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  • #346212

    Anonymous

    This is an exciting pre-print of a scientific study published by Lazaradis et al.

    Ancient human genomes suggest three ancestral populations for present-day Europeans

    ABSTRACT

    Analysis of ancient DNA can reveal historical events that are difficult to discern through study of present-day individuals. To investigate European population history around the time of the agricultural transition, we sequenced complete genomes from a ~7,500 year old early farmer from the Linearbandkeramik (LBK) culture from Stuttgart in Germany and an ~8,000 year old hunter-gatherer from the Loschbour rock shelter in Luxembourg. We also generated data from seven ~8,000 year old hunter-gatherers from Motala in Sweden. We compared these genomes and published ancient DNA to new data from 2,196 samples from 185 diverse populations to show that at least three ancestral groups contributed to present-day Europeans. The first are Ancient North Eurasians (ANE), who are more closely related to Upper Paleolithic Siberians than to any present-day population. The second are West European Hunter-Gatherers (WHG), related to the Loschbour individual, who contributed to all Europeans but not to Near Easterners. The third are Early European Farmers (EEF), related to the Stuttgart individual, who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model the deep relationships of these populations and show that about ~44% of the ancestry of EEF derived from a basal Eurasian lineage that split prior to the separation of other non-Africans.

    Some results

    European Early Farmer (EEF) mostly of near eastern origins

    Code:
    Maltese 0.932
    Ashkenazi_Jew 0.931
    Sicilian 0.903
    Sardinian 0.817
    Spanish 0.809
    —–
    Norwegian 0.411
    Icelandic 0.394
    Scottish 0.39
    Lithuanian 0.364
    Estonian 0.322

    Western Hunter-Gatherers (WHG). The component could be called European Hunter-Gatherers as it also peaks in eastern Baltic region.

    Code:

    Estonian 0.495
    Lithuanian 0.464
    Icelandic 0.456
    Belarusian 0.431
    Norwegian 0.428
    —–
    Spanish 0.068
    Greek 0.058
    Maltese 0
    Ashkenazi_Jew 0
    Sicilian 0

    Ancient North Eurasian (ANE) of south central Siberia

    Code:

    Estonian 0.183
    Scottish 0.182
    Hungarian 0.179
    Lithuanian 0.172
    Czech 0.167
    —–
    Bergamo 0.108
    Sicilian 0.097
    Ashkenazi_Jew 0.069
    Maltese 0.068
    Sardinian 0.008


    Code:

    EEF WHG ANE
    0.781 0.092 0.127 — Albanian
    0.931 0 0.069 — Ashkenazi_Jew
    0.593 0.293 0.114 — Basque
    0.418 0.431 0.151 — Belorussian
    0.715 0.177 0.108 — Bergamo
    0.712 0.147 0.141 — Bulgarian
    0.561 0.293 0.145 — Croatian
    0.495 0.338 0.167 — Czech
    0.495 0.364 0.141 — English
    0.322 0.495 0.183 — Estonian
    0.554 0.311 0.135 — French
    0.675 0.195 0.13 — French_South
    0.792 0.058 0.151 — Greek
    0.558 0.264 0.179 — Hungarian
    0.394 0.456 0.15 — Icelandic
    0.364 0.464 0.172 — Lithuanian
    0.932 0 0.068 — Maltese
    0.411 0.428 0.161 — Norwegian
    0.457 0.385 0.158 — Orcadian
    0.713 0.125 0.163 — Pais_Vasco
    0.817 0.175 0.008 — Sardinian
    0.39 0.428 0.182 — Scottish
    0.903 0 0.097 — Sicilian
    0.809 0.068 0.123 — Spanish
    0.746 0.136 0.118 — Tuscan
    0.462 0.387 0.151 — Ukrainian

    PCA Plot which includes some Slavic populations. For large resolution : http://s22.postimg.org/mjdyhlj41/6g9k.png

    [img width=700 height=356]http://s22.postimg.org/mjdyhlj41/6g9k.png”/>

    A few observations:

    ◦ European Early Farmer (EEF) comprises the bulk of the genetic stock of modern Europeans. Forms a very clear north-south cline. South Europeans are mostly this. Even then, North Europeans are around 30-40% of this component.

