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Thread: Massive paper on Stone age Europe and Eurasia. New HG ancestry in Steppe herders

  1. #51
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    1 members found this post helpful.
    Quote Originally Posted by Angela View Post
    That's a very healthy way to keep depression in check, as exercise releases natural endorphins. Anti-depressive drugs are of questionable use, imo, as some people have the opposite reaction to them, with them increasing the depression. So much so that the medications often come with the warning to cease taking if suicidal thoughts appear.

    My weakness is anxiety, inherited from my mother (my father didn't have an anxious bone in his body) although it's not generalized anxiety disorder; it's more a case of having a heightened anxiety reaction to very stressful situations (serious illness, even sometimes not so serious, or approaching death of a loved one, or myself for that matter, etc. being the most common one).

    It can extend to things like being pretty anxious when my children learned to drive and would get home very late. I would worry they'd drink too much or do too much weed or fall asleep at the wheel. Even though I missed them terribly, I was so glad when they moved out. :) What I didn't see didn't trigger me.

    Deep breathing and meditation are very helpful, and cognitive processes, like refusing to let your thoughts spiral into all the possible reasonable consequences of the situation. "Take everything one day at a time", is a cliché, but a helpful one.

    Interestingly, I'm drawn to other people who have some anxiety or can be a bit depressed at times. I find phlegmatic types really boring after a while, and I'm ashamed to say that when I'm with people who are like that, always calm and cheery, I sometimes wonder if they're pretending, or are really stupid, or have no experience of the darker aspects of reality, or are on the autism spectrum or something. It's like positivity that is so extreme it's toxic. Mean, and undoubtedly wrong, I know, but I'm being honest.
    Angela you're just a typical Italian or Greek overprotective mother. Nothing more nothing less.

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    Based on my interest if some racist ideas are true, I did a search for strongly with mental disorders associated variants in living populations some years ago. I did not find any variant that was very common in any living population based on the average population data about the SNPs on NCBI.

    It is true, that the alleles for some heritable mental disorders are more present in some populations, but not the really striking variants. They are rare everywhere.

    But some populations have some kind of allele more often.

    For example Africans have the most alleles associated with poor education attainment, the same goes for Neanderthals. Allele sharing of Neanderthals and Africans is a general trend that is extended to ancestry components, physical traits and many other things.
    I personally do not understand, why Neanderthals and Denisovans are associated with “Out of Africa” populations, they appear totally Archaic African in so many ways.

    Ashkenazi Jews are associated with Schizophrenia, a fact which was often used by Antisemites: https://www.haaretz.com/.premium-ash...enia-1.5294333

    I did once an ancient PCA based on 244 SNPs that are associated with physical, metabolic, immunologic and mental traits like Introversion, Anxiety Disorder, Antisocial Behavior, Psychopathy, Depression, Creativity, Autism, Intelligence and various addictions.
    Direct use of alleles converted to numbers, no conversion to population components, a very pure PCA, but with 7.16% imputed alleles. I imputed them by hand based on the average values of all other populations for the SNP. One could say I used “ancient global values” so this smooths them a little too strong. I have also a program for imputation, but this program is an extremist in my opinion, I don’t like to use it and it cannot impute all alleles I need.


    The PCA:





    As you can see, I didn't want to believe it, but physical, metabolic and mental traits go hand in hand and there seems to be a significant association between mental traits and heritage/population.
    But there is a large spectrum of variation between European, Middle Eastern, Caucaisan and South Asian populations, while East Asians, Africans and mesolithic European HGs are more separated.

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    3 members found this post helpful.
    Quote Originally Posted by Stefano View Post
    These are indeed really strange charts.
    Also why is Uk divided in small areas and france and italy are taken as one? They have far more internal diversity than UK.
    And egypt and italy the same steppe admixture? ridiculous. The farmer in north africa is suspiciously high too.
    How can geneticist and academics produce such results? unbelievable

    Probably because for France and Italy they used some kind of average, I don't know, while not for UK. I guess the main focus of this paper is not so much regional divisions within a country, and that's understandable, UK might be the exception perhaps because the paper was funded or co-funded with UK money. I don't know. But these are the least of the problems, I think. Whereas this chart has very implausible results. Maybe it's me who has problems with my vision, there is more WHG in China than in south-eastern Europe and Italy, EHG has its peaks in Finland and Mongolia, CHG has its peak between Pakistan and India, Yamnaya is widespread in non-European countries where it has never been found, Farmer ancestry seems too high in North Africa... I really don't know if it's a problem of metodology, of errors, of sloppiness of whoever graphically made the chart, but the fact that geneticists may produce results with little credibility is nothing new.

