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    Dienekes Pontikos has just released DIY Dodecad, a DIY admixture analysis program. You can download the files yourself. It runs on both Linux and Windows. Since I already have tools in Linux I decided to try out the Windows version, and it seems to work fine. It is somewhat limited in that you start out...
  • Your mother’s West Asian is 2 and your father’s West Asian is 3.9 (almost 4), yet, you are zero?..

    i already covered why this might be a real result and might not just noise extensively.

    http://blogs.discovermagazine.com/gnxp/2011/01/asian-in-all-the-right-places/

    but for DIY Dodecad it might be noise too. this should be used as a first pass i think.

    #2, he doesn’t have a south asian skewed reference set like zack. some of the ASI is padding your east asian. i’m probably 5-10% east asian, but dodecad is giving be 15%.

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  • Ian says:

    It gave me ather different results from what I got from Zack’s analysis. For example, on HAP South Asian + Onge was 42%, while DIYDodecad only showed me as 28% South Asian. Others were more similar – HAP showed me as 13% Southwest Asian, while Dodecad’s West Asian (9.77%) + Southwest Asian (2.94%) was 12.71%.

    Dodecad seems to think I am a lot more East Asian than does either HAP or 23andme. 23andme says 4% Asian. HAP says 2% East Asian, 1% Siberian. Dodecad, on the other hand, says 0.93% Northeast Asian and 5.80% Southeast Asian. That’s 7% – about twice what the others say.

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  • Your mother’s West Asian is 2 and your father’s West Asian is 3.9 (almost 4), yet, you are zero?..

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  • Over the past few months I was hoping more people would start doing what Zack Ajmal, Dienekes, and David, have been doing. There are public data sets, and open source software, so that anyone with nerdy inclination can explore their own questions out of curiosity. That way you can see the power and the limitations...
  • [...] reason I posted about how to run ADMIXTURE was that the more readers themselves were familiar with the biases of the program the more they [...]

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  • “Do people ever make pie charts for these things?” what else could be worse than that?

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  • Is the dataset listed above complete or might there be other popuations that were not included?

    Thanks

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  • 2) What information is actually contained within these files? ADMIXTURE’s page says it’s “multilocus SNP genotype datasets.” What the heck is that? What part of the genome are they examining for single nucleotide polymorphisms? Are these standard points for examination? How many points per individual?

    Each SNP is a single base-pair in the genome at which two alternative versions are measured. Given two possible alleles (say A and B), there are three possible genotypes (AA, AB, BB). The data are genotypes.

    The chromosome and base-pair coordinate is given in the map file. These coordinates are with respect to a genome build, such as hg18. http://genome.ucsc.edu/cgi-bin/hgGateway?db=hg18

    These SNPs were likely selected because they are otherwise well characterized, so in essence they are standardized.

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  • 1) What does “pedigree formatted” mean?

    http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped

    Are these beds, bims, and fams in a binary or ascii format? I assume binary because I wasn’t able to open them in a text editor.

    bed and bim are binary

    http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#bed

    Besides ADMIXTURE (which I can’t use because like most people in the world, I use Windows :) ), is there any way to read these files? Could I write a custom binary processor? Is there any ascii version of the data? Is that what the csv is?

    you can convert bed/bim to ped/map using plink (see links above)

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  • Hi Razib,
    Thank you for the quick answers. I hadn’t made it to your next post at the time of my comment! 27000 SNPs huh? That’s quite a bit of data. I see that I can open the bim and fam files in a text editor, so there’s hope I can import all of it into MATLAB and play with it. I’ll have to read your posts more carefully and do some investigation as to the meaning of each row of the file. We’ll see if anything comes of it.

    Cheers

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  • Besides ADMIXTURE (which I can’t use because like most people in the world, I use Windows ), is there any way to read these files? Could I write a custom binary processor? Is there any ascii version of the data? Is that what the csv is?

    no idea about windows. .bed is binary. the text version is .ped.

    What information is actually contained within these files? ADMIXTURE’s page says it’s “multilocus SNP genotype datasets.” What the heck is that? What part of the genome are they examining for single nucleotide polymorphisms? Are these standard points for examination? How many points per individual?

    the data have snps and individuals. also stuff like sex, phenotype, etc., but that’s extraneous for our purpose. in these data 27,000 snps per individual.

