Analyses of the Stuttgart genome

Below are the results of analyses of the Stuttgart genome. The Stuttgart sample is from an early Neolithic skeleton found at the Viesenhäuser Hof site in Stuttgart-Mühlhausen, Germany. The site belonged to the Linear Pottery culture, which is dated to 5500–4800 BC.

Stuttgart was female and belonged to mitochondrial haplogroup T2c1d1.

Stuttgart didn’t have any of the K12b Gedrosia component, which is associated with Y haplogroup R1b. She did have 29.29% of the K12b Caucasus component. The Caucasus component is associated with Y haplogroup G (along with J2 and R1a), and Europe’s first farmers belonged primarily to haplogroup G.

globe4

  • 96.76% European
  • 1.83% African
  • 0.72% Asian
  • 0.70% Amerindian

globe10

  • 48.17% Atlantic_Baltic
  • 42.77% Southern
  • 8.00% West_Asian
  • 0.60% Neo_African
  • 0.20% Palaeo_African
  • 0.18% East_Asian
  • 0.09% Australasian
  • 0.00% Amerindian
  • 0.00% Siberian
  • 0.00% South_Asian

globe13

  • 61.77% Mediterranean
  • 17.27% Southwest_Asian
  • 12.38% North_European
  • 6.72% West_Asian
  • 0.74% West_African
  • 0.55% East_Asian
  • 0.28% Palaeo_African
  • 0.27% Australasian
  • 0.02% East_African
  • 0.00% Amerindian
  • 0.00% Arctic
  • 0.00% Siberian
  • 0.00% South_Asian

K7b

  • 50.63% Southern
  • 43.57% Atlantic_Baltic
  • 4.66% West_Asian
  • 0.76% African
  • 0.38% East_Asian
  • 0.00% Siberian
  • 0.00% South_Asian

K10a

  • 65.73% Mediterranean
  • 21.22% Atlantic_Baltic
  • 7.16% West_Asian
  • 4.45% Red_Sea
  • 0.56% Sub_Saharan
  • 0.53% Southeast_Asian
  • 0.33% Palaeoafrican
  • 0.01% East_Asian
  • 0.00% Siberian
  • 0.00% South_Asian

K12b

  • 53.68% Atlantic_Med
  • 29.29% Caucasus
  • 10.54% Southwest_Asian
  • 5.23% Northwest_African
  • 0.51% Southeast_Asian
  • 0.47% North_European
  • 0.27% Sub_Saharan
  • 0.00% East_African
  • 0.00% East_Asian
  • 0.00% Gedrosia
  • 0.00% Siberian
  • 0.00% South_Asian

dv3

  • 57.08% Mediterranean
  • 17.27% West_European
  • 9.76% West_Asian
  • 9.54% Southwest_Asian
  • 5.63% Northwest_African
  • 0.35% Palaeo_African
  • 0.17% Southeast_Asian
  • 0.12% East_European
  • 0.05% Neo_African
  • 0.02% East_African
  • 0.00% Northeast_Asian
  • 0.00% South_Asian

MDLP K=5

  • 64.72% Paleo-mediterranean
  • 34.07% Caucasian
  • 1.17% South-Asian
  • 0.05% West-Eurasian
  • 0.00% East-Eurasian

MDLP K=6

  • 63.16% Paleo-Mediterranean
  • 34.78% Caucasian
  • 1.14% South-Asian
  • 0.92% West-Eurasian
  • 0.00% East-Euroasian
  • 0.00% North-West-Eurasian

MDLP K=7

  • 62.94% Paleo-Mediterranean
  • 34.98% Caucasian
  • 1.26% South-Central-Asian
  • 0.81% West-Eurasian
  • 0.00% Altaic-Turkic
  • 0.00% Paleo-Scandinavian
  • 0.00% Volga-Uralic

MDLP K=8

  • 62.33% Paleo-Mediterranean
  • 19.65% West-European
  • 17.10% Caucasian
  • 0.88% South-Central-Asian
  • 0.04% East-European
  • 0.00% Altaic-Turkic
  • 0.00% Paleo-Scandinavian
  • 0.00% Volga-Finnic

