Friday, April 16, 2010

Review — "Linking the sub-Saharan and West Eurasian gene pools: maternal and paternal heritage of the Tuareg nomads from the African Sahel"

As it has become customary on this site, we will hereby examine the material specifics of work that recently came out, by Pereira et al., giving us an idea of what aspects of the journal withstands scrutiny and what doesn't. Below, is the extract, to give an indication of what we are working with:

Linking the sub-Saharan and West Eurasian gene pools: maternal and paternal heritage of the Tuareg nomads from the African Sahel

Pereira et. al.

European Journal of Human Genetics advance online publication 17 March 2010.


The Tuareg have a nomadic lifestyle and according to some demographic reports they show reduced fertility in comparison with their neighbours.47, 48, 49 The data observed here for mtDNA and Y-SNP diversities are concordant with those independent reports, especially for the Tuareg living within the bend of the Niger.

The overall West Eurasian mtDNA gene pool in the Tuareg population as a whole (H1, H3 and V) seems to favour a North African heritage.50 The only exception is the absence of the otherwise rare U5b that might have rather come to Africa through the Near East, and then drifted to higher frequencies only in some isolated populations such as in the Egyptian oasis Siwa.51 The absence of U6 can further be explained by genetic drift during the expansion of this haplogroup within North Africa.51 Note that U6 was observed at low frequencies in several population groups from the Chad Basin, such as in the Nilo-Saharan Kanuri and the Afro-Asiatic Masa.35

Relationships with the peoples of Eastern Sudan (the Beja) as pointed to by the study of classical genetic markers2 cannot yet be disregarded here as there is still no mtDNA of the Beja people available for study. However, according to historical reports, the origin of the Beja is more likely to be traceable to the Arabian Peninsula52 and the West Eurasian mtDNA lineages seen in the Tuareg have a rather Iberian affiliation in the post-LGM, and probably expanded to North Africa first.30, 31 The weak Eastern African influence in Tuareg is further supported by the M1 haplotypes belonging to the lineages characteristic of the later Mediterranean expansion (M1b and M1a2a) and the presence of very few matches for sub-Saharan L haplotypes with East Africa. The main post-LGM Eurasian and M1a2a lineages found in the Tuareg favour North African origin with migration to its southern location in the Sahel between ~9000 and ~3000 years ago. The upper time limit is defined by the age of the M1a2a, (estimated here from the coding region diversity observed in the three Tuareg, two North and two south Mediterranean individuals at 8000±2400), and by the upper 95% confidence interval for the Tuareg V lineages having polymorphism 16 234 (8800 years ago); the lower limit is defined by the age of the Tuareg V lineages having polymorphism 16 234 (3600 years ago).

The dates obtained from the genetic data coincide well with climatic changes in the Sahara, which resulted in repopulation during the first half of the Holocene when by ~10 000 YBP (the Holocene climatic optimum) humid conditions and greening were established. The climatic optimum lasted until ~6000 YBP, when the shift towards more permanent aridity occurred, culminating with the formation of the current Sahara desert. This desertification could have entrapped Tuareg populations coming from North Africa to the Sahel belt together with other pastoralists such as the Chadic speaking peoples41 coming from East Africa and Fulani nomads6 coming from West Africa. In fact, by performing complete mtDNA sequencing of the L3f3 lineage, specific for Chadic-speaking groups of the Chad Basin, Černý et al41 estimated a local demographic expansion during the Holocene period at about 8000±2500 YBP. No doubt all populations arriving to the Sahel were further enriched by various admixtures of many other sub-Saharan lineages, an effect even more pronounced in the Chadic groups who adopted a sedentary lifestyle soon after their arrival to the fertile Chad Basin than in the Tuareg who remain nomadic until present.

It is curious that, at least for the Tuareg maternal gene pool, there are no mtDNA lineages connected with the Neolithic expansion from the Near East despite being present in considerable frequencies in other North African populations. For example, the conservation of the high frequency and remarkable internal variability of T1 haplotypes within the distant and relatively isolated Egyptian oasis of el-Hayez led to an estimation of local expansion at around 5138±3633 YBP.37 There are no indications yet of the ages of local expansions in the more central and western regions of North Africa, which could contribute further insights for its absence in the Tuareg population as a whole.

Interestingly, for the Y chromosome, the dominant haplogroup in North Africa as well as the Tuareg is E1b1b1b. This haplogroup was associated with Neolithic diffusion in North Africa, with an age estimation of 2800–9800 YBP,45 but the lower resolution of the Y chromosome tree did not allow us to investigate this issue further. Nonetheless, disregarding whether they are in fact Neolithic, the ages for the mtDNA and Y chromosome lineages of North African origin observed in southern Tuareg are consistent with the same period, between 9000 and 3000 years ago.
- Extract ends.

