Welcome to the J haplogroup project with an open access philosophy! We invite all members of the Y-DNA haplogroup J, from anywhere in the world, to join, and welcome all interested researchers to visit. We encourage everyone to freely share their Y-DNA data for our common benefit.
Welcome new co-admin Tim Janzen!
Thank goodness a co-admin has been found who will be able to bear some of the burden of managing this huge project. Tim has become a real expert in his subclade, J2a4h1a, L70+, and I'm very happy that he is willing to help out with that very active area of our project. No doubt he will be contributing some excellent material to this website as well.
New SNPs now available!
FTDNA has now added a number of new J SNPs to the Advanced Orders page. Here's the J section of the SNP listing:
J-L24 $49.00
* L70 $29.00
* L84 $29.00
J-M267 $29.00
* L134 $29.00
J-M304 $29.00
* L60 $29.00
J-P58 $49.00
* L92 $29.00
* L93 $29.00
Most of these SNPs are not expected to be of major importance, except for one -- L70. This is the SNP we've waited years for -- from the time when we first recognized the distinctive group of haplotypes that we then called "J2x." Once the deletion at DYS445 to 6 was found, we gave it the clade name, J2a1k. Research has shown it to be especially common in southeastern Anatolia and in southern Italy, among other places. It's also found to some degree in Greece, but mainly in Crete and the southern part of the mainland.
After many more permutations of discovery and amendment of the SNP tree, culminating with the discovery of L70 in the 23andMe results of one of our project members, and Thomas Krahn's development of this SNP for customer ordering, we have finally come to the day when FTDNA is able to offer you this SNP.
According to our data so far, L70+ is found only in persons who are L24+ and L25+. At the same time, it's correlated not only with having DYS445=6, but also, with having DYS462=8 or 10, and with a few exceptions, DYS391=9. DYS462 and DYS445 may be ordered from FTDNA as Advanced Orders.
Tim has also found that L70+ people have extra, partial alleles at DYS464, giving results such as 15.1, 14.1, or 16.1, but these are not reported by FTDNA on the project results table. The partial allele has been seen in results from SMGF.org, who do report them in all cases when they are found. If they are interested, FTDNA customers may either write to the company and inquire about their original tests of DYS464, to see if these partial alleles can be seen on the electropherogram of the results, or they may order the Advanced DYS464X test from Thomas Krahn's Genomic Research Lab in Houston.
L84 is an interesting SNP which has been found in one project member so far, kit 123476, who is L24+, but L25- (negative). This tells us that L24 and L25 are distinct branches on the phylogenetic tree. We'll be able to add L84 to the tree if we find any substantial number of people, who aren't very closely related to kit 123476, who are also L84+. So anyone who is not L25+, or L70+, has not already been found L24-, and is not positive for one of the other subclade SNPs such as M67, M319, etc., and has a J2a haplotype, is welcome to try and see if they could be L84+.
In J1, there are three new SNPs. Thomas has told me that he expects L92 and L93 to be rare. They were found in a P58+ person. I haven't yet been informed about L134! I hope to remedy that shortly. I'll report back when I know more.
L60 is a SNP that I happened to notice a couple of years ago in some data from a study that had tested a few random HapMap Y-SNPs in Amish populations that I'm descended from. Gareth Henson's work with the data made it possible for me to see that it was a J SNP. Further testing, and results from 23andMe, have shown that in all J samples, it is either positive or has failed to give results. I believe it's a SNP shared by all members of the J haplogroup, so its testing isn't a high priority.
Previous update:
FTDNA Updates its Phylogenetic Tree & Subclade Names
You'll see that many members of J2a now have new subclade names assigned to them! These represent a major advance that takes into account the new SNPs, L24, L25, L26, and L27.
This is the latest update of FTDNA's phylotree, but not the last. There was necessarily a cut-off date about 10 days before this tree was rolled out, and some major developments in our haplogroup unfortunately reached the point of being proven valid in the eyes of FTDNA a few days too late for the deadline. So, you'll see that in our project results table, I'm using the FTDNA clade names to start out with, but with a few additions.
I hope to post some tree diagrams here soon, but FTDNA's current tree, also recognized by the YCC, is available here: Y Chromosome Phylogenetic Tree
Thomas Krahn's more up-to-date version can be seen here:
Working Draft of the Y Chromosome Tree Below J-M304 This shows the latest version that FTDNA recognizes as proven, but it will be several more months before the official YCC tree and their computer system are updated to reflect all the new information.
Only those members of the project who have actually been tested for L24 and/or L25 will see the new clade name, J2a4h, next to their name. The rest of you remain in your existing sections of the results table, which indicate the SNPs I believe you will be positive for. Of course, you are encouraged to order these SNPs to confirm the assignment.
