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Thread: The Population Genomics Of Archaeological Transition In West Iberia

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    2 members found this post helpful.

    The Population Genomics Of Archaeological Transition In West Iberia

    now also West-Iberian DNA

    http://biorxiv.org/content/early/2017/05/10/134254

    after a long dry period, it is raining new publications today
    it will take me some time to digest

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    Is this just the abstract?
    Be wary of people who tend to glorify the past, underestimate the present, and demonize the future.

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    you can click 'download pdf'
    suplementary info I don't find

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    1 members found this post helpful.
    Chalcolithic Iberia seems to be dominated by I2a, maybe there is a link with megalithism
    R1b-P312 arrived in Iberia and become dominant in early bronze age (+/- 1700 BC)

    Last edited by bicicleur; 11-05-17 at 17:46.

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    Their ADMIXTURE analysis at K = 10 seems to exclude Yamnaya as a source of Bronze Age ancestry in the Portuguese individuals:



    I think if the CHG signal was there, ADMIXTURE would definitely pick it up since it is quite diverged.

    I find that a bit surprising to be honest - I used to think the Bronze Age in Iberia was pretty much derived from Central Europe where CHG ancestry should have been widespread after CW/BB movements. I take this to mean that bronze technology spread to Portugal over the Mediterranean and not through France & Spain.

    Also there's KO1 again:

    A reversal of this trend is seenin the later Neolithic and Chalcolithic individuals from Portugal and Spain, butintriguingly not in other Atlantic Neolithic samples from Ireland and Sweden. This isconfirmed by a Mann-Whitney test demonstrating that Iberian Neolithic samples receivesignificantly more (p=1.02x10-6) haplotypes from west European HG (Bichon, Loschbourand LaBrana) than KO1 relatively to Neolithic samples from elsewhere in Europesuggesting a more prolonged hunter-gatherer interaction at the littoral. In the transitionto the Portuguese Bronze Age, a second shift can be seen in relative hunter-gathererancestry with some increase in relative haplotype donation from KO1, which is seenmore prominently in the majority of post-Neolithic Eurasian samples, hinting at somedifference between the Portuguese Neolithic and Bronze Age.

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    1 members found this post helpful.
    There's more EHG, though...would that have come by way of the Med? Could there have been a group which was largely EHG, with little to no CHG, which was Indo- Europeanized and also made its way through Central Europe and ultimately to Iberia. I think it's clear that the old simplistic "kurgan" narrative doesn't fit southern Europe.

    Could bronze technology, like copper technology, have gotten there by cultural diffusion, or should we look at sites like El Agar? Do the dates fit? Were any of the tested samples from there?

    https://en.wikipedia.org/wiki/El_Argar

    "The collective burial tradition typical of European Megalithic Culture is abandoned in favor of individual burials. The tholos is abandoned in favour of small cists, either under the homes or outside. This trend seems to come from the Eastern Mediterranean, most likely from Mycenaean Greece (skipping Sicily and Italy, where the collective burial tradition remains for some time yet).From the Argarian civilization, these new burial customs will gradually and irregularly extend to the rest of Iberia.
    In the phase B of this civilization, burial in pithoi (large jars) becomes most frequent (see: Jar-burials). Again this custom (that never reached beyond the Argarian circle) seems to come from Greece, where it was used after. ca 2000 BC."


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    Quote Originally Posted by Angela View Post
    There's more EHG, though...would that have come by way of the Med? Could there have been a group which was largely EHG, with little to no CHG, which was Indo- Europeanized and also made its way through Central Europe and ultimately to Iberia. I think it's clear that the old simplistic "kurgan" narrative doesn't fit southern Europe.

    Could bronze technology, like copper technology, have gotten there by cultural diffusion, or should we look at sites like El Agar? Do the dates fit? Were any of the tested samples from there?

    https://en.wikipedia.org/wiki/El_Argar

    "The collective burial tradition typical of European Megalithic Culture is abandoned in favor of individual burials. The tholos is abandoned in favour of small cists, either under the homes or outside. This trend seems to come from the Eastern Mediterranean, most likely from Mycenaean Greece (skipping Sicily and Italy, where the collective burial tradition remains for some time yet).From the Argarian civilization, these new burial customs will gradually and irregularly extend to the rest of Iberia.
    In the phase B of this civilization, burial in pithoi (large jars) becomes most frequent (see: Jar-burials). Again this custom (that never reached beyond the Argarian circle) seems to come from Greece, where it was used after. ca 2000 BC."
    Is there excess EHG ancestry in those samples though? As I understand it, the imputation of steppe ancestry in those Portuguese samples is based on increased similarity to present day Orcadians, Chuvash and Lezgins. This could be caused by any number of things. Is there something in the supp. material that I've missed?