MDLP K=9

  • 62.78% Paleo-Mediterranean
  • 17.18% Caucasian
  • 17.06% West-European
  • 2.07% Paleo-Balkanic
  • 0.88% South-Central-Asian
  • 0.04% East-European
  • 0.00% Altaic-Turkic
  • 0.00% Paleo-Scandinavian
  • 0.00% Volga-Finnic

MDLP K=10

  • 60.69% Paleo-Mediterranean
  • 14.43% Iberian
  • 14.21% Caucasian
  • 7.83% British
  • 2.04% Paleo-Balkanic
  • 0.80% South-Central-Asian
  • 0.01% East-European
  • 0.00% Altaic-Turkic
  • 0.00% Paleo-North-European
  • 0.00% Volga-Finnic

MDLP K=11

  • 60.63% Mediterranean
  • 14.14% Iberian
  • 13.92% Caucasian
  • 8.21% Celto-Germanic
  • 2.03% Paleo-Balkanic
  • 1.05% South-Central-Asian
  • 0.01% East-European
  • 0.00% Altaic-Turkic
  • 0.00% Paleo-North-European
  • 0.00% Uralic-Permic
  • 0.00% Volga-Uralic

MDLP K=12

  • 60.00% Paleo-Mediterranean
  • 14.24% Iberian
  • 13.74% Caucasian
  • 8.82% Celto-Germanic
  • 2.04% Paleo-Balkanic
  • 1.14% South-Central Asian
  • 0.02% East-European
  • 0.00% Alatic-Turkic
  • 0.00% Balto-Finnic
  • 0.00% Paleo-North-European
  • 0.00% Uralic-Permic
  • 0.00% Volga-Uralic

MDLP K=13

  • 22.14% Altaic
  • 15.72% Paleo-Mediterranean
  • 15.59% Celto-Germanic
  • 9.93% Mediterrean
  • 8.44% East-Mediterranean
  • 7.27% South-Central-Asian
  • 6.87% East-European
  • 5.49% Iberian
  • 3.18% Baltic-Finnic
  • 2.95% Volga-Uralic
  • 1.11% Uralic-Permic
  • 0.94% Paleo-North-European
  • 0.39% Caucasian

MDLP K=14

  • 40.67% Mediterranean
  • 31.21% Paleo-Mediterranean
  • 10.99% East-Mediterranean
  • 7.84% Iberian
  • 6.61% Celto-Germanic
  • 1.52% Paleo-Balkanic
  • 0.64% Caucasian
  • 0.53% South-Central-Asian
  • 0.00% Altaic
  • 0.00% Balto-Finnic
  • 0.00% Balto-Slavic
  • 0.00% Paleo-Scandinavian
  • 0.00% Uralic-Permic
  • 0.00% Volga-Finnic

MDLP K=15

  • 40.84% Balkanic-1
  • 30.95% West-Mediterranean
  • 10.90% East-Mediterranean
  • 7.82% Iberian
  • 6.74% Celto-Germanic
  • 1.52% Balkanic-2
  • 0.65% Caucasian
  • 0.58% South-Central-Asian
  • 0.00% Balto-Finnic
  • 0.00% Balto-Slavic
  • 0.00% East-Altaic
  • 0.00% Paleo-North-European
  • 0.00% Uralic-Permic
  • 0.00% Volga-Uralic
  • 0.00% West-Altaic

MDLP World-22

  • 56.94% Atlantic_Mediterranean_Neolithic
  • 24.45% Near_East
  • 12.70% North-East-European
  • 4.81% West-Asian
  • 0.45% South-African
  • 0.32% Sub-Saharian
  • 0.14% Indo-Tibetan
  • 0.07% Pygmy
  • 0.06% Austronesian
  • 0.05% East-South-Asian
  • 0.01% Melanesian
  • 0.00% Arctic-Amerind
  • 0.00% East-Siberean
  • 0.00% Indian
  • 0.00% Indo-Iranian
  • 0.00% Mesoamerican
  • 0.00% North-Amerind
  • 0.00% North-European-Mesolithic
  • 0.00% North-Siberean
  • 0.00% Paleo-Siberian
  • 0.00% Samoedic
  • 0.00% South-America_Amerind

