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.

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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.

Saudi Arabian Y Chromosome Diversity and its Relationship with Nearby Regions

A new provisional study by Dr. Khalad Abu-Amero et al takes a detailed look at the genetic makeup of Saudi Arabians and provides a comparison with its geographical neighbours. Saudi Arabia has long been unsurveyed from a Y Chromosome Perspective and while many areas of the Middle East have been well studied, this new paper does shed light on the distribution of haplogroups in the Arabian Peninsula. Haplogroup J1, M267 was most frequent overall, representing 40% of the Y Chromosome samples. The authors are quick to note however, that Saudi Arabia is distinguished from its neighbours by higher levels of M172, Haplogroup J2. Haplogroup J2 was the second most frequent haplogroup found in the Study sample, representing 15.92% of the total. These J2 lineages were also tested for subclades M410, M47, M67, M92, M158, M339, M340, M12 and M241. The most frequent subclade of J2 was J2a, M410+ with the deletion at DYS 413 (rs34126399), which represented about 72% of all J2 in the study. M47 was also detected at 2.55% of the total or 16% of the J2 total. The higher levels of J2 found in Saudi Arabia were explained by the study's authors as being a result of Saudi Arabia's geographical proximity to the Fertile Crescent and northern boundary with the Levant. With respect to Haplogroup J1, the authors estimate, using a 0.00069 mutation rate, divergence ages for M267 at 11.2kya for Saudi Arabia and 11.3kya for Yemen, also noting these ages as significantly older than estimates for UAE, Qatar and Oman. This suggested a terrestrial colonization and spread of Haplogroup J1 in Saudi Arabia.

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Y chomosome Genetic Landscape of the Levant

A new study of Y chromosome haplogroup distribution in the Levant, appearing in the Annals of Human Genetics, establishes a complex pattern of haplogroup distribution, especially with haplogroups J1 and J2, and theorizes on a coastal-inland contrast differentiating J1 and J2 in the Levant. The study included the DNA of 5874 men from the Levant and neighbouring regions, and the results established a coastal-inland, east-west pattern of diversity and frequency distribution within the Levant. The study again shows the most frequent haplogroup in Lebanon is Haplogroup J2, with a frequency of 29.4%. In the South of Syria, in the cities of Damascus and Diraa, J2 was present at frequencies of 24% and 83.3% respectively. In Lebanon, J2 was found in its highest frequencies at Zahle (37.5%) in the Bekaa Valley and at Byblos (36.4%).

Haplogroup J1 was revealed to show a larger frequency but lower diversity in inland regions of the Levant. The authors note most of the interior, where higher frequencies of J1 were found, were arid with semi-desert conditions which support a lower population diversity. Consistent with previous analyses, coastal Levantine regions showed a high frequency of Haplogroup J2.

"The diversified J2 reduced-median network and high coastal frequency suggest a sustained and non-interrupted presence of this haplogroup along the Eastern coast of the Mediterranean"

Geographical Structure of the Y-Chromosomal Genetic Landscape of the Levant: A coastal-inland contrast

Jewish priesthood founded on limited paternal lineages

A new study of the Jewish priesthood (Cohanim) suggests the majority of contemporary Jewish priests descend from a limited number of paternal lineages, the 2 largest being in J1e (P58) and J2a (M410). Over 60% of Cohanim descend from one of these 2 paternal lines. Unfortunately the paper did not test for newly discovered SNP's L24 and L25 (rs35248080 and rs34534058), known to be found in a large set of J2 Ashkenazi Cohanim. These haplotypes were simply defined as J2a, M410 in this paper. The study identifies 2 principal founding lineages for Jewish priests, one in J1e (P58) dating back to a common ancestor who lived approximately 3190 years ago and another lineage in J2a (M410) dating back to a common ancestor who lived 4200 years ago. It is also interesting to see a 3rd lineage of Jewish priests from the island of Jerba defined by SNP M318 which also lies downstream of SNP's L24 and L25, also known as J2a4h.

The study was a long overdue followup to a 1997 study which identified a 6 marker Cohen Modal Haplotype. This new paper identifies an expanded 12 marker haplotype in J1 found in a large portion of Cohanim who carry the Y-Chromosome M267 (J1) SNP. The study also showed the likelihood of both the J1e and J2a genetic signatures dating back to before the Jewish diaspora since both signatures were found in Jewish communites from the Near East, Eastern Europe and the Mediterranean, communities which have been, for the most part, separated since roman times.

