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Tuesday, December 23, 2008

Y Chromosomes of Iberia reflect Sephardic and Moorish Origins?

A recent article in the American Journal of Human Genetics, The Genetic Legacy of Religious Diversity and Intolerance: Paternal LIneages of Christians, Jews and Muslims in the Iberian Peninsula attempts to estimate the percentage of Sephardic Jewish and Moorish origins in the present day Iberian population. The results yielded very surprising figures; that upwards of 20% of Iberian Y Chromosomes are of Sephardic Jewish origin and 10% could be of Moorish origin. The history of Iberia certainly records the presence and impact of these 2 cultural groups on the peninsula. This article represents the first attempt using genetics to estimate levels of religious conversion that happened during the Spanish Inquisition period. The study included 1140 DNA samples from Iberia, representing a hugely informative look at the haplogroups of Spain and Portugal as well as long awaited data on the Sephardic Jewish communities mostly originating from Belmonte, Bulgaria, Djerba, and Turkey. The data itself shows that of the 14 haplogroups found in the Sephardic Jewish community, M172, Haplogroup J2 is the most frequent haplogroup overall, representing 25% of this population group. This was followed closely by M267, Haplogroup J1 which represented 22% of the total. In the Iberian Peninsula, M172, Haplogroup J2 was most frequent in the south, 15% in Southern Portugal, 14% in Western Andalusia and 12% in Extremadura. Interestingly, the Balaeric Islands showed lower levels of M172, Haplogroup J2 in Majorca, Minorca and Ibiza at 8, 3 and 4% respectively.

One glaring observation which might challenge the conclusions of the article is the ratio of J:J2 found in the Sephardic Jewish population compared to that of the Iberian population. This ratio is 0.88 (22% vs 25%) in the Separdich Jewish population but only 0.125 (1% vs 8%) in the Iberian Population. If one was to assume the converted Jewish population of Iberia contained a similar genetic makeup to present day Sephardic Jewish communities, looking at Haplogroup J1 as a defining marker, the amount of Sephardic ancestry could not exceed 5% since J1 makes up 22% of present day Sephardic Jews but was found in only 1% of Iberians. From this perspective, the articles conclusions of a 20% Sephardic Jewish ancestry seem lofty. The study's approach was to look at the genetic markers of the Basque population, Moroccan population and present day Sephardic Jewish population to represent Iberian, Moorish and Sephardic ancestry respectively. It then compared this data with that of the 1140 Iberian Y-Chromosomes from the study. Again, the study seems to largely discount the possible input of Phoenician or other near eastern populations as a source for the present day genetic makeup of the Iberian Y chromosome data assuming both Phoenician and Greek impact would be in the eastern parts of Iberia and not in the West where most Haplogroup J2 and J is found. The authors also note a good degree of Haplotype sharing (exact matches) at 3.6% between Sephardic Jewish haplotypes and Iberian Haplotypes. The study also notes the Sephardic sample which is taken from a small group of individuals would have been subject to Founder effect, bottlenecks and other factors which might reduce haplotype diversity.

Looking at the impact of the Moors, the study does provide good evidence linking E3b (M81) to a Moorish population originating in North Africa. The low diversity of this genetic marker comparing North African and Iberian M81 haplotypes supports a very recent common origin, likely brought to Iberia by the Islamic Moors, who controlled the Peninsula for 700 years.

Overall the study does a good job of a very difficult task in attempting to uncover the genetic history of Iberia and how its recent history has had a profound impact on its present day population which undoubtedly includes both Sephardic Jewish and Moorish origins.

Monday, December 15, 2008

Update on rs35248080

The SNP found in Haplogroup J2, rs35248080 should likely split the M410 branch of J2 into 2 large subgroups. Those positive for rs35248080 seem to include all or part of 2 J2 clusters referred to as J2a1h (ISOGG) also known as J2a-Lambda (J2 Y-DNA Project) as well as another cluster, pre-J2a1h (Haplogroup J project) or J2a-Beta (J2 Y-DNA Project). Thus far haplotypes which are M67+ are negative for the SNP rs35248080, haplotypes in J2a that do not carry the deletion at DYS 413 are also negative. Participants in J2b are also negative. Haplotypes which carry a distintive 9 repeats at DYS 450 as well as 6 or 10 repeats at DYS 445 which define J2a1h/J2a-Lambda and pre-J2a1h/J2a-Beta respectively have tested positive for the new SNP. Testing is ongoing.

