Administrator/Researcher: Angela J. Cone
Costa Tsirigakis - Founder J2 Y DNA project & admin/researcher from 2006 - mid 2008
See bottom of page for Project Admin. information

Project Hypotheses
(Prepared November/December 2007)
(Presented February 2008)

Written in question form:-

Can J M172+ sub-clades be reliably predicted from extended haplotypes?
             The original aim of the J2 Y-DNA project was to answer the above question.
             At present the answer is "yes and no". We hope to quantify this answer more definitively very soon.

Do the haplotype clusters identified by the project correlate to true biological lineages?
   (ie. subclades).
             See the phase three analysis page for details of the haplotype clusters defined by the project.

Specifically:

A) Within J2b (M12/M102/M221/M314)

1. Is J2b-Delta is a true clade? If it is a true clade, is it separate from J2a-Alpha or is it nested within J2b-Alpha?
2. Is J2b-Zita a true clade? If it is a true clade, is it separate from J2b-Delta or is it nested within J2b-Delta? What is its relationship with J2a alpha? (answering this will depend on answers to 1.)
2. Is J2b-Gamma is in a separate grouping from, or is part of the same clade as J2b-alpha? could J2a-Gamma perhaps represent J M12+ M205- M241- haplotypes?
[The recent M241 testing results have found that: some haplotypes in Alpha, Delta and Zita clusters are M241- and most are M241+. A J2b-Gamma cluster haplotypes has been found to be M241+. This may mean that Alpha, Gamma, Delta and Zita clusters are artificial clusters. Further research is needed to see whether the M241- (that are also M205-) haplotypes can be distinguished from M241+ haplotypes]

B)Within J2a (M410)
       (Answers to the questions in bold, may alter the non-bold questions)

1. Do SNP's exist that separate J2a-Alpha from J2a-Beta?

2. Is J2a-Beta a true clade?, can a SNP be found to unite all in J2a-Beta? [[Yes! L24 and L25!!]]
3. Are some existing clades in the YCC tree (eg.M47) part of J2a-Beta?
[Yes,. for instance we know that M137 is part of J2a-Lambda cluster]

4. Can a SNP be found that defines J2a-Lambda? [[Yes!!, L70]]
5. Are some clusters within J2a-Beta more related to J2a-Lambda than others (eg. are the J2a-beta haplotypes that cluster with J2a-Gamma less related to J2a-Lambda than those that cluster more strongly with J2a-Lambda)
[[??]]
6. Can a SNP be found that defines J2a-Theta? Are some clusters within J2a-Beta more related to J2a-Theta than others? How are J2a-Theta and J2a-Lambda related in relation to the rest of J2a-Beta?
[[??]]

7. Is J2a-Alpha a true clade?, can a SNP be found to unite all in J2a-Alpha, or just some of J2a-Alpha? [??]
8. Are some existing clades in the YCC tree part of J2a-Alpha?

9.  How do M67- haplotypes that are currently in J2a-Alpha fit into the tree? (eg. haplotypes in J2a-Xi and J2a-Psi).
10. Is J2a-Delta a true clade?

(one of the main diagnostic features of J2a-Delta seems to be high values at DYS 458. High values can be seen in J1 - therefore perhaps high values in J M67+ reflect an ancestral character state of all J2, rather than a derived state within J M67+. If high values can be considered to be "ancestral", and low values can be considered "derived", - then it might be that J2a-Delta is "paraphyletic" and therefore not a true clade).
{{Whilst some M67- J2 haplotypes have high values at DYS458, other marker values distinguish those haplotypes from those J2 M67+ which have high DYS458 values.
J2 M67+ haplotypes that have high DYS458 values tend to cluster together in 67 marker diagrams. If J2a-Delta is defined on the basis of clustering at 67 markers, then it is therefore likely to be a monophyletic grouping within M67+}}


