Friday, June 22, 2012

Intra African Genome-Wide Analysis, V2

See Also : Intra African Genome-Wide Analysis, V1


Population References and First Pass K10 Analysis



K2 - K10 Analysis



MDS Plots



Second Pass K10 Analysis



Eurasian Proxy Analysis



Final ADMIXTURE Results Summary (GEDMatch Submission)

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86 comments:

  1. Andrew Oh-WillekeJune 22, 2012 at 1:36 AM

    Quick work. I'm impressed. It used to take months or years for new papers to get integrated into comprehensive overviews the way that you did in a matter of hours.

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    1. EtyopisJune 22, 2012 at 2:07 AM

      The publishers had the dataset in PLINK format already, so all I had to do was merge it with my previous dataset and re-run ADMIXTURE on it. I still need to run the MDS plots however, which I'll do tomorrow. In any event, the addition of the Nilotic and Omotic clusters at the expense of the West-central African and one of the pygmy clusters is quite interesting, also the fact that the minor East African cluster (East Africa 1) remained intact....

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    2. UnknownNovember 27, 2016 at 1:53 PM

      This comment has been removed by the author.

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  2. MajuJune 22, 2012 at 8:52 AM

    Hmm... interesting but up to a point. You did not run other K-levels (always useful to contrast) and you run the regional datasets only in supervised manner, what is a complementary way of analysis but one I consider less interesting than the unsupervised, where the intrinsic variation comes out on its own.

    Finally it'd be interesting to check vs. WEA populations at least Fst-wise, maybe in a separate analysis but it can give very interesting information in any case.

    Most interesting maybe is the main K=10 analysis that does bring to light several East African apparent components, even if we ignore the Hadza (what we should because their distinctiveness is clearly product of inbreeding) but again it could be better evaluated if we had some other K-levels to compare with.

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    1. EtyopisJune 22, 2012 at 10:04 AM

      Sorry for the moderation, I have trolls spamming this place, which left me with no choice.

      “Hmm... interesting but up to a point. You did not run other K-levels (always useful to contrast)”
      True, I didn't have the time to go through each K run, my computer is pretty slow too, I plan on doing that with the global dataset as time permits however.

      “and you run the regional datasets only in supervised manner,”
      That is absolutely not true Maju, where did you get that? I ran it exactly the same way as the Intra African Genome-Wide Analysis, V1, the only difference is that I added these 235 samples, which gave me a total of 1300, and that my genotyoping rate went down a bit, as I mentioned in the post, other than that this is an intercontinental unsupervised K=10 run just like V1.

      “what is a complementary way of analysis but one I consider less interesting than the unsupervised, where the intrinsic variation comes out on its own.”
      Again, it is unsupervised, please see above.

      “Finally it'd be interesting to check vs. WEA populations at least Fst-wise, maybe in a separate analysis but it can give very interesting information in any case.”
      Yes, as time permits, I will integrate the data to my global dataset and run it up to K=13, like I did here:
      Cross Validating and K Selection

      “Most interesting maybe is the main K=10 analysis that does bring to light several East African apparent components, even if we ignore the Hadza (what we should because their distinctiveness is clearly product of inbreeding) but again it could be better evaluated if we had some other K-levels to compare with. on Intra African Genome-Wide Analysis, V2”
      The main difference between the V1 run is that the Pygmy clusters collapse into one and the West-Central African cluster disappears, these are then replaced with the Omotic and Nilotic clusters. However, while the Eastern Pygmies come out with the full Pygmy cluster membership, the Western Pygmies (Biaka) appear to have a multiple membership in the Omotic, Khoisan, Eastern Pygmy and Eastern Bantu clusters. The North Africans also do not seem to be Dominated with just North African cluster any longer, instead the major East African cluster (East Africa2) has a much more significant assignment in them than in my first version run, also Ethiopians have less of the North African cluster , which goes to show how adding these new populations completely changes the overall dynamics, as I had suspected.....

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    2. MajuJune 22, 2012 at 10:37 AM

      "That is absolutely not true Maju, where did you get that?"

      Hmmm... otherwise you would not get Hadza component, even if it's a thin layer one pixel thick, anywhere but among the Hadza (and maybe some in the Sandawe). In the regional plots you must be using pre-determined "zombie" components obtained from the general African run.

      I'm not sure if "supervised" is the right word but otherwise you would not get most of those components for example among North Africans (which I am most familiar with) but instead internal subdivisions.

      That's also the case in the V1 exercise. Maybe you just run one single pan-African comparison and then cut up the graph by regions?

      "The North Africans also do not seem to be Dominated with just North African cluster any longer, instead the major East African cluster (East Africa2) has a much more significant assignment in them than in my first version run, also Ethiopians have less of the North African cluster , which goes to show how adding these new populations completely changes the overall dynamics, as I had suspected....."

      This part is potentially interesting although I gather from the PC graph that the two components are not too distinct from each other and must have quite low Fst distance between them. So I'm not really sure of its significance.

      It's difficult to evaluate with the data you produced but it's behavior is very similar to that of the Ethiopian-specific component I gathered in my analysis of North Africans (plus controls). Maybe a bit stronger in appearance (surely because other North African layers are eclipsed here) but overall quite similar: minor in North Africa in general with quite greater weight in Egypt and Libya (but still minor).

      This component I thought back in the day that it is indeed a deeply rooted Ethiopian component but also a the product of ancient admixture between West Eurasian back-migrants and Native Tropical Africans. Why?

      1. The component takes long to show up (only since K=10) and earlier it appears divided between the West African and the Arab component.

      2. The Fst values are almost exactly equidistant between West Eurasian (incl. most North African) components and Tropical African ones.

      So IMO this Ethiopian or East Africa 2 component is the homogenized product of an ancient admixture, surely dating to the Paleolithic.

      So in the end the dynamics has not really changed: it is with all likelihood the same component I detected in my little North African exercise, just that somewhat aggrandized in its influence because of a different focus in the analysis.

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    3. EtyopisJune 22, 2012 at 11:18 AM

      "Maybe you just run one single pan-African comparison and then cut up the graph by regions?"
      Exactly that is what I did, both V1 and V2 are Just 1 Pan-African run each @ K=10, both UNSUPERVISED, there is a clear distinction in the ADMIXTURE software for running supervised or Unsupervised runs, I chose the latter, No Zombie populations were involved, the regional graphs are strictly and only for ease of visualization. of the results. Any body can try the experiment on their own,
      I have already put up the link to the original Africa dataset (V1) here: http://ethiohelix.blogspot.com/p/public-data-sets.html

      All, one has to do is incorporate the data from Pagani, which you can find here: http://mega.bioanth.cam.ac.uk/data/Ethiopia/

      Then, when merging you have to flip the strands of about 8,000 SNPs or so otherwise it won't work.....

      I will respond to your other comments a little later...

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    4. MajuJune 22, 2012 at 1:40 PM

      "Then, when merging you have to flip the strands of about 8,000 SNPs or so otherwise it won't work....."

      Easily said... I can manage the 1000 genomes dataset but no idea beyond that.

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    5. EtyopisJune 22, 2012 at 2:06 PM

      Maju, when you first try to merge them WITHOUT flipping, PLINK gives you an error, but it also gives you a file with a list of the SNPs that are causing the problem, what you then need to do is take that file and save it as a .txt file, then run this command on the old dataset, i.e the one that you want to merge:
      plink --bfile Africa_Rev4_public --flip Africa_Rev6.txt --recode --make-bed --out Africa_Rev4_public_flipped

      what this command will do is take the file from the original, called "Africa_Rev4_public", flip the SNPs from the list that you saved as .txt file, called "Africa_Rev6.txt", and make a new .bed file called "Africa_Rev4_public_flipped". With this new file you will be able to merge with the Pagani set after you extract the common SNPs from there as they have over a million SNPs....

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    6. MajuJune 22, 2012 at 2:13 PM

      I really appreciate your help Etyopis but it really gets over my head. I need a windowed tutorial to be able to use almost any software. I'll leave the complications to the younger generation (or at least the ones who have a young mentality, eager to climb over the obstacles and learn in the process, as you do).

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    7. EtyopisJune 22, 2012 at 10:25 PM

      I have updated for K2-K10 run....

      Delete
  3. AnonymousJune 22, 2012 at 10:02 AM

    It looks like the authors of the study mistyped the identities of the individuals identified as being Afar. According to Table S1. Sample Size, Location, and Sociological Features of the Genotyped Populations in the supplementary data, these "Afars" speak an Agaw language, i.e. Xamtanga, and they're located in the Wag Herma zone in northern Amhara; they're are also referred to as highlander agriculturists.

    http://download.cell.com/AJHG/mmcs/journals/0002-9297/PIIS0002929712002716.mmc1.pdf
    http://en.wikipedia.org/wiki/Xamtanga_language
    http://en.wikipedia.org/wiki/Wag_Hemra_Zone

    I'm assuming that we didn't get any true Afar samples in this new study; but nevertheless, non-Beta Israel Agaw samples who are much more closer to the Afro-Semitic references, i.e. Amhara and Tigray, than the former.

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    1. EtyopisJune 22, 2012 at 10:33 AM

      Thanks for the information, I will look into it. It seems odd that the researchers (of which a couple are Ethiopian) would confuse Afars with agews from wag (the traditional place of the Wag-shum, heirs of the Zagwe Dynasty), this is not something even a lay Ethiopian would confuse, but like I said I'll look into it.

