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Thread: Genetic origins of the Minoans and Mycenaeans

  1. #831
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    Quote Originally Posted by Kale View Post
    The Mycenean samples are quite strange... they insist on 6-8% SSA admixture. If the results can be interpreted as accurate otherwise, the shift doesn't appear Anatolian like in the case of Peloponnese_N or Minoan, but rather Levantine.

    Greece_Mycenaean
    "Greece_Lassithi_Minoan" 50.85
    "Russia_Mezhovskaya_MLBA.SG" 19
    "Israel_Yehud_IBA" 18.75
    "Mota.SG" 6.55
    "Israel_Megiddo_IBA" 2.3
    "Jordan_AinGhazal_EBA" 1.8
    "Malawi_Hora_9000BP" 0.5
    "Cameroon_ShumLaka_900BP" 0.1
    "Malawi_Fingira_2500BP" 0.1
    "Russia_Krasnoyarsk_MLBA" 0.05
    "distance%=0.2987 / distance=0.002987"
    Columns:,Anatolia_Barcin_N,Levant_N,Iran_GanjDareh _N,CHG.SG,Taforalt,Vanuatu_ancient,PrimorskyKrai_B oisman_MN,Peru_Laramate_900BP,Karelia_HG,IronGates _Meso1,Yamnaya_Samara,Ust_Ishim.DG
    It's deamination damage.

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  3. #832
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    The currently available Mycenaeans do produce somewhat confusing f3 stats. We noticed it a while ago.

    https://eurogenes.blogspot.com/2019/...-approach.html

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  5. #833
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    If we take the SSA as deanimation damage, the rest seems plausible, it's not like it's asking for a bunch of Papuan ancestry or something weird. Say ~55% Minoan baseline, 20% Steppe_MLBA, 25% Levant_BA.
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  7. #834
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    Quote Originally Posted by Kale View Post
    If we take the SSA as deanimation damage, the rest seems plausible, it's not like it's asking for a bunch of Papuan ancestry or something weird. Say ~55% Minoan baseline, 20% Steppe_MLBA, 25% Levant_BA.
    Probably not deamination...

    Code:
    2REF_POPULATIONS                                             AMPLITUDE                               TIME(GENERATIONS)
    Kenya_Early_PN;Greece_Minoan_Odigitria	0.000888693 +/- 0.00025865      78.3257 +/- 26.1111 (Z=2.9997)
    PPNB;Malawi_Hora_8100BP_all	        0.00204149 +/- 0.00062006  	78.3257 +/- 26.1111 (Z=2.9997)
    Sardinia;PPNB	                        0.000684834 +/- 0.000143385 	78.3257 +/- 26.1111 (Z=2.9997)
    LD corr between 4 individuals is highly unlikely due to damage. ...and then to print out valid 2ref curves on top of that. Might look further into this just for the sake of seeing why Mota, works in so many admixture models involving Near eastern related ancestry. Don't really care that much about Greeks to further investigate the Mycenaeans without external motivation though.

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  9. #835
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    Sorry I'm not familiar with LD, can you explain what that output means?
    Also what do you mean about Mota working in many models of Near Eastern ancestry?

    Distance is a little better here, but no material difference.

    Greece_Mycenaean
    "Greece_Lassithi_Minoan" 53.85
    "Russia_Mezhovskaya_MLBA.SG" 18.5
    "Kenya_PastoralN_Elmenteitan" 12.25
    "Israel_Megiddo_MLBA" 11.15
    "Israel_Yehud_IBA" 3.9
    "Tanzania_Luxmanda_3100BP" 0.25
    "Kenya_PastoralN" 0.1
    "distance%=0.2703 / distance=0.002703"

