perjantai 20. maaliskuuta 2015

Estimating ancient genes among present-day European populations

Reich Lab's new Admixtools version 3 includes a new admixture calculator based on f4-statistics.  So here is my first effort to find out our Neolithic genetic admixtures.   This test is based on three European Neolithic sample groups:  Yamnaya culture samples,  Neolithic farmer samples from Hungary and Neolithic hunter-gatherer samples from Southern Scandinavia.  East-Asian samples were used additionally to find out possible Northeastern migrations.

So I had four admixture groups.  It wasn't enough, it became soon obvious that South Europeans had a fifth admixture dimension.  I tried to solve the problem and fit Near-Eastern samples to the model, because my previous test with Mixmapper showed a later Near-Eastern admixture in South Europe.  But at this time it didn't succeed.  Sure there is a solution and I'll try to find it later.  Just now some South European results show poor accuracy due to this unknown admixture proportion.  Best fit was obtained in Ukrainian, Belarussian, Cornwall and Basque results.   Results show elevated amounts of East Asian, which was the case also in Haak et al.  The reason is either in low-quality ancient samples or in the method itself. 

This new tool is exciting because it makes estimates fast and seems to have less problems caused by genetic drift, which are typical for admixture analyses.  But I have work to do to learn pros and cons. 

Download Excel-file here.


edit 20.03.15   Sardinian and Sicilian row names corrected.

edit 21.03.15  I did preliminary tests using HungaryGamba_HG, aka KO1, instead of Scandinavian hunter-gatherers.  KO1 was a hunter-gatherer found from Hungarian plain and lived around 5000 years ago and the genome is around as old as the Swedish hunter-gatherer Ajv58 used in my earlier test with other Scandinavian samples from the same period.

The result implies that KO1 shares less common ancestry with Yamnaya, Scandinavian obviously much more than KO1.  Replacing Scandinavian HGs by KO1 led to much higher Yamnaya and lower hunter-gatherer admixtures everywhere where the sum admixture of Yamnaya and Scandinavian HG was highest.   I am working with this but have not just now time to complete my tests.  

edit 21.03.15  Sorry about erroneous test, now corrected (underlined).  To be in a hurry is not a good thing.


4 kommenttia:

  1. "So I had four admixture groups. It wasn't enough, it became soon obvious that South Europeans had a fifth admixture dimension".

    I find your work, which I just begun to explore very interesting because it coincides with my impression: not a triangle but a pentagon. Replace Scandinavians HGs with the surely more direct reference of Scandinavian Neolithic peoples (semi-foragers), as you did, and it seems to work well.

    However I'm perplex that you don't seem to find that fifth component, even approximately, with Near Eastern samples. The Italian deviation should be to something like Palestinians, while the Balcanic deviation (less marked possibly) seems rather towards Anatolia.

    Notice that Scandinavian samples work well but that at least part of that deviation in Western Europeans actually owes to WHG (via reflux from Atlantic Chalcolithic). I'm not sure why you seem to get those East Asian residuals however.

    VastaaPoista
  2. Thanks, your pentagon looks good.

    Actually I have found the lacking Mediterranean dimension. As I wrote in my newer posts I found that Turkish without Asian match well for East Mediterraneans, implying obviously Anatolia. The rest of Turkish genetic profile is disregarded in analysis and Lebanese samples seems to fill the hole. But I have not yet profiled Western Mediterranean. Although pentagon can be reasonable with pure ancient genomes we probably need now a mixture of Near Easteners until we have Near Eastern ancient genomes.

    Yes, Scandinavian HG's owe a lot to WHG, but WHG is likely too old to cover present-day genomes. Using Admixture it works well, probably because Admixture doesn't tell the residual proportion. WHG comes from a time dimension x.

    VastaaPoista
  3. Let me explain: you are using a baseline of Yamna-Early Neolithic that is not represented in my graph but can easily be drawn as well: it goes over the Balcans and North Italy but leaves most Europeans "above" it, with clear extra tendency towards HGs in general. This can be mostly corrected using, as you do, Pitted Ware samples (I refuse to call them "hunter-gatherers", rather fishermen with pigs and possibly even some grain, and of course pottery and stable settlements) but notice that (from other data) these tend to Motala (SHG) rather than to Lochsbour/Braña (WHG) and that there is also an apparent tendency towards hardcore WHG, which in my graph is apparent in the First Neolithic - Megalithism side of the triangle and the pentagon. This extra WHG (possibly attributable to Megalithism) is what makes the difference between a Serbian and a German or between a North Italian and a Basque.

    Call it nit-picking but there seems to be distinct influence of three HG sources: Western, Scandinavian and Eastern all around, and over-simplifying this HG-influence diversity may introduce errors (for example in relation to Paleo-Siberian, Ma1-like, influence).

    However I agree that ideally more recent (and more mixed) pops. than Epipaleolithic ones are more likely to explain the variation in European admixture. Just that we work with what we have. An improvement you can already make however is to introduce another column (maybe removing the East Asian one, which is trivial except for the Chuvash) with Skoglund's Megalithic people from SW Sweden.

    VastaaPoista
  4. Maju "Call it nit-picking but there seems to be distinct influence of three HG sources: Western, Scandinavian and Eastern all around, and over-simplifying this HG-influence diversity may introduce errors (for example in relation to Paleo-Siberian, Ma1-like, influence)."

    I wouldn't call it nit-picking, because I see the difference between regional hunter-gatherer samples. Even Karelian and Samara HG's give different results, although grouped together as "EHG". We have always regional and consecutive differences. It would be good to use cultural names, as you did, but researchers use not those abbreviations. All Scandinavian hunter-gatherers seem to be somewhat mixed, but I prefer finding best fits instead of a theory about smallest amount of mixing factors. Sure it is also interesting to find out who were the first distinct populations in Europe after the Ice Age, but I am more interesting in history.

    VastaaPoista

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