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Thread: Ancient I-M253 samples list

  1. #331
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    I didn't realize that Allentoft actually mentioned I1 (or even I1a) at all for any of the samples - I couldn't find any reference to I1 or SNPs in either the manuscript, supplementary material or excel files. I had assumed that the labelling of these RISE samples (as well as SF11) as I1 came from the descriptions on the blog by Genetiker and then everyone quoted from there. I do see that there's a barplot which has the colours for I1, I1a on BaSca group in Extended Data Figure 6 near the end of the paper which I hadn't noticed before.

    A couple of other sources have listed these samples: Jean Manco's ancient samples list in the Wayback Machine here https://web.archive.org/web/20170825...zeagedna.shtml lists RISE179 and RISE175 from Allentoft 2015 as I rather than I1 for Y-DNA haplogroup on the Ancient European DNA of the Copper and Bronze Ages list, so I guess she didn't find it conclusive enough to call either of these samples as I1. Also, David Reich's lab at Harvard lists RISE175, RISE179, RISE210 and SF11 as I rather than I1 and doesn't list any haplogroup for RISE207 when I downloaded their dataset in April from here https://reich.hms.harvard.edu/downlo...blished-papers to it seemed that it wasn't definitive enough for them.

    As I've said several times in the forum, I'm against assigning the RISE samples definitively as I1 based on the low number of derived reads, especially when the majority of the positions are only one-read. It's entirely possible that these could have been I1, but for me there's not enough data to be sure. Same with BAB5 - not enough data. SF11 and BAL051 are a bit easier to categorize due to to multiple ancestral reads. The Allentoft 2015 RISE samples and BAB5 could have ancestral reads as well or they could all be derived. My hunch is that these individuals aren't the ancestors of modern I1 population and were essentially extinct lineage offshoots. But there's not really enough evidence to assign definitively one way or another. I am aware of people who label some of these samples as I1 without understanding the subtleties and raw data. I think it's safer to categorize these samples separately. If there's reanalysis of some of these samples, or new samples come to light that make this a bit less muddy, it'll be worth revising. But on current evidence, it's not enough for me.

    I'm still trying to get my head around where Allentoft et al got the I1a designation in Extended Data Figure 6 from. As far as I can tell, none of these samples have any reads (either ancestral or derived) for DF29 or phyloequivalent SNPs (which is how I would define I1a). Of course it's entirely possible that they're using an earlier version of the tree which defines I1a differently. I had a look at the ISOGG tree from 2015 and it looks that I1a is just defined by DF29 alone, although I1 above that is defined my much less SNPs than the current 312 on the YFull tree https://isogg.org/tree/2015/ISOGG_HapgrpI15.html - but may even be using an earlier reference than that - if you go back to 2006 I1 was then I1a and I2 was I1b https://isogg.org/tree/2006/ISOGG_HapgrpI06.html but can't really be that as Allentoft refers to I2. Perhaps I1a assignment comes from a further downstream SNP. I don't know. But analyzing the BAM file from scratch against the current YFull tree... yeah, not so much.

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  3. #332
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    Quote Originally Posted by deadly77 View Post
    I didn't realize that Allentoft actually mentioned I1 (or even I1a) at all for any of the samples - I couldn't find any reference to I1 or SNPs in either the manuscript, supplementary material or excel files. I had assumed that the labelling of these RISE samples (as well as SF11) as I1 came from the descriptions on the blog by Genetiker and then everyone quoted from there. I do see that there's a barplot which has the colours for I1, I1a on BaSca group in Extended Data Figure 6 near the end of the paper which I hadn't noticed before.

    A couple of other sources have listed these samples: Jean Manco's ancient samples list in the Wayback Machine here https://web.archive.org/web/20170825...zeagedna.shtml lists RISE179 and RISE175 from Allentoft 2015 as I rather than I1 for Y-DNA haplogroup on the Ancient European DNA of the Copper and Bronze Ages list, so I guess she didn't find it conclusive enough to call either of these samples as I1. Also, David Reich's lab at Harvard lists RISE175, RISE179, RISE210 and SF11 as I rather than I1 and doesn't list any haplogroup for RISE207 when I downloaded their dataset in April from here https://reich.hms.harvard.edu/downlo...blished-papers to it seemed that it wasn't definitive enough for them.

