Saturday, January 19, 2013

National Geographics Geno 2.0 Update.

The National Geographic's Genographic 2.0 Project is providing valuable information regarding our J-L24(M530) clade. I recommend taking the Geno 2.0 test over Family Tree DNA's (FTDNA's) Deep Clade test. Geno 2.0 will provide your current terminal branch of the Y-DNA tree, just as Family Tree DNA's Deep Clade test, however Geno 2.0, testing over 12000 Y-SNPs, may reveal, in addition, previously unknown branches.

I'm posting above the current J-L24 Y-DNA phylogenetic tree. It is quite different than the one I posted in December 2012! Just click anywhere on the chart for the full view. The chart was provided by Ludmila Ryabchenko, sponsor of FTDNA kit 171488 (Nickolay Ryabchenko). A clearer view of the chart can be found HERE.

What is new is the two large J-L25 branches(clades) defined by SNPs PF4888/PF5401 and F3133. They parallel our other major, in fact largest, J-L25 branch defined by the Z387 SNP (encompassing our DYS445=6 haplotypes). We suspect that most all members, subclusters, and subclades of J-L25(J2a4h2) will fall under the PF4888/PF5401, F3133, and Z387 branches of J-L25. This is a big step forward in our understanding of the J-L25 genetic tree. Currently, as seen in the J-L24 phylogenetic tree, PF4888/PF5401 unites the L243 clade with a new clade called PF5366/PF5368. In turn PF5366/PF5368 unites my own L229/L230/L264 clade with the L254/F659 clade. The L254/F659 clade also unites two other clades called M365.2 and CTS1489. Clearly we need additional testing of the PF4888/PF5401 clade in order to learn more about its genetic structure. We need at least one member of each of the L243 clusters (L243-alpha through L243-eta) to test (Geno 2.0 preferably with the possibility of finding new SNPs, but in the future FTDNA will offer individual SNPs for testing too). The L243 clusters can be seen in our FTDNA J-L24-Y-DNA Project Y-DNA Results section. The L243 clusters are numbered 02111 through 02117 (forest(dark) green clusters). We also need the many members of the L254 clade to test so that we can see how many are derived for the new F659 and CTS1489 SNPs.

A characteristic of the PF4888/PF5401 clade, first noted by David Dugas, is YCAII=19-23. It appears, so far, that all members of PF4888/PF5401 have YCAII=19-23.  This stands out from the ancestral state which is YCAII=19-22 found both in the F3133 and Z387 clades. This doesn't mean the PF4888/PF5401 clade is younger than the F3133 and Z387 clades. It just means that YCAII=19-23 happened early when PF4888/PF5401 was founded, while it did not happen in F3133 or Z387. In any event one can scroll through the J-L24-Y-DNA Projects Y-DNA Results section, observe YCAII, and see who might be PF4888/PF5401 via YCAII=19-23. One sees that the Cohen cluster (0214) and the Saudi-alpha cluster (0215) are likely also PF4888/PF5401 (but not tested yet). It would be good to see several members of the Cohen (0214) cluster take the Geno 2.0 test, hopefully we will find a SNP for this Jewish cluster that is L254-. The PF4888/PF5401 clade appears to have a European flavor and a significant Jewish component, but with lighter links to Lebanon and the Middle East. This may just be due to a lack of sufficient genetic testing from the area of the Levant (Lebanon, Syria, Jordan, Palestine, Israel, Cyprus, and Southern Turkey). Kamel Al Gazzah indicated that PF4888/PF5401 has an Ashkenazi component while F3133 a Sephardi component. However, interestingly, we observe that the Z387 clade has both Ashkenazi and Sephardi components.

F3133 appears to have more of a Middle Eastern flavor and a lighter European component. We will see how this pans out as more and more of our members test with Geno 2.0 or through FTDNA. Currently we have found that J-L192.2 shares F3133 with a new clade called F761. F761 currently includes the Ducas (L231) and Ward (L317) clades. Looking at YCAII=19-22 it appears that the Mughal-Timurid, Curtin, Al-Ahsaa, Najd, and Syrian-Anatolian clusters may also be F3133 and possibly F761. Again, it would be most helpful if at least one member of each of these clusters would take the Geno 2.0 test.

I'm looking forward to more Geno 2.0 results in the near future!

