Criticism of Jewish priesthood paper

Anatole Klyosov has written a comment (A comment on the paper: Extended Y chromosome haplotypes resolve multiple and unique lineages of the Jewish Priesthood by M.F. Hammer, D.M. Behar, T.M. Karafet, F.L. Mendez, B. Hallmark, T. Erez, L.A. Zhivotovsky, S. Rosset, K. Skorecki, Hum Genet, published online 8 August 2009) to Human Genetics in which he takes issue with the age estimation in the recent extended Cohen Modal Haplotype paper.

Klyosov correctly criticizes the authors for using the evolutionary mutation rate:

A common ancestor of all 99 Cohanim lived 1,075 ± 130 ybp, and this timing is reproducible for 9-, 32412-, 17-, 22- and 67-marker haplotypes. A much higher values of 3,190 ± 1,090 and 3,000 ± 1,500 ybp were obtained in the cited paper (Hammer et al. 2009) using incorrect methods and incorrect mutation rates.

However, it should be noted that the +/- 130ybp limit around the estimated age of Cohanim J-P58 is too small, and gives the false impression of great confidence in the age estimate, which is not really warranted by Y-STR markers.

Please note that Klyosov uses both a mutation-counting "linear" method, as well as a "logarithmic" method which relates age to the fraction of inferred ancestral ("base") haplotypes in a collection; the "linear" method produces age estimates of comparable error as the more commonly used ASD/variance methods, but the "logarithmic" method produces sufficiently worse (larger confidence intervals) estimates. You can easily modify the Y-chromosome Microsatellite Genealogy Simulator to test the performance of Klyosov's methods.

In conclusion: Klyosov is right to criticize Hammer et al. for using the evolutionary mutation rate. However, his methods do not warrant the strong conclusion that Cohanim J-P58's share a common origin in the last 1,000 years. See my own post on the Hammer et al. paper for my thoughts on the matter.

Finally, an updated look at Y-chromosomes of Jewish priests (Hammer et al. 2009)

We had expected an update on the early Cohen Modal Haplotype work for a few years now. That work had established the distinctiveness of the Cohen Y-chromosome gene pool relative to that of other Jews, which suggested common founders to the Jewish priesthood, but did not provide sufficient phylogenetic resolution: the genetic signature of the Cohens was a 6-marker haplotype that could be found in both haplogroups J1 and J2 and in non-Jewish populations at substantial frequency.

Thus, it became necessary to find a more stringent characterization of Cohen Y-chromosomes that would represent true founder effects in that population. The new paper seems to identify at least two such lineages, one in J-P58, which is a subset of J1, and one in J2a-M410*, and estimates that they were founded 3.2 and 4.2 thousand years ago.

I will comment on this further when I get a hold of the paper and supplementary material.

UPDATE: The authors use the evolutionary mutation rate, and thus the presented ages are overestimated significantly. However, there are reasons to doubt the germline-rate estimate of about 1,000 years for the J1 lineage:

• Demographic plausibility of growth to encompass nearly a third the Cohanim in about 1,000 years. I am not sure what the demic size of Cohanim is, but going from 1 individual to the current population size would require a consistent high growth over many generations. This seems implausible, unless there is indeed historical evidence for such a Cohen founder's descendants extraordinary success.
• The presence of the founding lineage in both Ashkenazim and Sephardim may suggest a common ancestor before the separation of these two populations.

In short, I am skeptical of the age estimates in this paper due to the use of the evolutionary mutation rate, but the wide confidence intervals of Y-STR based estimates, coupled with the knowledge of the lineage's wide geographical dispersal and high number of descendants may make us believe that the founder in question lived at an older time than ~1kya.

Pinpointing Jewish priestly founders to specific individuals, including Biblical ones, is not easy, as the Y-STR technology does not allow for anything resembling accurate age estimation. However, the paper is a welcome new study of a much-discussed topic, and adds significantly to our understanding.

