November 27, 2012

Ethiopian haploid genetics

Ethio Helix mentioned yesterday a doctoral thesis on Ethiopian haploid DNA:

Christopher Andrew Plaster, Variation in Y chromosome, mitochondrial DNA and labels of identity within Ethiopia. The Center of Genetic Anthropology, University College of London, 2012 (doctoral thesis) ··> LINK (PDF).

The study deals with the anthropology, ethnology and linguistics of the African state, and especially with the haploid genetics (although more in detail with the Y-DNA side of the matter than with mtDNA). It is very much worth reading for anyone interested on the anthropology and population genetics of Africa and in particular the Horn region.

Personally I find most interesting the fact that there seem to be some correlations between Y-DNA and mtDNA. The author mentions that there is such correlation in diversity but it seems apparent that there is some more than just that, as should be obvious for example in the following graphs:

Population codes are:
  • AF Afar (Cushitic, Afar region: 2)
  • AM Amhara (Semitic, Amhara region: 3)
  • AN Anuak (Nilotic, Gambela: 6)
  • ML Maale (Omotic, SPNN region: 10)
  • OR Oromo (Cushitic, Oromia: 8)

What I have in mind is, first of all, that those populations who have the most Eurasian (F-derived) Y-DNA lineages also have the most Eurasian (N, M) mtDNA ones. However there is noticeably greater apportion of mtDNA from Eurasia than Y-DNA - and most of that excess corresponds to mtDNA M (all of it M1).

In a simplistic scenario in which one or several waves from Eurasia would be the only element to consider, we would expect similar apportions for male and female lineages or even noticeably more immigrant Y-DNA. This is not the case and therefore it is perplexing.

After some thoughts on the matter I realized that the situation is similar, mutatis mutandi, to the one of North Africa. This probably means that the cause of both anomalies can well be the same: a relatively recent (Epipaleolithic?) expansion of Afroasiatic-speaking peoples with mostly African male lineages (typically E1b1b-M215). But notice that in North Africa also J1 (ultimately from West Asia) appears to be also important in the Afroasiatic phenomenon, as it is in the Horn (and certainly in West Asia), making the situation even more complex for interpretation.

In this regard it is worth mentioning that haplotype networks from this study show that while the Amhara and Oromo J1 is intermingled and diverse, the Afar J1 forms a very tight cluster, strongly suggestive of an ancient founder effect.

Another such apparent correlation could be Y-DNA E1 and E1b1a7 with specific subclades (?) of mtDNA L0/L1 (probably L0) and L2. At least the apportions are almost identical among the Anuak (but not among other groups, hence why I suggest specific subclades to be determined).

It is a pity that no more fine detail was achieved with mtDNA, especially the more purely African part of it, i.e. L(xM,N). Much better detail is provided instead for the once-backmigrant M and N derived lineages (table 5.9), from which I highlight the following (only >5% shown):
  • All M is M1 (overall: 10%, AM 17%, OR 13%, AF 9%, ML 6%)
  • R0(xHV) reaches 11% among the Amhara (all R0: 15%)
  • N1 reaches 7% among the Afar
  • U(xK) reaches 6% among the Afar (all U: 9%)
  • K reaches 6% among the Maale (all U: 9%)
  • The Anuak seem the most purely African population among this selection with only 3% of M1 and 0% N. 
I would seem that even the Omotic, the most remote Afroasiatic branch according to linguists (some even consider it a distinct family), have some Eurasiatic genetic influence. However I'd say that this influence is at least largely pre-Neolithic and has been subject to deep reshaping by internal African dynamics as suggested above. Still Neolithic and even maybe post-Neolithic layers of West Eurasian deposition are also apparent in the structure - always in my understanding.


Ethio Helix has updated with extra information not included in the thesis.  Notable is a graph with much greater detail on the Y-DNA haplogroup distribution.

The E1* block is now split between a number of E1b1b subclades and some important dose of E1b1c, which is the dominant lineage among the Maale (and hence maybe among other Omotic peoples). Among the E1b1b sublineages, the Afar are relatively dominated by E1b1b1e, while the Maale have an important bloc of E1b1b1c1 and the Oromo appear dominated by E1b1b1a1b.

The B bloc is also split in several subclades, all them only relevant among the Anuak (most of it B2a and most B2a within B2a1a.

It is also quite notable that some J(xJ1,J2) has been found among the Maale. For reference on this rare paragroup, I'll mention that another niche of J* is the nearby island of Socotra (74%, probably a verly local founder effect and specific lineage to be described) and there is also some J* reported among peninsular Arabs, some Turks, Greeks, Jews and a few others - but otherwise most Y-DNA J either belongs to J1 or J2.


  1. The most common interpretation of the distribution of haplogroups M and U in Africa is that M1 and U6, which are specific to Africa and common across North Africa and East Africa in linguistically Afro-Asiatic populations, represent back migrations to Africa, in Upper Paleolithic era that are not associated with any of the more recent Neolithic era migrations to Africa from Eurasia such as probably Bronze Age migration associated with the Ethio-Semitic language family. This expansion seems to have had a male counterpart of some manner of Y-DNA haplogroup E, the only Y-DNA haplogroup present at significant levels in all populations with M1 and/or U6 in significant amounts.

    All of the populations except the Nilotic Anuak are Afro-Asiatic linguistically, so it is unsurprising that the Anuak lack M1 and U. In terms of deep linguistic history it is widely assumed that in Ethiopia, Nilotic language family speakers migrated to the region at a time long after the Afro-Asiatic languages were established there. The E1b1a7 Y-DNA haplogroup found in the Anuak is a characteristic marker of Nilotic affiliation. The Nilotic population is also the only one in the sample with Y-DNA haplogroups B or E2 and the only one to completely lack Y-DNA haplogroup T.

