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Thread: The genetic history of Europeans (paper online August 2012)

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    The genetic history of Europeans (paper online August 2012)

    There is a new review paper out:
    Ron Pinhasi, Mark G. Thomas, Michael Hofreiter, Mathias Currat, Joachim Burger, The genetic history of Europeans, Trends in Genetics.

    The evolutionary history of modern humans is characterized by numerous migrations driven by environmental change, population pressures, and cultural innovations. In Europe, the events most widely considered to have had a major impact on patterns of genetic diversity are the initial colonization of the continent by anatomically modern humans (AMH), the last glacial maximum, and the Neolithic transition. For some decades it was assumed that the geographical structuring of genetic diversity within Europe was mainly the result of gene flow during and soon after the Neolithic transition, but recent advances in next-generation sequencing (NGS) technologies, computer simulation modeling, and ancient DNA (aDNA) analyses are challenging this simplistic view. Here we review the current knowledge on the evolutionary history of humans in Europe based on archaeological and genetic data.
    Dienekes sucks out the marrow. Crucial snippets from the paper:

    The inferred patterns of discontinuity between Neolithic and modern populations in Europe raise questions about which demographic processes reshaped European genetic variation after the Neolithic transition.... Future research should also reveal the effects of post-Neolithic demographic processes, including migration events, which preliminary data suggest had a major impact upon the distribution of genetic variation. These include events associated with Bronze Age civilizations, Iron Age cultures, and later migrations, including those triggered by the rise and fall of Empires.
    Last edited by Jean M; 08-15-2012 at 09:50 AM.

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    For French-speakers, there is a summary in French from Bernard.

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    The discontinuity makes sense, especially given Europe's history of waves of migration from Asia (a recurring theme throughout the millenia). I can see how farming would significantly impact on the DNA - farming supports more people per unit area than hunting. The same goes for the purported Indo-European invasions (although I'm undecided how much of it was due to military conquest vs cultural diffusion). Me, I think the situation was like Latin America in later centuries: A minority elite imposing (via force or unconscious / unintended cultural domination) their views on the natives. I believe the same pattern happened in Britain during the Germanic invasions. So while I think Europeans are majority native of the immediate region, there certainly was significant genetic diffusion into the European "blood stream".

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    On present knowledge, Europeans are largely descended from a mixture of inputs from the Near East at various times from 45000 years ago through to the Middle Ages. There was also a smaller input into Europe from other parts of Asia at various times from ancient to Middle Ages, bringing haplogroups that are relatively rare today in Europe, such as Y-DNA N and H.

    The Indo-Europeans actually spread into the rest of Europe from a homeland now just on the European side of the Europe/Asian border, but were themselves descended from a mixture of local hunter-gatherers and farmers with an origin in the Near East, as far as we know from ancient DNA. From what we know so far (and we do need much more data), they contributed the Y-DNA R1a1a1 (M417) and R1b1a2 (M269) that dominates Europe today. So far there is no sign of it elsewhere in Europe prior to the Copper Age. So the picture is more one of Indo-European mass movement than elite dominance, though it varies by region. We should also bear in mind that haplogroups that first arrived in Europe earlier could also travel later with the Indo-Europeans, making a very complex picture. For example the mtDNA haplogroup U5 is ancient in Europe. It predominates in the DNA found so far in people of the European Mesolithic. Yet most of it in the British Isles today probably arrived no earlier than the Copper Age.

    Mark Thomas has made a copy of the paper available online.
    Last edited by Jean M; 08-17-2012 at 11:44 AM.

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    Quote Originally Posted by Jean M View Post
    The Indo-Europeans actually spread into the rest of Europe from a homeland now just on the European side of the Europe/Asian border, but were themselves descended from a mixture of local hunter-gatherers and farmers with an origin in the Near East, as far as we know from ancient DNA. From what we know so far (and we do need much more data), they contributed the Y-DNA R1a1a1 (M417) and R1b1a2 (M269) that dominates Europe today.
    Though we're on the same page vis-a-vis the PIE dispersal from the Pontic-Caspian steppe, I'd like to know what evidence gave you the means to reach the conclusion that Y-DNA Haplogroup R1b-M269 was present on the steppes at that time.

