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Thread: Pinhasi et al-Ancient dna recovery

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    Pinhasi et al-Ancient dna recovery

    Thanks to Dienekes for the link:
    http://journals.plos.org/plosone/art...l.pone.0129102

    "Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone"

    The technical aspects are beyond me, but basically they can recover dna from remains in hotter and wetter climates.

    " These results suggest that it may be possible to obtain endogenous DNA from part C also for samples with relatively low amounts of endogenous DNA from hot environments, although extreme caution will be necessary in the interpretation of the results obtained from such samples."


    I hava a feeling very few will exercise extreme caution.
    :)

    Apparently the have a sample from Jordan 10,000 years ago and one from just around the time of the departure to Europe. It should be very interesting.


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    Apparently the DNA files are available online and Felix already has plans to analysis them.

    Do ctrl+F "AG037"
    http://www.y-str.org/p/ancient-dna.html

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    Very interesting and much needed, lets hope the technology keeps on growing at a fast pace. Exciting times

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    8,400 year old Female from Turkey. Her genome is of low coverage. Her results are consistent with what we heard about other Neolithic Anatolian.

    Dodecade K12b. See the Post
    12 ancestral populations 166770 total SNPs
    67 flipped SNPs
    0 heterozygous SNPs
    0 no-calls
    166356 absent SNPs
    0.002482 genotype rate
    mode genomewide

    ----------------------------
    FINAL ADMIXTURE PROPORTIONS:
    ----------------------------

    0.00% Gedrosia
    0.00% Siberian
    20.76% Northwest_African
    0.00% Southeast_Asian
    65.30% Atlantic_Med
    0.00% North_European
    0.00% South_Asian
    0.00% East_African
    0.00% Southwest_Asian
    0.00% East_Asian
    13.94% Caucasus 0.00% Sub_Saharan
    Dodecade K7b. See Post
    0.00% South_Asian 0.00% West_Asian
    0.00% Siberian
    0.00% African
    51.93% Southern
    48.06% Atlantic_Baltic 0.00% East_Asian
    MDLP K27. See the Post.
    0.00% Nilotic-Omotic
    0.00% Ancestral-South-Indi
    0.00% North-European-Balti
    0.00% Uralic
    0.00% Australo-Melanesian
    0.00% East-Siberean
    0.00% Ancestral-Yayoi
    41.12% Caucasian-Near-Easte
    0.00% Tibeto-Burman
    0.00% Austronesian
    0.00% Central-African-Pygm
    0.00% Central-African-Hunt
    0.00% Nilo-Saharian
    3.64% North-African
    0.00% Gedrosia-Caucasian
    0.00% Cushitic
    0.00% Congo-Pygmean
    0.01% Bushmen
    0.00% South-Meso-Amerindia
    55.24% South-West-European
    0.00% North-Amerindian
    0.00% Arabic
    0.00% North-Circumpolar
    0.00% Kalash
    0.00% Papuan-Australian
    0.00% Baltic-Finnic
    0.00% Bantu
    MDLP K14. See the Post.
    0,00 ANE0,00 ANI
    14,76 ASI
    33,48 Caucasian
    0,00 Mesolithic
    51,75 Neolithic
    0,00 East-Asian
    0,00 Subsaharian
    0,00 Near-East
    0,00 Pygmy
    0,00 Amerindian
    0,00 Papuan
    0,00 Siberian 0,00 Altaic
    Eurogenes AMI K8. See the Post.
    8 ancestral populations 101647 total SNPs
    0 flipped SNPs
    0 heterozygous SNPs
    0 no-calls
    101332 absent SNPs
    0.003099 genotype rate
    mode genomewide

    0.00% Amerindian
    0.00% Siberian
    18.44% Euro_HG
    0.00% Oceanian
    0.01% Sub-Saharan
    4.73% Southeast_Asian
    76.82% LBK 0.00% South-Central_Asian

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    I put her results in a spreadsheet along with Stuttgart's. Davidski got ANE K8 results for her, I also put them in the spreadsheet.

    BAR100(8400YBP Western Antolia) is the Red dot. She's just South of EEF.

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    Thanks, very interesting. So no Gedriosia but some Caucasus in 12b, but not a lot. I had a hunch that Gedrosia was more to the east.

    In K8 it says 18.44% Euro_HG. Does this equals to WHG roughly? It might mean that first contact with WHG was actually in Anatolia, as some of us suspected. Unless this person is from back migration from Balkans to Anatolia.

    We need the one 10,000 y old from Syria to confirm. This BAR100 looks so Neolithic Balkan like that it could be a back migration at that point.
    Be wary of people who tend to glorify the past, underestimate the present, and demonize the future.

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    Quote Originally Posted by Fire Haired14 View Post
    I put her results in a spreadsheet along with Stuttgart's. Davidski got ANE K8 results for her, I also put them in the spreadsheet.

    BAR100(8400YBP Western Antolia) is the Red dot. She's just South of EEF.
    Can you point to it with an arrow or a letter. I can't find it with my eyes. Sorry.

