February 23, 2013

Algerian haploid genetics

This new study has particular interest for data miners willing to dig in the supplemental materials. It also has some other points of interest that I will discuss below and its general approach is loosely alright. However there are many nuances to be discussed in depth on the very complex NW African genetic landscape in which their tentative conclusions seem to lack enough depth of analysis (who grabs too much, squeezes little). Hence the complexity is too big for me to go issue by issue offering a criticism, so I will leave most of that open for the discussion, if the readers wish so.

Asmadan Bekada et al., Introducing the Algerian Mitochondrial DNA and Y-Chromosome Profiles into the North African Landscape. PLoS ONE 2013. Open accessLINK [doi:10.1371/journal.pone.0056775]


Mitochondrial DNA

The mtDNA landscape of Algeria and Northwest Africa is dominated (using HVS-I only to estimate it) by R-CRS ("H/HV" in table S2) with levels of 18-34% (29% in Algeria) almost comparable to Western Europe (~45%). This fraction we know from previous studies to be composed almost only by H1, H3, H4 and H7, all them attributed by Cherni to be originated (judging on diversity) in SW Europe (Iberia, France). Along with them HV0/V (7% in Algeria, 5-9% regionally) must be mentioned as also plausibly to be from that part of Europe (4-7%).

Another notable lineage is U6 (typical and most diverse in NW Africa), which reaches frequencies of 11% in Algeria (somewhat less in neighboring countries). Outside this area is only notable in Levant (~1%) and Iberia (~1,4%).

M1 reaching 7% in Algeria (~1-4% elsewhere in NW Africa, <1% in Europe and Highland West Asia, 1.2% in Levant, 2.4% in Peninsular Arabia) is also very much worth a mention, especially because the authors find an specifically NW African node centered in Algeria (HT2):

Figure 3. Reduced median network relating HVS-1 sequences of subhaplogroup M1.
(...) Black circles correspond to haplotypes observed in Algeria, whereas grey triangles pentagons correspond to lineages found in Egypt. Haplotype observed both in Algeria and Egypt are indicated using a black triangle. Grey circles indicate haplotypes observed in other geographical regions. (...)

The pattern suggests an Egypt-centered expansion for this lineage, however notice that East African M1 was not considered. 

Synthesis of mtDNA haplogroups or paragroups found in NW Africa at frequencies >2.5% (see table S2 for details and the many low frequency lineages as well), nomenclature as in table S2 (but some annotations in [square brackets] by me), frequencies for Algeria first (in brackets NW African range):
  • HV/H[R-CRS]: 28.8% (17.9-34.2%)
  • HV0/HV0a/V: 6.7% (4.6-8.3%)
  • R0a: 0.8% (0.8-3.2%)
  • U3*: 3.2% (1.1-3.2%)
  • U6a[U6a*]: 1.9% (1.9-7.8%)
  • U6a1'2'3: 9.4% (2.6-9.4%)
  • K*: 1.6% (0.7-4.8%)
  • T1a: 3.5% (0.0-5.6%)
  • T2b*: 1.9% (0.0-2.2%)
  • J[*]/J1c/J2[*]: 3.8% (1.3-3.8%)
  • M1[*]: 7.3% (0.7-7.3%)
  • L3b[*]: 0.3% (0.3-2.8%)
  • L3b1a3: 1.3% (0.0-2.8%)
  • L3e5: 1.6% (0.0-2.9%)
  • L2*: 0.5% (0.0-4.1%)
  • L2a[*]: 0.8% (0.0-3.2%)
  • L2a1*: 1.3% (0.7-4.8%)
  • L2a1b: 1.3% (0.8-3.5%)
  • L2d: 0.0% (0.0-2.8%)
  • L1b*: 3.0% (2.7%-9.0%)
Notice that in nearly all cases L(xM,N) highest frequency correspond to West Sahara. The exceptions are L2a* (Tunsian "Andalusians") and L3e5 (Tunisians), suggesting maybe a local NW African deep rooting rather than ancient or recent flows from Tropical Africa. There are other lineages in the low frequency range in similar situation.

For this and other reasons I decided to color-code the list above according to my best guess about the origin of each lineage: NW African in deep red, Tropical African in brown, Egyptian in light brown, West Asian in green and European in blue. Unclear cases I left in black type.

Mini-update (Apr 19 2015): my rough estimate of ancient regional origins of Egyptian mtDNA (Notice that European lineages can be as ancient in North Africa as Oranian, c. 22 Ka ago):
  • Ancient North African: 13.7%
  • European: 35.5%
  • West Asian: 14.8 (includes those labeled above as unclear)
  • Tropical African: 7.7%
  • Egyptian: 7.3%
  • Low frequency lineages (not classified): 23%
(End of mini-update for mtDNA)

Y chromosome DNA

Algerian and NW African Y-DNA is overwhelmingly dominated by E1b1b1b (M81), reaching 44% in Algeria (44-67% in the region), which is a NW African specific lineage. The second most important lineage by frequency is J1 (M304) with 22% in Algeria (0-22% in the region, 6-22% if we exclude Libya). None of the rest of the lineages reaches 7%, excepted E1b1b1c (M123) but only in West Sahara (11%, elsewhere it is very minor).

List of Y-DNA haplo-/paragroups with frequencies above 2.5% anywhere in NW Africa follows (based on table S6). Same notation as with mtDNA (Algerian frequency first, NW African range in brackets):
  • E1a (M33): 0.6% (0.0-5.3%)
  • E1b1[*] (P2): 5.2% (0.7-38.6%)
  • E1b1b1[*] (M35): 0.6% (0.0-4.2%)
  • E1b1b1a4 (V65): 1.9% (0.0-4.8%)
  • E1b1b1b (M81): 44.2% (44.2-67.4%)
  • E1b1b1c (M123): 1.3% (0.0-11.1%)
  • F[*] (M89): 3.9% (0.0-3.9%)
  • J1 (M267): 21.8% (0.0-21.8%)
  • J2a2 (M67): 3.9% (0.0-3.9%)
  • R1b1a (V88): 2.6% (0.9-6.9%)
  • R1b1b1a1b[*] (U198): 2.6% (0.0-2.6%)
  • R1b1b1a1b1 (U152): 2.6% (0.0-2.6%)
Mini-update (Apr 19 2015): I color coded the Y-DNA above also by origin, same as with mtDNA, except that here light brown does not mean "Egypt" but "Nile basin" or "NE Africa", including Sudan and Ethiopia. I find easier to discern regionally that way with Y-DNA than with mtDNA. I consider the bulk of J1 (see below) and of R1b-V88 to have that origin but I can't discard minor J1 from more recent West Asian inflows nor some R1b-V88 arriving from Chadic peoples across the Sahara or Mediterranean origins (both lineages demand more detailed and dedicated research). NW African E1b sublineages are related to these Nile Basin ones but it's unclear how old they are in the region (I would say that E1b-M81 particularly is very old but not quite sure how much exactly). Totals by regional origin:
  • NW Africa: 46.1%
  • NE Africa: 31.5%
  • European: 5.2%
  • West African: 0.6%
  • Unclear (F*): 3.9%
  • Low frequency lineages (not classified): 12.7%
(End of mini-update for Y-DNA)

For more diverse samples of NW African Y-DNA (from previous studies), Wikipedia has a nice table.

