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Thread: I-A12974 Branch

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    I-A12974 Branch

    Iíve been intrigued by the new(ish) I-A12974 branch close to the root of I-L338 for a couple of reasons Ė personally because this may be where I split away from the rest of the I-L338 folks and procedurally because it flies rather close to SNPs that we may consider unreliable for Y-DNA phylogeny.

    YFull installed this new branch I-A12974 as a transition between I-L338 and two already established downstream branches I-Y33691 and I-Y12329 and this change to their phylogenetic tree first appeared in YTree version 7.08.01 (archived 21 October 2019) https://www.yfull.com/arch-7.08/tree/I1/ and remained on the YFull tree for the subsequent three versions of the tree, including the current version. Tracking back to version 7.07 of the YFull tree, archived 9 Sep 2019, I-A12974 doesnít appear and I-Y33691 and I-Y12329 are directly downstream of I-L338 along with I-Y15155 and I-S12289 https://www.yfull.com/arch-7.07/tree/I1/
    YFull tree v7.08.pngYFull tree v7.07.png

    Over on the FTDNA public haplotree, they have also recently installed A12974 as a transition branch at the same position, representing several of the kits that are on downstream branches at YFull (which FTDNA has labelled I-A2006 and I-S24090) as well as a few more that are not and from the country report, thereís one kit that is I-A12974 but not belonging to either of the two downstream branches. https://www.familytreedna.com/public...;name=I-A12974 Iím not sure when FTDNA installed this branch on their haplotree, as unlike YFull they donít seem to list archived versions. However, I donít think I-A12974 was on there in December.
    FTDNA Haplotree I-A12974.pngFTDNA Country Report I-A12974.png
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    FTDNA also lists FGC74335 as a phyloequivalent SNP to A12974. This grabbed my attention as FGC74335 was first reported in my own YElite test as one of my novel SNPs. However, FGC74335 is located at ChrY position (Hg38): 5457635, which is in the X-Y homologue region of Yp11.2. YFull tagged FGC74335 as homologous >95% (low confidence) among my novel SNPs when my results were first analyzed, but has since removed FGC74335 from my list of novel SNPs. YSEQ flagged FGC74335 as not recommended when Wish a SNP was ordered, stating 98.1% similar to chromosome X + 92343012 92344014. I’ve seen YSEQ reject several SNPs in this region, and YFull doesn’t appear to add them to their tree, although FTDNA have several examples on their haplotree.

    Looking up FGC74335 in the Groups view at YFull, I can see that most people in I-Z140 have the ancestral allele A or the position is not read (most likely Big Y Y500 kits). The only ones that show the derived allele G are my own two kits (YElite and WGS) and YF66605 on the I-Y33691 branch. For the others on that branch the position is not read as these are previous Big Y Y500 kits and the upgraded Y700 kits that are on the public YFull tree have not joined the I1-Z140 group at YFull. All three I-A8673 kits are Big Y Y500 with no read for this position. On the I-Y12663 branch, YF01814 is a Big Y Y500 kit that upgraded to Y700 or another test for the same individual, which is YF67369. FGC74335 is not read in the Y500 but is in the other test. However, the result is showing as ambiguous, with YFull reporting nucleotide “R”, which IUPAC uses to refer to A or G.
    Groups view Z140 tree position FGC74335.png
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    Back to A12974 – when I received my YElite results in the excel spreadsheet mapped to hg19, A12974 was listed as one of my derived novel SNPs, but then when the WGS results came in shortly after, the BAM file showed that the result for A12974 was ambiguous with 18A (ancestral) and 27T (derived). After Full Genomes realigned to hg38, I received the hg38 BAM file and that also shows ambiguous call for A12974, although this time with 31A and 22T. Going back to the Groups view at YFull, most people in the I-Z140 project are showing the ancestral allele A. Under I-L338 (xS12289), two of the I-Y15155 kits are negative with A, while all of the I-Y12329 kits that I can see are positive (T), except YF01814 which has no reading (although upgraded kit YF67369 does). For the kits that I can see on the I-Y33691 branch, YF09616 and YF07607 are ambiguous for A12974, although upgraded kit YF66605 for the latter individual shows positive (T) for A12974. Can’t see the results for YF65004 (upgraded kit for YF09616) or YF66752 as these kits haven’t joined I1-Z140 YFull group, but these may be positive for A12974 as well.
    Groups view Z140 tree position A12974.png
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    A12974 is located at ChrY position (Hg38): 10125784, which puts it pretty close to the centromere. A12974 won’t be available for Sanger single SNP testing at YSEQ because it falls in this region chrY:10072350..11686750. In recent years we’ve seen FTDNA use SNPs in regions that are highly identical such DYZ19, centromere, X-Y homologue region of Yp11.2, inside STRs, palindromes, etc. and in some cases YFull will tend to use these SNPs for branching, but less regularly and not for age estimation. YSEQ on the other hand tends to not recommend SNPs from these highly identical regions – I’ve seen Thomas Krahn say a few times that he doesn’t consider such SNPs reliable for Y-line phylogeny, given that there’s a higher probability of false mapping and that they’re prone to recombination events. And even if such a SNP has been inherited for several generations, there’s no guarantee that it won’t undergo recombination events in a future or parallel generation. Thomas has a presentation here https://www.yseq.net/images/2014-08_...THXOSoOraD2qB4 – it’s from a few years ago, but worth a view.

