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Thread: The mixed genetic origin of the first farmers of Europe

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    Quote Originally Posted by beyoku View Post
    Fairly new from where exactly? And how is "New" defined in age?
    Good question. The where is quite likely Near East and/or North East Africa, but when is more difficult to answer. But I'd guess, just a guess, it wasn't there for longer than 10.000 BP.

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    Quote Originally Posted by Riverman View Post
    Good question. The where is quite likely Near East and/or North East Africa, but when is more difficult to answer. But I'd guess, just a guess, it wasn't there for longer than 10.000 BP.
    You should take into consideration that He was Mtdna L3x quite localized to the HOA and M329 also pretty local.
    Both being about 35-40 thousand years old. He also contained high altitude genetic adaptation to the Ethiopian highlands.

    None of these facts support in North African southern migration and most definitely not a Near Eastern one.
    Then again, perhaps it is very possibly that Mota type ancestry is autochthonous to North East Africa and the Near East.

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    Quote Originally Posted by beyoku View Post
    You should take into consideration that He was Mtdna L3x quite localized to the HOA and M329 also pretty local.
    Both being about 35-40 thousand years old. He also contained high altitude genetic adaptation to the Ethiopian highlands.
    Local today, but the adaptations are an argument indeed. However, Mota is no "pure newcomer", but a locally admixed one after a couple of thousands years in place. The origin is of course not directly from the Near East, but with a stopover in North East Africa, if not being from there directly.

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    Quote Originally Posted by Riverman View Post
    Good question. The where is quite likely Near East and/or North East Africa, but when is more difficult to answer. But I'd guess, just a guess, it wasn't there for longer than 10.000 BP.
    That seems unlikely. The Malawi HG (~8000BP) from Skoglund 2017 have nearly half their ancestry from a Mota-like population and no evidence of recent admixture.

    Are you associating ANA/Neo-African-like ancestry exclusively with E/L3? BT/L3'4'6 seem like better candidates to me (maybe L2 as well and to a lesser extent L5). Most L3 lineages are deeply rooted in the horn/Rift-Valley, as are almost all L4 and L6 lineages, so any theory involving a "new" introduction would have to allow enough time for these lineages to diversify into what we see today, certainly much longer than 10,000 years.
    Last edited by blackflash16; 12-01-2020 at 03:56 PM.

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    Some quick comments about the OoA bottleneck and facts about the phylogenetic relationships of IBM that are clear as of now:

    Both the length of divergence and the size of the bottleneck probably had some role to play in the accumulation of drift among Eurasians vs Africans, the bottleneck was severe enough as to reduce heterozygosity in a single step among all Eurasians vis-a-vis Africans (i.e. serial founder effects post-OoA still matter somewhat but nothing mattered more than the original founder effect) and enriched weakly deleterious mutations throughout all Eurasians vs Africans, and Africans have by far the most population-specific variants, but its also true that the population divergence is very old and probably on par with divergences within Africa (i.e. there are also some private Eurasian-specific variants); the fact that its not clear exactly which African population best preserves an element closely related to the OoA expansion should also tell us as much.

    The original paper introducing Taforalt had a very clever and clean graphic which was incredibly illuminating even on its own:

    We know that all populations in Eurasia have their relationship with IBM increase monotonically as their relationship with Natufians increase. I.e. we have no indication that its possible for Eurasians to get closer to Natufian without getting closer to IBM. However, this isn't the case for Sub-Saharan Africans: within them there is no such linear relationship. I.e., it is actually possible for a SSA group to increase in affinity to IBM without increasing their affinity to Natufian. This rules out purely IBM --> SSA (its either IBM<-->SSA or IBM<--SSA). As it is, we know at least some of the ancestry of IBM (and probably quite a lot) forms a clade with the bulk of the ancestry of some groups of present-day Africans to the exclusion of Natufian and also characterizes those present-day Africans to the exclusion of other Africans, i.e. among modern populations this ancestry is characteristic first and foremost of a subgroup of present-day Africans. Secondly, from this we at least know that the distribution of this ancestry in Africa is not perfectly correlated with Natufian ancestry or IBM ancestry, i.e. the "African" side of IBM has its own admixture history among the populations of Africa independent of whatever IBM and Natufian went through.
    Last edited by Ryukendo; 12-01-2020 at 04:01 PM.
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    Quote Originally Posted by Ryukendo View Post
    Some Africans, the bottleneck was severe enough as to reduce the some private Eurasian-specific variants); the fact that its not clear exactly which African population best preserves an element closely related to the OoA expansion should also tell us as much.