    Or removing all Near Eastern groups

    Greece_Mycenaean
    "Greece_Lassithi_Minoan" 60.5
    "Russia_Mezhovskaya_MLBA.SG" 19.15
    "Kenya_PastoralN_Elmenteitan" 12.25
    "Egypt_ancient" 8.1
    "distance%=0.3091 / distance=0.003091"
    Columns:,Anatolia_Barcin_N,Levant_N,Iran_GanjDareh _N,CHG.SG,Taforalt,Vanuatu_ancient,PrimorskyKrai_B oisman_MN,Peru_Laramate_900BP,Karelia_HG,IronGates _Meso1,Yamnaya_Samara,Ust_Ishim.DG
    Last edited by Kale; 06-16-2020 at 06:25 AM.
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  11. #836
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    Quote Originally Posted by Kale View Post
    Sorry I'm not familiar with LD, can you explain what that output means?
    Also what do you mean about Mota working in many models of Near Eastern ancestry?
    One example, is in another thread, when modeling Pastoral_Neolithic samples in east Africa. Mota would serve as the best proxy for Ancient east African ancestry despite Kenya_LSA(for example) having geographical proximity. Also I fail to see much 2ref correlations with Kenya_LSA samples in the earlier PN populations, though its been postulated that they as locals mixed with incoming NorthEast Africans carrying Near eastern ancestry.

    about LD:
    Amplitude is the strength of the curve, the higher the amplitude the sore similar the two admixing populations are to the original two populations.
    Time is the date of the admixture event in generations, assuming a generation of 25 years the Mycenaeans in this run had admixture dating to roughly 2000 years prior to their existence.

    In this instance a handfull of samples were added to the run and only these five populations created a curve in three different combinations. Individually they'll all yeild different times based on the LD decay, but the times are averaged (or ommitted if too divergent) but weighed in relation to their respective Amplitudes and significance. So these admixing combinations are indicative of a singe admixture event. See this study.

    Another thing to note is that this is a quick and dirty run by me... I wasn't using this method for dating admixture or Identifying the admixing populations (which is somewhat what this method is used for.) I use it to rule out Admixture, cuz the test will definitely fail or not show African admixture in any capacity if there is none in Eurasian samples. Also, The test will fail if the population has noisy reads within itself, which is why holfelder couldn't date admixture within her Coptic sample (even though I can quite easily) and pendergast had to limit the amount of samples pooled in their runs to two each. In this case, the Mycenaean samples would produce too much noise to output a significant curve if they were damaged enough to show a whole 6% of false information. Not to mention they show 2ref curves with Africans on top of that.

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  13. #837
    According to the supplementary materials from a study of Reich :The ~14,000 year old Upper Paleolithic
    hunter-gatherer from Switzerland 12 can also be modeled as WHG+Mota, but has no significant
    evidence of Basal Eurasian ancestry (α=-0.9±5.1%), consistent with its close relationship to WHG 12
    (Fig. 1b).


    Is there something about Mota, we don't know yet?

    As far as I remember La Brana showed some SSA-like admixture too.
    However, Chad emphatically stated that there is no African admixture in any WHG at all. WHGs are indeed very removed from SSAs.

    Besides, one Anglo-Saxon sample from Roman Britain scored around 1% SSA. What is the reason behind these results that seem not to make any sense?
    Last edited by dr.sparco; 06-16-2020 at 11:59 AM.

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  15. #838
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    Quote Originally Posted by dr.sparco View Post
    According to the supplementary materials from a study of Reich :The ~14,000 year old Upper Paleolithic
    hunter-gatherer from Switzerland 12 can also be modeled as WHG+Mota, but has no significant
    evidence of Basal Eurasian ancestry (α=-0.9±5.1%), consistent with its close relationship to WHG 12
    (Fig. 1b).


    Is there something about Mota, we don't know yet?

    As far as I remember La Brana showed some SSA-like admixture too.
    However, Chad emphatically stated that there is no African admixture in any WHG at all. WHGs are indeed very removed from SSAs.

    Besides, one Anglo-Saxon sample from Roman Britain scored around 1% SSA. What is the reason behind these results that seem not to make any sense?
    Yes. But what I wonder...