    Note that his presentation says that highly identical regions are not necessarily bad data, but require a bit more caution. Maybe in the future we can make better judgement calls with better human genome reference or long read technology. There’s an article discussing sequencing the Y chromosome centromere here https://www.theatlantic.com/science/...encing/556034/ using nanopore sequencing which references this paper in Nature Biotechnology https://www.nature.com/articles/nbt.4109

    I had a go at looking up A12974 on YBrowse, zooming out to 1kbp, downloading the decorated FASTA file and pasting into UCSC BLAT against hg38 reference. Came up with this – if I’m reading this correctly, sequence is 94.7% similar to a sequence on chromosome 20.
    BLAT 10125284 to 1012683.png
    I’d be interested to hear what others think about this – is this a real branch that’s phylogenetically consistent, or is it fool’s gold? It’s not really necessary for either the I-Y33691 branch or the I-Y12329 branch as they have several more SNPs that describe their Y line phylogeny downstream of I-L338 without including A12974 or FGC74335. Although it does move them closer to each other (and possibly myself) than the I-Y15155/A1944 or I-S12289 branch. It doesn’t affect anything in genealogical records since it’s over 2500 years ago for all concerned and we all have a common ancestor at I-L338 anyway. So worth considering or overthinking something that may not be reliable?
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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    Quote Originally Posted by deadly77 View Post
    A12974 is located at ChrY position (Hg38): 10125784, which puts it pretty close to the centromere. A12974 won’t be available for Sanger single SNP testing at YSEQ because it falls in this region chrY:10072350..11686750. In recent years we’ve seen FTDNA use SNPs in regions that are highly identical such DYZ19, centromere, X-Y homologue region of Yp11.2, inside STRs, palindromes, etc. and in some cases YFull will tend to use these SNPs for branching, but less regularly and not for age estimation. YSEQ on the other hand tends to not recommend SNPs from these highly identical regions – I’ve seen Thomas Krahn say a few times that he doesn’t consider such SNPs reliable for Y-line phylogeny, given that there’s a higher probability of false mapping and that they’re prone to recombination events. And even if such a SNP has been inherited for several generations, there’s no guarantee that it won’t undergo recombination events in a future or parallel generation. Thomas has a presentation here https://www.yseq.net/images/2014-08_...THXOSoOraD2qB4 – it’s from a few years ago, but worth a view.

    Note that his presentation says that highly identical regions are not necessarily bad data, but require a bit more caution. Maybe in the future we can make better judgement calls with better human genome reference or long read technology. There’s an article discussing sequencing the Y chromosome centromere here https://www.theatlantic.com/science/...encing/556034/ using nanopore sequencing which references this paper in Nature Biotechnology https://www.nature.com/articles/nbt.4109