    Or to put it another way, it’s creating K fictitious populations that are as genetically distinct as possible, and showing the proportion each modern population has of these fictitious populations?

    yes

    4) Is it possible to specify that one of your K populations is completely one of the modern populations? Could you say, as an example, that you want the French and the Moroccans to show up as 100% one of the resultant clusters?

    yes. see follow up post.

    These bar charts that you end up with are rather hard to follow. Do people ever make pie charts for these things? How about a map of the Earth with the ranges of each of the K populations? You can clearly see in your K=12 map, for example, that the pink population is most prevalent in northeastern Europe and dissipates moving outward from there.

    yes. i have thought of that. need to get fluid with R’s map functions. i don’t want to learn GIS. the thematic heat maps are easy with paid software, but i’m not going to shell out $400 for that :)

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  • Thanks for this useful post. I am an engineer with a casual interest in genetics. So I have a decent math background but understand little about the domain. Up til now, all these admixture analyses have been like black magic to me. Now I at least have a bit better of an understanding. And yet, your post begs more questions…

    1) What does “pedigree formatted” mean? Are these beds, bims, and fams in a binary or ascii format? I assume binary because I wasn’t able to open them in a text editor. Besides ADMIXTURE (which I can’t use because like most people in the world, I use Windows :)), is there any way to read these files? Could I write a custom binary processor? Is there any ascii version of the data? Is that what the csv is?

    2) What information is actually contained within these files? ADMIXTURE’s page says it’s “multilocus SNP genotype datasets.” What the heck is that? What part of the genome are they examining for single nucleotide polymorphisms? Are these standard points for examination? How many points per individual?

    3) If I understand correctly, ADMIXTURE is doing is a cluster analysis? It’s crunching the data, finding the eigenvectors for the given K, and displaying the vector components of each population mapped onto the eigenvectors? Or to put it another way, it’s creating K fictitious populations that are as genetically distinct as possible, and showing the proportion each modern population has of these fictitious populations?

    4) Is it possible to specify that one of your K populations is completely one of the modern populations? Could you say, as an example, that you want the French and the Moroccans to show up as 100% one of the resultant clusters?

    5) These bar charts that you end up with are rather hard to follow. Do people ever make pie charts for these things? How about a map of the Earth with the ranges of each of the K populations? You can clearly see in your K=12 map, for example, that the pink population is most prevalent in northeastern Europe and dissipates moving outward from there.

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  • [...] RSS « Analyzing ancestry with ADMIXTURE, step by step [...]

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  • Thanks, I downloaded the script using a vista computer on another network. I still have no idea why I can not access it here. But I have it now. Garvan

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  • Thanks a bunch for this….can’t wait to graduate college so I can mess around with this…

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  • The Rstuff.R link gives me a 403 Forbidden error message. Could you check the link please?

    Thanks,
    Garvan

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  • Thanks Razib for this great tutorial! I’ve always wanted to play with this kind of things, and this post will save me a lot of time.

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  • Zack, yeah, the latest version of gtool, which shellfish depends on, seems to be broken. I downgraded to version 0.6.1 and it works fine: http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool_v0.6.1.html

    I’m using Python 2.6.6 as well, on Debian unstable.

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  • RK: I downloaded shellfish just for that reason, but it gives me (Python 2.6.6 on Ubuntu 10.10) errors in the initial conversion step. Have you been able to get it to work? I haven’t had time to look into it.

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  • hey, anyone can leave a question here. didn’t want 2 overload the post.

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  • yeah, i put the –extract stuff there. also, no issue with flipping when i did a test run. it seemed oriented 23andMe direction. haven’t used shellfish, but i’ll check it out.

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  • Wow, this is great — especially the merged dataset. Thanks for putting it together. I haven’t used the dataset, but shouldn’t you be filtering your 23andMe file for the SNPs found in the merged dataset? After all, the latter has many fewer SNPs than the former. Also, I’m not sure if it’s needed for this dataset, but people should familiarize themselves with how to flip strands when merging datasets.

    Have you ever used Shellfish to do PCA? It lets you create “loadings” for reference populations, so that you can see where samples fall on the dimensions generated by the reference data without changing the dimensions themselves. Basically, it’s like the advanced genetic similarity plot on 23andMe. I’m trying to create a loading for the HGDP populations, but now I may as well add these in.

