The hunt for ancient DNA

By Razib Khan | August 9, 2011 11:59 am

Ewen Callaway has a good survey of what’s been going down in ancient human genomics over the past year in Nature, Ancient DNA reveals secrets of human history. It’s not paywalled, so read the whole thing. Most of it won’t be too surprising for close readers of this weblog, but this part is new:

By comparing individual DNA letters in multiple modern human genomes with those in the Neanderthal genome, the date of that interbreeding has now been pinned down to 65,000–90,000 years ago. Montgomery Slatkin and Anna-Sapfo Malaspinas, theoretical geneticists from the University of California, Berkeley, presented the finding at the Society for Molecular Biology and Evolution meeting in Kyoto, Japan, held on 26–30 July.

Slatkin says that their result agrees with another study presented at the meeting that came from the group of David Reich, a geneticist at Harvard Medical School in Boston, Massachusetts, who was involved in sequencing both the Neanderthal and Denisova genomes. The dates also mesh with archaeological finds bookending early human migrations out of Africa to between about 50,000 and 100,000 years ago. Reich’s team is now developing tools to find signs of more recent interbreeding that might have occurred after humans arrived in Asia and Europe.

Remember that the Neandertal admixture seems present in all non-Africans. That pegs the admixture event very early, before the diversification of modern human populations. I wouldn’t put too much stock in any one value presented at a conference with a large confidence interval. From what I hear there will be much more on statistical genetic inferences of admixture timing over the next year, but if there’s one thing that the enormous yield from genomes constructed from ancient DNA has convinced me is that we should be really cautious of results which we can’t cross-check easily because of their time depth. I read a lot of papers by high-powered teams before 2010 on how the genomic evidence implied no admixture between modern human and archaic lineages, and gave them great weight. There’s only so much power in working back to the past from the present.

  • Eurologist

    I agree we will need to wait for more analyses and tighter time constraints to learn more from this, but the dates – if proven correct – do seem to exclude admixture in Africa, IMO. North African AMH were abundant during the wet phase ~130,000 – 100,000 years ago – and if the dates are correct, apparently did not carry “Neanderthal” admixture.

  • SPM

    The strange thing here is that in order for the genes to have been distributed so evenly among non-Africans, the interbreeding must have taken place in the Middle East and not in Europe. Why would this be when most Neanderthals lived in Europe? The only answer to that has to be that Neanderthals could not produce fertile offspring with humans, and that the interbreeding took place not with Neanderthals, but with a human/Neanderthal hybrid that had left Africa earlier, but did not manage to make it out of the Middle East. Other possible explanations which should be examined are that the genes may have been transferred between species by viral infections or that the DNA fragments thought to have been transferred was actually human DNA introduced into the sample by contamination.

  • SPM

    One other thing that needs to be checked is whether the HLA genes conferring resistance to various diseases could have arisen form the bacteria they protect against rather than from interbreeding. In other words, do they have the same HLA code block not because they interbred, but because because the genetic code block in both species had to match a block in the common virus or bacteria that the body was resisting?

  • dave chamberlin

    We might as well hold back opinions until new tools are developed and new findings come from them. The cool thing is we won’t have to wait long, as the nature article said, “ancient human genomics is moving at breakneck speed.” It is nice to see the collaborative effort in this area among researchers, they are sharing their data and working together. It is also nice to the John Hawks team so prominantly mentioned in the Nature piece, I have to say I am rooting for him and his Madison team to make a big splash in the field. He is kind of our home town boy as he frequently comments here and takes time to write a wonderful blog for all of us laymen fascinated by our now emerging long lost past.

  • Addison DeWitt

    Let’s not forget the Toba eruption 70,000 years ago. The climate change it caused wiped out many human populations across the globe. The strain that survived apparently had Neander genes, but what of those other now-extinct strains? I’m sure the genetic picture was a lot more diverse back then.

  • Raimo Kangasniemi

    “Remember that the Neandertal admixture seems present in all non-Africans.”

    There are several problems with this: First, the Neanderthal admixture is present in the few sampled Sub-Saharan African populations, but under 1 % level which why it’s closed off from results and a thousand popular science stories have thus given their readers a false impression that Sub-Saharan African populations would lack the Neanderthal heritage completely. Even a cursory look at blood types show that for example coastal regions of Sub-Saharan Africa show evidence of the long contact with other regions through maritime trade, settlement and colonialisation.

    Secondly, the samples are relatively limited globally, and tend to represent majority populations. Many interesting aboriginal populations that might represent a longer regional continuation than the sampled majority populations are not included. For example, in Europe, the French in the light of the new understanding of population history of Mesolithic and Neolithic Europe (and even beyond it) probably are not a good way to try to seek evidence of a possible second Neanderthal&modern Human admixture in Europe (beyond the first one that happened probably in the Middle East).

  • Eurologist

    “The strange thing here is that in order for the genes to have been distributed so evenly among non-Africans, the interbreeding must have taken place in the Middle East and not in Europe.”

    I think there are a number of things to ponder:

    – Just because there are “Neanderthal” genes, we don’t know for sure if the admixture was with Neanderthals or more general Heidelbergensis-like. For Denisovans, in particular, I think the latter is much more likely.

    – Neanderthals were late-comers to the Near and Middle East – other early humans were there for hundreds of thousands of years; (to me) convincing evidence points to Heidelbergensis-like people migrating East all the way to China between ~240,000 and 190,000 years ago, when the climate was rather moderate.

    – As such, I agree there is a possibility that AMHs from North Africa first admixed with Heidelbergensis-like people in the Middle East when the former where expanding during the wet phase from North Africa ~130,000 – 100,000 years ago (there were no Neanderthals there, then). Later AMHs could have then mixed with this group (perhaps related to y-haplogroup D).

    – There is very little evidence that Europeans *of any time* were dominated by people from the Near East or Mid East. Most European y-haplogroups seem to come from the Indian subcontinent – although some seem to have migrated back to the Middle East rather early. At any rate, admixture could have easily taken place at entry there, as well.

  • Deanna

    “Remember that the Neandertal admixture seems present in all non-Africans.”

    If Africans are the core/founding population would this statement not be more accurate in saying “non-continental Africans” or something simular…….it seems a bit misleading when the modern humans ARE African. I say that because this statement is being used to “prove” that Europeans are superior to Africans by people with racist intentions, a way to prove the uniqueness of Europeans.

  • Deanna

    Fall of the Neanderthals: Volume of Modern Humans Infiltrating Europe Cited as Critical Factor

    ScienceDaily (July 29, 2011) — New research sheds light on why, after 300,000 years of domination, European Neanderthals abruptly disappeared. Researchers from the University of Cambridge have discovered that modern humans coming from Africa swarmed the region, arriving with over ten times the population as the Neanderthal inhabitants.

    The reasons for the relatively sudden disappearance of the European Neanderthal populations across the continent around 40,000 years ago has for long remained one of the great mysteries of human evolution. After 300 millennia of living, and evidently flourishing, in the cold, sub-glacial environments of central and western Europe, they were rapidly replaced over all areas of the continent by new, anatomically and genetically ‘modern’ (i.e. Homo sapiens) populations who had originated and evolved in the vastly different tropical environments of Africa.
    http://www.sciencedaily.com/releases/2011/07/110728144928.htm

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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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