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    2. EtyopisJune 23, 2012 at 9:53 AM

      Looking at that table if it was indeed Agews from wag instead of the Afar they sampled, then the elevation listed would also be wrong, the elevation listed is more indicative of lowland areas, like where the Afar live and not where Wag or Lasta is , which is well in the Ethiopian highlands. I think it really was the Afar that were sampled, just a typo in some of the labelling like location, subsistence and language, or they could have physically sampled some Afars that were in wag but incorrectly listed their sampling locations instead of where the Afar are traditionally found.

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    3. AnonymousJune 24, 2012 at 10:19 PM

      idk These "Afar" samples are practically identical to other northern highlander ethnicities like the Amhara, Beta Israel, and Tigray. Surprising given their cultural and linguistic affinities, not to mention location; I find it very unlikley that the Afar, being lowland Cushites, are more similiar, if not identical, to Habeshas than they are to more closely related groups like the Somali who they happen to share a country with, i.e. Dijibouti.

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    4. MajuJune 25, 2012 at 8:26 AM

      @Anon: Djibuti is an artificial modern, post-colonial, state, which does not mean anything in ethnic or historical terms. Geographically, the Afar country is to the West of the Rift and bordering the Amhara and Tigray countries. It may be a peculiar lowland area but I doubt that lowland-highland distinction alone is so important.

      Anyhow Somalis are not that different from Afar or other Horner peoples, which are essentially (at K=10) a base of East Africa 2 with some Nilotic (and in some cases other stuff, notably North or West Africa affinity, although I bet the North Africa component hides an Arabian affinity instead).

      It's also very possible that Somalis from different areas have somewhat different compositions. It's surely not the same a Somali from Mogadishu than one from Somaliland, etc. Maybe Somalis from the Gulf of Aden area are also closer to the Amhara-Tigray, as well as to Arabs (not obvious but probably hidden in the North Africa affinity component).

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    5. EtyopisJune 25, 2012 at 9:34 AM

      Depends how you look at it, on a global level, K=14, (which I haven't published a post on), most of the Afroasiatic East Africans including the Somalis but excepting the omotics are quite similar, with about the same (+/-10%) composition of Nilotic/Omotic + South West Asian + North West African components. The South West Asian, although peaking in the inbred Bedouins, is likely a hybridized cluster of OOA +African Upper-Palaeolithic + S.West-Asian Neolithic, while the North West African is likely a hybridized cluster of European Palaeolithic + African + South West Asian.
      On an African level, as you can see in the current post, the Afar have slightly more East African2 and NiloSaharan than the highlanders, not by much, while the Somalis on top of having the highest East African2, also have more Nilo Saharan and West African than everyone else including the Wolayta and other Omotics (Perhaps a sign of Somali Bantu Introgression ??). Also, Afar/Saho is thought to be Linguistically 'ancestral' or diverged earliest from all other Lowland East Cushitic languages, and thought as one of the trifurcation components of Eastern Cushitic (the other components being Highland East Cushitic and Mogogodo/Tsamai languages)
      I will update this post with my 3D intra African MDS soon.....

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    6. AnonymousJune 25, 2012 at 10:10 PM

      @ Maju

      There are about twenty some Somali individuals from 23andme being circulated among the various active amateur bloggers interested in further comprehending the genetic affinities of NE Africans and Africans in general, inshallah, and they indicate a fairly straightforward story. These individuals are from an array of different locales throughout East Africa, i.e. from Djibouti to inner Ethiopia to eastern Ethiopia to Kenya, and all of the individuals have been extremely homogeneous so far.

      The highlander vs. lowlander distinction in NE Africa likely played a fundamental role in the sub-structure, in relation to Eurasian admixture, in the region. The relatively "recent" introduction of Yemeni-like gene-flow into NE Africa was likely stimulated by the agricultural potential in the highlands, something that wasn't the case in the arid and desert-like lowlands surrounding the northern highlands. So far, all sampled lowland groups, for example the Borana Oromo and Somali, have been notably divergent in relation to Beja, Agaw, and Afro-Semitic speaking populations in the Eastern Sudan, Eritrea, Tigray, Amhara, and northern Oromia.

      edit: According to this aforementioned study, the Somali samples are from Somaliland in northernmost Somalia. In addition, the Ethiopian Somali seem to be from the general Hararge region of Oromia, Ethiopia which borders the Afar region to the immediate south.

      At the end of the day, the fact that these "Afar" samples are listed as Xamtanga (Agaw) speaking, agricultural highlanders from the Wag Herma zone in northern Amhara, in addition to clustering in the same vicinity as other highlanders indicates that they are not Afar.

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    7. jes-rJune 26, 2012 at 12:16 AM

      @Etyopis
      ''On an African level, as you can see in the current post, the Afar have slightly more East African2 and NiloSaharan than the highlanders, not by much, while the Somalis on top of having the highest East African2, also have more Nilo Saharan and West African than everyone else including the Wolayta and other Omotics (Perhaps a sign of Somali Bantu Introgression ??).''

      You must be playing really stupid if you think that's the case. It's obvious that some of your clusters are unstable due to the fact that you did not prune for relatives. Also, if you play close attention to your own run the so-called ''Eastern Bantu'' cluster is not present in most Somalis. So before you claim any nonsense like this at least think critically.

      Also, here is a global run I did on the same Pagani data-set, including some Somali fiends from various backgrounds (both from the South and North), and the vast majority of Somalis have at higher K levels no West African whatsoever, while it is still very much present in Bantu East Africans and Nilotic Sudanese. Clearly indicating that Bantu ancestry is not present in most ethnic Somalis. See the spreadsheet below:

      https://docs.google.com/spreadsheet/ccc?key=0AqWOT2m6btAGdEpjTExTRG1NU1NKRnJfd3hOeWkwdkE#gid=8

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    8. jes-rJune 26, 2012 at 12:23 AM

      @Anonymous

      ''edit: According to this aforementioned study, the Somali samples are from Somaliland in northernmost Somalia. In addition, the Ethiopian Somali seem to be from the general Hararge region of Oromia, Ethiopia which borders the Afar region to the immediate south''

      Actually they are a random group of immigrants living in Pakistan per the study, they weren't sampled inside Somalia. I doubt they are from the same place, given the fact that none of them is closely related or shares significant IBD.

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    9. jes-rJune 26, 2012 at 12:32 AM

      @Maju,

      ''It's also very possible that Somalis from different areas have somewhat different compositions. It's surely not the same a Somali from Mogadishu than one from Somaliland, etc. Maybe Somalis from the Gulf of Aden area are also closer to the Amhara-Tigray, as well as to Arabs (not obvious but probably hidden in the North Africa affinity component).''

      No, not really, you shouldn't just assume things. They are basically the same. I have Somali friends from Southern regions who took a 23andMe test and they are basically identical to Northern Somalis. There is no ancestry difference them. There is no Arab ancestry whatsoever in Northern Somalis, which some people seem to sometimes incorrectly assume. Northern Somalis are actually ethnically a branch/sub-set of Southern Somalis who took up camel pastorlism about 2,000 years ago.

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    10. MajuJune 26, 2012 at 7:48 AM

      @Eze and Anon.: I take notice of your surely best informed comments and stand corrected. Thanks for the feedback.

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    11. EtyopisJune 26, 2012 at 10:28 AM

      @Eze
      "You must be playing really stupid if you think that's the case. It's obvious that some of your clusters are unstable due to the fact that you did not prune for relatives."
      Not sure what exactly you mean by unstable, but I have run the dataset several times and get the same results, I have also run it with cross validation, anybody can rerun this data as I have already posted the input files like I explained to Maju earlier. All the new Afroasiatic East Africans sampled from Pagani in my run (including both Omotics) have an average of 0.31% West African Cluster and 13.05% Nilotic, While the Ethiopian Somalis have 4.44% West African and 21.38% Nilotic, and the other Somalis have 3.46% West African and 22.81% Nilotic. So there is obviously higher affinity, which can not be simply explained by geography since Somalis are the Eastern most African Afroasiatics and all the remaining AA samples are geographically in between them and Nilotes, I simply proposed a possibility for this higher affinity relative to the other East Africans, as you recall also the L3 mtDNA Somali study from Soares earlier this year also had a handful of L3e samples in the Somali data.
      As far as the Eastern Bantu cluster missing in the Somali, yes, I did notice that, but the bantu Kenyans and the Luhya also had the West African as well as the Nilotic cluster in fairly significant amounts, in addition to the fact that the Eastern Bantu cluster is relatively close to the aforementioned clusters in terms of FST, thus making them more prone for probabilistic allele assignment confusion with each other.
      Like I said, it is just a possibility.........

      @ Anon:
      The Afar samples will be considered as Afar and nothing else unless you bring concrete proof from the publishers themselves that they indeed are not Afar.

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    12. jes-rJune 26, 2012 at 12:00 PM

      @Etyopis,

      It's not a possibility at all. There are several clues which completely refute that.

      Regarding that Soares study, they clearly included some actual minority groups and not only ethnic Somalis (there were some odd recent Eurasian lineages present as well). Just like in Ethiopia, not everyone is ethnically the same in Somalia. So it's useless to bring it up. However, we are dealing with homogeneous ethnic Somali Somalian samples in Pagani's study.