    As I've said several times in the forum, I'm against assigning the RISE samples definitively as I1 based on the low number of derived reads, especially when the majority of the positions are only one-read. It's entirely possible that these could have been I1, but for me there's not enough data to be sure. Same with BAB5 - not enough data. SF11 and BAL051 are a bit easier to categorize due to to multiple ancestral reads. The Allentoft 2015 RISE samples and BAB5 could have ancestral reads as well or they could all be derived. My hunch is that these individuals aren't the ancestors of modern I1 population and were essentially extinct lineage offshoots. But there's not really enough evidence to assign definitively one way or another. I am aware of people who label some of these samples as I1 without understanding the subtleties and raw data. I think it's safer to categorize these samples separately. If there's reanalysis of some of these samples, or new samples come to light that make this a bit less muddy, it'll be worth revising. But on current evidence, it's not enough for me.

    I'm still trying to get my head around where Allentoft et al got the I1a designation in Extended Data Figure 6 from. As far as I can tell, none of these samples have any reads (either ancestral or derived) for DF29 or phyloequivalent SNPs (which is how I would define I1a). Of course it's entirely possible that they're using an earlier version of the tree which defines I1a differently. I had a look at the ISOGG tree from 2015 and it looks that I1a is just defined by DF29 alone, although I1 above that is defined my much less SNPs than the current 312 on the YFull tree https://isogg.org/tree/2015/ISOGG_HapgrpI15.html - but may even be using an earlier reference than that - if you go back to 2006 I1 was then I1a and I2 was I1b https://isogg.org/tree/2006/ISOGG_HapgrpI06.html but can't really be that as Allentoft refers to I2. Perhaps I1a assignment comes from a further downstream SNP. I don't know. But analyzing the BAM file from scratch against the current YFull tree... yeah, not so much.
    I totally agree, I would rather define as accurately as possible based on the available evidence, assuming it is I1 or otherwise is "risky", a good example of bad calls going too far can be seen in a very recent pre-print from last year.

    In regards to some of the calls I found this through a link while scrolling through one of their supplementary excel files,
    https://genetiker.wordpress.com/2015...asian-genomes/

    Genetiker lists them as I1-FGC2435/Z2698, I1-M450/S109, I1-Z2765/CTS3506, apparently these are phyloequivalents and part of the SNP pool of M253. I would definitely say these are pre-I1, until perhaps a later date when (and if) they are tested again.

    I also found this link through the excel file: https://anthrogenica.com/showthread....ll=1#post89569

    I wonder how Genetiker managed to determine these results.

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  5. #333
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    Yes the biggest mystery of I1-DF29 in particular, is did it originate/assimilate with the Corder Ware or Single Grave groups and "hitched a ride", or did it originate during Nordic BA, or was it hunter gatherers in isolation somewhere in Scandinavia before CW and the Neoliths etc, did it get there with the Funnelbeakers or some kind of Neoliths. That's the most interesting question or mystery at this point which will hopefully be resolved eventually. I'm kinda surprised someone from Scandinavia hasn't tried to tackle this subject yet and lead in the research. I1 makes up around 40% of their Y DNA and it's the most frequent HG in that region, and it probably originated in that region, and experienced some kind of founder effect. Shouldn't some Scandinavian genetics research team try and figure out when, where, how and why? Cultural politics obstructing the curiosity or what?

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  7. #334
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    Quote Originally Posted by spruithean View Post
    I totally agree, I would rather define as accurately as possible based on the available evidence, assuming it is I1 or otherwise is "risky", a good example of bad calls going too far can be seen in a very recent pre-print from last year.

    In regards to some of the calls I found this through a link while scrolling through one of their supplementary excel files,
    https://genetiker.wordpress.com/2015...asian-genomes/

    Genetiker lists them as I1-FGC2435/Z2698, I1-M450/S109, I1-Z2765/CTS3506, apparently these are phyloequivalents and part of the SNP pool of M253. I would definitely say these are pre-I1, until perhaps a later date when (and if) they are tested again.

    I also found this link through the excel file: https://anthrogenica.com/showthread....ll=1#post89569

    I wonder how Genetiker managed to determine these results.
    Yes, that's the way I view it. I'd rather hedge on the side of conservative than "risky" - especially when it's quoted as being I1 as evidence for a theory.

    Cheers for the links. I'd looked at Genetiker's blog quite some time ago but not recently. All the SNPs mentioned are ones I found while doing analysis of the BAM files and listed in the posts on this forum and the map. Genetiker doesn't list the quality of these calls (for example if they're one read). If you look at the comments thread, there's an exchange with Erik Holmund where Genetiker had originally assigned haplogroup I1a3a2 (which is considerably further along than I1) for RISE175 and RISE179 and Erik Holmund asks if he has identified the SNPs BY351 or BY352, by reference to the current ISOGG tree of 2015. Genetiker then changes RISE175 and RISE179 back to I1.