    I had a go at looking up A12974 on YBrowse, zooming out to 1kbp, downloading the decorated FASTA file and pasting into UCSC BLAT against hg38 reference. Came up with this – if I’m reading this correctly, sequence is 94.7% similar to a sequence on chromosome 20.
    BLAT 10125284 to 1012683.png
    I’d be interested to hear what others think about this – is this a real branch that’s phylogenetically consistent, or is it fool’s gold? It’s not really necessary for either the I-Y33691 branch or the I-Y12329 branch as they have several more SNPs that describe their Y line phylogeny downstream of I-L338 without including A12974 or FGC74335. Although it does move them closer to each other (and possibly myself) than the I-Y15155/A1944 or I-S12289 branch. It doesn’t affect anything in genealogical records since it’s over 2500 years ago for all concerned and we all have a common ancestor at I-L338 anyway. So worth considering or overthinking something that may not be reliable?
    I would definitely post a pointer to this thread on a wider FTDNA post on the forum to make sure you get the necessary expertise. My only useful comment is that I take frequent screenshots from YFull, which has enabled me to chart the TMRCA changes on the S12289 branch. The last change there was in the past few weeks. Good luck because it looks to me that you're learning something about your own L338 line.
    Living DNA's former Cautious mode:
    Wales-related ancestry: 86.8%
    Cornwall: 8%
    North England-related ancestry: 5.2%
    Y line: Peak District, England. Big Y match: Scania, Sweden; TMRCA 1,280 ybp (YFull);
    mtDNA: traces to Glamorgan, Wales
    Mother's Y: traces to Llanvair Discoed, Wales

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    I lack the scientific acumen to give you a helpful answer; however, here is my opinion regarding the matter. At this moment in time with the minimal amount of folks in the databases I’m satisfied with just focusing on “reliable” SNPs that are found on both the Ftdna and YFull Haplotrees for phylogeny and age estimates. In the future as more men test and more patrilineal differentiation will be necessary I’ll delve deeper at said time into these “questionable” SNPs. I don’t really care about questionable SNPs that are millennia old because in terms of what I want to know there is not much diffference between a common patrilineal ancestor from 500 BC or a “questionable” common patrilineal ancestor from 420 BC.
    I would find these “questionable” SNPs to be more worthwhile similar to Y-111 STRs when you want fine detailed patrilineal differentiation within a genealogical timeframe when paper trails are incomplete.
    I1 (3200 BC - 2000 BC) Battle Axe Culture >
    DF29 > Z58 > Z59 > Z2041 > Z2040 >
    Z382 (1800 BC - 900 BC) Nordic Bronze Age >
    S26361 > S16414 > FGC24354 >
    FGC24357 (500 BC - 300 AD) Nordic Iron Age >
    FGC24356 > S10350 > FGC75802 >
    Y125947 LŁbeck, Germany >
    S21197 Ireland, Netherlands > BY149414 Scotland >
    BY188003 (1544 AD - 1875 AD) >
    BY188570 (Jean Wauthy 1908 AD) Belgium

    YFull id: YF15884

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    I would imagine that sometime in the future we may be able to use those SNPs in a more reliable fashion. Although, for the time being, I’m inclined to listen to Thomas Krahn and generally disregard them. Coincidentally, my match received his results yesterday and of the 12 Novel Variants we match (11 @ FT), two of them are in the centromeric region. So I’ve been wondering how to consider them. Mostly, I’ve been ignoring them but not always. Perhaps, as Deadly said, they’re useful for branching but not for dating. Hopefully, he’ll send his results to YFull and we can let them figure it out.


    Edit: After reading the article in the Atlantic, maybe the future is closer than I thought. Let’s hope!
    Last edited by JMcB; 01-23-2020 at 10:40 PM.
    Paper Trail: 43.8% English, 29.7% Scottish, 12.5% Irish, 6.25% German, 6.25% Italian & 1.5% French. Or: 86% British Isles, 6.25% German, 6.25% Italian & 1.5% French.
    LDNA: 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).
    BigY 700: I1-Z140 >I-F2642 >Y1966 >Y3649 >A13241 >Y3647 >A13248 (circa 620 AD) >A13242/YSEQ (circa 765 AD) >FT80854 (circa 1650 AD).

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    Quote Originally Posted by JonikW View Post
    I would definitely post a pointer to this thread on a wider FTDNA post on the forum to make sure you get the necessary expertise. My only useful comment is that I take frequent screenshots from YFull, which has enabled me to chart the TMRCA changes on the S12289 branch. The last change there was in the past few weeks. Good luck because it looks to me that you're learning something about your own L338 line.
    That's a good point as it's clearly not a scenario that's exclusive to I1. I have taken screenshots of my YFull pages over time - there are a few things that have been added or removed since the initial results unlocked, some changes stick around, some changes go away. It's good to see that some things are dynamic and being updated. Good value for a one-off fee for analysis.