UPDATE II: On the other hand, the J-P58* haplogroup was found in 325 of 2,099 non-Jews surveyed, but the extended Cohen Modal Haplotype (eCMH) in none (Table S2). If the eCMH founder lived 3+ kya, it would be strange indeed if he left no non-Jewish descendants, as it would imply zero conversion from that lineage to other religions. The lack of non-Jewish eCMHs does support the "Jewishness" of this lineage, but on the other hand, makes a very old age more difficult to accept.

My guess is that the eCMH founder lived in Roman times. This would simultaneously allow enough time to explain the lineage's geographical and demographic growth, while also explaining its limited penetration to non-Jewish populations.

Human Genetics doi:10.1007/s00439-009-0727-5

Extended Y chromosome haplotypes resolve multiple and unique lineages of the Jewish priesthood


Michael F. Hammer et al.

Abstract

It has been known for over a decade that a majority of men who self report as members of the Jewish priesthood (Cohanim) carry a characteristic Y chromosome haplotype termed the Cohen Modal Haplotype (CMH). The CMH has since been used to trace putative Jewish ancestral origins of various populations. However, the limited number of binary and STR Y chromosome markers used previously did not provide the phylogenetic resolution needed to infer the number of independent paternal lineages that are encompassed within the Cohanim or their coalescence times. Accordingly, we have genotyped 75 binary markers and 12 Y-STRs in a sample of 215 Cohanim from diverse Jewish communities, 1,575 Jewish men from across the range of the Jewish Diaspora, and 2,099 non-Jewish men from the Near East, Europe, Central Asia, and India. While Cohanim from diverse backgrounds carry a total of 21 Y chromosome haplogroups, 5 haplogroups account for 79.5% of Cohanim Y chromosomes. The most frequent Cohanim lineage (46.1%) is marked by the recently reported P58 T->C mutation, which is prevalent in the Near East. Based on genotypes at 12 Y-STRs, we identify an extended CMH on the J-P58* background that predominates in both Ashkenazi and non-Ashkenazi Cohanim and is remarkably absent in non-Jews. The estimated divergence time of this lineage based on 17 STRs is 3,190 ± 1,090 years. Notably, the second most frequent Cohanim lineage (J-M410*, 14.4%) contains an extended modal haplotype that is also limited to Ashkenazi and non-Ashkenazi Cohanim and is estimated to be 4.2 ± 1.3 ky old. These results support the hypothesis of a common origin of the CMH in the Near East well before the dispersion of the Jewish people into separate communities, and indicate that the majority of contemporary Jewish priests descend from a limited number of paternal lineages.
Electronic supplementary material The online version of this article (doi:10.1007/s00439-009-0727-5) contains supplementary material, which is available to authorized users.

Link

Muslim and Christian Lebanese or Hasty Conclusions in Human Population Genetics

On my post on Genetic Palimpsests, I argued that genetic interpretations about historical events are often suspect when done with very old markers:

Often, this historical reasoning can be shaky. For example, Spencer Wells has made tall claims about the Phoenicians, the Sea Peoples, and the Carthaginians in a National Geographic article which were based on the analysis of haplogroup J and E distribution in the Levant and North Africa.

The reason for this is the following. Suppose a marker is very old, much older than the historical phenomenon under study. In the case of the above-mentioned documentary, the ages of the markers used were about 7 times greater than either the appearance of the Sea Peoples or the Carthaginians. Thus, if we observe similarity between two populations based on such old markers, we cannot conclude that they have a common recent historical origin. This is why Spencer Wells' inspired study on The Phoenicians was wrong when it claimed:

The tests could confirm that men of Tyre-Christians and Muslims alike--are related to the ancient traders. Wells and Zalloua also took samples in other parts of the Phoenician world, where results may reveal the same lineage in areas of former colonies like Sardinia and Malta.

...

During the bloody civil war of the 1970s and 1980s, some groups used the name Phoenician as an ideological weapon. Certain Maronites, the dominant Christian sect in Lebanon, claimed a direct ancestry from the Phoenicians, implying that they held a more legitimate historical claim on Lebanon than later immigrants from the Arabian Peninsula. This inflamed many Muslims. The term Phoenician had turned into a code word for Christian rather than Muslim.

...

Could genetics show that modern Lebanese, both Christians and Muslims, share the same Phoenician heritage? That's one question this project, funded by the National Geographic Society, hopes to resolve.