    About languages I don't know. The samples are too early to be Celtic, hence they could be either Lusitanian IE or non-IE Paleohispanic. I think the samples come from southern Portugal close to historic Turdetanian-Tartessian territory.

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    Markoz, I have no clue how the methods work for the most part so I can't be of any assistance but they detected the increased steppe ancestry with two different ones (ChromoPainter/fineSTRUCTURE and D-stats), didn't they? Though the D-statistics they performed and refer to are in a supplement that doesn't seem to exist on the site. Didn't some methods model the Mako woman, which appears teal-less here, as part CHG and EHG by the way?

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    Quote Originally Posted by LATGAL View Post
    Markoz, I have no clue how the methods work for the most part so I can't be of any assistance but they detected the increased steppe ancestry with two different ones (ChromoPainter/fineSTRUCTURE and D-stats), didn't they? Though the D-statistics they performed and refer to are in a supplement that doesn't seem to exist on the site. Didn't some methods model the Mako woman, which appears teal-less here, as part CHG and EHG by the way?
    The results are essentially summarized in Fig. 3 . The issue with this is that it is based on present populations. Their evidence of steppe introgression seems to be (i) increased similarity to present day Orcadians, Lezgins and Chuvash and (ii) R1b in the Portuguese samples, which they see as a reliable indicator of steppe descent.

    I hope there's something better in the supplementary material, but I don't have much confidence.

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    Quote Originally Posted by MarkoZ View Post
    Is there excess EHG ancestry in those samples though? As I understand it, the imputation of steppe ancestry in those Portuguese samples is based on increased similarity to present day Orcadians, Chuvash and Lezgins. This could be caused by any number of things. Is there something in the supp. material that I've missed?

    About languages I don't know. The samples are too early to be Celtic, hence they could be either Lusitanian IE or non-IE Paleohispanic. I think the samples come from southern Portugal close to historic Turdetanian-Tartessian territory.

    I couldn't find a supplement. That's part of my problem with the conclusions: I want to see more of the stats.

    As to what they see happening in the Bronze Age, the Admixture run you posted shows a slight increase in "H/G".

    This is what they say in the body of the paper:
    "In the transition to the Portuguese Bronze Age, a second shift can be seen in relative hunter-gatherer ancestry with some increase in relative haplotype donation from KO1, which is seen more prominently in the majority of post-Neolithic Eurasian samples, hinting at some difference between the Portuguese Neolithic and Bronze Age."

    However, when discussing "steppe" intrusion they say:"Consistent with this, when comparing Portuguese Neolithic to Bronze Age samples, the former presented an excess of haplotype donation to Sardinian and Spanish (p=0.017). Northern/eastern ancestry is evident in the Bronze Age, with significantly increased enrichment in Chuvash, Orcadian (p=0.017), Lezgin and Irish (p=0.033)." All of those populations share EHG. However, Orcadians, Lezgin,and Irish also share CHG, don't they? What about Chuvash?

    Then they say the following:
    "A recurring feature of ADMIXTURE analyses of ancient northern Europeans is the appearance and subsequent dissemination within the Bronze Age of a component (teal) that is earliest identified in our dataset in HGs from the Caucasus (CHG). Unlike contemporaries elsewhere (but similarly to earlier Hungarian BA), Portuguese BA individuals show no signal of this component, although a slight but discernible increase in European HG ancestry (red component) is apparent. D-Statistic tests would suggest this increase is associated not with Western HG ancestry, but instead reveal significant introgression from several steppe populations into the Portuguese BA relative to the preceding LNCA (S4 Text, S6 Table). Interestingly, the CHG component in ADMIXTURE is present in modern-day Spaniards and to a lesser extent in the Basque population."

    They couldn't have worded this more confusingly, but I took this to mean that they believe that d-stats show that the slight increase in HG in the Iberian Bronze Age is not from western hunter-gatherers, but from steppe populations, which would imply EHG, yes? Yet, didn't they say above at least part of it came from Koros?

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    I guess the only explanation is that their 'steppe' component is identical to the component that's being referred to in the Pagani abstract. Whereas in the Reich papers 'steppe' always denotes the hybrid Yamnaya component.

