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

Link to taxonomy pages

Haplogroup J2 sub-clade Nomenclature

The information on this page is intended to make it easier for people to "cross reference"
the different nomenclature versions
.

The new YCC tree has now been published. The major difference between the Sengupta et al. 2006 nomenclature and the new official 2008 YCC tree, is the removal of DYS 413 - which confirms the conclusions made in the DYS 413 review. The reason why STR markers cannot be used as characters in the YCC tree is explained in the "cladistics" page (see the taxonomy pages for further details ).
The
other difference is that M327 has been repositioned as a subclade of J M92 (previously only positioned as a subclade of M67, parallel with M92 rather than being "downstream of M92), and three new SNP's have been added. There are two new SNP's "downstream" of J M410, - P81 and P279 - , and one new SNP "downstream" of
J M12/M102/M221/M314 - P84.
[added 3 April 2008]

Why are there so many different versions of nomenclature?
- Different versions of nomenclature can be confusing,
the purpose of this page is to reduce that confusion

In the field of science, it is perfectly valid for different scientists to use different versions of nomenclature. If the taxonomy of a group is revised, then other scientists are not automatically obligated to use that new nomenclature. As an extended form of peer review, it is perfectly valid for other scientists to choose to accept the new classification, or - if in their judgment, the new classification is not scientifically valid - not to accept the new classification.

The reason why this doesn't lead to confusion is because scientists reference the nomenclature used when they publish research papers. That way, there is never any doubt about which taxa are being referred to. More about this is explained in the "Taxonomy of the Human Y-Chromosome" pages. We intend this page to help reduce any confusion about nomenclature used for lineages within J2.

To be considered scientifically valid, a new taxonomic revision needs to conform to all the official nomenclature rules. Different branches of taxonomy (eg. Botany, Zoology) have their own official naming rules. In the case of Y-DNA, the official nomenclature rules were laid out by the YCC Consortium in 2003. One of the official rules is that all "characters" (eg. SNP's) must be "binomial" (ie. have only two character states - see this page for more information). Therefore, any Y-DNA classification that uses non-binomial characters (ie. STR markers) does not conform to the official YCC rules (and therefore is not scientifically valid).

If you look at the series of taxonomy pages that have been prepared, you will see that the YCC (2002) actually proposed two alternative forms of nomenclature - "by mutation" and "by lineage". The form of nomenclature that is usually used by the "genetic genealogy" community is the "by lineage" nomenclature. The J2 Y-DNA project now uses this dual system of nomenclature, and for the "by lineage" system it will be using the official 2008 YCC nomenclature (Karafet et al. 2008).

2008 YCC tree
Link to official research paper
(also see supplemental research data)
By lineage nomenclature
By
mutation
YCC 
2008
Sengupta
et al.

2006
FTDNA
2005
YCC
2003
  J2*    J2*   J2* J M172
  J2a*  J2a* J2a1*     J M410
  J2a1   J2a1a    J2a    J2a J M47
  J2a2*   J2a1b*    J2f*    J2f* J M67
  J2a2a*   J2a1b1    J2f1    J2f1 J M92
  J2a2a1   J2a1b3    J2f1a J M327
  J2a2b   J2a1b2    J2f2    J2f2 J M163
  J2a3   J2a1c    J2b    J2b J M68
  J2a4   J2a1d    J2c    J2c J M137
  J2a5   J2a1e    J2d    J2d J M158
  J2a6   J2a1f     J M289
  J2a7   J2a1g    J2k J M318
  J2a8   J2a1h    J2l J M319
  J2a9   J2a1i    J2g J M339
  J2a10   J2a2    J2h J M340
  J2a11   J2a1j     J M419
  J2a12     J P81
  J2a13 J P279
  J2b*   J2b*    J2e1*   J2e1* J M102
  J2b1   J2b1    J2e2 J M205
  J2b2*   J2b2*   J2e1b J M241
  J2b2a   J2b2a   J2e1a    J2e1a J M99
  J2b2b   J2b2b   J2e1c J M280
  J2b2c   J2b2c  J2e1b1 J M321
  J2b2d J P84

 


What happened to DYS 413??!!

A review completed by Angela Cone (the J2 Y-DNA projects administrator) showed that the inclusion of DYS 413 into the NRY phylogenetic tree was not valid. This conclusion has been independantly confirmed by the YCC (Karafet et al. 2008).
If it was valid to include a STR like DYS 413 in the YCC tree, then it would have been encorporated into the 2008 Karafet tree. The fact that it was excluded from the Karafet tree indicates that it cannot be included in Y-DNA trees according to the offical YCC nomenclature rules.

