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Thread: SNP Tracker

  1. #1
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    Iowa, USA
    Ethnicity
    English-Irish
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    United States of America
    Y-DNA
    R1B - BY31340
    mtDNA
    H1b1-T16362C

    SNP Tracker

    Greetings -

    I am curious as to where SNP Tracker: http://scaledinnovation.com/gg/snpTracker.html
    Obtains the data for SNP Placement. My terminal haplogroup is BY31340 and we all come from the same family line.
    None of us have data to indicate a match in Flanders which is where it places us on the map.

    Any ideas? The FAQ seems to indicate FTDNA but we are all in the Hadley Surname project and there are no other matches on YFull or Yree.
    Last edited by hadleyro; 05-08-2019 at 10:06 PM.

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     Cascio (05-14-2019)

  3. #2
    Junior Member
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    Iowa, USA
    Ethnicity
    English-Irish
    Nationality
    United States of America
    Y-DNA
    R1B - BY31340
    mtDNA
    H1b1-T16362C


  4. #3
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    The "Discussion" tab covers where they're supposedly from, answer is mostly from FTDNA and very few hand-curated locations from academic sources. The site looks like a Phylogeographer/Mygrations clone though, just with smoother and more visual appeal. The modern locations are LOT less exact, at least mine is pretty far off, and there's no zoom to see where they exactly go anyway. I don't understand how exactly Phylogeographer works now, it seems you have to pay to provide your ancestral location for it, which seems like it would have pretty much stopped contributions to Phylogeographer. Before that I think at least some of the project files with locations were publicly available?

  5. #4
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    Greetings -- I'm the author of SNP Tracker. Yes, the locations are based on user-reported paternal nationality plus ~150 ancient SNPs pinned to literature locations. I'm very well aware of the dilemma of such a tool: show people an approximation and cite all of the caveats, or show nothing? I decided on the former and have tried to clean up the data -- but it's not easy. In hadleyro's case, the reason for placement is that his terminal SNP ancestry almost exactly matches the massive bulk Anglo-Irish bias in FTDNA kits. One of the several things I do to try to improve the locations is to normalize away much of that bias, but in a case like hadleyro that means that the final location is really just bouncing around on the subtractive noise. Basically there's just not enough information available to do much better. Put 400 km circles around every dot and squint and you'll get a better view.

  6. The Following 7 Users Say Thank You to rkenobi For This Useful Post:

     deadly77 (05-14-2019),  digital_noise (05-14-2019),  emmental (05-14-2019),  JMcB (05-16-2019),  Theconqueror (05-15-2019),  Trelvern (05-16-2019),  vettor (05-14-2019)

  7. #5
    Registered Users
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    Australia
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    Italian Alpine
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    Australian and Italian
    Y-DNA
    T1a2b- Z19945 - Jura
    mtDNA
    H95a1 - Pannoni

    Australia Italy Veneto Friuli Italy Trentino Alto Adige Austria Tirol Germany Palatinate
    Quote Originally Posted by rkenobi View Post
    Greetings -- I'm the author of SNP Tracker. Yes, the locations are based on user-reported paternal nationality plus ~150 ancient SNPs pinned to literature locations. I'm very well aware of the dilemma of such a tool: show people an approximation and cite all of the caveats, or show nothing? I decided on the former and have tried to clean up the data -- but it's not easy. In hadleyro's case, the reason for placement is that his terminal SNP ancestry almost exactly matches the massive bulk Anglo-Irish bias in FTDNA kits. One of the several things I do to try to improve the locations is to normalize away much of that bias, but in a case like hadleyro that means that the final location is really just bouncing around on the subtractive noise. Basically there's just not enough information available to do much better. Put 400 km circles around every dot and squint and you'll get a better view.
    Are you also involved with ISOGG ?

