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Denisova and aDNA: an embarrassment of riches

As usual, I'm being a bit naughty- blogging when I have a ton of other work that needs attention. But I have to write about thoughts spilling out of my head following a new article in Science (paywall) pointed out by Ross Barnett (@DeepFriedDna). Also, it's my birthday, so I'll blog if I want to ;-)
OK, well this paper is a tantalising write-up of new results on the hominins at Denisova Cave, Altai, not yet published (but presented yesterday at a conference) by Svante Pääbo and team at the Max Planck Institute for Evolutionary Anthropology in Leipzig. Denisova hit the news big time in 2008 when it was announced that there was a "hominin X" there- a species in 2010 certainly identified as something different by DNA analysis of a tiny finger tip, and dubbed "Denisovans". I love this site because it's making everyone sit up, rub their eyes and take a look at the New World of human evolution- surprises wherever we look, even kicks in our collective academic asses; and today Neandertals are centre-stage.

Since 2010 there have several developments, with further 'Denisovan' individuals identified by DNA analysis of teeth. There's tons of interesting stuff to say about the Denisovan genetic sequencing from this site, which I don't want to go into detail on here- instead check out John Hawk's excellent coverage of this. I will underline John's position however, that right now things are fuzzy as to whether we should even be doing any species pigeon-holing at this site, given the fact that the 'Denisovans' sequenced so far (from different levels) seem to represent a highly diverse genetic population: more dissimilar to each other than any Neandertal was to another over their enormous geographical range.
The new research reported today relates to a toe bone, found in the same level as the finger-tip (but below Denisovan teeth) already identified using DNA as Neandertal, something which I remember Pääbo talking about at  the ESHE conference in Leipzig in 2011 and which was recently published. Detailed study of the toe sequence has found that it is pretty likely that this Neandertal individual was the result of a first-cousin union. Additionally, analysis of one Denisovan sequence shows that 17% was actually contributed by Neandertals, which is a very hefty amount, if I understand correctly and that about 4% came from YET ANOTHER "Hominin X" (or Z? No, that's zombies, right?), something maybe with a more ancient root. For context, 4% is the largest figure quoted for the amount of Neanderthal contribution to any living humans. Both results, Denisovan-Neandertal (and "X") breeding and apparent Neandertal-Neandertal in-breeding (I know, this gets confusing!) are really interesting to me for their wider implications, which get my brain spinning on several levels.

 This fabulous video by Mindy Petre and students comes from John Hawk's blog, I <3 it!

First, this is more data to add to our slowly expanding collection of facts for how Neandertals mated- there's a lot of attention given to how they might have got personal with modern humans thanks to the recent evidence that we did in fact, at some point, somewhere and to some extent, breed. However, I'm more interested in what Neandertals were getting up to with each other before we were on the scene- and now apparently, with other ancient hominins too. There's several lines of evidence that they had small, isolated populations (including the small size of living sites for one, as well as DNA), yet there is remarkable similarity in their material culture across large areas, coupled with very clear 'barriers' between regions too, especially in regard to totally different ways of making bifacial tools (the classic Mousterian vs. Keilmesser technologies).

I've been bothered for a long time what this mixed picture of genetics and archaeology implies. If they were in-breeding on a huge scale, with very localised populations that didn't travel far or encounter other groups, leading to low diversity in genetics and population separation, how could they have maintained apparently coherent cultural systems across very large regions? This picture is further complicated by the fact that we have repeated evidence (if not very frequent) for the long-distance transport of stone tools- up to several hundred kilometers in some cases. Either individuals (or whole groups) were moving the tools with them, or there was some kind of exchange of stone tools going on between groups. The second option is kind of anathema to many researchers, because trade and exchange has been built into models of what supposedly made the Upper Palaeolithic modern humans different to Neandertals*. But if  either scenario is true, trade between groups of Neandertals or actual long-distance mobility, then why are there such clear cultural barriers?

This is very tricky, and as usual, the answer is that more data is needed for us to better understand whether or not Neandertals were moving long distances, and what kind of mating pattern was typical- if any! Inbreeding is implied here, but in other areas, different strategies might have been going on, for example the recent (and highly disputed) suggestion of patri-local mating in a Spanish group. This complexity is only added to by the Denisovans getting in on the picture. In fact, what we have right now is a situation where we know more about that group as a population than any individual Denisovans- we still don't know what these people *looked like* beyond the uninformative finger tip, and some quite chunky teeth. I can't help wondering whether more complete skeletal remains, if we ever get any, will 'fit' the genetics evidence- will they look like Neandertals, like the older root populations of Homo heidelbergensis, or present a completely novel ancestral face, looking back at us?

Tourists approaching Denisova Cave, Altai. The woman looks a little knackered: maybe how human origins people feel right now with the relentless amazing new stuff coming from this site! Image: ЧуваевНиколай at ru.wikipedia [ CC-BY-SA-3.0-2.5-2.0-1.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons
I'm also finding it crazy that we have all this DNA data for the Denisovans, but at the moment, hardly any cultural material that we can assign *with confidence* to these people. There's a major game of archaeological catch-up to be played, which is going to be extremely tricky to pull apart. The base deposits from Denisova (Levels 22-21) are described as dated to the Middle Pleistocene (in this paper [paywall]), with Early Middle Palaeolithic archaeology, specifically including stone tool technology of Levallois and parallel-core reduction, the latter producing blades. There's also pretty generic-sounding retouched pieces: scrapers and notches- stuff we'd normally be happy assigning to early Neandertals. Above this, Levels 20-12 contain later Middle Palaeolithic artefacts, including parallel reduction and what's described as radial technology (presumably centripetal/discoidal), with a bit of Levallois still present and scrapers again.

It's the overlying Level 11 that the Denisovan teeth and finger bone come from. The archaeology is termed by the excavators "Initial Upper Palaeolithic", and has been dated using AMS radiocarbon to between 30-50,000 years ago (although it has to be said, all radiocarbon dates are somewhat suspect as the technique has been undergoing major refinements, with work by Thomas Higham at Oxford on the Ultrafiltration technique producing results which suggest many dates are too young). Level 11 again has parallel reduction, but now some Upper Palaeolithic-style tools are present, as well as bone tools. Significantly, a rather beautifully polished stone bracelet was found at the base of this layer. The layers further above this contain much more obviously Upper Palaeolithic assemblages, assumed to be produced by modern humans. So the Denisovans made cool stuff, right, like the Level 11 bracelet? Well confusingly, this is also the level that produced the Neandertal toe bone- apparently it's from low down, but this is where the bracelet was found.

So even at the type site for the Denisovan 'species', we can't know who made what; not the stone tools, the less-typically Neandertal artefacts like bone tools (although they most certainly did make these sometimes) or the unique bracelet. Perhaps more significantly, the DNA evidence is pointing to the Denisovans having a much larger population than the Neandertals- so where is the rest of their archaeological record? Are the Altai people outliers for that population, or central to its distribution? What about all those hundreds of Eurasian sites with archaeology that is a mix of Middle Palaeolithic/ transitional Initial Upper Palaeolithic, too old to be made by modern humans (we think!), but with no accompanying skeletal remains?

Right now it feels like Big Picture of Human Evolution is a runaway rollercoaster, flying along shiny new rails of DNA, following a route we can't see, with all the archaeologists hanging on by our fingernails to the back car. The speed at which things are changing is hard to keep up with, and that's set to continue. Hold on tight!

Geneticists at the front, archaeos at the back! Image: By Boris23 (Own work) [Public domain], via Wikimedia Commons


*It's true that modern humans were moving lithics further overall, in different forms (more often as raw nodules than 'finished' tools), as well as transferring stuff like shells- these are used most often to argue for exchange rather than actual group/individual mobility.

Comments

martine said…
Just wanted to say I really enjoyed your piece about the invention of clothing in the Guardian. It was lovely to see someone answering a child's questions properly and wondering why they didn't ask you to write the answer to the girl's original question.
Hi Martine,
Thanks for your comment, I enjoyed writing the Guardian piece, there's so much to say about this topic, and I remember from being young myself, it's the everyday stuff like "what did they wear" that fires children's enthusiasm about the past.

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