We’ve known about the Denisovans for about 15 years, since part of a finger was found in a Russian cave (the “Denisova Cave“) in 2008 and wasw published two years later. They were a hominin subspecies like Neanderthals. I consider these groups subspecies of H.sapiens because they both interbred with H. sapiens and left fertile offspring. Denisovans lived in Asia from about 300,000 to 25,000 years ago. (They may also have bred with Neanderthals.) They are considered a sister taxon to Neanderthals, which means that these two groups shared a common ancestor that had already branched off from the ancestor of “modern” H. sapiens.
Wikipedia gives a useful table of all the known remains of Denisovans, which are judged as a distinct group from DNA sequencing. We have small bits of bone, including teeth, parietal bones, mandibles, and limb bones (and now, according to the Nature article below, a rib bone) from the three locations—all caves—shown below from the Wikipedia map shown below:
And here’s a picture of the Denisova Cave in Russia where it all started:
Here’s a diagram of the route the Denisovans took as they colonized Siberia and SE Asia from the Middle East, as well as a “family tree” on the right showing the sister-group relationship of Neanderthals and Denisovans (the figure presumes that the common ancestor of the two was a different species, Homo heidelbergensis, which, confusingly. has been considered a subspecies of H. erectus or even H. sapiens.
Just as many Westerners have some Neanderthal DNA (I have a bit among my Ashkenazi genes), so some Asians and people from Oceania have Denisovan DNA. This shows the hybridization I talked about above. And if two groups meet, mate, and produce fertile hybrids, they’re considered by evolutionary biologists to be subspecies, not species. Unless, that is, they’re hominins, for paleobiologists love to split names and create new species, a practice that produces more excitement and fame than simply saying “we found a new subspecies of Homo sapiens.”
Well, we’ve known about the Denisovans for a while, so what’s new? This news report from Nature (click to read) gives us a bit more information, like what kind of food they ate, as well as reporting on a new Denisovan rib bone found this year.
The results aren’t that thrilling to me, but many people thrive on human paleobiology, and so here are some extracts from the news:
When life got tough, the Denisovans got tougher. The enigmatic ancient humans hunted birds, rodents, even hyenas, helping them to thrive high on the Tibetan plateau for well over 100,000 years.
Those conclusions emerge from a study of thousands of mostly tiny animal bones that provide an insight into life at Baishiya Karst Cave in China1 — only the second archaeological site known to host Denisovans, after the Siberian cave that gave the group its name. Denisovans are a sister group to Neanderthals, and might have once lived across Asia.
Many of the cave remains could be identified only by their protein signatures. This included a rib bone that represents a new Denisovan individual, one of just a handful known.
“Denisovans are dealing with the full suite of animals they’re surrounded with in order to survive in this quite harsh landscape,” says Frido Welker, an archaeological scientist at the University of Copenhagen who co-led the study, published in Nature on 3 July. “It’s at high altitude. It’s cold. It’s not a nice place to be as a hominin.”
The article they’re discussing, a new one also in Nature, is below: click on the screenshot to read it:
And here’s the paper’s abstract, which discusses not only the discovery of a new rib bone from the cave in Tibet, but also some scratches on associated animal bones, indicating that they’d been processed for food, presumably by Denisovans:
Using zooarchaeology by mass spectrometry, we identify a new hominin rib specimen that dates to approximately 48–32 thousand years ago (layer 3). Shotgun proteomic analysis taxonomically assigns this specimen to the Denisovan lineage, extending their presence at Baishiya Karst Cave well into the Late Pleistocene. Throughout the stratigraphic sequence, the faunal assemblage is dominated by Caprinae, together with megaherbivores, carnivores, small mammals and birds. The high proportion of anthropogenic modifications on the bone surfaces suggests that Denisovans were the primary agent of faunal accumulation. The chaîne opératoire of carcass processing indicates that animal taxa were exploited for their meat, marrow and hides, while bone was also used as raw material for the production of tools. Our results shed light on the behaviour of Denisovans and their adaptations to the diverse and fluctuating environments of the late Middle and Late Pleistocene of eastern Eurasia.
Here, from the paper, is a human-cut bird wing bone showing the scratches, probably made when feathers were removed. This happens to be a golden eagle. How did they catch it?
And here from the paper is a photo of the rib bone from a Denisovan also found in the Tibetan cave, along with a phylogeny showing that the rib is closely related to a Denisovan mandible found in the same cave. It’s not really earth-shaking that a Denisovan rib would be genetically similar to a Denisovan mandible found in a different level of the same cave, but it does add to the specimens we have. Note as well that Denisovans and Neanderthals are, again, placed by DNA analysis as sister groups: each other’s closest relatives.