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  17. #839
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    In view of the increased activity in recent threads which involve the discussion of the interplay between Sub-Saharan-related admixture (be it cryptic, a para-group relation or actual) and West Eurasian admixture (be it cryptic, a para-group relation or actual);

    A couple general points of guidance as an administrator:

    1. Don't assume the worst of each other. Nobody has the objective truth on any of these questions given the on-going deficiency in aDNA. This community differs from others in that the majority of users aren't interested in agenda-peddling and our administration is too inherently diverse to promote X position or diminish Y position. Treat the majority of those who disagree with you as well-intentioned counterparts with a different heuristic cognitive+evidence base package from yourself rather than an ideological enemy. Which leads me onto...
    2. Don't permit bad habits or past experience from other venues to be replayed over here. This administration has recognised that some of the newer participants in this forum, who were formerly active in other venues where such discussions regularly descended into inane bigoted flaming, are present in these discussions. To everyone involved (both the newer members and the longstanding ones who recognise them) Please do not assume that the positions taken on any particular topic are binary (i.e. a false dichotomy position). Such basic thinking is/was abound in other venues, but there's no sensible reason to replay those here.
    3. Recognise the limitations of your own perspective in discussions here. Given the absence of key aDNA, the majority of these discussions rest on conjecture and circumstantial evidence. Many outcomes are possible and the objective truth may eventually produce a very simple or vastly complicated picture.
    4. Don't be a slave to your own dogma or biases. We all have them (be they pre-conceived notions based on imperfect or circumstantial data, personal ideology, the list goes on). Promoting a given view with rigidity completely defies the point of participating here.


    One thread was already closed, infractions are coming, and we'll continue to uphold our Terms of Service, which all of you had agreed to upon registration here.

    Please comply with our Terms of Service, apply critical thinking to all perspectives, minimise personal biases and treat each other kindly - We'll all have an easier and far more productive experience.

    [Edit]: Removed four unproductive and personalised posts.
    Last edited by DMXX; 06-16-2020 at 03:59 PM. Reason: minor

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  19. #840
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    Quote Originally Posted by El-Maestro View Post
    One example, is in another thread, when modeling Pastoral_Neolithic samples in east Africa. Mota would serve as the best proxy for Ancient east African ancestry despite Kenya_LSA(for example) having geographical proximity. Also I fail to see much 2ref correlations with Kenya_LSA samples in the earlier PN populations, though its been postulated that they as locals mixed with incoming NorthEast Africans carrying Near eastern ancestry.

    about LD:
    Amplitude is the strength of the curve, the higher the amplitude the sore similar the two admixing populations are to the original two populations.
    Time is the date of the admixture event in generations, assuming a generation of 25 years the Mycenaeans in this run had admixture dating to roughly 2000 years prior to their existence.

    In this instance a handfull of samples were added to the run and only these five populations created a curve in three different combinations. Individually they'll all yeild different times based on the LD decay, but the times are averaged (or ommitted if too divergent) but weighed in relation to their respective Amplitudes and significance. So these admixing combinations are indicative of a singe admixture event. See this study.

    Another thing to note is that this is a quick and dirty run by me... I wasn't using this method for dating admixture or Identifying the admixing populations (which is somewhat what this method is used for.) I use it to rule out Admixture, cuz the test will definitely fail or not show African admixture in any capacity if there is none in Eurasian samples. Also, The test will fail if the population has noisy reads within itself, which is why holfelder couldn't date admixture within her Coptic sample (even though I can quite easily) and pendergast had to limit the amount of samples pooled in their runs to two each. In this case, the Mycenaean samples would produce too much noise to output a significant curve if they were damaged enough to show a whole 6% of false information. Not to mention they show 2ref curves with Africans on top of that.
    LD mixture analyses often produce unusual results even with high quality modern samples, so using something like this to prove that Mycenaeans had any sort of African admixture is flawed.

    We need to nip this in the bud right now, before some people get confused and actually believe that Mycenaeans were partly Sub-Saharan or eastern African.

    Please e-mail Iosif Lazaridis and Nick Patterson and ask them whether they've ever found any evidence of such admixture in their Mycenaean or Minoan samples, and if your LD admix analysis actually provides reliable evidence of such a thing.

    I hope they can talk some sense into you.
    Last edited by Generalissimo; 06-17-2020 at 10:58 AM.

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