Though FTDNA's current tree shows L24 and L25 on the same branch, we have now discovered that L25 is downstream of L24. J2a4h means L24+; a person who's additionally L25+ will be J2a4h1, but this extension of the tree does not yet show up in the clade names of FTDNA's current version. If you are L25+ you will, for now, be shown by FTDNA as J2a4h.
The further SNP, L70, will very soon be available for ordering. This clade is believed to include only the group (recently called "Cluster A") who typically have both DYS445=6 and DYS391=9. L70 is downstream from both L24 and L25. L25, downstream from L24, now has a small (possibly private) brother clade, L84, also downstream from L24.
There are several SNPs whose exact placement is not yet known. I believe M158 to be downstream from L24; we don't yet know if it is also downstream from L25. The SNPs M137 and M318 are known by tests at FTDNA to be downstream from L70; I believe M289 to be a brother clade to them, from indirect evidence provided to us by Stanford. It will only be possible to know M289's placement for sure if the folks at Stanford are able to provide a positive control sample for M289, or else test their sample for L70 themselves.
All samples so far that have DYS445=10 are positive for at least L24, and usually also L25. All samples that have DYS445=6 have been positive for both L24 and L25, and therefore will be within J2a4h1. The group who have DYS445=6 and DYS391=10 appear, beyond that, to be negative for L70 and other downstream SNPs. Thus, for now they will have the J2a4h1* clade name, with the additional qualifier of DYS445=6.
There is obviously much more to explain, but this will have to do for a preliminary news bulletin! Things will continue to evolve. I would advise everyone to get used to your clade names changing, because this isn't going to stop, but will probably accelerate. The best solution is probably for us to refer to clades by the name of their SNPs, rather than by names like "J2a4h1."
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News from last time
We've been so fortunate now that FTDNA's lab in Houston is now running at full speed. We found the first P279+ project member, N58704, and right afterward, the first P81+, 130992.
What's cool is that we've now discovered that P279+, unlike all the other J2a clades that project members belong to, has DYS413 values of 20+. It doesn't have that deletion at 413 that we now know corresponds to L26 and L27. This person is going to be tested for those SNPs soon. Their subclade will be put onto a different level of the tree, upstream of L26 and L27, while all the other J2a subclades are downstream of them. There are four other families who I've had clustered with the family of N58704, who may or may not belong to this same clade. It's very important that they order Deep Clade SNP tests, or upgrade any they've already had done with the Extended version which includes P279.
The time has come!
Finally, at long last! The new SNPs are here! Yes, the ones that we helped to discover, that are going to finally make J2a*, J2a1* and J2a1k (by whatever name) "official"! Note that the price is not going to ruin anyone's finances: only $29 a SNP.
We can all rejoice, but not everyone needs to order these SNPs, of course. Only those who are in the ambiguous territory of uncertain clade, between J2a* and J2a1*, or between J2a1* and J2a1k*, for example, really should test them. Others can test them if they like just to be able to get that stamp of authenticity, even if there wasn't any real doubt about their clade.
So who's the highest in priority to order them? Your category will already be labeled on the Results Table to let you know. Are you in one of these groups?
"J2a* candidates, need L26 & L27 tests"
"J2a1k or J2a1k1 candidates, need L24 & L25 tests"
These are the people most likely to benefit. But certainly not the only ones. You all in the category "J2 - Need to order more markers to be classified" would do well to order these - each case is individual, but if you order all four SNPs, it wouldn't hurt. Of course, I'd really like to see you all order at least 37 markers!
As far as the category, "J2a - subclade unknown, need Deep Clade SNP test", it won't be necessary for those of you who've already tested 67 markers, but for the rest, it certainly wouldn't hurt. You ought to order the Deep Clade tests too, though! They won't set you back that much.
More later! Thanks for your participation!
Previous news entry - lots of info
Now there will be changes in the subgroups themselves. In J2, we are delighted to have found a number of new SNPs -- four so far -- that have resolved some troublesome places in the phylogenetic tree. They weren't troublesome to us, but to the folks in Arizona who put together the YCC tree, which FTDNA uses for their official subclade names, only SNP mutations were acceptable to define a clade. That is why there has been the difference in your clade names -- J2a for FTDNA, J2a1 for us at ISOGG; J2a2 for FTDNA, J2a1b for us, etc. The most glaring problem was the omission of the large clade that has been defined by the deletion at DYS445, which we've called J2a1h for the last year (originally J2a1k), and its close relation, "pre-J2a1h."