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    Quote Originally Posted by Jean M View Post
    We should also bear in mind that haplogroups that first arrived in Europe earlier could also travel later with the Indo-Europeans, making a very complex picture. For example the mtDNA haplogroup U5 is ancient in Europe. It predominates in the DNA found so far in people of the European Mesolithic. Yet most of it in the British Isles today probably arrived no earlier than the Copper Age.
    This is precisely the question that I struggle with when analyzing data in the FTDNA U5 project - perhaps some of the U5 subclades now found at high frequency were either present among early farmers in the the Near East, or were incorporated into early farming communities in southeastern Europe at an early date and then spread throughout Europe during the Neolithic. Certain subclades of U5a1 and U5a2 in particular have very large populations in Europe today, while other subclades are extremely rare. Perhaps there are interesting things to be learned by focussing on subclades that have very unusual distributions today. And maybe some type of statisical analysis can cut through the noise. Hopefully ancient DNA will fill in some of the gaps.

    U5 is interesting because it seems to be found almost exclusively in Europe (with some very interesting exceptions) while other U subclades seems to have a wider distrubtion in Asia. The question I hope to see answered from ancient DNA is: Was U5 the dominant group in the first modern Europeans 45,000 years ago, or did it enter Europe at a later date?

    I've started updating the U5 results page with summaries of individual subclades. This is going very slowly as I try to include all of the recent Behar sequances (and sort out which ones are already in the U5 project and which are new). I'd appreciate any comments/corrections/suggestions on the text on the U5 results page.

    thanks,
    Gail

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    Quote Originally Posted by Humata View Post
    Though we're on the same page vis-a-vis the PIE dispersal from the Pontic-Caspian steppe, I'd like to know what evidence gave you the means to reach the conclusion that Y-DNA Haplogroup R1b-M269 was present on the steppes at that time.
    An addition to my previous message.

    The evidence from aDNA thus far presents a clear picture. aDNA has shown that Y-DNA Haplogroup R1a has been the predominant find from the Lichtenstein cave through to Eulau and Krasnoyarsk in Siberia with several sites in-between. This overlaps perfectly with the archaeological cultures in Eurasia associated with pastoral nomads who hypothetically spoke early Indo-European languages (Corded Ware<->Yamnaya<->Andronovo+Afanasievo).

    Haplogroup R1b-M269/U106, on the other hand, have been found in Western Europe only thus far (Bell Beaker remains and the Lichtenstein cave).

    The SNP evidence also reveals "phylogenetic dissonance" between R1a1a-M17 and R1b1a2-M269 within Europe. R1a1a-M17's SNP diversity is currently greatest on the western side of the Eurasian steppe. Even if sampling bias towards Europe is taken into account, the presence of key parahaplogroups (R1a1*-SRY10831.2 and R1a*-M420 in West Asia, Underhill et al.) not too far from East Europe does not contradict an expansion of R1a1a-M17 from the Pontic-Caspian steppe.

    The same cannot be said of R1b1a2-M269 when the presence of basal SNP's (especially R1b1a2a-L23) are all found south of the Caucasus mountains and the Caspian/Black Seas. Before tackling the erroneous stance regarding R1b's origin in an Iberian refugium, Vineviz in particular proved to the DNA-Forums community years ago that Y-DNA R1b-M269's diversity increases the further southeast one travels through Europe.

    When the totality of our current findings are considered, it is difficult to imagine a scenario where Indo-European-speaking men bearing R1b1a2-M269 existed on the steppe, which is what you stated, spoke the earlier Centum proto-branches and expanded westwards towards Europe only from above the Black Sea.

    A scenario more in-line with the information provided is that Haplogroup R1b1a2-M269 was a European-specific secondary (but major) lineage involved in the dissemination of Indo-European languages west of Yamnaya-influenced archaeological cultures.

    If I am relying on outdated information, I'd gladly hear what has surfaced recently.

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    Quote Originally Posted by Humata View Post
    Though we're on the same page vis-a-vis the PIE dispersal from the Pontic-Caspian steppe, I'd like to know what evidence gave you the means to reach the conclusion that Y-DNA Haplogroup R1b-M269 was present on the steppes at that time.
    As you know, we don't have that evidence from aDNA, so this is deduction from the end result i.e.

    1. Correlation of the distribution of both R1b-M269 and R1a1a with IE languages.
    2. Spread of the same two mutations for lactase persistence east and west, regardless of the predominant Y-DNA, suggesting intermarriage over a good long period before migrations east and west. If these alleles arrived on the steppe with dairy farming, there must have been interbreeding between the Cucuteni and steppe peoples, to disseminate these genes thoroughly before the migrations. There was much contact between the two cultures.
    3. The rare mtDNA haplogroup U2e seems Indo-European in its present distribution, though it is far older than PIE. It probably occurred among U2 hunter-gatherers roaming the steppe and forest-steppe around the Urals. U2e appears in remains from archaeological cultures of west and east linked to the Indo-Europeans: Bell Beaker (with R1b) and Andronovo (with R1a1a). It was also found in two Iron Age cemeteries, one near Qiemo, Xinjiang on the old southern Silk Road. In modern populations U2e reaches a peak of nearly 16% among the Kalash of Northern Pakistan, a polytheistic people who speak an Indo-European language.
    Last edited by Jean M; 08-18-2012 at 10:46 PM.