I would like to highlight the problematic of J1 in Africa in general (including NW Africa). While there is no reasonable doubt that J1 as a whole originated in West Asia, it is found at rather high frequencies in East/NE Africa (Sudan, the Horn, Upper Egypt) and NW Africa with only very limited (at best) company by J2. Instead West Asian populations show a much more balanced apportion of the two major J sublineages, even in Saudi Arabia the J1:J2 proportion is of 8:3, almost 2:1. We do see this kind of apportioning in Lower Egypt, suggesting a "recent" (Neolithic or later) demic colonization from West Asia but we see exactly but nowhere else in Africa, where J1 is found always much more frequently than J2 (if the latter is found at all). 

In my understanding this excludes colonization from West Asia after the Pre-Pottery Neolithic B, which seems the most plausible scenario for the spread of "Highlander" J2 into "Lowland" West Asia (probably dominated by J1 initially). So J1 in Africa (excepted Lower Egypt) cannot be argued easily to be of "recent" Neolithic, much less Semitic or Arab origin: it must be older. 

Also Ethio Helix commented in this very interesting discussion at his blog that Tofanelli 2009 found low diversity on NW African J1. However, to my knowledge, nobody has looked at NE/East African J1 diversity nor a proper study has been done on the substructure of this lineage in Africa. This leaves wide open the possibility that NW African J1 has a NE African origin, surely related to the expansion of Capsian culture or internal African Neolithic flows. 

While this matter is not properly addressed, researchers will oversimplify and imagine J1 as simply West Asian influx. It is ultimately of course but I strongly suspect that it has a secondary and distinct NE African center at the Nile basin and this is being totally ignored. 


Comparisons

This study offers several rough comparisons with nearby regions (but not West Africa), however they oversimplify some stuff (the already mentioned Y-DNA J1 or assigning all mtDNA L(xM,N) to East Africa, when it seems obvious that some lineages may be deeply rooted in NW Africa or others probably come from West Africa). For whatever it is worth anyhow, here there are two such questionable comparisons:

Table 2. Geographic components (%) considered in Y-chromosome and mtDNA lineages.

Figure 2. Graphical relationships among the studied populations.
PCA plots based on mtDNA (a) and Y-chromosome (b) polymorphism. Codes are as in Supplementary Tables S2 and S6.


See also:

45 comments:

  1. I can't reconcile the R1b haplogroups reported for Algeria with their publicly available haplotype info (Robino 2007 n=102 + Arredi 2004 n=47).

    The study says there were 15 R1b samples. That's correct, I counted 15 R1b samples in the haplotype data. As a little extra check, I also counted 69 E1b1b-M81 samples, and effectively the study says there were 69 E1b1b-M81 samples. It's only with respect to the subhaplogroups of R1b that things get weird.

    7 of 15 R1b haplotypes have 393=12, typical indicator of eastern R1b, such as M269* or L23*. Barely 2% or 3% of western R1b (U152, U106, P312*, etc.) have 393=12. So we are almost certainly looking at a minimum of 6 eastern lineages of R1b, and probably all 7. But the study says there are only 2 M269*/L23* samples. This is almost impossible.

    1 of 15 R1b haplotypes is R1b*/R1b1a*. But the study says there are 4 R1b*/R1b1a* samples. Another impossibility.

    Is there a way to change font in a post? If I could change the font to courier I could post the R1b haplotypes.

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    1. They tested them for SNPs, there should be no doubt. STR haplotypes are sometimes misleading in fact.

      "Is there a way to change font in a post?"

      I don't think so.

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    2. More precisely they say in the "Materials and methods" section:

      For updated subdivision of haplogroup R, SNP V88 was amplified and analyzed as in Cruciani et al. [40] and SNPs L11, L23, M412, M529, S116, U106 and U152 as in Myres et al. [45].

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    3. Actually, it's the other way around, SNPs are sometimes misleading, not haplotypes. A y-dna clade has a certain signature composed of several STR values which would be very unlikely to be all simultaneously off-modal, while in the case of an SNP, you're bounded by that one single end-node result, if it fails, you erroneusly end up with R1b* instead of R1b-U106, for example.

      I regularly observe obvious errors in studies between the reported haplotypes and their SNP haplogroups. It's usually of the end-node failure type, for example, F* instead of J, R1b* instead of R1b1b2, etc. But it's also quite common for completely unexplainable mix-ups, like G instead of R1b, which I never manage to understand how they managed to botch it up like that. A typical study will have a 2% or 3% error rate, it's very unusual for a study to not confuse at least a few samples. And a few studies are a disaster, with 10% or 20% error rates: Zalloua comes to mind.

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    4. No. You are very wrong in this. An SNP can happen twice, statistically speaking, once in many millions or maybe billions of years. STRs instead can perfectly happen many times in human terms instead. That's why we should never compare STR structure across haplogroups. Sometimes an STR defined cluster ends up being described as an SNP-defined haplogroup but other times STR-clustering only causes confusion.

      Trust me in this: SNPs matter much more than STRs, which are just relevant when SNPs are not known. If you don't trust my experience of many years reading and later also writing on this stuff, ask someone else you think experienced and trustworthy. But for all I know and since many years now, SNPs are the serious stuff and STRs are just an inexact reference. They don't "botch" anything: they test for SNPs.

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  2. So if J1 in east/northeast africa didn't arrive in the neolithic, with what cultural complex do you ascribe its migration to?

    Also how do you think the neolithic dispersals out of the levant affected the aforementioned region in terms of Y and mtdna? I always thought the majority of the J1 found in south europe, east and north africa were due to the spread of agriculture during that period triggered by the climatic change in the region leading to the greening of the saharan and arabian deserts?



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    1. First of all, Maju, you wrote: "While there is no reasonable doubt that J1 as a whole originated in West Africa". What? Typo?

      But back to your post. J1-L222 is the most common type of J1 in Arabia and North Africa. A recent giant study of Ethiopia (Plaster, 2012) tested 5000 y-dna samples from the country, including several hundred J1 samples. He didn't test for J1-L222, but J1-L222 has a distinctive haplotype, 391=11 + 388=17, which sets it apart from all other J1 clades, and since the study included this information, I was able to observe only 3 or 4 occurences of this combinations amongst the hundreds of Ethiopian J1 samples. This would kind of exclude a massive migration from anywhere in Arabia after the time in which J1-L222 became very common there (which I have no idea when it did).

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    2. If there would Neolithic evidence chronologically related with the PPNA of Levant, I would more easily accept a Neolithic origin but AFAIK there's no known African Neolithic until much later, so attribution to Neolithic is extremely problematic.

      Prior to that time we know that there are other genetic influences from Asia into NE/East Africa: mtDNA M1, X1, Y-DNA T... but the most notable is surely this J1. A possible time-frame for arrival might be at the origins of the LSA (Later Stone Age), which is the incorporation of "mode 4" (roughly the stone blade tech) to the African Paleolithic and is roughly equivalent to West Eurasian Upper Paleolithic. Africa may have quite old dates for this (50,000 BP?) but they are still more recent than those of Palestine and roughly the same as those of Europe. This is one possible window for the penetration of Asian (or Eurasian) lineages in general to NE and East Africa and is the window I generally imagine for mtDNA M1 for example.

      However it is very difficult to be certain: can possibly J1 be that old? I truly do not know nor I think there's way of knowing with any certainty at least by the moment. So maybe there were secondary flows West Asia → NE Africa later in the Upper Paleolithic/LSA that we still do not understand in archaeological terms. But what is clear to me is that there has been a flow of West Asian genetics into NE Africa and The Horn, with very minor penetration into East Africa proper and that this flows look pre-Neolithic (for reason of lack of J2 and also other West Asian lineages like G or even R1 other than R1b-V88). The matter seems to require more research, both archaeological and genetic.

