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Thread: Ancient I-M253 samples list

  1. #601
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    I should have all the samples sorted by subclade in this ancient I1-M253 spreadsheet. If anyone notice mistakes in SNP assignments, or samples missing from the spreadsheet, feel free to post it here.

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  3. #602
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    Quote Originally Posted by Pribislav View Post
    I should have all the samples sorted by subclade in this ancient I1-M253 spreadsheet. If anyone notice mistakes in SNP assignments, or samples missing from the spreadsheet, feel free to post it here.
    Nice work Pribislav - I have a few on my map that aren't on your spreadsheet, but they are low data ones. Birger Magnusson and his son Erik entombed at Varnhem Abbey - it's an earlier paper and the researchers only tested one SNP (M253) relevant to I1. But that's the same level of testing to BAB5, which is on the spreadsheet. On that note, I had listed BAB5 and the RISE samples from the Allentoft 2015 paper as pre-I1/I* - there's no ancestral I1-level SNPs as for SF11, BAL051, Car1 but I think if more were tested on BAB5 it would fall into that category given the date. The paucity of data in the RISE samples means it's difficult to say either way, so I've decided to be more conservative in their classification.

    The samples urm035 and urm045 from the Sigtuna paper weren't assigned a haplogroup in the manuscript. On going through the BAM files, the samples are low coverage with lots of no calls, but I'm satisfied that they cover enough derived reads for the I1 level SNPs. For subclades, urm035, picked up DF29 1G, Z2892 / CTS9848 1G as well as an ancestral call for Z2893 1G; urm045 had Z2893 1A, Z2892 / CTS9848 1G, Z61 1T. They're one-read SNPs, but given the low coverage, I think that might be as far as it goes for these two.

    The other ones are AE 1154 in Altenerding-Klettham and there are seven I1 samples from a skeleton collective from 4th - 5th centuries in the village of Görzig - although all of these are from a small number of STRs - no SNPs tested, so it's up to you if you include them.

    I hadn't included the ME_7 or KO_55 samples as I'm yet to find a reliable source for the data. Do you have anything?

    Regarding US14, the "colonist" found at Shohola Creek, Indian Cabin Ridge, Pennsylvania, I noticed that there were a couple of mentions of Z73 in some tables in that paper, but I haven't been able to verify that in the BAM file. I found US14 was no call for Z73 and the phyloequivalent SNPs at I-Z73: Z73, FGC8675, CTS743, L1301, CTS12940, FGC8671, Z2896, Y2926, Z2899, Z2901, FGC8668, FGC8669, S2137, V1812, V3142 and also upstream levels with no calls for CTS9352, CTS9477, Z2895, CTS7362, Z2903, FGC8667, Z60, Z61, CTS8647, Z62, Z59, Z58. Only downstream SNP I found was a one read for DF29+, but I'm satisfied that he's I1 with derived reads for 29 of the 312 SNPs on the I1 level. But I couldn't find anything that verified US14 as I-Z73. Could you check the BAM file and see if I missed anything?
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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  5. #603
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    I see deadly77 has finally disappeared from my list of 100 YFull SNP matches today. Good to see more S12289 testers, who have brought this about, but sad to see him go. Sadly only a couple of the new testers have the flags that I always enjoy for what they can potentially add to the picture of ancient movements.
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    Quote Originally Posted by JonikW View Post
    I see deadly77 has finally disappeared from my list of 100 YFull SNP matches today. Good to see more S12289 testers, who have brought this about, but sad to see him go. Sadly only a couple of the new testers have the flags that I always enjoy for what they can potentially add to the picture of ancient movements.
    Aha, but you're still on my list of SNP matches at YFull, JonikW. I guess that's because I have less close matches.

    You could always send your matches without the flags a message by clicking on the envelope icon next to their YFull ID and ask them if they would consider adding a flag.

    Interesting things going on at the base of I-L338. YFull appear to have grouped two of the L338+/S12289- subclades together with a new branch point at I-A12974. It seem a bit of an odd choice. In the groups view, 3 of the kits below I-Y12329 are listed positive (all though not all with read quality 100) with one n/a, while the two kits at I-Y33691 have ambiguous reads for the SNP A12974. In my own results, the SNP A12974 is ambiguous (18A, 27T). ChrY position (Hg38):10125784 would put it in the centromere as YSEQ defines it (and so wouldn't be available in their catalogue for Sanger sequencing). Five of my SNPs on the "Hg and SNPs" tab are listed at the I-A12974* level are listed but four of them are one star. "Age estimation" tab also has some of the SNPs listed more than once but weighted between I-L338 and I-YSC261 level or between I-A12974 and my kit number. Perhaps YFull aren't yet sure of some of the placements and things at this level will change in the future.
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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  9. #605
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    There's two main methods of ancient DNA analysis - "shotgun" sequencing which is similar in principle to a WGS or the "SNP Capture" enrichment assay approach, most commonly the 1240K SNP capture assay used by the Reich group and others. There's advantages and disadvantages to both approaches - we discussed a bit earlier in this thread around post #379 and there's a good discussion of merits and drawbacks of each in Kivisild's 2017 review in Human Genetics here https://link.springer.com/article/10...439-017-1773-z which is worth a read.

