October 23, 2010

Mitochondrial DNA H1 in North Africa

A new paper on mtDNA H1 has been published, detailing its presence and phylogeny in Africa.

Claudio Ottoni et al., Mitochondrial Haplogroup H1 in North Africa: An Early Holocene Arrival from Iberia. PLoS ONE 2010. Open Access. [LINK]

They ratify that African H1 is, as its sisters, of 'Iberian' (SW European) derivation  (something known at least for Tunisia since last year, see Cherni 2009) . They also add some detail on its phylogeny and frequencies. 

Maybe most notable is the high frequency (but low diversity) of the lineage found among Libyan Tuaregs, telling of some sort of specific founder effect. 

Of some interest is the description of three novel sublineages:  H1v, H1w and H1x, all them almost exclusive of Lybian Tuaregs (see fig. 1). 

Fig. 2 Frequency of mtDNA H1

The authors make the leit motiv of this paper their molecular clock estimates, which they calculate between 3400 and 11,500 years ago for all H1. If anybody needed further evidence of why the molecular clock methods are unreliable this is it: the only way Europe could have got a meaningful genetic influence on North Africa (and we are talking here c. 25% of the maternal ancestry, not counting K nor V) in this period would have been the Megalithic phenomenon. However, if that would be the case, where is the Y-DNA?

The only comparable Y-DNA is R1b1b2a2, which does exist in North Africa (along with some fossil I found in Guanches), looks of European origin too, but is found at much smaller frequencies (and lower diversity) than in Europe. There are no possible inputs between Megalithism and present day, as we know that Roman and Islamic conquests had minimal demic impact (nor they look likely origins for the dominant Y-DNA E1b1b1).

Additionally there is reasonably clear evidence of the existance of mtDNA H (and in general similar frequencies as today) at Taforalt some 12,000 years ago (Kefi 2005), which argues for an older arrival, surely at the genesis of Oranian culture, in the LGM.

Only the Oranian time-frame really seems to explain the deep and extended penetration of Iberian DNA in North Africa.


References:

R. Kéfi et al., Diversité mitochondriale de la population de Taforalt (12.000 ans bp - maroc): une approche génétique a l’étude du peuplement de l’afrique du nord. Anthropologie 2005. [PPT presentation direct download - Institut Pasteur]

L. Cherni et al., Post-last glacial maximum expansion from Iberia to North Africa revealed by fine characterization of mtDNA H haplogroup in Tunisia. American Journal of Physical Anthropology. Pay per view. [LINK]

H. Enafaa, V. M. Cabrera et al., Mitochondrial DNA haplogroup H structure in North Africa. BMC Genetics 2009. Open Access. [LINK]

For papers on H but not specifically related to Africa, see this post at Leherensuge (April 2009).

18 comments:

  1. "[I]f that would be the case, where is the Y-DNA?"

    It certainly wouldn't be unprecedented for invasive groups to have a much bigger Y-DNA than mtDNA impact. One can imagine a population with V, H1, K and R1b1b2a2 around 12,000 years ago, in which subsequent Berber and then Arab invaders replace a lot of Y-DNA, while not importing many women, instead seeking wives from the local population. Hence, Upper Paleolithic mtDNA and Neolithic or later Y-DNA.

    Given likelihood that polygamy was present somewhere between invasion and today, the effect could be exaggerated.

    One can also easily imagine that most of the ancestors of prior populations would have migrated out of the region in the face of climate change. We have Chadic language speaking and Nilo-Saharan language speaking pastoral populations who are believed to have migrated from not far from Tuareg territory into the Sahel and East Africa. Admittedly, migration out of North Africa has issues too. Why is there not more H1 and V and K in these parts of Africa then? But, if the migration were to Egypt (like African migrations to megacities of Africa today), they would have blended in to an already difficult to parse mix.

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  2. "It certainly wouldn't be unprecedented for invasive groups to have a much bigger Y-DNA than mtDNA impact. One can imagine a population with V, H1, K and R1b1b2a2 around 12,000 years ago, in which subsequent Berber and then Arab invaders replace a lot of Y-DNA, while not importing many women, instead seeking wives from the local population. Hence, Upper Paleolithic mtDNA and Neolithic or later Y-DNA".

    Almost exactly my point in fact. Thanks for explaining it further.

    I may conceive even more complex scenarios but that is the basic idea anyhow.

    "Why is there not more H1 and V and K in these parts of Africa then?"

    Well, this needs deconstructing a bit the North African mtDNA pool:

    - H and V, more than 25%, are probably accounted for at the Oranian genesis, if this one had some sort of Iberian influence.

    - U6 is surely of early Aurignacoid arrival (Dabban industries) from West Asia. 15%?