Let's start with a statement that Pereira et al. make in the abstract provided for the journal at hand:
"On the other hand, the Y chromosome SNPs data show that the paternal lineages can very probably be traced to the Near Eastern Neolithic demic expansion towards North Africa, a period that is otherwise concordant with the above-mentioned mtDNA expansion."
What is one to make of the Pereira et al.'s (2010) reference to a "Near Eastern" origin above? The answer is that the said authors meant by it just as it sounds like: "Near Eastern". Obviously, the line of question at hand is not so much as a demand for learning the definition of the Euro-centered political/geopolitical construct  of  the so-called "Near East", but so much as a call to question, the far-fetched claim about "Near Eastern" origins of Tamazight speakers of western Africa, including Tamasheq (Tuaregs) nomads, whom they compare to the Beja, another group whose origins they dubiously trace to the Arabian peninsula. As ridiculous as it may sound, from the looks of it, the authors are interpreting the African haplogroup E1b1b1b (a.k.a. E3b2-M81) as a "Neolithic" marker of "Near Eastern" rather than the conventional understanding of its African origin. The present author of this blog supposes that this is the reason they find it "interesting". If so, conversely, the present author finds it interesting, how a typical African marker turned into a "Near Eastern" one.

As a simple matter of fact, neither the quadro-entity of hg E1b1b1b, Tamazights, Tamasheq (Tuareg) nomads, and Beja nomads are found in the Arabian peninsula, at least not as autochthonous groups. All are rare to absent in the Arabian peninsula. Hg E1b1b1b is generally absent in the Arabian peninsula, save for the few sporadic spots which became host to historic era immigrants from coastal northwestern Africa, like say the "Mizrachim" Sephardic Jews of coastal northwestern Africa, elements of which can be found in Israel. That is the only context in which any hg E1b1b1b subclade makes its presence in the so-called "Near East". The basal clades of the marker are restricted to Africa, not to leave out the haplogroup's diversity. Likewise, neither Tamazight nor Beja language are spoken in the Arabian peninsula.

Getting back to that matter of why Pereira et al. find it interesting that the "dominant" male haplogroup of coastal northwest Africans and the Tamasheq ("Tuaregs") happens to be of the characteristic "Berber" marker of hg E1b1b1b, when such an understanding is otherwise conventional wisdom and therefore, to be the expected turn of results; let's think about it for a moment: Getting an understanding of why these authors feel that way may also explain why they would even bother to entertain an Arabian peninsula origin of the Beja, even though no such group is native to that area. The invocation of the Beja has a role to play here: Since the Beja (Bedawi) have been claimed to show close relationship with the Tamasheq/"Tuareg" in one study [specifically by Sforza] that used select autosomal markers, the authors brought them up perhaps to support their idea of the supposed arrival of Tamasheq/"Tuaregs" first from coastal north Africa, and then their settlement in the Niger Bend areas upon the desertification of the Sahara in the mid-Holocene era.

They try to buttress this viewpoint, from what the present author can discern, by turning to what they call "Eurasian component" of Western African Tamasheq/"Tuaregs", again NOT the Libyan or northwestern Saharan Tamasheq/"Tuaregs", but the ones in the noted "sub-Saharan" African countries. The markers that they are leaning on are hgs H1, H3 and V.

Pereira et al. seem to be of the mindset that the Y-markers came to coastal north Africa via the "Near Eastern" Neolithic diffusion, and then in coastal northwest Africa, mtDNA from the Iberian peninsula were picked up, with some contribution from a "Near Eastern" Neolithic mtDNA gene pool [albeit not significant in the western African Tamasheq ("Tuareg"), according to the said authors' own observations], which they seem to identify with the expansions of M1, hence calling it a late "Mediterranean expansion".

Few other things to take into account:

Hg M1 markers...

  • The M1 markers implicated in the extract are actually of the Eastern African types, and not the typical coastal northwestern African examples. While the authors here do seem to entertain an ultimate eastern African origin for the M1 clades that they mentioned on the one hand, from the language in the extract provided, it appears that they were describing a coastal north African flow of the marker on the other hand, i.e. presumably before its heading for the Sahel in western Africa. In other words, notwithstanding the acknowledgment that their mentioned M1 sub-clades originate in eastern Africa, Pereira et al. are treating the M1 sub-clades here as "northern markers".

  • *More insight into hg M1 expansion across coastal northern Africa, eastern Africa and the so-called "Near East" had recently been posted here: Following Trails of the Cro-Magnon - II

    The Beja...