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  • Since I know plenty of friends are getting, or just got, their V3 results, I thought I'd pass this on, Open-ended submission opportunity for 23andMe data (#2): Also, Zack has more than 30 individuals in HAP. The "cow belt" is still way underrepresented. The only Bengalis in the data set are my parents.
  • Anonymous • Disclaimer says:

    Please could somebody tell me how to get the autosomal data from 23andme? The only options available to download raw data are

    - mitochondrial DNA
    - only the Y chromosome
    - or all DNA (chromosomes 1-22, X, Y, and mitochondrial).

    I have search on the Internet but there are no instructions to get the autosomal data.

    I only need a link. Thanks in advance.

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  • wow! I am excited about this since I didn’t think I could figure out how to do admixture on my own. I hope he takes me, even though Ashkenazim have been studied so much already!

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  • Just got my Dodecad results back. Seems I have a 1.5% South Asian admixture interesting! My west Asian admixture is at 14.4% interesting enough seems to be close to double the % average that the Irish_D dodecad group have.

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  • Hi Razib, how are you? Do you know anyone accepting people with multiple-european groups ancestry? I am felling discriminated! Maybe I need some affirmative action :) Thanks!

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  • Yeah they received it on Jan 11.

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  • a month since it arrived? 5 weeks seems like a plausible turnaround right now from arrival.

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  • I am still waiting. It’s been a month so I likely have another 2-4 weeks to go. I suck at patience.

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  • pconroy: Sure, get them to send their data.

    Razib: Not just half-brown, I am accepting quarter and less too. :)

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  • heez accepting half-brownz, so i think it would be useful.

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  • Raz,

    I have 1 half Bengali relative from the US and 2 half Indian relatives in the UK – do you want me to reach out to these? Or are they much use to a study like the Harappan one?

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  • Dienekes did another run of his data with K = 64. He posted a huge plot with the two largest dimensions of variation. He also posted an accompanying spreadsheet with the coordinates of where the Dodecad samples were. So I found my own position pretty quickly. Before going to that, I thought I'd repost a...
  • [...] One of the great things about the mass personal genomic revolution is that it allows people to have direct access to their own information. This is important for the more than 90% of the human population which has sketchy genealogical records. But even with genealogical records there are often omissions and biases in transmission of information. This is one reason that HAP, Dodecad, and Eurogenes BGA are so interesting: they combine what people already know with scientific genealogy. This intersection can often be very inferentially fruitful. [...]

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  • I am aware that a few people have done three dimensional MDS plots and have seen one or two. I’d be curious to hear what people think about their usefulness.

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  • No, but whatever it is, it’s only a minor portion of other Indian samples – so IMO it must be due to:
    1. Isolation by distance – like Sardinia – which is not likely
    2. Isolation by religion/caste – like Assyrian
    3. Ancient substrate
    4. Exogenous to India – like Austronesian admixture

    I guess there is some likelihood of #1 or #2 – if the sample was all sourced from an isolated mountain village or religious minority, but usually in understudied areas, samples are from cities, and rarely rural areas.

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  • u wouldn’t happen to know what the detailed origin of the north kannadi sample is, would you?

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  • Razib,

    Very interesting, as this would fall in line with my speculation that the mystery component of the North Kannadi could be Austronesian – and depending on how one defines Austronesians and their expansion – slow boat/fast boat etc – they could be seen as South East Asian + Oceania or at least island South East Asian

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  • In the open thread someone asked: "Any recent stuff on the genetics of Ethiopians." That prompted me to look around, because I'm curious too. Poking around Wikipedia I couldn't find anything recent. A lot of the studies are older uniparental lineage based works (NRY and mtDNA). Ethiopia is interesting because unlike almost all other Sub-Saharan...
  • If you had male mediated Austronesian settlement in coastal Mozambique, which were later overrun by male Bantu’s, then Arabs from Oman, there would be little evidence in uniparental markers, now would there?!

    Not a lot, but given that you have discernable Khoisan uniparental traces, you wouldn’t expect there to be a huge autosomal component and less than 1% uniparental markers at all. Also, I would be quite surprised if there wasn’t at least some exploratory comparison of a Madagascar component to the Mozambique unique component that wasn’t reported in the final product because it wasn’t a match.

    Matilda’s makes a case with which no one disagrees that there is a substantial Eurasian genetic component in Ethiopia, which may include some Y-DNA sub-haplogroups of E found in Euraisans. But, she doesn’t even begin to argue that Y-DNA haplogroup E is non-African, and indeed, clearly identifies some varieties of it with African Niger-Congo populations in the post you cite, which is the mainstream view.