A summary from the News & Views piece of how scientists decided which species the animal bones came from (they used protein sequences from collagen rather than DNA to do this), and which animals they ate:
Proper excavations of the cave revealed more signs of occupation: dirt from the site dating to between 100,000 and 45,000 years ago contained DNA sequences from maternally inherited cell structures called mitochondria, matching those of the Denisova Cave remains. The dig, led by archaeologist Dongju Zhang at Lanzhou University in China, also uncovered thousands of mostly fragmentary animal bones.
To identify more than 2,000 of these remains, Zhang, Welker and their colleagues chemically analysed collagen protein signatures, which vary between animals. Especially common were caprines (the subfamily that includes goat and sheep) as well as wild yak, horses and gazelle. Carnivores, including wolves and foxes, also turned up in the mix.
Many of the bones from the cave, including those of hyena, caprines and golden eagles (Aquila chrysaetos), contained cut-marks and other signs of human predation. Even rodents and hare were probably hunted: a marmot (Marmota) leg bone was split open, potentially to harvest its marrow. Such small, speedy animals wouldn’t have been easy to catch, says Zhang, and bringing down carnivores such as hyenas would have taken moxie.
And here’s the Tibetan cave, Baishiya Karst Cave. It’s no wonder they call these hominins “cavemen”. Where else could you get shelter from the rain and wind and a place to process your catch? And cook it, too, for there’s evidence that both the Denisovans and the Neanderthals could probably make fires.
What more do we know now? Well, we know what the Denisovans ate, which is really no surprise. Callaway tries to give his piece more oomph by saying that we now know the Denisovans’ “survival secrets”, but of course they had to eat something. But knowing what they ate is better than nothing. And we also have more bones, though as yet they haven’t yielded much new information. There’s more to come as excavations proceed, but the N&V ends rather lamely:
. . . . scientists’ picture of Denisovans is becoming less opaque thanks to information gleaned from dirt and shards of bone subjected to cutting-edge DNA and protein analysis, says Brown. “Denisovans are essentially, at the moment, a biomolecular population.”
The remains Zhang and her colleagues analysed are from pre-pandemic excavations of Baishiya Karst Cave. But the researchers are now back excavating the enormous cavern, hoping to find more insights into Denisovan life. “We haven’t reached the bottom,” says Zhang.
Perhaps I’ve gotten jaded, for the discovery of a new subspecies of humans in Eastern Asia, one that probably went extinct like the Neanderthals, truly is a surprise.
Actually, to be in a noticeably different layer of sediment fill does imply quite a substantial difference in time. Either the environment in the cave needed to change, altering the nature of sediments laid down in it, or the environment outside the cave needed to change enough to change the supply of sediment into the cave.
Or, for a third option, one bone was found below a widespread (within the cave) ash or burning or charcoal layer in the cave’s stratigraphy, and the other bone was found above the same “marker horizon“.
Unless the remains were found together (and preferably articulated) you can’t be more than hopeful that they are associated. Reporting genetic proximity is worthwhile.
I also note that the name given is “the Baishiya Karst Cave” (my emphasis). Most caves are found in areas of “Karst topography” (the name derives from a Balkan region of limestone landscape with a well developed set of structures – caves carrying rivers ; relict towers and cavern-collapse gorges ; sink holes ; resurgences ; and other signs of landscape controlled by chemical corrosion of limestones), so describing it as “karstic” implies to me that there are other caves in the area which are not karstic (so, lava flow tunnels ; boulder-ruckles ; human excavation in soft sandstones (see Cappadocia in Turkey). Which is a bit odd.
A cave being described as “karstic” suggests the presence of “flowstone” – deposits of calcium carbonate minerals, which can cover parts of the floor sediments, artefacts, fossils, and even wall paintings. Such “flowstone” is potentially datable by the uranium-series method [wiki], and by covering this but not that can be very useful in resolving the dating of a site. A number of cave paintings have been dated this way, where part of a painting has “flowstone” growing over it. U-series dating is particularly useful in the 30ka to 100ka interval, between the upper limits of carbon dating, and the lower limits of (say) K-Ar dating.
I’m trying to remember how the original Denisova cave deposits were dated. They did establish that one of their bone fragments was from thousands of years different to another (see above comments) and that these two periods of Denisovan occupation were separated by a period of Neanderthal occupation – but how those dates were established, I forget. That comment on a specifically karstic cave makes me suspicious about work still in the pipeline.
I saw some mention in the last few days about Denisovans, but wasn’t motivated to follow it. This might have been it. Interesting, but not earth-shattering.
Just an addition: In Denisova cave, some morphologically undiagnostic bones turned out to be from three different populations (ancient modern humans, Neandertals, and Denisovans), and one individual turned out to be a F1 generation Denisovan-Neandertal mix.
I am afraid the proteomic analysis in this case means that again, ancient DNA probes have failed on a specimen from a Chinese cave, despite its being climatically suited to ancient DNA conservation.
There are so many questions that could be answered if the many morphologically interesting, genealogically enigmatic pleistocene skulls from China would yield DNA.