      Secondly, look at K7 of my run here:

      https://docs.google.com/spreadsheet/ccc?key=0AqWOT2m6btAGdEpjTExTRG1NU1NKRnJfd3hOeWkwdkE#gid=5

      The Somalia Somali samples in here get on average get 0% 'Omotic', 54% 'Nilo-Saharan', 0% 'West African', 46% 'Arabian/Red Sea'.

      If you look at the same sheet, Luhya Bantus and Nilotic Sudanese still have a high fractions of West African ancestry, while it's not present in Somalis.

      Clearly we are dealing with something very ancient that simply can't be explained by recent Bantu or Nilotic slavery. Also, if you know anything about Somali history you should know that slavery was only a fairly recent event (instigated by Arab/Portuguese merchants) which can't have affected the main nomadic ethnic Somali population who didn't participate in it. The fact that these Somalian samples show an equal distribution of these clusters also goes completely against such crazy ideas. A population affected by recent slavery would behave like those Yemeni Arab samples from Behar who behave very heterogeneous, this is not the case with these homogeneous Somalian samples.

      What is very clearly is that Somalis from Somalia lack a hunter-gatherer affinity that's present in Omotic people. This is also clearly visible in your PCA plots.

      What possibly could explain this is that the original Cushites were an Upper Egyptian or North Sudanese-like population with both Nilo-Saharan and North African genetic affinities that entered the Horn. The Cushites who entered the highlands encountered Omotic people and mixed with them, while those who entered the semi-arid lowlands probably didn't encounter Omotic people and hence the lack of Omotic and/or significant hunter-gather ancestry in most present-day eastern lowlanders. Considering that the Cushitic ethnogenesis has been placed in North Sudan by some this could very will be true.

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    13. AnonymousJune 26, 2012 at 12:03 PM

      Yes! Xamtanga/Agaw speaking Afars from Weg Herma zone, Amhara who somehow abandoned their nomadic way of life and took up farming in the northern highlands. lol Some of us are attempting to contact the authors for further clarrification.

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    14. EtyopisJune 26, 2012 at 1:04 PM

      @ EZE,
      I am not discounting your theory but I just processed your data @K7, The ESomalis(17) had the 'West African' on Median at 0.00% while the Somalis(23) had it at 0.00%, my Global K7 run however begs to differ, the Esomalis(17) had the West African or Cluster6 at 7.35%, while the Somalis(23) had it at 7.16%, again higher than the other Pagani East African AA samples average. My global dataset had a lot more entries from around the world too (184, N=2967), versus yours (59, N=852), the global cluster break down was also very different, Omotic and Nilo-Saharan have not broken up and they don't break up even at K14, and there was no Arab cluster but rather a West Asian cluster that peaked in the Basques and Sardinians, In addition there was a papuan/SouthAsian cluster as well as a San/Pygmy one. My K7 Global results are available here .

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    15. jes-rJune 26, 2012 at 1:44 PM

      Etyopis,

      Well, my run was focused primarily on Africa and West Eurasia and I also used ~160,000 SNPs (99% call rate, --geno 0.01 and --indep-pairwise 50 5 0.3) instead of the ~26,000 SNPs you used.

      Also, as I said before there is something wrong with your clusters because you still haven't pruned out those Aari, Hadza, Maasai relatives (siblings and first cousins!) out. Since Ethiopians have Omotic ancestry this would work in favor of Ethiopians and pushing alleles of non-Omotic mixed Somalis into other clusters. So prune out those relatives, get an Omotic and Nilo-Saharan cluster in an intra-African or intra-Africa-West Eurasia run, and then compare your results to mine. It should be roughly the same.

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    16. EtyopisJune 26, 2012 at 2:09 PM

      Eze,
      I am not going to cherry pick samples, if it is an African run, then all continental African populations I have available will be included, within reason off-course, like the well acknowledged and obvious inbred Tunisian and Moroccan jew samples were discarded, likewise if it is a global run then ALL global populations I have available will be included, I am trying to get a full picture of population structure on an African and Global level and not tidbits here and there, the density of your SNPs were definitely larger than mine, I'll give you that, but so did the run included in the Pagani study have higher density SNPs, yet my results just as there's shows a slightly higher level of Nilotic and West African in the Somali samples than the remaining E. African AA samples, starting from K4 and up for West African and from K6 and up for Nilotic.

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    17. jes-rJune 26, 2012 at 2:47 PM

      Who said anything about cherry picking samples? All I said is to remove samples with IBD/PI_HAT > 0.125, which is basically step 1 when one performs an admix/structure run (you basically keep forgetting this).. Anyhow, with a few distinct non-inbred East African clusters the Pagani Somalia samples show no Bantu ancestry at all, which is basically what this whole argument started about.

      What possibly could explain those patterns you notice is either 1) A very old but minor Nilo-Saharan-Cushitic admixture event which affected the proto-South Lowland E. Cushitic group when they expanded southwards thousands of years ago. OR.. 2) A higher retention of Nilo-Saharan/Egyptian related ancestry from the original Cushitic expansion from North Sudan into the Horn. In the Ethiopian highlands this was lowered by both Omotic/hunter-gather and by a second wave of North African or Southwest Asian admixture. This to me does not seem like a far-fetched idea, but quite possible.

      Delete
  4. LankJune 22, 2012 at 12:26 PM

    Why do the Behar et al. Amhara and Tigray have less East-Africa1, along with more East-Africa2 and North-African than the new Amhara and Tigray samples? The East-Africa1 component is higher in all of the Behar samples (Jews and Oromos as well) than the Pagani samples.

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    1. EtyopisJune 22, 2012 at 12:45 PM

      Yeah you are right, although the differences are about ~5% ,Here are more exact percentages, the populations to the right are the peaking populations of each cluster
      Entry = EtA
      UniquePop # 6 / 57
      N = 7
      K = 10

      Means

      Cluster3 43.91% Somali
      Cluster10 25.82% mozabite
      Cluster9 14.72% South-Sudan
      Cluster4 6.73% maasai
      Cluster7 3.93% ARI-B
      Cluster1 2.30% hadza
      Cluster6 1.03% luhya
      Total 100.00

      Medians

      Cluster3 42.79% Somali
      Cluster10 26.62% mozabite
      Cluster9 14.20% South-Sudan
      Cluster4 6.11% maasai
      Cluster7 4.20% ARI-B
      Cluster1 1.86% hadza
      Total 96.54
      Closest Population EtT

      Entry = EtA-P
      UniquePop # 7 / 57
      N = 26
      K = 10

      Means

      Cluster3 52.81% Somali
      Cluster10 19.38% mozabite
      Cluster9 13.30% South-Sudan
      Cluster7 6.45% ARI-B
      Cluster4 2.68% maasai
      Cluster1 1.72% hadza
      Cluster8 1.21% san-nb
      Cluster2 1.04% dogon
      Total 100.00

      Medians

      Cluster3 52.46% Somali
      Cluster10 19.53% mozabite
      Cluster9 13.35% South-Sudan
      Cluster7 5.88% ARI-B
      Cluster4 3.10% maasai
      Cluster1 1.80% hadza
      Total 97.46
      Closest Population EtT-P

      Entry = EtT
      UniquePop # 11 / 57
      N = 5
      K = 10

      Means

      Cluster3 45.89% Somali
      Cluster10 25.09% mozabite
      Cluster9 14.40% South-Sudan
      Cluster4 5.72% maasai
      Cluster7 2.52% ARI-B
      Cluster6 2.44% luhya
      Cluster2 1.57% dogon
      Cluster1 1.29% hadza
      Total 100.00

      Medians

      Cluster3 45.22% Somali
      Cluster10 25.23% mozabite
      Cluster9 13.45% South-Sudan
      Cluster4 5.54% maasai
      Cluster6 2.76% luhya
      Cluster7 2.49% ARI-B
      Cluster1 1.52% hadza
      Cluster8 1.16% san-nb
      Total 97.38
      Closest Population EtA

      Entry = EtT-P
      UniquePop # 12 / 57
      N = 21
      K = 10

      Means

      Cluster3 53.93% Somali
      Cluster10 21.06% mozabite
      Cluster9 12.72% South-Sudan
      Cluster7 5.07% ARI-B
      Cluster4 1.87% maasai
      Cluster2 1.67% dogon
      Cluster6 1.13% luhya
      Total 100.00

      Medians

      Cluster3 54.23% Somali
      Cluster10 21.69% mozabite
      Cluster9 12.90% South-Sudan
      Cluster7 4.74% ARI-B
      Cluster4 1.26% maasai
      Total 97.50
      Closest Population EtA-P

      contd....