Wednesday, November 26, 2008

Elamo-Harappan origins for Haplogroup J2 in India?

The presence of Haplogroup J2 in India, including the subclades M410 and M241 has been an often overlooked clue to the origins of M172. Sengupta et al, in 2005 worked to explain the presence of M172 in India. Their paper provides an immediate acknowledgement of the proposed spread of proto-Elamo-Dravidian speaking peoples into India originating from the Indus Valley and southwest Persia. The idea that M172 may have been carried into India with proto-Elamo-Dravidian groups is supported by the frequencies of Haplogroup J in one of the only remaining Dravidian Speaking ethnic groups in the Iranian Plateau, the Brahui. 28% of the Brahui, an ethnic Dravidian speaking group from Western Pakistan were found to carry the mutation defining Haplogroup J. Overall Haplogroup J2 in India represented 9.1% of this very populous nation. In Pakistan, M172 accounted for 11.9% of the Y-Chromosomes typed. Sengupta's paper broke down the frequencies of Haplogroup J2 into various caste and language groups. J2 was found to be significantly higher among Dravidian castes at 19% than among Indo-European castes at 11%. J2a-M410 in particular may be a strong candidate for a proposed migration of proto-Dravidian peoples from the Iranian Plateau or the Indus Valley since J2a M410 is a very high component of the haplogroup J2 chromosomes found in Pakistan. Over 71% of the M172 found in Pakistan was M410+.

Another interesting characteristic in the distribution of M172 and more specifically, M410, in India was its higher frequencies in Upper Caste Dravidians. M410+ chromosomes were found in 13% of Upper Caste Dravidians. Sengupta goes on to suggest an Indian origin of Dravidian speakers but from a Y chromosome perspective, the paper seems to acknowledge M172 arriving in India from Middle Eastern and Indus Valley Civilizations.

Despite an apparent exogenous frequency spread pattern of J2a toward North and Central India from the west, it is premature to attribute the spread to a simplistic demic expansion of early agriculturists from the Middle may also reflect subsequent Bronze Age Harappans of uncertain provenance.

Subclades of M172 such as M67 and M92 were not found in either Indian or Pakistani samples which also might hint at a partial common origin. And while there may be multiple events and origins for M172 lineages in India, it does seem likely that the Indus Valley and Elamo-Dravidian speaking groups may be the origin of some of the M172 found in India today.

Friday, November 14, 2008

Y chromosomes of Sicily

In May of 2008, Cornelia Di Gaetano et al submitted an article to the European Journal of Human Genetics studying the Y chromosome makeup of the island of Sicily. Sicily has one of the highest frequencies of Haplogroup J2 (M172) in the mediterranean. J2-M172 made up 33% of the Y chromosome signatures on the island and was non-randomly distributed occurring at higher frequencies in the eastern areas of the island. This distinction was evident in the subclades, M67 and M92, which have previously been linked to Greek and proto-greek colonization. Both M67 and M92 were twice as frequent on the eastern portion of Sicily which displays more archaelogical traces from the Greek classic era. Even the paragroup of undistinguished J2 haplotypes (M172) was more than twice as frequent in Eastern Sicily. One of the more interesting subclades, referred to as J2a1k (DYS445=6) showed an interesting non-random distribution in Sicily. This subclade is also commonly referred to as J2a1h (ISOGG) or J2a-Lambda (J2 DNA Project). Most striking was differences in frequencies between Mazara Del Vallo and Sciacca. Mazara Del Vallo is a port city established by the Phoenicians in the 9th century B.C. while Sciacca, known as Thermae in Greek times, was founded in the 5th century B. C. by the Greeks. These 2 cities, founded by different groups are only 57 KM apart. Yet 11.11% of the Y chromosomes in Mazara del Vallo were J2 M172 with DYS 445=6 while this subclade was absent from the sample data from Sciacca. Trapani, another port city in Western Sicily also exhibited high levels of J2-M172 with DYS 445=6 at 9.09%. This subclade was absent from the inland cities of Santa Ninfa and Piazza Armerina and the northern Sicily town of Caccamo. The data seems to suggest that J2a1h (J2a1k)'s distribution is stronger in coastal regions of Western Sicily and more rare in inland and Eastern parts of the island. The sole exception to this trend was the data from Troina which did report 10% J2 M172 with DYS 445=6. Overall the non-random and high levels of J2 on the island of Sicily seem to reflect the complex history of the island and might represent multiple migrations by multiple groups over various periods of the islands history.

