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We are all Denisovans now!

Since 2010 the combination of improvements in genomic technology and ancient DNA have totally revolutionized our understanding of the human past through genetic techniques. In the 2000s there was a “live debate” about archaic introgression into modern human genomes, in large part because the techniques were not powerful enough to answer the questions that were being asked (nevertheless, many thought they really knew the answer already!).

With the sequencing of the Neanderthal in 2010 we saw that non-Africans seemed to carry more Neanderthal alleles than Africans, which was suggestive evidence of archaic admixture. Before the end of the year, the Denisovans were discovered, and it was clear that their impact was significant in the Papuans (and to some extent Oceanians generally). These discoveries were a shock already, but over the years more and more subtle discoveries have occurred. To some:

– Researchers believe that the Neanderthals have some ancestry from a basal modern population (a group that diverged a long time ago)

– Lots of debate about whether greater estimated Neanderthal fraction in East Asians was due to a second admixture or dilution of the original admixture by later mixing in West Eurasians, or, differential natural selection in different populations (I lean toward the middle position)

– It is clear that there is some Denisovan ancestry in East and South Asians, as well as in peoples of the New World. And, it seems quite clear that these admixtures were from different branches of the Denisovan group of humans

– It seems quite likely that Papuans may have multiple admixture events from Denisovan populations or from people related to the Denisovans

– There is lots of circumstantial evidence that Neanderthals and Denivosons may harbor ancestry from earlier human lineages that were present in Eurasia when their ancestors pushed out of Africa ~750,000 years ago

– Lots of evidence for deep ancestry admixture within Africa

– Basal Eurasians. What are they? We still don’t know!

Add to that list a new paper, The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes:

…humans outside of Africa trace about 2% of their genomes to admixture from Neanderthals, which occurred 50–60 thousand years ago1. Here we examine the effect of this event using 14.4 million putative archaic chromosome fragments that were detected in fully phased whole-genome sequences from 27,566 Icelanders, corresponding to a range of 56,388–112,709 unique archaic fragments that cover 38.0–48.2% of the callable genome. On the basis of the similarity with known archaic genomes, we assign 84.5% of fragments to an Altai or Vindija Neanderthal origin and 3.3% to Denisovan origin; 12.2% of fragments are of unknown origin. We find that Icelanders have more Denisovan-like fragments than expected through incomplete lineage sorting. This is best explained by Denisovan gene flow, either into ancestors of the introgressing Neanderthals or directly into humans…

The power of the Icelandic dataset is that they got really high coverage genomes, 30x, and phased them together to generate a lot of confident haplotypes. 3.3% Denisovan out of the 2-3% that’s archaic is really small. But if you have enough data you can find it.

They had to do simulations and run some HHMs to get here. I’m not sure I believe it. But I also think it’s plausible. The two models they present are:

– Denisovans mix into Neanderthals who mix into humans

– A Denisovan related population mixes into early non-African humans just before they mixed with Neanderthals

As time goes by I suspect we’ll find many small details of past interaction.

8 thoughts on “We are all Denisovans now!

  1. @Razib
    You think it’s possible this Denisovan in Irish comes from the East Eurasian part of ANE?

  2. @thejkhan

    I have long thought that ydna K2 entered Central Asia from Iran/Pakistan, then travelled clockwise around the Himalayas, into South Asia and then back to Central Asia. This was the only way I could make sense of the distribution and relationships of the K2 haplogroups and associate Q & R with ANE.

    The problem (until now) was that it predicted a non-zero Denisovan contribution to Europeans…

  3. How about Icelanders having some East Asian ancestry? Was that accounted for and would the ratio found allow that source for the gene flow from Denisovan-like populatons?

  4. @thejkhan unlikely seeing as tianyuan’s genome (best proxy for AEA component of ANS/ANE) didn’t reveal any detectable Denisovan segments.

  5. @Joshua

    New paper has 3% Denisovan for Tianyuan, and ANE is suggested to have Denisova since 2016 at least.

    “Denisova-related (but not excess Neanderthal) gene flow into MA1, with an inferred mixture proportion of 1.2%, or 1.0% Denisova-related ancestry (95% confidence interval 0.4–1.6%; see Materials and Methods) in MA1 after dilution by eastern Eurasian gene flow”

  6. @Obs, I think we’d probably need ideally a good sub-sample of people with hefty proportions of East Eurasian ancestry to be sure – 27,566 Han / Bengali / whatever genomes, ideally probably both. Then you could see the Denisovan fragments fall off in a predictable way.

    It seems like it wouldn’t to me, naively. Say you have admixture from some ENA ancestor (not necessarily the main one for either East Asia / South Asia, but some relative) into some long distant ancestral stream into Iceland (say EHG) then…

    … if that ENA related admixture stands overall at 3% of Icelandic ancestry today (which would be a high estimate I think, but maybe not!) and 3.3% archaic fragments, it would scale up to the expectation that Denisovans would contribute 100% of archaic fragments to East Eurasian groups.

    Which they probably don’t.

  7. What’s the consensus now on on what exactly constitutes “East Asian” ancestry (i.e., Han-like or Ami-like)? Do East Asians derive most of their ancestry from an Onge-like or a Tianyuan-like source?

  8. You think it’s possible this Denisovan in Irish comes from the East Eurasian part of ANE?

    yes

    How about Icelanders having some East Asian ancestry? Was that accounted for and would the ratio found allow that source for the gene flow from Denisovan-like populatons?

    zero evidence. very well studied population. nordic+british isles. that is all. (perhaps some distant from finnic, but most icelander nordic is norwegian)

    What’s the consensus now on on what exactly constitutes “East Asian” ancestry (i.e., Han-like or Ami-like)? Do East Asians derive most of their ancestry from an Onge-like or a Tianyuan-like source?

    tianyuan. check older posts on this blog

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