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    2. EtyopisJune 22, 2012 at 12:47 PM

      Entry = EtO
      UniquePop # 8 / 57
      N = 7
      K = 10

      Means

      Cluster3 41.12% Somali
      Cluster9 24.63% South-Sudan
      Cluster10 10.76% mozabite
      Cluster4 9.35% maasai
      Cluster7 4.42% ARI-B
      Cluster6 2.73% luhya
      Cluster1 2.69% hadza
      Cluster2 1.71% dogon
      Cluster8 1.62% san-nb
      Total 100.00

      Medians

      Cluster3 41.65% Somali
      Cluster9 26.84% South-Sudan
      Cluster4 9.84% maasai
      Cluster10 9.64% mozabite
      Cluster7 3.80% ARI-B
      Cluster6 3.35% luhya
      Cluster1 2.78% hadza
      Cluster8 1.85% san-nb
      Cluster2 1.60% dogon
      Total 101.64
      Closest Population EtO-P

      Entry = EtO-P
      UniquePop # 9 / 57
      N = 21
      K = 10

      Means

      Cluster3 45.78% Somali
      Cluster9 17.36% South-Sudan
      Cluster10 15.15% mozabite
      Cluster7 11.65% ARI-B
      Cluster4 3.38% maasai
      Cluster5 1.75% pygmy
      Cluster1 1.69% hadza
      Cluster8 1.50% san-nb
      Cluster2 1.08% dogon
      Total 100.00

      Medians

      Cluster3 47.19% Somali
      Cluster9 17.52% South-Sudan
      Cluster10 15.23% mozabite
      Cluster7 11.99% ARI-B
      Cluster4 2.25% maasai
      Cluster1 1.66% hadza
      Cluster5 1.63% pygmy
      Cluster8 1.15% san-nb
      Total 98.91
      Closest Population EtA-P

      My suspicion is that it has to do with the intersection of the old (my V1 dataset) SNPs with the Pagini data, as I noted in my post the resulting dataset incurred a slight loss (~7%) in the genotyping rate....

      Delete
  5. MarnieJune 23, 2012 at 12:32 AM

    Interesting. Having had a quick look at the Pagini paper, its focus is Ethiopians. Outside Ethiopia, it heavily samples the Maasai and a few other Nilotic speakers. Other Nilo-Saharan speakers of the Sahel are not sampled, so I think that may throw off an ADMIXTURE run.

    In any case, your ADMIXTURE run does show that the Maasai are a eclectic group. Tishkoff indicates that in her papers as well. Interestinly, your ADMIXTURE run also shows that the Gumuz, who linguistic evidence indicates speak a very early form of Nilo-Saharan (Ehret), do show up as being mostly Nilo-Saharan (Nilotic).

    It be good if there were a few more Afroasiatic samples. The Beja are obvious in their absence. (They are in Tishkoff.)

    ReplyDelete
    Replies
    1. EtyopisJune 23, 2012 at 9:58 AM

      I also took a look at their model based analysis, in essence the difference between this run and theirs are in (a) SNP density (theirs was much higher) and (b) populations sampled, I believe this run had more populations included in it, the software they used off-course was ADMIXTURE, same as here. In terms of populations in their dataset, the only one I do not have included here are the French, other than that, this dataset actually had more Central Africans, including the Bulala, fang, hema... ; more Southern Africans, including the Pedi, Nguni and Xhosa; more West Africans, including the Dogon, Fulani, Hausa, Bambaran.... and more North Africans, including the Libyans, Algerians and Various Moorrocans.

      That said, there was congruency in population structure and the progression of the K variable between this run and theirs, however, the congruency breaks down at K=6 and on, if you notice on their run the Pygmies first split off at K=5, but then at K=6 the pygmies do not form their own cluster and instead the omotics and Hadza create their own cluster, however in my run the pygmies still maintain their cluster at K=6 while the Hadza emerge with a new cluster as well and Omotics do not get their own cluster till K=7, so from here on (i.e. K=6) we start getting different components (some what to an extent), including the fact that in their run the Lhuya and Bantu Kenyans do not get their own cluster, which I named 'Eastern Bantu', and off-course my run goes up to K10, while theirs stops at K9, I still have room for a couple of clusters according to the CV error values generated by ADMIXTURE for my dataset.

      As far as the cluster naming Nilo Sahran vs. Nilotic, although model-based cluster names are fluid and not set in stone, yes I agree Nilo Saharan may have been more appropriate.

      Delete
  6. MarnieJune 23, 2012 at 12:47 AM

    Looking again at your ADMIXTURE chart for East Africa, I believe Nilotic should be renamed Nilo-Saharan.

    ReplyDelete
  7. jes-rJune 25, 2012 at 8:22 AM

    Overall an interesting admix run, although it looks like you haven't pruned for relatives (PLINK IBD/PI_HAT > 0.125), which is a must in order to get more stable clusters. A large portion of the Blacksmith Ari, Hadza, and Maasai are siblings and/or first cousins.

    ReplyDelete
    Replies
    1. EtyopisJune 25, 2012 at 10:52 AM

      True, I have not run IBD neither on this Dataset or the previous one (V1), however, I get the same general cluster progression as the authors do, Like I explained earlier to Marnie, however, they, i.e. Pagani 2012 did do some IBD pruning on their dataset, so I am not sure it would make a big difference.

      Delete
    2. jes-rJune 25, 2012 at 11:24 AM

      I don't think Pagani 2012 did any IBD pruning in their structure data set, because from the chart it includes many Hadza, Maasai, and Blacksmith Ari, who otherwise wouldn't make it with an IBD/PI_HAT > 0.125 criteria. You can test it out yourself, if you do it correctly you should end up with only few/handful of them. Ari cultivators are mostly outbred though.

      Delete
    3. EtyopisJune 25, 2012 at 11:50 AM

      Read the Materials and Methods section of the study (if you have access to it):

      “The merged data set was pruned to remove SNPs in high LD (r2 > 0.1), and ADMIXTURE analyses were run as described33 after removal of samples showing high relatedness (PLINK identity-by-descent score >= 0.125) with any other sample in the same population (1 Amhara, 2 Ari Cultivators, 6 Ari Blacksmiths, 3 South Sudanese, and 1 Gumuz).34 Cross vali-dation was used to estimate the optimum number of clusters (K).”

      They even have the 13 individuals they removed labeled in their .fam file, (even though I did not take them out for my run):

      ARIBLACKSMITH13IBD ARIBLACKSMITH13IBD
      ARIBLACKSMITH14IBD ARIBLACKSMITH14IBD
      ARIBLACKSMITH15IBD ARIBLACKSMITH15IBD
      ARIBLACKSMITH16IBD ARIBLACKSMITH16IBD
      ARIBLACKSMITH18IBD ARIBLACKSMITH18IBD
      ARIBLACKSMITH17IBD ARIBLACKSMITH17IBD
      ARICULTIVATOR23IBD ARICULTIVATOR23IBD
      ARICULTIVATOR24IBD ARICULTIVATOR24IBD
      GUMUZ20IBD GUMUZ20IBD
      SUDANESE22IBD SUDANESE22IBD
      SUDANESE24IBD SUDANESE24IBD
      SUDANESE23IBD SUDANESE23IBD
      AMHARA26IBD AMHARA26IBD

      Delete
    4. jes-rJune 25, 2012 at 12:56 PM

      Using plink IBD >= 0.125 I am only left with 5 Hadza and 7 Blacksmith Ari. However, if I look at the admix chart in the study, I count 17 Blacksmith Ari and 16 Hadza, which is basically all of them. Despite what they have said in the Material and Methods section they did not actually perform this simple task.

      Delete
  8. jes-rJune 25, 2012 at 10:24 PM

    By the way, what's up with 'Omotic' in the Biaka, it doesn't make any sense.

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    Replies
    1. EtyopisJune 26, 2012 at 12:06 AM

      Yes, that is one of the major conundrums of this run I have been trying to reason with.
      If you notice in my previous run the Biaka and Mbuti pygmies had made completely independent clusters, then, with the addition of the Nilotic and Omotic samples, only the Mbuti Pygmies retained the cluster. However, if you look at the MDS plots (particularly C1-C2) that I posted earlier today you can see a clear distinction between Mbuti and Biaka Pygmies, the biaka pygmies seem less 'Hunter Gatherer' like and pull towards the remaining Africans on C2, hence when the Omotics were added into the mix and they occupy almost the same position on the vertical (C2) axis as the Biaka pygmies, the uniqueness of the Biaka Pygmies is blurred. So in the ADMIXTURE run, the biaka pygmies are composed in almost equal proportions of Omotic, Eastern Bantu and Pygmy with a bit of SAN, this kind of make sense in relation to where they are on the PCA plots. The Eastern Bantu cluster is also different from my V1 run too, I believe it has more indigenous rift valley and other ancient elements as it is wide spread throughout Africa.
      So basically, right now I am inclined to think that Omotics may have some type of deep rooting HG ancestry with pygmies in Eastern Africa, the mbuti Pygmies became Isolated and Biaka pygmies picked up some other African elements, but perhaps the addition of other diverse samples in Africa may yet again change this....

      Delete
    2. EtyopisJune 27, 2012 at 12:36 AM

      By the way, I actually got the Biaka Pygmy cluster back and lost the Eastern Bantu cluster, I homogenized the Intra-African dataset using my studentization method, removed all samples that had studentize >2 for any cluster from the previous run, this took out 405 samples from across the dataset leaving me with 895 . The standard deviations also dropped across clusters and samples by >50%!.

      The interesting thing with this new run is that the East African2 cluster is so close to the North African cluster that the Egyptians are now almost exactly 50/50. East Africa2 also peaks almost simultaneously in the Afar and Somali, instead of just the Somali. The North Africa cluster peaks in Northwest Africa (with the Mozabites) at 89% and declines in North East Africa (Egypt) to about 50%, and in Northern Ethiopia to about 17%.

      The other interesting thing also is that the Wolayta are 42.4% Omotic, which makes much more sense, and the results (at least at K10) look more similar to the publication than my first run did, last time (V1) my studentization method did not work so well and did not have an impact on the run, but this time it really did its job removing outliers and homogenizing populations, you can check out the full results here.