...

That result delights Zalloua; it supports his belief that both Muslim and Christian Lebanese populations share an ancient genetic heritage.

"Maybe now we can finally put some of our internal struggles to rest," he says.

It is clear from this article that the two possible outcomes of the study were not treated equally: the idea that Muslims and Christians are alike "delights", while the idea that they are not is demonized as contributing to sectarian violence and civil war in Lebanon.

Science should be about the facts, not about wishful thinking. The science of population genetics does have the potential to be used for political reasons, but that is no excuse for drawing unsubstantiated conclusions based on what is politically useful.

The results of the National Geographic study were never published in a peer reviewed journal, so they did not undergo the normal process of scientific scrutiny. However, it is clear why the results were not sufficient: the markers used were ancient. One cannot conclude a recent origin of two populations sharing a common ancient marker, because differences can be revealed when other, more recent, markers are used.

Indeed, in a different study (pdf) which studied more derived markers, the difference between Christian and Muslim Lebanese was made apparent:

The PC plot suggested the presence of four main groups (Fig. 3a): 1) North Africa, Figure 2 Genealogical relationships of the selected UEPs. Nomenclature as suggested by YCC (2002). 2) Near East/Arabs (including Muslim Lebanese and Ashkenazi Jews), 3) Central-East Mediterranean grouping, including Christian Lebanese and 4)West Mediterranean.

What is the reason for these conclusions? The most striking difference between the Christian and Muslim Lebanese is within haplogroup J, i.e., the haplogroup supposed to reflect their common heritage. Muslims have 56.4% of J, while Christians have 44.2%, but this is distributed 30.8%/25.6% among haplogroups J*(xJ2) and J2 in Muslims and 9.3%/34.9% among Christians. It is the high frequency of J*(x2) which indicates the substantial Arab ancestry among the Muslims compared to the Christians. So, indeed Christians appear to descend more from the pre-Arab populations of Lebanon, and presumably the Phoenicians, compared to the Muslims who are more similar to other Arabs.

The literature is full of similar hasty conclusions. The Cohen Modal Haplotype debacle is another case in point. In this case, a simple 6-locus STR haplotype in a YAP- background was taken to be indicative of Aaronic biblical ancestry, a conclusion which did not withstand further scrutiny. At present, 10 years after the Y-DNA Aaron proposition made its appearance, no evidence in support of this theory has been presented; customers of genetic testing companies dabbling in "Jewish ancestry" are expectedly at a loss.

Similarly, haplogroup R1a1 has been proposed as indicative of Viking, Slavic, Kurgan, Ukranian Paleolithic, Indo-Aryan, etc. expansions although very little is known about its phylogeny since the Upper Paleolithic.

Of course R1a1 may have hidden phylogenetic structure that could be linked to the various proposed population expansions, and Aaron's Y chromosome may have been inherited by some bearers of the CMH. But the case needs to be made.

DNA Testing: In Our Blood.

Newsweek has an article titled "DNA Testing: In Our Blood", which offers layman's introduction to the world of population genetics and geneaological testing.

From the article:

The research led Skorecki's team to Africa, where they tested members of the Lemba tribe, a group that believed they were descended from the Biblical land of Judea. Some of their DNA matched the Cohan signature. "We share a common paternal ancestry," says Skorecki. In 2001, Father Bill Sanchez, a Roman Catholic priest in Albuquerque, N.M., discovered he closely matched the Cohan signature, too. Sanchez's Jewish roots go back to Spain (his mother's heritage is Native American). Today he keeps pictures of his Christian and Jewish ancestors on his wall; in November he traveled to Israel. Now his niece Jessica Gonzales, 24, wants to go. Raised Catholic, she wants to learn more about her family roots. "I've been reading a lot about Judaism," she says.

I don't know the specifics of Father Sanchez family origins, but I have to wonder when Skorecki et al. will finally decide to come clean about the significance of their "Cohen signature" and the little-known fact that it is neither a Jewish nor a Cohen-specific signature. I have a feeling that there are quite a lot of people out there who've been "reading about Judaism" based on false beliefs created by dubious science.

