Chronology of Ksar Akil

PLoS ONE 8(9): e72931. doi:10.1371/journal.pone.0072931

Chronology of Ksar Akil (Lebanon) and Implications for the Colonization of Europe by Anatomically Modern Humans

Katerina Douka et al.

The Out-of-Africa model holds that anatomically modern humans (AMH) evolved and dispersed from Africa into Asia, and later Europe. Palaeoanthropological evidence from the Near East assumes great importance, but AMH remains from the region are extremely scarce. ‘Egbert’, a now-lost AMH fossil from the key site of Ksar Akil (Lebanon) and ‘Ethelruda’, a recently re-discovered fragmentary maxilla from the same site, are two rare examples where human fossils are directly linked with early Upper Palaeolithic archaeological assemblages. Here we radiocarbon date the contexts from which Egbert and Ethelruda were recovered, as well as the levels above and below the findspots. In the absence of well-preserved organic materials, we primarily used marine shell beads, often regarded as indicative of behavioural modernity. Bayesian modelling allows for the construction of a chronostratigraphic framework for Ksar Akil, which supports several conclusions. The model-generated age estimates place Egbert between 40.8–39.2 ka cal BP (68.2% prob.) and Ethelruda between 42.4–41.7 ka cal BP (68.2% prob.). This indicates that Egbert is of an age comparable to that of the oldest directly-dated European AMH (Peştera cu Oase). Ethelruda is older, but on current estimates not older than the modern human teeth from Cavallo in Italy. The dating of the so-called “transitional” or Initial Upper Palaeolithic layers of the site may indicate that the passage from the Middle to Upper Palaeolithic at Ksar Akil, and possibly in the wider northern Levant, occurred later than previously estimated, casting some doubts on the assumed singular role of the region as a locus for human dispersals into Europe. Finally, tentative interpretations of the fossil's taxonomy, combined with the chronometric dating of Ethelruda's context, provides evidence that the transitional/IUP industries of Europe and the Levant, or at least some of them, may be the result of early modern human migration(s).

Link

Genomewide diversity in the Levant (Haber et al. 2013)

Razib points me to a new paper (and its associated data, consisting of Christian, Druze, and Muslim Lebanese).


Genome-Wide Diversity in the Levant Reveals Recent Structuring by Culture

Marc Haber et al.

The Levant is a region in the Near East with an impressive record of continuous human existence and major cultural developments since the Paleolithic period. Genetic and archeological studies present solid evidence placing the Middle East and the Arabian Peninsula as the first stepping-stone outside Africa. There is, however, little understanding of demographic changes in the Middle East, particularly the Levant, after the first Out-of-Africa expansion and how the Levantine peoples relate genetically to each other and to their neighbors. In this study we analyze more than 500,000 genome-wide SNPs in 1,341 new samples from the Levant and compare them to samples from 48 populations worldwide. Our results show recent genetic stratifications in the Levant are driven by the religious affiliations of the populations within the region. Cultural changes within the last two millennia appear to have facilitated/maintained admixture between culturally similar populations from the Levant, Arabian Peninsula, and Africa. The same cultural changes seem to have resulted in genetic isolation of other groups by limiting admixture with culturally different neighboring populations. Consequently, Levant populations today fall into two main groups: one sharing more genetic characteristics with modern-day Europeans and Central Asians, and the other with closer genetic affinities to other Middle Easterners and Africans. Finally, we identify a putative Levantine ancestral component that diverged from other Middle Easterners ~23,700–15,500 years ago during the last glacial period, and diverged from Europeans ~15,900–9,100 years ago between the last glacial warming and the start of the Neolithic.

Link

Y-chromosomes of Maronites from Lebanon

The freely available supplementary material contain a real treasure trove of Y-STR haplotypes for different populations of Lebanon and from Iran.

UPDATE: The paper uses the wrong Zhivotovsky et al. "evolutionary" mutation rate, hence their age estimates are inflated 3-fold. Hence, their conclusion that religion differences were superimposed on an already structured population is also wrong, in my opinion.

The write, for example that:

The Christian–Muslim split dated to 3475 (2000–6025) ybp for pooled Muslims and 3325 (1875–4225) ybp for pooled Christians.

Divide these by 3 and you get about 1.2ky which is quite close (given the huge confidence intervals, of course) to the arrival of Islam to the country. Once again, the genealogical mutation rate conforms with history, while the "evolutionary" one suggests a speculative scenario about the supposed long-term maintenance of structure on which the Islam-Christian distinction was superimposed.

