimation models predict 1400–2900 years of overlap between Homo sapiens and Neandertals prior to their disappearance from France and northern Spain. Scientific Reports, v. 12, article  15000; DOI: 10.1038/s41598-022-19162-z). Their study is partly an attempt to shed light on the ‘authorship’ of the novel technology. The results suggest that the Châtelperronian (Ch) started around 45 ka and had disappeared by ~40.5 ka, along with the Neanderthals themselves. Early AMH artefacts are known as proto-Aurignacian (PA) and bear some resemblance to those of Châtelperronian provenance. The issue revolves around 3 conceivable scenarios: 1. the earliest AMH migrants brought the PA culture with them that Neanderthals attempted to copy, leading to their Ch tools; 2. Neanderthals independently invented the Ch methodology, which AMH adopted to produce PA artefacts; 3. both cultures arose independently.

Djakovic and colleagues have found that the data suggest that the proto-Aurignacian first appeared in the area at around 42.5 ka. Maps of dated human remains and artefacts for six 400-year time ranges from 43.4 to 39.4 ka show only Neanderthal remains and Châtelperronian artefacts from the earliest range (a in the figure). Two sites with proto-Aurignacian artefacts appears in NW Spain during the next ‘slot’ (b) then grow in numbers (c to e) relative to those of Châtelperronian provenance, which are not present after 40 ka (f) and neither are Neanderthal remains. These data suggest that local Neanderthals may have made the technological breakthrough before the appearance of the AMH proto-Aurignacian culture, which supports scenario 2 but not 1. They also suggest that the sudden appearance of Ch in France and Spain and the abandonment of earlier Neanderthal artefacts known as Mousterian could indicate that the Ch culture may have been introduced by Neanderthals migrating into the area, perhaps from further east where they may have been influenced by the earliest known European AMH in Bulgaria: i.e. tentative support for 1 or 2.

However, well documented as Djakovic et al.’s study is, it considers only 17 sites across only a fraction of Europe and a mere 28 individual artefacts each from Neanderthal and AMH associations (56 altogether). More sites and data are bound to emerge. But the study definitely opens exciting new possibilities for cultural ‘cross fertilisation’ as well as the proven physical exchange of genetic material: the two seem very likely to go hand-in-hand. Seven thousand years (~350 generations) of mutual dependence on the resources of southern Europe surely signifies too that the initially distinct groups did not engage in perpetual conflict or ecological competition, as with small numbers of both one or the other would have been extinguished within a few generations.

 See also: Devlin, H. 2022. Neanderthals and modern humans may have copied each other’s tools. The Guardian, 13 October 2022; Davis, N. 2020. Humans and Neanderthals ‘co-existed in Europe for far longer than thought’. The Guardian, 11 May 2020.

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

Relationships between modern humans and Neanderthals

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Before 40 thousand years (ka) ago Europe was co-occupied by Neanderthals and anatomically modern humans (AMH) for between five to seven thousand years; about 350 generations – as long as the time since farming began in Neolithic Britain to the present day. Populations of both groups were probably low given their dependence on hunting and foraging during a period significantly colder than it is now. Crude estimates suggest between 3,000 to 12,000 individuals in each group; equivalent to the attendance at a single English Football League 2 match on a Covid-free winter Saturday afternoon. Moving around Europe south of say 55°N, their potential range would have been around 5 million square kilometres, which very roughly suggests that population density would be one person for every 200 km2. That they would have moved around in bands of, say, 10 to 25 might seem to suggest that encounters were very infrequent. Yet a hybrid Neanderthal-Denisovan female found in Siberia yielded DNA that suggested a family connection with Croatia, 5,000 km away (see: Neanderthal Mum meets Denisovan Dad, August 2018); early humans moved far and wide.

