Denisovan – Earth-logs

Symbolic art made by Denisovans (?)

Published on August 29, 2019August 29, 2019 by zooks777Leave a comment

The deep soil by a permanent spring in a vegetable allotment on the edge of the small town of Lingjing near Xuchang City in Henan Province, China has provided a wealth of stone artefacts and bone fragments to a depth of 10 m (see Denisovan(?) remains in the garden, March 2017). Optically stimulated luminescence (OSL) dating of mineral grains shows that the last time that the deepest soils were exposed to sunlight was between 78 to 123 ka. Long before the first arrival of anatomically modern humans (AMH) in China the site had been much as it is today, a human habitation site. Among the bones were fragments of the crania from five human individuals, perhaps either Homo erectus descended from the earliest arrivals in China or more recent Denisovans closely related to the Neanderthals of western Eurasia. Reconstruction of the two most complete crania hinted at the second possibility by resemblance to Neanderthal anatomy yet the complete lack of evidence that Neanderthals travelled so far to the east.

denisovan arft — Top: lines etched through ochre veneer on a rib bone from Lingjing, China; bottom: hashed lines carved on a faceted block of hematite from Blombos Cave (Credit: Li et al 2019; Fig. 3 and Chris Henshilwood)

So far there have been no reports of DNA from these enigmatic fossils, but some of the bones from the deepest layers show etched, roughly parallel lines (Li, Z et al. 2019. Engraved bones from the archaic hominin site of Lingjing, Henan Province. Antiquity, v. 370, p. 886-900; DOI: 10.15184/aqy.2019.81). Analysis shows that they were deliberately made after the bones had been defleshed: the fragments have thin veneers of red ochre through which the deep scratches reveal white bone. They are not cut marks, but the scratches on previously reddened bone suggest some form of design. This is by no means the earliest symbolic art, for shells associated with Eugene Dubois’s ~500 ka old ‘Pithecanthropus’ (Homo) erectus remains from Trinil, Java are similarly engraved (see Art from half a million years ago. December 2014). Yet the Lingjing engravings predate the oldest know symbolic art from the Blombos Cave of South Africa that was produced by AMH who lived in about 75 ka ago. Neanderthal artistic ability has shown up at many sites (see Human evolution and migrations, March 2011; May 2016; February 2018)

An ability to express mental concepts of some kind in a durable way now seems to have characterised at least four human species over the last half-million years.

See also: Schuster, R. 2019. Prehistoric Art or Doodle? 110,000-year-old Engraved Bones Create New Mystery (Haaretz, 31 July 2019); Denisovan(?) remains in a Chinese garden (Earth-logs, March 2017)

Denisovan on top of the world

Published on May 6, 2019July 2, 2019 by zooks777Leave a comment

Who the Denisovans were is almost completely bound up with their DNA. Until 2019 their only tangible remains were from a single Siberian cave and amounted to a finger bone, a toe bone three molars and fragment of limb bone. Yet they provided DNA from four individuals who lived in Denis the Hermit’s cave from 30 to more than 100 thousand years ago. The analyses revealed that the Denisovans, like the Neanderthals, left their genetic mark in modern people who live outside of Africa, specifically native people of Melanesia and Australia . Remarkably, one of them revealed that a 90 ka female Denisovan was the offspring of a Denisovan father and a Neanderthal mother whose DNA suggested that she may have come from the far-off Balkans. Living, native Tibetans, whose DNA has been analysed, share a gene (EPAS1) with Denisovans, which regulates the body’s production of haemoglobin and enables Tibetans and Nepalese Sherpas to thrive at extremely high altitudes (see The earliest humans in Tibet).