      ...

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    3. ...

      "... how do you think the neolithic dispersals out of the levant affected the aforementioned region in terms of Y and mtdna?"

      Lineages like mtDNA K, T, J... seem Neolithic (although in some cases I'm unsure of their exact origin: West Asia or somewhere in Europe or...?) In the Y-DNA side it is possible that some small fraction (but not the majority) of all that J1 that correlates to the frequencies relative to J2 in West Asia (as well as J2 itself) may have arrived with Neolithic or also later Semitic flows (Phoenicians and Arabs). But in general African Neolithic, maybe with some exception sin Egypt, seems very much African (again with the reservation needed for lack of enough research).

      "I always thought the majority of the J1 found in south europe"...

      No. In Iberia for example there is very little and I think that's also the case of Italy. There is some more in Greece and the Balcans but still low in comparison to J2. There's people who think otherwise but IMO the Neolithic Y-DNA with West Asian origin in Europe is essentially E1b-V13, G2a (both documented in Cardium Pottery sites of Languedoc and Catalonia) and J2 (not documented in aDNA yet), with minor presence of J1 in the SE. Add to that North African E1b-M81 in West Iberia (and some scattered offshoots elsewhere), which might also be pre-Neolithic (but not Islamic because it's much more common in NW than in SE Iberia, cf. Adams 2009).

      J1 is clearly centered in what I call Lowland West Asia, with an ill-explained dense pocket in the Eastern Caucasus (Azerbaijan, Daghestan) and then in the already discussed parts of Africa and with lesser frequencies Highland West Asia and parts of the Caucasus. An old map is can be seen in Semino 2004 but a complementary map with the inclusion of the Daghestani pocket you can find here. For African details I'd visit Ethio Helix because he has very nice well-documented charts.

      Probably (in my opinion) J1 coalesced at the early UP of Palestine and spread from there in various ill understood waves. As PPNA, which is the Palestinian Neolithic, did not have much influence in terms of expansiveness at least, I think it spread mostly before that time but the processes are not well understood.

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    4. "First of all, Maju, you wrote: "While there is no reasonable doubt that J1 as a whole originated in West Africa". What? Typo?"

      Typo. Thanks for noticing. I'm rushing to correct that. I meant West Asia, naturally.

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    5. "But back to your post. J1-L222 is the most common type of J1 in Arabia and North Africa".

      Are you sure? That would be evidence of something. Not sure what but I would have to revise my hypothesis for sure.

      Could you produce a source or reference (preferably a free access one)?

      "I was able to observe only 3 or 4 occurences of this combinations [likely J1-L222] amongst the hundreds of Ethiopian J1 samples".

      That's a very interesting information. So Ethiopian J1 is not "Arab" but (on some other undetermined source or ground) you claim that North African one is instead.

      I'm all ears to what you say on this because it is a level of detail that I haven't managed so far. I would just like to see it with my own eyes. So if you have a paper that is important here and not open access, I beg you to send me a copy to lialdamiz[at]gmail[dot]com. Thanks for all.

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    6. Maju, this is the result of FTDNA being ahead of the curve. Similar to how we already knew about L51, L11, and L23 before geneticists finally started testing it, in fact, if you'll recall, the Myres study of R1b only tested for those 3 SNP on the insistence of several people from dna-forums.org who had tested with FTDNA. Anyhow, for quite a while now L222 is being tested by FTDNA, and you can find the results in the FTDNA Arabian J1 Project webpage:

      http://www.familytreedna.com/public/arabian_ydna_j1_project/default.aspx?vgroup=arabian_ydna_j1_project&section=yresults

      Also of interest is the FTDNA J Project:

      http://www.familytreedna.com/public/Y-DNA_J/default.aspx?vgroup=Y-DNA_J&section=yresults

      Notice that L222+, in the Arab Project page, is underrepresented because of samples that didn't test for L222. These samples make up the first half of the results page, and are all indicated as being haplogroup J1. Make sure to include all the samples by writing 3000 in the Page Size box at the top of the webpage. The second half of the page are the samples that tested for the presence of L222, and these samples are indicated by haplogroups J1c3 and deeper (there are also a couple of rare J1c2). L222+ is J1c3d2. You can see that it makes up about half of the Arabian J1. And you can also see the evident haplotype difference between L222+ and L222-: L222+ almost always has 391=11 + 388=17 (or 18), while L222- almost never has both values simultaneously.

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    7. I have checked the J1 list and (notwithstanding error on my side) I see:
      J1*-M267: Egypt 5, NW Africa 5 (Mor 2, Alg 1, Tun 2)
      J1c3d-L147.1 (J1b2b) - Egypt 2, NW Africa 1 (Tun)
      J1c3d2-L222.2 (J1b2b1) - Egypt 1, NW Africa 1 (Tun)

      The sample is small but it does not say on first read what you claimed, with most NW African J1 falling in the J1* zone (100% in Algeria and Morocco). I don't have time right now to check for haplotypes, which in this case is very advisable, but I'll check later.

      Anyhow, the overall sample is tiny, especially in comparison with the oil-rich countries of the Arabian Peninsula and one can imagine that the most well-off families of the region tend to be more arabized than the bulk of the population. We cannot ignore this potential bias every time we deal with commercial samples.

      ...

      Wait, quick look at haplotypes at J1*:
      Egypt: 2 11/17, 1 11/18, 1 10/15, 1 10/16
      Morocco: 1 11/17, 1 12/17
      Tunisia: 1 11/19, 1 10/17
      Algeria: 1 10/16

      So there is at least a sizable fraction of haplotypes not looking L222+ in this sample. Only 3/10 (mostly in Egypt).

      In the L147.1 group:
      Tunisia: 1 14/17
      Egypt: 1 14/11, 1 15/11

      So in total, and assuming that your haplotype correlation is correct, there apportion would be:

      J1-L222 (presumed): NW Africa 2, Egypt 3
      J1-other: NW Africa 5, Egypt 5

      Not exactly what you said.

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    8. I thought we were talking about Arabia, you can see in the Arab Project page that it's filled with Saudis, Kuwaitis, etc. After all, the concept of a mass J1 migration to Ethiopia always involves the Arabian peninsula, not Northwest Africa.

      Anyhow, regarding what you observed about Northwest Africa, yes, you're absolutely right, but there's a good reason. The ysearch results are self-reported and this produces, in some regions, notable biases. For example, Eastern European samples are mostly American Ashkenazi Jews, and Spanish samples are mostly Latin Americans. Northwest Africa is one of the regions with a notable bias of this sort, specifically at least 1/3 of the samples are North African Jews, and they have a lot of J1 samples, but which notably lack L222+. But if we take a look at published studies, about 80% of Northwest African J1 has the distinctive L222+ haplotype 391/388 = 11+/17+, which actually implies more than 90% of their J1 belongs to L222+, since obviously some samples will have a mutation to 391=10 or 388=16. Another thing, because I remember your comment about EthioHelix mentioning a study (Tofanelli?) that found very reduced diversity in Northwest African J1: almost all the Northwest African J1-L222+ actually belongs to a specific Northwest African L222+ clade. So already we have at least one subclade within L222, and yes, it's very, very low diversity, and it's very common in North Africans, from Saharawi all the way to Benghazi.