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  • [...] Comment of the week, in response to The genetic affinities of Ethiopians: First of all, you should know that Behar’s Oromos were sampled in areas neighboring the Kenyan [...]

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  • Andrew said:

    Interesting theory, but it is completely contradicted by the facts.
    Austronesian mtDNA and Y-DNA, which has a well characterized profile, would stick out like a sore thumb in Mozambique.

    I wasn’t talking about uniparental markers, but autosomal DNA, which is where the unique component in Mozambiques was discovered.
    If you had male mediated Austronesian settlement in coastal Mozambique, which were later overrun by male Bantu’s, then Arabs from Oman, there would be little evidence in uniparental markers, now would there?!

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  • Also, here’s a pretty good blog post by Matilda on this very subject:

    http://mathildasanthropologyblog.wordpress.com/2008/03/04/caucasian-africans/

    Her blog focuses on the genetics of Northern Africa mostly.

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  • Andrew,

    I think Y-DNA E originates in the Southern Fertile Crescent, probably with the Natufian Culture and brought Afro-Asiastic languages to Africa, along with agriculture.

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  • I have spoken of my somewhat atypical, for a South Asian, genetic results before. Recently Dienekes performed some cluster analysis which confirmed the initial findings, while adding a little detail: I am DOD075. The Southeast Asian component is modal in Malays, while the East Asian component is modal in the North Chinese. Vietnamese and Cambodians...
  • Razib,
    This is a fantastic analysis of your heritage using DNA. I’ll have to look into doing the same for mine over the weekend.

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  • Dear Rajib,
    Where can we get a check like this done in India? What might be the cost? $1000?

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  • OT, but the ‘The 10,000 Year Explosion’ just got reviewed (positively) in the prestigious Financial Times.

    http://www.ft.com/cms/s/2/e3465a8a-19e1-11e0-b921-00144feab49a.html

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  • In the open thread someone asked: "Any recent stuff on the genetics of Ethiopians." That prompted me to look around, because I'm curious too. Poking around Wikipedia I couldn't find anything recent. A lot of the studies are older uniparental lineage based works (NRY and mtDNA). Ethiopia is interesting because unlike almost all other Sub-Saharan...
  • But, Eastern Africa is also the ancesteral home, perhaps of Southern Africa hunter-gatherers, Nilo-Saharans and Niger-Congo language speakers

    I assume here you are referring to the origin of modern humans as a whole, am I right? If yes, I must state that enough time has passed for the divergence of those groups you mention and their language families.

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  • “Sure Omotic is spoken at the fringe of the Cushitic language area, but I would not say that Afroasiatic influence should be weakest there, considering that it seems likely to be close to the area from which proto-Afroasiatic originally spread.”

    Every imaginable arrangement of the phylogenetic tree for the origin of the major families Afroasiatic languages has been proposed by credible leading linguists and none have won a consensus, although the validity of the macrofamily (apart from the question of whether Omotic is Afro-Asiatic, or that if it is that is belongs in the same group as Cushitic or not) is fairly solid.

    Points of origin for the Afro-Asiatic language family have been proposed for everywhere from its far Northern extent in the North Levant to the expanse of East Africa, Sudan, Egypt, and perhaps even in the Sahara (if it has links to a diaspora population from Green Sahara period in the early Holocene). There is a fair degree of consensus on the main subfamilies, but not about their relationships or places of origin.

    This lack of consensus from the linguists make population genetics, ancient climate studies, and archaeological culture associations, and the analogies we can draw from cases where we understand how languages have spread elsewhere, are especially important in informing our understanding of the period in this region.

    In most historical cases, some combination of the spread of agricultural technology or other technological complexes, mass religious movements, mass migrations of peoples (away from or to something that is a very good reason), or conquest seem to explain how language families become widespread. Of course, in Africa, somebody has to speak the “original” language of modern humans (or for that matter the last common language of modern humans, which might not be the same thing) so one of the language families could be that language (then again, maybe that language, like Sumerian, the original written language is now dead and has no recognizable descendants).