MDLP Ancient Roots K17

  • 59.82% Ancestral_Mediterranean_EEF
  • 24.48% West_European_HG
  • 8.00% Ancestral_East_European_ANE
  • 5.72% Caucasian-Basal
  • 0.47% Ancestral_Sami-Finnic
  • 0.21% Uralic
  • 0.20% Archaic_African
  • 0.20% Near-East-Basal
  • 0.18% Ancestral_South_Indian
  • 0.14% African_Sub_Saharian
  • 0.13% Ancestral_North_Indian
  • 0.13% Melano-Austronesian
  • 0.10% Ancestral_West_Siberian
  • 0.09% Circumpolar
  • 0.07% South_East_Asian
  • 0.03% Amerindian
  • 0.02% Ancestral_East_Siberian

MDLP Ancient Roots K18

  • 50.03% Mediterranean
  • 27.97% North_West_European
  • 9.30% Afroasiatic
  • 6.02% Caucasian
  • 2.90% Roma
  • 2.65% East_European
  • 1.08% South_East_Asian
  • 0.02% Sami-Finnic
  • 0.01% Archaic_African
  • 0.01% Melano-Austronesian
  • 0.00% Amerindian
  • 0.00% Arctic
  • 0.00% East_African
  • 0.00% East_Siberian
  • 0.00% South_Central_Asian
  • 0.00% South_Indian
  • 0.00% Volga-Uralic
  • 0.00% West_Siberian

MDLP K23b

  • 54.44% European_Early_Farmers
  • 29.44% Caucasian
  • 9.37% Near-East
  • 5.63% North-African
  • 0.43% European_Hunters_Gatherers
  • 0.12% East-Siberian
  • 0.10% Khoisan
  • 0.08% Amerindian
  • 0.07% Austronesian
  • 0.06% Archaic-Human
  • 0.05% Melano-Polinesian
  • 0.04% South-East-Asian
  • 0.03% Paleo-Siberian
  • 0.02% Altaiс
  • 0.02% Ancestral-South-Indian
  • 0.02% Austroloid
  • 0.02% East-African
  • 0.01% African-Pygmy
  • 0.01% Ancestral-North-Eurasian
  • 0.01% Ancestral-North-Indian
  • 0.01% Archaic-African
  • 0.01% Arctic
  • 0.01% Subsaharian
Advertisements
Posted in Uncategorized
3 comments on “Analyses of the Stuttgart genome
  1. Alberto says:

    Something does stand out: For the first time (as far as I know, but I could be wrong) a genome from this time and place show some West Asian admixture (in k7b it’s 4.66%, not a lot, but above the noise level I’d say).This is in contrast with Ötzi, Gökhem farmers or modern Sardinians, which have ~0%.

    Quite interesting… Early European Farmers (up until now) didn’t show West Asian admixture. But all modern day populations from West Asia do show this admixture in high percentage. This means that by the time of the first migrations into Europe from the Near East (Levant and/or Mesopotamia), they didn’t have this admixture, but later at some point they got it (and to a high degree).

    When and where from did this West Asian admixture come from? And why this Stuttgart farmer shows it already but later Gökhem farmers don’t? Or is this West Asian admixture just a Red Herring?

  2. genetiker says:

    The West Asian components basically lump together the K12b Caucasus and Gedrosia components. A sufficiently large amount of the Caucasus component will show up as some of the West Asian components, but if the amount of the Caucasus component is small enough, little to none of the West Asian components will show up. Stuttgart had a large amount of the Caucasus component, so she also had some of the West Asian components.

    You can see the positive correlation between the Caucasus component and the West Asian components in the results below.

    This is in contrast with Ötzi, Gökhem farmers or modern Sardinians, which have ~0%.

    Ötzi had some of the West Asian components. Some of the Gökhem farmers had small amounts of some of the West Asian components. Sardinians have 4.1% of the globe13 West Asian component.

    Early European Farmers (up until now) didn’t show West Asian admixture.