European Journal of Human Genetics advance online publication 1 December 2010; doi: 10.1038/ejhg.2010.177

Influences of history, geography, and religion on genetic structure: the Maronites in Lebanon

Marc Haber et al.

Cultural expansions, including of religions, frequently leave genetic traces of differentiation and in-migration. These expansions may be driven by complex doctrinal differentiation, together with major population migrations and gene flow. The aim of this study was to explore the genetic signature of the establishment of religious communities in a region where some of the most influential religions originated, using the Y chromosome as an informative male-lineage marker. A total of 3139 samples were analyzed, including 647 Lebanese and Iranian samples newly genotyped for 28 binary markers and 19 short tandem repeats on the non-recombinant segment of the Y chromosome. Genetic organization was identified by geography and religion across Lebanon in the context of surrounding populations important in the expansions of the major sects of Lebanon, including Italy, Turkey, the Balkans, Syria, and Iran by employing principal component analysis, multidimensional scaling, and AMOVA. Timing of population differentiations was estimated using BATWING, in comparison with dates of historical religious events to determine if these differentiations could be caused by religious conversion, or rather, whether religious conversion was facilitated within already differentiated populations. Our analysis shows that the great religions in Lebanon were adopted within already distinguishable communities. Once religious affiliations were established, subsequent genetic signatures of the older differentiations were reinforced. Post-establishment differentiations are most plausibly explained by migrations of peoples seeking refuge to avoid the turmoil of major historical events.

Link

Coastal-inland differences in Y chromosomes of the Levant

More on this after I get a hold of and digest the information in the paper.

Just a quick comment, based only on the abstract, that the Levantine populations should be studied in a European context as well, as they have been influenced by prehistoric populations from the Aegean, Greeks, Romans, medieval Crusaders, or Ottomans of various origins.

UPDATE: The paper has several supplementary figures and tables.

In Figure S1 we see the biallelic markers used in this study, and their representation in the various populations. It is a chronic problem with studies of this sort to undertype samples; there are phylogeographically informative markers within haplogroups G, L, E1b1b, and J2 for example, which would have added important information about the specific affinities of these haplogroups in the studied populations.


Inspit of these deficiencies, we may still make some useful observations. For example, IE-speaking Iranians have largely the same haplogroups as Arabs, but a much higher representation of haplogroup J2 compared to J1. The converse is true for all Arabs except the Lebanese. But, we do know, that even in Lebanon itself, Muslims have a higher J1/J2 ratio than Christians, and Islam was the main vehicle of Arabization in the region. The Christians are descended from the pre-Arab Byzantine Greco-Aramaic populations (with an addition of Western European Y-chromosomes in some Christian communities, which would not have substantially upset the J1/J2 balance).

It is fairly clear to me that in the Middle East, Greek and Iranian-settled regions have a higher J2/J1 ratio than regions with solid Semitic or NE Caucasian populations where J1 predominates.

UPDATE II (Aug 27):

The paper reports a near zero frequency of haplogroup J1 in Tunisia and Morocco, after an earlier study by the same authors. However, a different study (Onofri et al.) on Moroccan and Tunisian Y chromosomes report 20 and 35% respectively, which is in agreement with an earlier study on North African Y-chromosomes (Arredi et al.) The discrepancy in the J1 frequency seems too large to have arisen by chance given the sample sizes, and it would be interesting to see how it may have arisen.

Annals of Human Genetics doi:10.1111/j.1469-1809.2009.00538.x

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

Mirvat El-Sibai et al.

Abstract

We have examined the male-specific phylogeography of the Levant and its surroundings by analyzing Y-chromosomal haplogroup distributions using 5874 samples (885 new) from 23 countries. The diversity within some of these haplogroups was also examined. The Levantine populations showed clustering in SNP and STR analyses when considered against a broad Middle-East and North African background. However, we also found a coastal-inland, east-west pattern of diversity and frequency distribution in several haplogroups within the small region of the Levant. Since estimates of effective population size are similar in the two regions, this strong pattern is likely to have arisen mainly from differential migrations, with different lineages introduced from the east and west.

Link

More on Lebanese Phoenicians or mixing Science and Politics

The BBC has a story on Divided Lebanon's common genes.

Dr Zalloua says in Lebanon the Phoenician signature is distributed equally among different groups and that the overall genetic make-up of the Lebanese is proving to be similar across various backgrounds.

"Whether you take a Christian village in the north of Lebanon or a Muslim village in the south, the DNA make-up of its residents is likely to be identical," says Dr Zalloua.