    FWIW, my bet is that Afro-Asiatic languages have their roots in the expansion of Fertile Cresent, Sahel or Ethiopian agriculture since agriculture seems to be the main driver of macrolanguage groups whose origins can’t be traced to the historic era. And, given (1) their area of spread, (2) the anomolous R1b Y-DNA haplogroup frequency of predominantly pastoral Chadic speakers found neither in other Afro-Asiatic language speakers or other African linguistic groups at high frequencies (suggesting back migration to Africa from an area outside the Afro-Asiatic language area probably accompanied by language shift and a lack of connection to Sahel crops), and (3) the narrow geographic scope of Ethiopian origin domesticates relative to the Afro-Asiatic territory: my money would be on Afro-Asiatic as part of the Fertile Cresent farming and herding package (i.e. with the main expansion starting ca. 6000 BCE or perhaps a couple of thousand years later depending on the latest archaeological finds).

    This would put the most likely place of origin for Afro-Asiatic languages in either the Nile Valley or the Levant (there is no evidence that other places that were part of the Near Eastern Neolithic ever spoke Afro-Asiatic languages in the earliest historically documented periods or before then).

    Coptic, as the first written Afro-Asiatic language, is a particularly strong contender as an epicenter of African fertile cresent agriculture, with historically attested boating technology, with easy access to Berber, Semitic, Coptic, Chadic, Cushitic and Omotic regions via sea coasts and rivers. A common source language for all of the major families would help also explain the lack of a tree-like structure amongst them that one would expect if Semitic languages were at the root of all of the Afro-Asiatic languages in a Levant origin scenario.

    It is certainly possible that Afro-Asiatic languages could have originated in Ethiopia and worked their way via the Red Sea and/or Nile and/or Green Sahara to North Africa and the Near East. But, what would the Ethiopians have done that would have brought them to the cultural dominance that would have led to linguistic dominance across this wide region? I guess coffee, but I don’t really believe that.

    Yes, genetically, Y-DNA E1b1 some parts of which trace Afro-Asiatic languages seem to have origins in Eastern Africa and perhaps Ethiopia. But, Eastern Africa is also the ancesteral home, perhaps of Southern Africa hunter-gatherers, Nilo-Saharans and Niger-Congo language speakers, so the notion that the linguistic roots of Afro-Asiatic languages, even though it spawned other linguistically very different groups, isn’t very convincing.

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  • One more footnote on Y-DNA E origins in Africa.

    Y-DNA haplogroup E also splits from the Eurasian haplogroups descended from CF, at the very base of the Y-DNA tree (just after A and B) and split very neatly from D which is Asian. So, if Y-DNA haplogroup E originated in Eurasia, it would have to have made the split right at the very dawn of the Out of Africa moment, and there is evidence from the 1000 Genomes project that the CF/DE split may be even more ancient than earlier Y-DNA analysis had suggested. So, any scenarios in which Y-DNA haplogroup E arises any time in the last 50,000 years is falsified.

    Thus, any scenario with a non-African Y-DNA haplogroup E origin has to explain why it completely disappeared everywhere else in almost all of its varieties, without even a single individual in billions and billions whose ancestry is not attributable to recent immigration in all of Asia, despite the fact that one’s Y-DNA haplogroup was invisible after just a few generations until the last decade or two.

    Notably, while there are major branches of the Y-DNA and mtDNA trees that are found in Asia but not in Europe, there are no major branches of the Y-DNA or mtDNA trees that are found in Europe but not in Asia as is the case with Y-DNA haplogroup E.

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  • marcel, good idea.

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  • anon, please use a distinctive handle. adding a number to your handle would do. it is hard to track comments from a generic user.

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  • “I also wonder if the mystery component in Mozambique is Austronesian, likewise if Austronesians are the mystery component in the North Kannadi – who knows, but if I’m right, it would provide the stepping stones for Austronesians ending up in Madagascar, as I think a direct voyage is unlikely.”

    Interesting theory, but it is completely contradicted by the facts.

    Austronesian mtDNA and Y-DNA, which has a well characterized profile, would stick out like a sore thumb in Mozambique. But, Mozambique is 78% Y-DNA haplogroup E1b1, 7% Y-DNA haplogroup E2, and 15% Y-DNA haplogroup B2a, none of which are found at all among Austronesians. See, e.g.,
    On the mtDNA side: “From the north came sequences that may have been involved in the Bantu expansion (from western, through eastern, to southern Africa), such as members of haplogroups L3b, L3e1a and a subset of L1a. The dating of the major component of Mozambican mtDNAs, the subset L2a of haplogroup L2, displayed an age range compatible with the Bantu expansion. The southern influence was traced by the presence of sequence types from haplogroup L1d, a probable relict of Khoisan-speaking populations that inhabited the region prior to their displacement by the Bantu-speaking incomers.” http://www.ncbi.nlm.nih.gov/pubmed/11806853 There are no Austronesians in Austronesia with mtDNA haplogroup L.