    Edit: I found her. She looks less WHG than EEF farmers. It might be true than that mixing mixing of ENF and WHG happened in Anatolia. Interesting question is what Y-hg were WHG in Anatolia? C, F or even I2?
    I have a feeling that I'm rushing to much into unknown... :)

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    Thanks for doing this, Fire Haired.

    Is this the link? I don't see a PCA.
    https://docs.google.com/spreadsheets...it?pli=1#gid=0

    I don't want to rain on anyone's parade but I don't think this can be relied upon. The results seem to be all over the place, don't they? I mean, if you go by Dodecad K-7b she's almost identical to Stuttgart...about a four percent difference, which would mean there was almost no admixture in Europe. (Lazardis did say it might only be a few percent difference.) Yet there's a big difference in K-12b results.

    So, as far as I'm concerned, this doesn't settle much of anything.

    Does anyone have a map showing where the sample was found?

    For comparison, this is the map from Haak et al for the Neolithic spread into Europe (Renfrew used to think that the Indo-European languages moved into Europe with the farmers.).
    Haak et al map of Neolithic and Anatolian IE.jpg

    It's basically the same as Paschou et al:
    http://www.pnas.org/content/111/25/9211.abstract

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    She's of very low coverage. BTW, she's from the Western edge of Turkey, right next to Greece. I haven't been given an exact location though.

    Here's a spreadsheets with her and Stuttgarts ADMIXTURE results. According to ANE K8 Stuttgart is around 90% Neolithic Antolian and 10% WHG. But, BAR100 is of very low coverage, and so her results may not be realistic. I'm can't wait for the 10,000YBP Syrian. If it's of good coverage we might see Off the Charts levels of Basal Eurasian.

    https://docs.google.com/spreadsheets...Pak/edit#gid=0

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    There's also a Late Neolithic Female from Turkmenistan that will be analysed. That'll be very interested, and probably ANE-rich.

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    Quote Originally Posted by Fire Haired14 View Post
    She's of very low coverage. BTW, she's from the Western edge of Turkey, right next to Greece. I haven't been given an exact location though.

    Here's a spreadsheets with her and Stuttgarts ADMIXTURE results. According to ANE K8 Stuttgart is around 90% Neolithic Antolian and 10% WHG. But, BAR100 is of very low coverage, and so her results may not be realistic. I'm can't wait for the 10,000YBP Syrian. If it's of good coverage we might see Off the Charts levels of Basal Eurasian.

    https://docs.google.com/spreadsheets...Pak/edit#gid=0
    Well, that's right on the proposed route according to Paschou et al and Haak...from the juncture of southeast Anatolia/Northern Levant all along the coast, some peeling off for Cyprus maybe, others hitting the Greek islands and mainland Greece, and then bifurcating from there.

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    Quote Originally Posted by Fire Haired14 View Post
    She's of very low coverage. BTW, she's from the Western edge of Turkey, right next to Greece. I haven't been given an exact location though.
    This might as well be true, screwing the results. However her WHG/Near Eastern from K8 run makes sense. She is closer to epicenter of farmer's homeland, therefore have more Near Eastern than Stuttgart does. K12b makes sense if we imagine that she is from different and later wave of migration than Stuttgart. Her tribe first went south to (Egypt?)picking some N-W African hunter-gatherer admixture and later migrated north to Anatolia. At time when most of Caucasus admixture left Anatolia for some reason. Or part of her genome containing more Caucasus is missing.

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    Davidski keeps updating his post. In "Identity by Decent" he was able to use more SNPs than in ADMIXTURE. The results are consistent with ADMIXTURE. She's closest to South Europeans: Tuscan, Sardinian, Basque, and Spanish_Murcia. This and ADMIXTURE confirm to me she's ancestral to EEF. Most South Europeans today are probably 50%+ Neolithic Anatolian, and all other Europeans should be just under 30% at the least.

    https://docs.google.com/spreadsheets...gid=1507216515

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    Quote Originally Posted by Fire Haired14 View Post
    Davidski keeps updating his post. In "Identity by Decent" he was able to use more SNPs than in ADMIXTURE. The results are consistent with ADMIXTURE. She's closest to South Europeans: Tuscan, Sardinian, Basque, and Spanish_Murcia. This and ADMIXTURE confirm to me she's ancestral to EEF. Most South Europeans today are probably 50%+ Neolithic Anatolian, and all other Europeans should be just under 30% at the least.

    https://docs.google.com/spreadsheets...gid=1507216515
    Probably not ancestral, but containing the same or most ancestry (ancestral genes) as EEF folks.

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    This is almost as interesting as the 101 genomes from Allentoft et al. study. The Dodecad K12b is the one that particularly got my attention.

    If the data is reliable, then it would appear that Near Eastern Neolithic farmers brought most of the Atlantic_Med admixture to Europe. This is important because it means that this admixture, which peaks in the Basques and Sardinians (70-75%), is therefore not native to Europe.

    In the same way, those Neolithic farmers carried 21% of Northwest_African admixture. Modern Maghrebans have 35-45% of Northwest_African and 20-25% of Atlantic_Med admixture, and all of it could ultimately have been inherited from Anatolian or Levantine Neolithic farmers (some of it via the Phoenicians and Arabs).

