Month: October 2022

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.

Origin of animals at a time of chaotic oxygen levels

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Every organism that you can easily see is a eukaryote, the vast majority of which depend on the availability of oxygen molecules. The range of genetic variation in a wide variety of eukaryotes suggests, using a molecular ‘clock’, that the first of them arose between 2000 to 1000 Ma ago. It possibly originated as a symbiotic assemblage of earlier prokaryote cells ‘bagged-up’ within a single cell wall: Lynn Margulis’s hypothesis of endosymbiosis. It had to have happened after the Great Oxygenation Event (GOE 2.4 to 2.2 Ga), before which free oxygen was present in the seas and atmosphere only at vanishingly small concentrations. Various single-celled fossil possibilities have been suggested to be the oldest members of the Eukarya but are not especially prepossessing, except for one bizarre assemblage in Gabon. The first inescapable sign that eukaryotes were around is the appearance of distinctive organic biomarkers in sediments about 720 Ma old. The Neoproterozoic is famous for its Snowball Earth episodes and the associated multiplicity of large though primitive animals during the Ediacaran Period (see: The rise of the eukaryotes; December 2017).

The records of carbon- and sulfur isotopes in Neo- and Mesoproterozoic sedimentary rocks are more or less flat lines after a mighty hiccup in the carbon and sulfur cycles that followed the GOE and the earliest recorded major glaciation of the Earth. The time between 2.0 and 1.0 Ga has been dubbed ‘the Boring Billion’. At about 900 Ma, both records run riot. Sulfur isotopes in sediments reveal the variations of sulfides and sulfates on the seafloor, which signify reducing and oxidising conditions respectively.  The δ13C record charts the burial of organic carbon and its release from marine sediments related to reducing and oxidising conditions in deep water. There were four major ‘excursions’ of δ13C during the Neoproterozoic, which became increasingly extreme. From constant anoxic, reducing conditions throughout the Boring Billion the Late Neoproterozoic ocean-floor experienced repeated cycles of low and high oxygenation reflected in sulfide and sulfate precipitation and by fluctuations in trace elements whose precipitation depends on redox conditions. By the end of the Cambrian, when marine animals were burgeoning, deep-water oxic-anoxic cycles had been smoothed out, though throughout the Phanerozoic eon anoxic events crop up from time to time.

Atmospheric levels of free oxygen relative to that today (scale is logarithmic) computed using combined carbon- and sulfur isotope records from marine sediments since 1500 Ma ago. The black line is the mean of 5,000 model runs, the grey area represents ±1 standard deviations. The pale blue area represents previous ‘guesstimates’. Vertical yellow bars are the three Snowball Earth events of the Late Neoproterozoic (Sturtian, Marinoan and Gaskiers). (Credit: Krause et al., Fig 1a)

The Late Neoproterozoic redox cycles suggest that oxygen levels in the oceans may have fluctuated too. But there are few reliable proxies for free oxygen. Until recently, individual proxies could only suggest broad, stepwise changes in the availability of oxygen: around 0.1% of modern abundance after the GOE until about 800 Ma; a steady rise to about 10% during the Late Neoproterozoic; a sharp rise to an average of roughly 80% at during the Silurian attributed to increased photosynthesis by land plants. But over the last few decades geochemists have devised a new approach based on variations on carbon and sulfur isotope data from which powerful software modelling can make plausible inferences about varying oxygen levels. Results from the latest version have just been published (Krause, A.J. et al. 2022. Extreme variability in atmospheric oxygen levels in the late Precambrian. Science Advances, v. 8, article 8191; DOI: 10.1126/sciadv.abm8191).

Alexander Krause of Leeds University, UK, and colleagues from University College London, the University of Exeter, UK and the Univerisité Claude Bernard, Lyon, France show that atmospheric oxygen oscillated between ~1 and 50 % of modern levels during the critical 740 to 540 Ma period for the origin and initial diversification of animals. Each major glaciation was associated with a rapid decline, whereas oxygen levels rebounded during the largely ice-free episodes. By the end of the Cambrian Period (485 Ma), by which time the majority of animal phyla had emerged, there appear to have been six such extreme cycles.

Entirely dependent on oxygen for their metabolism, the early animals faced periodic life-threatening stresses. In terms of oxygen availability the fluctuations are almost two orders of magnitude greater than those that animal life faced through most of the Phanerozoic. Able to thrive and diversify during the peaks, most animals of those times faced annihilation as O2 levels plummeted. These would have been periods when natural selection was at its most ruthless in the history of metazoan life on Earth. Its survival repeatedly faced termination, later mass extinctions being only partial threats. Each of those Phanerozoic events was followed by massive diversification and re-occupation of abandoned and new ecological niches. So too those Neoproterozoic organism that survived each massive environmental threat may have undergone adaptive radiation involving extreme changes in their form and function. The Ediacaran fauna was one that teemed on the sea floor, but with oxygen able to seep into the subsurface other faunas may have been evolving there exploiting dead organic matter. The only signs of that wholly new ecosystem are the burrows that first appear in the earliest Cambrian rocks. Evolution there would have ben rife but only expressed by those phyla that left it during the Cambrian Explosion.