      By the way, yesterday, after I posted my comment, I went and downloaded the J1 page (the general one, not the Arabian), and was surprised to see that, though generally correct, there are too many 11/17 samples in the L222- category. There should be almost none. L222+ has other distinctive modals, and judging from those other STRs I was able to see that these L222- with 11/17 belonged to the same clade as the L222+ 11/17. So now I'm wondering, is L222+ a downstream SNP that catches most but not all of the samples that belong to the 11/17 clade, or did the project manager of the J1 Project mess up? I'm going to write to them at rootsweb and I'll post back here what they tell me.

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    9. You implied, or I understood so, that L222 was dominant in NW Africa. You said before:

      "J1-L222 is the most common type of J1 in Arabia and North Africa".

      I asked you for confirmation/source and you then mentioned the FTDNA list. So I checked (a bit in a hurry) and it does not look like L222 is particularly strong in North Africa.

      "After all, the concept of a mass J1 migration to Ethiopia always involves the Arabian peninsula, not Northwest Africa".

      You mentioned Ethiopia also, not reflecting the modern Arabian J1 pool, but, in contrast, you mentioned North Africa, as I quote above. But, well, a misunderstanding, I guess.

      "... at least 1/3 of the samples are North African Jews, and they have a lot of J1 samples, but which notably lack L222+".

      That doesn't help us much, does it?

      "But if we take a look at published studies, about 80% of Northwest African J1 has the distinctive L222+ haplotype 391/388 = 11+/17+"

      Which studies? Be specific, please.

      ... "almost all the Northwest African J1-L222+ actually belongs to a specific Northwest African L222+ clade".

      That I was expecting in a sense, although I imagined the clade originating at the Nile. Whatever the origins, this implies a very marked founder effect, what seems incompatible with recent Arab flows, which should be more diverse in origin and have less dramatic impact (as the substrate populations were already densely settled). It might be Neolithic after all but, if so, it'd need to be from a very specific high J1 population like Negev Bedouins (hypothetically descendants of Harifians). Any idea of what clade/s do these Bedouins have?

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    10. “Anyhow, the overall sample is tiny, especially in comparison with the oil-rich countries of the Arabian Peninsula and one can imagine that the most well-off families of the region tend to be more arabized than the bulk of the population. We cannot ignore this potential bias every time we deal with commercial samples.

      This statement I highly agree with, especially the last part, we see these types of sweeping conclusions being made from commercial samples of E1b1b as well, when we know that a majority of these samples are of European descent, or those whom can afford these tests but they are not at all representative of where the lineage actually dominates in frequency, simply because there are not enough participants from where the lineage is common in. Conclusions made from commercial samples of other lineages like R1a and R1b are far more believable to me because these lineages are actually some of the most common in Europe, and the participants reflect this reality.

      WRT to J-L222 (formerly known as J1c3d2), I can not say where it is most common without a formal study, but I had analyzed the haplotypes with my program about seven months ago and had found 84 haplotypes with a self declared country of origin as follows:

      Saudi Arabia 47
      Kuwait 10
      Tunisia 7
      Iraq 3
      United Arab Emirates 3
      Algeria 2
      Turkey 2
      Lebanon 2
      Sudan 2
      Qatar 2
      Oman 2
      Syrian Arab Republic 1
      Egypt 1


      What I did find however was that these haplotypes were only 0.16 – 0.23 times as old as all the J-M267 haplotypes combined.

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    11. Here's the study about North Africa, curiously it was Tofanelli (2009), which I mentioned in this thread already but for some other reason:

      http://www.nature.com/ejhg/journal/v17/n11/abs/ejhg200958a.html

      Or just go straight to the xls file with the haplotype data:

      http://www.nature.com/ejhg/journal/v17/n11/extref/ejhg200958x1.xls

      I don't think any study has tested L222, yet, a situation very similar to the L51/L11/L23 SNPs, that were known for several years, thanks to FTDNA, before geneticists finally caught up with that knowledge.

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    12. @Kalupitero: I've downloaded the xls file and take notice of your previous comment about "the distinctive L222+ haplotype 391/388 = 11+/17+" in order to parse them when I gather some time (tomorrow hopefully). Thanks. I'll comment further when and if I'm ready.

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    13. Sorry I though it was more data. I can quickly see that, following the two marker rule you say, your model is confirmed.

      However, if you look at the haplotype network in figure 3 (use the HTML version because the grey colors of the PDF are confusing), it seems very apparent that J1, judging on those 20 STR markers, had a single star-like expansion and the apparent center is at the large node which is mostly NW African with a small Qatari slice. Seen as that one could easily imagine that J1 expanded from NW Africa. Of course further sampling should clarify this and find a more likely center (probably in Palestine) but still one wonders why a supposedly derived haplogroup such as J1b2b1-L222.2 (ISOGG name) appears so extremely central in the haplotype network.

      I'm even more puzzled now than before. Is the two markers method really indicating what you say? If so, how do you conciliate its centrality in the star-like haplotype network with the quite derived state in the SNP one?

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    14. 19 out of 28 of the NW Africans (Moroccans + Tunisians) in the Tofanelli worksheet have the “11/17” pattern on 391/388 mentioned by kalupitero above. In the FTDNA database, (from what I downloaded several months ago) , 67/84 SNP tested J-L222 haplotypes harbor the pattern of “11/17”. So from these results you can not conclude that ALL the 19/28 NW African samples in Tofanelli were J-L222 +, but you can extrapolate by the probability that 15/28 of the NW Africans in Tofanelli have a good chance of being J-L222+, nothing for sure without an SNP test however. Interestingly, all the haplotypes that had this pattern “11/17” also had 22/22 exclusively on YCAII, a pattern first documented in Semino (2004).

      The TMRCA estimate on the J-L222+ ftdna haplotypes are below.

      Dataset:J1c3d2
      Marker list:49markerlist
      Sample size:84

      Pedigree/Familial Rates Summary
      Years/Generation:28 - 33
      TMRCA Range:1287 - 2658
      Mean TMRCA:1817
      Median TMRCA:1687
      SD:463

      Coalescent_Detail =

      {
      [1,1] = Chandler;49 Markers; Generations(Median)--80.554 Generations(Modal)--80.554
      [1,2] = Stafford;49 Markers; Generations(Median)--48.432 Generations(Modal)--48.432
      [1,3] = Burgarella_Navascues;49 Markers; Generations(Median)--63.43 Generations(Modal)--63.43
      [1,4] = Ballantyne;49 Markers; Generations(Median)--45.967 Generations(Modal)--45.967
      [1,5] = Zhivotovsky;49 Markers; Generations(Median)--232.74 Generations(Modal)--232.74
      }

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    15. Compare with R1b. U106 has 390=23 + 492=13. But all its other STRs are common with the general R1b modal. If you built a haplotype network of R1b, the U106 clade probably wouldn't show up, because the noise factor is drowning out the real signal of its presence (390 and 492). I'm not saying this as a fact, but as a possible explanation.

      Delete
    16. Just for the fun of it, as I don't really believe in TRMCA calculations but among them I think that Zhivotovski is the most reasonable by a lot, the Zhivotovski method age estimate (at 30 years per generation) is 6990 years, c. 5000 BCE. With a bit of stretching (which fits well with my way of thinking, as I think that Z. did not go far enough with his corrections) this would be compatible with either Neolithic or also pre-Neolithic (Capsian) scenarios but not at all with historical ones (Islam, Phoenicians). If we are to use the quite broken "molecular clock" hypothesis, then this is my stand within it.

      Just for the record the other mentioned TRMCAs are in years: Chandler: 2415 (c. 400 BCE), Stafford: 1452 (c. 650 CE - but notice that it is shorter than the pedigree, what makes no sense whatsoever), Burgarella: 1902 (c. 100 CE) and Ballantyne 1380 (c. 600 BCE, again more recent than the pedigree, ergo nonsense).