The reason why STR markers cannot be used as characters in the YCC tree is explained in the "cladistics" page. To view the pages that contain the review of DYS 413 (and the associated taxonomic pages), click here.

The project began its review of DYS 413 in response to the fact that one of its members received a DYS 413 result of 18 23. This member has not yet been SNP tested, but falls within the cluster J2b-Zita. We have verified with the testing company that this is not a clerical error. The lab has re-examined the original results electropherograms, and the reported results do correspond to what is seen in the results electropherograms.
It would be interesting to know whether there are others who fall within the cluster J2b-Zita that have similar DYS 413 values, or whether it was an isolated occurrence. So far, all others in J2b-Zita who have had DYS 413 tested have had normal results.
We acknowledge that it is still possible that this was just a lab error. However, the results of the review of DYS 413 done by Angela Cone suggest that if it was lab error, the frequency of similar "lab errors" in haplotypes from several haplogroups would suggest that DYS 413 is an unreliable marker to test. It is more likely that the reported results are accurate. As suggested in the review, If Sengupta et al. 2006 had tested all haplotypes for DYS 413 (instead of just the "J2 related lineages") then they themselves would undoubtedly have found that the deletion event seen in J M410+ haplotypes was not a unique event. Sengupta et al. 2006 found more than 20% of haplotypes were within haplogroup O, - it would be very interesting know whether all haplogroup O haplotypes have DYS 413 values of 17,17.

What? are you saying DYS 413 isn't useful anymore?!?!?!

The project still considers that DYS 413 is a very useful marker, - but just can't be used in the NRY tree (in the way the NRY tree is currently defined), and thus cannot be included within the official YCC "by lineage" or "by mutation" nomenclature. As mentioned in the review of DYS 413, we hope that the YCC can devise some additional complimentary nomenclature that can be used for markers that are valid within the context of a portion of the tree (but not valid within the context of the whole NRY phylogenetic tree). Perhaps such as the Greek character notations that were used in Haplogroup E3b* (and also by this project in its cluster analysis). There are other STR markers that are equally useful, and this alternative form of notation could be used to denote the groupings that these markers define also.

    * Now E1b1b1

It is now known that a new marker (S57) is more-or-less equivalent to DYS413<18. If S57 is found to have occurred in the Y-DNA tree either earlier than, or after the DYS413 deletion, then the J2 Y-DNA project will include this marker in a modified form of YCC nomenclature. If they are found to be synonomous, the J2 Y-DNA project will not be including DYS413 in any form of nomenclature. Until more information is available, the project will treat nomenclature as if they (DYS413<18 & S57) are synonomous. From a theoretical perspective though, the project is not making this assumption - ie. I'm not claiming the two mutations occurred at the same time, - in fact it's more than likely that they did occur at different times... what remains to be seen is whether any lineages remain that have one but not the other (or whether those lineages became "extinct"/daughtered out).

What about S57?

S57 is a new SNP marker that was discovered by Ethnoancestry. This new SNP seems to be positioned in the J2 Phylogenetic tree more-or-less equivalently to the DYS413 deletion (but not all J2 subclades have been tested for S57 yet). This new marker was not discovered in time to be included in the official Karafet et al. tree and we hope that enough will be known about the placement of this new marker when the J2 tree is next officially updated in a Journal publication. Until then, the official nomenclature designation of haplotypes that are S57+ will be " J S57+ "or "J2a /-S57/ " (as per the official YCC guidelines - see page 345 of YCC 2003).

What about DYS 445?

The J2 Y-DNA project acknowledges the biological validity of a cluster of haplotypes with DYS 445=6, which is more-or-less equivalent to a true biological clade.
This biological grouping was first identified by Athey and Schrack (unpublished data), and has been recognised by geneticists such as Peter Underhill (eg. King et al. 2008). This biological grouping was independantly identified as J2a-Lambda cluster, by the J2 Y-DNA project in its January 2007 cluster analysis. J2a-Lambda cluster is a sub-cluster of a wider cluster named J2a-Beta cluster, haplotypes in which tend to have DYS 445 values of 10, and DYS450 values of 9 (this was stated on the updates page on 29 April 2007).

However, because this grouping is as yet only defined by a STR, YCC nomenclature therefore cannot be legitimately used to notate its presence (since the official YCC rules effectively state that all taxonomic characters must be binomial). This may seem pedantic - however, official Taxonomic rules are official Taxonomic rules, and DYS 455 is definitely not a binomial character (a fact which is underscored by looking at the raw data from King et al. 2008).

The graph below shows the DYS445 values observed in the J2a* haplotypes found in the King et al. 2008 study (found in the supplementary "sm_tables1.xls" file). It is important to note that one haplotype in the J2 Y-DNA project has a DYS445 value of 11. This graph clearly shows that it would be tenuous to claim that DYS445 is a binomial character.