The general heterogeneous composition of Hgs seen in our Sicilian data is consistent with similar patterns observed in other major islands of the Mediterranean, like Sardinia and Crete, possibly reflecting the complex histories of settlements in these islands during the Holocene.


Friday, October 31, 2008

Phoenician Footprints in the Mediterranean

Pierre Zalloua and the Genographic Consortium have been hard at work trying to retrace the steps of the Phoenician civilization which dominated trade in the Mediterranean 2 to 3 thousand years ago. From their homeland in the Levant, they established colonies and trading posts throughout the Mediterranean eventually disappearing into history. Zalloua et al are attempting to find some genetic trace of the phoenicians by examining the Y chromosome of men from areas of known Phoenician settlement. Their results link haplogroup J2 and 6 specific Y chomosome haplotypes as having contributed >6% to the present day Y chromosome gene pool of the specific populations studied. The paper focuses on Malta, Tunisia and Southern Spain as phoenician influenced regions spreading from a Phoenician Heartland in present-day Lebanon. Some of the highest levels of Haplogroup J2 are provided in the supplemental data including 28% J2 in the area defined as the Phoenician Heartland, 22% in the neighbouring periphery regions, 37% in Cyprus, 32% in Malta, 14% in Coastal Tunisia and 11% in Southern Spain. Tunisia, in the eyes of the authors provided a valuable contrast:

The excess of J2, PCS1+, PCS2+, and PCS3+ (Phoenician Colonization Genetic Signatures) in coastal Tunisia, the site of Carthage, compared with inland Tunisia is particularly salient, because these lineages are considerably more rare in North Africa than in Southern Europe. It also suggests that the Roman destruction of Carthage did not eliminate the Carthaginian gene pool. Further support for the PCS+ haplotypes' spread with the Phoenicians is illustrated by their generally high frequency among the Phoenician contact sites across the Mediterranean basin (Figures 1D–1F).

The authors used a variety of control tests to estimate the impact of Neolithic, Greek and other population migrations the the studied regions. They noted that only one Haplogroup, J2 consistently scored significantly in all their Phoenician-colony tests across the range of colonization sites. They also identified 6 specific 7 marker haplotypes they believed associated with the Phoenician expansion but acknlowledged that the limited phylogenetic resolution of the haplotypes (their small size) would pick up signatures not necessarily involved with Phoenician expansion. They also hope that future identification of SNP's may lead to the discovery of some rare but distinctly Phoenician genetic signatures. The link to the full paper is on the left side in the links section.

Thursday, October 30, 2008

Haplogroup J2-M172 in Iran

A 2008 Paper written by Nasidze et al, Close Genetic Relationship Between Semitic speaking and Indo-European speaking Groups in Iran, works to demonstrate that geography plays a much stronger role than language in determining genetic relatedness. The paper focuses on comparisons between the Bakthiari, an indo-european speaking population of Iran and Iranian Arabs. The Haplotype frequency table quickly demonstrates that the level of M172, Haplogroup J2 is fairly evenly distributed througout Iran's geography and the population groups studied. In fact, it is the most common Haplogroup found in Iran overall and in the above listed study, present in 28% of Iranian Arabs and 25% of the Bakthiari. A full table of the haplogroup frequencies can be viewed here

While there are some differences with respect to Haplogroup G, paragroup F* which includes J1 (M267) and Haplogroup T (M9), the authors go on to state:

The Iranian Arab group shows close affinities with the Bakhtiari and other Iranian Indo-European-speaking groups for both mtDNA and the Y chromosome. In fact, for both mtDNA and theYchromosome, all of the Indo-Europeanspeaking and Semitic-speaking groups from West Asia exhibit generally low levels of differentiation (i.e. Fst values are less than 0.05). The significant correlation between mtDNA and NRY Fst values, as shown by the Mantel test, further indicates that there are no substantial differences between patterns of mtDNA and NRY variation in this region of the world. The lack of significant differentiation between west Asian Semitic-speaking and Indo-European-speaking groups indicates that language has not been a substantial barrier to gene flow in this part of the world.