    This might explain how it ended up in southern Portugal in an early BA context, since both Balkan & Scandinavian HG seem to carry inflated 'steppe' ancestry relative to the westernmost 'post-Franco-Cantabrian' hunters.

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    Central European BB without Iberian ancestry and Iberian post-BB without steppe ancestry (as EHG + CHG). Something must be wrong here or there isn't?
    "What I've seen so far after my entire career chasing Indoeuropeans is that our solutions look tissue thin and our problems still look monumental" J.P.Mallory

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    2 members found this post helpful.
    Berun, they're saying there was no CHG in Bronze Age Iberia, although there is now, not even in those Bronze Age R1b1 samples. Using their own definition of "steppe" ancestry, which apparently doesn't include CHG like ancestry, theysay there is a bit of steppe in Bronze Age Iberia, but not much.

    The conclusion is unsurprising. Look how little Yamnaya-steppe, defined as EHG and CHG, there is in modern Spaniards. Only the Greeks, Albanians and Sardinians on that chart have less. I'm just not convinced there's no CHG in Martiniano's steppe component.

    Spanish North is basically Spanish Basque...
    Last edited by Angela; 12-05-17 at 04:11.

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    Quote Originally Posted by MarkoZ View Post
    Their ADMIXTURE analysis at K = 10 seems to exclude Yamnaya as a source of Bronze Age ancestry in the Portuguese individuals:



    I think if the CHG signal was there, ADMIXTURE would definitely pick it up since it is quite diverged.

    I find that a bit surprising to be honest - I used to think the Bronze Age in Iberia was pretty much derived from Central Europe where CHG ancestry should have been widespread after CW/BB movements. I take this to mean that bronze technology spread to Portugal over the Mediterranean and not through France & Spain.

    Also there's KO1 again:
    Again, by analyzing admixtures, I concluded that CW wasn't the source. It looked more like Baden Culture/Hungarian BA (like) people from North Balkans came to Iberia. If there is a connection to steppe and Yamnaya and IE language, it could be only through SW Yamnaya, which could have contained more WHG than EHG, and didn't mix much with Iranian Farmer (CHG like). Now it even makes more sense when we know that Baden was in center of R1b WHG.

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    Quote Originally Posted by Angela View Post

    Then they say the following:
    "A recurring feature of ADMIXTURE analyses of ancient northern Europeans is the appearance and subsequent dissemination within the Bronze Age of a component (teal) that is earliest identified in our dataset in HGs from the Caucasus (CHG). Unlike contemporaries elsewhere (but similarly to earlier Hungarian BA), Portuguese BA individuals show no signal of this component, although a slight but discernible increase in European HG ancestry (red component) is apparent. D-Statistic tests would suggest this increase is associated not with Western HG ancestry, but instead reveal significant introgression from several steppe populations into the Portuguese BA relative to the preceding LNCA (S4 Text, S6 Table). Interestingly, the CHG component in ADMIXTURE is present in modern-day Spaniards and to a lesser extent in the Basque population."

    They couldn't have worded this more confusingly, but I took this to mean that they believe that d-stats show that the slight increase in HG in the Iberian Bronze Age is not from western hunter-gatherers, but from steppe populations, which would imply EHG, yes? Yet, didn't they say above at least part of it came from Koros?
    What they are saying is that they can't reconcile completely Admixtures with DStats. Their admixtures show no Steppe ancestry, where they expect to see CHG, but D Stats do show some. More confusion is that modern Spaniards show quote a bit of CHG.

    I think all is good. Iberian BA will show influence of Hungarian BA, and will show a bit of CHG (Iranian Farmer). Not much because SW Yamnaya didn't get much.

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    Anyone remember the archaeological context for BR1? He was largely EEF and EHG. He's one of the reasons I started suggesting that perhaps there was a reservoir of largely EHG people who were Indo-Europeanized and then moved west.