407458aa.2 — The Baishiya Karst Cave in eastern Tibet, with Buddhist prayer flags (credit: Dongju Zhang, Lanzhou University )

Part of a hominin lower jaw unearthed by a Buddhist monk in 1980 from a cave on the Tibetan Plateau, at a height of 3280 m, found its way by a circuitous route to the Max Planck Institute for Evolutionary Anthropology in Leipzig in 2016. It carries two very large molars comparable in size with those found at the Denisova Cave, and which peculiarly have three roots rather than the four in the jaws of non-Asian, living humans. East Asians commonly show this trait. This and other aspects of the fossil teeth resemble those of some uncategorised early hominin fossils from China. Dating of speleothem calcium carbonate with which the jaw is encrusted suggests that the fossil dates back to at least 160 thousand years ago, around the oldest date recovered from Denisova Cave; during the glacial period before the last one. So the individual was able to survive winter conditions worse than those experienced today on the Tibetan Plateau. Further excavation in the cave found numerous stone artefacts and cut-marked animal bones (Chen, F. and 18 others 2019. A late Middle Pleistocene Denisovan mandible from the Tibetan Plateau. Nature, v. 569, published online; DOI: 10.1038/s41586-019-1139-x).

Unfortunately the Tibetan Jaw did not yield DNA capable of being sequenced, so the issues of inheritance of the ‘high-altitude’ gene and wider relatedness of the individual could not be checked. However, one of the teeth did contain preserved protein that can be analysed in an analogous way to DNA, but with less revealing detail. The results were sufficient to demonstrate that the mandible was consistent with a hominin population closely related to the Denisovans of the Siberian cave.

No doubt a path has already been beaten to the Tibetan cave, in the hope of further hominin material. To me the resemblance of the Tibetan fossil jaw to other hominin finds in China, including those from Xuchang, summarised here, is exciting. None of them have been subject to modern biological analysis. Perhaps the ‘real Denisovan’ will emerge from them.

Read more on Human evolution and migrations

Detecting the presence of hominins in ancient soil samples

Published on April 30, 2017 by zooks7771 Comment

Out on the plains countless herbivores fertilise the ground by continual urination and defecation. A friend’s sheep are doing just that in the small field that came with my current home while they are keeping the grass under control. Millions of hectares of prime agricultural land in China are kept fertile through disposal of human night soil from ‘honey wagons’ every day; it is even fed to fishes in small ponds. Such a nice economy also donates the DNA of the animal and plant inhabitants to the soil system. In 2015 analysis of environmental DNA from permafrost in Siberia and Alaska produced ‘bar codes’ for the now vanished ecosystems of what was mammoth steppe during the climate decline to the last glacial maximum and the subsequent warming. The study revealed mammoth and pre-Columbian horse DNA and changes in the steppe vegetation, from which it was concluded that the steppe underwent regional extinction pulses of its megafauna linked to rapid climate ups and downs connected with Dansgaard-Oeschger cycles. It was but a small step to see the potential for studying distribution and timing of various hominins’ occupation of caves from the soils preserved within them, without depending on generally very rare occurrences of human skeletal remains.

The Max Planck Institute for Evolutionary Anthropology in Leipzig, now famous for extracting DNA from Neanderthal, Denisovan and possibly H. antecessor fossils, has applied the environmental DNA approach to sediments from 7 caves in France, Belgium, Spain, Croatia and Russia that span the period from 550 to 14 ka (Slon, V. and 30 others 2017. Neandertal and Denisovan DNA from Pleistocene sediments. Science, v. 356 (online publication); doi:10.1126/science.aam9695). The sites had previously yielded fossils and/or artefacts. All of them contained mitochondrial DNA from diverse large mammals, four including archaic human genetic material supplied by Neanderthal individuals and Denisovans in the case of the Denisova cave. A key finding was Neanderthal mtDNA in one sedimentary layer that contained no skeletal remains – decay of a body was probably not involved. In two cases the DNA was from more than one individual. A variety of tests showed that surprisingly large quantities of DNA survive in soil and that it is spread evenly in sediment rather than being present in spots – an indication of derivation from urine, excreta or decayed soft tissue.