Iran shows some of the highest levels of Haplogroup M172 in the world. When one factors in the population of Iran, it may be one of the most populous countries of men bearing the mutation defining Haplogroup J2. But did Haplogroup J2 originate in Iran? This topic is far more complicated and most sources simply indicate its origin as the Northern Portion of the Fertile crescent which could include the northern Levant, Anatolia, Syria, Iraq or Iran. Certainly many subclades of Haplogroup J2 have likely developed outside Iran. Reguiero et al typed their DNA samples in Iran for numerous subclades of J2 which were not found to be present including M137, M158, M163, M280, M318, M319, M321, M339 and M340. These subclades more likely developed and spread from another area of the Near East. Thus Iran is likely not the source region for these particular subclades but could still be one of a few geographical regions of origin for some of the earliest M172 bearing men.

Thursday, October 23, 2008

Correlations in the spread of Viticulture and Haplogroup J2

Recently, I came across a few books which discussed the history of Viticulture and its spread. I was amazed at the similarity in its spread with that of Y-Chromosome Haplogroup J2 (M172). The earliest evidence of Wine Making found to date originates from Hajji Firuz Tepe in the Zagros Mountain Range, Northern Iran. A Wine Jar, with a volume of about 9 liters (2.5 gallons) was found together with five similar jars embedded in the earthen floor along one wall of a "kitchen" of a Neolithic mudbrick building, dated to ca. 5400-5000 B.C. Chemical Analysis determined the residue in the jars was Wine. Some of the highest levels of M172 are found in this area of Iran, 24.24% in Northern Iran according to Regueiro et al. But certainly M172 and the earliest signs of viticulture are not restricted to this remote area of the Near East. Early evidence of viticulture exists in the Levant and later with the Phoenicians and Isrealite populations, the Sumerians, Akkadians and Hittites of Anatolia.

Common discussion on J2 states that it started to spread in the Northern Fertile Crescent during the Neolithic Period. King et Al noted a strong correlation in precipitation levels and associated levels of J2a (M172+ M410+) within the Middle East, stating:

The genetic memory retained in the extant distributions of Y-chromosome haplogroups J1-M267 and J2a-M410 within the FertileCrescent significantly correlates with regional levels of annual precipitation in a reciprocal manner. The statistically significant correlations of Y-chromosome haplogroups, precipitation levels and domestic lifestyle are pronounced. The spatial frequency distribution of haplogroup J2a coincides closely with regions characterised by >400mm of annual precipitation capable of supporting settled agriculture, while haplogroup J1-M267 distributions correlate inversely with semi-arid regions characteristically used by
Thus, King et al have established that M410's spread seems to correlate with rainfall. It would then make sense that viticulture would likely mirror this spread since about 400 mm is also the level of annual precipiation required to support the farming of Wine Grapes (General Viticulture, Albert Julius Winkler p 395). And this is what we see; that viticulture mirrors the proposed spread of M172, M410 through the Near east during the bronze age.

Wine making spread to Crete during the Minoan period and then later to Italy with the Etruscans and to Iberia with the Phoenicians. It was an integral component of the economy and social culture of the proto-greek civilizations and the phoenicians who both went on to settle other mediterranean coastal regions. And tracing the spread of Viticulture from its origins to its spread before the Roman period, we can see te highest levels of Haplogroup J2 today correlate with the geographical centres of all these civilizations. While viticulture may not represent the first wave of M172 migrants to Europe, M172 certainly played a strong role in bringing Viticulture to Europe with such civilizations as the Minoans, Greeks and Phoenicians.

Thursday, October 16, 2008

Important new SNP's in the J2 tree

23 and Me has been offering testing using a new chip which scans the Y chromosome for over 2000 SNP's. 2 of these could be very significant to the structure of Haplogroup J2, M172. The first, rs34126399, seems to represent an SNP downstream of M410. This SNP was discussed in 23 and me's blog here. Testing done by Dr. Peter Underhill suggest that this SNP is equivalent to the deletion at DYS 413. And thus, it would appear that a major branch of the J2 structure will return at some point to the YCC haplogroup tree.

The second SNP being found in some J2 participants with 23 and me is rs35248080. Less is known about this marker except that it lies downstream of rs34126399 (ISOGG-J2a1). From the testing results received to date, we do know that one participant from the cluster pre-J2a1h (Haplogroup J project FTDNA) or J2a-Beta (J2 DNA project) is positive for this SNP. This group carries some distinctive repeats at DYS 445 and 450 and testing through Family Tree DNA has been ongoing for some time. We also know that 1 participant in Haplogroup J2a2 (ISOGG-J2a1b) which carry the M67 SNP and another in Haplogroup J2b (M205+) were negative for rs35248080. Thus it appears that this SNP could split J2a1's into 2 fairly large branches. Exactly which subclades and clusters are positive for this SNP will only be determined with more testing.

