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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.