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Thread: Recent radiation within R-M269 led to high Y-STR haplotype resemblance

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    Recent radiation within R-M269 led to high Y-STR haplotype resemblance

    Maarten H. D. Larmuseau et al., Recent Radiation within Y-chromosomal Haplogroup R-M269 Resulted in High Y-STR Haplotype Resemblance, Annals of Human Genetics, Volume 78, Issue 2, pages 92–103, March 2014

    http://onlinelibrary.wiley.com/doi/1...12050/abstract

    Y-chromosomal short tandem repeats (Y-STRs) are often used in addition to Y-chromosomal single-nucleotide polymorphisms (Y-SNP) to detect subtle patterns in a population genetic structure. There are, however, indications for Y-STR haplotype resemblance across different subhaplogroups within haplogroup R1b1b2 (R-M269) which may lead to erosion in the observation of the population genetic pattern. Hence the question arises whether Y-STR haplotypes are still informative beyond high-resolution Y-SNP genotyping for population genetic studies. To address this question, we genotyped the Y chromosomes of more than 1000 males originating from the West-European regions of Flanders (Belgium), North-Brabant and Limburg (the Netherlands) at the highest resolution of the current Y-SNP tree together with 38 commonly used Y-STRs. We observed high resemblance of Y-STR haplotypes between males belonging to different subhaplogroups of haplogroup R-M269. Several subhaplogroups within R-M269 could not be distinguished from each other based on differences in Y-STR haplotype variation. The most likely hypothesis to explain this similarity of Y-STR haplotypes within the population of R-M269 members is a recent radiation where various subhaplogroups originated within a relatively short time period. We conclude that high-resolution Y-SNP typing rather than Y-STR typing might be more useful to study population genetic patterns in (Western) Europe.

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    This is contradicted by the difference between the Most Recent Common Ancestor calculated by STRs and by SNPs. It is true that we are yet discussing about the time to assign to a single SNP (3-4 generations or 8-10?), but many samples of aDNA found in Europe (hgs. G and E above all) let us think that the STRs time should have been multiplied for a 2.5 factor.
    Perhaps you know that I, from many years, tried to explain this fact by my 3 or 4 golden principles:
    mutations happened around the modal
    there is a convergence to the modal as time passes
    only sometime a mutation goes for the tangent
    rarely there are multistep mutations.
    Last edited by Rathna; 02-25-2014 at 08:00 AM.

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    If they're only typing STRs using the standard forensic 17-marker Y-Filer set, then yes, they won't find much if any to differentiate between sub-clades with any degree of confidence. Maximizing STRs (i.e. 111 markers) in tandem with high-resolution Y-SNP typing would be preferred, but then theirs may be a cost-based conclusion.

    More data will always be better.

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    Quote Originally Posted by VinceT View Post
    If they're only typing STRs using the standard forensic 17-marker Y-Filer set, then yes, they won't find much if any to differentiate between sub-clades with any degree of confidence. Maximizing STRs (i.e. 111 markers) in tandem with high-resolution Y-SNP typing would be preferred, but then theirs may be a cost-based conclusion.

    More data will always be better.
    The study deals directly with "subtle patterns in a population genetic structure" and I don't think that even 111 markers are good for that if the only choice is between those and high-resolution Y-SNP genotyping, especially if cost is considered. 111 STR markers won't always tell us that a person definitely belongs to a subclade. Only Y-SNP testing can tell us that. 111 STR markers are better for more recent ancestry, 20 generations, not "subtle patterns in a population genetic structure"

    You can see which STR markers and which SNP markers the authors used by going to http://onlinelibrary.wiley.com/doi/1...12050/suppinfo and by downloading the supporting info at http://onlinelibrary.wiley.com/store...x?v=1&5545d1bb

    Dienekes also has an image with the SNP markers at http://1.bp.blogspot.com/-E1MMnc_de-.../larmuseau.png

    It makes me very happy to see that they included P312 and Z195 which have been missing from many previous studies but is very common in Western Europe.

