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Thread: Ancient I-M253 samples list

  1. #281
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    Or it could be nothing because there is no real Y-DNA in this sample. If you look at Table 1 in the paper, Ble008 has the most coverage out of all the samples, more than three times the coverage of Ble007, but Ble007 has 2.65 times more Yseq than Ble008. Also, comparing the ratios of Yseq to Xseq across the samples, the ratio of Y:X for Ble004 and Ble008 is pretty low compared to Ble007.

    I've loaded up the BAM files of all three samples from this paper into IGV and checking them for I1 SNPs. A third of the way through and there is zero evidence for Y-DNA haplogroup I1 in any of these three samples. So far, Ble 007 has a lot more calls in Y chromsome than Ble008 or Ble004. All of the positions where there is a read are ancestral for I1 so far.

    I also took a look into the X chromosome of Ble008's BAM file - a lot of positions were visually heterozygous which to me indicates that there are two X chromosomes.

    I'd say Ble008 and Ble004 are female and the Y-DNA calls are probably homologous with X chromosome or autosomes. Ble007 is male but not haplogroup I1 (or even pre-I1 so far).

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  3. #282
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    I figured as much, the study even mentions possibilities of contamination and the items they are testing are extremely old.
    Y-DNA: I-A14097(Scotland),
    Big Y: I-F2642>Y1966>Y3649>A13241>Y3647>A14097 (1,850 YBP)
    mtDNA: pending (Westeremden, Netherlands)
    Other lines:
    R-M222 x2, R-L21 x2, I-M223, R-S1141, R-U198 & R-U106, mtHg J1c3
    Known ancestry
    Paternal: Britain & Ireland, France and Germany
    Maternal: Netherlands

  4. #283
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    Quote Originally Posted by deadly77 View Post
    I was having a chat with forum member Celt_?? and he asked me if I knew of any Google Maps with the locations ancient Hg I locations. He shared a link to one that Rocca had prepared for ancient R1b-U152. It looked like a pretty nice way to summarize the data, so I thought I'd have a go at putting one together for the ancient I1 samples that we've discussed in this thread.

    Try this out and see if the link works: https://www.google.com/maps/d/viewer...4350000038&z=3

    If you click on one of the pins on the map or the name in the left-hand menu, should pop up with more information. I've put together a brief summary of the context, selected Y-DNA SNP calls, reference to the relevant publication and if appropriate a link to the YFull tree for four of the sampls.

    Please let me know if you find mistakes, information that is missing, etc. There's also a few options for colour coding, icons, etc. that I haven't incorporated yet. I included the pre I1 samples - I'll probably colour code them different. Not sure if it's better to colour code by different subclades or time period. I'm thinking the latter may be a better option given that some of them the subclade assignment is limited by the design of the sequencing or the quality of the ancient sample, but I'm open to suggestions.

    I'm seeing this map just now , how behind am I...

    Very nice work! I also like the skull and crossbones for lineages we are sure died out and the question marks for the presumably pre-I1 lineages. I've been pondering the exact path that the (pre-I1?) I1 haplogroup took in Europe, obviously they've found various pre-I1 lineages from Scandinavia, Iberia and Hungary so that's a large spread. How exactly did I1 end up in northern Europe? Did it come up through a mixing of Linear Pottery Culture with what was to become Funnelbeaker and then from there at some point it was firmly rooted in Scandinavia? Or are the pre-I1's found in Central Europe and Iberia both extinct branches and some lineage of pre-I1 eventually produced I1-M253 in Scandinavia?

    I guess for now it's just hypotheticals and a lot of head scratching. For now I suppose I1 folk should be pleased with what has been found so far, at least there is a decent amount of I1-M253 in Migration Period and the Medieval era!
    Y-DNA: I-A14097(Scotland),
    Big Y: I-F2642>Y1966>Y3649>A13241>Y3647>A14097 (1,850 YBP)
    mtDNA: pending (Westeremden, Netherlands)
    Other lines:
    R-M222 x2, R-L21 x2, I-M223, R-S1141, R-U198 & R-U106, mtHg J1c3
    Known ancestry
    Paternal: Britain & Ireland, France and Germany
    Maternal: Netherlands

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  6. #284
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    Quote Originally Posted by spruithean View Post
    I'm seeing this map just now , how behind am I...