    Bringing it up again as Wing Genealogist very kindly extracted the Y-SNPs that are included in the design of the assay - see post here https://anthrogenica.com/showthread....l=1#post612520 and spreadsheet here https://docs.google.com/spreadsheets...it?usp=sharing

    I volunteered to identify I1 SNPs to the spreadsheet, since I have them in hg19 position, and I was also curious how extensive the 1240k SNP capture assay was at covering the I1 SNPs.

    Of the 312 phyloequivalent SNPs at the I1 branch (before subclades), the 1240k SNP capture covers 149 of those (48%) - that's a lot more than I thought having looked at several ancient I1 samples where 1240k SNP capture was used. DNA damage/fragmentation was likely a bigger factor than SNP capture assay.

    At I-DF29 level, 3 SNPs (DF29/S438, Z2891/V1614, Z2891/V1614) are covered, while other three are not, so that's 50%.

    Of the three main I-DF29 downstream branches, I-Z58 and I-Z63 are covered by their single SNP (no phyloequivalent SNPs on those branches) while for I-Z2336, Z2336/CTS6364 is covered while phyloequivalents Y2592 and Y2593 are not.

    I'm not going to go through all 2123 subclades and 7555 SNPs that are on the YFull tree, but I can take a look if anyone's especially interested in anything in particular. Or you can take a look on Wing Genealogist's spreadsheet if you know hg19 position for the SNP of interest. I would guess that more lately discovered SNPs and subclades are less likely to be in the 1240k SNP capture assay.

    General takeaway is that there's more than enough I1 SNPs in the 1240k SNP capture assay to identify ancient remains as at least I1. Lack of calls in several samples that we know about are probably more due to damage to the sample in the centuries or millenia post-mortem, how it's been stored (temperature, acidic soil, etc.) than the assay. 1240k SNP capture may be less good at covering downstream branches.
    Last edited by deadly77; 11-27-2019 at 12:27 PM. Reason: DNA damage/fragmentation was likely a bigger factor than SNP capture assay. sentence was incomplete
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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  11. #606
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    Quote Originally Posted by deadly77 View Post
    There's two main methods of ancient DNA analysis - "shotgun" sequencing which is similar in principle to a WGS or the "SNP Capture" enrichment assay approach, most commonly the 1240K SNP capture assay used by the Reich group and others. There's advantages and disadvantages to both approaches - we discussed a bit earlier in this thread around post #379 and there's a good discussion of merits and drawbacks of each in Kivisild's 2017 review in Human Genetics here https://link.springer.com/article/10...439-017-1773-z which is worth a read.

    Bringing it up again as Wing Genealogist very kindly extracted the Y-SNPs that are included in the design of the assay - see post here https://anthrogenica.com/showthread....l=1#post612520 and spreadsheet here https://docs.google.com/spreadsheets...it?usp=sharing

    I volunteered to identify I1 SNPs to the spreadsheet, since I have them in hg19 position, and I was also curious how extensive the 1240k SNP capture assay was at covering the I1 SNPs.

    Of the 312 phyloequivalent SNPs at the I1 branch (before subclades), the 1240k SNP capture covers 149 of those (48%) - that's a lot more than I thought having looked at several ancient I1 samples where 1240k SNP capture was used. DNA damage/fragmentation was likely a bigger factor than SNP capture assay.

    At I-DF29 level, 3 SNPs (DF29/S438, Z2891/V1614, Z2891/V1614) are covered, while other three are not, so that's 50%.

    Of the three main I-DF29 downstream branches, I-Z58 and I-Z63 are covered by their single SNP (no phyloequivalent SNPs on those branches) while for I-Z2336, Z2336/CTS6364 is covered while phyloequivalents Y2592 and Y2593 are not.

    I'm not going to go through all 2123 subclades and 7555 SNPs that are on the YFull tree, but I can take a look if anyone's especially interested in anything in particular. Or you can take a look on Wing Genealogist's spreadsheet if you know hg19 position for the SNP of interest. I would guess that more lately discovered SNPs and subclades are less likely to be in the 1240k SNP capture assay.