      Delete
    3. jes-rJune 27, 2012 at 11:54 AM

      Results look more stable now, only thing that's still odd is 'East Africa 2', which looks like a small IBD-caused cluster.

      Delete
    4. MajuJune 27, 2012 at 1:47 PM

      @Eze: "East Africa 2" or "East Africa 1"?

      The small cluster is EA1 actually (deep purple).

      IMO EA2 (orange) is the product of ancient WEA-EAf admixture (based on what I have seen elsewhere, explained in a previous comment), so maybe EA1 exists "to compensate", so to say, as a still non-admixed/non-homogenized aboriginal affinity zone. In the end it's all a matter of affinity, not "true divisions".

      Delete
    5. jes-rJune 27, 2012 at 1:52 PM

      Oops, meant to say 'East Africa 1'.

      Delete
  9. EtyopisJune 27, 2012 at 11:31 AM

    Updated for K10 run with a newer outlier removed dataset.

    ReplyDelete
  10. LankJune 27, 2012 at 12:00 PM

    Interesting new results. However, I think when you have clusters that are obviously Eurasian-influenced (East-Africa2 and North-Africa), it's important to use Eurasian references. That would make it more believable that they may actually represent real ancestral populations.

    ReplyDelete
  11. MarnieJune 28, 2012 at 3:04 AM

    Have you had a look at Tishkoff?
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2947357/

    If you look at Figure 4 in this paper:
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2947357/figure/F4/

    you can start to compare the components you are getting with the components generated in the Tishkoff paper. One of the important things that was done in that paper was that extensive Eurasian datasets were included.

    The "components" that appear in Tishkoffs African populations are:

    Niger-Kordofanian component
    Nilo-Saharan component
    Afroasiatic component
    Ouldeme component (Cameroon)
    Baka component
    Khoesan/Mbuti component
    Hadza component
    Sandawe component
    Dogon component (West Africa)
    Fulani/Indian component
    Middle East component
    European component

    Tishkoff didn't pick up an Omotic or Cushitic component because she didn't have enough samples from those populations. Your "East Africa 2" is probably a Cushitic component. However, to get a better idea, I agree with "Lank" that you need more samples from Eurasia.

    With the exception of the the Cushitic and Omotic components appearing, your data appears to replicate the work of the Tishkoff paper. (A minor note is that due to her more extensive sampling, she's picked up more substructure in a few populations like the Dogon and Fulani, which don't appear in your runs.)

    ReplyDelete
  12. EtyopisJune 28, 2012 at 10:06 AM

    Appending this new data from Pagani to a global data set does not show much of a difference in African structure than without the addition of the Pagani dataset, even going all the way up to K14 . The Nilotic and Omotic components do not split as they do when looking at it from an African level, the one difference on a global level is that where as before (appending Pagani) the East African component used to peak in the Maasai, now the East African or rather best named Nilo-Omotic, peaks with the Gumuz and ARI-Blacksmith. Other than that, Ethiopians and other East African Afro Asiatics appear to be largely composed of this Nilo-omotic and a South West Asian Cluster (which likely itself is a hybrid of OOA +African Paleolithic and South West Asian Neolithic), with an additional bit of a cluster that peaks in North West African. The reason I can not observe much substructure in Africa on a global level, could potentially be due to a general Eurasian-Bias of the SNPs used .

    With respect to Tishkoff 2009, a more apples to apples comparison with this run would be to compare it with the intra African STRUCTURE run, (Figure S13 supplemental material) , although, this would still not be an apples to apples comparison with this run as Tishkoff used Autosomal Microsatellites instead of SNPs, nevertheless in that figure;
    K2 – East and North Africans are differentiated from other Africans
    K3 – Hadza split
    K4 – Baka Pygmies split
    K5 -Nilo Saharans split (interesting that Afroasiatics have some Nilo Saharan here)
    K6 – North Africans split from AfroAsiatics
    K7 – Mbuti Split
    K8 – Sandawe Split
    K9 – Fulani Split
    K10 – Can't really tell from the Chart
    K11- Looks like a cluster forms centered around east African Cushitics

    Personally I think, that the East African1 cluster I keep getting has something to do with the Sandawe, but I can't prove it, yet.............

    ReplyDelete
  13. MarnieJune 28, 2012 at 12:56 PM

    As I was looking at your latest runs last night, I also thought that East Africa 1 had a Sandawe association. The Sandawe do get there own component at low K values in Tishkoff's runs. However, in your runs, East Africa 1 appears at low level and is quite widely distributed, so it would be a stretch to infer a Sandawe association with your data set.

    It's true that the Pagani data set doesn't extend the evidence for African substructure outside Ethiopia. Regarding Ethiopia, the Pagani data set shows substructure within Afroasiatic samples - Omotic, Cushitic, Semitic, North African.

    Regarding the "Omotic-Nilotic" component: Tishkoff notes that the Maasai are likely descended from both Nilotic and Afroasiatic groups. The archaelogical evidence strongly supports contact between Afroasiatic and Nilotic groups over the last 8,000 years. Therefore, although there is a long pattern of contact between these two groups, it it probably confusing to assign an Omotic-Nilotic component for the Maasai.

    If you could get samples for the Songhai or other Nilo-Saharan groups who moved early into West Africa, you might be able to tease out evidence that Afroasiatic - Nilo-Saharan contact has occured within the last eight thousand years, and more likely within the last six thousand years.

    There's some information on my blog about the separate but proximate economies of Afroasiatic and Nilo-Saharan speakers.
    (www.linearpopulationmodel.blogspot.com)

    I have to say that I think that you are doing a good job on this run. I've only recently started following your blog. I hope your next posts are as carefully constructed and well presented as this one.

    ReplyDelete
  14. jes-rJune 30, 2012 at 10:22 PM

    Etyopis,

    Could you try do some experiments with TreeMix on this new data? Perhaps you can find something interesting.

    ReplyDelete
    Replies
    1. EtyopisJuly 1, 2012 at 12:34 PM

      I had to unload R from my computer because it was using a conflicting library with that of the linear algebra library of the main computation software I use (Octave), in addition, due to the small size of memory I have on my machine, Treemix was not able to process the more voluminous global dataset I had, I therefore removed that as well. If you or anybody has Treemix and R loaded on your machine, I can prepare and upload the input files as well as the command line instructions I used in my previous Treemix analysis and you can run it on the new intra African dataset and see the differences (if there are any).

      Delete
    2. jes-rJuly 4, 2012 at 10:00 PM

      I'm currently traveling and kinda busy. I will look into it perhaps later on. Thanks for the info anyhow.

      Delete
  15. EtyopisJuly 19, 2012 at 1:50 PM

    Updated for different Eurasian proxy scenarios.....

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    Replies
    1. MajuJuly 19, 2012 at 3:36 PM

      Most interesting exercise, Etyopis. Thanks.

      I'd say it is clear that there is a West Eurasian influence in North Africa and to lesser extent The Horn. But that this one is difficult to quantify using only one proxy, probably for reasons like:

      · Various distinct sources of Eurasian backflow into Africa
      · Locally important specificities vanishing in some cases (for example the "North Africa" component disappears in the Palestinian comparison but not the others, what may be critical in interpretation - you might want to do a K=11 instead of a K=10, in order to attempt to retain the K=10 Africa-only distinctions).
      · Your call...

      In North Africa at least the Japanese component is a regular fraction (c. 25%) of the French component in the respective panels. This correlation is not retained in East Africa (dropping to c. 13%) probably again because some key African component vanished in one but not the other (checked: no "East Africa" component in the French comparison).

      You'd surely get a simpler comparison if using K=11 for the comparisons with Eurasians (but K=10 for Africa only).

      In any case I think that it can be deduced that:

      1. There is a clear West Eurasian flow into Northern Africa and The Horn. This is NOT generic ancestral (OoA) Eurasian affinity by some Africans because then the Japanese and French values would be similar and they are not even close.

      2. This can be quantified (tentatively and roughly) using the French comparison in North Africa (so the North African component is not eclipsed). The result could be:
      · Egypt (Delta): c. 56% [c. 60% in my own exercise with two distinct WEA comparisons]
      · Libya: c. 46% [c. 45% in my exercise]
      · Morocco-N: c. 36% [c. 30%]
      · Morocco-S: c. 16% [c. 6%]

      Another issue is that the North African component, by Fst looks as just another West Eurasian component and not just another African component. It should add but that's another story.

      I do not dare to estimate the apportion of West Eurasian influx in the Horn because in one case the East African component and in the other the East African one are hidden by the "compaction" effect. In my December exercise I got very low values (4%, all Arabian) but the North African component was important prior to the coalescence at K=10 of an Ethiopian-specific component (with Fst signal of being homogenized ancient admixture) and this North African component is of WEA affinity (by Fst distances, very clearly).

      But interesting anyhow in the sense that it really discards the OoA affinity hypothesis you suggested in previous discussions. It's really unlikely that something so old can be retained after bottlenecks and areal homogenizations (by means of normal "inbreeding" with your neighbors and drifting away from your geographically distant relatives).

      Delete
    2. EtyopisJuly 19, 2012 at 4:33 PM

      “But interesting anyhow in the sense that it really discards the OoA affinity hypothesis you suggested in previous discussions.”

