Genographic Project yields informative new branches for J-M530

The new Genographic Project's Geno 2.0 test contains over 12,000 SNP's on the Y Chromosome.  A good level of participation from J-L24/L25 or M530 as L24 is referred in published papers, has resulted in new branches and twigs for this subclade of J2 which peaks in frequency in Eastern Iran (Yazd, 17%+ J-M530).  Below is a draft tree of J-L25 with the new SNP's and their theorized positions:

New SNP's that reveal new branching include F3133, F761, PF4888, PF5401, PF5366, PF5368, PF5456 along with a large number of SNP's which reinforce existing branches.  Of most interest are the newest branches near the top of L25-PF4888/PF5401 and F3133.  These 2 new branches seem to divide a large section of J-L24, L25 in half and the task in the coming months will be to test these new mutations on various other clusters of J-L24 (M530).

The Genographic project description for L25 with a map view origin in Western Turkey seems different from the research of Grugni 2012 which identified M530 as originating in Iran, peaking in frequency in eastern Iran (Yazd 17%+) and peaking variance in both the south and north of Iran.  Geno 2.0 reports J-L25 frequencies as follows:

Branch: L25 

Age: Bronze Age

Location of Origin: West Asia

With the trade of goods produced in the Bronze Age, members of this lineage moved first into the Mediterranean and then on to Europe, where it is present at low frequencies.
Today, this line is present most often in Tunisia (10 to 11 percent), Azerbaijan (9 percent), Macedonia (5 percent), and Malta (4 to 5 percent). It is about 4 percent of male lineages in Armenia, Kuwait, and Jordan. It is between 3 and 4 percent of the male population in Iran.

Note: This branch is not accompanied by a major movement on the map, and research on this branch is continuing.

Such a high number of new SNP's will assist in determining various migrations for this subclade of J2 which has such a strong connection to the Middle East.

Ancient Migratory Events in the Middle East-Y Chromosome Variation of Iranians

A very comprehensive new study on Y-Chromosomes in Iran is shedding light on Haplogroup J2 and the origins of its subclade, M530, also known as L24 and defined by the SNP rs35248080.  The study looks at various population groups in Iran and the spread of Y-Chromosomes.  From a J2 persective, M410, L26, M530 (L24), M67 and M92 were studied along with M205 and M241 in Haplogroup J2b.  The results showed an ancient background mainly composed of J2a subclades, along with an influx of M92 from Asia Minor into certain groups in Iran.  Overall Haplogroup J comprised 31.4% of all modern Iranians combined; with J2 making up 22.5% of the population, the overwhelming majority of that being M410+ (J2a).  From the paper:

In particular, the recently described J2a-M530 shows high frequencies in the Zoroastrians of Yazd (17.6%) and Tehran (15.4%), and in Persians of Yazd (17%).  J2a-M47 reaches frequencies higher than 5% in Yazd, Mazandaran, Khuzestan and Fars....Among the different J2a haplogroups, M530 is the most informative as for ancient dispersal events from the Iranian region.  This lineage probably originated in Iran where it displays its highest frequency and variance in Yazd and Mazandaran.

Also of interest in the paper, some ancient deep rooted lineages from IJ-M429 were observed in the Iranian Plateau.  This of course, forms a solid foundation for the theory of the spread of humans from Iran over the course of history into both India, other parts of the Middle East and elsewhere in Europe.  M530 however, showed a curious diffusion from a fairly clear origin in Iran.  While it did spread early to Turkey and the Levant where subcaldes Z387 and L70 (distinguished in part by DYS 391=9) likely arose, the authors report an almost complete absence of M530 from Iraq in table S3 (only 1.3% in Baghdad, 0% in Marsh Arabs).  It is also absent from 4 of 11 regions referenced from Turkey/Asia Minor and almost completely absent from many areas of Europe with the exception of Italy where migrations of M530 subclades Z387+ and L70+ from Anatolia likely occurred.  Was this uneven distribution through the near east the result of  climate, topography or other civilizations?  The paper does not address this issue and the age estimates and theorized spread discussed in the paper do not seem to correlate with the uneven results reported.  Nevertheless, the paper provides invaluable data on Iran; it is the second major paper to address J2a-M530 and provides a window into theY-chromosome makeup of modern day Iran with genetic clues to a very ancient presence of Humans in the country.

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1000 Genomes Project yielding informative SNP's for Haplogroup J2

The 1000 genomes project, with data freely available to the scientific community, is providing a multitude of informative markers to the Y-DNA Tree. Within J2 a number of new SNP's have been identified, including Z387 which may split current haplogroup J2a4h (L24, M530). Within this subclade of J2, some key clusters were identifiable by Short Tandem Repeats, especially at DYS 445 where values of 6 and 10 are largely observed whereas most M172 derived haplotypes carry repeats of 12 at this marker. Testing is still in its initial stages but results thus far are showing that DYS445=6 haplotypes are Z387 derived and DYS 445=10 haplotypes are ancestral for this SNP. Previously, a marker, L70, had identified a large subset of the DYS 445=6 haplotypes, with the exception of one cluster. Z387 may turn out to be an informative Y-SNP which identifies most or all J2a4h haplotypes with the apparent deletion at DYS 445=6.

Y Draft Tree graphic courtesy of Thomas Krahn, DNA-Fingerprint. A number of other 1000 genomes SNP's within Haplogroups J1 and other subclades of J2 are being researched by a variety of projects including the Y-Haplogroup J project at Family Tree DNA headed by Bonnie Schrack.