  • While some genetic infiltration has taken place into the autochthonous gene pool of the Beja, the bulk of their Y-DNA lineage is of M78, BUT these are not the examples found in the Arabian peninsula; rather, these are the examples mainly found in the African Horn. The bulk of Beja M78 markers carry the V32 binary marker [see for example, Hassan et al. 2008].

  • The Beja language is considered to be a standalone sub-phylum of the Cushitic branch, and hence, not Semitic. The Arabian peninsula is dominated by Semitic languages.

  • The west African Tamasheq or "Tuaregs"...

    The study that the present author posted on this site earlier about the largely west African component of west African Tuareg mtDNA related the following, to recall:

    West African Tamasheq/"Tuaregs":
    The mitochondrial data of the Northwest African populations (Berber from Morocco and Algeria, Moroccans, West-Saharans, Mauritanians, Tuareg) show a mosaic composition of mtDNA types, with a pronounced gradient of sub-Saharan lineages from north to south: at the one extreme, the Berbers from Morocco have a predominantly European (Iberian) affinity, while at the other extreme, the Tuareg are closely related to sub-Saharan West Africans as represented by several Senegalese groups in this study, whereas the West-Saharans and Mauritanians are somewhat intermediate. It is remarkable that the Tuareg bear little mitochondrial resemblance to the Berber populations, although they speak a Berber language. - Rando et al. 1998 [mtDNA analysis of Northwest African populations reveals genetic exchanges with European, Near Eastern and sub-Saharan populations]
    One should not think for a moment that Rando et al. (1998) were alone in their findings about western African "Tuaregs"; the following from Claudio Ottoni et al. (2009) essentially tells the same story:
    Of note is that the other Tuareg sample described in the literature (Watson et al., 1996) (Western Tuaregs) did not show a close genetic relationship with the Libyan Tuaregs, implying a genetic heterogeneity of the Tuaregs. This difference appears to be primarily caused by the low frequency (8%) of the European component in the Western Tuaregs, characteristic of northern African populations. After the removal of the H and V haplotypes, the Libyan Tuaregs showed a strong affiliation with the Eastern populations, while the Western Tuaregs associated more with the Central and Western African populations. - Claudio Ottoni et al. 2009, First Genetic Insight into Libyan Tuaregs: A Maternal Perspective.
    *While Claudio et al. have their own shortcomingsa  matter that may be saved for another discussion, what is appealing about their findings is the fairly comprehensive range of their Tamasheq ("Tuareg") population samples, spanning western Africa to coastal central-north Africa, and thereby giving a noticeable mtDNA structuring that takes shape in the form west-to-east or vice versa gradients and south to north or vice versa gradients. In the west-to-east genetic structuring, western African "Tuaregs" more readily related to other western Africans and central Africans, while by removing the hgs H and V from the Libyan "Tuareg" sample, the Libyan-situated "Tuaregs" more readily related to eastern African populations. As noted here (click to the link) before, this pattern is suggestive of expansions of ancestors of contemporary Imazighen populations as a migrating group whose demography was likely biased towards male constituents; females of their destination points or from the vicinities thereof were then later integrated into the Imazighen nomads. So, we see distinctive patterns between Libyan "Tuaregs" and the western African "Tuaregs". The western African Tuaregs, just as Rando et al. found out, cluster with other western Africans. What does this then tell us? It tells us that the findings of authors in the intro post is the one that is out of character, if we are compelled to judge the results on such grounds.

  • Even Pereira et al.'s own observations hint on the very real possibility that they are only seeing a snapshot of a bigger picture...
  • The weak Eastern African influence in Tuareg is further supported by the M1 haplotypes belonging to the lineages characteristic of the later **Mediterranean** expansion (M1b and M1a2a) and the presence of very few matches for **sub-Saharan** L haplotypes with East Africa. - Pereira et. al.
    What else do these "sub-Saharan" L types match with then? Why, very likely the central and western African examples!

    Hint on what these L types are, may be found in the authors' emphasis on Chadic speakers carrying L types.

  • They theorize that the Tuaregs could have started in the North, and then descended down, based on H and V markers, which they date to around 8000 YBP or so, but guess what? That specific L haplogroup (L3f3) that they do mention in the extract provided, also dates to about the same time frame, or falls within the same window of time frame!

  • What does all this mean at this point? Their theory has little basis to it. This may very well be hinted on by Pereira et al.'s own puzzlement in the following:
    It is curious that, at least for the Tuareg maternal gene pool, there are no mtDNA lineages connected with the Neolithic expansion from the Near East despite being present in considerable frequencies in **other** North African populations. - Pereira et. al.
  • It puts them in a difficult position, because their mental attitude seems to be one of a demic diffusion from the "Near East" in the Neolithic times along the coastal areas of North Africa, whereupon in the far west Maghreb, they'd pick up European mtDNA marker types. This then will have been followed up with the mid-Holocene aridity of the Sahara, prompting the ancestors of Tuaregs to seek refuge in the Sahel, where they would mix with "sub-Saharan" Africans. This absence of "Neolithic" mtDNA markers in Sahel/"sub-Saharan" west African Tuaregs upsets that theory, in addition to the other little details just noted. 

