Monday, February 26, 2018

Looking at Supp Info

Started looking at the Supplementary Info from the "Beaker Phenomenon and the Genomic Transformation of Northwest Europe".

Extended data (this paper)

Look at these numbers for the percentage of R1b.  Significant that of 34 British Neolithic, 0% are R1b 

- 27/27 Czech Beakers (whaaat)
- 20/21 British Beakers
- 6/6     French
- 8/9     Polish 
- 6/15   Spaniards are R1b
- 2/2     Swiss
- 7/7     Netherlands

- 23/26 Germany
- 1/1     Italy

Several of the above non-R1b lineages of Beakers are labeled P1, CT, CF, BT and F and then labeled as negative for this and that.  I imagine that's as far as they could be read with damage.  Any guesses as to what they would likely be?

- 6/13   Hungary

Hungary is a mixed bag and should be.

- 0/2     Portugal

Kind of ironic for a stylistic tradition that synthesizes contact between Portugal and Morocco.  But as the new Spaniards in the final paper show, every new genome adds a twist to the story.  Speaking of Portugal, two papers are out on Portuguese Bell Beaker and those explain a lot. 


  1. You can be virtually certain that the origin population for the Bell Beakers was almost entirely disjunct on the male side from the origin population for Corded Ware and from the origin population for Indo-Aryans.

  2. "Iberian Beaker-associated individuals without a genome-wide signal of steppe ancestry
    belonged mainly to haplogroups I2 and G2 (Supplementary Table 4), both present in
    high frequencies in European Neolithic farmers273,278–280 and also in Iberian Copper Age
    populations. Haplogroup G2 probably entered Europe from the Near East during the
    Neolithic expansion, and haplogroup I2 was likely introduced into the Neolithic
    population through admixture with European hunter-gatherers. Two Iberian individuals
    (I0257 and I0261) without steppe ancestry belonged to haplogroup R1b but likely not to
    R1b-L23 and therefore not to R1b-S116/P312. Similar R1b haplogroups (ancestral for
    L23) were present in low frequencies in Europe during the Neolithic period, as they
    have been previously observed in both central Europe (I0559) and Iberia (I0410)273.
    Interestingly, 4 Beaker-associated males from Iberia belonged to R1b-M269, and the
    two with higher coverage could be further classified as R1b-S116/P312. These 4
    individuals displayed a clear signal of steppe ancestry in the autosomes, highlighting the
    association between R1b-M269 and steppe-related genetic affinities. These individuals
    represent, to our knowledge, the earliest observation in Iberia of R1b-M269 and R1bS116/P312,
    lineages that dominate the Y-chromosome composition in present-day
    Iberian populations.
    Outside Iberia, Beaker Complex individuals present a striking uniformity in paternal
    lineages, with 87 out of 93 males (excluding relatives) belonging to haplogroup R1b
    (Supplementary Table 4). Where R1b downstream mutations could be determined
    (n=60), all but two males belonged to R1b-S116. The six individuals outside Iberia
    without R1b Y-chromosomes were excavated in Hungary (n=4), Germany (n=1) and
    England (n=1). Interestingly, most of these individuals presented low amounts of steppe
    ancestry in the nuclear genome as compared to other individuals from the same regions
    (Figure S2a).
    Another striking observation is the haplogroup composition of Neolithic males in
    Britain (n=34), who displayed entirely I2a2 and I2a1b haplogroups. Thus, there is no
    evidence at all for a contribution to Neolithic farmers in Britain of the Y chromosome
    haplogroups (e.g., G2) that were predominant in Anatolian farmers and in
    Linearbandkeramik central European farmers.
    We detect 28 males who belonged to R1b-L21/M529, all of them dated to the Beaker
    and Bronze Age periods and excavated in Britain. This matches the high frequency of
    this clade in modern populations from the British Isles.
    We finally comment on three individuals with uncertain attributions:
    -Sample I0261 can be assigned to haplogroup R1b1a based on mutations
    R1b1a:L1345:21558298G->T; R:F652:23631629C->A and R:M651:9889199G->A.
    Haplogroups I, G, R1a and R1b1a1a2a can be excluded due to the presence of ancestral
    alleles for I (CTS11979:23401471C->T), G (M3600:21954611G->A,
    PF3134:15275200C->G), R1a (L145:14138745C->A) and R1b1a1a2a (L23:6753511G>A).
    Thus, it seems that I0261 belonged to R1b, but not to the R1b-S116/P312
    (R1b1a1a2a1a2) clade that is present in most Beaker-associated individuals outside
    -Sample I0257 can be assigned to haplogroup R1b1 based on derived alleles at
    mutations R1b1 (L1349: 22722580T->C) and R (P224:17285993C->T,
    L1347:22818334C->T). Haplogroups I, G and H can be excluded due to the presence of
    ancestral alleles for I (CTS2193:14214481G->T, PF3641:7688470 T->C,
    PF3660:8466652G->A), G (CTS1283:7309873T->G, CTS2016.1:14155765G->A,
    CTS2125:14190447A->G, CTS4761:15802681C->T, CTS9011:18615020A->T,
    M3474:7930724C->A, PF3134:15275200G->C) and H (M2942:17887908A->G). This
    individual and I0261 could belong to the same haplogroup, but for I0257 we cannot
    exclude any R1b1 subclade."