    ◦ Western Hunter-Gatherers (WHG) make up most of what's left. Combined with EEF, the pair seem to account for over 80% of what modern Europeans are comprised of genetically. Again forms a north-south cline peaking up top in some sort of circum-Scandinavian zone. Is actually absent in some South European populations. Consistent with the archaeological landscape of Europe during prehistory (i.e. Neolithic era farming technology reaching the Baltic region last).

    ◦ Ancient North Eurasian (ANE) matches WHG's pattern but seems to generally peak more in the Baltic-Carpathian zone better. Again, some South Europeans have very little of this component.

    WHG and WHG/ANE: indigenous European hunter-gatherers
    EEF: mixed European/Near Eastern Neolithic farmers
    ANE/WHG: Proto-Indo-European invaders from the Eastern European steppe
    ENA/ANE: early Uralics from the Volga-Ural region
    EEF/WHG/ANE: late Indo-Europeans (ie. Celts, Germanics and Slavs)

    #426252

    Anonymous

    Croatians :  56% EEF: mixed European/Near Eastern Neolithic farmers ,  29% WHG and WHG/ANE: indigenous European hunter-gatherers ,  14% ANE/WHG: Proto-Indo-European invaders from the Eastern European steppe.

    I notice a significant difference between the two South Slav groups in this study , Bulgarians and Croatians with Bulgarian EEF being around like 77%.  Why the huge divergence? Is there any data on the other neighboring South Slavs?

    Did I read this correctly?

    #426253

    Anonymous
    Quote:
    Croatians :  56% EEF: mixed European/Near Eastern Neolithic farmers ,  29% WHG and WHG/ANE: indigenous European hunter-gatherers ,  14% ANE/WHG: Proto-Indo-European invaders from the Eastern European steppe.

    I notice a significant difference between the two South Slav groups in this study , Bulgarians and Croatians with Bulgarian EEF being around like 77%.  Why the huge divergence? Is there any data on the other neighboring South Slavs?

    Did I read this correctly?

    EEF for Bulgarians is 71.2%.

    The results I came across were showing Croats genetically more similar to other southern Slavic ethnicities than Bulgarians.

    The chart below was prepared by Vadim Verinich who maintains the MDLP project. The chart is based on autosomal DNA data and the samples were obtained from scientific studies . It's likely similar samples for European ethnicities were used by V. Verenich and in the study above.

    Larger resolution: http://s16.postimg.org/3pgg08k11/mbqrex.jpg

    [img width=700 height=341]http://s16.postimg.org/3pgg08k11/mbqrex.jpg” />

    #426254

    Anonymous

    Belarussian has the highest concentration of NE European. Along with Belorussian goes Polish , Ukrainian , and most Russian. Seems like other South Slavs are pretty similar to Croats. In that graph it looks like the Western South Slavs ( Croats , Bosnians, and Slovenes) show a very similar distribution while Bulgarians, Macedonians , and Montenegrins show another with Serbs somewhere in between.  I'm mostly looking at Atlanto-Med and NE European but notice a higher frequency of 'West Asian' in Bulgarians and Macedonian. All very interesting.

    #426255

    Anonymous
    Quote:
    Belarussian has the highest concentration of NE European. Along with Belorussian goes Polish , Ukrainian , and most Russian. Seems like other South Slavs are pretty similar to Croats. In that graph it looks like the Western South Slavs ( Croats , Bosnians, and Slovenes) show a very similar distribution while Bulgarians, Macedonians , and Montenegrins show another with Serbs somewhere in between.  I'm mostly looking at Atlanto-Med and NE European but notice a higher frequency of 'West Asian' in Bulgarians and Macedonian. All very interesting.

