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Thread: The new way to look at Ancient mtDNA

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    Lightbulb The new way to look at Ancient mtDNA

    I have been very frustrated with how academics and amateurs online view ancient mtDNA. To most what really matter is the frequency of large and old haplogroups, such as H and U, compared to modern people which is plain ridiculous. This has caused many to make wrong conclusions about ancient people based on their mtDNA. For example many believe Bell beaker from Germany was mostly Iberian-like because of its high frequency of mtDNA H, but if you look more deeply into it's mtDNA you'll see it's very similar to German Corded ware, Unetice, Bronze age Pontic Steppe, and Bronze age central Asia.

    All we have to learn about ancient mtDNA is "Ancestral Journeys", which only gives the haplogroup label of samples, year, era, and cultural affinity. We don't know what extra mutations each sample had, haplogroup frequencies, haplotypes in ancient mtDNA, and Ancestral Journeys is wrong on some of its haplogroup labels. It is impossible to compare ancient mtDNA to modern mtDNA in any meaningful way using Ancestral Journeys. Enthusiasts online are kept in the dark when it comes to ancient mtDNA, because of a lack of convenient resources.

    Because of those reasons I created "Ancient mtDNA package", which has every Upper Palaeolithic-Bronze age mtDNA sample on Ancestral Journeys(except for a few), fully analysed.

    EDIT 7 hours later: I understand the old link I gave has limited access. This new one though gives you full access, and you can even download it into a word document and save it on your computer.

    Ancient mtDNA package

    There are 6 sections in the Ancient mtDNA package:

    1.Ancient mtDNA reference: This is a spreadsheet with all the samples I analysed accorded to age(except for hunter gatherers) and or region. I enbolded likely founder effects in the same color. I only considered samples from the same site as possible founder effects.

    The last section of the spreadsheet is "Likely false results".They're all from old studies. I kept them in the spreadsheet so we will at least consider they may have some validity. I'm suspicious many of the samples from Iberia in general, which are mostly from old studies, have false results.

    2.Haplogroup Frequencies: This has a spreadsheet showing haplogroup frequencies for every subgroup in "Ancient mtDNA reference". I only put frequencies for haplogroups which can be defined by HV1, or CR if the vast majority of samples from that section were tested for a specific CR SNP.

    3.Map of Haplogroup Frequences: Here I show haplogroup frequencies on a map.

    4.Haplotypes: In this file every haplotype in "Ancient mtDNA reference" are presented on Google documents.

    5.Map of Haplotype: In this File I have a map of the haplotypes for every haplogroup. I only display haplotypes which are shared between more than one sample. I don't treat popular haplogroups, such as U5 as haplotypes.

    6.Sources: In this File are all my sources. It also has all my personal notes, which will probably be hard to understand.

    I'll continuously edit the Ancient mtDNA package as new samples come in, and as I think of better ways to present ancient mtDNA. I will also use this method with modern mtDNA, so that we can directly compare it to ancient mtDNA. I think this will be the new way people will look at mtDNA in general, because it's the most detailed way possible.

    I suggest everyone who is interested in human prehistory put this on their Google Drive or Download it to Microsoft office.

    EDIT 1 hour later: I understand that some of my labels are inconstant. For example sometimes I call Mid-Late Neolithic Central Europe, Late Neolithic Central Europe. Often I abbreviated culture names on the maps. I can't correct some of my inconsistencies, and so hopefully anyone who reads it will be able to still understand the information.

    BTW, don't forget to use Ctrl+F.
    Last edited by Krefter; 01-11-2015 at 08:12 PM.

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    Something interesting I noticed looking at ancient mtDNA, is that all the various cultures from Neolithic Central Europe ranging some 2,000 years had mtDNA which is hard to distinguish from each other. Funnel beaker and Bernberg have more typical WHG mtDNA(U5b) than earlier Neolithic cultures and lack N1a1a, but that's it. Bronze age east Europeans though had a totally different mtDNA structure.

    Brandt. 2013 sampled the same region of Germany ranging the Mesolithic-Bronze age, and the only obvious change after the Neolithic occurs in the Bronze age with Corded ware, Bell beaker, and Unetice cultures. All three have obvious EHG(east European hunter gatherer) mtDNA and share other haplotypes(T1a, W6, J2b, J1b1a1, N1a1b) with Bronze age east Europeans that are either non-existent in Neolithic Central Europe or very very rare.

    Add to this with genomic evidence that Bronze age Germans were mostly of Yamna origin, ANE ancestry, Y DNA R1, there's no disputing a massive East European migration into western Europe during the Bronze age.

    Bronze age Central Asians look like they also were of mostly Bronze age east European maternal heritage, suggesting a related people also migrated east into Asia. It's incredible how archaeology and linguistics are matching up with DNA so nicely.

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    BTW, here's a life-like reconstruction of Mesolithic Europeans; Loschbour; who had mtDNA pre-U5b1a and Y DNA pre-I2a1b. We know what hair-eye-skin color he had, so this is probably very realistic.



    All but 3 samples from European hunter gatherers belonged to mtDNA U, and two are probably from east Asian admixture.

    If I had to guess on what mtDNA clades are of ANE origin, I would say U4 and U2e(and various U2 clades in south and west Asia). The U5a in Mesolithic east Europe and the Baltic is probably of WHG origin, because most U5 from central Europe's first farmers was U5a, and they lacked ANE ancestry. U4 was also found in one sample from Neolithic Hungary, but still I think it can be associated more with ANE than U5a.

    I wouldn't be suprised if U8(inclu. K), U7, U3, U1, U2, U6, etc. in the Middle east and south Asia are connected to their WHG and ANE-like ancestry. ~38,000 year old Russian K-14, belonged to U2-his own basal clade, and was mostly from an ancestral clade of ANE and WHG. mtDNA U might be the ANE-WHG lineage.