Wednesday, December 26, 2012

J2a-L24(M530) Y-DNA Genetic Tree

I'm posting below the current J-L24 genetic tree. It is quite different than the one I posted in Mar 2009! It will change significantly in the next year as we find even more J-L24 branches (SNPs: Single Nucleotide Polymorphisms) as a result of the National Geographic Societies Genographic Project which currently tests an amazing 12064 Y-SNPs. If you are interested in finding your branches of the Y-Tree, both near and far, I recommend the Geno 2.0 Project.  All your Y-DNA results can be downloaded to Family Tree DNA. Also you can download all results to your own computer (it is your data after all).

Here is the current J-L24 Y-Tree (click to see full image):

Tuesday, December 4, 2012

More Comments on Grugni et al (2012)

In the J-L24 Blog of 28 Nov 2012 I mentioned that Grugni et al (2012) found L24(M530) at 12.2% frequency in Lebanon and that this lent support to the Phoenicians providing early movement of L24(M530) Y-chromosomes westward into the Mediterranean Sea islands and coastal countries and also onward to the coast of Portugal and beyond.

There are several comments that need to be added concerning the statement above. First of all, the 12.2% applies to people living in Lebanon today. It says nothing about the L24(M530) percentage (frequency) 100 years ago or 3600 years ago at the very beginning of the Phoenician maritime trading culture. There is no way to know what the L24(M530) frequency was in Phoenicia 3600 years ago of course.  All we can say is that if the L24(M530) frequency is 12.2% today in Lebanon then it was possibly some similar frequency 3600 years ago. It gives us some fragile evidence for the presence of L24(M530) in Phoenicia (Lebanon) thousands of years ago. It is not definitive. It makes me think however that every Galley, every Bireme, that left a Phoenician port probably had one or more L24(M530)'s aboard for a time period lasting over 1000 years. If nothing more, it "fires the imagination", but definite proof of Phoenicians being L24(M530) it is not.

The second comment is that the Phoenicians are only one of numerous possibilities for the movement of L24(M530) haplotypes, as indeed we know they did move, from their ancient origins in Iran (L24(xZ387) map). Prior to the Phoenicians there were the Minoans, a maritime power in the Aegean Sea. The Aegean Sea lies on the west side of Turkey and we already know of the L24(M530) presence in Turkey. The Y-DNA of Crete is discussed in the paper by King et al (2008). There is also an interesting post on Crete in Mathilda's Anthropology Blog. In King et al (2008) we find 5 cases out of 193 randomly selected haplotypes from Crete's Heraklion Prefecture (north-central and central Crete) that were found to be DYS445=6. 2008 was just before we learned of L24 and L25, but we know now that DYS445=6 is found only within haplogroup L24(M530), subclade L25, and subclade Z387. So right away we can say that L24(M530) is indeed found in Crete today and likely L24(M530) has been in Crete for some time, and possibly even during the time of the Minoans. So the Minoan mariners might also have been a source for the early spreading of L24(M530) Y-chromosomes. In fact King et al (2008) found 13 cases of DYS445<=10 all of which I believe are derived for L24(M530) and L25. Hopefully at some point these Cretan DYS445<=10 haplotypes will be tested for M530 which I am sure will provide even stronger evidence of L24(M530) in Crete. The Minoans and Ancient Greeks very likely played an early role in the frequency and high diversity of L24(M530) haplotypes we see today in Apulia, Italy as found by Grugni et al (2012). Later the Roman armies and auxiliaries played a role. Possibly even the Carthaginians under Hannibal (Battle of Cannae) played a role. Later still the Byzantine Empire, over a period of about 1000 years, very likely played a role in the movement of L24(M530) Y-chromosomes. Certainly the Jewish people played a role too, possibly a major role as we find Jewish subclades and subclusters throughout L24(M530) today. In any event, very likely, it was through multiple ways, in space and time, that L24(M530)'s moved from the Middle East into Europe. It wasn't by one isolated single event.

Wednesday, November 28, 2012

Comments on the J-L24 aspects of Grugni et al (2012)

Some highlights, links, and comments of the haplogroup J-L24(M530) aspects of the Grugni et al (2012) paper are given below.

