LineageDeepClade

Note: updated on 9-14-12, 9-25-12, 11-14-13 & again on 12-8-13

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12-8-13 - the Big Y test is no longer on sale.  The price is $695

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As of 11-9-13, there are two ways to test yDNA Deep Clade:

1. The National Genographic "2.0" - for $159 - which tests about 12,000 known ySNPs and will position you within the known yTree.  It also includes an assessment of your geographic/ethnic heritage and some other interesting things.

2. The FTDNA "Big Y" - for $499 - which tests for nearly 25,000 known SNPs, plus a very significant unexplored portion of the yChromosome.  The results of this testing should identify many, many new SNPs and add significantly more Deep Clade branching - providing yet another major advance in learning.  (available only to existing FTDNA yDNA customers at this time)

Whichever you choose - the LOGIC listed below is valid - but the details need to be interpreted for the actual test you choose.  (I have done both - and also did the first version of the FTDNA "Walk through the Y")  Terry 

End of 11-14-13 Update

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These are exciting times for Deep Clade SNP testing of yDNA results.  The advances in the detail of SNP-tested Haplogroups has progressed at astonishing speed over the past couple of years and we expect the pace will increase even more during the next years.  (my own Haplogroup definition has progressed from a simple R1b to the R1b1a2a1a1b3c2 Deep Clade)

So - you are thinking it's time that you jump in and get Deep Clade SNP-tested .  Is there a "better" or "best" way to test?   I think there is. 

Here is my recommendation - which assumes that you are matching other men at 37 or 67 markers:

  1. Communicate with all of your yDNA matches

    1. Explain that you should work together as a group to do the Haplogroup Deep Clade testing - as it is probable that all of you will have an identical outcome. 
    2. It will be cheaper to test strategically only one or a few men as a group (and then each man who chooses, can simply test the defining (terminal) SNP to confirm his perfect match)
  2. Work together as a Group

    1. Assess your group's current level of Deep Clade knowledge and identify any additional testing already underway.  (if WorldFamilies prepares your Results Table - your group is made up of the men in your Surname Lineage - plus any matches at 37 or 67 markers who are not in the project.)  Note: get the matches not already in the project to join - as there are also benefits to looking at shared marker mutations to identify branching within the Lineage!
    2. Collect donations from all who are willing to participate (FTDNA can hold the Funds)
    3. If you already have one or more men in your Lineage who are SNP tested (their Haplogroup is reported in green text instead of red), then you already have a degree of learning.  The "longest" Haplogroup is the current level of learning for your Lineage. 
    4. It's also possible that one or more of your men has also been testing individual SNPs to extend the Haplogroup definition even further (which may or may not be reported on the Project Results Page)
    5. If you have men already SNP-tested - have them join their FTDNA Deep Clade project and communicate with the project administrator - as he will possibly have some advice and will certainly want to know of your Group effort.
  3. Test Strategically

    1. Ironically, whether your group already has done some Deep Clade testing or not - the next testing your group should do is to test one of your Group at National Geographic's Genographic Project.
    2. The test is called "Geno 2.0" and is the "ultimate" Deep Clade test on the market.  It is expected to be much more defining than the Deep Clade test currently offered by FTDNA.

      1. If one of your Lineage was tested initially at National Genographic (their kit number starts with "N") then the cost of testing them is $179 - a slight discount
      2. If no one in your Lineage was tested at National Genographic, the cost of testing one of your group will be $199.  (pick one man as your volunteer - maybe the one who donated the most or the one who started the Deep Clade project)
  4. Confirm the Deep Clade

    1. Once you have the initial Deep Clade result from the Geno 2.0, you'll know the probable Deep Clade of the entire Group (Lineage). 
    2. You'll want to test additional Group members to confirm they are all the same.

      1. Probably, FTDNA will quickly be offering individual SNPs - and individuals can test only the terminal SNP to confirm their match. 
      2. If you can't do the inexpensive test on a single terminal SNP, then selectively test men who are the "most distant" from the first man tested - as these are the most likely to have a difference
    3. If some of the men don't test positive for the terminal SNP, this will be an indication of Deep Clade branching within the Lineage.

      1. This is particularly exciting, as you will have identified a formal test to determine which branch of the Lineage a man belongs to (which will be more accurate than marker matching) 
      2. You'll need to test a number of men in the group to find the correlation between marker mutations and the Lineage branch
    4. Individuals can each test if they choose to have formal confirmation of their Deep Clade - or they can simply conclude that they have the same Deep Clade as their close yDNA matches
  5. Join your Deep Clade Project(s): 

    1. Join the formally SNP-tested men to their relevant FTDNA Deep Clade project - to share the learning
    2. Look Carefully - there may be more than one relevant Deep Clade project for you.  (I belong to 3)
  6. Keep Going - this can't be the last step!