Until I saw the data above, I was under the belief that in haplogroup J2, all non J2a-Lambda cluster haplotypes had DYS445 values of 10 or greater (and no J2 haplotypes had ever been observed with values of 7 8 or 9). Thus it seemed that the values of 6 in J2a-Lambda cluster haplotypes clearly represented a STR deletion, that could be more-or-less considered equivalent to a UEP. However, the values above may be more suggestive of normal STR variation, rather than a UEP.

I had been prepared to encorporate DYS445 into nomenclature, in much the same way that this project is now encorporating S57 (eg." J DYS445=6 " or " J2a//-DYS445=6// "). However, based on this new information, I will defer making my decision about encorporating Lambda cluster into a modified/complimentary form of nomenclature, until more information is available. I will provide an update regarding this issue in September/October 2008. Until then, it will remain in this project identifiable as J2a-Lambda cluster.

(See the "cladistics" page for more information about difficulty of using STR's as UEP's, especially the section on binomial distributions that is halfway down the page. The last sentance on the "cladistics" page I think is very relevant).

The material below was written in October 2007, before the release of the 2008 YCC tree. The discussion is now "moot" but is retained here for interest.

But... you still refer to J2a and J2b

At present we are using a slightly modified version of the "by mutation" nomenclature. For instance rather than referring to M12 as J M12+ we will refer to J2b (or J2b M12).

We began writing this review before the start of rumours of an upcoming new FTDNA version of the tree. For all we knew, it could have been a long while before a new scientifically valid version of the NRY Phylogenetic tree was produced. We wanted to use a valid system in the meantime, but still preserve maximum information. We still believed that the taxonomic changes which resulted from the discovery of M410 were valid, we just weren't sure that all the changes downstream of M410 were valid (nor were we sure that Sengupta's decision to make M12 and M102 synonymous was valid). We decided it would be more valid to use the J2a/J2b labels in conjunction with the "by mutation" nomenclature, than revise the nomenclature ourselves. In effect we'd use a hybrid version of the two nomenclature systems. Use one system for everything "downstream" of the disputed tree structure, and the other system for everything "upstream".

Our use of J2a/J2b in the "by mutation" nomenclature may change, depending on what nomenclature the new FTDNA tree assigns to M12 v's M410. It is very possible that the two labels may get switched - either version could be considered equally valid, as outlined below. Again we think that the YCC needs to better clarify the official manner in which name changes are done (or revise the nomenclature themselves on an annual basis, as they originally proposed in 2002).

Is M410+ J2a or J2b?? Is M12+ J2b or J2a??

In early 2006 the paper by Sengupta et al. was published. They referred to M410+ as J2a and M12+ as J2b. However, later that year Regueiro et al. published research in which M12+ was referred to as J2a and M410+ was referred to as J2b. The nomenclature used by Sengupta et al. 2006 and Regueiro et al 2006 contradict each other. Interestingly, Dr Peter Underhill (one of the members of the YCC) was a co-author on both research papers.

The question is which version is more valid? Either could be considered more valid than the other, depending on different rules used in Taxonomy. Greater clarity about specific rules for naming Y- Chromosomal lineages would be helpful.

Using the J2a label for M410 could be considered the most valid, according the taxonomic rule of priority (in which the earliest published name for an equivalent lineage has priority. The Sengupta et al. paper was published before the Regueiro et al. paper. Therefore the Sengupta et al. nomenclature has priority.

On the other hand, - the M12 SNP was discovered prior to the discovery of the M410 SNP, so it could be legitimately argued that the M12/M102 lineage should be assigned the "J2a" label, and M410 assigned the "J2b" label.

However, if the original YCC paper is consulted, it can be seen that they generally label the lineages with less "tip haplogroups" first, and those with more "tip haplogroups" last. That is why (for instance) the lineage named "K" was labeled K rather than (for instance) G. There are more tip haplogroups within M410 - therefore it would be more valid to call M12+ J2a, and M410+ J2b. On the other hand, it may be that principle of having divisions with more tip haplogroups last was only relevant for the initial structuring of the tree, and might not apply to revisions.

Although it seems that it might be more valid to call M12+ J2a and M410+ J2b, we decided that overall it was better for us to leave the J2a v's J2b labels as they commonly used, and let the experts decide. We shall see how it is treated in the new NRY tree presented at the FTDNA conference. We do hope that both M410 and M241 are included (and it would be rather nice if FTDNA tested for them as well - would be rather interesting to see if any M172+ M12- M410- haplotypes are found).

 

 

 

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This work can be freely cited, if it is attributed to:
The J2 Y-DNA project
http://www.j2-ydnaproject.net

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