The Grugni paper found that L24(M530) occurred at a frequency of 10.00% out of 130 random samples in Konya, Turkey. These are probably Z387 (DYS445=6) haplotypes.  We don't know at this time. I have communicated with Dr. Grugni and Professor Semino regarding SNPs we have found within L24 and Dr. Grugni has agreed to test L25, Z387, and L70 on her datasets. Tests are underway at this time. The variance of the Konya, Turkey haplotypes is moderate at 0.326. Variance is a mathematical procedure that is used to test the simularity of the haplotypes. If the variance is 0.0 then the haplotypes are identical. As the variance increases the haplotypes become increasingly different (there is no limit). Variance is also used to estimate the age of a group of haplotypes. The Grugni paper provides calibrated age estimates in their Table S7. Age of microsatellite variation and Standard Error within the main haplogroups.

The Grugni paper found that L24(M530) occurred at a frequency of 12.20% out of 41 random samples from Lebanon. The variance was however lower at 0.200. The high frequency in Lebanon is interesting and it lends support to the Phoenicians as providing early movement of L24(M530) haplotypes westward into the Mediterranean Sea Countries as well as the coast of Spain and Portugal, the British Isles, and possibly even Ireland.

The Grugni paper found that L24(M530) occurred at a frequency of 12.24% in the Hormozgan Province of Iran. The variance was moderate though at 0.333 in this southwestern corner of Iran. Hormozgan Province is important to J-L24(M530) because it stands as a gateway from the Gulf of Oman, Arabian Sea and Indian Ocean, into the Persian Gulf. Perhaps it is through Hormozgan that today we find J-L24(M530) Y-chromosomes in Bahrain, Qatar, Kuwait, United Arab Emirates, Oman, and of course Saudi Arabia. Most important is the maritime port city at Bandar Abbas.  Perhaps Bandar Abbas is the link to J-L24(M530) Y-chromosomes we find today in Kerala, India? Bandar Abbas was an active maritime port city even during the reign of Darius the Great (586 and 522 BCE). Marco Polo visited Bandar Abbas in 1272 and 1293 and reported widespread trading activities. European colonialists landed in the region in 1497 for the first time headed by Portuguese explorer Vasco da Gama. The Portuguese controlled the area for a while but then the trading empires of the Dutch and English East India Trading companies took over. These various contacts with European nations and trading companies were no doubt conduits for movements of some J-L24(M530) haplotypes.

The highest L24(M530) frequency observed, anywhere in the world, was for Zoroastrians in the city of Yazd, Iran. The frequency was 17.5% out of a random sample of 80. The Persians of Yazd also showed an L24(M530) frequency of 17.5%. Zoroastrians of Tehran showed an L24(M530) frequency of 15.4%.  Other areas of Iran showed high frequencies as well, higher than found anywhere else in the extensive set of countries studied in the paper. It seems clear that Zoroastrians and Persians are important groups in our ancient L24(M530) paternal ancestry.

Iran then is our most ancient paternal homeland, but can one point to a specific area within Iran as the origin of L24(M530)?  Yes, it is possible from the variance. The place of highest variance, highest diversity of haplotypes, is likely the place of origin of L24(M530). Our L24(M530) origin appears to be with the people occupying the Mazandaran Province of Iran where the variance was found to be 0.730. Indigenous peoples include the Mazanderani who occupy the southern coastal plains of the Caspian Sea and the near by Alborz mountains. A closely related ethnic group are the Gilakis. The Gilaki are found in Mazandaran province and also in the Gilan Province just west of Mazandaran Province. These people are the oldest members of L24(M530) and I wonder how many will be found to carry the L25 SNP which is immediately downstream of L24(M530). So far in our FTDNA J-L24-Y-DNA Project we have found only two confirmed haplotypes who are L24+ and L25-. The second highest variance (0.651) was found among Persians/Zoroastrians of Yazd and Fars Provinces. The Mazanderanis people and the Persians are no doubt paternally related. I look forward to seeing Dr. Grugni's L25 test results. Perhaps we will find some cases being L24+ and L25-.