    - L(xM,N), 25%?, is surely at least in large part original from the region (Aterian) or arrived with Capsian culture because it is found aboundantly in Guanche mummies from Canary Islands. A small fraction can possibly be attributed to more recent flows (slave trade and such).

    The remainder are what we could loosely call "Neolithic haplogroups" in the Euro-Mediterranean context: W, J, T and K. I am not sure they are strictly Neolithic (could be partly Epipaleolithic, specially in North Africa, where Capsian pre-dates but continues through Neolithic).

    In the Y-DNA facet, there's basically E1b1b1 and J1, with some others as minorities (notably R1b1b2a but also J2 and T). I think J1 is Epipaleolithic (Capsian - the E1b1b1/J1 'Afroasiatic' exchange seems bidirectional) and that may also be the case for some E1b1b1. However I have not yet pondered well if E1b1b1 (some clades?) could be older, from the Aurignacoid period maybe.

    The dimension of the Y-DNA swap looks excessive to me: from (at least) 25% to less than 5% is a (gender biased) genocide (reduction of more than 80%!). Not impossible but something I find hard to believe, so I hope eventually to achieve a better understanding of the matter.

    Maybe in North Africa we have to ponder also different conjectural densities as in Europe. In Africa, the Nile basin may have acted as demographic pump/refuge the same as the Franco-Cantabrian Region did in Europe. But I don't know if this conjecture stands the reality check yet.

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  3. "The dimension of the Y-DNA swap looks excessive to me: from (at least) 25% to less than 5% is a (gender biased) genocide (reduction of more than 80%!)."

    I'm not sure that I'm as struck by that as being implausible, particularly given the relatively small size of the population involved now and presumably even smaller population then.

    If you have generations where the outsiders have 4 wives each, and the locals have 1 wife each, and a lot of locals go without wives and are exiled (a bit like the population dynamics of polygamous groups in Southern Utah/Northern Arizona today), you can get this result in not so many generations.

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  4. "If you have generations where the outsiders have 4 wives each, and the locals have 1 wife each"...

    That scenario is simply not credible in pre-Neolithic conditions. Not even in Neolithic ones or later.

    Even in societies where polygyny is allowed, most men still have one wife only, two at most. And they are not "outsiders" anyhow.

    This kind of scenario would require a very extreme and sustained sexual apartheid for, which is not viable even in the most elaborate forms of oppression, such as those appearing in the Metal Ages.

    "and a lot of locals go without wives and are exiled"...

    Where would they go? I make no sense of this, as it is not just inviable in pre-Neolithic conditions but it's likely to cause massive social disintegration as the young have to murder the old (or the locals kill the outsiders) in order to get wives. This kind of extreme injustice can only be supported up to some extent in very elaborate patriarchal societies, which cannot exist before property and therefore wealth accumulation.

    That kind of inequalities can only be post-Chalcolithic (late Neolithic), as it's in this period when social stratification first appears. But even in such cases this extreme view you propose would not be viable.

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  5. A more likely scenario would be one in which there was a true demographic wave (Capsian), whose members effectively replaced the natives, maybe by brute force, but took at least some wives from the invaded peoples.

    It'd be a wave of advance dominated by males (patriarchal at least to some extent) which would consider the natives, specially the native males, a nuisance at best and an enemy to exterminate at worst. There were no mechanism to enforce social inequality before (advanced) Neolithic but different "tribes" could have generally hostile relations to each other anyhow. It would not be an individualized "success" but one of ethnic groups as a whole, because only "tribes" and "clans" could control territory in such "pre-civilized" conditions.

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  6. To me the, fact that there are mtDNA hg H, U5, V (and J1b1) in Fulbe population from Burkina Faso (a country below Mali), Chad and Cameroon * (about 8.1 % as a whole in these tests) is another proof of their ancient arrival in north Africa. I think they were in the gene pool of the green Sahara populations (mixed with subsaharan populations). I think when it dried they migrated, some reaching Egypt and participated in the birth of the ancient egypt civilization (there are elements to support this theory (archeological and even linguistical IIRC)). It could explain the presence of Y-DNA R1b1b2 ** and a few rare I and mtDNA H and U5 (there was also a U4 in the study I've seen, so who knows) in present Egypt - If my memory doesn't betray me, they are all present though in very low frequency.