Tuesday, October 7, 2008

Pronounced Westward Maritime Diffusion of J2a (M410)

When looking at the diffusion of Haplogroup J2a, M410, westward into Europe, one aspect of this westward spread becomes quite clear. M410+ ancestors used a maritime and coastal route to move west. Considering how J2a arrived in Western Europe to places like Italy, France and Spain one sees 2 possible routes-by land and by sea. The frequencies of J2a in regions that lie between Western Europe and its' origin in the Near East show that a land route to western Europe was quite unlikely. Di Giacomo et al 2006 studied the Y Chromosomes in the Czech Republic through which the Danube river flows. J2a M410 accounted for only 3.5% of the total in the sample set of 257 individuals. In another study published in 2005, Marjanovic et al looked at Y chromosomes in Croatia, Bosnia and Serbia. J2 (xJ2b) lineages accounted for only 3.5% of their sample involving 256 males from these regions. These rates of course are in very sharp contrast to what we see on islands of the mediterranean which show rates of J2a over 20%. Capelli et al, while studying Y chromosomes of the Mediterranean, noted J2 was present in 21% of their Maltese sample, 36.9% of their sample from Cyprus, and ~28% of Sicilian Samples. Even North African regions, such as Tunisia showed over 10% J2.

Many authors including Di Giacomo have noted this maritime or littoral spread of Haplogroup J2. Looking at J2, and specifically at J2a's frequencies from East to West, certainly provides ample support for a maritime spread of J2 into Europe from its origin in the Northern Fertile Crescent.

Thursday, October 2, 2008

Diffusion of M319, J2a8 (YCC) Subclade

One particularly interesting branch of Haplogroup J2, is M319, also referred to as J2a8(YCC) or J2a1e(ISOGG). This SNP was first reported in 2004 by Shen et al in their study of the Samaritans. A link to this paper can be found on the right. M319 was found in 3 samples from their study, 2 Moroccan Jewish and 1 Iraqi Jewish males living in Israel. Further studies which tested for M319 found it to be absent in Iran but quite prevalent (8.8%) in Crete (minoan tablet pictured at right). This branch of J2 does appear to be fairly rare, being found in only a handful of cases of Iberian, Swiss and Italian origin from public databases. M319 haplotypes often show a distinctive value at DYS 413a, where they are seen to carry 16 repeats as opposed to 17 which is normally found in J2a haplotypes that are DYS 413 derived. King and Underhill, in their 2008 paper, Differential Y chromosome Anatolian Influences on the Greek and Cretan Neolithic hint at a bronze age arrival of M319 in Crete and a possible origin in Syro-Palestine or Anatolia saying

In turn, 2 distinctive haplogroups, J2a1h-M319 and J2a1b1-M92, have demographic properties consistent with Bronze Age expansions in Crete, arguably from W/NW Anatolia and Syro-Palestine

Certainly finding M319, albeit rarely, in the Mediterranean, while not being detected in Iran or mainland Greece might support a post-neolithic origin and/or expansion from Syro-Palestine or some other nearby coastal region. There is no shortage of evidence of the ties between the Minoan civilization and Southern Anatolia and the Levant.

Tuesday, September 30, 2008

What is an SNP and what is M172?

For many of us who have tested our Y Chromosome for genealogical purposes or to discover our paternal ancestral origins, these are questions that might be considered basic and possibly even uninteresting. But since this is our first blog post, we might as well start with the basics so everyone can be brought up to speed.

SNP stands for a Single Nucleotide Polymorphism and it refers to a DNA sequence variation that occurs in a single Nucleotide (A C T or G) in the genome sequence. When one of these changes in some way, we call this a Single Nuleotide Polymorphism or SNP for short. These SNP's, when found on the Y Chromosome, can be used as markers of descent on the paternal tree of life, thus acting as a way of determining relatedness among different people.

So, what is M172? In short, it would be the 172nd Y chromosome SNP discovered by scientists. It is also referred to as Haplogroup J2 and is a genetic marker carried by men originating from a region ranging from India to Spain. All men carrying this genetic marker share a common paternal line ancestor. Haplogroup J2 or M172 is especially frequent in men from the Near East and the eastern Mediterranean. This blog will try to unravel the story of M172 and his descendents, discussing specific branches of Haplogroup J2 and the peoples who spread this marker from the Neolithic right through Roman times.