    Last edited by Pax Augusta; 12-05-22 at 14:07.

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    4 members found this post helpful.
    Quote Originally Posted by Doggerland View Post

    For example Africans have the most alleles associated with poor education attainment, the same goes for Neanderthals.
    You may want to check your "sources" again.

  5. #55
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    Quote Originally Posted by Archetype0ne View Post
    I know its speculative rn. But how would you say the 9700 Kotias Klde J2b this paper mentions relates to UP Caucasus?
    Really hard to tell, we only know that CHG(Kotias Klde)=Dzudzuana +ANE. Also the new samples doesn't provide us new Y-DNA for UP Caucasus because she is a female with mtDNA U4`9, which is a very rare clade. UP Caucasus could have many Y-Haplogroups but most likely seems G because of it's closeness to Anatolian farmers.

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    Quote Originally Posted by firetown View Post
    You may want to check your "sources" again.


    My sources are NCBI, Neanderthal and modern African DNA files.

    rs11743006 A = Lower mathematical ability
    rs12640626 G = Bad education attainment, lower household income
    rs8049439 C = Lower intelligence
    rs2966 C = Bad education attainment
    rs11588857 G = Bad education attainment, lower math ability, lower household income
    rs438895 G = Bad education attainment
    rs4950 G = Bad leadership ability

    AfroAmerican
    rs11743006CC
    rs12640626GG
    rs8049439CT
    rs2966CC
    rs11588857GG
    rs438895AG
    rs4950GG

    African(Includes North Africa)
    rs11743006CC
    rs12640626GG
    rs8049439CT
    rs2966CC
    rs11588857GG
    rs438895AG
    rs4950GG

    MbutiPygmy
    rs11743006CC
    rs12640626GG
    rs8049439CC
    rs2966CC
    rs11588857GG
    rs438895GG
    rs4950GG

    San
    rs11743006CC
    rs12640626AG
    rs8049439CC
    rs2966CC
    rs11588857GG
    rs438895AG
    rs4950GG

    ShumLaka
    rs11743006CC
    rs12640626AG
    rs8049439TT
    rs2966CT
    rs11588857GG
    rs438895AG
    rs4950GG

    Neanderthal
    rs11743006CC
    rs12640626GG
    rs8049439CC
    rs2966CC
    rs11588857GG
    rs438895GG
    rs4950GG

    Denisova
    rs11743006CC
    rs12640626GG
    rs8049439CC
    rs2966CC
    rs11588857GG
    rs438895GG
    rs4950AA

    Gorilla
    rs11743006CC
    rs12640626GG
    rs8049439CC
    rs2966CC
    rs11588857GG
    rs438895GG
    rs4950GG

    AverageEuropean
    rs11743006CC
    rs12640626AG
    rs8049439TC
    rs2966CT
    rs11588857GG
    rs438895AA
    rs4950AA

    AshkzenaziJews
    rs11743006CC
    rs12640626AG
    rs8049439TT
    rs2966CT
    rs11588857GG
    rs438895AA
    rs4950AA

    EastAsians
    rs11743006CC
    rs12640626AA
    rs8049439TT
    rs2966TT
    rs11588857AG
    rs438895AA
    rs4950AA

    I think the data speaks for itself.

    So I don’t understand why people think Neanderthals where in any way superior. They had a different brain shape, but this was due to a more primitive brain development, and not because they where more intelligent:

    https://www.cell.com/current-biology...822(18)31470-2

    The SNPs that are associated with Neanderthal head shape, are very rare today and are most present in Indigenous African and Siberian populations, according to NCBI data:

    rs28445963 C

    Old data from 1000 genomes:

    In Europeans: 0.004
    In Africans: 0.0
    In East Asians: 0.1

    But:

    Indigenous Africans: 0.5

    "African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations.", Genome Biol, 2019 Apr 26;20(1):82

    Siberians 0.5

    Registration date: 19-Nov-2014
    University of Southern California

    rs72931809 T

    Indigenous Africans according to the study: 0.62 (More than half)

    It seems that the alleles where rarely tested, because they are not included in the most DNA Chips that are commonly used. The newer studies are based on Whole Genome Sequencing, 1000 genomes was not.
    The most indigenous Sub Saharan Africans could carry one of the neanderthal alleles, if most people are heterozygote.

