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Whole genomes of ancient farmers and hunter-gatherers

A new preprint uses about a dozen ancient genomes to create a model of the origins of Europeans and European farmers more precisely. The big deal here is that they aren’t relying on the same old SNP-array, but using the whole genome. This allows for some more explicit model-building and testing. I do think explicit model creation is something that needs to be done. A lot of the work today is data-first, and there needs to be more “theory”.

The mixed genetic origin of the first farmers of Europe:

While the Neolithic expansion in Europe is well described archaeologically, the genetic origins of European first farmers and their affinities with local hunter-gatherers (HGs) remain unclear. To infer the demographic history of these populations, the genomes of 15 ancient individuals located between Western Anatolia and Southern Germany were sequenced to high quality, allowing us to perform population genomics analyses formerly restricted to modern genomes. We find that all European and Anatolian early farmers descend from the merging of a European and a Near Eastern group of HGs, possibly in the Near East, shortly after the Last Glacial Maximum (LGM). Western and Southeastern European HG are shown to split during the LGM, and share signals of a very strong LGM bottleneck that drastically reduced their genetic diversity. Early Neolithic Central Anatolians seem only indirectly related to ancestors of European farmers, who probably originated in the Near East and dispersed later on from the Aegean along the Danubian corridor following a stepwise demic process with only limited (2-6%) but additive input from local HGs. Our analyses provide a time frame and resolve the genetic origins of early European farmers. They highlight the impact of Late Pleistocene climatic fluctuations that caused the fragmentation, merging and reexpansion of human populations in SW Asia and Europe, and eventually led to the world’s first agricultural populations.

The supplements are worth reading too. It’s all there.

No mention of Basal Eurasians. The last author told me on Twitter that they weren’t needed, but Iosif Lazaridis (also on Twitter) disagrees, naturally.

+5

7 thoughts on “Whole genomes of ancient farmers and hunter-gatherers

  1. Perhaps the other curated set of WGS released by Dublin+Cambridge group in October could be useful to extend the question of Basal Eurasian and their model, as includes EHG (ZVEJ31), CHG (KK1), African, Upper Palaeolithic Eurasian and American samples – https://www.biorxiv.org/content/10.1101/2020.10.27.351692v1.full.pdf+html

    (Or maybe bioinformatics differences between panels prevent this).

    Interesting that their study of Neanderthal ancestry looks to indicate decline of total by 5% since neolithic (upper limit of diverse panel of European and SW Asian samples looks lower, so not just panel inc. SW Asian samples w/ some African ancestry). Not sure how that could happen though (no admixture source that makes sense which hits all modern Europe+SW Asia, would have been detected in capture aDNA already).

    Suggestion of relatively deep structure between WHG and Iron Gates HG in different refugia by 26kya is interesting!

  2. Matt, the decrease in Neanderthal ancestry could just be selection against existing alleles, so people with fewer ones reproduced more. Why? The neolithic selection went against HG traits like not being to deal with a high carb diet, and likely selected to protect against communicable diseases etc.

    The separation time of 26k years could indicate when the main villabruna cluster and villabruna-like ancestry in west Europe split. Relating to that, I don’t think that the team even mentioned Aurignacian vs villabruna type ancestry in magdalenian and post magdalenians for some reason.

  3. @Dathang, yep, actually considered that one and could be, just seems like a lot for selection (maybe my guess of how many surviving Neanderthal linked variants are selectively neutral is off).

    They didn’t discuss anything that they don’t have Whole Genome Sequences for I don’t think, incl. samples from Spain during late UP. (Some ppl had some trouble getting this one I think as seem to think they’re just ignoring lots of capture adna, but authors r aware it exists, just not using it).

  4. In that case while it adds something new to the table, it cannot be used to upturn things that they didn’t cover.

  5. Indeed.

    Do find it interesting that author Escoffier on twitter implies that Basal Eurasian not needed due to different modelling with Site Frequency Spectrum, possible due to having WGS…

    But didn’t the momi2 model (from https://www.repository.cam.ac.uk/bitstream/handle/1810/293968/momi2-1.pdf) use SFS and find a Basal Eurasian pulse? What’s the difference here? Some difference in data? Would be important for what we think f-statistic based graphs can tell us if there is a real inconsistency.

  6. @DaThang, I think you asked me a little while ago in comments about f and d statistics, saw this paper on biorxiv that is aimed at correcting current estimators of f and d* for inbreeding and population size biases, and as it had a good introduction to what the stats are, thought it might be useful – https://www.biorxiv.org/content/10.1101/2020.11.20.391367v1 – “Properties and unbiased estimation of F- and D-statistics in samples containing related and inbred individuals” (20-11-2020).

    Useful as lays out what each stat is and that D stats are basically just f4 stats with a specific normalisation denominator to make them function as a test of admixture.

    Also, off topic again, but something else that makes me go hmmm from a recent paper: the supplement to Ning 2020 paper (https://www.biorxiv.org/content/10.1101/2020.10.12.336628v1.full) features a mention on page 72 of the supplement of an attempt to create a dataset, using high coverage shotgun samples, that is free of biases found in the usual capture dataset used for adna. When building graphs they then note: he four graphs generated in an automated way on the set of neutrally evolving sites were very similar, and included several well-known admixture events: for instance, the Neanderthal gene flow into all non-Africans, the West Eurasian gene flow into Native Americans, and the basal Eurasian gene flow into Caucasian and Middle Eastern groups. On the other hand, two “unconventional” admixture events shared by all four “winning” graphs were as follows: a 10% gene flow from an American or Siberian source into the Caucasian hunter-gatherer (Kotias) (and another one they try to explain). A geneflow from a Native American related population seems plausible from what we know of West Siberian Hunter Gatherer interactions. Albeit they have fewer samples to work with on that set…

    * Current stats based on estimations of these stats, not directly computing as per theoretical model.

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