    FWIW, there are also no Austronesian linguistic traces in Mozambique. http://en.wikipedia.org/wiki/Languages_of_Mozambique All of the indigeneous languages of the region are Bantu languages. Portugese and English are lingua franca of trade and of the educated classes. “Small communities of Arabs, Chinese, and Indians speak their own languages (Indians from Portuguese India speak any of the Portuguese Creoles of their origin).” None of those languages are Austronesian.

    While autosomal DNA don’t precisely track either Y-DNA or mtDNA, it would be essentially impossible for the predominant component of Mozambique’s autosomal DNA to be Austronesian (an arrival that is only about 1000 years old, give or take) without leaving any trace in Y-DNA, mtDNA, or any linguistic trace.

    By comparison, autosomally, Madagascar is about 66% East African and 33% Asian, http://www.nature.com/jhg/journal/v53/n2/full/jhg2008213a.html and the uniparental mtDNA and Y-DNA mix is close to 50-50 between Borneo and East Africa. http://news.mongabay.com/2005/0708-wildmadagascar.html There is clear Austronesian linguistic influence in Madagascar that is specific to Borneo.

    * * *

    “I predict that once more discoveries are made Y-DNA E will be shown to be Eurasian.”

    This is basically impossible given the data we already have strongly disfavoring this scenario.

    The latest study of Y-DNA E1b1, “strongly supports the hypothesis that haplogroup E1b1 originated in eastern Africa.” http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016073 Similarly, E2 is found outside Africa only on a narrow strip of the Red Sea coast of Arabia. http://forwhattheywereweare.blogspot.com/2011/01/some-new-insights-in-phylogeny-of-y-dna.html and E1a is exclusively African. All of the examples basal Y-DNA paragroup DE* are found in West Africa or Tibet, with Y-DNA haplogroup D having an a peculiar but almost exclusively Asian distribution and Y-DNA haplogroup E having an almost exclusively African distribution. Y-DNA haplogroup E is not found in any place in Asia where its sister clade, Y-DNA D is found.

    Only a few fairly high level branches of the Y-DNA haplogroup taxonomy are found outside Africa.

    * Essentially all Y-DNA haplogroup E1b1 is found in people of European descent has haplogroup E-V68 or E-V257 or E-M123, found on three of the nine branches of Y-DNA haplogroup E-M215, the rest of which are exclusively African. The other main branch of haplogroup E1b1, E-V38/V100 is exclusively African and is the predominant haplogroup of West Africans, Bantu language speaking Southern Africans, and of East Africans.

    ** E-V257 consists of E-M81 and E-V257*. E-M81 is characteristic of North African Berbers, and is also found at lower frequencies in Central and Southern Iberia (within Iberia with a mostly Western distribution, but with some presence in the East but very low in the SE). E-V257* is found (at low frequencies) in Iberians (Cantabrians and Andalusians), Corsicans, Sardinians, Marrakesh Berbers and Borana (Oromo) from Kenya. It is found nowhere else in Europe.

    ** E-M123 is found in much of Afro-Asiatic language speaking Africa, is most common in Arabia, and is found at low frequencies in Europe and West Asia in areas that roughly correspond to holdings of the Islamic empire at its peak. It is not found in Asia or in most of Europe and is even absent from Iberia.

    ** E-V68 consists of E-M78 and E-V68* (found only in Sardinians). E-M78, which is half of one of nine branches of the two main branches of the Y-DNA E1b1 haplogroup family tree, is the only kind of Y-DNA E found at any frequency among people outside Africa in areas not historically under Moorish rule in people who are not recent immigrants. In Arabia and Iran it becomes less frequent the further one gets from the Gate of Tears and the Sinai. In Europe, it becomes less frequent the further one gets from Greece. By the time you get to India and all points East, and by the time you cross the Urals, E-M78 vanishes entirely. It is also essentially absent from the Atlantic and Baltic Coasts of Europe. E-M78 is also found in the Afro-Asiatic language speaking parts of Africa and in the same parts of Iberia where E-M81 is found.