    1. It's likely that additional learning will occur after the Geno 2.0 information, which will mean the group will want to again pursue even more Deep Clade testing - again strategically. (hmmm - if it's Geno 2.0 now - does that mean that "Geno 2.5" or "Geno 3.0" is coming soon?)
    2. Do WTY on one of your men as a last resort (see Thomas Krahn's comment below)

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Updates 9-14-12:

A. Geno 2.0 vs WTY:

I ran this article by Thomas Krahn at FTDNA to see what he thought about Geno 2.0 vs WTY (Walk through the Y testing being done at FTDNA to search for new SNPs) and received this reply:

"Yes, the Geno 2.0 is also helpful when someone has already had a WTY because the chip contains thousands of Y-SNPs that haven't been covered by the WTY. The likelihood that you'll find something "absolutely new" is somewhat lower than at the WTY but at least Geno 2.0 will confirm the position and the upstream tree structure for the well characterized WTY samples. Many upstream SNPs still need to be characterized and we may find further branching points that will split up a row of previously synonymous SNPs.

I like your Deep Clade strategy outline very much and it'd help my laboratory to not get clogged with redundant SNP tests if everybody used that strategy.

You might add the WTY testing as the very last resource for finding a defining SNP, if everything else was unsuccessful to reach te desired resolution to solve a genealogical question."

B. Other Components of Geno 2.0

I wrote this Blog posting to discuss yDNA Deep Clade testing strategy, but as the discussion is heavily focused on Geno 2.0, it's appropriate to mention other outcomes you will get from testing with Geno 2.0:

  • Define percentage of your genome affiliated with specific regions of the world (ethnicity)
  • Get your mtDNA Deep Clade
  • Learn the history and migration of your mtDNA and Y-DNA haplogroups
  • Find out if you have Neanderthal or Denisovan ancestry.

Update 9-25-12:

Thomas Krahn answered question from Bill Hurst and CeCe Moore that were printed on the ISOGG DNA-Newbie list today:

A. Bill Hurst wrote:  Thanks for the explanation. For the record, how does a Deep Clade test compare with the Geno 2.0 and WTY?

Thomas Krahn responded: 

From a Y chromosome perspective Geno 2.0 essentially will replace the DeepClade test because almost every SNP from the Deep Clade works on the Geno 2.0 chip. The few that did not work yet can be either subsidized with synonymous SNPs or if really needed they can be done with a single individual SNP order.

I'm not sure if FTDNA will continue the traditional "Deep Clade" test in the future when Geno 2.0 is available, however I strongly recommend to go with Geno 2.0 . Even if the price for a Deep Clade test is lower than Geno 2.0 you'll get much more value per dollar (even though I'm just looking at Y-SNPs).

Technically the Deep Clade was done with some quantitative PCR method in PCR plates whereas the Geno2.0 will use the Illumina bead chip technology.

The WTY program will be unaffected by Geno 2.0 . Sure there are plans to expand WTY and have some successor to it. However the parameters and the platform is not set in stone yet.
 

B. CeCe Moore added her comments:  That was the impression that I got on the Geno 2.0 webinar with Spencer and Elliott. My mistake. Did you design them all yourself? That is, no doubt, a very large undertaking.

Thomas Krahn responded:

Geno 2.0 was a team effort. Elliott was focusing on the mtDNA, Eran (from National Geographic) was focusing on the autosomal SNPs (including Neanderthal, Denisova etc.) and I did the Y-SNPs. Elliott was also leading the evaluation process (wetting the chip as Spencer puts it).

The difficulty was not really the high number of SNPs but rather selecting the best ones for genealogical and anthropological purpose. I started off with a contingent of 15000 SNPs that Spencer wanted for the Y chromosome and I tried to make sure that all SNPs from the existing tree and whatever we had available from the WTY and other internal sources was included on the chip. Then I selected the ones from the most reliable external sources and filled them up with data that was extracted from the 1000 genomes public datasets (excluding regions that are considered problematic from a recombination mechanism standpoint).

From the > 25000 Y-SNPs that I had available at that time we filtered out the ones that gave the best scores with a prediction tool provided by Illumina. However we always tried to keep all SNPs from the YCC and Draft Tree in our selection. After several iterations I was able to convince Spencer to increase the Y contigent to 18000 SNPs at the time when we submitted our final choice to Illumina. Many of the today known Z series SNPs have been included in the selection, however I cannot discuss each individual one. There will be other good Z series SNPs that we'll be missing because not all currently available 1000 genomes data were available at that time. Off course all new findings from the WTY and all verified Z markers that were discovered in the mean time will be considered for the next version of the Geno chip.

The future of Y SNP testing after Geno 2.0 will be essentially:

1.) Test Geno 2.0 or predict your Y haplogroup as good as possible from Y-STR results.

2.) If necessary use individual Y-SNP tests to determine your fine haplogroup (to the last twig of the current knowledge if you want).

3.) If you still can't solve a Y haplogroup question consider to apply for a WTY run and hopefully find a new SNP that will solve your question and/or contribute to further research and for inclusion in the next Geno Chip.