    There were a few interesting things going on with the "Hg and SNPs" tab and the "Age Estimation" tab recently - wish I had taken some of those screenshots. You probably see similar in your results - under "+ known SNPs" for the "Age Estimation" tab, some of the SNPs were being counted 2 times but assigned to I-YSC261 and I-L338 with a weight attached to each - for example DF77/S1969 assigned to I-L338 level with a weight of 0.846 and the same SNP assigned to the I-YSC261 level with a weight of 0.154. This says to me that they're not completely sure level these SNPs should be on since everyone who is I-YSC261 is I-L338. I guess we won't know for sure unless someone breaks up the block of phylogenetic SNPs. On the "Hg and SNPs" tab, most of them are listed as "level I-L338 <-> I-YSC261"

    I also have a private SNP that's not novel because it appears on the YFull tree as a recurrent SNP in haplogroup O. YFull was flipping that between my kit number and I-A12974 with a weight assigned to each, but the I-A12974 level has now dropped out of that. Should have taken some screenshots of that before it changed.
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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    Quote Originally Posted by mwauthy View Post
    I lack the scientific acumen to give you a helpful answer; however, here is my opinion regarding the matter. At this moment in time with the minimal amount of folks in the databases I’m satisfied with just focusing on “reliable” SNPs that are found on both the Ftdna and YFull Haplotrees for phylogeny and age estimates. In the future as more men test and more patrilineal differentiation will be necessary I’ll delve deeper at said time into these “questionable” SNPs. I don’t really care about questionable SNPs that are millennia old because in terms of what I want to know there is not much diffference between a common patrilineal ancestor from 500 BC or a “questionable” common patrilineal ancestor from 420 BC.
    I would find these “questionable” SNPs to be more worthwhile similar to Y-111 STRs when you want fine detailed patrilineal differentiation within a genealogical timeframe when paper trails are incomplete.
    This is largely where I am with these, and very much agree with the strategy of concentrating on the reliable SNP candidates first and then looking at the more questionable ones later that Thomas Krahn outlined in the presentation linked in #4. And for sure, A12974 and FGC74335 don't have any recent genealogical influence. The I-Y33691 folks have between 17 and 20 SNPs on the YFull tree that are suitable for age estimation (plus several more on the YFull tree) that track their descent from I-L338 while I have 17 different ones in the same category so we can chart our divergence from each other without including A12974 or FGC74335 as a stepping stone. Although I must admit that I'm interested if this I-A12974 is reliable in a phylogenetic sense in terms of the architecture of the tree. More curious than practical for genealogy and it may be chasing ghosts that may not be real.
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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    Quote Originally Posted by JMcB View Post
    I would imagine that sometime in the future we may be able to use those SNPs in a more reliable fashion. Although, for the time being, I’m inclined to listen to Thomas Krahn and generally disregard them. Coincidentally, my match received his results yesterday and of the 12 Novel Variants we match (11 @ FT), two of them are in the centromeric region. So I’ve been wondering how to consider them. Mostly, I’ve been ignoring them but not always. Perhaps, as Deadly said, they’re useful for branching but not for dating. Hopefully, he’ll send his results to YFull and we can let them figure it out.


    Edit: After reading the article in the Atlantic, maybe the future is closer than I thought. Let’s hope!
    Indeed, there's an element of opinion on whether these type of SNPs are reliable or not. FTDNA and YSEQ are easiest to predict as it seems (at least to me) FTDNA are using all that are found as long as the positives/negatives are consistent across branches in their own database and YSEQ have set their red lines in a more conservative approach. I agree with you that I lean a bit closer to the YSEQ view, as Thomas Krahn explains his reasoning but I haven't yet seen similar from anyone associated with FTDNA. It's the others (YFull, FGC, Alex Williamson's Big Tree, etc.) that are a bit harder to predict because I'm not sure what their accept/reject criteria are. For example, I can understand why YFull aren't including FGC74335 on their tree due to homology with the X chromosome. But I'm not sure why they use A12974 and give it four stars out of five in their rating. Figured best was to send them an email and ask them, so will see if they respond.

    Yes, I thought that was an interesting article in the Atlantic - an easier read than the Nature Communications paper itself, which I haven't had a full go at yet. Better references sequences are probably what we'll be able to apply to our own data in the future. Long read will involve a extra NGS test but the price is a bit rich for me currently. As well as the more difficult regions, can see it being better for the longer INDELs and STRs which we're probably not using as much as we could due to the limitations of current technology, not to mention an even more limited pool to compare with.
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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