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    Quote Originally Posted by Angela View Post
    Anyone remember the archaeological context for BR1? He was largely EEF and EHG. He's one of the reasons I started suggesting that perhaps there was a reservoir of largely EHG people who were Indo-Europeanized and then moved west.
    I must have had a temporary brain freeze or maybe making dinner at the same time isn't such a good idea. :)

    Bronze Age I: 1,980–2,190 BC, a woman, K1c1 mtdna, from Bronze Age Mako Culture, eastern Hungary. It wasn't far from Vucedol, and, strangely on one of the tributaries of the Koros. :)

    Cristina Gamba et al says:

    "
    Our two Bronze Age samples, BR1 (1,980–2,190 cal BC) and BR2 (1,110–1,270 cal BC) fall among modern Central European genotypes. Within this period the trade in commodities across Europe increased and the importance of the investigated region as a node is indicated by the growth of heavily fortified settlements in the vicinities of the Carpathian valleys and passes linking North and South26. These two Bronze Age genomes represent the oldest genomic data sampled to date with clear Central European affinities."

    https://www.nature.com/articles/ncomms6257

    It was some of the modelers, I think, who suggested she could be modeled without CHG, if I remember correctly.

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    Quote Originally Posted by Angela View Post
    I must have had a temporary brain freeze or maybe making dinner at the same time isn't such a good idea. :)

    Bronze Age I: 1,980–2,190 BC, a woman, K1c1 mtdna, from Bronze Age Mako Culture, eastern Hungary. It wasn't far from Vucedol, and, strangely on one of the tributaries of the Koros. :)

    I got 3 BA Hungarians. Two of them show Baloch, which is definitive steppe or CHG or Iran Neolithic. Big change from Copper Age to BA, but not as pronounced as CW up North. Surprisingly BR1 doesn't show Baloch, and looks like only mixture of WHG with EEF.
    First dude is CA for comparison.
    F999930 CO1 F999933 BR2, J-M67 M681225 BR1 M631469 RISE349
    Hungary, Apc-Berekalja I 4.8kya Hungary, Ludas-Varjú-dűlő, 3.3kya EBA Hungary 1,980–2,190 BC Hungary MBA [2034-1748 BC] T2b3 -
    Run time 7.06 Run time 15.13 Run time 10.55 Run time 3.16
    S-Indian - S-Indian - S-Indian - S-Indian -
    Baloch - Baloch 3.15 Baloch - Baloch 5.64
    Caucasian 19.26 Caucasian 14.73 Caucasian 5.45 Caucasian 13.81
    NE-Euro 16.74 NE-Euro 46.18 NE-Euro 56.15 NE-Euro 38.22
    SE-Asian - SE-Asian 0.2 SE-Asian 0.49 SE-Asian -
    Siberian - Siberian - Siberian - Siberian -
    NE-Asian - NE-Asian - NE-Asian - NE-Asian -
    Papuan - Papuan 0.18 Papuan - Papuan -
    American - American - American - American -
    Beringian - Beringian - Beringian - Beringian -
    Mediterranean 55.37 Mediterranean 31.73 Mediterranean 34.48 Mediterranean 34.63
    SW-Asian 8.52 SW-Asian 3.33 SW-Asian 3.1 SW-Asian 3.94
    San - San - San - San -
    E-African - E-African - E-African - E-African -
    Pygmy - Pygmy - Pygmy - Pygmy -
    W-African 0.1 W-African 0.48 W-African 0.3 W-African 3.75

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    1 members found this post helpful.
    If BA Hungary/Balkans invaded Iberia, it will be very hard to show genetically, because they were quite alike, both a mixture of EEF with WHG. Just BA hungarians have a bit of typical steppe, typical Central/East Yamnaya. It will dilute very quickly once they arrived in Iberia. Researchers have to dig deep to distinct and smallest mutations to figure it out. Likewise finding matching clades of Y DNA of both could be helpful too.