    Very nice work! I also like the skull and crossbones for lineages we are sure died out and the question marks for the presumably pre-I1 lineages. I've been pondering the exact path that the (pre-I1?) I1 haplogroup took in Europe, obviously they've found various pre-I1 lineages from Scandinavia, Iberia and Hungary so that's a large spread. How exactly did I1 end up in northern Europe? Did it come up through a mixing of Linear Pottery Culture with what was to become Funnelbeaker and then from there at some point it was firmly rooted in Scandinavia? Or are the pre-I1's found in Central Europe and Iberia both extinct branches and some lineage of pre-I1 eventually produced I1-M253 in Scandinavia?

    I guess for now it's just hypotheticals and a lot of head scratching. For now I suppose I1 folk should be pleased with what has been found so far, at least there is a decent amount of I1-M253 in Migration Period and the Medieval era!
    Cheers - the map is definitely a work in progress. I was trying to keep organized with an excel spreadsheet, but it was getting a bit messy. Celt?? shared a link to Rocca's ancient R1b-U152 map which is a really nice piece of work and I thought this might be a better way to organize the I1 samples that we know about and get them into some kind of format before the hoped for avalanche of ancient I1 samples to be sequenced in the future (hoping here, rather than believing, but oh well...) One thing I like is being able to look at the map data as a whole and then click on individual samples and get a lot more detail just on that sample. I found the spreadsheet was a bit difficult to isolate the data of one sample without being a little overwhelmed.

    I went for the skull and crossbones for the ancient samples that were before the estimated TMRCA of modern I1 and had confirmed ancestral reads among the I1 SNPs, and I went for question marks with the ones which don't have ancestral I1 SNPs but have less than 15% of the relevant I1 SNPs with derived read. Things may change if we get more definition or branching between the break off from I and the TMRCA of I1. Not everyone agrees with me - I had some negative feedback regarding this map in a Facebook group. But I made the map for my own records and organization. If other folks find it useful, great. Regardless, I'm not the police of who is I1 and who is not I1.

    As to whether the pre-I1 samples contributed as ancestor to the I1 TMRCA line or not, I think it's too difficult to say. The large number of no calls among the I1 SNPs for these samples adds a lot of uncertainty. I think we'd have a better idea if we had a greater percentage of those SNPs called and we had more examples in total. That way we'd have a greater consistency over the order of the mutations and that may allow us to define some samples as extinct lineages. My hunch is that BAL051, BAB5, SF11 are not direct ancestors of I1 TMRCA, but right now, not enough data to say for sure.

    But yeah, I think that the pre-I1 lineages were more geographically spread than just Scandinavia. I think there will be more found in other locations around Europe. I think it's possible that there were more than one mini-bottleneck that didn't make it to the I1 TMRCA. My own feeling is that during the migration of R1b into and through Europe, the Y lineage that became I1 became incorporated among those people and his Y descendants "hitched a ride" with that group, despite much more diverse earlier origins that aren't with that group. I'd say that's why the population expansion from the TMRCA (which doesn't neccesarily need to be in Scandinavia) into diverse descendant subclades occurs around the same time. I think thats also why we don't find I1 ancient samples in isolation in the majority of the locations that we have data for - almost always found with R-U106 in particular. But again, the small number of ancient I1 samples means that it's difficult to draw any meaningful conclusions with confidence. Again, not enough data. We have what we have for now, hopefully we have more samples with better sequencing in the future.

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  8. #285
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    Quote Originally Posted by deadly77 View Post
    Cheers - the map is definitely a work in progress. I was trying to keep organized with an excel spreadsheet, but it was getting a bit messy. Celt?? shared a link to Rocca's ancient R1b-U152 map which is a really nice piece of work and I thought this might be a better way to organize the I1 samples that we know about and get them into some kind of format before the hoped for avalanche of ancient I1 samples to be sequenced in the future (hoping here, rather than believing, but oh well...) One thing I like is being able to look at the map data as a whole and then click on individual samples and get a lot more detail just on that sample. I found the spreadsheet was a bit difficult to isolate the data of one sample without being a little overwhelmed.
    I certainly agree that it makes it much easier to get a visual representation of the distribution of the ancient samples so far. Charts with data are good when just pure data is needed, but some of us like that visual for sure. It definitely looks like if we get more and more samples it will be easier to track via the map.