Also, from the article:

Last fall, Wells packed up 500 blood-collection tubes, needles, alcohol wipes and cheek swabs and headed off to Chad, one of the project's first testing sites, where he took 300 DNA samples from towns and villages around the country. Thirty-five to 40 came from members of the isolated Laal community, whose population, at fewer than 750, is declining. Wells fears that this community will die out within the next 10 to 30 years, taking with it valuable DNA and cultural traditions and an ancient language—information that could provide critical insights into the first people to live in Central Africa more than 40,000 years ago. "We can use DNA to figure out some of these great mysteries, to make sense of the past," says Wells.

I guess I was right about Dr. Wells' activities in my New Year's predictions... and their name is Laal. Now, let's hope that Dr. Wells and his team will find some time to devote to the other 6,000,000,000-750 of us.

Criticism on papers regarding Jewish genetics

A. Zoossmann-Diskin has a new article in Homo in which he casts significant doubt on the practices of population geneticists publishing on the subject of Jewish origins, with an emphasis on the purported "Ashkenazi Levite" haplotype. While I have also criticized the identification of the so-called Cohen Modal Haplotype whose alleged correspondence with the Aaronic line of priests is invalid, this new article casts some even more serious doubt on a long string of research results. I will comment on the subject after a careful reading of the paper.

UPDATE

The point of the article is that the frequency of the LMH in the original publication is much less than that in the later publication. In the initial publication it is 21% among Ashkenazi Levites and it becomes 42% in the later publication.

So, either:

1. Significant typing errors occurred in the first publication, and the 21% frequency is widely off-the-mark. Did they publish an erratum, a letter to the editor, an announcement on their website, correcting this error? Or did they allow their result to stand in the scientific literature, even though they knew it had serious errors?

or:

2. They used a biased convenience sample in their second article which just so happened to have twice the frequency of the LMH?

So, either the researchers botched the first publication and kept quiet about their mistake, or they massaged their second sample to increase the frequency of the LMH.

I would be interested in any alternative interpretations.

HOMO - Journal of Comparative Human Biology
(Article in Press)

Ashkenazi levites’ “Y modal haplotype” (LMH) – an artificially created phenomenon?

A. Zoossmann-Diskin

Abstract

The article on the Y chromosomes of Ashkenazi Levites (Behar et al., 2003. Am. J. Hum. Genet. 73, 768–779) is the fourth in a series on the Y chromosomes of the three Jewish male castes: Cohanim (priests), Levites (priests’ helpers) and Israelites (lay people). It became apparent that there is a problem with omission of samples when the second article “Origins of Old Testament priests” (Thomas et al., 1998. Nature 394, 138–140) was published. In the fourth article a remarkable 55% of the Ashkenazi Levite samples from the earlier 1998 study are not included. This causes the “Levite modal haplotype” to double its frequency from 21% of the Ashkenazi Levite sample in 1998 to 42% of the Ashkenazi Levite sample in 2003. The authors offer three main explanations:

(1) The studies are independent using different sample sets.

(2) Typing errors and poor quality exclude samples from future studies.

(3) Correction of typing errors means that some samples are classified under different haplotypes.

The explanations offered to the problem of omitting samples from subsequent studies after their haplotypes or partial haplotypes are known, are not convincing. Consequently their sample sets cannot be considered random and non-biased. At the least, these laboratories have bad practices of sample handling and many typing errors, which are enough to invalidate their studies.

Link

On Genetic Palimpsests

Most of the genetic markers used in human phylogeographic studies have been dated to the prehistoric period, and the majority of them are of Upper Paleolithic origin.

Lately, subclades identified within some human lineages on the Y-chromosome have crossed the Neolithic barrier, and in even rarer cases, "signatures" of historical events, such as the dominance of the Mongols, the Manchu, or the Ui Neill.

As a result, most markers are suitable for examining events of human prehistory, and not of historical ethnic groups.

Of course, scientists have tried to apply genetic information to historical processes, e.g., in the case of Jewish origins, but it turns out that the "Jewish gene" or Cohen Modal Haplotype actually turns out to to be much older and not particularly Jewish after all.