      Not at all Maju, the problem with West Eurasians is that they have a distinct African Affinity on a global level as I have clearly demonstrated in my K2 Global run, they can not be assumed as a pure non-African proxy for Africans because they are already related with Africans, I.e they are not 'pure' from the start of the formation of the West Eurasian cluster @K3, this unwarranted notion of 'pure West Eurasians' is a residue of scientific racism that started a couple of hundred years ago, escalated during colonialism and later on found itself upheld in the Annals of Eugenics (now called the Annals of Human Genetics).

      Now, I have acknowledged on several occasions that migrations into Africa after OOA have occurred in several instances (Paleolithic, Neolithic and Historical) according to uni-parental markers (mtDNA U, H, N … YDNA J,R... and so-forth), however these migrations did not occur in a unidirectional manner, but rather bi-directional (YDNA E1b1b, Helicobacter pylori, Li & Durbin ….).

      Therefore, I still hold the opinion that these components are best viewed as being composed of layers of different events of human migrations, the primary one or the foundation of them all being Out of Africa.

      Delete
    3. MajuJuly 20, 2012 at 12:33 AM

      Your K=2 global run only detects East Asians and some very diverged "Paleo-Africans" (not really liking this word but I can't think of any better). All the rest appear as an hybrid artifact that is, in my opinion, meaningless. What Admixture says, very specially for the 50-50 populations, is "neither this nor that" - nothing else.

      So with Europeans it says: "not really East Asians but 75% chance of being East Asians and 25% of being African", and so on with the other populations.

      "Therefore, I still hold the opinion that these components are best viewed as being composed of layers of different events of human migrations, the primary one or the foundation of them all being Out of Africa."

      Not at all: autosomal genetic clusters are generated by inbreeding, this can be intense and recent or extense and ancient but only looking at the clusters you'll never discern one and the other. You need a multidimensional apporach looking at every angle (in autosomal data: diversity, Fst distances between components, etc. - but also to haploid data, which is most informative on its own right).

      Based on haploid DNA the primary division should be Khoisan and the rest, then Pygmy (and maybe some neighbors) and the rest, then West Africans and the Rest and only then Eurasians vs Africans. But that is not what you get when you apply Admixture because Admixture is not that smart after all and samples and other issues (like re-homogenization of ancient admixture... or recent intensive cousin marriage) also matter.

      There is indeed a small amount of African admixture in West Eurasians (and not East Asians) but (1) this one varies clinally (so you may want to use Scandinavians instead of Palestinians as proxy if you are concerned by that) and (2) it is small enough not to show up in most autosomal runs. It's something rather subtle, more obvious in haploid genetics in fact.

      In any case if these apparent levels of (West) Eurasian back-flow would be (in any large fraction) just significant of c. 100,000 years old ancestral affinity, we'd see that the French and Japanese bars would be identical or almost, instead it totally looks like the Japanese bar is nothing but a low quality for generic Eurasian backflow (i.e. a pale shadow of the real WEA backflow).

      I don't think you can detect autosomal affinity from that old between separated groups. For one simple reason: it is not discernible from generic human (H. sapiens) affinity. Based on haploid genetics, even Pygmies had surely not diverged much from the main population in East and Central Africa when the OoA happened, only Southern African Aboriginals (Khoisan) were probably distant enough to be noticeable but (1) later admixture would have smoothed that difference and (2) I'm not sure how we could design the relevant exercise.

      But in any case just my opinion.

      Delete
    4. EtyopisJuly 20, 2012 at 9:52 AM

      You can't have your cake and eat it too. The fact of the matter is that @ K=2 before the formation of the West Eurasian cluster, West Eurasians appear to be composites of a non-African and African component, then at K=3 they start belonging completely to a West Eurasian component, this component also happens to be intermediate between the East Asian and African components in terms of Fst, albeit slightly closer to the East Asian component.

      BTW, it was not only my run that shows a significant African component in West Eurasians at K=2 but also the STRUCTURE run of Behar (2010), matter of fact at K=2 in that run, West Eurasians belong almost completely to the African cluster, but in my humble opinion, the dataset I used has more global populations sampled including more Eurasians and Africans and is more accurate (though it has less SNPs).

      So like I said you can't have your cake and eat it too, if you want to use the West Eurasian signal generated from model-based algorithms as the source of non-African input in Africans, then you must also admit that the same West-Eurasian signal is formed from a synthesis of African and non-African inputs.

      Delete
    5. MajuJuly 20, 2012 at 12:30 PM

      I've always argued that such a misunderstanding of cluster analysis is useless and misleading. And that is why you in other cases apply that method, whose name I do not recall, to hint at which number of clusters is optimal, i.e. the most realistic representation of the analyzed samples. Typically is >10 (13 or so?) for a global sample. That is the real analysis.

      What do you think it would happen if we compare birds, mammals and lizards at K=2? That one of the three clusters would show up as intermediate (not sure which, depends on sample sizes and such), same with global population analysis.

      It's not "my" cake, it's "the" cake in any case.

      "this component also happens to be intermediate between the East Asian and African components in terms of Fst, albeit slightly closer to the East Asian component".

      Haven't checked intensively but that is exactly my point: the "normal" OoA Fst distance is c. 0.200, while major (East-West) intra-Eurasian distances are of the order of c. 0.150 and intra-West-Eurasian Fst values are between 0.060 and 0.110 (say an average of 0.85).

      IMO these distances represent roughly the successive divisions:

      1. c. 0.200 around Out of Africa time (c. 130-80 Ka ago)
      2. c. 0.150 around "Eurasian Expansion" time (c. 80-55 Ka. ago)
      3. c. 0.085 around Western Eurasian colonization time (c. 55-30 Ka ago)

      This should be much more accurate than your K-estimates, which are the wrong way of looking at the problem.

      [The main exception is when it totally looks like a component is product of homogenization after ancient admixture, as can happen when an Ethiopian or Fulani specific component coalesces (depending on samples and K level), eclipsing an African and Eurasian component by Fst values, with Fst values that are intermediate. In this case I think the best explanation is ancient homogenized admixture - unless you can suggest a better one - but in any case is a very localized interpretation problem].

      "the STRUCTURE run of Behar (2010), matter of fact at K=2 in that run, West Eurasians belong almost completely to the African cluster"

      Actually it is vice versa (and not 'almost' but 'totally'): Africans are undersampled and absorbed in the West Eurasian cluster. That's why there is no cline (because no African is closer to East Asians than to West Eurasians, while the opposite is true). Just that, confusingly the cluster is painted in brown (it should be blue but whatever).

      Check it all you want, Behar's "brown" K=2 cluster splits in two (brown and blue) at K=3 with no "border change". Your blue (African) cluster does not split in two like that: they represent different things: yours is really an African component (because your African sample is large), while Behar's is a West Eurasian one (and undersampled Africans are forced into it 100%).

      In other words K=2 is not good enough and will vary a lot depending on sampling strategies (try undersampling East Asians for example). Actually K=3 etc. are not very informative either (we need K>10, probably K>13 to be in the safe zone) but K=2 is ridiculously confusing to the extreme.

      "the same West-Eurasian signal is formed from a synthesis of African and non-African inputs".

      Apparently not, because even with undersampled West Eurasians (your latest trial with just a few French, for example), West Eurasians appear neatly distinct, just like Pygmies or Khoisan. Also the Fst distance to Africans is invariably very high, in the OoA levels (Fst>0.180 zone I mention above). It must be somewhat diluted but it is at very low levels, nothing too obvious.

      Delete
  16. AnonymousJuly 28, 2012 at 1:17 PM

    Minor-moderate Western Eurasian gene-flow into the Horn of Africa is evident and from the looks of it ADMIXTURE k=10 (Africa V2b + French) seems to be the most informative. We can logically assume that the French cluster acts as a reliable proxy for legitimate West Eurasian ancestry in North Africa/NE Africa regardless of the probability that the French cluster itself contains traces of ancient African gene-flow. Nevertheless the North African cluster seems to act as a signature for complex bidirectional Afro-Eurasian gene-flow, either be it in North Africa, NE Africa, or Western Eurasia.

    The Japanese run is also very interesting, although the North African cluster in this case is much more African than in previous runs; likely indicating the exclusivity of the Japanese cluster in comparison to the French in terms of "Eurasianess".

    I personally think it's safe to assume that Highlander NE Africans, i.e. groups like the Tigray, Amhara, and Beta Israel, are approximately around ~30% Western Eurasian, in contrast to lowlanders at about ~15% Eurasian. In addition, coastal North Africans like the Mozabite seem to be somewhere around 1/3rd African. This would mirror the results documented in Tishkoff et al. 2009 and imho seems to be the most probable and realistic scenario.

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    Replies
    1. EtyopisJuly 30, 2012 at 12:13 PM

      "We can logically assume that the French cluster acts as a reliable proxy for legitimate West Eurasian ancestry in North Africa/NE Africa regardless of the probability that the French cluster itself contains traces of ancient African gene-flow."

      What kind of 'logic' is that? Paradoxical logic? LOL!

      Delete
    2. EtyopisJuly 30, 2012 at 12:26 PM

      And by the way, the French had more than 'Traces of African Gene-flow' in my K2 global Analysis at 29% African.

      Delete
    3. MajuJuly 30, 2012 at 12:47 PM

      Your K2 analysis is pointless. It would be useful ONLY if you'd measured admixture between two well defined groups, anything else it's just effect of forcing third, fourth, fifth, etc. groups into an A or B false dichotomy.