    General takeaway is that there's more than enough I1 SNPs in the 1240k SNP capture assay to identify ancient remains as at least I1. Lack of calls in several samples that we know about are probably more due to damage to the sample in the centuries or millenia post-mortem, how it's been stored (temperature, acidic soil, etc.) than the assay. 1240k SNP capture may be less good at covering downstream branches.

    Thanks for the info! Going forward the two SNPs I care most about identifying in ancient I1 are:

    I-Z382 (Nordic Bronze Age)
    Hg 19: 3680849 : G to C

    I-FGC24357 (Nordic Iron Age)
    Hg 19: 17709753: G to A
    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 for the info! Going forward the two SNPs I care most about identifying in ancient I1 are:

    I-Z382 (Nordic Bronze Age)
    Hg 19: 3680849 : G to C

    I-FGC24357 (Nordic Iron Age)
    Hg 19: 17709753: G to A
    Z382 is covered in the 1240k SNP capture assay. Phyloequivalent SNPs Y2171/FGC24330 and Z2037 at the I-Z382 level are not covered. FGC24357 is not covered.

    Not that this guarantees that Z382 would definitely be read in a 1240k SNP capture assay for an ancient sample. But there's a better chance of having a result here.
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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    Quote Originally Posted by deadly77 View Post
    Z382 is covered in the 1240k SNP capture assay. Phyloequivalent SNPs Y2171/FGC24330 and Z2037 at the I-Z382 level are not covered. FGC24357 is not covered.

    Not that this guarantees that Z382 would definitely be read in a 1240k SNP capture assay for an ancient sample. But there's a better chance of having a result here.

    Thanks! There were two ancient I1 samples in the Viking Paper that tested positive for I-Z2040 which is the parent clade of I-Z382 . When the data is eventually released for those samples hopefully we will get confirmation for I-Z382 which is missing from the Isogg Haplotree.
    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! There were two ancient I1 samples in the Viking Paper that tested positive for I-Z2040 which is the parent clade of I-Z382 . When the data is eventually released for those samples hopefully we will get confirmation for I-Z382 which is missing from the Isogg Haplotree.
    Ah - this won't apply to the VK samples from the Viking preprint as the researchers from that paper used shotgun sequencing rather than the 1240k SNP capture assay.

    Huh, didn't realize that Z382 wasn't on the ISOGG tree. I'm not sure what the procedure for getting SNPs on the ISOGG tree involves. There should be enough evidence from several samples to have Z382 added to ISOGG tree. Ybrowse lists 30 derived reads by Sanger sequencing and there must be enough Big Y that are derived for this SNP. That is, unless there is some other reason why ISOGG did not accept this SNP. Perhaps contact the ISOGG administrator and ask them.

    But yes, we'll have a better idea when the BAM files become available. Even if Z382 is no call, there may be reads for phyloequivalent or downstream SNPs that would provide information by proxy.
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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    I've been working with Hunter Provyn to get some of the ancient I1 samples into his Phylogeographer tool. The tool uses the YFull tree as it's main data source, but you can see the supplemental ancient samples here https://phylogeographer.com/ancient-samples-map/ with a filter for haplogroup (rough filter for now).

    So far, updated the locations for the five I1samples on the YFull tree, then added additional samples for SSJ-A2, SSG-A3, DAV-A9 (Iceland); 84005, urm035, urm045 (Sigtuna); NO3423 (Anglo-Saxon); AED249, STR486 (Bavaria); CL63 (Collegno); R110, R1286 (Rome).

    For the pre-I1 samples BAL051, SF11, Car1, RISE175, RISE179, RISE210, BAB5 we're trying a slightly different approach - we've added these samples as haplogroup I and also included the positive and negative I1 SNPs into the dataset and then adjust the algorithm to account for that so that such samples don't pull the origin point of I1 as much as they were before. The tool doesn't yet support the logic for splitting clades by positives and negative SNPs, but going to give this a try and see how it works going forward.

    Not added to Phylogeographer.com: SzO/540 and K2/26 from Hungarian conqueror paper, STR241 from Bavaria or US14 from Pennsylvania as they are all pretty low coverage. And US14 would likely throw the geographical skew a bit as well. Likewise Birger Magnusson and his son Erik entombed at Varnhem Abbey where they only tested M253. Also didn't include AE 1154, E864/I or the samples from the skeleton collective from 4th - 5th centuries in the village of Görzig as those were STR data only with no SNPs.

    Also not included yet: the VK samples from the Population genomics of the Viking World preprint. Since we don't have the BAM files for these samples yet, the actual subclade may change after review and I'd rather not add all of these samples twice (since there are a lot of them).
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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