Neolithic Migrations in the Near East and Aegean

Dr. Roy King has contributed a very interesting chapter to a 2009 book, Ancient Human Migrations, where he provides some insight into the earliest migrations of Haplogroups J1 and J2. He applies linguistic and archeaological research to the current spread, diversity and frequency of Y-Chromosome haplogroups J1 and J2 to theorize on their deepest origins. Among some of the noted general observations was the trade in Obsidian dating from 9000BC originating from sources near Lake Van in Eastern Anatolia and found in the southern Levant.


His observations on Haplogroup J2 are especially interesting, noting its highest variance which is one component of a possible origin, being found in South Eastern Anatolia, Northwestern Iraq, the Mediterranean and among Palestinians living in coastal Israel. He notes these variances are higher than in other areas such as Iran and the Caucasus where high levels of J2 are also found. Using STR mutation rates of .0007 per generation (rates theorized by Zhivotovsky et al), he theorizes an expansion of J2 between 19,000 and 25,000 BCE presumably placing J2 during the Last Glacial Period at refugia areas in the middle Euphrates and southern Levant. From there, he theorizes, J2 was well positioned to participate in the Neolithic Expansion to areas like Southeastern Europe, the Caucasus, Iran and India.

Dr. King also notes an interesting correlation with a subclade of Haplogroup J2, M67, and place names in the Aegean, Balkans and Italy while citing a deeper origin for subclade M67 in Northern Syria or southern Anatolia. The age and spread of M67 seems associated with proto-greek substratum in the Aegean.

Some of the most interesting theories put forth in the chapter deal with linguistics. While noting that multiple haplogroups are likely involved in the spread of languages through the middle east, Dr. King noted a correlation between very old Middle Eastern languages of uncertain origin and Haplogroup J2 while at the same time theorizing that Haplogroup J1 may have been involved in spreading Semitic languages through the region. These old languages possibly linked to J2 are known to have existed in Mesopotamia and the Northern Levant and this substratum is sometimes referred to as "Banana" languages due to their syllabic duplication.

Underlying both these migrations, there may have been a population dating to the LGM characterized by J2 Y lineages whose set of languages is unknown but may have included syllabic reduplication in their morphology... Immediately after the LGM, southeast Anatolia, northern Syria and coastal Palestine may have provided refugia to populations marked by J2 lineages of uncertain linguistic character.

Haplogroup J2, M172 in Antalya, Turkish Republic

Timur Serdar and Demircin Sema authored a recent study on the Y chromosomes of Antalya, which is located on the southern coast of Anatolia. Haplogroup J2 was most frequent in this study of 75 unrelated males found at a frequency of 26.6%. The J2 data was consistent with an earlier study by Cinnioglu et al which found 24% J2 in southern Anatolia. Haplogroup T (K* in the study) was next most frequent at 13.3% and this data differed from Cinnioglu's data which found only 3.3% Haplogroup K in southern Anatolia.

The first record of Antalya was as Attalia, a greek city founded approximately 150BC by Attalos II, King of Pergamon.

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Oldest Village in the Middle East uncovered in Iran

Iran's Press TV is reporting that Iranian and English archeologists have uncovered what they believe to be the oldest village in the Middle East in Kermanshah Province, Western Iran. Carbon dating on discovered objects in the village date to 9800BC and evidence suggests the site was inhabited until 7400BC according to Hassan Fazeli, director of Iran's Archeology Research Center. According to Fazeli, such evidence strenthens the theory that Iran was one of the main Neolithic centres of the Middle East.

Some of the highest frequencies of Y chromosome Haplogroup J2, also associated with the Neolithic are found in Iran.

CNN features genetic work of the Genographic Project's research in Lebanon

Genographic Project Principal Investigator Pierre Zalloua was recently featured on CNN's "Inside the Middle East" program. Pierre discusses the discoveries made by the Genographic team about the Phoenicians, the mysterious ancient maritime culture from the first millennium BCE.

FTDNA releases updated Haplogroup J2 tree

Family Tree DNA has updated their nomenclature for the various subclades of Haplogroup J2a. They have incorporated the new L24 and L25 SNP's which refer to rs35248080 and rs34534058 respectively. They have also updated the position of P279 above the deletion at DYS 413, which is represented by L26 (rs34126399). This update thus recognizes L24/L25, a sizeable branch of haplogroup J2 which previously was only identified by FTDNA as J2a (M410). However, they'll need to revise yet again, as research from Thomas Krahn seems to show some haplotypes are L24 positive or derived but L25 negative or ancestral. He has also identified a further SNP in these haplotypes which is being called L84. DNA fingerprint seems to show one of the more up to date Haplogroup J trees here . The DNA fingerprint tree is also more legible in part, since it references the SNP 's by name and not by a constantly evolving numbering system.