      Incidentally I was thinking of you when I discussed recently Khoisan autosomal genetics (on Pickrell 2012, open access).

      Why? Parltly because you have been stubbornly adamant of misreading the usual L-shaped global PCA (with the usual sampling strategy), a misreading that is essentially the same you are doing here with your K=2 discourse. But all that, I insist, depends on sampling strategies largely, so for Behar 2010 Europeans did not appear as intermediate of Africans and East Asians but as their own pole, in which (undersampled) Africans were subsumed by default. Pickrell offers us another different viewing angle with his oversampling of Khoisan and generally African peoples and using Eurasians (both West and East Eurasians) as control.

      Pickrell's global PCA (legend) makes an L-shape but, unlike the graphs we are most used to, the angle of the L is not in Europe or West Asia at all but in the non-Khoisan Africans pole, while Eurasians do cluster together (with Europeans slightly "more African" than East Asians, yes but just a bit).

      Because of the oversampling of Khoisan and other Africans, this is IMO actually a more reflective analysis of the overall Human structure, which is essentially African, with an Eurasian-plus offshoot.

      Pickrell also has a an Admixture analysis, in whose K=2 level French (the only non-African sample in this case) make up one component and the other corresponds to the Ju|'hoan. But that is trivial and I mention only as counterpoint, because K=5 is, among those levels studied, the one probably more reflective of reality.

      Of course greater depths should give an improved understanding, because Humanking or just the African part of Humankind cannot be described as admixture of any two simple components but as a large array of various populations (and subpopulations) firstly differentiated by means of millenary isolation (relative inbreeding or endogamy) and only secondarily, in some cases at least, admixed with each other. You cannot describe 13 or 28 components with just two simple shades of color: no way!

      Delete
    4. EtyopisJuly 30, 2012 at 12:55 PM

      Maju, instead of attacking my sampling strategies why don't you propose what the correct number of samples and geographical allocations should be for a global Analysis? After all, there are only a finite number of people/groups of people in the world. And then, you could simply perform a K2 analysis on that and we could compare notes.

      Delete
    5. MajuJuly 30, 2012 at 3:51 PM

      Don't take it personally, I beg you, but you are in clear error in some interpretations which are forced and not well done.

      In any case it's not your sampling strategy: your sampling strategy is fine, as long as you acknowledge it is one among many possible and don't over-read or misread some of the analysis. One analysis will only give you one viewpoint and we need many different viewpoints to understand even a bit the multidimensionality of actual human population genetics.

      We can't get a phylogeny out of autosomal DNA: we get very rough approximates at best or totally distorted results at worst... because the "real tree" is not any tree but an irregularly dense hyper-web. The tree model assumes just divisions and not mergers and that can only happen with simplified genealogies like purely paternal (Y-DNA) or purely maternal (mtDNA) ones.

      "After all, there are only a finite number of people/groups of people in the world".

      Seven billion individuals in the extreme, 7000 language-defined ethnicities or some 40,000 dialect defined populations, some 250 polities, tens of thousands of provinces or regions, etc...

      And each group is imprecisely related with the rest. The number may be finite but it's certainly not two.

      The method of optimizing the number of clusters in an Admixture analysis, you know well (cross-validation), better than me. You know that the cross-validation value seldom legitimizes less than a dozen clusters for any sizable and distinct number of samples. Anything less than a low cross-validation value is useless in any case, because it's forcing third categories into false dichotomies. It's like demanding the color blue to split between green and red: the result is identical to that of grey between black and white but it's a false result; it's like forcing the direction up to be defined in terms of left or right, etc.

      "And then, you could simply perform a K2 analysis on that and we could compare notes".

      You can't use K=2 as meaningful unless you are actually comparing two basic groups and intermediates, for example HGDP samples YRI (Nigerians), CEU (Utah Whites) and ASW (African Americans), in which these last can effectively be described as a linear admixture of the other two (or very similar ancestral populations). But I have just mentioned two different examples of global K=2 analysis that are not coincident with your K=2 analysis or among them: just because samples are different everything changes.

      There is no simple duality in Humankind: there is a branching and seeding of populations like (simplified): (1) proto-Khoisan, (2) proto-Pygmy, (3) proto-West Africans, (4) proto-Eurasians, etc., including their (often disparagingly diverse) subgroups. But then there is interaction among them or lack of it... re-homogeneization (partial neutralization of the process of divergence) or increased drift (simplest process) - or even both. That can't be read in a K=2 graph. At best it gives a very blurry impression.

      You have been doing a great job analyzing African and other human genetics but in this you are radically wrong: misusing the instruments of analysis much as an illiterate could read "crossroads" in the letter X.

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    6. EtyopisJuly 30, 2012 at 4:52 PM

      “as long as you acknowledge it is one among many possible and don't over-read or misread some of the analysis”

      That is the thing right there, I do not think it is one among many possible results, when you divide the world into 2 genetic poles, you will always get 1 result, and that is Africans on one side of the pole and East Asians/Amerinds on the other side of the Pole, I agree that the corresponding compositions you would get for the populations in between would vary depending on sampling, but I also believe that the dataset I used has more of the 'in between' populations than what is currently out there and is thus the most accurate, there may off-course be variations on the results depending on the SNPs used as well, but I am fairly convinced that it is fairly accurate. One way you can check is by measuring the clinal differentials, a well represented dataset should have the least Average clinal differential @ K=2.

      “The number may be finite but it's certainly not two.”

      Yes, but the minimum you could divide it is into two, everything else proceeds from there.

      “Anything less than a low cross-validation value is useless in any case,”

      The cross validated result is the optimized (K-optimum) final result where the maximum likelihood plateaus for a given dataset, that does not mean that the results generated for K< K-optimum are meaningless, the final result is a direct consequence of the previous K values. For example, give me a random genome typed for those same SNPs that I used in my global analysis and @ K=2 I would be able to tell you if he/she falls into the African, EastAsian/Amerind or intermediate between the two clusters, @ K=3 I would tell you if he/she falls in the West Asian, East Asian, African or clusters intermediate thereof, and so forth for 4>=K<=optimum, but the fundamental genetic split of humanity is at K=2, that is the BASIS and it is by no means meaningless.

      “There is no simple duality in Humankind”

      I respectfully disagree in terms of genetics here Maju.

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    7. MajuJuly 30, 2012 at 6:05 PM

      "when you divide the world into 2 genetic poles, you will always get 1 result, and that is Africans on one side of the pole and East Asians/Amerinds on the other side of the Pole"...

      That is not what Behar 2010 (where Africans are relatively undersampled) gets: he gets a West Eurasian and an East Asian pole at K=2. The African pole only shows up at K=3. But as Africans are invariably closer to West Eurasians (if nothing else because West Eurasians have minor, often subtle, African admixture all around), Africans appear as wholly in the Eurasian cluster.

      The behavior is extremely different to your own K=2 experiment.

      I must say that, back in the 1990s, even someone of the height of Cavalli-Sforza misinterpreted similar results to your own the way you did: he did suggest in some works that Europeans or West Eurasians would be a mixture of 2/3 Asian blood and 1/3 African blood but that's not really true and nobody after him or even himself later on have reclaimed such result. It is a simplistic misinterpretation. I always wondered how could he arrive to such conclusions but reading you, I now understand how, and which was his error.

      "Yes, but the minimum you could divide it is into two"...

      That's an arbitrary division. It's like dividing people in Ireland between blonds vs redheads, or blonds vs brunettes, or redheads vs brunettes... something is lacking all the time. It's like dividing the realm of life between plants and animals and then saying that sponges or bacteria or viruses are something in between. You can only divide a reality in two if all (or at least most) cases (samples) cluster in two clearly defined zones and that is often not the case.

      For example when you compare European subpopulations and a Nigerian control, there is always a simple dichotomy (although the second dimension may stretch ones or the others, depending on relative internal genetic diversity of each sample contrasted with the Nigerian control). That's easy. But when you get Moroccans in the equation it becomes more complicated because even if Moroccans may have some European or West African genetic influences, they also have their own unique elements, that get them out of the dichotomy if you allow for that to happen. (See here for actual graphs illustrating these examples).

      (cont.)

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    8. MajuJuly 30, 2012 at 6:06 PM

      (...)

      "The cross validated result is the optimized (K-optimum) final result where the maximum likelihood plateaus for a given dataset, that does not mean that the results generated for K< K-optimum are meaningless"...

      They can be really close to meaningless and they certainly do not automatically mark the first branching in the "tree of Humankind". The higher the cross-validation value, the more distant from the optimum, the more irrelevant and confusing it is.

      "... but the fundamental genetic split of humanity is at K=2, that is the BASIS and it is by no means meaningless".

      You only get two poles, which are rather determined by the sampling strategy: oversampled real clusters such as (typically) East Asians, West Eurasians, West Africans... tend organize the rest. However genetic difference also weights and so even relatively under-represented real clusters like may be Pygmies or Khoisan in some cases, also produce polarities. I can't really explain how that happens because, as you know, maths are not my strong point - but I know from experience that it happens that way.

      But when extremely undersampled, even very distinct populations like Khoisans (we used to see them in very low numbers until recently), may appear as (false) "admixture" of other clusters.

      Whatever the case, those poles have been determined, all the rest is forcibly aligned with them depending on whom they resemble more gene by gene. There's no "grey component" indicating which genes or AIMs could not be aligned (it'd be a good idea however), otherwise you'd see in your K=2 (and all other K=2 graphs) how most of the samples would be essentially "grey" (= neither this nor that).

