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 J2a-Zita a true clade? If it is a true clade, is it separate from J2a-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?

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?
3. Are some existing clades in the YCC tree (eg.M47) part of J2a-Beta?

4. Can a SNP be found that defines J2a-Lambda?
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).
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? 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 M413 deletion that occurred in J2a?
(S57 - recently discovered by Ethnoancestry might fulfil the above role - more testing is required to verify this)
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?

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. At present, FTDNA has not given full details on how this new initiative will work, - the details that they have shared so far can be seen here (From Thomas Krahns FTDNA conference presentation).
We also acknowledge the continuing valuable SNP discovery research done by Ethnoancestry (...and of course the valuable Scientific research by the Academic Community)