Outside of Iran I have already indicated the relatively high frequencies of L24(M530) found in Turkey and Lebanon, and there are several other countries worthy of comment. The first that stands out is Italy where L24(M530) is observed throughout. In fact the highest frequency of L24(M530) is 6.98% out of a random sample of 86 people in Apulia, which is higher than all places tested in Turkey except for Konya, Turkey. In fact Apulia, Italy shows the 3rd highest variance (0.552) observed in this study of L24(M530). This is remarkable because this degree of variance indicates and ancient age of the haplotypes in Apulia. In fact the Grugni paper indicates the Apulia L24(M530) haplotypes have an age going back 19500+/-5200 years ago (Table S7). The error is large at +/-5200 years but still even the minimum age is quite old for these L24(M530) haplotypes in Apulia. The 19.5+/-5.2 thousand years ago age indicates the Upper Palaeolithic (Late Stone Age). The Neolithic period begins about 8000 years ago. The Neolithic makes more sense to me because when I look at Apulia using Google Earth I see an area rich in farming. An explanation to this puzzle could be that L24(M530) Neolithic farmers moved into Apulia in more recent times, less that about 8000 years ago, but they just happened to have diverse haplotypes which we see today. It is not necessarily true that L24(M530) has been in Apulia for 19.5+/-5.2 thousand years (since the Upper Palaeolithic). Here is a brief summary of Prehistoric Italy. In fact when I check the published 9 marker haplotypes (6 out 86 random samples in Apulia are L24(M530)) 3 of them (50%) are very clear J-L70 haplotypes and J-L70 appears to have it's origin in Southern Turkey or Northern Syria about 3000 to 4000 years ago (my own estimate). Another sample is clearly L25 and may be L254 or L243. The remaining two haplotypes are unusual and I cannot resolve their position under L24 with just 9 markers tested. In any event it appears to me that L24(M530) in Apulia is more Neolithic or even Bronze Age than Upper Paleolithic.

Another country of interest is Israel. In Israel 7.32% out of a random sample of 82 Ashkenazi Jews were found to be L24(M530) and 4.65% out of a random sample of 43 Sephardi Jews were found L24(M530). This is in agreement with our own J-L24-Y-DNA Project where we see evidence of Jews throughout the subclades of L25. A notable Jewish subclade of L25 is L254. Also Jewish clusters and subclades are found within subclades L243 and L70. It will be interesting to learn the history of these various Jewish clusters and subclades of L25 and to see how they may or may not be connected.

Iraq is curious due to the low percentages of L24(M530) found there. Not one L24(M530) was found in 143 random samples of the Marsh Arabs of Iraq and only 2 L25(M530) were found in 154 (1.30%) random samples from Baghdad. This seems odd because Iran shares a good part of it's western border with Iraq. Perhaps L24(M530) haplotypes moved through the most northern parts of Iraq (Kirkuk, Erbil, Mosul)? It would be interesting to test L24(M530) in these northernmost areas of Iraq, and also the northern area of Iran at Urmia and Tabriz.

Poland is also interesting because no L24(M530)'s were found in a random sample of 99 people in Poland. This seems odd too because in our J-L24-Y-DNA Project we have 22 L24(M530) cases with ancestry from Poland (a number with Jewish ancestry). It could be that having ancestry from Poland and actually living in Poland are two different things? It could be with the overwhelming numbers of Y-DNA haplogroups I and R in Poland that L24(M530) is indeed difficult to detect? Also a factor could be the connection of L24(M530) with the Jewish people. The Holocaust was certainly a factor and the subsequent movement of Jews out of Poland another factor.

Spain is another country showing 0.00% of L24(M530) in this Iran study by Grugni et al (2012).  No cases of L24(M530) were detected in 93 random samples from Andalusia, 55 random Basque samples, and 29 random Catalan samples. Not one L24(M530) out of 177 total random samples tested. This is remarkable, because here I am an L24(M530) person with paternal ancestry from Basque Country (Spain). Perhaps L24(M530)'s left Iberia after 1492 CE and made their way to the New World and today their descendants are found in the America's! I suspect if Dr. Grugni and her colleagues were to test random samples from Veracruz and Puebla Mexico that they would be surprised to find L24(M530) in sufficient numbers, probably yielding a good idea of the L24(M530) frequency in Iberia before 1492. It would be an interesting experiment anyway. It would not fail I think, because today in the J-L24-Y-DNA Project there are 25 L24(M530)'s, out of 384 members (6.5%), with paternal ancestry from Iberia. They are Hispanics with more recent ancestry from Mexico, Central and South America.

Currently I am entering the Grugni et al (2012) 9 marker L24(M530) haplotypes into my J2 database and I will try to find matching subclades and clusters for them. I'll report on this later.