      It's a true pity that no Admixture-like program or variant showing what is not aligned with any of the components exists. It would be of great help.

      Cheers.

      Delete
    9. EtyopisJuly 31, 2012 at 10:10 AM

      “That is not what Behar 2010 (where Africans are relatively undersampled) gets: he gets a West Eurasian and an East Asian pole at K=2. The African pole only shows up at K=3.”

      This is actually not true at all, since I have the behar samples as a subset of my dataset I had also attempted running ADMIXTURE on just the Behar Subset, and clearly one of the K2 poles is African and NOT West Eurasian, hence why they painted the cluster brown, I.e same colour as the African cluster in K3, in my simulation, I get approximately what Behar gets, for example the French were 77.6% African in my run, where as in Behar '10 the French get ~95% African, similarly in my run the Russians get 69.8% African, where as in Behar '10 the Russians get ~80% African. I attribute the slight differences to 2 things, (1) The volume of SNPs used and (2) The Software used; Behar used STRUCTURE, I used ADMIXTURE.

      “Africans appear as wholly in the Eurasian cluster.”

      You obviously have it the other way around...

      “You only get two poles, which are rather determined by the sampling strategy: oversampled real clusters such as (typically) East Asians, West Eurasians, West Africans... tend organize the rest.”

      You are doing too much speculation with very little validation/experimentation, for example take the 3 poles that appear in a K3 global run and then run K2 on that particular dataset, what do you get? In-fact, I did this for 220 West Africans, 375 Europeans and 503 East Asians, guess what I got, the French were 64% African and 36% East Asian. So the poles never change, cluster distribution for in-between populations may change depending on the quantity and diversity of the in-between populations sampled, if I included more Africans in the Above run then the French would have less African and more East Asian, if I include more South Asians (who are related to aborigines) then It would change again, adding more middle easterners would also yet again change the results, but the poles NEVER change.

      Delete
    10. MajuJuly 31, 2012 at 10:22 AM

      I'll get to you later, when I do some experimental exercise but for sure that the poles do change depending on samples and so on. Just try with 200 Africans, 10 Europeans and 10 Japanese... or with 200 Eurasians and 10 Africans... or...

      Delete
  17. UnknownAugust 23, 2012 at 2:47 PM

    Etyopsis, is there anyway you can upload your merged dataset used for this run, so that i can try it with experiments on my own, for new worlders = ) This would be great, this is Lemba.

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    Replies
    1. EtyopisAugust 30, 2012 at 4:00 PM

      I have uploaded the file under Africa Dataset (V2) on the Public Datasets/Resources page.

      Delete
  18. UnknownDecember 9, 2014 at 10:19 AM

    Hi. Im still just trying to understand my results..Im new to the DNA side of genealogy. My mom is mostly black with a small 15% white, and my dad is a European mix (all white)...

    Here are my results:
    Kit Number: F372029 Iteration: 206 Delta-Q: 5.714213e-08 Elapsed Time: 8.75 seconds



    Population Chr--> 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
    Nilo-Saharan 7.8% 17.7% 4.4% 7.2% 5.1% - 10.6% 1.6% 10.0% - 6.7% 0.4% 4.9% 18.5% - 2.2% 18.5% 4.0% - - 4.2% -
    North-Africa 3.2% 16.7% 6.7% 5.6% 8.0% 14.7% 11.0% 16.1% 5.8% 14.7% 17.2% 15.2% 15.5% 22.6% 25.9% 23.4% 33.5% 27.0% - 15.7% 5.4% -
    Mbuti-Pygmy - - - 2.7% - - - - - 0.3% - 1.3% - - - - - - 5.4% 0.4% 1.5% -
    Eastern-Bantu 15.5% 1.3% 11.9% 13.2% 8.2% - 7.9% 23.4% 8.1% 11.6% 16.7% 14.4% 7.1% - 21.0% 21.4% 2.4% 21.9% - 11.5% 13.1% 22.4%
    Khoi-San - - - - - 3.5% 3.1% 1.8% - - - 0.1% - - - - 4.6% 0.7% - 8.2% - 0.8%
    West-Africa 13.1% 20.9% 30.0% 17.4% 24.5% 27.1% 26.6% 16.2% 26.4% 26.7% 16.0% 15.6% 8.3% 11.8% 5.8% 17.2% 16.7% 16.3% 20.6% 9.0% - 8.5%
    Hadza - - - - 2.9% 6.1% 3.0% 2.8% - 4.2% 1.8% 3.8% 2.5% 0.5% - 3.6% - 2.1% - 4.6% - 8.7%
    Biaka-Pygmy - - - 0.5% - - - - 3.4% 3.3% - 11.5% 12.2% 10.5% 3.8% 1.2% - - - 2.4% - -
    French 47.9% 39.3% 47.0% 53.4% 46.9% 36.2% 37.8% 38.1% 46.3% 39.2% 41.6% 37.6% 49.0% 36.1% 28.7% 31.0% 24.3% 28.0% 74.0% 48.2% 75.8% 59.7%
    Omotic 12.4% 4.1% - - 4.4% 12.4% - - - - - 0.1% 0.6% - 14.9% - - - - - - -
    Number of SNPs eval: 1977 2305 1846 1777 1717 1684 1355 1586 1302 1398 1248 1317 1157 883 780 811 552 846 269 620 423 276

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    Replies
    1. MajuDecember 9, 2014 at 3:50 PM

      I was also perplex at first because the "French" results score are in most cases well under 50% (and should be >50%). But if you add to the "French" the "North African" affinity component (which is also West Eurasian, as the Tropical African affinity in real North Africans would be reflected in other categories), then you have reasonable results in this aspect (or so it seems to me): all "white" scores are above 50%, as should be. The "North African" affinity can indicate a degree of Mediterranean ancestry, as in Greek, Italian or Iberian (or West Asian too).

      Notice that for earlier generations a random element is at play: you inherit one chromosome from your mother and one from your father but each of these are random remixes of your grandparents, etc. (recombination), so the "white" ancestry inherited from your mother can vary: in one chromosome it can be 0% and in another 90% (I'm actually spotting that figure in chr. 21).

      As for the African side, it seems quite mixed but not sure how informative are these categories anyhow. For whatever is worth, my impression is that the Eastern African components are quite heavy, suggesting a maybe Mozambican-dominated ancestry. But compare with other Afro-descendants for safety (after due pondering).

      Hope this helps.

      Delete
  19. UnknownDecember 28, 2014 at 10:33 AM

    Sorry to be a plonker!!! BUT when I run dna through your tool - they come up pretty equal without differentiation. My Mother i law should show up some African (or possibly Caribbean) if the family story and some old photos are to be believed. On the European (French) - African tool she shows 15% African and pretty much the rest European. BUT me and my Father i law come up pretty similar - which we shouldn't do. Am I using/interpreting this incorrectly?

    ReplyDelete
  20. UnknownSeptember 17, 2016 at 9:43 AM

    Would my phased data or unphased data be more accurate. My daughter phased her kit so her maternal kit which is me is about 7 percent more african than my unphased it. which one would be more accurate

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  21. UnknownSeptember 17, 2016 at 9:44 AM

    I used the plus french

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  22. UnknownNovember 29, 2016 at 12:20 PM

    Hello, DNA testing revealed that I was 74% Sub -Saharan West African, 1.7% East Asian/Native American, 18% European, 0.2% Middle Eastern/North African. EhioHelix k10 + Palestinian run shows an 89.89% Palestinian percentage. What does this mean? I am inexperienced with this. Your help is appreciated.

    Thank You

    ReplyDelete
  23. lisalebittMarch 25, 2017 at 2:38 PM

    Can you explain my numbers to me please?
    Thank you.

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  24. AnonymousJuly 22, 2017 at 2:06 PM

    Can you add a calculator to filter the native american imput out? its confusing as I dont know where my native goes. thank you.

    ReplyDelete
  25. ahabeshaethioMarch 19, 2018 at 11:10 AM

    I'm Northern Ethiopian (Habesha). 23&me shows I have 3% Middle East/North African in me and remainder East African. Is it more accurate to use the African Only calculator or +Palestinian?

    ReplyDelete
  26. UnknownApril 29, 2018 at 4:49 AM

    What is:
    East-Africa 2 and East-Africa 1?

    ReplyDelete
  27. UnknownJuly 24, 2018 at 9:03 PM

    Why are Egyptians classified as French or predominantly French of the the reference population chart? Is it because they are genetically more similar to Palestinians than they are to Algerians?

    ReplyDelete
  28. AmyFebruary 24, 2019 at 11:23 PM

    This comment has been removed by the author.

    ReplyDelete
  29. Rabbi Dr. Norbert WeinbergDecember 26, 2019 at 5:14 PM

    I am 98-99% Ashkenazic Jewish ( based on MyHeritage and FTDNA analysis) with a smattering of Finn/Central Asian genetic material. I ran my kit through Gematch on your Ethio-Helix+Palestinian, and I find this breakdown: Biaka-Pygmy 1.99 Pct; Palestinian 88.25 Pct; Omotic 8.38 Pct, and a smattering of others. Since Ashkenazic Jews and Palestinian Arabs share a large amount of ancestral DNA, would this result be consistent with that finding?



    UNDER DEVELOPMENT:



    ReplyDelete

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