Saturday, December 20, 2014

Poll Closed (split decision)

This poll will stay open till Christmas Eve.  Please include justification in the comments section if you dare.

*Update*  I am unable to update the poll, however the "Heavy Pastoral" option, not overweight pastoralists, I have a brief explanation.  The Early Pastoral in North Africa is characterized by the introduction of domesticated bos taurus primagenius, aka Longhorn.  The Middle Pastoral begins around 4000 B.C. and ends around 3100 B.C. or thereabouts.  The Middle Pastoral is characterized by dairying [here] and bovid rock art.

What is the origin of mtdna H among Malians, Libyans, Algerians, Mauritanians, Burkinabe, etc?


  1. I would guess it's connected to Neolithic Euros somehow, because the H clades they share with Europe. I doubt any of the H is Paleolithic, but who knows. I know very little about the subject so....

    NW Africa is interesting to me because they are a mostly west Eurasian population living in Africa, and they have a different but related story to tell than west Asia, south-central Asia, and Europe. I'm excited about any further research on NW Africa.

    I suspect they're of mostly recent(7000BC whatever) Near eastern decent.

    1. But, in the European Neolithic, while H is present, it is uncommon, and the frequencies of H are pretty high in NW Africa.

  2. FWIW, I'm not sure how a "heavy pastoralist" differs from an ordinary one other than that a heavy pastoralist has to wear XXL shirts. Yeah, I know that this isn't what you mean, but I really have no idea what you do mean by the term. Do you mean cow herders v. goat and sheep herders?

    1. Ha ha. Admittedly (and fairly) this population is a little more ambiguous. These people were Near Easterners who entered North Africa about 4500-5000b.c. This begins the pastoral phase loosely defined by rock art, pottery and lithics.

  3. I voted 'other'. I suspect that haplogroup H has always been present in Africa.

    1. Perhaps, but why is it generally found in clusters with West Asian haplogroups? How much of it is native vs. Holocene immigration?

    2. It depends what we define as being 'West Asian' versus 'African' I suppose. How many tens of thousands of years ago did it back-migrate, or did it even leave Africa in its entirety or did some of it linger in the border zones? Ok, if mtdna H entered Africa from West Asia and then later spread to Burkina Faso and Mali, I think that we should expect to see significant frequencies of H in Egypt &/or Horn of Africa, however Egypt and Ethiopia both have extremely low frequencies. Also, H's predecessor HV is found at peak African frequencies in Burkina Faso and Niger, but again Egypt and Ethiopia have the lowest frequencies in Africa. So in my opinion mtdna H in the Sahel is likely derived from either Africa or Europe, but not West Asia. I believe that Berbers have some quite high diversity of H and it has been in those populations for some quite considerable time. And then I look at a variety of other genetic markers which point to potential or even likely prehistoric migrations from Africa directly into Europe anywhere between 5kya and 25kya+.

  4. From Kefi, 2005: Diversité mitochondriale de la population de Taforalt (12.000 ans BP – Maroc), see here:,d.d24
    H is present in Morocco 12,000 years ago.

    1. Taken at face value and assuming continuity, does this suggest the major Western clades of Europe and other regions arose in North Africa?

  5. "Taken at face value and assuming continuity, does this suggest the major Western clades of Europe and other regions arose in North Africa?"

    If this actually were true, and there is always a chance that it *could* be, I can't see many people accepting it. A lot of genetics and anthropology bloggers and their readers likely wouldn't. I'm interested to find out the truth, even if it is unorthodox or unpopular.

    1. Seeing Haplogroup H in Taforalt around the turn of the Holocene is very plausible. It appears they originated in the Near East, but were unrelated to Natufians.

      What doesn't exactly jive though, is that H, V, JT and U6 were recovered from the rock shelter. (Again, very plausible), but this puts V at its maximum age or beyond.

      Modern sub-clades of H in North Africa aren't restricted to this continent and these are pushed to their age limits (still plausible to have continuous waves of immigration throughout the Holocene)

      As you've said, I just want a definitive answer. But H1, H1b, H3, H5a, H6b, H8, etc... These are the haplogroups appearing in the Sahara. Either they originated here or immigrated. I'm interested to see how others see this.

    2. Of course, I recognize that actual, ancient DNA is the true gauge of its age, not estimations.

      To clarify, I am always skeptical about dis-articulated human remains in a context with multiple levels of habitation and pottery styles. I just see a lot of people taking the Nestea plunge in studies. I don't want different results, I want better results.

  6. A look at the dating and phylogeny of specific subclades of mtDNA U6 suggest an Upper Paleolithic arrival of it in NW Africa, and while Berbers in NW Africa have several varieties of mtDNA L, some of which are probably recent arrival via trans-Saharan slave trade, at least one of the main mtDNA L varieties in Berbers in NW Africa is also Upper Paleolithic.

