K = 13 admixture analysis of ancient Near Eastern genomes

Below is a plot for a K = 13 admixture analysis that includes 45 ancient Near Eastern genomes.

This analysis produced five Caucasoid components. Three of them are similar to components in the preceding K = 12 analysis, while a fourth represents Western European hunter-gatherer DNA, and a fifth represents DNA from the hunter-gatherers of Eastern Europe and Western Siberia, and the later Copper and Bronze Age populations of Eastern Europe.

Over the past week I began to suspect that the Caucasus-related pine green component appearing in large amounts in European samples in my recent K = 13 analyses, which I thought was linked with the spread of R1b-L51 people, was somehow spurious. This analysis, along with others I’ve done over the past few days, confirms my suspicion. The plot below shows most European populations as having only small amounts of the Caucasus-related pine green component.

all-13-8-1

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6 comments on “K = 13 admixture analysis of ancient Near Eastern genomes
  1. norah4you says:

    Reblogged this on Norah4you's Weblog and commented:
    Thanks to Genetiker who let me reblogg this.
    Genetiker have by now presented so many essential analysis re Ancient Genome that I during the day will start a new page on my blogg. If you from tomorrow June 30 2016 look up on the top of the blogg you will find an index as well as later on links to information told long ago which most historians believe could have happened but most likely didn’t. Well they were wrong as I see it reading the analysis.

  2. Anon says:

    Seems more accurate than the other two. Wish you would use a calc that better breaks up WHG/ANE, though. Based on most other calcs there’s no way modern Europeans, IEs, Khvalynsk/Samara are more Mal’ta/Afontova Gora than WHG, unless there was significant drift towards WHG affinity but I don’t see why/how that could happen.

    The Eskimo peaking orange and Amerindian red in Neolithic Levantines(and some modern MENA pops) is weird.

    Also, any thoughts on not all middle paleolithic Europeans(25k-40k BC) having the South Indian dark green? 3 of the 5 that don’t seem to be in Italy. Makes me think it might have something to do with Basal Eurasians, although couldn’t it also just be they’re low coverage SNP wise and got wonky results because of it? Pavlov 1 seems to be almost a full WHG yet he’s 30k years old, which seems unthinkable.

    • Genetiker says:

      Seems more accurate than the other two.

      They’re all accurate. Each shows different aspects of the data.

      Wish you would use a calc that better breaks up WHG/ANE, though.

      I don’t use calculators. I use unsupervised admixture analyses. The computer figures out the optimal set of genetic clusters itself, based on the data.

      Based on most other calcs there’s no way modern Europeans, IEs, Khvalynsk/Samara are more Mal’ta/Afontova Gora than WHG, unless there was significant drift towards WHG affinity but I don’t see why/how that could happen.

      The medium blue component is not a Mal’ta and Afontova Gora component. Most of the samples in the cluster represented by the component are Pit Grave and Afanasevo samples, so the component is mostly defined in terms of those samples. The Mal’ta and Afontova Gora samples are somewhat genetically related, so they lie partially within the same cluster, and show some of the medium blue component, but they also show some other components. The large amount of the medium blue component appearing in the modern European samples in this plot is an indication of the large genetic impact that the Indo-Europeans must have made.

      The Eskimo peaking orange and Amerindian red in Neolithic Levantines(and some modern MENA pops) is weird.

      It’s just noise.

      Also, any thoughts on not all middle paleolithic Europeans(25k-40k BC) having the South Indian dark green? 3 of the 5 that don’t seem to be in Italy. Makes me think it might have something to do with Basal Eurasians, although couldn’t it also just be they’re low coverage SNP wise and got wonky results because of it? Pavlov 1 seems to be almost a full WHG yet he’s 30k years old, which seems unthinkable.

      No, I really don’t think there’s any meaningful pattern there.

  3. Olympus Mons says:

    Yeah. You find it first. And i asked you to follow up but you didn’t care. Now they are all happyn and thrilled at eurogenes because ryukendo find it by other means…. I told you.

  4. DYS389ii says:

    Nice work
    How do you do admixture when the various samples have different quality and SNP counts ?
    Whicj programme do you use ?

    • Genetiker says:

      How do you do admixture when the various samples have different quality and SNP counts ?

      I include all samples in my dataset regardless of how many SNPs they have. ADMIXTURE gives good results for samples with as few as even 100 to 1,000 SNPs.

      Whicj programme do you use ?

      ADMIXTURE.

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