      Excluding the two nonsense estimates (you can't run faster than light, i.e. the pedigree estimate), the options are: (1, pedigree): late Roman era, (2, Chandler and Burgarella): late Phoenician era, (3, Zhiv.): Neolithic, (4, my skepticism): Capsian or whatever. And we are talking here only the alleged L222 subset, not all North African J1.

      Note: I'm sure someone will be quick to say that I have discarded the two "nonsense" estimates precisely because they fit with Islamic/Arab expansion. Well, not really: I understand that the pedigree is the fastest possible one (hence the need for corrections like Zhivotovski's because we can't be sure that the "clock" runs always or even at all at max. speed). You cannot be faster than the faster thing of that kind and Stafford's and Ballantyne's methods are (also I dislike Stafford quite a bit, finding him a dishonest or at best self-deluding geneticist).

      ...

      Then there is that other issue of the supposedly derived North African haplotype being at the center of the star-like haplotype structure. It cannot be as Kalupitero says, that there is "noise" because the network, if done properly, implies that every single STR change creates a new cluster, joined to the one (or ones) closest in overall 20 markers haplotype.

      It still can be (and often happens) that the real root is not at the apparent center but at one branch, but that would only remove one branch from the starlike structure and all the rest still seem to go through that central node phylogenetically.

      What may happen instead is that the STR markers used are not the ideal ones for this particular haplogroup, creating a network that does not fit SNP-based phylogenetic reality. That is a problem we cannot surely address here however, gentlemen, needing specialized research.

      It does seem to devalue in any case the insight power of an STR based approach, at least until more significant STR markers are found/chosen.

      Delete
    17. “the Zhivotovski method age estimate (at 30 years per generation) is 6990 years, c. 5000 BCE.”

      I wouldn't multiply Z-estimates by 30 yrs/generation (like I would for the others) since the mutation rate itself is estimated 0.00069 specifically for 25 years.

      “also I dislike Stafford quite a bit, finding him a dishonest or at best self-deluding geneticist”

      I don't even know him really, his rates are the only ones in my calculator with no accompanying publication, but apparently his mutation rate set is simply just a compilation of other ones, I just used it because it has broad marker coverage and all of them were put together in one convenient spread sheet, there are many more mutation rate sets that I could include, but many of them are for < 20 markers, which is not a wide enough coverage for what I'm looking for.

      “What may happen instead is that the STR markers used are not the ideal ones”

      That is a possibility, look at my experiment here on how drastically TMRCA estimates and thus diversity are affected when different combinations of markers and size are used. There is also the Swiss software Arlequin that many geneticists use to estimate microsatellite diversity, I just haven't gotten around learning (or downloading) it yet.

      Delete
    18. If your primary product is number of generations, as you mentioned, then we should multiply all results for the same factor (generation time), which is generally accepted to be in the range you say (30 years to simplify). That Zhiv. chose another factor should not affect the method as such, especially when comparing with other methods, because the primary result is given in number of generations.

      I find your experiment interesting and somewhat revealing. I also suspect that there is still some margin for research in Y-DNA J1, very especially in Africa (also Palestine, which may well be the ultimate origin of this haplogroup overall).

      Anyhow, can you fathom any good explanation as to why two methods produce age estimates more recent than the pedigree rate? I am a bit shocked by that: they should not.

      Delete
  3. "Lineages like mtDNA K, T, J... seem Neolithic (although in some cases I'm unsure of their exact origin: West Asia or somewhere in Europe or...?) In the Y-DNA side it is possible that some small fraction (but not the majority) of all that J1 that correlates to the frequencies relative to J2 in West Asia (as well as J2 itself) may have arrived with Neolithic or also later Semitic flows (Phoenicians and Arabs). But in general African Neolithic, maybe with some exception sin Egypt, seems very much African (again with the reservation needed for lack of enough research). "

    I still dont understand the J1/J2 relation you are speaking of since If I'm not mistaken, the frequency of J2 in the levant is not that high when compared to adjacent regions like the fertile crescent and the caucasus/turkey. Could it not have been that J2 became a player in the levant later in the neolithic, ie post neolithic dispersal of agriculture? I think it would make sense, since the J1 E1b1b1 link/combination (ie usually they are found together) IMO points to it being dispersed during the neolithic.

    Also If I'm not mistaken the region was a cosmopolitan hub in the early neolithic as a consequence of the mushabian migration there most probably bringing m123 and other e1b1b1 derived lineages to the levant.. the mushabian kebaran merged population was always what I thought to be the best candidate for 'proto afroasiatic' given its cosmopolitan nature and its central position for redispersal into north west and eastern africa during the neolithic waves of migration... hence why I thought it triggered the migrations of m81 and m78 west and south respectively from egypt (if I'm not mistaken, the dispersal of both those clades was dated to the neolithic).. Making the modern north africans essentially a combination of early capsian culture, the new neolithic afroasiatics, and the ibero-maurusians in the coastal region.


    So I guess my second question to you is if that conclusion isn't in line with the data, then with what culture would you ascribe the proto afroasiatic speaking population given its postulated date of origin during the mesolithic and subsequent dispersals dated to around the early neolithic? And what markers would you ascribe to that migration?

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    Replies
    1. No time now. I'll get to you later.

      Delete
    2. "I still dont understand the J1/J2 relation you are speaking of"...

      Just check Wikipedia (simplified and reorganized list of J2 frequencies):

      Highland West Asia:
      Iraq - 43.6%
      Iran - 25%
      Turkey - 24.2%

      Levant:
      Lebanon - 29.4%
      Syria - 20.8%
      Ashkenazim - 19%
      Israel-Akka - 18.6%
      Jordan - 14.6%

      Peninsular Arabia:
      Saudi Arabia - 15.9%
      Oman - 10.0%
      UAE - 10.3
      Qatar - 8.3%
      Yemen - 9.6

      a map.

      By comparison J1 is found at the following frequencies (again simplified from Wikipedia):

      Highland West Asia:
      Iran - 3.2%
      Turkey - 9.0%
      Iran - 11.3%
      Kurds-Iraq - 11.8%
      Iraq-Nassiriya - 26.8%

      Levant:
      Jews (non-Cohanim) - 14,9%
      Lebanon - 18.9%
      Palestinians - 32.7%
      Syria - 33.6%
      Jordan - 35.5%, 48.7%, etc.
      Palestinians-Akka/Acre 39.2%
      Jews (Cohanim) - 46.0% (quite arguably Aaron's lineage was a J2 variant)
      Negev Bedouins - 67.9%

      Arabian Peninsula:
      Kuwait: 33.3%
      Saudi Arabia: 33.3%, 40.1%
      UAE: 34.8%
      Oman: 38.0%
      Qatar: 58.3%
      Yemen - 72.6%

      So it seems obvious that J1 has in general a more southernly distribution than J2 but that both exist in notable frequencies in all the region (except Iran, where J1 is minor). For example in Saudi Arabia the J1:J2 apportion is 2:1 or at most 3:1, in Jordan roughly the same. Only in Yemen the proportion goes extreme: 7:1. In the reverse, we have the 2:5 of Turkey or the 2:3 of Lebanon. In any case, any of these populations or a pooled compendium of them would have carried both lineages and not only or almost only J1.

      ...

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    3. "Could it not have been that J2 became a player in the levant later in the neolithic, ie post neolithic dispersal of agriculture?"