Although the study does not add to knowledge of hominin genetics, it confirms that the methodology is sufficiently advanced and efficient to detect hominin presence in fossil-free sediment. So this approach seems set to become a standard for many sites, such as that from California reported in the previous post, which suggest a human influence, or any cave sediments for that matter. Although skeletal remains are essential for reconstruction of bodily characteristics, hominin phylogeny seems set to cut loose from fossils. Hitherto suspected species’ presence in the time period where DNA analysis is feasible may be detected, such as Asian H. erectus. It may become possible to map or extend the geographic ranges of Denisovans and Neanderthals. Perhaps species new to science will emerge.

More on late Pleistocene hominin genetics here

Wade, E. 2017. DNA from cave soil reveals ancient human occupants. Science, v. 356, p. 363.

Prehistoric human DNA is found in caves without bones in ‘enormous scientific breakthrough’

Pre-sapiens hominins reached North America?

Published on April 27, 2017 by zooks777Leave a comment

In 1991-2 palaeontologists excavated a site near San Diego, California where broken bones had been found. These turned out to be the disarticulated remains of an extinct mastodon. One feature of the site was the association of several large cobbles with bones of large limbs that seemed to have been smashed either to extract marrow or as source of tool-making material. The cobbles showed clear signs or pounding, such as loss of flakes – one flake could be fitted exactly to a scar in a cobble – pitted surfaces and small radiating fractures. The damage to one cobble suggested that it had been used as an anvil, the others being hammer stones. Broken pieces of rock identical to the hammer stones were found among the heap of bones. No other artefacts were found, and the bones show no sign of marks left by cutting meat from them with stone tools. The breakage patterns of the bones included spiral fractures that experimental hammering of large elephant and cow bones suggest form when bone is fresh. Other clear signs of deliberate breakage are impact notches and small bone flakes. Two detached, almost spherical heads of mastodon femora suggest that marrow was the target for the hammering and confirmed the breakage was deliberate.

Since the sediment stratum in which the remains occurred consists of fine sands and silt, typical of a low-energy river system, the chances that the cobbles had been washed into association with the mastodon are very small. The interpretation of the site is that it was the result of opportunistic exploitation of a partial carcase of a young adult mastodon by humans. In the early 1990s attempts were made to date the bones using the radiocarbon method, but failed due to insufficient preserved collagen. That the site may have been much older than the period of known occupation of North America by ancestors of native people (post 14.5 ka) emerged from attempts at optically stimulated luminescence dating of sand grains that can suggest the age of burial. These suggested burial by at least 60 to 70 ka ago. It was only when the uranium-series disequilibrium method was used on bone fragments that full significance of the site emerged. The results indicated that they had been buried at 130.7±9.4 ka (Holen, S.R. and 10 others 2017. A 130,000-year-old archaeological site in southern California, USA. Nature, v. 544, p. 479—493; doi:10.1038/nature22065 – full paper and supplements available free)

Not only is the date almost ten times that of the earliest widely accepted signs of Homo sapiens in the Americas, the earliest anatomically modern humans known to have left Africa are around the same age, but restricted to the Levant. The earliest evidence that modern humans had reached East Asia and Australasia through their eastward migration out of Africa is no more than 60 ka. The date from southern California is around the start of the interglacial (Eemian) before the one in which we live now. It may well have been possible then, as ~14 ka ago, to walk across the Bering Straits due to low sea level, or even by using coast-hugging boats – hominins had reached islands in the Mediterranean and the Indonesian peninsula certainly by 100 ka, and probably earlier. But whoever exploited the Californian mastodon marrow must have been cold-adapted to achieve such a migration. While the authors speculate about ‘archaic’ H. sapiens the best candidates would have been hominins known to have been present in East Asia: H. erectus, Neaderthals and the elusive Denisovans.

Surely there will be reluctance to accept such a suggestion without further evidence, such as tools and, of course, hominin skeletal remains. But these long-delayed findings seem destined to open up a new horizon for American palaeoanthropology, at least in California.