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    2. The Iberian xP312 are intriguing, especially given the age and spread of V88 from Southern Europe in the paper that came out last week.
      Call me paranoid but is someone teasing us or is it a coincidence?

  3. "CT, CF, BT and F"

    CT, CF and F are basically telling you nothing more than that they are not DE and not A or B.

    BT only excludes A.

    A and B are African Y-DNA clades. F also excludes a Asian C clades.

    1. But I'd assume this means they're not certain of assignment below these macrogroups due to damage?

    2. That would be my guess. There is no other reason I can think of to make such a vague assignment. Honestly, it would be better to remove them from the Y-DNA sample entirely unless your main purposes was to show that they weren't recent African immigrants.

  4. P1 is ancestral to Y-DNA Q (mostly Native American) and Y-DNA R (which are sister clades). In this context, P1 is almost certainly some type of Y-DNA R1 and realistically, probably R1b.

  5. What are the 2 new papers on Portuguese BB ?
    Did you mean archeology papers ?

    1. These are from a symposium in 2017. Some of the other papers may be uploaded as well. I haven't checked yet.

  6. Rob.
    Can you model I6601?
    Try to see if any balkans in it...

    so, back at Eurogenes you all are approching Shulaveri, right? - Remember, shulaveri proper most likely came from balkans. Yes might have Barcin, but should have a good chunk of WHG.

    1. We dont have SS dat yet, so its hard to say. Arm Chalc had probable northern influences, so it isn;t a good proxy for preceding S.S.

      I6601 : LCA i2a male

      "Iberia_MN" 89.8
      "Tiszapolgar_ECA" 9.95
      "Bonda" 0.25

      Largely a continuity from local Middle Neolithic, plus admxiture from Balkans via Italy (here underestimated - more like 30-40%)

  7. The second paper on Portuguese Beaker you listed shows that their influence in North Central Portugal is late, and not very connected to the Meseta - they even say "the apparent isolation from Northern Meseta (regarding Ciempozueos style)". Most of the BB pots seem to be from Fraga da Pena, just about 15km from my father's village, whereas other sites have very few.

    Haven't fully read the paper, but the conclusion states "the faint presence of beakers in Beira Alta (that can be associated to an also pale manifestation of those other expressions) may correspond to a slower and more conservative course and, simultaneously, to dynamics of resistance to the social change in progress."

    After this, it shouldn't be surprising that none of those BB samples in Portugal are R1b- eventhough they are just 2, so not very significant. Even today West Iberia has a lower concentration of this haplogroup than the East

    1. When the draft first came out I thought then that it would take a long while to figure Iberia out due to the size of the Peninsula, the earliness of the Beaker phenomenon, and even in Portugal the very different stories from site to site. Even with the final paper we see how quickly the situation changes with just a few more remains.

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    3. André,
      Since you mention current population.
      Do you know that portugal has the highest percentage of M269(×p312) that only matches in Brittany and North france. And the 2200bc , DF27 (father) has no, i repeat no, Z195 (son) which has the same TrMc as the father(DF27). They actually new each other.

      It just makes a strange east to west migration of r1b