      Can you suggest a process (or several) for that? I can only think in PPNB but maybe I am blind to something.

      "... the mushabian migration"...

      Thanks for mentioning the Mushabian because I "had heard bells but did not know where" (Spanish phrase for loose, imprecise knowledge). However, reading at Wikipedia it seems that it suggest more an Africa → Levant migration (which may well be at the origin of proto-Semitic, I guess), related to the presence of E1b1b lineages in West Asia and later into Europe as well.

      Notice please that the Kebaran and therefore the Mushabian too are Upper Paleolithic cultures and not yet Neolithic. Their alleged merge would have created the Natufian that is already Mesolithic (only arguably showing the first signs of agriculture).

      So if we talk of Mushabian, Kebaran or even Natufian, we are not really talking of Neolithic but of some of its most direct precursors.

      "... he mushabian kebaran merged population was always what I thought to be the best candidate for 'proto afroasiatic'"...

      Rather proto-Semitic. Afroasiatic originates beyond almost any doubt in the Nile Basin, where most of its linguistic diversity remains. As I understand it, the (or maybe some of the) peoples of the Southern Levant in the Natufian-PPNA period surely spoke proto-Semitic. A very strong candidate is the Harifian culture (semi-desert variant of Natufian), which, already in PPNB times, would be at the origins of the Circum-Arabian Pastoralist Complex (CAPC), which in turn preludes the Semitic invasions partly documented historically (Sumer) of the early 4th millennium BCE.

      But the expansion of Afroasiatic should be a mostly African issue, with that exception.

      "Making the modern north africans essentially a combination of early capsian culture, the new neolithic afroasiatics, and the ibero-maurusians in the coastal region".

      AFAIK there is no serious archaeological evidence of any Neolithic migration from West Asia to Africa in general, much less to NW Africa. Prove me wrong if you can, of course. Certainly some concepts and crops/cattle were introduced but that can also be done by mere cultural diffusion or with minimal, almost invisible, migrations - even easier of the main vector shared language family and customs (circumcision anyone?) and had been involved in Mesolithic proto-farming of some sort as I have seen suggested on occasion for Sudan and Upper Egypt.

      "... then with what culture would you ascribe the proto afroasiatic speaking population"...?

      I don't know. Either my knowledge of Nile Basin prehistory is too weak (it is) or there has been not enough research on the matter (also). I associate proto-Berber with Capsian and I have already explained proto-Semitic and Semitic probable genesis above. About the rest I must admit I just do not know enough, and I wonder if anyone does. It should be in any case a culture or complex emerging from either Sudan or Ethiopia, and we should be able to track it to the Natufian/Harifian and Capsian, via Egypt probably. That's my understanding.

      Anyhow, to finish, I'd like to mention that in the Wikipedia list mentioned above, we can see a dense pocket of J1 in the Khartoum area 74.3% (notice that the so-called Sudan-Arabic only have 17.1%). I'm not really knowledgeable but I know that there are interesting Mesolithic cultures in that area (Ancient Nubia) that sometimes have been claimed to influence further North. I would explore that way for the origins of NW African J1 and also at least a branch of the AA languages.

      Delete
  4. I'm probably misunderstanding but could it be the J1 was a first wave followed by a later J2 wave in most places but not north africa because the J1 wave who settled in the Nile Delta created a barrier - perhaps through higher population density brought about by unusually high levels of food resources?

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    Replies
    1. I am in agreement that J1 must have expanded into at least some parts of Africa before J2 expanded onto "Lowland West Asia". But the true question is when. My estimate for the J1 waves is that they look very much pre-Neolithic, while the J2 wave may well be Neolithic instead (PPNB). This tempo also allows for whatever founder effects because population densities were relatively low.

      Delete
    2. "My estimate for the J1 waves is that they look very much pre-Neolithic"

      Yes. I was thinking Deltas and flood plains might be the optimal places for foragers leading to relatively high population densities while at the same time - before irrigation is developed - those same areas might be quite marginal for farming.

      Delete
  5. Interesting new paper, which I haven't had a chance to look in detail to yet, though I think you mean J1 (M267) and not J1 (M304) as M304 is upstream of both J1 and J2. And actually the E-M81 range for NW Africa should be 44.2 -100 % and not 44.2-67.4%, although that is what the publication shows, but this publication combined the Tunisian berbers and Arabs together from Fadhlaoui-zid et al. 2011 , but the source publication shows the berbers to belong to 100% E-M81.

    In any event, briefly about the J1/J2 ratio you have brought up several times, if most or a significant majority of J1 haplotypes was brought into NAfrica with the expansion of the Islamic caliphates, then firstly, the source area of expansion (Saudi) today has a ratio of ~ 2.5 Abu-Amero (2009), (however Yemen has 7.5 !), here in the data you presented now, both Morroco and Algeria have ~ 4.8 while Egypt has ~ 3.1, so actually we see an ascending cline of this ratio going from Saudi to Egypt to NW Africa, which would be what to expect, if the newly incoming J1 into these areas is combining with pre-existing, likely Neolithic, type of J1 in the area. But this is all IF we were to assume that the people of Saudi had about the same composition of YDNA lineages in the early middle ages that we see today, a big leap of faith in itself....

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    1. You are right about M304. I just took the first marker of the list, thinking they'd be interchangeable (i.e. like M267 and L225) but it seems not. They list as markers of J1: "M304,M267,P58,M365,M368,M369", of which only M267 is actually of that branch. I'm going to correct that immediately. Thanks for noticing.

      Re. the E-M81 range, I followed the table. They probably pooled several Tunisian populations so only the average is shown.

      Regarding the J1/J2 ratio. There is still a very theoretical possibility that the NW African J1 can be sourced to a single extreme population like Yemen or maybe the Negev Bedouins. But this is a very extreme claim and I would ask in turn for some extra evidence such as haplotype concordance or some other supporting evidence. Otherwise it looks like the proverbial burning nail.

      "in the data you presented now, both Morroco and Algeria have ~ 4.8 while Egypt has ~ 3.1"

      "But this is all IF we were to assume that the people of Saudi had about the same composition of YDNA lineages in the early middle ages that we see today, a big leap of faith in itself...."

      I don't know why should it have changed too much. Nor I know why people expect a desert like Arabia to produce game-changing masses of colonists, as the Arab hypothesis needs.

      In any case, I suggest you to read the comments also because there has been interesting extra info and debate going on before you joined.

      Delete
  6. "Can you suggest a process (or several) for that? I can only think in PPNB but maybe I am blind to something. "
    Bronze age expansions? Chalcolithic period interactions (Ghassulian culture?) etc all of those are possibilities considering the northern and southern parts of the levant were in a great deal of contact during that period

    "Thanks for mentioning the Mushabian because I "had heard bells but did not know where" (Spanish phrase for loose, imprecise knowledge). However, reading at Wikipedia it seems that it suggest more an Africa → Levant migration (which may well be at the origin of proto-Semitic, I guess), related to the presence of E1b1b lineages in West Asia and later into Europe as well."

    It could not be the protosemitic group because protosemitic was dated to the middle neolithic ~6000 bc and its expansions to the bronze age... Rather protosemitic was dated to that period (between 18,000 and 10,000 bc which conicides with the mushabian kebaran peak period.. ).. hence why the sinai/negev region seems the most ideal.. with the harifian culture being the first indication of contact from that culture with others deeper in africa.

