Ancient ancestry - K11 Ancients Common and rarer Alleles, and a fresh assessment

Emmanuel Benner - Prehistoric Man Hunting Bears

Above image by Emmanuel Benner the Younger [Public domain], via Wikimedia Commons

The new K11 Ancients Common and Rarer Alleles tests are being run by Dilawer Khan, creator of the Gedrosia stable of admixture calculators available on GEDMatch.com, and of the EurasianDNA.com website.  This new test uses a new set of principles, based on using ADMIXTURE to produce more reliable ancient results.  I commissioned him to run my own 23andMe file through the tests, to produce the following results and PCA's/

PCA for Common Alleles (my position "Norfolk"):

PCA for Rarer Alleles (my position "Norfolk"):

The K11 Ancients common Alleles results should reflect the older ancestry most accurately.  In summary, that gave me:

  1. 48.6% Neolithic Farmer
  2. 26.5% Copper Age Steppe Pastoralist
  3. 24.9% Western Hunter-Gatherer

Thank you Dilawer.

How have other tests seen similar admixture?

I previously commissioned David Wesolowski (Eurogenes stable on GEDMatch and of Eurogenes Blog) to run my raw file through his K7 Basal-rich test.  He produced the following results:

  1. 57.1% Villabruna-related
  2. 28.8% Basal-rich
  3. 14% Ancient North Eurasian.

These are two very different tests, of admixture between different sets of population, of different time periods.  What I do find interesting is the 14% percentage of ANE (Ancient north Eurasian) relates quite favourably to what I understand it's admixture percentage is to Yamna or Steppe pastoralist.  Dilawer gives me 26.5% Steppe.   I have previously heard that the Yamna were circa 50% ANE, and the remainder of mixture of other Western Eurasian Hunter-Gatherer groups, including Caucasus Hunter-Gatherers.

The K11 Ancients test does suggest that I have a surprisingly high amount of ancestry from the Neolithic Farmers, that were in Europe previous to the arrival of the Steppe migrants around 4,900 years ago.  This is actually consistent with my other Ancient admixture test results.  The K7 Basal-rich test for example, had given me 28.8% Basal.  The Basal Eurasians are a hypo-theoretical "ghost" population that was among the founding admixture of the Neolithic Farmers, in a similar way that the ANE were among the founding admixture of the Steppe Pastoralists.  Again then, the two tests do tally reasonably well in determining where my personal percentages of ancient DNA  originate.

Why do I have so high percentages of Neolithic Farmer and Basal Eurasian I do not know.  My DNA flavour is a slight extreme, and atypical even for an English person, and more so for a Briton.  My recorded genealogy is all SE English, mainly East Anglian.  I would love to see the results of other East Anglians, as I suspect to them, that I am not such an extreme.  However, even if this was the case, it doesn't explain why modern East Anglians would have lower Steppe, and more Neolithic than either West British, Scandinavians, or even ancient DNA from Anglo-Saxons.  Higher percentages of Neolithic ancestry today are usually found to the South, peaking in Sardinia, then Iberia.  A favoured explanation is that the SE English could have had a lot of input from the South, via the French during Norman and Medieval periods.  I'm not totally convinced - yet.

A third new ancient admixture test that I might use here in the MDLP Project Modern K11.  On GEDMatch Oracle, it proposes a number of genetic distances to ancient DNA samples:

1 British_Celtic @ 6.948432
2 Bell_Beaker_Germany @ 8.143357
3 Alberstedt_LN @ 8.426399
4 British_IronAge @ 9.027687
5 Halberstadt_LBA @ 10.273615
6 Bell_Beaker_Czech @ 12.190828
7 Hungary_BA @ 12.297826
8 Nordic_MN_B @ 12.959966
9 British_AngloSaxon @ 12.993559
10 Nordic_BA @ 13.170285