Haplogroup J in the Gulf of Oman

A paper from Cardenas et al 2008, Y-Chromosome diversity characterizes the Gulf of Oman, analyzes the Y Chromosome diversity for clues to the origins of present day peoples of this region. This part of the world has played a key role in many migratory episodes leaving Africa for Eurasia. Certainly Arabia served as a conduit for the first migrations out of Africa however, the data suggest that the during the Neolithic era, contact with the Levant and Mesopotamia contributed to the very high levels of Haplogroup J found in the Persian Gulf. Just north of the Persian Gulf lies the Fertile Crescent, stretching from Egypt in the West to Iraq in the East. This region is recognized as the birthplace of agriculture during the Neolithic period. While the region was fertile, ancient international trade existed for minerals and other resources. Archaelogical evidence in the form of Ubaid pottery, dated 7000yBP shows ancient contact between the Persian Gulf, Mesopotamia and the Arabian Gulf. Clues from Y Chromosome data, such as the presence of E3b subclade M34 suggest ancient contact between Yemen and the Levant or Egypt. The presence of Haplogroup J2, M172 at frequencies over 10% in UAE could be an indication of migrations from Mesopotamia and/or the Levant.

By far the most frequent haplogroup throughout the Arabian Peninsula is Haplogroup J1 defined by SNP M267. In this study it was found at rates of 58% in Qatar, 72% in Yemen and 34% in UAE. M172 on the other hand was found at rates of 10.3% in UAE, 9.6% in Yemen and 8.4% in Qatar. The authors go on to conclude that the Neolithic period helped disperse Haplogroup J into the Arabian peninsula from the north. They also note the highest levels of diversity seem to emanate from the Persian Gulf coastal areas of UAE, Southern Iran, Oman and South Pakistan.

YCC J2a13 P279 likely resides above 413 deletion

The YCC Subclade J2a13 (ISOGG J2a1j) defined by the SNP P279 has been found derived in one FTDNA Haplogroup J project participant who's paternal line originates is Southern France. It is among the first examples of this very rare subclade found to date, and the result will also likely allow ISOGG researchers to more properly place this subclade on Y chromosome tree. The reason is that this participant carries values of 22 and 22 at DYS 413. This marker, DYS 413, in J2, is usually found with values at or near 17 and it is believed this deletion event represents a division of J2 which is likely now defined by SNP's L26 and L27 (L26=rs34126399). Thus, the P279 result shows that P279 is a branch of J2 which falls into the group that does not carry these SNP's, L26 and L27.

The participant only has one 1 step mismatch from Syria on public databases including YHRD, SMGF and Ysearch.

Evidence of a Cultural diffusion of agriculture in Southeast Europe

A recent paper by Battaglia et al, Y chromosomal evidence of the cultural diffusion of Agriculture in Southeast Europe, attempts to measure the impact of Neolithic farmers from the Middle East on Southeastern Europe to determine if these farming technologies were spread to Europe more through cultural contact or through migrations of Near Eastern peoples into Europe. The neolithic expansion into europe is a complex process likely involving multiple migrations and cultural diffusion over a period of time starting around 9000BC. In this study, Y Chromosome data was collected from 16 regions of South East Europe. The findings suggest that Haplogroup J2b-M241 correlates with the Neolithic period, has a different migration and origin from J2a-M410 and that J2b-M241 may have been involved in the process of admixture with Mesolithic peoples, thus being among the first peoples to introduce agriculture to Euorpe.

Levels of J2a-M410 were very low through the areas studied with little correlation of subclades. J2b frequencies showed a spike in Albania at 14.5% and was found in Greece and the Czech republic at rates of around 4%. The findings of the authors suggest that Haplogroups I and E-V13 were representative of Mesolithic peoples already present in the region who adopted the farming technologies introduced by near eastern farming colonists. From SE Europe where this cultural contact took place, agriculture then spread through Europe crossing the Adriatic into Italy.

Although southeast europe shows considerable archaeological evidence of the Neolithic transition, our Y-Chromosome results provide biological evidence of complexity in the transition to farming in terms of the contrasting influences of pioneering agriculturalists and Mesolithic foragers.