    * http://findarticles.com/p/articles/mi_qa3659/is_200602/ai_n17186281/

    It goes well with the non-subsaharan skeletons found in Niger and Mali (at least in this case he was associated with the mechtoids (cro-magnoids of north Africa).

    about Mali (Hassi-el-abiod), in french : http://www.persee.fr/articleAsPDF/bmsap_0037-8984_1988_num_5_4_1681/article_bmsap_0037-8984_1988_num_5_4_1681.pdf?mode=light

    about Niger : http://dienekes.blogspot.com/2008/08/kiffians-and-tenerians-from-sahara.html

    ** IIRC there are a few R1b1b2, I'm not wrong am I? It probably also explain the King Tut R1b1b2 lineage - if officially confirmed, that is - (I've read a post (I tink it was from Aargiedude but I'm not sure), saying the datae could favorized a ht15 flavor rather than a ht35 despite the fact that it's kind of counter-intuitive, at first sight).

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  7. The data is not very clear, Wagg. First Cerný says 8.7% of WEA haplos, incl. H and V, but then the figure is repeated and only U6, U5 and J1b are mentioned - which are more likely to have an ultimate West Asian origin (U6 via North Africa, of course).

    Also all the paper deals with the Fulani, which are a special population original form Westernmost Africa (Futa Toro and Futa Djallon, in Senegal and Guinea respectively) and who expanded only recently (17th-18th century) filling the gap left by the Songhai Empire and the weak imperialist Moroccan rule.

    The other papers are more interesting though not new to me in contents. However it says little on light of modern West Africans being clearly from a different stock. The case for these Saharan "Caucasoids" seems to be that they vanished in the 6th millennium and the new colonization when fertility returned was "Negroid" from the East.

    In general little of West/Central African genetics seems to point to NW Africa but rather to the Nile basin. However there is some R1b1a-V88 (the Chadic/Italian/West Asian haplogroup) in North Africa but does not look diverse enough (all is R1b1a* and concentrated at Siwa oasis, Egypt).

    I am thinking anyhow that Y-DNA E1b1b1 was already present in North Africa at the Oranian genesis. This would explain its presence in some parts of Iberia (West and specially NW, including Asturias and Cantabria) arriving possibly (with mtDNA U6) in the context of Oranian genesis and the complexities of Iberian Gravetto-Solutrean. If some E1b1b1 is ancient in NW Africa, we would not require such a massive gender-biased genocide as suggested above. Some other clades of E1b1b1 and, of course, J1, would be the ones implied in the Capsian flow (with mtDNA in the categories of L(xM,N) and U6a - and whatever else).

    Parallel to this Capsian flow would have been the Chadic colonization of Central Africa with Y-DNA R1b1a and some other WEA genetics.

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  8. @ Maju : "only U6, U5 and J1b are mentioned"

    U5 is more likely to have a west Asian origin?

    I thought it was the haplogroup that wouldn't generate any debate.
    Why not paleolithical Europe as origin?
    After all there are U5 in north Africa nowadays too, and the Kefi paper makes it quite credible it was in the Taforalt samples, apparently.

    "which are a special population original form Westernmost Africa (Futa Toro and Futa Djallon, in Senegal and Guinea respectively)"

    Weren't some U5 found in Senegal? I remember reading it in a study at Dienekes' a few months ago. Did I misread?

    Anyway, here's an interesting bit related to the matter :

    http://en.wikipedia.org/wiki/Fulbe#Origins_and_spread

    "Interestingly, rock paintings in the Tassili n'Ajjer suggests the presence of proto-Fulani cultural traits in the region by at least the fourth millennium B.C. Scholars specializing in Fulani culture believe that some of the imagery depicts rituals that are still practiced by contemporary Fulani people (*)."

    (*) http://www.metmuseum.org/toah/hd/fula_2/hd_fula_2.htm

    "I am thinking anyhow that Y-DNA E1b1b1 was already present in North Africa at the Oranian genesis."

    So do I, but by looking at the frequency of the supposed haplogroups in Kefi et al. 2005, I tend to think it was a minority.

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  9. Sorry, I misquoted at the beginning and in the last part of the post, my comment on the presence of E1b apply mostly to the Taforalt and the north of Morocco, even though I think these "cromagnoid" populations went quite further east (and south, including quite possibly south-west).

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  10. "U5 is more likely to have a west Asian origin?"

    AFAIK it's not too common in North Africa not even SW Europe, where it seems old but minor (see aDNA studies on Portugal and Morocco).

    I am not sure at this point if U5 has a European or West Asian origin but I suspect it spread with Gravettian culture in Europe. It is frequent enough in West Asia as to consider that area as possible origin, really.

    "After all there are U5 in north Africa nowadays too, and the Kefi paper makes it quite credible it was in the Taforalt samples, apparently".

    Kéfi mentions two U6 and eleven CRS sequences labeled as "H or U". These CRS sequences have been found in R0, HV, H1, H2a (of course) and U*. This last is most rare anyhow and is not U5 but something else. In principle I consider the CRS sequences to be H1, specially on light of other four sequences labeled as H and other two as V, together making up most of the mtDNA pool of Taforalt (others are: U6, JT and one "other").