    I went for the skull and crossbones for the ancient samples that were before the estimated TMRCA of modern I1 and had confirmed ancestral reads among the I1 SNPs, and I went for question marks with the ones which don't have ancestral I1 SNPs but have less than 15% of the relevant I1 SNPs with derived read. Things may change if we get more definition or branching between the break off from I and the TMRCA of I1. Not everyone agrees with me - I had some negative feedback regarding this map in a Facebook group. But I made the map for my own records and organization. If other folks find it useful, great. Regardless, I'm not the police of who is I1 and who is not I1.
    Ah, ok I see. I certainly agree with the choice to define the pre-TMRCA ancient I1 as pre-I1 or label them with question marks or skulls. I1 by definition to me is the haplogroup with 309 defining mutations and a rather young TMRCA, so everything prior to that can't literally be I1.

    As to whether the pre-I1 samples contributed as ancestor to the I1 TMRCA line or not, I think it's too difficult to say. The large number of no calls among the I1 SNPs for these samples adds a lot of uncertainty. I think we'd have a better idea if we had a greater percentage of those SNPs called and we had more examples in total. That way we'd have a greater consistency over the order of the mutations and that may allow us to define some samples as extinct lineages. My hunch is that BAL051, BAB5, SF11 are not direct ancestors of I1 TMRCA, but right now, not enough data to say for sure.
    I don't think we may ever be sure whether those lineages are ancestral to modern I1, we don't even have any idea what the chronological order is for the SNPs that are phyloequivalent for M253. I'm also not sure we'll ever know considering soil in Scandinavia can be rather destructive to genetic material (same goes for parts of Britain, notably the new Saxon Tomb). I have seen the current I1 origin theory via Eupedia and some various comments on Eurogenes and elsewhere that it is believed I1 or pre-I1 was present in Mesolithic Central Europeans with the LBK culture which eventually led into the Funnelbeakers and Corded Ware and the eventual rise of Nordic Bronze Age and Germanic cultural development. However, I don't think we have enough to make assumptions yet.

    But yeah, I think that the pre-I1 lineages were more geographically spread than just Scandinavia. I think there will be more found in other locations around Europe. I think it's possible that there were more than one mini-bottleneck that didn't make it to the I1 TMRCA. My own feeling is that during the migration of R1b into and through Europe, the Y lineage that became I1 became incorporated among those people and his Y descendants "hitched a ride" with that group, despite much more diverse earlier origins that aren't with that group. I'd say that's why the population expansion from the TMRCA (which doesn't neccesarily need to be in Scandinavia) into diverse descendant subclades occurs around the same time. I think thats also why we don't find I1 ancient samples in isolation in the majority of the locations that we have data for - almost always found with R-U106 in particular. But again, the small number of ancient I1 samples means that it's difficult to draw any meaningful conclusions with confidence. Again, not enough data. We have what we have for now, hopefully we have more samples with better sequencing in the future.
    That is actually quite reasonable and it would explain some of the diversity, distribution and the non-isolated finds. A hitched ride with the R1b folk would make sense indeed!

    Admittedly I'm pretty chuffed to share a paternal lineage to some degree with some of those recent aDNA finds (Avar-era Hungarian, Conqueror-era Hungarian, Longobards, Icelanders, Baiuvarii, etc). It's definitely not something I'd anticipated back in the early genetic genealogy days, that's for sure.
    Y-DNA: I-A14097(Scotland),
    Big Y: I-F2642>Y1966>Y3649>A13241>Y3647>A14097 (1,850 YBP)
    mtDNA: pending (Westeremden, Netherlands)
    Other lines:
    R-M222 x2, R-L21 x2, I-M223, R-S1141, R-U198 & R-U106, mtHg J1c3
    Known ancestry
    Paternal: Britain & Ireland, France and Germany
    Maternal: Netherlands

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  10. #286
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    Quote Originally Posted by deadly77 View Post
    Or it could be nothing because there is no real Y-DNA in this sample. If you look at Table 1 in the paper, Ble008 has the most coverage out of all the samples, more than three times the coverage of Ble007, but Ble007 has 2.65 times more Yseq than Ble008. Also, comparing the ratios of Yseq to Xseq across the samples, the ratio of Y:X for Ble004 and Ble008 is pretty low compared to Ble007.

    I've loaded up the BAM files of all three samples from this paper into IGV and checking them for I1 SNPs. A third of the way through and there is zero evidence for Y-DNA haplogroup I1 in any of these three samples. So far, Ble 007 has a lot more calls in Y chromsome than Ble008 or Ble004. All of the positions where there is a read are ancestral for I1 so far.

    I also took a look into the X chromosome of Ble008's BAM file - a lot of positions were visually heterozygous which to me indicates that there are two X chromosomes.