    On October 18, 2008 Dienekes posted Why Y-STR haplotype clusters are not clades which brought this problem to my attention back then. http://dienekes.blogspot.com/2008/10...s-are-not.html Recently Mike Walsh has posted spreadsheets to try and help R1b people determine their subclade based on STR markers and others have been posting modals in Ysearch. So far I have found it is best to just get people to order SNP tests even if they have a 37 or 67 marker match with another person because the STR markers seem to vary too much. That doesn't mean that at some point there won't be an easy match of 67 STR markers with a specific SNP but in the meantime the the consumer both need to be used and for "subtle patterns in a population genetic structure" high-resolution Y-SNP genotyping should be used.

    edit: I want to state that I applaud what Mike Walsh has done with the spreadsheet and anyone that has posted a modal in Ysearch. They have been helpful in determining what can and can't be done with STR markers.
    Last edited by ArmandoR1b; 02-25-2014 at 01:16 PM.

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    Their median joining network diagram shows just how meaningless STRs are at such high level to trace deep ancestry. Most of the relationships are between samples that, from an SNP perspective, we know have little to do with one another.

    IMO, even 111 STRs are insufficient to rectify these discrepancies with an acceptable level of confidence. The 600 STRs that FGC offers are nice, but when one has a full list of SNPs, STRs become superfluous.
    Paternal: R1b-U152 >> L2 >> FGC10543 >> PR5365, Pietro Rocca, b. 1559, Agira, Sicily, Italy
    Maternal: H4a1-T152C!, Maria Coto, b. ~1864, Galicia, Spain
    Mother's Paternal: J1+ FGC4745/FGC4766+ PF5019+, Gerardo Caprio, b. 1879, Caposele, Avellino, Campania, Italy
    Father's Maternal: T2b-C150T, Francisca Santa Cruz, b.1916, Garganchon, Burgos, Spain
    Paternal Great (x3) Grandfather: R1b-U106 >> L48 >> CTS2509, Filippo Ensabella, b.~1836, Agira, Sicily, Italy

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    For a moment there I thought we had been subject to some sort of solar radiation :0)

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    Its nice to have another paper concluding this although STR wizards like Ken N realised this many years ago and the vast majority in this hobby came to a broad consensus that this was the case several years ago. I wonder if they had a stab at dating this 'radiation' of M269. One of the interesting things in SNP counting dating by Michal and others is that M269 seems to have existed for a considerable time before it expanded and left clades that survive today.

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    Its not really my area of knowledge but I tend to get the same impression that STRs have taken things as far as they could in terms of new knowledge and the future looks like its going to be SNP based. Still, we owe a big debt to all those people in this hobby who have done so much amazing work using STRs to take their use to the maximum, untangle the human story and keep us all interested over the years.

    Quote Originally Posted by Richard A. Rocca View Post
    Their median joining network diagram shows just how meaningless STRs are at such high level to trace deep ancestry. Most of the relationships are between samples that, from an SNP perspective, we know have little to do with one another.

    IMO, even 111 STRs are insufficient to rectify these discrepancies with an acceptable level of confidence. The 600 STRs that FGC offers are nice, but when one has a full list of SNPs, STRs become superfluous.

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    Quote Originally Posted by Rathna View Post
    This is contradicted by the difference between the Most Recent Common Ancestor calculated by STRs and by SNPs. It is true that we are yet discussing about the time to assign to a single SNP (3-4 generations or 8-10?), but many samples of aDNA found in Europe (hgs. G and E above all) let us think that the STRs time should have been multiplied for a 2.5 factor.
    Perhaps you know that I, from many years, tried to explain this fact by my 3 or 4 golden principles:
    mutations happened around the modal
    there is a convergence to the modal as time passes
    only sometime a mutation goes for the tangent
    rarely there are multistep mutations.
    you left one out

    mutations happened with geographical change


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    Quote Originally Posted by vettor View Post
    you left one out

    mutations happened with geographical change
    It is possible, but I don't know any serious study that investigated this by a scientific point of view. I think we should add that it seems that mutations are more frequent with the age of the father, and surely there are haplotypes (or haplogroups) which mutate faster or slower than others.
    But all this makes STRs to be used with care. The same happened in the mtDNA, in fact usually mutations are calculated on average, but we should add also the number of meioses: a rare haplotype mutates slower than a more diffused one, and where it is rare there are more possibilities it goes extinct, and where it is more diffused that only a few lines survive, and the few survived ones cumulate many SNPs (and STRs variance) in the knots.

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