    A second package of mtDNA clades arrives in NW Africa as a package and strongly suggests an arrival from Iberia to NW Africa across the Strait of Gibraltar in the Epipaleolithic: mtDNA U5b1b, H1, H3 and V, all of which are rare further east. The Taforalt mtDNA H and V probably arrives in this wave. Notably the Berbers and Saami of northern Finland share both mtDNA U5b1b and V, which are also present at elevated levels in coastal areas of the Netherlands and Belgium. The presence of these clades up and down the Atlantic maritime coastal route, and their absence in areas between NW Africa and the Levant, disfavors of North African terrestrial or coastal maritime route for the women bearing this mtDNA. This narrative is corroborated by examples of Epipaleolithic mtDNA H from both Greece and Basque Spain. The absence of mtDNA H or V in Upper Paleolithic or post-LGM hunter-gathers, however, tends to support that notion that the Franco-Cantabrian refugium may have lacked mtDNA H or V, with this arriving from the east only once the LGM thaws and facilitates expansions of hunter-gatherer/maritime hunter-gatherer/proto-farmers (who systemically cultivated wild plants showing no signs of domestication and may have keep animals like rabbits that were indistinguishable from the wild type).

    Of course, this isn't to rule out subsequent mtDNA contributions from the Bell Beaker era through the historic era, or the impact of secondary migrations. Mali and Burkina Faso may have had major demic impacts from the North in the era of Medieval trade kingdoms such as the one based in Timbuktu. Phoenician, Punic, Roman, and Vandal contributions, collectively were surely not negligible either.

    It is also worth noting that Berber Y-DNA clades are much younger than Berber mtDNA clades, suggesting a male dominated conquest and replacement of pre-existing men, while leaving the mtDNA pool in the region more stable.

    It is also worth noting that Berbers and Egyptians are much closer to each other in autosomal DNA than they are to Chadic or Cushitic people, that the R1b-V88 found in Chadic people cannot be the source of the R1b clades of Western Europe, and that the mtDNA L clade that is distinct to Chadic people is absent in North Africa including NW Africa. Thus, the Copper Age Y-DNA R1b expansion in Western Europe cannot have its source in any African population. European clades of R1b in NW Africa today are almost certainly a result of N to S migration.

    The fact that R1b expanded in concert with a major increase in the percentages of mtDNA H which was present but not especially common in the first wave Neolithic in Europe, also suggests that the R1b expansion involved R1b men and mtDNA H women expanding as colonizing families from the point of Bell Beaker ethnogenesis in Iberia, rather than an arrival of mtDNA H "warrior women" from North Africa.

    It is possible that Bell Beaker ethnogenesis in Iberia may have involved proto-Bell Beaker maritime R1b male migrants taking women from Iberia and NW Africa who were mtDNA H dominated due to quirks of local geography and then expanding from there as a unit, however. But, it is also possible that the founding Iberian Bell Beaker population include founding families of R1b men and mtDNA H women and was not male dominated. I don't think that we have good evidence to distinguish those two models yet.

  7. @ Andrew - "Notably the Berbers and Saami of northern Finland share both mtDNA U5b1b and V, which are also present at elevated levels in coastal areas of the Netherlands and Belgium. The presence of these clades up and down the Atlantic maritime coastal route, and their absence in areas between NW Africa and the Levant, disfavors of North African terrestrial or coastal maritime route for the women bearing this mtDNA."

    No doubt you are referring to this paper:
    "Saami and Berbers—An Unexpected Mitochondrial DNA Link"

    In actual fact the 'unexpected' mtdna link encompasses Saami, Berbers, and also Fulbe (Fulani), Italians, Spanish, and Yakuts:-

    "Seven of the new sequences (one Berber from Algeria, two Italian, one Spanish, and three Saami) clustered into U5b1b, the subclade encompassing the Yakut and Fulbe mtDNAs. The Saami and the Yakut mtDNAs formed a minor branch distinguished only by the transition at nt 16144, the Berber and the Fulbe mtDNAs clustered in a second minor branch also characterized only by control-region mutations, and the Italian and Spanish mtDNAs formed other minor branches."

    Looking at HLA haplotypes, I believe that I have found one which links all of the above, namely: A*01:01-B*37:01-C*06:02.
    I am very confident that it originated in Africa. A*01 has reached high frequencies in certain populations both outside Africa as well as inside, but its diversity is greatest within Africa (Kenya, Uganda, Sudan, Guinea Bissau, Senegal, Mali, Tunisia, Morocco); B*37 reaches peak world frequencies in Central African Republic Mbenzele pygmies, Cameroon Baka Pygmies, Burkina Faso Fulani, Cameroon Bakola Pygmies, and Cameroon Sawa; C*06 reaches world peak in Sudan, Morocco, Kenya, Uganda, Cameroon Bakola Pygmy, Cameroon Bamileke, Tunisia, etc.

    1. I wasn't referring to that paper as a sole source, although it is one of them. I've looked at about five papers on point.