10. Is there a SNP that separates J2a-Gamma from the rest of J M67+
[??]
11. Is there a SNP that unites the J M67- haplotypes that have DYS 395S1 15,15 , with J M67+?
(or are the DYS 395S1 values of these haplotypes and those of M67+ haplotypes "identical by character state" rather than "identical by descent" - ie. via. "convergence") [??]
12. Is there a SNP that defines J2a-Sigma? Are there additional SNPs that clarify the relationship of J2a-Sigma compared to other J M67+ haplotypes?
13. Is there a SNP that defines J2a-Omega? Are there additional SNPs that clarify the relationship of J2a-Omega compared to other J M67+ haplotypes?
14. Is there a SNP that defines J2a-Mu? Are there additional SNPs that clarify the relationship of J2a-Mu compared to other J M67+ haplotypes?

15. Is there a SNP that defines J2a-Zita? [yes, J2a-Zita haplotypes are M319+] Is J2a-Zita more related to haplotypes within J2a-Alpha or J2a-Beta? [??]

16. Can a SNP be found that is equivalent to the primary DYS413 deletion that occurred in J2a?
[ Yes!!,Two -> L26 & L27]]
17. How paraphyletic are J2a haplotypes that do not have the DYS 413 deletion?. Are some of these haplotypes more related to the J2a with the DYS 413 deletion? Can SNPs be found to unite some of the J2a without the deletion with the J2a with the deletion?

[So far all haplotypes that don't have the DYS413 deletion are negative for both L26 & L27, & vice versa, so at present the three seperate mutations seem to me phylogenetically equivalent]

Answering this additional question will depend on the answers in bold above
18. How do J2a haplotypes that have the DYS 413 deletion, but are neither in J2a-Alpha or J2a-Beta fit into the tree?

Hopefully FTDNA's new initiative"the walk on Y project" will help us answer the questions/hypotheses above. Additional questions will be added over time.

We also acknowledge the continuing valuable SNP discovery research done by both Ethnoancestry and FTDNA (...and of course all the valuable Scientific research by both the Academic Community, and the Genetic Genealogy Community... the more both communities work together, the greater the information that will be learned).

Update (2 October 2008): In the last year, two new DNA companies ( 23andme and Decodeme) that measure thousands of SNP's on different chromosomes, have started business. These include (for males) SNP's on the Y-Chromosome. Many of the SNP's that are tested on the Y-Chromosome are ones that are not placed yet in the Y-tree. These SNP's have names like "rs34276300"

As a result of comparing different results, people have found that some of these SNP's do give useful new information for the Y-DNA tree. For instance, we now know that the SNP "rs34276300" has an important place in the R1b portion of the Y-DNA tree (as do at least two other SNP's). When the YCC Y-DNA tree is updated, this SNP will be included in the Y-DNA tree with the SNP name (it's also currently named "S116" by Ethnoancestry)

So far, one new SNP has been detected in J2a by 23andme. This new SNP is apparently found in most J2a's, and is currently known by the number rs34126399.
According to tests done by Dr Peter Underhill, this new SNP is equivalent to the DYS413 deletion. Presumably this SNP will be given an official SNP name in the Y-DNA tree when the YCC tree is next updated. There is a short article about this new SNP in the 23andme blog which can be seen here.

It would be very interesting to know whether any of the other Y-DNA SNP's tested by either 23andme or decodeme might fit into the haplogroup J part of the Y-DNA tree.

[Update: 18 March 2009 - Yes!! we now have 2 SNP's which correlate with J2a-Beta cluster, (L24 & L25) and there is another SNP being tested which likely correlates with J2a-Lambda cluster (and yes, it is a clade within J2a-Beta).
rs34126399 is now named L27, and L26 is rs34459399 (and is exact same mutation that Ethnoancestry named S57).

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Angela Cone - Co-administrator from mid 2006 - mid 2008
Administrator from mid 2008 - Present
Click here to read about Angela.

Costa Tsirigakis - Founder J2 Y DNA project & admin from 2006 - mid 2008