    I don’t think there’s a  genome-wide study specific to Croats. However, there is a sample or two for Croats which different authors use obtaining similar results. So yes, Bosniaks and Slovenes are more similar to Croats than Bulgarians. Another study confirms it.

    Genetic variation in the Sorbs of eastern Germany in the context of broader European genetic diversity (2011) by Veeramah et al. : http://www.slavorum.com/forum/index.php?topic=4802.msg75049#msg75049

    #426256

    Anonymous

    I wonder how they determine these % for russians for example who are such a heterogeneous population as well as many others.

    #426257

    Anonymous
    Quote:
    I wonder how they determine these % for russians for example who are such a heterogeneous population as well as many others.

    The percentages were obtained using Admixture software commonly used in scientific studies : http://www.genetics.ucla.edu/software/admixture/

    Three Russian populations were used in this chart. Northern Russians, Russians (I am guessing from central European Russia) and Russian Cossacks from southern Russia.

    Some notes on samples and admixture analysis for the chart above: http://magnusducatus.blogspot.com/2012/09/behind-curtains-mdlp-world-22-showcase.html

    #426258

    Anonymous

    Specifically, ADMIXTURE uses a block relaxation approach to alternately update allele frequency and ancestry fraction parameters. Each block update is handled by solving a large number of independent convex optimization problems, which are tackled using a fast sequential quadratic programming algorithm. Convergence of the algorithm is accelerated using a novel quasi-Newton acceleration method. The algorithm outperforms EM algorithms and MCMC sampling methods by a wide margin. For details, see our publications.

    chinese much? I plead guilty! ;D

    #426259

    Anonymous

    However this study doesn't reveal anything new, just confirms things that we have already known :D

    Actually it shows that most of European countries are made of 50% Neolithic Proto-European farmers and 50% incoming hunter-gatherer Indo-Europeans.

    0.561     0.293 0.145 — Croatian
    0.462     0.387 0.151 — Ukrainian
    0.418    0.431 0.151 — Belorussian

    I guess the amounts are pretty similar…after all when Croats arrived they did assimilate Latin and Celto-Illyrian population in Dalmatia…but even with that the amounts obviously show still a similar composition to other Slavs…meaning we pretty much all share the same story of arriving to a land and assimilating the natives into our composition.

    #426260

    Anonymous

    It's nice to get this confirmation because occasionally some non IE speakers of Europe are suggesting Indo-Europeans had little genetic influence on north Europeans when in fact there is a significant influence, while some western Europeans have been suggesting there's no Siberian genetic influence in western European populations.

    Most European populations are homegeneous in comparison to the world let alone Slavic populations, which are from eastern Europe but the aim of the study wasn't about comparing the European populations in terms  of  the 3 components.

    #426261

    Anonymous

    However high amount of Ancient North Eurasian (ANE) of south central Siberia in Scottish people 0.182

    Rather interesting. But then again its probably due to Vikings (composed of Scandinavians and Slavs) raids and settlements across Scotland.

    #426262

    Anonymous
    Quote:
    However high amount of Ancient North Eurasian (ANE) of south central Siberia in Scottish people 0.182

    Rather interesting. But then again its probably due to Vikings (composed of Scandinavians and Slavs) raids and settlements across Scotland.

    Northern and eastern Europeans have a higher amount of ancient north Euroasian (Siberian) admix. It could have been due to the fact that Celts from the British Isles migrated from eastern Europe or as you suggested  –  the influence of the Vikings. There's another recent study on genetics (mtDNA) showing not a smooth transition between between early neolithic farmers and modern Europeans i.e. there was no gradual assimilation : http://dienekes.blogspot.com/2013/10/ancient-central-european-mtdna-across.html

    #426263

    Anonymous

    The Early European Farmers had probably something like 15-25% WHG ancestry.

    #426264

    Anonymous

    Nicely organised map from David Wesolowski

    http://imagizer.imageshack.us/a/img539/5260/IqLK2V.png

    [img width=820 height=453]http://imagizer.imageshack.us/a/img539/5260/IqLK2V.png” />

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