Even with old markers, it is still possible to reason about historical events. For example, the theories of white nationalist Arthur Kemp about the widespread prevalence of black African slavery in the classical world have been squarely defeated by the near-complete absence of Sub-Saharan African markers in the Italian and Balkan peninsulas. Similar theories propagated by Gustav Kossina and the Aryan-Nordic camp about the Northern European origin of the Indo-Europeans of India have similarly been defeated, since Indians completely lack haplogroup I chromosomes that are frequent in European Nordic populations.

So, even though the markers in question are very old (I is of Upper Paleolithic age), we can still reason historically with them.

Often, this historical reasoning can be shaky. For example, Spencer Wells has made tall claims about the Phoenicians, the Sea Peoples, and the Carthaginians in a National Geographic article which were based on the analysis of haplogroup J and E distribution in the Levant and North Africa.

For example, he found that there was little impact of Phoenicians on Carthage, but his conclusions are based on the paucity of haplogroup J in modern North African populations, who are a much broader-group than the socially and geographically constrained group of the ancient Carthaginians. Similar claims were made regarding the non-impact of the Sea Peoples in the Levant, but again, this is based on the similarity between coastal and non-coastal populations.
But, for all we know subdivisions of haplogroup J and other Near Eastern markers may differ between coastal and non-coastal populations, or perhaps, the Sea Peoples did initially affect the coastal peoples, but later their genes diffused into non-coastal populations, removing the distinctiveness of the two.

Let us take a further example of Sicily. The island of Sicily was colonized initially by farmers, and later by Greeks and Phoenicians. All three groups are believed to have contained some "Neolithic" markers, such as haplogroups J, E3b, and G, so any inferences about the relative contributions of the three groups are on very shaky ground.

For example, Semino et al. proposed that only 7% of Calabrian Y-chromosomes are of Greek with the assumption that J2a and E3b represent Anatolian and Greek lineages respectively. But, the frequency of E3b in modern Peloponnesians is not necessarily representative of its frequency in the very specific ancient city states and medieval Greek populations that colonized Southern Italy, and J2a may have arrived in Calabria either from Anatolia, e.g., during the Neolithic, or from Greece, during the age of colonization.

Things become even more complex when we turn to the Balkans or to Anatolia. For example, I playfully recounted some random facts about Phrygo-Armenians, but these hardly scratch the surface of the problem. Hittites, themselves either native or intrusive, were unseated by Phrygians, who were conquered by Persians, who were conquered by Macedonian Greeks, who were conquered by Romans, who were conquered by Turks. Not to mention the Galatians of Ancyra, or the ubuiquitous Armenians of the Byzantine Empire, or even the Jews of both the ancient and more recent origin, and of course the Turks themselves as well as imported Muslims from former provinces or vassals of the Ottoman Empire. And, of course, we should not forget that present-day Anatolians are only a subset of very recent Anatolians, several million of who were liquidated or deported following World War I.

These remarks underscore the near hopelessness of untangling historical patterns on the basis of phylogeography. Is there a way out?

Part of the solution will consist of performing huge studies with large sample sizes and very recently derived genetic markers, augmented by separate genome-wide autosomal clustering methods that may unmask latent genetic components that may be correlated with historical groups. Such studies will be very costly, even though the price of DNA testing is likely to go down, because ultimately the hard work of sample collection has to be done and paid for.

The ultimate solution, would be some significant progress in ancient DNA extraction. At present, mtDNA is the only game in town, and inferences from mtDNA are always up for grabs, due to the potential for contamination, uncertainties about selection, and of course the simple fact that ancient civilizations were largely patriarchal.

An even more exciting development would be the discovery -in modern human populations- of the genetics underlying common human variation in metric and morphological traits. Then, by examing ancient skeletal remains, we will be able to estimate the genetic identity of populations even if DNA cannot be directly observed.

The technical challenges are enormous, but -in my opinion- are not the main challenges at all. As hinted in Genetic vs. Mythical Origins, the study of the past forces us to question our ideas of descent and ethnicity. In the end, will it lead to an erosion of ethnic identity, or to its reinforcement along genetic and hence "objective" lines?