You can find more information on hominin migration here.

https://www.newscientist.com/article/2129042-first-americans-may-have-been-neanderthals-130000-years-ago/

When Did Humans Get To America? New Find Pushes Debate Back 100k Years

Denisovan(?) remains in the garden

Published on March 5, 2017 by zooks777Leave a comment

On the edge of the small town of Lingjing near Xuchang City in Henan Province, China, local people have long practiced intensive vegetable gardening because the local soil is naturally irrigated by the water table beneath the flood plain deposits of the Yinghe River. In the mid 1960s, around a small spring, they began to find dozens of small stone tools together with animal bones. Only in 2005, after the spring had stopped flowing, did systematic excavation begin (Li, Z.-Y. et al. 2017. Late Pleistocene archaic human crania from Xuchang, China. Science, v. 355, p. 969-972; doi: 10.1126/science.aal2482) About 3.5 m below the surface tools and bone fragments, including one with a carved representation of a bird, occurred just above the base of the modern soil profile. Radiocarbon dating of charcoal from the layer clustered around 13 500 years ago, just before the start of the Younger Dryas cooling episode; probably products of modern humans, although no human remains were found in the layer. Continued excavation penetrated sediments free of fossils and tools down to a depth of 8 m, when stone tools and bone fragments began to turn up again through the lowest 2 m of sediment. Optically stimulated luminescence (OSL) dating of mineral grains, which shows the last time that sediments were exposed to sunlight, produced much older dates between 78 to 123 ka. The thousands of stone flakes and cores, and cut marks on the animal bones found through the fossil-rich layer suggests that this was a site long used for tool making and food preparation, that had begun in the last interglacial period. Among the bones were fragments of the crania of as many as five individual humans.

Who were they? Their age range is tens of thousands of years before anatomically modern humans began to migrate into east Asia, so they are likely to have been an earlier human group. Homo erectus is known to have inhabited China since as early as 1.6 Ma ago and may be a possibility. The other possible group are the Denisovans, known only from their DNA in a small finger bone from a cave in eastern Siberia. Fragments of Denisovan DNA are famously present in that of many living indigenous people from eastern Asia, Melanesia and the Americas, but hardly at all in west Asians and Europeans. They also interbred with Neanderthals and may share a common ancestor with us and them, who lived about 700 ka ago.

Map showing the proportion of the genome inferred to be Denisovan in ancestry in diverse non-Africans. The color scale is not linear to allow saturation of the high Denisova proportions in Oceania (bright red) and better visualization of the peak of Denisova proportion in South Asia. (Credit: Sankararaman et al./Current Biology 2016; http://dx.doi.org/10.1016/j.cub.2016.03.037) — Map showing the proportion of the genome inferred to be Denisovan in ancestry in non-Africans. The color scale ranges from black – 0, through greens – present to red – highest . (Credit: Sankararaman et al./Current Biology 2016; http://dx.doi.org/10.1016/j.cub.2016.03.037)

Unfortunately the human bones are completely fragmented and lack any teeth, jaw bones or elements of the face. However, the Chinese-US team used sophisticated computer refitting of CT-scanned fragments to reconstruct two of the crania, revealing one individual with prominent brow ridges and a flat-topped skull extended towards the back, similar to that of Neanderthals but with a much larger brain than H. erectus. The semi-circular canals associated with the ears, but used in balancing, are well preserved and also resemble those of Neanderthals. Yet east Asia has yielded not a single Neanderthal fossil. Could these be the elusive Denisovans? Even if more diagnostic bones turn up, especially teeth, such is the state of late hominin taxonomy that only DNA will provide definitive results: the Denisovans are defined entirely by DNA. The authors, perhaps wisely, do not speculate, but others may not be able to resist the temptation.

For more information on recent human evolution see here.

Gibbons, A. 2017. Close relative of Neandertals unearthed in China. Science, v. 355, p. 899; doi: 10.1126/science.355.6328.899

Human Skull Fossils from China Have Surprising Traits

Human evolution: bush or basketwork?