Neolithic Patrilineal Signals on the Armenian Plateau

A recently released study on the Y-Chromosomes of Armenians from four distinct regions, the Ararat Valley, Gardman, Lake Van and Sasun shows a predominence of the J2-M172 haplogroup, combined with R1b, G2 and E1b1c1. The paper indicates settlement and population expansion dating back to the neolithic. This study , undertaken by Herrera, Underhill, Regueiro and others, recorded frequencies, calculated variance and compared these figures with neighbouring populations in an attempt to understand the migrations of the most frequent haplogroups observed within a neolithic context.

Frequencies of J2-M172 were very high, at 30% in the Gardman Region of present day Azerbaijan and 29% in the Lake Van region of eastern Turkey. J2a-M410(xM67) was the most frequent haplogroup subclade observed. A single P279 haplotype (J2a3), an extremely rare sublcade of J2 was also observed. Haplotype diversity, often used to determine the age of a particular haplogroup, was highest in neighbouring Palestine, followed by Crete, Syria, Greece and Lebanon. These figures, the authors suggest, could be indicative of an arrival of J2 chromosomes to the Armenian Plateau from the Levant possibly coinciding with the expansion of Agriculture.

The data observed in the Armenian Plateau, while carrying frequencies of Haplogroup J2 common in other areas of the Middle East, showed a much higher level of R1b, a correlation not observed in neighbouring populations like Iran, Iraq and the Levant. The authors suggest both R1b and J2, combined with other haplogroups E1b1b1-M35 and G2a are all indicative of Neolithic expansions and migrations. Yet R1b stands out from this group as it shows a very different frequency and spread from J, E and G haplogroups, which are much more frequent in the Fertile Crescent.

Genetic Diversity on the Comoros Islands show Seafaring Influence on Settlement

A recent Study in the European Journal of Human Genetics explores the rich and diverse history of the peoples of the Comoros islands. The Comoros islands are situated in the western Indian Ocean off the coast of Tanzania. Y chromosome and mitochondrial analysis showed a strong male genetic influence from South Asia and the Middle East, the latter attributed by authors to be as a result of settlement of Shirazi Persian Traders on the islands some 1000 years ago.

J2a, M410 was detected at a rate of 7% on the sample set of 381 Y Chromosomes. Interestingly, rare J* (xM172 xM267) was also found among samples from the Comoros.

The J1 and J2 data along with G2a and E1b1b data is attributed by authors to have come directly from a Middle Eastern origin and mostly from Shirazi Traders from the city of Shiraz in present day Iran.

By 1000 YBP, the Shirazi, traders with origins in the Persian city of Shiraz in present day Iran, had established themselves on the island of Kilwa. The Shirazi were responsible for the generalisation of Islam on the Swahili coast by 500 YBP. They had built mosques on Kilwa, Zanzibar and Anjouan by 800 YBP...A possible source of the Northern Y chromosomes is therefore the Shirazi traders from Southern Iran who established trading posts on the Comoros by 800 YBP.
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Haplogroup J2 subclade M340 downstream of P279

Recent testing at Family Tree DNA has confirmed that a very rare subclade of J2, M340 reported in Anatolia in the paper "Excavating Y-Chromosome Haplotype Strata in Anatolia" has been shown to reside downstream of an equally rare subclade P279. Both P279 and M340 reside upstream of L26 and L27, SNP's derived in many but not all M172 haplotypes.

To date only 4 cases of the P279 subclade (formerly referred to as J2a3) have been reported FTDNA as well as 2 cases from published data. King and Underhill reported M340 in a sample from region 8-Western Coastal Anatolia. Other known cases to date are also from Anatolia, Syria, and single samples have been reported with origins in Southern Russia and Southern France.

The coming of the Greeks to Provence and Corsica

A new paper released by King, Underhill, Chiaroni et al tries to unravel the Y chromosome contribution of ancient greek settlements to the Southern French regions of Provence and Corsica. Their conclusions in analyzing the data is that upwards of 17% of the paternal lineages in Provence could be of Ancient Greek origin. The study itself focuses on E1b1b V-13 as the signature greek marker. Their conclusions also suggest that southern France had little contribution from the Neolithic period. However, how they arrived at these conclusions, while they may be valid, could be, in part, erroneous. Southern France, especially around the testing areas along the Rhone was not simply a Roman territory, it was part of "Rome" itself, with senatorial representation. The study tries to negate the contribution of E-V13 from Roman sources by comparing Provence to other Roman conquered areas such as Spain and England. This comparison is apples and oranges as southern France was far more tightly integrated into the Roman Empire than most other areas outside present day Italy. Therefore, some of the E-V13 found in southern france may be indicative of Roman settlement and not just of Greek origin.

The paper also suggests that Haplogroup subclades G2a3a-M406 and J2a4h-M530 are indicative of Neolithic migrations. And therefore the absence of these subclades suggests little or no Neolithic contribution to the present day genetic makeup in Provence. This assumption can lead to false conclusions as G2a3a and J2a4h are likely indicative of multiple origins from the Middle East and based on certain dating methods could be indicative of post-neolithic migrations. So, the authors conceivably could be looking at the right haplogroups but the wrong subclades to estimate Neolithic contributions to the present day genetic makeup of Southern France.

Criticisms aside, the authors provide solid evidence that Greek settlement in southern France is evidenced in today's genetic makeup of men from the region. There are some clear correlations of haplotypes and their study involves a much deeper analysis both of subclades and haplotype STR's allowing for more accurate comparisons. Combined with archaelogical evidence, viticulture and historical knowledge, this region of southern France carries with it, traces of ancient Greek origins in their genes as well.

Looking at J2-M172, the authors found 10% derived M172 haplotypes in their sample study. 8% were derived for M530, J2a4h with 445=6 while 2% were derived for J2a4b, M67. Many J2 subclades were completely absent from the region including J2a4b1-M92, J2a4h with 445=10, J2a*, J2a4* and all subclades of J2b.

Link to Paper