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

Haplogroup J2 in the Maronites of Lebanon

A recent paper by the genographic consortium, Influences of History, Geography and Religion on Genetic Structure: The Maronites of Lebanon, demonstrates again the ancient and deep link between Haplogroup J2 and Lebanon. M172, Haplogroup J2 was the most frequent haplogroup found in all 3 Lebanese groups-Lebanese Muslims, Orthodox and Maronites. The frequency of Haplogroup J2 in the Lebanese Maronite community was 34.74%, one of the highest frequencies of M172 published to date. The study also showed however that Haplogroup J2 was found in 26.23% of Lebanese Muslims and 25.85% of Lebanese Greek Orthodox also being the most frequent haplogroup in these respective communities. The aim of the study was to describe the genetic structure of Lebanon and the effect of how social history may have contributed to genetic differentiation between these Lebanese religious groups. While the study did show some minor variance between the communities genetic structure, it revealed no significant distinction of major haplogroups. Supplemental data however did show that J2-M172 with DYS 391=9, often a characteristic of the L70 subclade of YCC Haplogroup J2a4h was almost completely limited to the Lebanese Christian population.


The Maronite community in Lebanon dates back to the 5th Century and is among the first Christian communities in the Near East. The liturgical language of the Maronite Church is Aramaic (Syriac). Their initial settlements were in the Mountains of Lebanon where they remained relatively isolated until the time of the Crusades. They are one of the largest Christian sects in Lebanon. The very high presence of Haplogroup J2-M172 among Maronites strongly suggests J2 was among the founding lineages of the community.

New L267 SNP may define distinct cluster of J2a4

Family Tree DNA's Walk Through the Y program has yielded hundreds of new SNP's that are helping to define the Y-Chromosome Tree. One such SNP, named L267 was recently found in a participant in the program whose paternal origin lies in Calabria, Southern Italy. The mutation, an A to G transition at position 2948591 on the Y chromosome is thus far, unique to this participant. The mutation was not found in other participants from other J2a4 subclades, J2-M67 and J2-L25 (rs34534058). Thus, it appears L267 could define a subclade under J2a4.

Similar haplotypes come largely from Eastern Anatolia and Armenia indicative of the possibility of a more recent spread from Anatolia to Italy for this cluster. The cluster can be viewed in the Haplogroup J project's results identified as J2a4 Cluster C. Further testing of this SNP is in progress.

Additional SNP's have also been identified in J2a4h (L25) including L192.2, L229, L230, L231, L243, L254 and L264 which so far look to define clusters within this subclade of J2, M172.

Indian Muslim population shows genetic affinity with non-Muslim Indian Geographic Neighbours

A 2009 study by India's National DNA Analysis Centre shows Indian Muslims display a genetic affinity with their neighbouring Non-Muslim populations along with low levels of Arabian, Central Asian and Iranian admixture. The study sampled 431 Indian Muslims from Uttar Pradesh, Gujarat, Andhra Pradesh and Tamil Nadu. The results showed distinctions between the Muslim communities based on geographic origins and a greater affinity to their neighbouring non-muslims than to each other. However, the study also does note a contribution to the genetic structure of Indian Muslims coming from Iranian and Arabian populaitons. The study does show some distinctive Y-DNA haplogroup frequencies especially in Haplogroup J:


Most noteworthy were the J2, J2a and JxJ2 frequencies of the Indian Shia population which were substantially higher than those of Indian Non-Muslims.

The spread of Islam in India was predominantly cultural conversion association with minor but still detectable levels of gene flow from outside, primarily from Iran and Central Asia, rather than directly from the Arabian Peninsula.

Traces of sub-Saharan and Middle Eastern lineages in Indian Muslim populations

Phylogeographic Analysis of Paternal Lineages in NE Portuguese Jewish Communities

ABSTRACT

The establishment of Jewish communities in the territory of contemporary Portugal is archaeologically documented since the 3rd century CE, but their settlement in Tra´s-os-Montes (NE Portugal) has not been proved before the 12th century. The Decree of Expulsion followed by the establishment of the Inquisition, both around the beginning of the 16th century, accounted for a significant exodus, as well as the establishment of crypto-Jewish communities. Previous Y chromosome studies have shown that different Jewish communities share a common origin in the Near East, although they can be quite heterogeneous as a consequence of genetic drift and different levels of admixture with their respective host populations. To characterize the genetic composition of the Portuguese Jewish communities from Tra´s-os-Montes, we have examined 57 unrelated Jewish males, with a high-resolution Y-chromosome typing strategy, comprising 16 STRs and 23 SNPs. A high lineage diversity was found, at both haplotype and haplogroup levels (98.74 and 82.83%, respectively), demonstrating the absence of either strong drift or founder effects. A deeper and more detailed investigation is required to clarify how these communities avoided the expected inbreeding caused by over four centuries of religious repression. Concerning haplogroup lineages, we detected some admixture with the Western European non-Jewish populations (R1b1b2-M269, 28%), along with a strong ancestral component reflecting their origin in the Middle East [J1(xJ1a-M267), 12%; J2-M172, 25%; T-M70, 16%] and in consequence Tra´s-os-Montes Jews were found to be more closely related with other Jewish groups, rather than with the Portuguese non-Jewish population.

The Portuguese NE Jews display a much closer genetic relation to Jewish populations of Europe and the Middle East, especially other Sephardic groups, than to the Portuguese population. However, it should be pointed out that the high frequencies of haplogroup R1b1b2, less frequent in other Jewish populations, indicate a significant level of admixture with non-Jewish Iberian populations.

Link

Family Tree DNA's Walk the Y yields new SNP's for Haplogroup J2

A program by Family Tree DNA, Walk through the Y, was set up late last year to allow customers to search for new SNP's or branches to their respective Y-DNA haplogroups. Recent testing on a number of Haplogroup J2 participants has yielded 9 new SNP's, many of which will prove to be phylogenetically informative in branching current subclades. Below is a list of SNP's found to date:

• L207.1 A6813448G found in J-L70 and J-L25 participants. May be synonomous with J-L24 or L25.
• L210 A15001591T found in one J-M67 participant.
• L212 T21120853C found in J-M67 and J-L25 participants.
• L218 deletion at 20199329 found in J-M67 participant.
• L227 C6919963T found in J-M67 participant.
• L228 C7831358T found in J-M67 and J-L25 participants.
• L229 C6813447T found in one J-L25 participant, ancestral in another.
• L230 G20327921A found in one J-L25 participant, ancestral in another
• L231 C13524835G found in one J-L25 participant, ancestral in J-M67.

It is likely more SNP's will be found as a more thorough analysis of the results has yet to be done. Also, results from other J2 participants have yet to arrive. SNP's can be used to determine the branchin within the Y-Chromosome tree and it is likely some of these SNP's will determine new terminal branches under J-M67 and J-L25.