More on the Cohen modal haplotype

A few days after my previous post on the Cohen modal haplotype, here is an abstract from the October ASHG meeting which essentially confirms my main points, that the CMH is not indicative of Hebrew ancestry and is split between J1 and J2 lineages.

An Updated World-Wide Characterization of the Cohen Modal Haplotype.

J.E. Ekins et al.

Since the definition of the Cohen Modal Haplotype (CMH) in 1998, the 6 SNP-6 STR genetic motif has been utilized to infer connections of contemporary individuals and communities to the ancient Hebrew population. The elucidation of the YCC SNP Phylogeny has allowed cataloguing of chromosomes compatible with the original CMH definition into several different Y-SNP subclades. Haplogroup membership was determined for 266 samples matching at ≥5 of the CMH STR alleles, defined as the Cohen Modal Haplogroup (CMHg). The bulk of the CMHg chromosomes were observed in J1 (53.0%) and J2 (43.2%), with a small portion falling outside of haplogroup J (3.8%). Members of the CMHg were observed throughout the world, with significant frequencies in various Arab populations: Oman (20.1%), Iraq (15.2%), Palestine (9.5%). Coalescent simulations were performed for CMH chromosomes within each SNP haplogroup using 24 STR loci. Estimates within J1 [6.5kybp(4K-12K)] and J2 [13kybp(7K-27K)] were substantially deeper than previous figures obtained from a heavily weighted Jewish sampling, indicating a likely origin of the compound haplotype prior to the establishment of the Hebrew population. The significant presence of CMH chromosomes in deeply divergent clades J1 and J2 (>20kybp), indicates the present CMH definition is not sufficient to distinguish lineages that likely arose by parallel IBS mutations. An expanded STR definition is proposed which allows differentiation between CMH-compatible chromosomes in J1 and J2. The inference of Jewish ancestry based on the original CMH definition should be performed with caution as subjects may be falsely categorized into the eponymous CMH lineage when the true origin is in the deeply divergent IBS branch. These observations underscore the importance of using updated SNP classifications when utilizing the CMH to infer ancestry in Jewish populations, or the use of the expanded STR definition.

Link

What was really Aaron's lineage? (Cohen modal haplotype)

One of the first spectacular applications of Y-chromosome testing was the discovery that Jewish Cohanim exhibited a particular Y-chromosome haplotype, called the Cohen Modal Haplotype (CMH). Jewish Cohens are believed to be descended from the priests of biblical Israel by patrilineal descent, and hence their Y chromosomes should be descended from that of Aaron, the first priest.

In retrospect, the first letter announcing this discovery supported its case by showing a spectacular difference between Cohanim and non-Cohanim Jews. The Cohanim had trace frequencies of haplogroup E3b, and a particular DYS19 allele at high frequency. This finding did prove different histories for priests and non-priests. However, it did not prove descent from a single individual because the YAP- DYS19B combination is not a monophyletic lineage.

In another study, the authors discovered a more extended version of the same haplotype (DYS19-14, DYS388-16, DYS390-23, DYS391-10, DYS392-11, DYS393-12) at high frequency in the Lemba of Southern Africa, as well as in Jews. This was interpreted as evidence for a Jewish origin of the Lemba. This seems likely, given the anomalous existence of a Middle-Eastern haplotype and the oral history of the Lemba. However, once again, it was not proven that people belonging to the CMH were all descended from the biblical Aaron.

A small note: if two men have the same haplotype, it does not mean that they are descended from the same ancestor. This is due to the fact that microsatellites defining haplotypes mutate quite fast, so two unrelated men may have the same haplotype by chance. In fact, the probability of such an accident increases as the number of microsatellites decreases.

The Cohen modal haplotype belongs to a Y-chromosome haplogroup called J or HG-9. A haplogroup is defined by a unique event polymorphism, and men who belong to the same haplogroup are indeed descended from a single man. But, in the case of J, that single man lived more than 10,000 years ago, long before the time of Aaron. However, J is split into two lineages that are also more than 10,000 years old: J2 (or Eu9) and J1 (or Eu10).