    "Weren't some U5 found in Senegal?"

    Yes I think so: one single person? The sub-haplogroup anyhow did not look Western European anyhow (if I remember correctly): it was somewhat mysterious (but an erratic probably in any case).

    "So do I, but by looking at the frequency of the supposed haplogroups in Kefi et al. 2005, I tend to think it [E1b1b1] was a minority".

    Maybe but let's remember that Taforalt is in Northern Morocco, not far from Iberia. It is possible, likely I'd dare say, that it does not represent well the overall genetics of North Africa back then. Taforalt mtDNA pool is very similar to that of modern locals (so says Kéfi at least), but it is probably quite different from other peoples of the wider region.

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  11. Re. E1b1b1, the M81 subclade (E1b1b1b) is absolutely NW African, with penetration (as I said before) into West Iberia. Instead M76 (E1b1b1a) is much more widespread and can be speculated to be the "Capsian" (or Afroasiatic) clade. The third major sub-haplogroup, M123 (E1b1b1c) looks rather specifically Semitic to me, with greatest concentrations in Palestine. Ref. Semino 2004.

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  12. About the U5 from Senegal : "The sub-haplogroup anyhow did not look Western European anyhow (if I remember correctly)"

    Ok, I'll try to get more informations about it.
    Still, I'm not convinced yet of its oriental origin at all.

    http://mathildasanthropologyblog.wordpress.com/2008/06/30/mitochondrial-dna-in-cameroon/

    "In fact, the non-L sequences found in the Fulbe from Cameroon differ substantially from those found among the Berbers, since they belong to the U5 haplogroup (which has a very broad distribution in Eurasia). The fact that the U5 Fulbe sequence (transitions at np 16189, 16192, 16270, and 16320) is a one-step derivative of mtDNA types found in Moroccans (Brakez et al., 2001), Saharawi, and Tunisians (Plaza et al., 2003) suggests that this population had some genetic contact with North African populations. "

    From : http://www.upf.edu/cexs/recerca/bioevo/2005BioEvo/BE2005-Coia-AJPA.pdf

    Moreover, as rare as they are, U5s in north Africa rather seem to have more in common with the European one (at the very least some of them) : "Saami and Berbers—An Unexpected Mitochondrial DNA Link" (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1199377/)

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  13. What I see in Achilli 2005 (fig. 1) is that U5b1b looks Italian-North African, with projections to Saami, Spain and Fulbe. I'd say that U5b is an Italian clade from that data but it's probably not complete information on the haplogroup.

    The second link is broken and I see as no surprise that the Fulbe and only them (not the Chadic peoples high in R1b1a) have also some of that U5. I'd say it had a Neolithic spread to Iberia (from Italy) and to the Fulbe (from North Africa). I can't say exactly how this lineage migrated between Italy and North Africa but I would suspect that through West Asia rather than the sea (unless it's a Neolithic expansion, what I find unlikely).

    The data of Achilli doesn't suggest me a migration via Iberia for this clade. But who knows?

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  14. Hi.
    Do you know the type of R1b and the type of west eurasian mtDNA hgs in this article about Tuaregs from Mali, Niger and Burkina Faso?:

    http://www.nature.com/ejhg/journal/v18/n8/abs/ejhg201021a.html

    The Dienekes' article doesn't give all the informations and there's a paywall.

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  15. No. I read about it at Dienekes but no idea. R1b without further description does not say much anymore, does it?

    My best hunch is R1b1a, common around Chad Lake but also found in North Africa. But it could also be West European R1b1b2a, which is also found in North Africa at similar low frequencies.

    More interesting to me is that the bulk of the Y-DNA pool is made of E1b1b1b (M78), the NW African clade and E1b1a (M2), a Tropical African clade, very common in West Africa.

    For that reason I do not understand when the authors say that "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".

    Excepting maybe some minor frequency clades (under 2%), all looks African or maybe European (R1b), because there is very little R1b1b in North Africa that can be considered part of the West Asian clade (per haplotype, cf. Alonso 2004). The data is hence inconsistent with the claim.

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  16. Erratum: M81, not M78 (otherwise the identification is correct). Also minor (one individual) clades are all 2.1% not "under 2%".

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  17. Thanks anyway.

    "More interesting to me is that the bulk of the Y-DNA pool is made of E1b1b1b (M78), the NW African clade and E1b1a (M2)"

    Very "polarized", Y-DNA haplogroup-wise (E1b1b1b on one side (Tgor & Tgos) and mostly E1b1a* + R1b on the other side (Ttan)).

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  18. True, I did not notice. The Ttan are also the ones having all the R1b, so I imagine that it's R1b1a and has a "Chadic" connection somehow.

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