Two additional reviews of the Grugni et al (2012) paper can be found here:
Dienekes Anthropology Blog,
Haplogroup J2 (M172) Blog.

Saturday, November 24, 2012

Recent J-L24 Scientific Papers

There is a recent scientific paper having, so far, the most comprehensive information regarding the origins of our own J-L24 clade. In this paper L24 is called M530.  In the scientific community the official clade name is taken from the first published paper to discuss it and it turns out that Dr. Roy King was the first to discuss our L24 clade in a scientific paper The Coming of the Greeks to Provence and Corsica and he called it M530 in accordance to the nomenclature used by Stanford University. I think after over 3 years it is almost too late for us to shift from the L24 to the M530 name, maybe slowly, but just remember that L24 and M530 are one and the same mutation, clade, and branch of the Y-chromosome tree.

The paper is by Grugni V, Battaglia V, Hooshiar Kashani B, Parolo S, Al-Zahery N, et. al. (2012, Ancient Migratory Events in the Middle East: New Clues from the Y-Chromosome Variation of Modern Iranians. PLoS ONE 7(7): e41252. doi:10.1371/journal.pone.0041252. Here is a link to the paper: Ancient Migratory Events in the Middle East: New Clues from the Y-Chromosome Variation of Modern Iranians. The paper is free to download and don't forget to download the extensive supporting information files. This paper along with Dr. King's paper places our J-L24 (M530) haplogroup firmly within the population genetics scientific arena. We can expect to see more papers discussing J-L24(M530) in the future. A great step forward for our clade!

I wrote a summary of the L24(M530) aspects of the paper and it is posted on the The J-L24-Y-DNA Project News Section for 14 Nov 2012. I will repost my comments here later as individual news items in the FTDNA Project News section cannot be linked to.

I had an very enjoyable time studying and thinking about this interesting paper by Grugni et al (2012) and I hope that you will too.

Saturday, November 3, 2012

I'm Back (03 Nov 2012)!

I have not posted for some time, but I'm hoping to do much better in the future! In March 2009 I created a project website with Family Tree DNA (FTDNA).  It is called the J-L24-Y-DNA Project . I have spent a good deal of my free time working on that project, and with tasks associated with that project. This blog though will allow me to do things that are just more difficult to do via the FTDNA project.
Best Wishes to one and all!

Thursday, March 5, 2009

Who should test Y-DNA J2a SNPs L24-L27 & L70?

Figure 1 above (click on image to expand) shows the positions of the recently discovered Y-DNA J2a SNPs designated as L24,L25,L26, L27, and L70 by FTDNA. L70 is not included in FTDNA's haplotree yet. A rough draft of the most current J-tree can be seen at the DNA-Fingerprint website here (scroll down to the section regarding the J-M304 tree).

Those Y-DNA haplogroup J people who are J2, have DYS413<=18-18 (to make sure you are at least J2a, if J2a-M410 was not tested), and/or have DYS450=9 (specifically) should at some point consider testing L24 through L27 to help confirm their status for these SNPs. Currently only FTDNA & 23andMe test the L24 through L27 SNPs. Hopefully other companies will incorporate these SNPs in the future as well. If you are J2, but are not estimated or confirmed J2a, then you can estimate if you are J2a by checking your haplotype using Whit Athey's haplogroup predictor by inputting your haplotype: (link) ... If overall, according to Whit's predictor, you have a high probability of being J2 and zero or very low probability of being J2b, then likely you are J2a! If J2a is indicated then at some point please test L24 though L27. If you need additional advice or have questions then send me an email and I will try to help (aburto (@) san (dot) rr (dot) com).

If you have tested FTDNA's 67 marker set and you have DYS413<=18-18 and DYS450=9 then absolutely test L24 through L27 and L70 (available soon hoepfully) when feasible as you are likely a prime candidate to test positive for one or more of those SNPs!

However, please note:
FTDNA now offers testing of L24 through L27 via a "Deep Clade Extended" test at a very reasonable price! Testing of M137, M158, M318 may (I am not certain of this) also be included as these SNPs define important subclades of L24/L25. You can see the "Deep Clade Extended" offer from FTDNA via the Haplotree page or the "Order Tests & Upgrades" page.
[posted 21 March 2009]