If the people who have the CMH are always in Eu9 or in Eu10, then the CMH really reflects priestly descent. But, if it is found in both, then by definition the CMH does not in itself reflect priestly descent, because the common ancestor of a Eu9-CMH and a Eu10-CMH lived earlier than 10,000 years ago, i.e., much earlier than the putative time of Aaron's priesthood (~3 thousand years).

This brings us to yet another study (pdf) which discovered a high frequency of the CMH in Jews. According to this study:

The most-frequent haplotype in all three Jewish groups (the CMH [haplotype 159 in the Appendix]) segregated on a Eu 10 background, together with the three modal haplotypes in Palestinians and Bedouin (haplotypes 144, 151, and 166).

This would suggest that the CMH belonged to J1. However, the author only identified that most CMHs belonged to J1. In the appendix of the same study, it is shown that haplotype 108 is also the CMH, but belongs to haplogroup J2.

Admittedly, 22 CMH-bearing Jews from the study belong to J1, and only 3 ones belong to J2, but this clearly demonstrates that the CMH is not in itself evidence of priestly descent. In principle, Aaron could have been either J1 or J2.

More importantly, the occurrence of the CMH in Cohanim overestimates their descent from Aaron, because at least some of the CMH bearers belong to J1 and some to J2, and they can't both be descended from Aaron.

At this stage, it would appear that we could conclude that the "real" priestly lineage was J1+CMH, because J1+CMH is more frequent than J2+CMH in Jews. Things are however not that simple.

In yet another study the authors state that:

By typing a limited number of Italian Cohanim (A. N. unpublished obs.) for the STRs used here, we determined that the Cohen Modal Haplotype (`an important component in the sharing of Ashkenazic and Sephardic Israelite Y chromosomes', Thomas et al. 2000) does indeed belong to network 1.2.

Network 1.2 falls under the J2 haplogroup. Hence it appears that Cohen Jews, as opposed to Jews in general may belong mainly to haplogroup J2.

At present, no new published information is available on this matter. Several studies have now proven that the CMH occurs in both J1 and J2 backgrounds and does not represent a single lineage. Moreover, Jews themselves are split between the J1 and J2 varieties.

More importantly, the CMH was first identified because of its high frequency compared to other haplotypes. The strength of this evidence is diminished by the finding that CMH chromosomes belong to two unrelated lineages. Furthermore, the dating of CMH chromosomes to Aaron's time should be reconsidered, and the molecular variation within J1 and J2-background CMH and its neighbors should be considered separately.

In conclusion, the true genetic identity of Aaron remains elusive.

UPDATE:

I just discovered the supplementary materials of this comprehensive article on Ashkenazi Jewish Y-chromosome variation.

According to my count, 28 of the Jewish CMHs belong to J1 (6.3%) and 25 belong to J2 (5.7%). This casts further doubt to the CMH as Aaron's lineage, and even if the CMH was Aaron's lineage, it raises the question as to whether he belonged to J1 or J2.

UPDATE II:

In Anatolia, the CMH occurs in:

2 x J2*, 1 x J2f1, 5 x J2f* (total 8 x J2 or 1.5%)
7 x J1* and 1 x J1c (total 8 x J1 or 1.5%)

It is noteworthy that in region 6 (south), 4/33=12% belong to the J1-CMH.

UPDATE III:

Among Armenians, the CMH occurs at a frequency of 1.9%, ranging up to 4.4% in the West region.

Y-chromosome Lineages from Portugal, Madeira and Açores

A very interesting new paper on Portuguese Y-chromosomes. Three important conclusions are derived from the study of Sub-Saharan African, E3b, and J1 lineages in Portugal. The Sub-Saharan component seems to be small (0.7%) unlike the corresponding mtDNA component. The E3b lineages are highly heterogeneous, and include various sub-types, including the Aegean E-M78 cluster α as well as North African E3b2 and Middle Eastern E3b3. Interestingly, the North African component seems to be primarily of earlier Berber rather than historical Moorish origin:

North African component at least for mtDNA, is mainly concentrated in the North of Portugal. The mtDNA and Y data indicate that the Berber presence in that region dates prior to the Moorish expansion in 711 AD. Our Y chromosome results are also consistent with a continuous and regular assimilation of Berbers in North of Portugal. This argues against previous interpretations of Moorish mediated contributions, based on Y chromosome data (Bosch et al. 2001; Pereira et al. 2000b; Cruciani et al. 2004) and provides an alternative view of an earlier Berber presence in the North of Portugal.