    I'd say Ble008 and Ble004 are female and the Y-DNA calls are probably homologous with X chromosome or autosomes. Ble007 is male but not haplogroup I1 (or even pre-I1 so far).
    Regarding No3423 I-DF29. The Anglo Saxon cemetery at Norton North East England was not christian. It was dated from at least the mid sixth century, and was pagan, with associated grave goods.

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    Quote Originally Posted by Paul333 View Post
    Regarding No3423 I-DF29. The Anglo Saxon cemetery at Norton North East England was not christian. It was dated from at least the mid sixth century, and was pagan, with associated grave goods.
    Was it really a pagan burial? Should we really consider it an Anglo-Saxon then? Would it possibly be a Viking burial then?

    Here is part of the supplementary data for the burial:

    1.3 Norton on Tees
    Two Anglo-Saxon cemeteries were excavated in the village of Norton, Teesside, north east England. They
    were located 200m apart and one of these, Norton East Mill, dated to the pagan Anglo*Saxon period
    (550*-650AD), while the adjacent cemetery, Norton Bishopsmill, dates to 650*-910AD and was Christian.
    The pagan cemetery contained 120 burials, many of which were furnished with grave goods, while the
    Christian burial ground contained the unfurnished burials of 100 skeletons. Analysis of the skeletal
    remains has revealed differences in the age and sex distributions as well as the pathology at the two sites
    47,48
    I seem to remember NO3423 being from Bishopsmill.
    Last edited by spruithean; Today at 12:42 AM.
    Y-DNA: I-A14097(Scotland),
    Big Y: I-F2642>Y1966>Y3649>A13241>Y3647>A14097 (1,850 YBP)
    mtDNA: pending (Westeremden, Netherlands)
    Other lines:
    R-M222 x2, R-L21 x2, I-M223, R-S1141, R-U198 & R-U106, mtHg J1c3
    Known ancestry
    Paternal: Britain & Ireland, France and Germany
    Maternal: Netherlands

  12. #288
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    Quote Originally Posted by spruithean View Post
    Was it really a pagan burial? Should we really consider it an Anglo-Saxon then? Would it possibly be a Viking burial then?

    Here is part of the supplementary data for the burial:



    I seem to remember NO3423 being from Bishopsmill.
    I agree. I'm sure he was from the Christian period from what we read at the time.
    Living DNA Cautious mode:
    South Wales Border-related ancestry: 86.8%
    Cornwall: 8%
    Cumbria-related ancestry: 5.2%
    Y line: Peak District, England. Big Y match: Scania, Sweden; TMRCA 1,280 ybp (YFull);
    mtDNA: traces to Glamorgan, Wales, 18th century. Mother's Y line (Wales): R-L21 L371

  13. #289
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    Quote Originally Posted by Paul333 View Post
    Regarding No3423 I-DF29. The Anglo Saxon cemetery at Norton North East England was not christian. It was dated from at least the mid sixth century, and was pagan, with associated grave goods.

    Quote Originally Posted by spruithean View Post
    I seem to remember NO3423 being from Bishopsmill.

    Quote Originally Posted by JonikW View Post
    I agree. I'm sure he was from the Christian period from what we read at the time.

    Norton Bishopsmill, dates to 650–910 AD and was a Christian Anglo-Saxon cemetery excavated in the village of Norton, Teesside, northeast England 14. We sampled 3 individuals from burials of 100 skeletons and selected the best preserved, NO3423, for the present study (Supplementary Notes 1 and 2 and Supplementary Fig. 1).

    https://www.ncbi.nlm.nih.gov/pmc/art...comms10326.pdf
    Last edited by JMcB; Today at 03:43 AM.
    Known Paper Trail: 45.3% English, 29.7% Scottish, 12.5% Irish, 6.25% German & 6.25% Italian. Or: 87.5% British Isles, 6.25% German & 6.25% Italian.
    LivingDNA: 88.1% British Isles (59.7% English, 27% Scottish & 1.3% Irish), 5.9% Europe South (Aegian 3.4%, Tuscany 1.3%, Sardinia 1.1%), 4.4% Europe NW (Scandinavia) & 1.6% Europe East, (Mordovia).
    FT Big Y: I1-Z140 branch I-F2642 >Y1966 >Y3649 >A13241 >Y3647 >A13248 (circa 930 AD) >A13242/YSEQ (circa 1075 AD) >A13243/YSEQ (circa 1660 AD).

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