    We know that all populations in Eurasia have their relationship with IBM increase monotonically as their relationship with Natufians increase. I.e. we have no indication that its possible for Eurasians to get closer to Natufian without getting closer to IBM. However, this isn't the case for Sub-Saharan Africans: within them there is no such linear relationship. I.e., it is actually possible for a SSA group to increase in affinity to IBM without increasing their affinity to Natufian. This rules out purely IBM --> SSA (its either IBM<-->SSA or IBM<--SSA). As it is, we know at least some of the ancestry of IBM (and probably quite a lot) forms a clade with some groups of present-day Africans to the exclusion of Natufian and also characterizes those present-day Africans to the exclusion of other Africans, i.e. among modern populations this ancestry is characteristic first and foremost of a subgroup of present-day Africans. Secondly, from this we at least know that the distribution of this ancestry in Africa is not perfectly correlated with Natufian ancestry or IBM ancestry, i.e. the "African" side of IBM has its own admixture history among the populations of Africa independent of whatever IBM and Natufian went through.
    I would say West Africans have some IBM ancestry, this is constently showed up by positive Neanderthal alleles, but it has little do with the ANA within IBM and Natufian groups.

    And that the fact modern SSA populations have some sizeable admixture from neo-clades, clades closer to ANA and Eurasians than deeper and divergent clades they also carry, has little to do with proper IBM gene flow and later post-Neolithic Eurasian gene flow in SSA populations.

    So we should separate things clearly when arguing over this.

    If we take East Africa for example, the situation is more complicated than in West Africa. East Africa and South Africa has thousands of groups of different lifestyle with various post-Neolithic Eurasian ancestries that range from Khoisans in Namibia to Maasais in Kenya.
    Last edited by Echo; 12-01-2020 at 05:33 PM.

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    deleted.
    Last edited by Ryukendo; 12-01-2020 at 04:51 PM.
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    Quote Originally Posted by Echo View Post
    I would say West Africans have some IBM ancestry, this is constently showed up by positive Neanderthal alleles, but it has little do with the ANA within IBM and Natufian groups.

    And that the fact modern SSA populations have some sizeable admixture from neo-clades, clades closer to ANA and Eurasians than deeper and divergent clades they also carry, has little to do with proper IBM gene flow and later post-Neolithic Eurasian gene flow in SSA populations.

    So we should separate things clearly when arguing over this.

    If we take East Africa for example, the situation is more complicated than in West Africa. East Africa and South Africa has thousands of groups of different lifestyle with various post-Neolithic Eurasian ancestries that range from Khoisans in Namibia to Maasais in Kenya.
    West Africans do have ibm, around 12 to 13 percent
    Neolithic model:
    Distance: 3.2366% / 0.03236553
    35.6 Early_European_Farmer
    26.0 Iberomaurusian
    13.8 Levant_Arabian
    11.2 Africa_Mesolithic
    6.8 Steppe_Pastoralist
    3.6 Iran_Neolithic
    3.0 Caucasus_Hunter-gatherer

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    Quote Originally Posted by TuaMan View Post
    Out of curiosity, how much IBM do modern North Africans have using qpAdm?
    The Mozabites seem to be in the 30-18 range. It seems to fluctuate pretty wildly depending on which populations I use for the models. This is excluding all the Iberomaurusian in Levantine populations. I don't we will be able to get a clearer picture until we can get a more pristinely ANA sample.

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    Quote Originally Posted by Mnemonics View Post
    The Mozabites seem to be in the 30-18 range. It seems to fluctuate pretty wildly depending on which populations I use for the models. This is excluding all the Iberomaurusian in Levantine populations. I don't we will be able to get a clearer picture until we can get a more pristinely ANA sample.
    It's not that easy to model them indeed but yeah they are most likely within this ballpark.

    G25 spreedsheet.

