Ust’-Ishim & the Old Race

There’s a new report out in Nature, on the DNA results from a 45,000 AMH skeleton found in Western Siberia.  It’s the oldest radiocarbon-dated modern human outside Africa and the Middle East.

The Neanderthal admixture is there,  about the same amount as today, but in larger blocks than in people today.  Less shuffled, so we now have a better estimate on the admixture date: 50-60,000 years ago.  The skeleton confirms the new lower estimate of the human mutation rate, about 1.2 x 10-8 per generation.   He’s equally related to Andaman islanders, Amerindians, Han Chinese, that Mal’ta Siberian ANE boy, and Old European hunter-gatherers (La Brana), but somewhat more distant from modern Europeans (French and Sardinians), because of this basal Eurasian component from the Middle East (found in the EEF, the original farmers of Europe).  These Basal Eurasians would have had to split from the AMH population that did the main expansion out of Africa before they left, so the split must have been well over 60,000 years ago. That doesn’t tell us exactly when the Basal Eurasians left Africa, however.  Could have been as long ago as the Shkul and Qafzeh skulls, roughly 100,000 years ago, could actually have been far more recent.

We know that there was an expansion of modern humans into the Middle East ~100,000 years ago – so the simplest explanation is that the Basal Eurasians are descended from that early expansion. Otherwise we have to posit three different expansions of modern humans out of Africa, one of which failed after a while. If they left that early, looks as if the Basal Eurasians didn’t sufficient moxie to displace archaic humans over most of Eurasia (while the later dispersal did) .  On the other hand, they do seem to have invented agriculture.

Finding a decent-quality ancient sample that is a good representative of those Basal Eurasians, as the Mal’ta boy is of the ancient Siberians, would sure help clarify things.

Chris Stringer is quoted as saying that the study offers compelling evidence that living non-Africans descend from a group that left Africa about 60,000 years ago – but in fact it strengthens the case that there were in actuality at least two different successful expansions of anatomically modern humans out of Africa.

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30 Responses to Ust’-Ishim & the Old Race

  1. Michael says:

    It seems interesting that these Basal Eurasians split from the other Out-Of-Africans well before 60,000 years ago, yet all of them seem to have exactly the same amount of Neanderthal admixture (based on early european farmer genomes). How is that compatible with the 50-60,000 year estimate from this genome? Did Neanderthals at that time just decide to join whatever modern human groups they could find?

    • Karl Zimmerman says:

      No one has DNA from a Basal Eurasian yet, just Early European Farmers. And IIRC, at least Otzi has a higher proportion of Neandertal ancestry than any modern human.

      This may imply that Basal Eurasians were actually significantly more Neandertal than even Otzi. Which sort of makes sense provided the Near East was the site for virtually all the admixture, as the Basal Eurasians could stick around for a bit longer and interbreed with Neandertals more, while the rest of the Eurasians either migrated to somewhere Neandertal-free around Central Asia, or for other reasons maintained a reproductive barrier.

      On the other hand, this should/would suggest that modern-day Europeans, and particularly Near Easterners without significant SSA admixture, should have a bit more Neandertal DNA than East Asians, when the converse actually appears to be true. So Otzi’s high percentage may have come from some fluke extra admixture which happened within the Near East among his WHG-like ancestors, with basal Eurasians actually showing depressed admixture (perhaps because they were actually in North or East Africa for significant periods).

  2. JB says:

    Seriously with the graphic? Some of us like to share these posts with our friends.

  3. somebody says:

    Interesting post! Exciting to live in a time where these things are being figured out. Thanks Professor

  4. TWS says:

    Has there been DNA studies done of Skhul and Qafez?

  5. ziel says:

    He was given a very Borgesian name.

  6. dave chamberlin says:

    As usual with important science news stories of this subject matter John Hawks has a great write up here http://johnhawks.net/. 20,000 years older than the next oldest AMH DNA, wow. It sure looks like that extra moxie that AMH got right around 60,000 years ago came from hybridization with Neanderthals, yep, sure does. But cautious scientists can’t suggest that even as a possibility because it insults the folks south of the Sahara who mostly missed out on the cavorting with Neanderthals.

    • Matt says:

      In the modern day, it looks like Bantu Africans have some “moxie” that Oceanians don’t. Neanderthal admixture is past its sell by date?

      On the divergence dates of Basal Eurasian from the Derived Eurasian clades.

      If we look at the Lazaridis’ paper’s tree models for Basal Eurasian, the shared drift between Dervied Eurasian groups (Onge, a Han-ish Amerind ancestor, Old European hunter gatherers and north Eurasians) prior to their divergence for which Basal is excluded is given a figure of 25 vs their prior shared divergence of all Eurasians from Mbuti given a figure of 171.

      This figure of 25 is then about 40% of the size subsequent non-shared drift between WHG and East Asian populations, where each population has about an additional 60 of drift from one another and BE on top. So if divergence between WHG and East Asians takes from around 50,000 BC to 4,750 BC (when we have the Loschbour sample), or 45,000 years, perhaps BE diverged from their ancestors 18,000 years before that?

      This doesn’t fit that closely with the Neanderthal mixture event being shared between Basal and Derived Eurasians and occuring only around 10,000 to 15,000 years before, so perhaps that estimate is a little short.

      Also, wouldn’t we expect some a bottleneck effect of small early Derived Eurasian expansion populations, compare the Native Americans, to what was likely for their Siberian ancestors?

      • dave chamberlin says:

        You are talking over my head which isn’t all that hard since I’m internet educated rather than formally educated on this subject. But thanks for the comment, now I have some work to do to understand what it is you are saying. I am sure you are right that the evolution of human “moxie” is far more complex than what I or anyone knows. We live in interesting times when one bone that happened to have it’s DNA preserved because of it’s location, presumably in Siberian permafrost for most of it’s exsistance, adds considerably to our limited knowledge of our very distant human past.

      • dearieme says:

        “it looks like Bantu Africans have some “moxie” that Oceanians don’t”: in what sense? Can you explain?

        • dave chamberlin says:

          I took Matt’s point to be that Bantu Africans are agriculturists and as such they are more advanced culturally than some of the hunter gatherer groups which comprise some of the Austronesians or Oceanians. These new names for new groups are coming thick and fast it is hard to keep up with them, the link I gave above starting dnatribes makes it much easier to understand. I took his real point to be that while introgression from Neanderthal genes could be responsible for increased intelligence that helped lead to virtual world domination by this hybridized 98% AMH 2% Neanderthal mix that originated 50,000 to 60,000 years ago it is far from the whole picture and also just an unproven hypothesis. It cannot be as simple as once we grabbed from the Neanderthals some intelligence increasing genes we took over. The complex truth is far more than that. The plot thickens with the discovery of every new bone that contains very old DNA.

          • Just sayin' says:

            At least some of those groups like Melanesians hybridized with both Neanderthals and Denisovans, instead of just Neanderthals.

            Or at least, that’s what they were claiming last year, it may have changed again.

  7. Frito Bandito says:

    Are middle easterners basal eurasians?

  8. Greying Wanderer says:

    Atlantic coast vs Egypt/Arabia/East Coast?

    • Greying Wanderer says:

      E & C?

    • Michael says:

      But it looks like the Basal Early Farmers grew crops from the Levant area, mixed with hunter-gatherers that were not from Western Europe, and spread from the middle-east. They didn’t enter Europe from the Atlantic side. Or are you suggesting that the larger “main” wave entered Eurasia from the Atlantic side?

      • Greying Wanderer says:

        Not really, I’m still digesting and simply have a bad habit of thinking aloud.

        I do think the Atlantic coast is a dog that isn’t barking because all the evidence will be under the sea but not necessarily from this time period.