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    So the steppe clans wiped out all Iberian men and the dark phenotype that exists today is passed down from the WHG traits retained by Neo women.

    However, I would guess that the Scandinavia replacement was due to climate changes. That area is prone so cold snaps. The filling populations would have been from the Steppe who mixed with local Neolithic elsewhere, maybe Germany

    Or, were there multiple Scandinavia depops since that time? The great migration period coinciding with the fall of the Roman empire was accompanied by a devastating cold period in Scandinavia.

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    1 members found this post helpful.
    PCA based on 10 skin color related SNPs:

    https://i.ibb.co/Zc86yTj/Skin-Color-PCA.png

    But there is a limitation: This PCA excludes SNPs that are linked to hair and eye color, some of them also have an influence on skin color.

    Clustering as a tree:

    https://i.ibb.co/QmTjtJG/Skin-Color-PCATree.png

    Because there are different SNPs for light skin color, not everybody who had light skin color is near each other. For example east Asians have other alleles and PAST(The program) takes that into account and don’t place them near the Europeans.

    Skin color can be used to differentiate between Africans, Asians and other groups, but it is generally a bad indicator for European ancestry in the last 10.000 years. It is not possible to address modern European peoples skin color to specific ancient populations, because they were too diverse.

    For example my Wife and I will not be in the same cluster according to the program, because we have different skin color alleles, both light skin, but not the same tone. She has for example one SNP heterozygote for an African related skin color allele, so she is placed in a much lower branch of the tree.

  9. #59
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    Quote Originally Posted by Doggerland View Post
    PCA based on 10 skin color related SNPs:

    https://i.ibb.co/Zc86yTj/Skin-Color-PCA.png

    But there is a limitation: This PCA excludes SNPs that are linked to hair and eye color, some of them also have an influence on skin color.

    Clustering as a tree:

    https://i.ibb.co/QmTjtJG/Skin-Color-PCATree.png

    Because there are different SNPs for light skin color, not everybody who had light skin color is near each other. For example east Asians have other alleles and PAST(The program) takes that into account and don’t place them near the Europeans.

    Skin color can be used to differentiate between Africans, Asians and other groups, but it is generally a bad indicator for European ancestry in the last 10.000 years. It is not possible to address modern European peoples skin color to specific ancient populations, because they were too diverse.

    For example my Wife and I will not be in the same cluster according to the program, because we have different skin color alleles, both light skin, but not the same tone. She has for example one SNP heterozygote for an African related skin color allele, so she is placed in a much lower branch of the tree.
    Interesting, when you combine the snps for cultural achievement and evolution of skin tone. Your wife is closer to Yamnaya snps than yourself(Cucuteni–Trypillia culture/Globular Amphora culture/Trichter(-rand-)becherkultur)

    .
    When comparing--Cucuteni–Trypillia culture/Globular Amphora culture/Trichter(-rand-)becherkultur with Yamnaya skills in mobility-metallurgy/carpentry/animal husbandry/ Elshanka type pottery(long distance steppe wagons/iron burials/proto Dom2 horses) achievement with dense settlements.
    Suum cuique---Rubiconem suum


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    Quote Originally Posted by etrusco View Post
    Local Neolithic farmers admixed with incoming pastoralists in eastern, western, and southern Europe whereas Scandinavia experienced another near-complete population replacement. Similar dramatic turnover-patterns are evident in western Siberia
    I wonder how they still have Neolithic Farmer ancestry then.
    They should only have Yamnaya component.

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    Quote Originally Posted by Mmiikkii View Post
    I wonder how they still have Neolithic Farmer ancestry then.
    They should only have Yamnaya component.
    The invading population was already mixed with EEFs. Yamnaya itself gets up to 18% EEF.

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