Well, all this is about to change. By analyzing data from 23andMe test results, with the invaluable assistance of Adriano Squecco's spreadsheets, we've been able to identify some SNPs that Thomas Krahn, head of FTDNA's Genomics Research Center, has named L24, L25, L26, and L27. These will be changing the J2 landscape considerably.
Thomas' tests on a representative group of subjects have determined that so far, everyone tested who is a member of either J2a1h or pre-J2a1h, are positive for the L24 (rs35248080)and L25 (rs34534058) SNPs, while all others tested are negative for them. Thus, a new clade on the phylogenetic tree will be defined by these two SNPs.
The L26 (rs34459399) and L27 (rs34126399) SNPs have already been tested by other labs, and are undergoing confirmation at the GRC.
L26 was discovered earlier by Ethnoancestry, who named it S57, but its technical details (rs number, etc.) were not made public at that time. EA has now confirmed that S57 is rs34459399. A number of our project members were pioneers in being tested for this SNP, and their results demonstrated that it occupied the same place in the tree as the deletion at DYS413, which for years has defined J2a1. All members of J2a*, who were positive for M410 but did not have a deletion in their DYS413 marker, have tested negative for S57 (L26), while members of J2a1 and its subclades, who do have that deletion, were all positive for S57(L26).
L27 has been tested at Stanford by the Underhill lab, as described by Dr. Roy King in his blog posting and discussions on 23andMe's Spittoon blog, The Origin of Farming in Europe: A View from the Y Chromosome, where he states, in reply to my query,
"You are indeed correct – according to tests we conducted in Dr. Peter Underhill’s laboratory at Stanford University, rs34126399G is equivalent to the DYS413 deletion that defines J2a1. Thus the map reflects both the distribution of the DYS413 deletion and rs34126399G. As I wrote in the blog, rs34126399G captures the circum-Mediterranean migration of the first farmers in Europe and the Near East."
The next step was to incorporate the new SNPs into the ISOGG tree. This has been done, and you can see the result here: Y-DNA Haplogroup J and its Subclades - 2009
We decided to retire the name J2a1h, which could be confusing since it has been used in some scientific papers to refer to M319+, and instead, we will be going back to the name we originally used, J2a1k. The membership of the new clade, though, will be expanded from that clade's original definition. We had used the criteria of DYS445=6 to define it, and only later discovered the broader group of related haplotypes which have DYS445=10. Now, this broader group will take the name J2a1k, while the more narrowly defined group, which shares a more recent common ancestor, will be known as J2a1k1.
The members of our project have a very special opportunity to be on the cutting edge of scientific discovery. Please consider ordering:
* L24 and L25 if you are a member of J2a1* or especially, the new J2a1k or J2a1k1
* L26 and L27 (L26 only if you haven't yet tested S57) if you're a member of J2a* or J2a1*
Reminder
I URGE every member of our project to PLEASE enter the name of your earliest known paternal ancestor, or at least your surname, in the box on your "User Preferences" page! There are so many empty spaces on our Y Results table. I may be able to see who you are, but please give a thought to your fellow J haplogroup and sub-clade members! They really want to know something about your family and its origins.
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Please note that we have a General Fund for contributions to the project. Donations will be gratefully accepted, and will go to enable upgrades to the tests of members who do not have the financial means to pay for them. These members, for example, may live in countries where the exchange rate with the dollar and the pay scale do not permit them to spend the amount on DNA testing that others fortunately can afford. Since this fund is just getting established, funds will be very limited, and will be applied to cases that can make the greatest contribution to answering crucial research questions.
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PUT YOURSELF ON THE MAP!
We would like to encourage everyone to put yourself on the map, which appears under "Y Results," below the haplotype chart. In order to do this, you'll need to:
1. Go to the "Setup Preferences" tab in your personal page.
2. At the bottom of that Setup page, there are places to enter the name of your earliest paternal ancestor, AND the latitude and longitude of his place of origin.
3. This latitude & longitude may be found in several places. One of them can be found by following the link provided by FTDNA, right there. You may need to use the Internet Explorer browser and re-enter the name of the city and country, when you get to the external mapping website. This should provide the latitude and longitude.
4. You'll need to copy the decimal version (for example, latitude 47.083 and longitude 7.696) instead of the old form that gives degrees and minutes.
5. Paste the decimal numbers into the latitude and longitude boxes on your Setup page.
6. Be careful! A mix-up between latitude and longitude, or an omission of a needed negative sign (-), could result in your dot appearing in the middle of the Atlantic Ocean, the Sahara Desert, etc.
7. Now you can go back to our J haplogroup project Y Results page, and you should be able to see your dot appear on the map! Click on the "+" sign to zoom in on the map, and "-" to zoom out. You can also switch to a lovely satellite photo for the background, using the button on the upper right-hand side. Enjoy!
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