      HLA haplotypes aren't great for inferring ancestry, because they are fitness enhancing and subject to positive selection, unlike ancestry informative mtDNA haplogroups which show every sign of being fitness neutral. The dynamics of the transmission of HLA haplotypes therefore are quite different - single instances of gene exchange are likely to grow dramatically and unlikely to be lost in genetic drift in the same way.

    2. "HLA haplotypes aren't great for inferring ancestry.."

      Reasonable explanation quoted elsewhere:
      "HLA has an advantage over mtDNA and Y chromosome. It is known in humans and most animals that heterozygous selection coefficients act on HLA to preserve alleles and haplotypes in the population. The Ne * ploidy is effectively 5 or more times greater than mtDNA and 10 or more times greater than the Y chromosome. Therefore small pop-sized based exclusions or patrilinear preferences (as seen with Y chromosomes in some studies) are not a problem with HLA. HLA has been able to resolve some issues, for example in cases where mtDNA says group X came from place A, and Y says group X came from place B, HLA has been able to show that A came from both place A and place B and that mtDNA was a result of female founders from A and male founders from B and even estimated the ration of female to male founders."

      From Wikipedia:
      "An HLA haplotype is a series of HLA "genes" (loci-alleles) by chromosome, one passed from the mother and one from the father[..]
      These haplotypes can be used to trace migrations in the human population because they are often much like a fingerprint of an event that has occurred in evolution[..]
      There are 100,000s of extended haplotypes, but only a few show a visible and nodal character in the human population."

      "because they are fitness enhancing and subject to positive selection"

      After 40+ years of extensive research, we know about the myriad of diseases which HLA confers susceptibility to. Yet I know of just two life-threatening conditions for which HLA is known to play a protective role, namely B*53 with malaria in West Africa and B*18 which is somewhat protective against mother-to-child HIV1 transmission. That is pretty much it in terms of what we know has been selected for, in terms of thousands of HLA alleles and haplotypes.

      The University of Geneva's Department of Genetics & Evolution's AGP Lab are using HLA currently in research projects funded by the Swiss National Science Foundation:-
      ""The AGP lab is involved in many research projects on human genetic evolution with the objective to understand better the dispersal of modern humans around the world and the mechanisms of their biological differentiations. Information from other disciplines, namely archaeology, paleoanthropology and linguistics, are also used to investigate the relationships between biological and cultural evolution. The team principally works in silico by developing computer tools and performing data analysis. One of the main polymorphisms used is HLA, but other genetic markers are also analyzed (mtDNA, Y chromosome, nuclear STRs, etc). Since several years, a big effort is devoted to the improvement of the HLA characterization of human populations from a methodological point of view and the maintenance of large databases."

      HLA still being used around the world in studies today:-
      "Distribution of HLA-A, -B and -DRB1 Genes and Haplotypes in the Tujia Population Living in the Wufeng Region of Hubei Province, China" [PLoS One 2012]

    3. Thanks for posting this Chris.

      I think there is more to be gleaned from genomics than the sole study of uniparental markers and autosomal PCA analysis, each of which has its limitations. That's why I've been looking to other ancestry driven DNA, which may greatly augment what we know.

      It takes a lot of mental and rhetorical gymnastics to explain Rhesus negative blood frequencies in Berbers compared to Irishmen. It's impossible to suggest the Berbers are "half-Irish" (so to speak) and then have almost double the frequency. (anyone wanting to dismiss with an endogamous explanation needs to read the previous sentence ten times)

      A cursory look a HLA haplotypes seems to indicate a big fat arrow going North into Europe. Hopefully, Monday I can link to the papers I have.

  8. "A cursory look a HLA haplotypes seems to indicate a big fat arrow going North into Europe."

    That's certainly what I can see. I'm glad that you can see it too.

    I only look at some data and notice patterns, but I don't attempt to tie the data in with any archaeology, linguistics, cultures, historical invasions, etc. (Others can do that better than I can). I try not to crow-bar the data to fit any pre-existing theories at any rate.

    I have HLA data on more than 1000 Spanish migrants in Germany, with over 1000 haplotypes.

    Out of the top 20 highest frequency haplotypes, no fewer than 8 of those are definitely derived from North Africa at any points within the last 20kya, if not 12kya.

    One of those HLA haplotypes which correlates to some degree with bell beaker distribution in my opinion is: A*29:02-B*44:03-C*16:01-DRB1*07:01-DQB1*02:01

    This one is in strong linkage disequilibrium all the way from Morocco to Denmark.*29:02:01:01*16:01:01*16#A29-Cw.2A16-B44

  9. "A cursory look a HLA haplotypes seems to indicate a big fat arrow going North into Europe."

    I think (?) it's pretty much accepted that the Atlantic Megalith culture had extensive links to NW Africa so is this arrow south to north exactly or coastal from southern Iberia.