    Target: Mozabite:HGDP01255
    Distance: 2.6122% / 0.02612177
    37.4 Iberia_N
    19.2 MAR_Taforalt
    15.8 Yamnaya_RUS_Samara
    13.4 Yoruba
    13.2 Levant_PPNB
    1.0 Levant_Natufian

    Target: Mozabite:HGDP01255
    Distance: 4.2356% / 0.04235623
    45.2 TUR_Barcin_N
    22.8 MAR_Taforalt
    16.0 Yamnaya_RUS_Samara
    11.6 Yoruba
    4.4 Levant_Natufian

    Target: Mozabite:HGDP01254
    Distance: 4.3738% / 0.04373845
    37.4 TUR_Barcin_N
    32.0 MAR_Taforalt
    11.4 Levant_Natufian
    10.0 Yamnaya_RUS_Samara
    9.2 Yoruba

    Target: Mozabite:HGDP01253
    Distance: 3.0094% / 0.03009409
    45.6 TUR_Barcin_N
    36.2 MAR_Taforalt
    9.0 Yoruba
    7.2 Yamnaya_RUS_Samara
    1.0 Levant_Natufian
    1.0 Levant_PPNB

    Guanches.

    Target: Canary_Islands_Guanche:gun008
    Distance: 2.9125% / 0.02912505
    36.4 Iberia_N
    25.4 MAR_Taforalt
    13.8 Levant_Natufian
    11.2 Yamnaya_RUS_Samara
    6.6 Yoruba
    5.2 Levant_PPNB
    1.4 Dinka

    Target: Canary_Islands_Guanche:gun005
    Distance: 4.5027% / 0.04502681
    35.6 TUR_Barcin_N
    32.6 MAR_Taforalt
    13.4 Yamnaya_RUS_Kalmykia
    12.8 Levant_PPNB
    5.6 Yoruba

    Target: Canary_Islands_Guanche:gun005
    Distance: 4.3767% / 0.04376697
    36.6 Iberia_N
    24.2 MAR_Taforalt
    15.0 Levant_Natufian
    14.8 Yamnaya_RUS_Samara
    6.0 Yoruba
    1.8 Levant_PPNB
    1.6 Dinka

    Replacing Yamnaya by Bell Beaker Iberia/Bell Beaker Italy and Iran N by Bronze Age Levant.

    Target: Mozabite:HGDP01255
    Distance: 2.8386% / 0.02838608
    32.0 Bell_Beaker_Iberia
    22.8 MAR_Taforalt
    21.8 TUR_Barcin_N
    12.6 Yoruba
    8.6 Levant_PPNB
    2.2 IRN_Ganj_Dareh_N

    Target: Mozabite:HGDP01255
    Distance: 2.4991% / 0.02499064
    34.2 Bell_Beaker_ITA
    21.2 MAR_Taforalt
    19.2 Iberia_N
    12.2 Yoruba
    9.8 Levant_JOR_EBA
    3.4 Levant_PPNB

    Guanches.

    Target: Canary_Islands_Guanche:gun005
    Distance: 3.9952% / 0.03995161
    26.8 MAR_Taforalt
    23.0 Iberia_N
    16.8 Levant_PPNB
    22.4 Bell_Beaker_Iberia
    6.2 Yoruba
    3.0 IRN_Ganj_Dareh_N

    Target: Canary_Islands_Guanche:gun005
    Distance: 3.4849% / 0.03484882
    29.0 Bell_Beaker_Iberia
    27.2 MAR_Taforalt
    16.5 Levant_PPNB
    13.6 TUR_Barcin_N
    6.8 Yoruba
    1.4 Levant_JOR_EBA
    0.8 Levant_Natufian

    Target: Canary_Islands_Guanche:gun005
    Distance: 2.9671% / 0.02967083
    43.2 Bell_Beaker_ITA
    29.0 MAR_Taforalt
    9.2 Iberia_N
    6.6 Levant_PPNB
    5.4 Levant_JOR_EBA
    5.0 Yoruba
    1.6 Dinka

    Target: Canary_Islands_Guanche:gun005
    Distance: 2.9704% / 0.02970405
    28.0 MAR_Taforalt
    25.4 TUR_Barcin_N
    22.0 Bell_Beaker_NLD
    17.4 Levant_PPNB
    5.2 Yoruba
    1.0 Dinka

    Replacing Iran_N with Minoan_Lasithi.

    Target: Canary_Islands_Guanche:gun005
    Distance: 3.6871% / 0.03687070
    27.0 Bell_Beaker_Iberia
    26.0 MAR_Taforalt
    18.0 Iberian_N
    12.4 Levant_Natufian
    10.2 GRC_Minoan_Lassithi
    6.4 Yoruba

    Tried to keep the lowest fits.
    Last edited by Echo; 12-02-2020 at 07:06 AM.

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