I hope this helps, Thomas

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Links: Family Tree DNA and National Geographic's Geno 2.0

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Terry

p.s. I wasn't smart enough to do this for my own Barton Lineage I.  I simply jumped in and ordered my Geno 2.0 test.  However, I'll follow my own recommendations for my other ancestral surnames!

GENO 2.0

Good advice, Terry! Thank you. I had not considered using GENO 2.0 to define lineages. That could be a very useful tool.
Doris

Haplo group

I have traced my Conklin lineage to my "brick wall": Richard Conklin b.12/21/1787 in New Jersey, m. 1815 Sarah Beers b. 12/21/1795. Lived in Lawrence Twp., Clearfield County, PA, and had 7 children.
I submitted for yDNA test at 37 markers, and was told that I do not belong to either of the 2 main New England Conklin families.
I was told my Haplo Group is J2. What does that mean, and how do I find out who my test matches?

yDNA test - no matches at all

Richard - your query doesn't really belong here - but I'll answer it anyway as other folks also have no matches. 

There are a number of resources available to researchers who are trying to understand their results.  Here are a couple: 

  1. You should do the "Interactive Tour" in your personal page at FTDNA.  FTDNA also has an extensive set of FAQs which are quite good. 
  2. WorldFamilies provides "DNA the Smart Way" at www.worldfamilies.net/smart   I encourage you to scan all of the pages of "Smart" and then to read the parts that seem relevant.

We have a section at Smart which specifically focuses on folks with no matches at all. I strongly encourage you to read that section.

http://www.worldfamilies.net/resultsfaq#nomatch

As far as the subject of this blog entry - Deep Clade testing - as long as you have no matches, you'll have to carry the entire burden yourself if you pursue your Deepest Clade.  Otherwise, the blog entry is fully relevant to you.  Join the J2 Haplogroup project and see if you find anything useful there.

One additional comment - your results profile seems to include only one marker - 456 -  that is far enough away from the "norm" to possibily be hiding your matches by itself.  (you could have a genetic distance (GD) of 3 from your otherwise matches at that one marker alone - and you are only allowed a GD of 4 to be considered to have a match at 37 markers.  While that difference of 3 would be counted as a GD=3. it might be only one mutation, which would mean counting it as a GD=1)  So - after you upload your yDNA results to ySearch, try searching for your matches without using DYS456 to see if that helps you locate any matches.

Terry

ps If some of the suggestions mentioned above exceed your knowledge - please do the Interactive Tour at FTDNA and look at their FAQs and/or WorldFamilies "Smart"

Very well written. A great

Very well written. A great description of probably the most intelligent way to go about the hunt for a terminal SNP.

Deep Clade Test

Excellent write-up of the topic. Well done. I will use it as a reference for my DNA talks.
Bonny

Geno 2.0 Pricing

Terry,
I too quickly ordered the Geno 2.0 test when it first was announced at the $199.95 price. Later, when I heard that those previously tested by NG were being offered a discount, I emailed NG to point out that although I had first been tested by FTDNA and therefore did not have an 'N' number, I had paid ($99 I believe) to transfer DNA from FTDNA to NG for inclusion in its program. NG immediately replied that I qualify for the reduced $179 price and its records have been corrected.

Z94

I have tested with FTDNA, Geno2 and 23andme and I am down to Z94. How much is each test going to cost to get me to the bottom of the ISOGG tree as published up until December of this year? I am already back to Z94 at about 3000 bce and R1a1a1b2 and a few other minor clade letters.

Dave Place
Co Admin Place surname site FTDNA

Z94

You can test the Terminal SNP (as defined on the ISOGG Tree) at FTDNA through your personal kit page for $39

Very high Y-DNA match without a family finder match

I wonder how many others have matched 209/111 and the same surname and yet not found another surname match in the Family Finder? I have not had even other Y-DNA matches due to a rather unusual DYS390 number of 24 when almost all the people in my general group show 25. I think I have a true mutation. I even had FTDNA retest that one allele and it came back the same 24! I am beginning to wonder if I should include all DYS390-25 matches to expand my possible matches. I just ordered the Z2124 SNP test for $39 so that will at least get me on to a new branch of the tree and hopefully eliminate the need to do at least 5-6 more SNPs to get to the bottom of the most recent ISOGG Tree that was published in late November. I hope someone else in our Place surname group will consider the Big Y and publish what they find. I am most interested in getting my own Kit N9119 into Yorkshire with a paper trail of course:-)

Dave Place
Co Admin Place surname site FTDNA

Very high Y-DNA match without a family finder match

Matches on yDNA who are also matching on Family Finder when it is more than 4 or 5 generations back to their most recent common surname ancestor are unusual - because the amount of autosomal DNA passed down to each descendant is likely insufficient to generate a FF match

Using a mutation at a single marker that is rare to search for your genetic yDNA family isn't going to be productive.  The best suggestion I can make is to use the FTDNA comparison guidelines.  You can get a little "wiggle room" if several of you are matching and each of you has mutations vs the Lineage modal by comparing each man to the modal instead of to each other

Terry