Using 4 populations approximation:
1 Bell_Beaker_Germany + Bell_Beaker_Germany + Corded_Ware_Germany + Hungary_CA @ 1.085814
2 BenzigerodeHeimburg_LN + BenzigerodeHeimburg_LN + Corded_Ware_Estonia + Hungary_CA @ 1.089547
3 Alberstedt_LN + Bell_Beaker_Germany + Corded_Ware_Germany + Hungary_CA @ 1.117882
4 Bell_Beaker_Germany + BenzigerodeHeimburg_LN + Hungary_CA + Srubnaya_LBA @ 1.149613
5 Bell_Beaker_Germany + British_IronAge + Hungary_CA + Karsdorf_LN @ 1.185312
6 Alberstedt_LN + BenzigerodeHeimburg_LN + Hungary_CA + Sintashta_MBA @ 1.226794
7 Nordic_BattleAxe + Hungary_BA + Hungary_CA + Karsdorf_LN @ 1.234930
8 Nordic_BattleAxe + BenzigerodeHeimburg_LN + Hungary_CA + Unetice_EBA @ 1.238376
9 Alberstedt_LN + Hungary_BA + Hungary_CA + Yamnaya_Samara_EBA @ 1.247371
10 Bell_Beaker_Germany + Hungary_CA + Nordic_LN + Srubnaya_LBA @ 1.268124

If I look at four population distances, then based on the samples available in the test, I'm looking pretty European Bell Beaker, with Corded Ware and Yamna appearing. My closest single population in the samples is a surprising British Celtic!  More samples from the European Neolithic might turn those results around.

My Basal-rich K7 Results

David Wesolowski of the Eurogenes Blog, has created a new ancient admixture calculator, the Basal-rich K7.

In his blog, he states: "The Basal-rich K7 is the best ancient ancestry test that I've been able to come up with. It correlates strongly with latest research reported in scientific literature. And, in fact, in some instances it probably trumps latest scientific literature.

For instance, Broushaki et al. 2016 characterized Early Neolithic farmers from the Zagros Mountains, Iran, as 62% Basal Eurasian and 38% Ancient North Eurasian-related (Figure S52). This, considering formal statistics like the D-stat below, with AfontovaGora3 (AG3) as the ANE proxy, is unlikely to be correct, despite the fact that AG3 is a relatively low quality sample.".

Villabruna-related

The Villabruna cluster represents the DNA found in 13 individuals in Europe from after 14,000 years ago.  They were Late Ice Age hunter-gatherers.  They appear to have links with the Near East.  The current thought is that they replaced earlier groups of hunter-gatherers in Europe.  The DNA of people in the Middle East and Europe pulled together at this time, and they may represent an expansion from the South-East.  Much of the Aegean Sea would have been dry, with low sea levels (glaciation), so the migration may have been easy.  It is believed that they had dark skin, and blue eyes.  They were possibly, the last hunter-gatherers of Europe and the Middle East.  They may have contributed to our DNA both through or either, later Asian or European admixtures.

David gives the English average as 56.7%.  My result is 57.1%

Basal-rich

The Basal Eurasians are a hypothetical "ghost" population derived from DNA studies.  It is suggested that they splintered from other modern humans 45,000 years ago, presumably outside of Africa, somewhere around the Middle East.  They significantly contributed DNA to the Early Neolithic Farmers of the Fertile Crescent and Anatolia, and consequently, on to all of us modern West Eurasians.  

 David gives the English average as 26.5%.  My result is 28.8%

Ancient North Eurasian

Another Ice Age hunter-gatherer "Ghost" population, but this one has been associated with human remains and an Upper Palaeolithic culture (Mal'ta-Buret') at Lake Baikal, Siberia.  We know that it significantly contributes to modern West Eurasians, through earlier admixture on the Eurasian Steppes.  Copper Age pastoralists then carried it westwards into Europe with their later expansion.

David gives the English average as 16.6%.  My result is 14.0%

Others

David gives the English averages as SE Asian 0.15, Oceanian 0.07, East Eurasian 0.00% and Sub Saharan 0.00

My results are SE Asian 0.00, Oceanian 0.01, and Sub Saharan 0.05

Comparison with other testers

A remarkable similarity has been observed between many of my East Anglian atDNA results and a Norman tester.  On K7, we are almost identical.  Indeed, we are often closer to each other in results, than I am to other British, and he is to other French.

I'm increasingly recognising that although my East Anglian heritage should in theory bring me closer to North German and Scandinavian results, in practice, compared with other Britons, I am pulled more to the south - to France, and even to Southern European.  Hence, I tend to receive lower ANE than many British, Irish, or Scandinavian, and more Early Neolithic Farmer in ancient admixture tests, than would be expected.

Other than Norman admixture, I struggle to explain this with either known paper recorded ancestry (252 direct ancestors from East Anglia and SE England - 100% English), or with known regional history.