The likely appearances of Neanderthals and anatomically modern humans when they first met between 50 and 40 thousand years ago. (Credit: Jason Ford, New York University)

A sparsely populated land can be wandered through with little fear other than those of predators, sparse resources or harsh climate and lack of shelter. But it still seems incredible for there to have been regular meetings with other bands. But that view leaves out knowledge of good places to camp, hunt and forage that assure shelter, water, game and so forth, and how to get to them – a central part of hunter-gatherers’ livelihoods. There would have been a limited number of such refuges, considerably increasing chances of meeting. Whatever the physiognomic differences between AMH and Neaderthals, and they weren’t very striking, meeting up of bands of both human groups at a comfortable campsite would be cause for relief, celebration, exchanges of knowledge and perhaps individuals of one group to partner members of the other.

As well as that from Neanderthals, ancient DNA from very early European AMH remains has increasingly been teased out. The latest comes from three individuals from Bacho Kiro Cave in Bulgaria dated to between 45.9 to 42.6 ka; among the earliest known, fully modern Europeans. One had a Neanderthal ancestor less than six generations removed (perhaps even a great-great grandparent 60 years beforehand). Because of the slight elapsed time, the liaison was probably in Europe, rather than in the Middle East as previously suggested for insertion of Neanderthal genes into European ancestry. The genetic roots of the other two families stemmed back seven to ten generations – roughly 100 to 150 years (Hajdinjak, M. and 31 others 2021. Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry. Nature, v. 592, p. 253–257; DOI: 10.1038/s41586-021-03335-3). The interpretation of these close relationships stems from the high proportion of Neanderthal DNA (3 to 4 %) in the three genomes. The segments are unusually lengthy, which is a major clue to the short time since the original coupling; inherited segments tend to shorten in successive generations. The groups to which these AMH individuals belonged did not contribute to later Eurasian populations, but link to living East Asians and Native Americans. They seem to have vanished from Europe long before modern times. The same day saw publication of a fourth instance of high Neanderthal genetic content (~3 %) in an early European’s genome, extracted from a ~45 ka female AMH from Zlatý kůň (Golden Horse) Cave in Czechia (Prüfer, K. and 11 others 2021. A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia. Nature Ecology & Evolution  DOI: 10.1038/s41559-021-01443-x). In her case, too, the Neanderthal DNA segments are unusually lengthy, but indicate 70 to 80 generations (~2,000 to 3,000 years) had elapsed. Her DNA also suggests that she was dark-skinned and had brown hair and brown eyes. Overall her genetics, too, do not have counterparts in later European AMH. The population to which she belonged may have migrated westwards from the Middle East, where one of her ancestors had mated with a Neanderthal, perhaps as long as 50 ka ago. But that does not rule out her group having been in Europe at that time. A later modern human, dated at 42 to 37 ka, is a young man from the Petştera cu Oase cave in Romania, whose forbears mixed with Neanderthals. His genome contains 6.4% of Neanderthal DNA, suggesting that his Neanderthal ancestor lived a mere 4 to 6 generations earlier, most likely in Europe, and was perhaps one of the last of that group.

The data suggest that once modern humans came into contact with their predecessors in the Middle East and Europe, mixture with Neanderthals was ‘the rule rather than the exception’. Yet their lack of direct relationship to later Europeans implies that AMH colonisation of Europe occurred in successive waves of people, not all of whom survived. As Palaeolithic specialist Chris Stringer of the Natural History Museum in London cautions, of these multiple waves of incomers ‘Some groups mixed with Neanderthals, and some didn’t. Some are related to later humans and some are not’. Even five thousand years after ‘first contact’, relations of modern humans with Neanderthals remained ‘cordial’, to say the least, including with the last few before their extinction.

