Family links among the Neanderthals of Siberia

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.

The DNA of some old mammoths

The only positive outcome of the thawing of permafrost is that it exposes remains of ancient animals in a virtually intact state, most famously those of the woolly mammoth (Mammuthus primigenius). But not so well-preserved that anyone could be induced to feast on its thawed-out meat. Tales of select groups being served mammoth at banquets are almost certainly apocryphal, but several have tasted one, and found that the meat smelled rotten and tasted awful. Mammoth bones, being so large, are regularly found and most museums in the Northern Hemisphere display their enormous teeth. DNA from three species of these extinct elephants has been sequenced – North American and European woolly mammoths and the North American Columbian mammoth that thrived on the more temperate central plains. But they lived about 12 to 100 thousand years ago. Now genetic data are available from three molar teeth found in permafrost in the Chukochya river basin in northern Siberia. (van der Valk, T. and 21 others 2021. Million-year-old DNA sheds light on the genomic history of mammoths. Nature v.591, p. 265–269; DOI: 10.1038/s41586-021-03224-9).

Wooly mammoth tooth offered for sale at Christie’s in 2015, which fetched £2750 (Credit: Christie’s on-line archives)

The mammoth molars have been dated at 0.68, 1.0 and 1.2 Ma (conservative estimates), far older than a horse dated between 560 and 780 ka that yielded DNA several years back. The sheer mass of the teeth and the fact that they had been preserved in frozen soil shielded genetic material from complete breakdown, but it was nonetheless heavily degraded to fragments no more than 50 base pairs long. This presented a major challenge to the team of palaeogeneticists’ reconstruction of the three mammoths’ genomes. Comparing the genomes with those of far younger woolly mammoths and their closest living relatives, Indian elephants, reveals that the ancient beasts were cold-adapted and probably had woolly coats. Two of the genomes suggest direct ancestry to both later woolly mammoths, whereas the third – the oldest – can  be linked to the enormous Columbian mammoth (M. columbi) that lived on mid-American grasslands during the Late Pleistocene. During glacial maxima when sea levels were ~100 m lower than at present Siberian faunas could easily have migrated into and colonised the Americas, using the Beringia land bridge across the Bering Strait. An early migration by the oldest Siberian mammoth could have given rise to the Columbian mammoth, later crossings to the American woollies. In fact it seems that genetic strands from the two younger Siberian mammoths also entered the DNA of M. columbi at some stage in its evolution.

Interesting as these revelations are about Arctic ice-age megafaunas, finding human remains that predate a few 10’s of ka in permafrost is unlikely. Modern humans and  Neanderthals are known to have migrated through Arctic Siberia, and perhaps Denisovans did too. Some individuals may have been unfortunate enough to have fallen into boggy ground that froze to form permafrost. However, there is no evidence for older human species having moved north of about 40°N since the first Africans entered 1.8 Ma ago. In any case, without the protection of massive bones, human DNA would probably have degraded more quickly than did that of these old mammoths.

See also: Roca, A.L. 2021. Million-year-old DNA provides a glimpse of mammoth evolution. Nature, v. 591, p. 208-209; DOI: 10.1038/d41586-021-00348-w; Black, R. 2021. Oldest DNA sequenced yet comes from million-year-old mammoths (Smithsonian Magazine, 17 February, 2021)

Arctic climate in the run-up to the Great Ice Age

Around 3.6 Ma ago a large extraterrestrial projectile slammed into the far north-east of Siberia forming crater 16 km across. The depression soon filled with water to form Lake El’gygytgyn, on whose bed sediments have accumulated up to the present. A major impact close to the supposed start of Northern Hemisphere glacial conditions was a tempting target for coring: possibly two birds with one stone as the lowest sediments would probably be impact debris and boreal lake sediments of this age are as rare as hens’ teeth. The sedimentary record of Lake El’gygytgyn has proved to be a climate-change treasure trove (Brigham-Grette, J and 15 others 2013. Pliocene warmth, polar amplification, and stepped Pleistocene cooling recorded in NE Arctic Russia. Science, v. 340, p. 1421-1426).

El'gygytgyn, Russia, is a impact crater with a...
Lake El’gygytgyn impact crater. (credit: Wikipedia)

The team of US, Russian, German and Swedish scientists discovered that the sedimentary record was complete over a depth of 318 m and so promised a high resolution climate record. The striking feature of the sediments is that they show cyclical variation between five different facies, four of which are laminated and so preserve intricate records of varying weathering and sediment delivery to the lake. The sediments also contain pollens and diatom fossils, and yield good magnetic polarity data. The last show up periods of reversed geomagnetic polarity, which provide age calibration independent of relative correlation with marine isotope records.

A host of climate-related proxies, including pollen from diverse tree and shrub genera, variations in silica due to changes in diatom populations and organic carbon content in the cyclically  changing sedimentary facies are correlated with global climate records based on marine-sediment stable isotope. These records reveal intricate oscillations between cool mixed forest, cool coniferous forest, taiga  and cold deciduous forest, with occasional frigid tundra conditions through the mid- to late Pliocene. Compared with modern conditions NE Siberia was much warmer and wetter at the start of the record. Around the start of the Pleistocene sudden declines to cooler and drier conditions appear, although until 2.2 Ma ago average summer conditions seem to have been higher that at present, despite evidence from marine proxies of the onset of glacial-interglacial cycles in the Northern Hemisphere.

In detail, Lake El’gygytgyn revealed some surprises including rapid onset of a lengthy cold-dry spell of tundra conditions between 3.31 to 3.28 Ma. The first signs that the lake was perennially frozen appear around 2.6 Ma, well before evidence for the first continental glaciation in North America, presaged by signs around 2.7 Ma that winters consistently became colder than present ones. Overall the lake record presents a picture of a stepped shift in climate in the run-up to the Great Ice Age. Lake El’gygytgyn seems set to become the standard against which other, more patchy records around the Arctic Ocean are matched and correlated. Indeed it is the longest and most detailed record of climate for the Earth’s land surface, compared with 120 and 800 ka for the Greenland and Antarctic ice-caps.

Modelling their findings against likely atmospheric CO2 levels the authors provide grist to the media mill which focuses on how the late Pliocene may be a model for a future warm Earth if emissions are not curtailed, with visions of dense polar forests