But, from another older BBC story referring to the actual study:

The team analysed the Y chromosomes of 926 Lebanese males and found that patterns of male genetic variation in Lebanon fell more along religious lines than along geographical lines.

and from the study itself:

In the present study, 926 Lebanese men were typed with Y-chromosomal SNP and STR markers, and unusually, male genetic variation within Lebanon was found to be more strongly structured by religious affiliation than by geography.We therefore tested the hypothesis that migrations within historical times could have contributed to this situation. Y-haplogroup J*(xJ2) was more frequent in the putative Muslim source region (the Arabian Peninsula) than in Lebanon, and it was also more frequent in Lebanese Muslims than in Lebanese non-Muslims. Conversely, haplogroup R1b was more frequent in the putative Christian source region (western Europe) than in Lebanon and was also more frequent in Lebanese Christians than in Lebanese non-
Christians.

If a Christian village and a Muslim village are likely to have "identical" DNA makeup, then why is genetic variation strongly structured by religious affiliation and not by geography?

Since contradictions don't exist in nature, the explanation is simple: in the published scientific article, which had to go through peer-review, someone could not claim that there are no differences between Christian and Muslim Lebanese. But, to the polloi of Lebanon, it is apparently alright to sell a vision of national unity and identity.

I don't know what % of modern Lebanese are descended from Phoenicians, but I detest the idea of mixing science with politics.

More on the topic of "Lebanese Phoenicians":

1. Muslim and Christian Lebanese or Hasty Conclusions in Human Population Genetics
2. Christian and Muslim Lebanese do differ from each other after all
3. "Phoenician" Y-chromosomes

Christian and Muslim Lebanese do differ from each other after all

Like I said they did in 2007. BBC has a story about this:

The team analysed the Y chromosomes of 926 Lebanese males and found that patterns of male genetic variation in Lebanon fell more along religious lines than along geographical lines.

A genetic signature on the male chromosome called WES1, which is usually only found in European populations, was found among the Lebanese men included in the study.

"It seems to have come in from Europe and is found mostly in the Christian population," said Dr Spencer Wells, director of the Genographic Project.

"This is odd because typically we don't see this sort of stratification by religion when we are looking at the relative proportions of these lineages - and particularly immigration events."

He told BBC News: "Looking at the same data set, we saw a similar enrichment of lineages coming in from the Arabian Peninsula in the Muslim population which we didn't see [as often] in the Christian population."

Lebanese Muslim men were found to have high frequencies of a Y chromosome grouping known as J1. This is typical of populations originating from the Arabian Peninsula, who were involved in the Muslim expansion.

As I predicted, the finding of similarity between Christian and Muslim Lebanese in the older National Geographic story on Wells' and Zalloua's work was premature, based on their common possession of Y-haplogroup J, because it did not look at downstream markers which differentiate between Christians and Muslims. As I observed based on the work of Capelli et al., it is the overrepresentation of Y-haplogroup J*(xJ2), which comprises almost entirely of J1 chromosomes that is the mark of the Arab descent of Muslim Lebanese.

I will post the abstract of this study and any further comments when I see it.

UPDATE: The Genographic project has its own page on this research, as well as a link to the paper (pdf).

Y-Chromosomal Diversity in Lebanon Is Structured by Recent Historical Events

Pierre A. Zalloua et al.

Lebanon is an eastern Mediterranean country inhabited by approximately four million people with a wide variety of ethnicities and religions, including Muslim, Christian, and Druze. In the present study, 926 Lebanese men were typed with Y-chromosomal SNP and STR markers, and unusually, male genetic variation within Lebanon was found to be more strongly structured by religious affiliation than by geography.We therefore tested the hypothesis that migrations within historical times could have contributed to this situation. Y-haplogroup J*(xJ2) was more frequent in the putative Muslim source region (the Arabian Peninsula) than in Lebanon, and it was also more frequent in Lebanese Muslims than in Lebanese non-Muslims. Conversely, haplogroup R1b was more frequent in the putative Christian source region (western Europe) than in Lebanon and was also more frequent in Lebanese Christians than in Lebanese non-
Christians. The most common R1b STR-haplotype in Lebanese Christians was otherwise highly specific for western Europe and was unlikely to have reached its current frequency in Lebanese Christians without admixture.We therefore suggest that the Islamic expansion from the Arabian Peninsula beginning in the seventh century CE introduced lineages typical of this area into those who subsequently became Lebanese Muslims, whereas the Crusader activity in the 11th-13th centuries CE introduced western European lineages into Lebanese Christians.

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.