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Thread: Ancient I-M253 samples list

  1. #821
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    Quote Originally Posted by Strider99 View Post
    Hello. This may be a dumb question, but I was wondering, which sample in Mittnik et al 2019 was assigned to I1? I looked through the supplementary materials but I could not find the I1 sample. I know there's a Mittnik et al 2018 as well, could I have been looking at the wrong study? This is the one I searched in: https://science.sciencemag.org/conte...6/731.abstract
    Lech_EBA OBKR_117_d was the sample. It isn’t I-L258, it’s I(xI1).

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  3. #822
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    Quote Originally Posted by Strider99 View Post
    Hello. This may be a dumb question, but I was wondering, which sample in Mittnik et al 2019 was assigned to I1? I looked through the supplementary materials but I could not find the I1 sample. I know there's a Mittnik et al 2018 as well, could I have been looking at the wrong study? This is the one I searched in: https://science.sciencemag.org/conte...6/731.abstract
    To be clear, the authors of that paper didn't assign that sample to I1 - rather to I - see supplementary table S1. Someone ran the raw data through an automated extraction tool, saw that that sample (OBKR 117) had a positive result for L258 which is downstream of I1, assigned the sample as I1 on that basis. Later on, Generalissimo posted (see post #519 on page 52 much further up in the thread) that this sample was negative for multiple SNPs on the I1 level and so the L258 result isn't phylogenetically consistent with that. Also positive for S294 which is downstream of I2, so those two positive results can't both be correct. The L258 result is a one read SNP and likely a false positive or a recurrent SNP. This shows why it's important to check for phylogenetic inconsistencies, especially in ancient DNA where there are more no calls and low read depth, either by assay or DNA damage post mortem (or both).
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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    Ftdna Haplotree now has I-L758 + 31 SNPs > I-M170 + 178 SNPs > I-Z2699 + 38 SNPs > I-M253 + 268 SNPs. There doesn’t appear to be anyone in the Ftdna database as I-L758* or I-Z2699* so I’m assuming these Haplotree changes are based on academic samples?

    My question is which samples were used to make these Haplotree changes and what kind of overall Y chromosome coverage did they have?
    I-DF29: ool009 Skane, Sweden 1930-1750 BCE

    Z58, Z59, Z2041, Z2040, Z382, FGC24333

    S26361: VK532 Zealand, Denmark 200-375 CE

    S16414, FGC24354, FGC24357, FGC24356, S10350

    FGC75802/BY19383: VK446 Funen, Denmark 800-1050 CE

    Y125947, S21197, BY149414, BY188003, BY188570

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    Quote Originally Posted by mwauthy View Post
    Ftdna Haplotree now has I-L758 + 31 SNPs > I-M170 + 178 SNPs > I-Z2699 + 38 SNPs > I-M253 + 268 SNPs. There doesn’t appear to be anyone in the Ftdna database as I-L758* or I-Z2699* so I’m assuming these Haplotree changes are based on academic samples?

    My question is which samples were used to make these Haplotree changes and what kind of overall Y chromosome coverage did they have?
    Yeah, this is splitting up I, so "pre-I". This probably comes from three pre-I samples (two monozygotic twins, samples I2483 and I2484, and another infant KremsWA3) that Pribislav mentioned in the Ancient DNA Discussion thread here https://anthrogenica.com/showthread....l=1#post719076
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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    Quote Originally Posted by deadly77 View Post
    Yeah, this is splitting up I, so "pre-I". This probably comes from three pre-I samples (two monozygotic twins, samples I2483 and I2484, and another infant KremsWA3) that Pribislav mentioned in the Ancient DNA Discussion thread here https://anthrogenica.com/showthread....l=1#post719076

    Thanks. That explains I-L758 + 31 SNPs being “pre-I.”

    I wonder which sample was “pre-I1” with I-Z2699 + 38 SNPs?
    I-DF29: ool009 Skane, Sweden 1930-1750 BCE

    Z58, Z59, Z2041, Z2040, Z382, FGC24333

    S26361: VK532 Zealand, Denmark 200-375 CE

    S16414, FGC24354, FGC24357, FGC24356, S10350

    FGC75802/BY19383: VK446 Funen, Denmark 800-1050 CE

    Y125947, S21197, BY149414, BY188003, BY188570

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    Quote Originally Posted by mwauthy View Post
    Thanks. That explains I-L758 + 31 SNPs being “pre-I.”