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    Fascinating reconstruction. He looks a bit like a northern European mixed with a central Asian, but much more robust.
    Y-DNA: I1* (Ware, Hertfordshire)
    MT-DNA: U5a1b4 (Boughton Aluph, Kent)
    Father's MT-DNA: J1c8 (Wolverhampton, Staffordshire)
    Grandfather's MT-DNA: H1b (Littlehampton, Sussex)

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    Quote Originally Posted by Anglecynn View Post
    Fascinating reconstruction. He looks a bit like a northern European mixed with a central Asian, but much more robust.
    His skull is very exotic and non-Caucasoid looking to me. Loschbour's reconstruction could pass as someone with a serious tan in Europe today, maybe there are alot of WHG facial features around. today.

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    Maybe someone will do a reconstruction of Stuttgart. It'd be interesting if there are well-persevered skulls from MA-1's people, so we can have an idea what WHG and ANE people looked like. I'm sure there are well persevered skulls from the Neolithic Near east, who can represent "Near eastern" ancestry.

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    I'm defiantly going to put this interesting EHG and Yamna-type mtDNA from Neolithic and Bronze age Siberia into the ancient mtDNA package eventually.

    file:///C:/Users/hp/Downloads/9783110266306.93.pdf

    By glaring at mutations I didn't see any U5a2a, but I did see U2e1b, U5a1a'g, U5a1h, U5a2c3(or U5a2d1), and U5a1d2b.

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    What makes you think that the results from Linatzeta Cave are "likely false"?



    By the way if you are wondering what "CT" means in the case of HV-C14766T, it means that it tested for both alleles C and T, which likely means that the result if contaminated, hence why it is testing for both alleles. Now Linatzeta is spot on indicating HV=>H, granted is only based on a single defining mutation for HV and H, but at the same time the likelihood that this haplogroup isn't H would mean that is a nonH haplogroup which is negative for 12308 and 3197 which define U and U5, is also negative for T, K. So I'm willing to bet that it is an H result, even with the 2 SNPs only. Also this was the only sample that was tested for every single SNPs.

    Holy shit!!! I just realized something, they tested it for the LP-13910 mutation, I missed the damn column, and it was C/C, so the Mesolithic Basque sample was likely lactose intolerant. I can't believe I hadn't notice this before!

    So the one sample from 6000 BC in the Basque country was 13910-C/C, yet in 3000 BC the Southern part of the Basque Country was already showing a good amount of T/T folks. Pre-Beaker site from SJAPL, Southern Alava dating to 3000 BC yields 13/19 C/C, 4/19 T/T, and 2/19 T/C, Longar 2500 BC in Navarra 1/7 T/T and 6/7 C/C.
    Last edited by jeanL; 01-12-2015 at 12:03 AM.

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    Quote Originally Posted by jeanL View Post
    What makes you think that the results from Linatzeta Cave are "likely false"?



    By the way if you are wondering what "CT" means in the case of HV-C14766T, it means that it tested for both alleles C and T, which likely means that the result if contaminated, hence why it is testing for both alleles. Now Linatzeta is spot on indicating HV=>H, granted is only based on a single defining mutation for HV and H, but at the same time the likelihood that this haplogroup isn't H would mean that is a nonH haplogroup which is negative for 12308 and 3197 which define U and U5, is also negative for T, K. So I'm willing to bet that it is an H result, even with the 2 SNPs only. Also this was the only sample that was tested for every single SNPs.

    Holy shit!!! I just realized something, they tested it for the LP-13910 mutation, I missed the damn column, and it was C/C, so the Mesolithic Basque sample was likely lactose intolerant. I can't believe I hadn't notice this before!

    So the one sample from 6000 BC in the Basque country was 13910-C/C, yet in 3000 BC the Southern part of the Basque Country was already showing a good amount of T/T folks. Pre-Beaker site from SJAPL, Southern Alava dating to 3000 BC yields 13/19 C/C, 4/19 T/T, and 2/19 T/C, Longar 2500 BC in Navarra 1/7 T/T and 6/7 C/C.
    I was wondering what LP stood for.

    I think that study has false results because it is totally inconsistent with recent studies and has contradicting calls. Many of those samples are positive for U and H, and whatever else. Close to 40% of the samples from Neolithic Basque and Navarre Spain have R*(xR0, U5, U4, U2, JT, etc.), which is out of the ordinary for any west Eurasian population. There's a streak of L3, N, or M samples from Neolithic and Mesolithic Iberia, and their only similarity is they come from the same old studies.

    There are several shared haplotypes across ages in old studies from Iberia and Ukraine, which were not found in recent studies in the same region.

    In the next few years as Mesolithic genomes and mtDNA come in from Iberia, I bet it'll pretty much all be U and WHG. But I'm ready for a surprise.

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    Quote Originally Posted by Krefter View Post
    I think that study has false results because it is totally inconsistent with recent studies and has contradicting calls. Many of those samples are positive for U and H, and whatever else. Close to 40% of the samples from Neolithic Basque and Navarre Spain have R*(xR0, U5, U4, U2, JT, etc.), which is out of the ordinary for any west Eurasian population. There's a streak of L3, N, or M samples from Neolithic and Mesolithic Iberia, and their only similarity is they come from the same old studies.
    The Linatzeta results do not have contradicting calls. Now one thing to remember is that the mt-DNA haplogroups in Northern Europe in the post-Ice Age period would be but a subset of those in Southern Europe. I'm certain that the Linatzeta results are 100% real, in fact the C/C in the LP-13910 is in line with other WHGs such as Loschbour and La Braña.

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