As is normal, the stratigraphy of cave deposits is complex. If anything, they’re worse than flood plains.
Very interesting post and good images always helpful. Thank you, enjoyed it greatly with morning coffee.
So fascinating – great to review this story – it is becoming less abstract with the accumulating “middle-world” material evidence, so amazing, I appreciate this writeup …
Thanks, PCC(e), for another very interesting post. Can we not look forward to recipes in Bon Appetit magazine for blanquette de marmot and similar components of the Xiahe diet,?
I am sure there are recipes for marmot in modern China, judging from what is sold at wet markets.
Thank you for sharing this.
Very cool, thanks for posting this.
The more we know the better, so thanks for shedding more light on the Denisovans.
“Just as many Westerners have some Neanderthal DNA (I have a bit among my Ashkenazi genes), so some Asians and people from Oceania have Denisovan DNA.”
All “Westernens” and most of humanity have some Neanderthal DNA, except sub-Saharan Africans (not withstanding the result of some later mixing). As far as I know East Asians have a bit more than Europeans. Neanderthal mixture is an universal property of the Eurasian (and in extension the Native American and Australia – Oceanian) population, but not all the inherited genes are the exact same, suggesting multiple mixture events (or – in part – differential selection).
At the other hand Denisovan DNA is specific to East Asians and Oceanians + Papua and Melanesians have much more of it, forming a kind of hotspot that does not have paralel in the distribution of Neanderthal ancestry.
I was going to comment that between “Indians” and “Chinese”, you’re close to a majority of humanity. But between copying part of your comment and the “comment box” loading, I wondered – what is the evidence for Denisovan (and for that matter, Neanderthal) ancestry in “sub-continental” populations.
It remains a valid point though. Western parochialism tends to forget that India is a bigger population than the “West”, however you define it.
Did the North-East Siberian population that people the Americas (recent blow-ins excepted) pass through Neanderthal-populated regions in the Levant/ Persia and pick up a Neanderthal admixture before their dispersal east then south?
I was also going to say that we (as a species) have had an interesting ancestry – but then I thought – how many non-human species have been subjected to this level of scrutiny? Has – for the only example i can think of off the top of my head – the Asiatic and European lion had such a nit-picking survey of their genomes, from their Pleistocene remains?
Assuming that the clade of “lion” originated in Africa – which I’m not 100% confident on.
We, Homo.sap.sap may have a thoroughly normal history of spread, isolation, differentiation-without-speciation, re-spread. Knowing that requires knowing the detailed genetic history of several species. (As my data-engineer instructor used to say – one measurement is a measurement ; two is a disagreement ; three, you start having some confidence. This was when a measurement could cost hundreds of thousands of dollars in rig time.)
“I was going to comment that between “Indians” and “Chinese”, you’re close to a majority of humanity.”
Indians are not East Asian and as far as I know they do not have Denisovan ancestry. (By and large, there are some minority ethnic groups there with a lot of eastern ancestry.) Many people do not realize this, but the main Indian population is closer genetically to Europeans than to the Chinese. Because of mixing and migration there is hardly any clear border, but by and large it can be said that genetically Eurasia is divided into West Eurasia and East Eurasia, not Europe vs. Asia.
“Did the North-East Siberian population that people the Americas (recent blow-ins excepted) pass through Neanderthal-populated regions in the Levant/ Persia and pick up a Neanderthal admixture before their dispersal east then south?”
Yes, but also Neanderthals were at large in Central Asia. In fact we have multiple different age Neanderthal remains from the Denisova cave itself. I believe we do not have enough samples to map the “border” and its changes, but most of Central Asia was likely Neanderthal territory most of the time. And ancient East Siberians definitely passed through there.
Another important thing to remember is that the first peopling of America is closer to us in time than to the first peopling of Central Asia and Siberia. There were population movements, mixings, formations during that time, so the Neanderthal mixture happened long before the much later first people of America even existed as a separate population within Asia.
“We, Homo.sap.sap may have a thoroughly normal history of spread, isolation, differentiation-without-speciation, re-spread. Knowing that requires knowing the detailed genetic history of several species. ”
Yes. You should look up the study about the mitochondrial DNA of Palaeoloxodon antiquus. They found that although the species was more similar to Asian elephants in their appurtenance, their mitochondrial DNA is nested inside the variation of modern African elephants. An interesting story.
Useful perspective. Humans seem (in a small sample) be unexceptional. That’ll be uncomfortable reading for people who believe humans to be exceptional.
Fascinating! Thank you Jerry. This is why your blog is the best because it is the only place we can get vital information like this. Keep up the good work, mate.
Thanks I enjoyed the read, great job.
Good review of recent finds. The complex origins and mixture of humanity over the eons of time is very difficult to sort.! With time, new techniques and persistence more details will come to light. A very interesting and complex history of mankind is certain.
David a. Lee MD
Very interesting. Thanks for posting.