    It seems to me that the way Genetiker views it is that if a sample is positive for any of the I1 SNPs, that sample is haplogroup I1, regardless of the quality of those calls (if they're one read or if they are in regions where the BAM file shows a lot of mutations in the same region), the quantity of derived calls on the I1 group of SNPs, and ignoring if there are disconfirming ancestral SNPs in the I1 block or derived calls for non-I1 haplogroups - as is the case for his analysis of SF11 which Genetiker labels "Stora Förvar 11 belonged to Y haplogroup I1~M253." here https://genetiker.wordpress.com/more...ora-forvar-11/

    So, by that line of thinking, a single positive one read SNP in the I1 block qualifies a sample as I1. And that's the case for RISE207 which has a a derived single call for M450/S109 and no call for all other I1-defining SNPs. Which is why Genetiker has listed this sample as I1-M450/S109 in his list. It seems that the Allentoft et al researchers view this the same way and list RISE207 baSca I1 in that list from the forwarded Anthrogenica forum post of Bernard on that link you shared. And Haak et al. in the BAL051 also use that criteria for I1.

    Conversely, Jean Manco's list, David Reich's dataset, GuČ nther et al. don't go this far with labelling these samples as I1 and are a bit more conservative. I'm closer to that side of things than Genetiker/Allentoft et al/Haak et al. I guess it's a question of taxonomy and classification.

    As for how Genetiker managed to determine these results, to me it seems that he downloads the BAM file and looks up the positions using a BAM viewer. I'm essentially doing the same thing, just with a bit more detail in regard to read quality calls, a more conservative haplogroup classification and without the overt supremacism.

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    I found this in a thread about Haplogroup N and the various associations of it: https://anthrogenica.com/showthread....l=1#post567729

    Definitely seems like Allentoft et al's stuff has gotten around quite a bit with the perhaps confused haplogroup designations.

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    Quote Originally Posted by spruithean View Post

    I1 is really a sort of strange haplogroup in all seriousness, it's somewhat common or dominant in a certain range of Europe, yet it doesn't appear in aDNA as often as R1b, R1a, G, E, etc perhaps due to where these people lived and their funerary practices be that burying their dead in soil that doesn't preserve genetic material or cremating their dead.
    It's quite likely that lack of numbers is the main reason we see no Neolithic or Mesolithic I1 in ancient DNA record before the now visible star-like expansion. For all we know no more than ten men with ancestral I1 were simultaneously alive at any point between 15,000 bp and the metal ages.

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    Quote Originally Posted by Shaikorth View Post
    It's quite likely that lack of numbers is the main reason we see no Neolithic or Mesolithic I1 in ancient DNA record before the now visible star-like expansion. For all we know no more than ten men with ancestral I1 were simultaneously alive at any point between 15,000 bp and the metal ages.
    I agree that the most reasonable cause is low numbers. We can however definitely say there were almost positively more than 10 living at any given time. There may have been bottlenecks down to a handful of men but the per generation male/female birth rate + survival to reproductive age would have wiped them out. It's got to be a combination of low numbers and, for instance, location. It's not out of the question that they were a localized minority HG among cultures we know of either.

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    Quote Originally Posted by xenus View Post
    I agree that the most reasonable cause is low numbers. We can however definitely say there were almost positively more than 10 living at any given time. There may have been bottlenecks down to a handful of men but the per generation male/female birth rate + survival to reproductive age would have wiped them out. It's got to be a combination of low numbers and, for instance, location. It's not out of the question that they were a localized minority HG among cultures we know of either.
    I'm not saying this literally happened but statistically we don't need a population size greater than 1 at a certain point in post-Mesolithic past to explain the modern I1 frequencies. Many modern lineages could have been hanging by a thread for a long time before some fortunate event caused a star-like expansion.

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    I found this thread when searching for information about the origin of I1. At that time I knew about the Hungarian and Iberian finds (BAB5 and BAL0051) and also knew that there were a few finds from the Nordic bronze age. So there were at least a few traces of I1 to keep in mind when thinking about its origin. But now I have learned that all these finds are dubious. So now I know even less than I knew before I came here. The mystery deepens.

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    It's not that they are necessarily dubious, it's more that approaching the samples with caution and being rather conservative with the haplogroup calls is the safest bet. BAL051, SF11, BAB5 and the Nordic Bronze Age samples are all important pieces to the history of I1 (for all we know those Nordic Bronze Age I1's may very well be actual legitimate I1, a few people seem to think so). With a MRCA of 4600 ybp the Bronze Age or Late Neolithic is when the haplogroup expanded, but before that there could have been several "I1-esque" lineages roaming about. YFull has a formed date of 27500 ybp, so that's an early split from I-M170, and a lot of time between then and when the first modern I1 lineage appeared.

    Of course most of our ancient modern I1 is in the Migration/Medieval period, so that's at least something, but also kind of expected.

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