    No, they did, and the earlier the samples are, they more of it they show. So we know that the Caucasus and West Asian components were in the Near East at the time of the migration to Europe.

    And why this Stuttgart farmer shows it already but later Gökhem farmers don’t?

    The Gökhem farmers lived far to the north of Stuttgart, in Sweden, and they lived 2,000 years later. Their first farmer Caucasus and West Asian alleles had become much more diluted by admixture with Y hg I hunter-gatherers.

    Ötzi lived 1,700 years after Stuttgart, and his first farmer Caucasus and West Asian alleles had become somewhat diluted as well.

    Stuttgart

    29.29% Caucasus
    8.00% West_Asian (globe10)
    6.72% West_Asian (globe13)
    4.66% West_Asian (K7b)
    7.16% West_Asian (K10a)
    9.76% West_Asian (dv3)

    Ötzi

    22.3% Caucasus
    5.7% West_Asian (globe10)
    6.0% West_Asian (globe13)
    1.4% West_Asian (K7b)

    Gökhem 5

    13.82% Caucasus
    0.01% West_Asian (globe10)
    0.00% West_Asian (globe13)
    0.04% West_Asian (K7b)
    1.83% West_Asian (K10a)
    2.02% West_Asian (dv3)

    Gökhem 4

    11.51% Caucasus
    0.01% West_Asian (globe10)
    0.02% West_Asian (globe13)
    0.03% West_Asian (K7b)
    0.01% West_Asian (K10a)
    8.16% West_Asian (dv3)

    Gökhem 2

    9.33% Caucasus
    0.00% West_Asian (globe10)
    0.00% West_Asian (globe13)
    0.00% West_Asian (K7b)
    0.00% West_Asian (K10a)
    0.00% West_Asian (dv3)

    Gökhem 7

    3.09% Caucasus
    0.01% West_Asian (globe10)
    0.02% West_Asian (globe13)
    0.00% West_Asian (K7b)
    0.00% West_Asian (K10a)
    0.00% West_Asian (dv3)

  3. Alberto says:

    Yes, in k12b the Caucasus component takes parts of what in K7b is West Asian and Southern. That’s why I don’t like k12b so much.

    In K7b, Ötzi does show a low 1.4% West Asian admixture, but all Gökhem and modern Sardinians show ~0%, though all show high amounts of Southern. Also Loschbour or La Braña show 0%. In contrast, modern day Near Eastern populations show high amounts of both Southern and West Asian admixture (Assyrians: 50% West Asian, 40% Southern. Lebanese: 39% West Asian, 44% Southern). So really it doesn’t seem like EEF were a mixture of these two populations. The only two options are that EEF came from North West Africa (unlikely) or that Near Eastern populations got the West Asian component later during the mid-late Neolithic.

    This speculation is also mentioned in this study: http://arxiv.org/abs/1312.6639v2 (page 67 of the PDF, when commenting on K=15 results). Though in this study they link it to Ancient North Eurasian, which seems a mistake (this component is much higher in Lebanon – or South Italy- than in Lithuania, so it can’t be an ANE influence).

    Also EEF were mostly haplogroup G, while in the Near East now J is much more common.

    So my question: What if there were 4 ancient Caucasoid populations?

    – The Northern (Atlantic_Baltic) in all Europe (including Kazakhstan). They could be divided in West (most of Europe) and East (East Ukraine, Russia, Kazakhstan) branches.
    – The Southern, in North Africa and Near East, probably extending east to the western and southern parts of Iran (could also be divided in 2 subgroups, one in North Africa and the other Middle Eastern).
    – The South Asian, in India and Pakistan.
    – The West Asian, in Central Asia (Uzbekistan, Turkmenistan, Tajikistan, Kyrgyzstan,…)

    In this scheme, there would have been 2 big migrations: first Southerners into Europe, and later West Asians (from Central Asia) into South and West Asia (from North of India to Egypt).

    Just a hypothesis trying to explain the West Asian admixture origin. No idea how could this theory work out for people who know much more details than me. But I just found it interesting to think about it.

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

Categories
%d bloggers like this: