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Big Thinking about BIG Y and Y-DNA Phylogenetics

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  • Ann Turner
    replied
    My request is not about phylogenetic tree design -- although I do think collapsible / expandable outlines like mtDNACommunity are handy.

    Will FTDNA continue to add numbers to the L series for newly discovered SNPs?

    I'm hoping we'll be able to contact people who match some or all of any private SNPs discovered -- that is, SNPs downstream of the most derived haplogroup assigned a label.

    Leave a comment:


  • S9 H9
    replied
    Originally posted by JohnG View Post
    I think there are two types of people in this - those that want to be part of the research/arguments/discovery and those that just want to know results.

    For the 'just the results' folks, something like the Genographic migration slides is probably great.
    As someone who "just wants to know the results" I can say for sure that what I do not want is the "Genographic migration slides".

    Rather, I'd like to do a Big Y test in the future, but my desire is to:
    1. Provide any corrective needed to the current family tree; and
    2. Connect by deepest Y ancestor (currently in the 16th century) to his deeper ancestors.


    To accomplish this though many people in the I2a2a clade will need to be tested, so it's not something that will give me results soon. It may takes thousands of men testing (of which hopefully some will have really well researched trees) before I can get to where I want to go.

    Thus what in the long run will help me, and others analogously with similar interests, is if the I-M223 project can find a way to incorporate the tsunami of Y SNPs that are coming.

    How the various Y projects will incorporate the diverse types of testing is going to be a challenge, I think. Many discovered SNPs may hang in "private" limbo for years before enough tests are reported for an academic researcher or ISOGG anoints a new subclade. Another issue is how/if Big Y will discover any STRs, and what if a new set of STRs from Big Y or FGC tests become the norm, different than the current Y-67 test? How does one measure "closeness" on a genealogical scale given a diverse set of Y data?

    Leave a comment:


  • ajmr1a1
    replied
    Some enhancements are needed for the "Advanced SNP Test Ordering"
    page.

    SNPs that are offered to me as being "available for testing" do not seem to take into account my Geno 2.0 results.

    For example, allowing me to order M458 is pointless since Geno 2.0 shows me to be M458- and Z280+.

    I think that the Advanced SNP Test Ordering page should be based on
    an experimental draft tree that is as current as possible.

    Leave a comment:


  • ajmr1a1
    replied
    Originally posted by D.Clade View Post
    Whatever style that is chosen, a dynamic and current tree based on always new data is absolutely needed now. Some unnecessary SNP testing is occurring from Geno 2.0 customers.
    Right you are!

    It is critical to be as up-to-date as possible with an experimental y-tree in order for project administrators to appropriately recommend single SNP, Geno or BigY testing in the most effective way possible.

    This means including all new SNP discoveries from other sources.

    Not everyone can afford the BigY or FullY but some will want to participate
    through single SNP testing.

    Leave a comment:


  • Applegatej1
    replied
    I like the trees at mtDNAcommunity and PhyloTree. The ISOGG tree is hard on my eyes and easily misread. Heatmaps are great, but I would be happy with a tree that could keep up. Possibly indicate what a SNP is downstream of without first defining a subgroup with it.

    Leave a comment:


  • D.Clade
    replied
    Chris Morley's An experimental computer-generated Y-chromosomal phylogeny, leveraging public Geno 2.0 results and the current ISOGG tree
    has been extremely useful. People look forward to seeing their kit in the next version and that encourages SNP testing.
    For the average and advanced user, Mike W's R1b phylogenetic trees are great visuals. Easy on the eyes.
    Whatever style that is chosen, a dynamic and current tree based on always new data is absolutely needed now. Some unnecessary SNP testing is occurring from Geno 2.0 customers.
    Thanks for working on this.

    Leave a comment:


  • JohnG
    replied
    time machine

    I think there are two types of people in this - those that want to be part of the research/arguments/discovery and those that just want to know results.

    For the 'just the results' folks, something like the Genographic migration slides is probably great. I can go back from my surname and known genealogy to the fuzzier times. I think of it as a sort of time and space line, or machines. Go back and forth in time by moving a cursor, showing the time and spatial location most likely associated with a change in SNPs or groups of SNPs. Maybe have another panel that shows the SNP tree, but be able to focus on the big picture, the story first.

    For those who like the work in process, maybe there is a different view, more statistical, more able to reference things like the NIH SNP database.

    Leave a comment:


  • Rebekah Canada
    started a topic Big Thinking about BIG Y and Y-DNA Phylogenetics

    Big Thinking about BIG Y and Y-DNA Phylogenetics

    Hi,

    I have asked this before in other places, but I want to step up the concept thinking. What do the experts in Y-DNA haplogroups and typical project members want from BIG Y results? Here are some examples to get things started:

    There is a Phylogenetic tree for mtDNA at http://www.mtdnacommunity.org/human-...phylogeny.aspx. If your Y-DNA SNP results were included in this type of tree, what would you like about it? What would you dislike?

    ISOGG has their Y-DNA Tree, http://www.isogg.org/tree/. What do you like about it? What do you dislike?

    23andMe has a phylogenetic tree for Y-DNA? Have you used it? Do you like it?

    Geno 2.0 has Y-DNA migration maps for part of their user experience. They also have basic heatmaps for key branches. Do you like them? What could make them better?

    The FullY group is building a Y-DNA Phylogenetic tree? What do you think of it?

    CeCe Moore has blogged about Full Genomes Corp.'s F-Y results files. Have you read the post? Do you have results? What is useful?

    What would your average project member understand from each of these? What is missing? What else is out there?
    Last edited by Rebekah Canada; 15 December 2013, 12:51 PM. Reason: copyedit
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