Finally, the J lineages in Portugal are mainly in the J2 clade, but there is a substantial presence of the J1 clade as well, which is found in Arabs and Jews and not as often in European populations. The Portuguese J1 chromosomes cluster around the Cohen Modal Haplotype, rather than the known modal haplotypes of the Arabs. Therefore, it seems probable that these were introduced by Sephardic Jews, rather than Arabs.



Annals of Human Genetics (OnlineEarly)

Y-chromosome Lineages from Portugal, Madeira and Açores Record Elements of Sephardim and Berber Ancestry

Rita Gonçalves et al.

Summary

A total of 553 Y-chromosomes were analyzed from mainland Portugal and the North Atlantic Archipelagos of Açores and Madeira, in order to characterize the genetic composition of their male gene pool. A large majority (78-83% of each population) of the male lineages could be classified as belonging to three basic Y chromosomal haplogroups, R1b, J, and E3b. While R1b, accounting for more than half of the lineages in any of the Portuguese sub-populations, is a characteristic marker of many different West European populations, haplogroups J and E3b consist of lineages that are typical of the circum-Mediterranean region or even East Africa. The highly diverse haplogroup E3b in Portuguese likely combines sub-clades of distinct origins. The present composition of the Y chromosomes in Portugal in this haplogroup likely reflects a pre-Arab component shared with North African populations or testifies, at least in part, to the influence of Sephardic Jews. In contrast to the marginally low sub-Saharan African Y chromosome component in Portuguese, such lineages have been detected at a moderately high frequency in our previous survey of mtDNA from the same samples, indicating the presence of sex-related gene flow, most likely mediated by the Atlantic slave trade.

Link

Haplogroup E3b and Ancient Jews

Jews have been widely distributed for thousands of years. Therefore, any single group of Jewish descent cannot in itself tell us much about the genetic composition of Ancient Jews (*)

Previously, I had suggested that the presence of Y-haplogroups Q,R1a in Ashkenazi Jews may have been introduced by a Turkic population in Eastern Europe, and hence was not present in Ancient Jews.

A recent study on Samaritans , a group which split from Jews in BC times, indicates that these belong wholly to haplogroup J, with the exception of the Cohen Samaritans who belong to haplogroup E3b. But, since Cohens in general belong to haplogroup J (which contains the Cohen Modal Haplotype), the E3b Samaritan Cohen is probably the result of some (possibly ancient) admixture event.

The Lemba of Southern Africa are physically Negroid, but the presence in their gene pool of the Cohen Modal Haplotype indicates that they are of Jewish origin. They possess 2.9% of haplogroup E3b, which however may have been introduced by other populations of Africa.

The Bene Israel of India also have traditions of Jewish descent, and they also have a high frequency of the Cohen Modal Haplotype, substantiating these claims. They lack haplogroup E3b, and the authors of the linked study suggest that they split from other Jews before E3b entered the Jewish gene pool.

The Cohens themselves have patrilineal descent, therefore they ought to represent in principle a more "pristine" gene pool of Jewish origin than other Jews who only have (almost always) matrilineal Jewish descent. They only have 1.5% of haplogroup E, in contrast to about 18% in lay Jews.

In conclusion, it's probable that ancestral Jewish groups lacked at some stage haplogroup E3b. If this turns out to be the case, then by additionally subtracting the possible Turkic/Slavic admixture (Q+R1a), as well as other clades of possible (Indo-)European origin, it appears that the ancestral Jews belonged primarily (**) to clades of haplogroup J.

(*) By Ancient Jews, I mean "as ancient as can be determined". Ethnic groups are not static entities, and undergo continuous processes of admixture.
(**) Primarily, or even exclusively at the most ancient stage.