  • Additionally, they mistake an African-specific Y gene pool with "Near Eastern" Neolithic demic diffusion. Northwest African M78 markers cannot be from the "Near East", because northwest African M78 gene pool is actually more diverse than those in the Levant, where the "Neolithic farming" revolution is supposed to have started, i.e. if we are to go by data that Cruciani et al. (2007) give us. Not to leave it out here, but even E-M81 (E1b1b1b) is rare to absent in the "Near East". In this idea, Pereira et al. may well have drawn inspiration from Arredi et al. (2004): 

  • Arredi et al.(2004) ran off with the theory that hg E1b1b1 markers first arrived in northern Africa in tandem with "Afro-Asiatic" speakers moving in from the "Near East", having citing outdated linguistic theories [like that of Diamond and Bellwood (2003)] of "Near Eastern" origins of "Afro-Asiatic" as their source of inspiration; this was the thesis of their study. They seemed to be tacitly implying that the characteristic E-M81 emerged along the path of this migration, with relative diversity of the clade decreasing as one moved to the far western corner of the continent. Of course, Arredi et al. (2004) did not account for the microsatellite distinctions in hg J clades, the other marker that is generally implicated in "Neolithic farming" subsistence for the so-called "Near East" aside from hg E1b1b1markers, that Semino et al. pointed out the same year. Much of northern African hg J clades appear to be more of post-Neolithic historic extraction, esp. during Arabic expansions, than Neolithic extraction, even though the coalescent age of the J1-M267 sub-clades when considered together point to initial dispersions within the vicinity of Neolithic time frames;  this latter observation is true for the more recent "Near Eastern" chromosomes as well. The older clades were better preserved in European and Ethiopian samples, according to Semino et al., and hence, the most likely markers of Neolithic era expansions. Moreover, Arredi et al.'s hypothesis is contemptuous of the facts mentioned above, to reiterate, about the restriction of hg E1b1b1b markers to Africa, the absence of Tamazight as an autochthonous "Near Eastern" language and of any languages therein in the "Near East", that serves as the root stratum of Tamazight. Lastly, as pointed out here time and again, northern Africa did not adopt large scale farming subsistence at the same time or within the logical or expected time frame that it should have, in the event that one should entertain the idea of Neolithic demic diffusion in tandem with the spread of agricultural subsistence from the so-called "Near East".

    What Pereira et al. may be seeing, if anything is to be made of it, is a portion of the "sub-Saharan" west African "Tuareg" gene pool that was attained from interactions between those Niger River bend "Tuaregs" and the more northern west Saharan groups. It is not inconceivable, since paternal and cultural relationship exists between these groups. The patterns seen in west African "Tuaregs" is obviously reflective of the Imazighen bio-history as nomads, and so, in order to get a fairly comprehensive picture of the uniparental DNA structuring in such groups, it is necessary to deal with large sample sizes that are not from just one or two spots, but spanning the general territories that are known for Tamasheq ("Tuaregs") communities. Rando et al. and Claudio et al. had done this to some degree or another, and hence, their relatively more consistent findings in DNA structuring. Pereira et al. may be suffering from what Cherni et al. described as "patchy" DNA sampling work. However, western African "Tuaregs" in the main, cluster with western Africans where mtDNA is concerned. As we've seen, two studies already attest to this, and as shown above, there are also hints in Pereira et al.'s own findings that this is the case.

    Keep an eye on possible updates in future!

    Pereira et al. (2010), Linking the sub-Saharan and West Eurasian gene pools: maternal and paternal heritage of the Tuareg nomads from the African Sahel.

    Rando et al. (1998), mtDNA analysis of Northwest African populations reveals genetic exchanges with European, Near Eastern and sub-Saharan populations.

    Claudio et al. (2009), First Genetic Insight into Libyan Tuaregs: A Maternal Perspective.

    —Hassan et al. (2008), Y-Chromosome Variation Among Sudanese: Restricted Gene Flow, Concordance With Language, Geography, and History.

    —Semino et al. (2004), Origin, diffusion, and differentiation of Y-chromosome haplogroups E and J: inferences on the neolithization of Europe and later migratory events in the Mediterranean area.

    — Arredi et al. (2004), A Predominantly Neolithic Origin for Y-Chromosomal DNA Variation in North Africa. 

    Personal notes; 2009, 2010.

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