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    Quote Originally Posted by LeBrok View Post
    I got 3 BA Hungarians. Two of them show Baloch, which is definitive steppe or CHG or Iran Neolithic. Big change from Copper Age to BA, but not as pronounced as CW up North. Surprisingly BR1 doesn't show Baloch, and looks like only mixture of WHG with EEF.
    First dude is CA for comparison.
    F999930 CO1 F999933 BR2, J-M67 M681225 BR1 M631469 RISE349
    Hungary, Apc-Berekalja I 4.8kya Hungary, Ludas-Varjú-dűlő, 3.3kya EBA Hungary 1,980–2,190 BC Hungary MBA [2034-1748 BC] T2b3 -
    Run time 7.06 Run time 15.13 Run time 10.55 Run time 3.16
    S-Indian - S-Indian - S-Indian - S-Indian -
    Baloch - Baloch 3.15 Baloch - Baloch 5.64
    Caucasian 19.26 Caucasian 14.73 Caucasian 5.45 Caucasian 13.81
    NE-Euro 16.74 NE-Euro 46.18 NE-Euro 56.15 NE-Euro 38.22
    SE-Asian - SE-Asian 0.2 SE-Asian 0.49 SE-Asian -
    Siberian - Siberian - Siberian - Siberian -
    NE-Asian - NE-Asian - NE-Asian - NE-Asian -
    Papuan - Papuan 0.18 Papuan - Papuan -
    American - American - American - American -
    Beringian - Beringian - Beringian - Beringian -
    Mediterranean 55.37 Mediterranean 31.73 Mediterranean 34.48 Mediterranean 34.63
    SW-Asian 8.52 SW-Asian 3.33 SW-Asian 3.1 SW-Asian 3.94
    San - San - San - San -
    E-African - E-African - E-African - E-African -
    Pygmy - Pygmy - Pygmy - Pygmy -
    W-African 0.1 W-African 0.48 W-African 0.3 W-African 3.75
    And there we go! We have synergy, LeBrok. I have to take you away from work more often. :)

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    Quote Originally Posted by Angela View Post
    Berun, they're saying there was no CHG in Bronze Age Iberia, although there is now, not even in those Bronze Age R1b1 samples. Using their own definition of "steppe" ancestry, which apparently doesn't include CHG like ancestry, theysay there is a bit of steppe in Bronze Age Iberia, but not much.

    The conclusion is unsurprising. Look how little Yamnaya-steppe, defined as EHG and CHG, there is in modern Spaniards. Only the Greeks, Albanians and Sardinians on that chart have less. I'm just not convinced there's no CHG in Martiniano's steppe component.

    Spanish North is basically Spanish Basque...
    The chart displays a 20% of steppe ancestry in actual Spanish people, so I would expect a possible 10% of CHG in such Portuguese samples at least. But ok, steppe warriors manage to arrive into Portugal without needing their CHG component and the Bell Beaker package arrived to Central Europe without any Iberian gene, just by TV broadcasting. It's irony not about you but about what I'm perceiving how Yamnayists are taking the different scenarios...

    By the way the last mtDNA paper dealing with BA Iberia found no steppe ancestry. It's a pity that some genetists are't worshipers of the holy cows.

  22. #22
    MarkoZ
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    I suppose CHG in present day Iberians could have arrived with Urnfield and La Tène-Hallstatt movements, the latter of which were indubitably Indo-European.


  23. #23
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    1 members found this post helpful.
    Quote Originally Posted by MarkoZ View Post
    I assume CHG in present day Iberians could have arrived with Urnfield and La Tène-Hallstatt movements, the latter of which were indubitably Indo-European.

    Celts are suspected to have arrived in Iberia 600 BC.
    Some of their genes should still be present in todays Iberians.

  24. #24
    MarkoZ
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    Quote Originally Posted by bicicleur View Post
    Celts are suspected to have arrived in Iberia 600 BC.
    Some of their genes should still be present in todays Iberians.
    I think this should be the most reasonable date for the Celtic arrival in Iberia. Has DNA from La Tene sites been published to date? I suppose they would be heavy in CW aDNA like those Central European Bell Beakers?

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    Population genomics of archaeological transition in west Iberia

    Published: July 27, 2017

    http://journals.plos.org/plosgenetic...l.pgen.1006852

    We analyse new genomic data (0.05–2.95x) from 14 ancient individuals from Portugal distributed from the Middle Neolithic (4200–3500 BC) to the Middle Bronze Age (1740–1430 BC) and impute genomewide diploid genotypes in these together with published ancient Eurasians. While discontinuity is evident in the transition to agriculture across the region, sensitive haplotype-based analyses suggest a significant degree of local hunter-gatherer contribution to later Iberian Neolithic populations. A more subtle genetic influx is also apparent in the Bronze Age, detectable from analyses including haplotype sharing with both ancient and modern genomes, D-statistics and Y-chromosome lineages. However, the limited nature of this introgression contrasts with the major Steppe migration turnovers within third Millennium northern Europe and echoes the survival of non-Indo-European language in Iberia. Changes in genomic estimates of individual height across Europe are also associated with these major cultural transitions, and ancestral components continue to correlate with modern differences in stature.
    Father's Mtdna H95a1
    Grandfather Mtdna T2b24
    Great Grandfather Mtdna T1a1e
    GMother paternal side YDna R1b-S8172
    Mother's YDna R1a-Z282

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