    I wonder which sample was “pre-I1” with I-Z2699 + 38 SNPs?
    That would be SNPs that the pre-I1 samples SF11 (10 SNPs) , BAL051 (13 SNPs) and Car1 (19 SNPs) are positive for, which would be 42 although there are some duplicates where the same SNP is found in more than one sample (eg. Z2699 is 2C for BAL051 and 1C for Car1) and some of FTDNA's I1 SNPs may not be on the YFull tree, which I used as reference when I went through the BAM files.

    Not sure if this is really appropriate - it implies that the relationship between these pre-I1 samples is closer than they are in that they form a clade by themselves, while in reality they might be disparate lines with a common ancestor much further back. The large number of no calls make it more difficult to confidently call that. BAL051 is ancestral for FGC2433 while SF11 is derived for FGC2433 while that SNP is included in the phylogenetic block. YSC0000301 is listed in the phylogenetic block but only observed in SF11 sample and not in Car1 or BAL051.
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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    The way the haplotree is set up, it can also give the impression that the pre-I1 samples on the I-Z2699 branch are ancestors of the main I1 branch, which I think is misleading as they are more likely to be a side branch - ie, not ancestors of the later I1 but sharing a common ancestor further back. Richard Miller made this graphic a while ago which demonstrates the idea of branches (lines) that died off betterthan text. I1 age estimation.jpg

    Although with the coverage of these three samples, many of the I1 SNPs are no call - these no calls account for more than 80% of the I1 SNPs in each of these samples, which would give us a clearer picture of when these samples branched away from the main I1 branch. What would be really interesting would be if FTDNA could find derived SNPs in these samples that no modern I1 was positive for. That would establish divergence, but with the low coverage many of such SNPs would be one-read SNPs and assigning these with any confidence versus one read false positives would be a bit risky.
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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    Thanks for the clarifications, guys. Much appreciated! God bless.

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    Hi, I was wondering something about the sample oll009 from Malmström 2019. He was dated to 1930-1750 BC. Is he Battle Axe or just Late Neolithic, culturally speaking? I noticed that in Deadly77's I1 list on Google Drive (great and informative compilation btw), he's marked as "LNBA".

    His tomb that had previously been a Funnelbeaker passage tomb was destroyed converted to a stone cist during the LN. Inside it they found both Funnelbeaker artefacts, Battle Axe artefacts and more typical Late Neolithic artefacts like a bronze disc and a flint dagger.

    Which material culture would you say oll009 is the most associated with? His Y-DNA is I1 but the guys buried next to him were R1a, right? Additionally, he's not like Funnelbeakers autosomally, but instead about 50% Yamnaya. Is he just broadly Late Neolithic Scandinavian, or was he a Battle Axe man?

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    Quote Originally Posted by Strider99 View Post
    Hi, I was wondering something about the sample oll009 from Malmström 2019. He was dated to 1930-1750 BC. Is he Battle Axe or just Late Neolithic, culturally speaking? I noticed that in Deadly77's I1 list on Google Drive (great and informative compilation btw), he's marked as "LNBA".

    His tomb that had previously been a Funnelbeaker passage tomb was destroyed converted to a stone cist during the LN. Inside it they found both Funnelbeaker artefacts, Battle Axe artefacts and more typical Late Neolithic artefacts like a bronze disc and a flint dagger.

    Which material culture would you say oll009 is the most associated with? His Y-DNA is I1 but the guys buried next to him were R1a, right? Additionally, he's not like Funnelbeakers autosomally, but instead about 50% Yamnaya. Is he just broadly Late Neolithic Scandinavian, or was he a Battle Axe man?
    Glad you like the I1 map. I had a look at the map and I don't see "LNBA" listed, so not sure why you say he's marked as "LNBA" - perhaps that's from another site?

    oll009 was Scandinavian Late Neolithic, based on the radiocarbon dating. From the items found at the site at Ölljsö, it looks like this burial site was used and reused by successive cultures over several time periods from Funnelbeaker to Battle Axe to late Neolithic, hence the variety of grave goods. The supplementary material says that at least 14 different individuals were buried at this site, although only three appear to have been DNA sequenced. The paper had oll009 and oll010 as Scandanavian Late Neolithic and oll007 (dated quite a bit earlier - between a few hundred and a thousand years older) to Battle Axe. So none of these three samples were funnelbeaker culture, although the site itself is characterized as such. Perhaps we would see more from funnelbeaker, etc. from this site if more of those had been sequenced

    No, the "guys" buried next to oll009 were not R1a - at least among those that were sequenced. oll007 and oll010 were female, and thus don't have a Y-DNA haplogroup. The two R1a samples listed in the paper were from different sites - ber1 was from Bergsgraven, Östergötland, Sweden and poz81 was from Obłaczkowo, Wielkopolska, Poland. Both of these samples are between a few hundred to a thousand years older than oll009.
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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