    Genetic drift could explain why some genes, which now make up the Atlantic_Med admixture, ended up being present at higher frequencies in Southwest Europe, while another set of genes from Neolithic farmers survived at much higher frequencies in Northwest Africa. From a modern standpoint it could look like the two have different origins, but it may just be one big family whose genes got divided early between two continents then evolved separately for thousands of years.
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    I hope one day they standartize those things. I have a feeling what is EEF and ENF and what not changes from study to study...
    Making it difficult to compare.

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    I agree, we need some standard here.
    And a simple number telling what coverage there is.

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    Quote Originally Posted by arvistro View Post
    I hope one day they standartize those things. I have a feeling what is EEF and ENF and what not changes from study to study...
    Making it difficult to compare.
    Totally agree with you. Samples are far too small to be able to have a good idea and population set ups and densities to be able to claim if someone was a farmer or a hunter gatherer, besides we still need to decipher other ancient dna from North Africa, middle east and southern Europe to be able to come close to any kind of accuracy and get the big picture..

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    Quote Originally Posted by Maciamo View Post
    This is almost as interesting as the 101 genomes from Allentoft et al. study. The Dodecad K12b is the one that particularly got my attention.

    If the data is reliable, then it would appear that Near Eastern Neolithic farmers brought most of the Atlantic_Med admixture to Europe. This is important because it means that this admixture, which peaks in the Basques and Sardinians (70-75%), is therefore not native to Europe.

    In the same way, those Neolithic farmers carried 21% of Northwest_African admixture. Modern Maghrebans have 35-45% of Northwest_African and 20-25% of Atlantic_Med admixture, and all of it could ultimately have been inherited from Anatolian or Levantine Neolithic farmers (some of it via the Phoenicians and Arabs).

    Genetic drift could explain why some genes, which now make up the Atlantic_Med admixture, ended up being present at higher frequencies in Southwest Europe, while another set of genes from Neolithic farmers survived at much higher frequencies in Northwest Africa. From a modern standpoint it could look like the two have different origins, but it may just be one big family whose genes got divided early between two continents then evolved separately for thousands of years.
    I think the NorthWest African score was noise. This Neolithic Anatolian is of very low coverage. All her results make sense except the NorthWest African score. It could be real, I don't know. In all the other tests she doesn't score any African. So, it could be like you said she didn't have NW African ancestry, NW Africans have decent from her people and African ancestry.

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    the coverage is low, noise will be imporatant
    but it is dangerous to speculate which part is noise and which not

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    so the Neolithic sample looks basically EEF. So as many people (including me) have suspected the WHG type ancestry was already found in the earliest farmers in Western Asia.

    And it really points more and more to the fact that EEF was slowly being replaced by an Afro_Asiatic shifted version of EEF. I remember saying the first time under Dienekes comment section that an East African shift probably happened.

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    Quote Originally Posted by Fire Haired14 View Post
    8,400 year old Female from Turkey. Her genome is of low coverage. Her results are consistent with what we heard about other Neolithic Anatolian.

    Dodecade K12b. See the Post


    Dodecade K7b. See Post


    MDLP K27. See the Post.


    MDLP K14. See the Post.


    Eurogenes AMI K8. See the Post.

    And also so much to "European character" was brought to BaArmenia by Yamna. It was good that I never accepted the theory of some other.


    Another thing. The sample with allot of NW African could be one of those late Neolithic samples who were already receiving Afro_Asiatic influx as by the paper (it was replaced by a very Middle Eastern and North African type ancestry).
    Last edited by Alan; 23-06-15 at 18:35.

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    Quote Originally Posted by Alan View Post
    Another thing. The sample with allot of NW African could be one of those late Neolithic samples who were already receiving Afro_Asiatic influx as by the paper (it was replaced by a very Middle Eastern and North African type ancestry).
    Do you know what would make some sense? If this girl with NW African admixture would have turned to be from E1b1b, J or T group who obviously entered Europe much later than G2a people. G2a coming from Northern part of Fertile Crescent which bordered with Caucasus admixture people. E1b1b coming from South part of this fertile crescent, closer to Africa.

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    Quote Originally Posted by LeBrok View Post
    Do you know what would make some sense? If this girl with NW African admixture would have turned to be from E1b1b, J or T group who obviously entered Europe much later than G2a people. G2a coming from Northern part of Fertile Crescent which bordered with Caucasus admixture people. E1b1b coming from South part of this fertile crescent, closer to Africa.
    As a girl she couldn't turn out with ydna but I got your point. :)

    E1b for her father would, J or T however not. Since J obviously chop through the rest of Western Asia during the Bronze and Iron Age. I am pretty convinced J2 started off from the Iranian Plateau.

    the only T we found so far on the other hand was late Neolithic and a very Yamna like signature to it with no NW African admixture.

    But than as Maciamo pointed out this "NW African admixture" could simply mean that the NW African component received genes from her relatives.

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