Published on January 8, 2014 by zooks777Leave a comment

Analysis of DNA from ancient humans has revealed its power decisively in the last few years, and especially at the beginning of 2014 with publication of the sixth full genome of an individual who was not an anatomically modern human (Prüfer, K. and 44 others 2014. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature, v. 505, p. 43-49). The newly sequenced material came from a toe bone found in the Denisova Cave in the Altai Mountains of southern Siberia; the same location made famous in 2010 by genetic evidence for unknown late hominins, the Denisovans . The bone occurred in the same layer of cave sediment, dated at 50.3 ka, which yielded the Denisovan finger bone, but from a lower sublayer. So there is no firm evidence that both groups cohabited the cave.

The genome reveals that the individual was female and related to the three Neanderthals from Croatia and another infant Neanderthal from the Caucasus, also analysed previously by Svante Pääbo’s team at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany (Note that the toe-bone team also includes co-workers from US, Chinese, Austrian, French and Russian institutions). The closest statistical link is to the Caucasian infant Neanderthal’s DNA. Interestingly, it proved possible to demonstrate that the Siberian Neanderthal woman was from a population that was clearly inbred, her parents having been related at the level of half siblings. Her mtDNA shows that she shared a common ancestor with all 6 Neanderthals from whom mtDNA has been analysed.

Comparing genomes from the single Denisovan, the 5 Neanderthals and living humans from sub-Saharan Africans gives an estimated 550 to 765 ka time of divergence of a population leading to anatomically modern humans from the progenitors of Neanderthals and the Denisovan. The Neanderthal-Denisovan split was roughly 380 ka ago. It was already known that non-African living humans contain genetic evidence for past interbreeding with Neanderthals and that some people in Asia, Australia, Melanesia and the Philippines had acquired genes from Denisovans. More refined comparisons now show Oceanians to have 3 to 6% Denisovan make-up with Asians in general sharing 0.2%. Neanderthal to modern non-African gene flow is now estimated at between 1.5 and 2.1%, with Asians and Native Americans being at the high end. Neanderthals and Denisovans also interbred, but only at the level of about 0.5% inheritance. However, that genetic sharing involved DNA regions known to confer aspects of immunity and sperm function, that also made their way into living non-African humans.

Since the common ancestor of Neanderthals and Denisovans left Africa long before modern humans appeared on the scene it would be expected that living Africans’ genomes would show the same level of similarity with both the now extinct groups, if all three originally shared a common ancestor. A surprising outcome from comparison of Neanderthal and Denisovan genomes with those of living sub-Saharan Africans is that there is a significant bias towards Neanderthal rather than Denisovan comparability. There are three possibilities for this bias. After the Neanderthal-Denisovan split the former group may have continued to interbreed with the group leading to modern Africans (and indeed to modern non-Africans): that would require Neanderthal genetics to have originated in Africa before they migrated to Eurasia. Secondly, the gene flow could have been from the ancestors of modern humans to Neanderthal progenitors, making descendant Neanderthals more like modern humans. Prüfer et al. suggest that the evidence is less supportive of both and weighs towards a third possibility; that the Denisovans interbred with an unknown contemporary hominin, whose genetic make-up was yet more different from that of all three known groups of the late Pleistocene and therefore their common ancestor . This may have been Homo antecessor or possibly H. erectus who survived until as late as 20 ka in SE Asia.

Family tree of the four groups of early humans living in Eurasia 50,000 years ago and the gene flow between the groups due to interbreeding. Image credit: Kay Prüfer et al.

As other commentators on the paper (Birney, E. & Pritchard J.K. 20113. Four makes a party. Nature, v. 505, p. 32-34) have observed, ‘…Eurasia during the late Pleistocene was an interesting place to be a hominin, with individuals of at least four quite diverged groups living, meeting and occasionally having sex.’ All this arises quite convincingly from the genetics of only 7 ancient individuals, to show that it may no longer be appropriate to consider human evolution as a tree or a bush linking permanently separated species. Either it is the history of a single, polymorphic species – remains of 1.7 Ma old Homo georgicus show clear evidence of such polymorphism – or a better metaphor for human development is an interwoven basket or twine. Rumour has it that attempts are being made to sequence an H. antecessor dated at 900 ka from Gran Dolina Cave in the Atapuerca Mountains in Northern Spain: as they say, ‘Watch this space’!

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