    Hence why I think the idea of a nile basin origin of afroasiatic is problematic because there were no known migrations out of africa during the neolithic to establish semitic, rather all migrations from that period were into africa.. (the earliest migration out, like I stated before was the mushabian kebaran one which would have likely brought m123 to the levant.. from there it dispersed south with the semtiic languages while m78 and m81.. which are linked to the neolithic, would have migrated south and west respectively (ofcourse cushitic being much earlier in their migration than the berbers)

    I think this fits the time periods perfectly and hence why I had a problem with an older J2 introduction in the levant, or else we would have seen similar J2 amounts in these afroasiatic offspring (namely berbers and cushitics).


    AFAIK there is no serious archaeological evidence of any Neolithic migration from West Asia to Africa in general, much less to NW Africa. Prove me wrong if you can, of course. Certainly some concepts and crops/cattle were introduced but that can also be done by mere cultural diffusion or with minimal, almost invisible, migrations - even easier of the main vector shared language family and customs (circumcision anyone?) and had been involved in Mesolithic proto-farming of some sort as I have seen suggested on occasion for Sudan and Upper Egypt."

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    1. The normal interpretation of Ghassulian is that it is a merge between PPNB and the CAPC and its dates are almost totally coincident with the spread of Semitic to Mesopotamia. Indeed Ghassulian seems to have its early origin in the North but it would be hard to explain with it the J2 expansion into Peninsular Arabia.

      "It could not be the protosemitic group because protosemitic was dated to the middle neolithic ~6000 bc and its expansions to the bronze age..."

      Semitic expansion is clearly Chalcolithic (Ghassulian, Akkadians). The estimated age for proto-Semitic may well be wrong or, if correct, it may ignore a previous phase, call it proto-proto-Semitic.

      Whatever the case there is much more to Afroasiatic than Semitic, which is a peripheral, albeit influential, branch only.

      "Rather [proto-Afroasiatic] was dated to that period (between 18,000 and 10,000 bc which conicides with the mushabian kebaran peak period.. )"

      Or the Capsian culture also, which is late UP to Neolithic. You seem too focused only on West Asia. These represent surely only some of the many branches of Afroasiatic: (proto-)proto-Berber with Capsian, Egyptian Mushabian maybe with proto-Egyptian and Natufian/Harifian for the (proto-)proto-Semitic. For the rest we'd need to dig on the archaeology of Sudan, The Horn and the Chad basin. And the ultimate source is almost for sure in the Middle Nile (Sudan-Ethiopia) but, as we have little idea of the prehistory of those regions, we can't say much more in term of material cultures (yet).

      "I think the idea of a nile basin origin of afroasiatic is problematic because there were no known migrations out of africa during the neolithic to establish semitic"...

      Didn't you just mention the Mushabian? Per Wikipedia: "The Mushabian culture (alternately, Mushabi or Mushabaean) is suggested to have originated along the Nile Valley prior to migrating to the Levant, due to similar industries demonstrated among archaeological sites in both regions but with the Nile valley sites predating those found in the Sinai regions of the Levant.[1]"

      The reference is Bar Yosef 1987 (PPV).

      There you have the migration out of Africa you are denying. Similarly the Capsian probably originated in the Upper Egyptian oases (I read something long ago but can't recall the reference).

      ... "rather all migrations from that period were into africa.."

      Nothing really demonstrated that looks too impacting, really.

      Delete
  7. BTW I made a typo in the first post.. when i said 'rather proto semitic was dated to that period' (third paragraph).. it should be rather proto afroasiatic..





    ""Can you suggest a process (or several) for that? I can only think in PPNB but maybe I am blind to something. "
    Bronze age expansions? Chalcolithic period interactions (Ghassulian culture?) etc all of those are possibilities considering the northern and southern parts of the levant were in a great deal of contact during that period

    "Thanks for mentioning the Mushabian because I "had heard bells but did not know where" (Spanish phrase for loose, imprecise knowledge). However, reading at Wikipedia it seems that it suggest more an Africa → Levant migration (which may well be at the origin of proto-Semitic, I guess), related to the presence of E1b1b lineages in West Asia and later into Europe as well."

    It could not be the protosemitic group because protosemitic was dated to the middle neolithic ~6000 bc and its expansions to the bronze age... Rather protosemitic was dated to that period (between 18,000 and 10,000 bc which conicides with the mushabian kebaran peak period.. ).. hence why the sinai/negev region seems the most ideal.. with the harifian culture being the first indication of contact from that culture with others deeper in africa.

    Hence why I think the idea of a nile basin origin of afroasiatic is problematic because there were no known migrations out of africa during the neolithic to establish semitic, rather all migrations from that period were into africa.. (the earliest migration out, like I stated before was the mushabian kebaran one which would have likely brought m123 to the levant.. from there it dispersed south with the semtiic languages while m78 and m81.. which are linked to the neolithic, would have migrated south and west respectively (ofcourse cushitic being much earlier in their migration than the berbers)

    I think this fits the time periods perfectly and hence why I had a problem with an older J2 introduction in the levant, or else we would have seen similar J2 amounts in these afroasiatic offspring (namely berbers and cushitics).


    AFAIK there is no serious archaeological evidence of any Neolithic migration from West Asia to Africa in general, much less to NW Africa. Prove me wrong if you can, of course. Certainly some concepts and crops/cattle were introduced but that can also be done by mere cultural diffusion or with minimal, almost invisible, migrations - even easier of the main vector shared language family and customs (circumcision anyone?) and had been involved in Mesolithic proto-farming of some sort as I have seen suggested on occasion for Sudan and Upper Egypt."

    Well certainly the introduction of proto berber into northafrica from egypt would indicate some dispersal of neolithics considering m81 was dated to a dispersal from the east during that timeframe...

    In terms of archaeology, I admitedly don't know much about the capsians to comment on it, though I did some arbitrary reading and there were some evidence of contact between the ibero maurisians and the nile valey (page 3 of this study: http://www.researchgate.net/publication/226996851_Early_and_Middle_Holocene_Environments_and_Capsian_Cultural_Change_Evidence_from_the_Tlidjne_Basin_Eastern_Algeria )

    I'd have to read more about it to comment, but at least from a cultural and genetic position, there was definately influence from the east...

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    1. "... the introduction of proto berber into northafrica from egypt would indicate some dispersal of neolithics"...

      Not if with the Late UP, Epipaleolithic and finally also Neolithic Capsian culture, as I think.

      Delete

  8. "Semitic expansion is clearly Chalcolithic (Ghassulian, Akkadians). The estimated age for proto-Semitic may well be wrong or, if correct, it may ignore a previous phase, call it proto-proto-Semitic."

    I doubt the dating is wrong as its been the agreed date from multiple sources (see Kitchen et al 2009) and would coincide with the formation of the CAPC during the late PPNB/Harifian period that would coincide with the dates IMO.. Protosemitic must have been brought by the harifians in that case then.

    In terms of proto-proto semitic, it still would be limited by the dating of PAA itself which is between (the earliest) 16,000 bc and (the latest) 7000 bc

    So I guess in that case you're right (interms of overfocusing on west asia and mushabian/kebarans being PAA), I guess I was looking at the dates of origins of the cultures which was throwing things off since 10,000 bc is much too early for any downstream afroasiatic languages to have arisen...

    thus in light of that probably the Halfan culture in egypt corresponds to the protoafroasiatic homeland, especially considering the apparant link between them and the maghreb (the problem with this link, again is that it's too early for the introduction of protoberber.. the sources I read said the ibero maurisian culture and the halfan had links, but it was during the UP which again corresponds with protoafroasiatic not proto berber.. so honestly I'm not sure what culture can link the two other than just an arbitrary neolithic population)..