  9. Fourth doorman of the apocalypse says:

    OT, but it looks like the older topics are not getting much attention.

    Is it possible that immunity to pathogens operates in a manner that many do not appreciate:

    1. When pathogens find a chink in our armor there is very little that those who are genetically susceptible to that attack can do,

    2. So, the pathogen largely kills off all those that are genetically susceptible,

    3. In cases where we do have genetically mediated methods to defeat pathogens, our immune system benefits from bootstrapping, as when, say, a mother transfers antibodies or whatever to her child in her milk. Bootstrapping might be the wrong concept here, maybe it is simply giving the child a head start without the billions of dollars being spent.

    • Richard Sharpe says:

      I recall some people saying that Viruses/pathogens seem to evolve towards less virulence over time, but is it possible that the following is what is happening:

      When a virus with a new trick first encounters a population, the population could be considered to consist of Completely susceptible individuals (C), Partially susceptible individuals (P) and Immune individuals (I) because of natural variance. (See, for example, CCR5-Δ32).

      Thus the population N = C + P + I.

      After a few rounds of application of the virus, the number of C + P individuals would surely be greatly reduces, and it looks like virulence has reduced, but what has happened is that the virus has selected for immunity to itself and it has to find a new trick.

      • Richard Sharpe says:

        Actually, I guess the virus is less virulent over time, but it did not evolve to become less virulent, the structure of the population evolved under the selection pressure applied by the virus.

        • erica says:

          Huh?
          My understanding is that pathogens, at least the very sturdy ones, mutate frequently, and some strains outcompete others, depending, of course, on the environment.

          Human response to those pathogens have effects on which strains survive and/or prosper.

          If an incapacitating pathogen which kills its host is shed through means such as diarrhea or vomit or blood and those bodily fluids are carelessly handled by their caregivers, even taken down to the local river to be washed, that strain of the pathogen will outcompete less virulent strains. Absent modification of host behavior, that strain prospers.

          If people take care to isolate the infected hosts and take care to destroy the dirty bedding, clothes, etc. that have been contaminated by bodily fluids, the virulent strain of the pathogen will lack means of transmission, and other, m ore benign strains will be favored by selection.

          • Richard Sharpe says:

            That’s what I used to think until I checked out that stuff on CCR5-Δ32, and there is some interesting stuff there, like:

            The highest frequency of the mutation exists in Ashkenazi Jews, with the overall frequency of the CCR5-Delta32 allele is elevated 13.7% on average.

            (You will have to click through to the CCR5-Δ32 link in the above article.

            Now, mutation is not a magic word that makes everything happen. It depends on where the mutation happens, that is where in the genome and where in space.

            Viruses have to do several things:

            1. They have to gain entry to cells in their host’s bodies because they need the cellular machinery to replicate.
            2. They need to disable the hosts defenses in some way or otherwise they die.

            3. They need to escape the host to go on and infect other hosts.

            Look at HIV and the CCR5-Δ32 mutation above. So, lets say that one or more (million) HIV virus particles in one host actually have a mutation that allows them to target those individuals who have the CCR5-Δ32 mutation. What then? Well, they will likely die out because they can no longer gain entry to the cells in the current host’s body. More over, these mutations only occur during replication, it seems to me.

            Now, of course, HIV is a bit of a one-trick pony, it seems, at least compared with Ebola, however:

            A. There seems to be people who can defeat Ebola without the sorts of herculean efforts that we undertake in some of our hospitals in the West, and this, it seems to me is very likely genetic. There might even be those who are immune because the have a mutation that affects the entry portals Ebola uses and that mutation does not cause a large reduction in functioning.

            B. The same arguments apply. How is the Ebola virus to develop mutations for evading the defenses of host type B when it is in, and successful in, host type A?

            Thus we can divide populations up into those that are completely susceptible, those who are partially susceptible, and those who are immune.

            However, a word of caution. I might be full of shit. People have told me that before.

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