There is a clear, empirical link between redox shifts and very large-scale glacial and deglaciation events. Seeking a cause for the dramatic cycles of climate, oxygen and life is not easy. The main drivers of the greenhouse effect CO2­ and methane had to have been involved, i.e. the global carbon cycle. But what triggered the instability after the ‘Boring Billion’? The modelled oxygen record first shows a sudden rise to above 10% of modern levels at about 900 Ma, with a short-lived tenfold decline at 800 Ma. Could the onset have had something to do with a hidden major development in the biosphere: extinction of prokaryote methane generators; explosion of reef-building and oxygen-generating stromatolites? How about a tectonic driver, such as the break-up of the Rodinia supercontinent? Then there are large extraterrestrial events … Maybe the details provided by Krause et al. will spur others to imaginative solutions. See also: How fluctuating oxygen levels may have accelerated animal evolution. Science Daily, 14 October 2022

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.

Amber, palaeontologists and a military dictatorship

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Most people are familiar with the term ‘blood diamonds’, meaning diamonds clandestinely exported from areas infested by the lethal activities of military and paramilitary forces. Indeed such conflicts are often fuelled by the large profits to be made from trading diamonds.  One such source was in Sierra Leone during the civil war of 1991-2002. Others include Liberia, Côte d’ Ivoire, Angola and the Democratic Republic of Congo. Like illicit money, gemstones can be ‘laundered’ and find their way into conventional trade. To some extent the blood diamond trade has been slowed down by a programme of certification of packaged uncut diamond ‘rough’ by bona fide producers, and banning the sale of uncertified rough. The Kimberley Programme has been criticised because certificates can be issued in corrupt ways, so that blood diamonds probably still make their way to the international diamond markets: certification may hold no fears for those who force people to ine at gun point. However, because diamonds often show geochemical signatures and minute inclusions of other minerals that are unique to individual pipe-like intrusions of kimberlite that carry deep-mantle material to the surface. So, it is technically possible – but costly – to check for suspect rough. Such controls do not apply to other gemstones. A major source of very-high value gems is Myanmar (formerly Burma), whose widely condemned military dictatorship may be engaged in their unethical trade, including smuggling to neighbouring Thailand and China to avoid scrutiny.

Foot of bird chick preserved in Cretaceous amber from Kachin, Myanmar. Credit: Pinterest, Xing Lida, China University of Geosciences)

Myanmar is well endowed with sedimentary deposits that contain amber, the solidified resin from a variety of now extinct trees. Oddly, completely clear amber has low intrinsic value: it is semi-precious, albeit attractive. But it often contains inclusions of vegetation fragments, insects, feathers and small vertebrates, of interest to palaeontologists. Myanmar amber is especially interesting as it is dated to the Middle Cretaceous (~130 Ma), older than that found around the Baltic Sea (Eocene ~44 Ma), which was the main source for European jewellery since the 12th century, and that from Canada (Upper Cretaceous ~80 Ma). Myanmar amber has been used decoratively and medicinally in China since the 3rd century CE, and in Europe since prehistoric times. It is attractive but quite common, so historically amber never commanded high prices but was widely used as a trade item. Since the publicity attending the supposed extraction of dinosaur DNA from the bodies of reptile parasites to resurrect dinosaurs in Steven Spielberg’s 1993 film Jurassic Park, public and scientific interest in amber has boomed. It is primarily the exquisite preservation of encased organisms that piques the interest of palaeontologists. Papers that rely on the Myanmar amber have grown in number over the last ten years, despite the country being infamous for military repression of tribal and religious groups in its rural areas.

One of the most conflict-riven areas is the northern state of Kachin where the most interesting amber to palaeontologists is collected by the Kachin people of the Hukawng Valley. Government forces have been in conflict with the Kachin Independence Army since the 1960s, most particularly for control of the amber industry. A recent paper has focussed on the ethical issue of publications based on fossil-bearing amber from the area (Dunne, E.M. et al. 2022. Ethics, law, and politics in palaeontological research: The case of Myanmar amber. Communications Biology, v. 5, article no. 1023; DOI: 10.1038/s42003-022-03847-2).

In 2010 the military began forcibly to take over mines in Kachin.  Between 2014 and 2021 the annual number of publication underwent a tenfold growth from between 10 to 15 to over 150, despite the fact that in 2015 the government in Yangon prohibited removal of fossils from the country. But the export laws exempt gemstones, so the growing demand for fossiliferous amber is clearly reflected in its supply to foreign scientists.  Rare specimens that include vertebrate remains command prices up to US$100,000. The Myanmar amber trade is now estimated at around US$ 1 billion per annum. The Myanmar military took over all the mines in 2017, and is clearly the main supplier to palaeontologists.

In the seven-year period, only 3 papers out of 872 included contributors from Myanmar, which also suggests an element of ‘parachute science’: unsurprisingly Myanmar-based scientists also find it difficult to visit the Kachin area. Before 2014 most of the 69 publications involved scientists in the US; since then, the top spot has been occupied by Chinese scientists who have amassed 417. It seems clear that there is a web of contacts linking together the source of Myanmar amber, its market and science. In 2020 the Society of Vertebrate Paleontology called for a moratorium on publishing data from Kachin sources. But since then there is little sign that palaeontologists have taken any notice.

See also: Ortega, R.P. 2022. Violent conflict in Myanmar linked to boom in fossil amber research, study claims. Science v. 378, p.10-11; DOI: 10.1126/science.adf0973 (This commentary includes opinion that seeks to mitigate the views of Emma Dunne and colleagues)