    In terms of matching Y-DNA and mtDNA proportions across the five populations, the mostly likely pairing seems to be Y-DNA A3b2b and mtDNA L2. This pairing might be the profile of one African population that admixed with other populations in the region at some point. The admixture seems to have largely bypassed the Omotic peoples, whose low but non-trivial levels of L2 could easily have a source of bride exchange with neighboring Nilotic and Cushitic populations. Perhaps the A3b2b/L2 people were involved in Cushitic ethnogenesis, either as a substrate or superstrate population in that process.

    As expected, the Semitic Amhara have elevated levels of J1 and J2 relative to the other populations, but the amount of elevation relative to the two Cushitic populations (the Afar and Oromo) is surprisingly modest, for what is commonly seen as a male dominated wave of migration that produced a language shift in Ethio-Semities who previously spoke Cushitic languages.

    Y-DNA E1/mtDNA L3* seems like the most likely profile for a founding/background population in Ethiopia, with other haplogroups found in Cushitic, Semitic or Nilotic speaking populations (including J1 and J2 but perhaps not J*) but much less common in Omotic language populations seen as intrusive subsequent waves.

    1. While I though in some aspects in a way similar to what (I think that) you say initially, it all changed when I realized the parallel with North Africa. So now I think mostly in the following draft:

      1. Pre-OoA stage (L3(xM,N), L2, L4, L5, L0...)
      2. Early UP backmigrant wave from West Asia: M1, U6, X1 and maybe others like U1... In the Y-DNA side I'd speculate with R1b-V88, J* and J1 subclades, T (but with lots of caution on the male side, which is much harder to gauge). This wave might well have triggered the LSA in general.
      3. Only for NW Africa (maybe with extension up to Egypt but not farther), Oranian wave with important genetic input from SW Europe: mtDNA H1, H3, H4, H7 and V apparently. Y-DNA R1b-M269 and I (the first exists in NW Africa at levels of c. 10%, the latter is rare but was common among Guanches according to ancient DNA). Possible smaller counter-flow of mtDNA U6 and Y-DNA E1b-M81 to Iberia then.
      4. Late UP/Epipaleolithic Afroasiatic expansion (from somewhere in the Nile basin), dominated by Y-DNA E1b-M78 but also J1 (which either was imported then from Asia or was already in Africa since the early UP); diverse in the mtDNA side (for instance U6a shows a signal of backflow Westward according to Maca-Meyer 2006). Later Neolithic hypothetical flows from West Asia (??) may confuse this a bit, bringing stuff like mtDNA K, W, etc.
      5. A final, rather thin, Semitic layer(s) with some J1 and notably the J2 signal. Also some West Asian specific mtDNA like R0a and some extra M1.

      "bride exchange"

      If you read the thesis it has an extensive section on inheritance of identity and while the mother side was less strong (excepting precisely some Omotic peoples like the Dizi) in general previous generations were almost always attached to their ethnicities by both sides. However that is quite less common nowadays (localized "globalization", you know - but still larger groups keep their ethnic homogeneity much better).

      "As expected, the Semitic Amhara have elevated levels of J1 and J2 relative to the other populations, but the amount of elevation relative to the two Cushitic populations (the Afar and Oromo) is surprisingly modest".

      That's why I insist in considering J1 a generic Afroasiatic lineage also in Africa and also since immemorial times (Late UP), together with E1b-M78. Prior to Neolithic these populations expanded, something that is obvious in the case of Capsian culture (NW Africa) but that may include even founder effects in SE Europe (Greece with extension to Albania and such), later carried around by the Neolithic flows, surely not anymore Afroasiatic in language (but uncertain).

      "Y-DNA E1/mtDNA L3* seems like"...

      Look at the update because the homogeneous appearance of the E1* bloc is very misleading. Surely that is also the case with L3*, L2, etc. Sadly the study lacks sufficient depth but don't let yourself be misled by such hyper-wide catch-all categories. Caution there!

      There is much more in that paper and certainly in the still semi-explored Horner genetic landscape than meets the eye in a quick look. It is very interesting for a full read and still there are many blanks asking to be completed.

  2. To me, especially in the context of the origin and evolution of y-DNA E, the AN (Anuak/#6) are the most interesting ones. They are completely different regarding their E make-up: the only ones with significant E2 and huge E1b1a7, and also the only B-carriers and have almost no Eurasian mt-DNA. Perhaps studies like this one can eventually illuminate the origin and timing of the different E-subgroups.

    1. Partly true. But the E1b1c dominant among the Maale is also very curious. That lineage is also strictly African and found only in small amounts in other Afroasiatic populations.

      This E1b1c was last listed by ISOGG in 2010 with the marker M329. Now it is also an E1b1a variant, specifically E1b1a2.

      So I'd say that both the Anuak and the Maale (and by extension the Nilo-Saharan and the Omotic wider families probably) are interesting in the way you mean, complementary to each other.

  3. "This E1b1c was last listed by ISOGG in 2010 with the marker M329. Now it is also an E1b1a variant, specifically E1b1a2".

    Yes, the author seems to be using an old nomenclature, which makes it difficult to follow all the ins and outs. But the study is interesting.

  4. Wow eurocentrist are obsessed with Haplogroup E!!!!

    1. Who are you calling "eurocentrist" and why?

      Also what is the problem with people being interested in one of the largest haplogroups and most widely distributed of Humankind, one that incidentally has been in Europe since Neolithic times?

      And where do you see the "obsession"?

      Should I have thrown your comment to the trash bing as pointless trolling? Maybe. I'll give you the chance to explain or apologize first, as I'm not familiar with you yet.


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