    European = 99.2%......Central Asian = 0.8% ....Yfull - 1460BC, Jura caves
    Father's Mtdna .........T2b17
    Grandfather's Mtdna .......T1a1e
    Sons Mtdna .......K1a4o
    Maternal Grandfather paternal......I1d-P109...CTS6009
    Maternal side Grandfather .......R-S8172
    Wife's Ydna .....R1a-Z282

    My Path = ( K-M9+, TL-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS54+, CTS8862+, Z19945+, Y70078+ )

  8. #6
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    Nope, though I've asked. From what I can see, ISOGG is pretty moribund.

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     JMcB (05-16-2019)

  10. #7
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    Quote Originally Posted by rkenobi View Post
    Greetings -- I'm the author of SNP Tracker. Yes, the locations are based on user-reported paternal nationality plus ~150 ancient SNPs pinned to literature locations. I'm very well aware of the dilemma of such a tool: show people an approximation and cite all of the caveats, or show nothing? I decided on the former and have tried to clean up the data -- but it's not easy. In hadleyro's case, the reason for placement is that his terminal SNP ancestry almost exactly matches the massive bulk Anglo-Irish bias in FTDNA kits. One of the several things I do to try to improve the locations is to normalize away much of that bias, but in a case like hadleyro that means that the final location is really just bouncing around on the subtractive noise. Basically there's just not enough information available to do much better. Put 400 km circles around every dot and squint and you'll get a better view.
    I've considered writing a somewhat similar tool for some time to give myself an excuse to try out some data visualization libraries. Pretty sure there's a 50% chance that if I did I'd organize the samples and finish my pipeline to import everything into my database but spend so much time curating the data that I wouldn't have time to spend on the dataviz presentation aspects that motivated me in the first place.

    Have you tried improving location by using any sort of criteria for weighting ancient samples?

  11. #8
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    As the documentation says, about 120 ancient SNPs have specific pinned locations based on my reading of the literature and some educated guesses. SNPs in between such pinned SNPs are linearly interpolated by time, which is equivalent to an assumption of constant-travel-velocity. As long we we're earlier than horse domestication ~5000 ybp, that's reasonable (the grand average over 19,000 SNPs is about 0.2 km/year).

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     vettor (05-16-2019)

  13. #9
    Registered Users
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    Location
    Australia
    Ethnicity
    Italian Alpine
    Nationality
    Australian and Italian
    Y-DNA
    T1a2b- Z19945 - Jura
    mtDNA
    H95a1 - Pannoni

    Australia Italy Veneto Friuli Italy Trentino Alto Adige Austria Tirol Germany Palatinate
    Quote Originally Posted by rkenobi View Post
    As the documentation says, about 120 ancient SNPs have specific pinned locations based on my reading of the literature and some educated guesses. SNPs in between such pinned SNPs are linearly interpolated by time, which is equivalent to an assumption of constant-travel-velocity. As long we we're earlier than horse domestication ~5000 ybp, that's reasonable (the grand average over 19,000 SNPs is about 0.2 km/year).
    I see your program also runs mtdna ................not sure if many know about this

    anyway I have no issue with my mtdna being in the eastern alps as it matches other programs/sites .............i do have 50% of my mtdna in south sweden and gotland as well ,
    would this mean that these swedes came from the eastern alps?
    I have found one ( of the 5 ) which was born in 1930 and died in sweden


    European = 99.2%......Central Asian = 0.8% ....Yfull - 1460BC, Jura caves
    Father's Mtdna .........T2b17
    Grandfather's Mtdna .......T1a1e
    Sons Mtdna .......K1a4o
    Maternal Grandfather paternal......I1d-P109...CTS6009
    Maternal side Grandfather .......R-S8172
    Wife's Ydna .....R1a-Z282

    My Path = ( K-M9+, TL-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS54+, CTS8862+, Z19945+, Y70078+ )

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     jdean (05-16-2019)

  15. #10
    Gold Class Member
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    Quote Originally Posted by vettor View Post
    I see your program also runs mtdna ................not sure if many know about this.
    Ah, have to change the symbol over to female, took an embarrassingly long time to work that one out : )))))

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