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 update news

Project Research fund

Explanation of the Scientific process

Haplogroup J2 nomenclature
Updated July 2008

J2 Y-DNA Project Hypotheses

Analysis results (first phase - 4th July 2006)
--Network diagrams--

Analysis results (second phase - 30 July 2006)
--Marker analysis--

Analysis results (third phase - February 2007)
--Cluster analysis-- (updated February 2008)



The Independant J2 Y-DNA project has been completed, so has ceased to have an active members area. The FTDNA J-M172 group continues to operate, and haplotype results, admin contact etc. can be found here

The final analysis results of the Independant J2 Y-DNA project can be seen here.

Angela Cone
29 July 2013

We have modal values in the third phase analysis page, and we have marker frequency distributions in the phase two analysis pages.

The project also wishes to clearly delineate between unconfirmed preliminary results, and results that have been sufficiently confirmed by proper scientific methodology. An outline of the scientific method used by all legitimate scientific researchers can be seen on this page.
The Project wishes to advance knowledge, and not inadvertantly perpetuate misinformation. When we present our results, we will endevour to make clear whether they are preliminary results, or fully confirmed results.

§ For some people, "privacy" also extends to not wanting their haplotype shown in public. This project respects that different people have different privacy comfort levels (for a multitude of different reasons). Members can choose whether their haplotype is shown in the public domain, or whether it remains "private" and viewable by members only.

The map below shows the Geographical origins of the J2 Y-DNA project members
(note: the Geographical origins of people who DNA test are not representative of the global population, therefore the member frequencies of J2 in different countries is
not a scientific representation of the relative population frequencies that occur in those countries.)

Red=J M12+ (SNP tested)
  (pale red/pink = J M12 predicted)

Blue=J M67+ (SNP tested)
Grey=J M67- , J M12- (SNP tested)*
  (white = J M410 predicted)

Last updated: February 2008
(prepared in November 2007)


First phase results (Network diagrams).
(last updated October 2007)

The overall aim has been to use the network diagrams as a form of exploratory data analysis, - to gain a visual representation of the likelihood that we'll be able to predict sub-clades from Haplotype results.

The general conclusion that can be made at this time is that it is much easier to differentiate J2b haplotypes from the rest of J2, some J2a(xJ2a2) haplotypes can be easily identified as being J2a(xJ2a2), and for some haplotypes it may be difficult to conclusively predict whether they are J2a2 or J2a(xJ2a2). More specific conclusions will be added as the study progresses.
This confirms the long held suspicion by many J2 researchers that J2b is most easily distinguished from the rest of J2. This distinct seperation between the two main haplotype clusters in J2 makes perfect sense in light of the discovery of M410 (by Sengupta et al. 2006), and the phylogenetic division of J2 into J2a and J2b.

The second phase of analysis (see link to results above) has begun to quantify which marker values are most useful in predicting subclades (and ultimately what combinations of markers). Already it appears that there are two main clusters within J2b, and at least 3 different clusters within J2a2. In addition there are multiple potential clusters within the paraphyletic J2a(xJ2a2).

The third phase of analysis (see link to results above) has begun to validate the results of the second analysis phase, and has also begun to define & label clusters of haplotypes. Whether or not these clusters represent true biological groups will be tested in the future. We will progressively outline and test hypotheses related to the various clusters.

A new version of the Y-chromosome phylogenetic tree was presented at the FTDNA conference (20 & 21st October 2007). This new tree was published in a scientific journal in early 2008. After this tree was published there was a change in the "by lineage" nomenclature.
Usually we put a "key" to the node colour coding on the network diagrams. This time we instead put the key to the colour coding in a seperate box to the right. That way, - we were able to easily update the key with the new nomenclature.

12 marker Phenogram.
Last Analysed: October 2007

(306 haplotypes)


25 marker Network diagram.
Last Analysed: October 2007

222 haplotypes


37 marker Network diagram.
Last Analysed: October 2007

(153 haplotypes)

In the J M410+ Confirmed (or predicted) diagram above, J2a-Gamma cluster and the various clusters within J2a-Beta cluster are indicated. It can be seen that there is one sub-branch in the network diagram that contains a mixture of those in J2a-Gamma cluster and a portion of those in J2a-Beta cluster. The fact that some J2a-Gamma cluster haplotypes and J2a-Beta haplotypes cluster tightly together was not previously seen in the 37 marker diagrams. It is evident now due to the fact that additional members in both J2a-Beta and J2a-Gamma now have 37 markers. This finding will be investigated further over the next couple of weeks, and we will discuss it in depth at the supplementary update which is currently scheduled for late October/early November 2007.

67 marker Phenogram
Last Analysed: October 2007

(68 haplotypes)


Network Diagrams created using "Network" (produced by Fluxus-Engineering)
Phenograms created using "Splits tree" (produced by Algorithms in Bioinformatics
© 2007 University of Tübingen
D. H. Huson and D. Bryant, Application of Phylogenetic Networks in Evolutionary Studies , Mol. Biol. Evol., 23(2):254-267, 2006

FTDNA YCC 2005 nomenclature
Sengupta et. al (2006) nomenclature


Creative Commons License
This work is licensed under a
Creative Commons Attribution-No Derivative Works 3.0 License.
This work can be freely cited, if it is attributed to:
The J2 Y-DNA project

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