    "Didn't you just mention the Mushabian? Per Wikipedia: "The Mushabian culture (alternately, Mushabi or Mushabaean) is suggested to have originated along the Nile Valley prior to migrating to the Levant, due to similar industries demonstrated among archaeological sites in both regions but with the Nile valley sites predating those found in the Sinai regions of the Levant.[1]""

    The mushabians came into the levant during the UP so they were too early to bring protosemitic, I think rather protosemitic was spoken with the harifians (initially arising from around fayum) who brought it east when they fused with the PPNB..

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    1. The date of c. 6000 BCE coincides well with the formation of the CAPC, which is generally considered to be at the origins of Semitic. However there must have been other previous transitions before that proto-Semitic or first Semitic proper from which all known Semitic languages hang.

      "In terms of proto-proto semitic, it still would be limited by the dating of PAA itself which is between (the earliest) 16,000 bc and (the latest) 7000 bc"

      7500 BCE actually (mentioned in Wikipedia without reference). But several proposed ages are in the range of c. 10-11,000 BCE, although the 16,000 BCE date also appears several times. So the oldest fraction 10-16,000 BCE is probably the correct one (or at least the most favored by linguists in general). That is in all cases pre-Neolithic and very distant from CAPC proto-Semitic, allowing for not just one but several intermediate evolutive states.

      "The mushabians came into the levant during the UP so they were too early to bring protosemitic"...

      They probably brought proto-proto-proto-Semitic instead. Most phylogenetic proposals place Semitic in the same branch as Egyptian, what makes all sense with this perspective. The plausible stages would be:

      1. Mushabian (still "Egypto-Semitic"?)
      2. Natufian/Harifian (proto-proto-Semitic)
      3. CAPC (proto-Semitic)
      4. Ghassulian, Akkadians (and others?) (Semitic proper)

      In parallel to the Mushabian but surely from a more southernly origin (Egyptian Nubia I've read some times) Capsian would have brought the early seed of Berber to NW Africa. Other less well documented (or known to us) processes in the Sahel would have generated the various other branches.

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  9. I've made the following xls file (600 KB) to better understand the L222+ clade of J1.

    http://www.sendspace.com/file/oj3rno

    It's based on the data from the J Project. In North Africa (exc. Egypt) 25 out of 27 J1 samples are L222+. In the Arab peninsula it's 156 out of 237.

    About 85% of L222+ have 391=>11 + 388=>17. About 5% of L222- have the same combination, but I suspect most of these are misclassified and are really L222+. Going back to the implications for Ethiopia, in the 2012 Plaster study, about 600 J1 samples were found in Ethiopia, and only 4 of them had this haplotype signature, which is so low it even suggests they're all probably L222- who randomly mutated to 391=>11 + 388=>17. Given that L222+ makes up 1/4 or 1/3 of the y-dna of any part of Arabia, from Kuwait to Yemen, this means that there is virtually 0.0% Arabian ancestry in Ethiopia since the moment at which L222+ became so common in the peninsula.

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    1. Thanks: it is a good synthesis of your viewpoint in the form of data. Let us notice that NW Africa is not the only place with a 100% (or >67% in some places) 11/17 haplotype (the presumed L222 haplogroup - I'm not yet 100% sure it is) but Sudan also has that signature. Instead Egypt is 0%, and so is Palestine, Israel (Jews?), Iraq, Iran, Ethiopia (? n=1!), and in general the Caucasus, Europe and Pakistan.

      So what we get is that the haplotype 11/17 (J1-L222?) is restricted (with the exception of Lebanon) to Arabia, Sudan and NW Africa.

      This again does not look like Islamic expansion, because we would expect Arab invaders to have got at least some of this kind of impact in the Fertile Crescent and Egypt, so it should have another explanation and either Sudan (which fits better with my hypothesis) or Lebanon (which does with the "Phoenician model", that would correspond to the TRMCAs obtained with the Chandler and Burgarella methods) are probably intermediate.

      Again I find Lebanon problematic because there should be more J2 (and also some more other J1 types, etc.) but at least Phoenicians did actively colonize much of the NW African coast, skipping Egypt and Cyrenaica, and that we know for a historical fact, so if you are able to believe that the genetic landscape of Lebanon has changed so much since Phoenician times, that could be a reasonable model, especially with the high incidence of Tunisia. But then southernmost Iberia (also colonized by Phoenicians), Ibiza, Malta, Cyprus should be evidence to look for confirmation. It does not seem to be the case at least in Iberia, with levels of overall J(xJ2) that are at most of 3% (East Andalusia, Valencia and Southern Portugal) and 0% in the Phoenician colony of Ibiza, far in any case from the 8-28% that the same paper (Adams 2008) reports for North Africa or the 7-22% reported here (except Libya).

      The alternative is of course Capsian (or maybe some undocumented Neolithic branch) via Sudan, possibly related to the expansion of R1b-V88 to Central Africa also via Sudan (most likely) and also in relation to Afroasiatic expansion (different founder effects but both original from West Asia ultimately).

      As for the Ethiopian case, I can't say much, just agree with you that it does not seem particularly related to either Arabia nor Sudan (nor North Africa). In Tofanneli's study it seems that they are many different haplotypes, some of them related to SW Asian ones (or European ones too) but others with any known relation, much as it happens with European ones. This contrast is very perplexing indeed but one (Ethiopia, Europe) talks of many small low-impact migrations and the other (Sudan-NW Africa) a single strong founder effect instead.

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  10. Maju , I think there was an afro-asiatic linguistic doctor who claimed Berber was closest branch to Semitic witin the whole family syntaxically and grammatically , infact the grammar of Berber is almost identical to that of Semitic , while Ancient Egyptian is much more divergent. The propotion of common roots in between Coptic-Semitic is not significantly higher than Berber-Semitic suggesting that while being neighbours , the mutual influence was not hgiher (may have been different before as we know Arabic whiped out Coptic but not Berber , so modern Berber may have more Semitic influence than pre-Islamic Coptic) but overall , Berber stands closest branch to Semitic. So how to explain it? Was there really a Mushabian still "Egypto-Semitic"? as you said? Is it possible the Egyptian Delta had a nother branch whiped , closer to Semitic-Berber out by AE during the first Dynasty or this a theory not to even think about? This is hard to tell.

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    1. I don't have any strong opinion on the matter of internal AA structure, I have just read a bit here and there and I know that specialists don't seem to agree among themselves.

      If your doctor's theory is correct (which I cannot evaluate), maybe there was, as you say an Upper-Lower Egypt duality also in languages initially. But there may also be other interpretations, like a common origin in the steppes vs. an Egyptian origin in the Nile banks, influence of Phoenician, a late (and undocumented) invasion of proto-Berbers from somewhere else (Egypt?, Sudan?), where they spoke a language now lost related to Semitic, etc.

      I can't really say.

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  11. Just some more data about J1 in Morocco from Alvarez 2014 "Y-chromosome analysis in a Northwest Iberian population: unraveling the impact of Northern African lineages."

    These data are interesting as usually Moroccan samples studied are endogamic and isolated groups whereas samples below are from costal cities (except Figuig oasis). Alvarez used haplogroup predictor here for these samples from other studies but nevertherless quite interesting:

    J1 frequencies:
    Rabat (n=267) : 21.3%
    Casablanca (n=166) : 15.7%
    Figuig Oasis (n=96) : 29.2%
    El Jadida (n=49) : 8.2%

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