See also: Gibbons, A. 2021. More than 45,000 years ago, modern humans ventured into Neanderthal territory. Here’s what happened next. Science, v. 372, News article; DOI: 10.1126/science.abi8830. Callaway, E. 2021. Oldest DNA from a Homo sapiens reveals surprisingly recent Neanderthal ancestry. Nature, v. 592, News article; DOI: 10.1038/d41586-021-00916-0. Genomes of the earliest Europeans (Science Daily, 7 April 2021). Bower, B. 2021 Europe’s oldest known humans mated with Neandertals surprisingly often (ScienceNews, 7 April 2021)

Why did anatomically modern humans replace Neanderthals?

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Extinction of the Neanderthals has long been attributed to pressure on resources following the first influx into Europe by AMH bands and perhaps different uses of the available resources by the two groups. One often quoted piece of evidence comes from the outermost layer in the teeth of deer. Most ruminants continually replace tooth enamel to make up for wear, winter additions being darker than those during summer. Incidentally, the resulting layering gives away their age, as in, ‘Never look a gift horse in the mouth’! Deer teeth associated with Neanderthal sites show that they were killed throughout the year. Those around AMH camps are either summer or winter kills. The implication is that AMH were highly mobile, whereas Neanderthals had fixed hunting ranges whose resources would have been depleted by passing AMH bands. That is as may be, but another possibility has received more convincing support.

Neanderthal populations across their range from Gibraltar to western Siberia were extremely low and band sizes seem to have been small, even before AMH made their appearance. This may have been critical in their demise, based on considerations that arise from attempts to conserve threatened species today (Vaesen, K. et al. 2019. Inbreeding, Allee effects and stochasticity might be sufficient to account for Neanderthal extinction. PLoS One, v. 14, article e0225117; DOI: 10.1371/journal.pone.0225117). The smaller and more isolated groups are, the more likely they are to resort to inbreeding in the absence of close-by potential mates. There is evidence from Neanderthal DNA that such endogamy was practised. Long-term interbreeding between genetic relatives among living human groups is known to result in decreased fitness as deleterious traits accumulate. On top of that, very low population density makes finding mates, closely related or not, difficult (the Allee effect). A result of that is akin to the modern tendency of young people born in remote areas to leave, so that local population falls and becomes more elderly. The remaining elders face difficulties in assembling hunting and foraging parties; i.e. keeping the community going. Many Neanderthal skeletons show signs of extremely hard, repetitive physical effort and senescence; e.g. loss of teeth and evidence of having to be cared for by others. Both factors in small communities are exacerbated by fluctuating birth and death rates and changed gender ratios more than are those with larger numbers; i.e. random events have a far greater overall effect (stochasticity). Krist Vaesen and colleagues from the Netherlands use two modern demographic techniques that encapsulate these tendencies to model Neanderthal populations over  10,000 years.

By themselves, none of the likely factors should have driven Neanderthals into extinction. But in combination they may well have done so, even if modern humans hadn’t arrived around 40 ka. Completely external events, such as epidemics or sudden climate change, would have made little difference. Indeed the very isolation of Neanderthal bands over their vast geographic range would have shielded them from infection, and they had been able to survive almost half a million years of repeated climate crises. If their numbers were always small that begs the question of how they survived for so long. The authors suggest that they ran out of luck, in the sense that, finally, their precariousness came up against a rare blend of environmental fluctuations that ‘stacked the odds’ against them. It is possible that interactions, involving neither competition nor hostility, with small numbers of AMH migrants may have tipped the balance. A possibility not mentioned in the paper, perhaps because it is speculation rather than modelling, is social fusion of the two groups and interbreeding. Perhaps the Neanderthals disappeared because of hybridisation through choice of new kinds of mate. Some closely-related modern species are under threat for that very reason. Although individual living non-African humans carry little more than 3% of Neanderthal genetic material it has been estimated that a very large proportion of the Neanderthal genome is distributed mainly in the population of Eurasia. For that to have happened suggests that interbreeding was habitual and perhaps a popular option

See also: Sample, I. 2019. Bad luck may have caused Neanderthals’ extinction – study. (Guardian 27 November 2019)

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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