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    Quote Originally Posted by GailT View Post

    U5 is interesting because it seems to be found almost exclusively in Europe (with some very interesting exceptions) while other U subclades seems to have a wider distribution in Asia. The question I hope to see answered from ancient DNA is: Was U5 the dominant group in the first modern Europeans 45,000 years ago, or did it enter Europe at a later date?
    My feeling is that U5 did not enter Europe, but arose there. Behar 2012 estimates its age as 30,248 year before the present. That would be too young to arrive with the first modern humans. U5 appears in Europe and U6 in North Africa. So that's a clue that some U* was in the Levant area and split into groups, some moving north into Europe, and some south into North Africa, where the geographically distinctive mutations arose.

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    Quote Originally Posted by Jean M View Post
    As you know, we don't have that evidence from aDNA, so this is deduction from the end result i.e.

    1. Correlation of the distribution of both R1b-M269 and R1a1a with IE languages.
    2. Spread of the same two mutations for lactase persistence east and west, regardless of the predominant Y-DNA, suggesting intermarriage over a good long period before migrations east and west. If these alleles arrived on the steppe with dairy farming, there must have been interbreeding between the Cucuteni and steppe peoples, to disseminate these genes thoroughly before the migrations. There was much contact between the two cultures.
    3. The rare haplogroup U2e seems Indo-European in its present distribution, though it is far older than PIE. It probably occurred among U2 hunter-gatherers roaming the steppe and forest-steppe around the Urals. U2e appears in remains from archaeological cultures of west and east linked to the Indo-Europeans: Bell Beaker (with R1b) and Andronovo (with R1a1a). It was also found in two Iron Age cemeteries, one near Qiemo, Xinjiang on the old southern Silk Road. In modern populations U2e reaches a peak of nearly 16% among the Kalash of Northern Pakistan, a polytheistic people who speak an Indo-European language.


    We do have mtDNA however and it is interesting. Take a look at Ancient Western Eurasian DNA. If you look at Dnieper-Donets you see a mixture of haplogroups that we can guess were retained from their time as hunter-gatherers (including some Central Asian) and some that we can guess came from wives from the adjacent Neolithic cultures with origins in the Near East. So even at that period, people were mixing.
    mtDNA is another side of the puzzle, as is the prevalence of an autosomal trait (lactase persistence via the 13910T mutation).

    1. The correlation between R1b-M269 and R1a-M17 with IE languages is only so in Europe. Large swathes of the Near-East which do not speak Indo-European languages (particularly the Levant and Mesopotamia) do not agree with a wholesale association between the two. Furthermore, populations in Asia who reside in key regions populated by Andronovo-descended groups (particularly Altaians and the Kyrgyz) nearly completely lack R1b-M269.*

    2. That the two populations underwent extensive intermarriage over an extended period of time is but one possibility rather than a demographically charted process. A single population event with subsequent cultural interactions could also account for the sharing and eventual transmission of these genes into different portions of Eurasia. Lactase persistence acts as an excellent example of how selective processes take place, but the nature of this selection hasn't been determined.

    3. mtDNA Haplogroup U2e's appearance in aDNA is very telling, but as you stated, its' origins predate PIE. What complicates the matter further is that mtDNA U2e was present across the steppe long before either Afanasievo or Andronovo expanded deeper east. I have covered this quite extensively in my write-up on the Baraba forest-steppe, as well as the confirmed interaction between genetically North European-like and East Eurasian hunter gatherers along a "migration corridor". Even more confusing are the cultural interactions between Eurasian steppe and Kazakh hunter gatherers pre-Andronovo, opening the possibility for some mtDNA U2e to spill its' way into South-Central Asia without having anything to do with Indo-Europeans.

    The most compelling piece of evidence that not every layer of mtDNA U2e should be associated with the Indo-Europeans is its' presence in the Hami cemetery, located in China's Xinjiang province, dating back to 4000 B.C.;

    Evidence that a West-East admixed population lived in the Tarim Basin as early as the early Bronze Age.
    Li C, Li H, Cui Y, Xie C, Cai D, Li W, Mair VH, Xu Z, Zhang Q, Abuduresule I, Jin L, Zhu H, Zhou H. Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, PR China. BMC Biol. 2010 Feb 17;8:15.


    ...Unless the Tocharians got there a few thousand years earlier than comparative linguistics tells us.

    * I vaguely recall one very downstream R1b-M269 Altaian in an earlier study. Will post results if found.

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