    ** The only place ancient Y-DNA haplogroup E specimens have been found outside of Africa is the Canary Islands in 2000 year old samples. http://dienekes.blogspot.com/2009/08/ancient-y-chromosomes-from-canary.html and then only in the E-M78 and E-M81 haplogroups found in nearby North Africa.

    * It is possible to imagine that some men with the E-M78 haplogroup left Africa for the Arabian Pennisula, and then backmigrated to Africa bringing a major cultural innovation such as the Fertile Crescent package of crops and the Afro-Asiatic languages with them that made their descendants common in the Afro-Asiatic language area, and that these men were also among those who were part of the Danubian Neolithic expansion. Similarly, it is conceivable that E-M123 arose in Arabia from people with ancestors in Africa.

    But, it is almost impossible to imagine a plausible scenario in which Y-DNA haplogroup E as a whole arose outside Africa; the evidence instead points strongly to an Eastern African origin. Its almost total lack of diversity outside Africa, geographical spread and frequency outside Africa all point decisively to an African origin.

    The vast majority of people with Y-DNA haplogroup E speak languages not spoken outside Africa.

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  • Anonymous • Disclaimer says:

    The Oromo do carry a variety of Eurasian lineages. Maternally macrogroup M & N, paternally J & T, and they have significant levels of an E1b1b subclade which originated in Northern Africa (E1b1b1a) near Libya/Egypt and migrated backwards to the Horn of Africa.

    It is actually likely that E1b1b1a originated in Northeastern Africa (Upper Egypt/Northern Sudan). Not that much of a difference, but anyway.

    It is possible that the upper paleolithic Ethiopians were similar to other Nilotic populations on the genomic level and that ancient back-migrations from Arabia caused the modern Ethiopians like the Amhara and Oromo to stream more towards West Eurasians. Tishkoff noted that this scenario is a possibility.

    It is indeed possible. But we don’t have any appropriate samples, so it’s impossible to say anything about that right now. The Maasai have a significant amount of recent shared ancestry with Afroasiatic speakers, and Bantu admixture. Some proper Nilotic samples would be great!

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  • Razib:

    Could you post a glossary of acronyms and other jargon, with a link on your main page. I’m new to your blog, with no background in genetics. At this point, I am blipping over things like PCA, much like Linus van Pelt did (IIRC) when he was reading War and Peace or the Brothers K, and came to another long Russian name. It would be irritating to your longer time readers, not to mention yourself, if you explained these things each time, but a permanent glossary page, with a link to it on the right would be helpful.

    Thanks

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  • What kind of scenario could be a fit to those fact? Here is a simple one. Given that Ethiopian Oromo have substantial Southwest Asian admixture not attributable to the Ethio-Semitic language transition about 2800 years ago, but similar in character, while the Maasai do not, one possibility is that the Afro-Asiatic Cushitic languages may be an artifact of a similar pre-historic language transition that took place more than 2800 years ago (i.e. 800 BCE) that caused most Ethiopians to transition from some pre-Cushitic language to to Cushitic languages in connection with a population influx from Southwest Asia.

    The Oromo do carry a variety of Eurasian lineages. Maternally macrogroup M & N, paternally J & T, and they have significant levels of an E1b1b subclade which originated in Northern Africa (E1b1b1a) near Libya/Egypt and migrated backwards to the Horn of Africa.

    It is possible that the upper paleolithic Ethiopians were similar to other Nilotic populations on the genomic level and that ancient back-migrations from Arabia caused the modern Ethiopians like the Amhara and Oromo to stream more towards West Eurasians. Tishkoff noted that this scenario is a possibility.

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  • Anonymous • Disclaimer says:

    did you note the clustering of the tigray with the ahmara in the PCA? were the ‘central cushitic’ then simply always closer to the semitic speakers than ‘eastern cushitic’?
    I did. By the way, it’s Amhara. :)

    It depends on which East Cushitic reference is being used. But yes, closer than to Behar’s Oromo samples from southernmost Ethiopia. That is the only possible explanation, since many Amharas and all Ethiopian Jews were Central Cushitic speakers a few centuries ago. It is also telling that almost all Amharas cluster firmly with the Tigray samples, since Tigray people have an older Semitic-speaking history on average, while the Amharic language has had a massive recent expansion (the Oromo language as well, by the way). Unless the Amhara samples are not representative at all, which I doubt.

    The main region where Amharas have mixed with Oromos is the southern parts of the Amharic-speaking region, Shewa and thereabouts. That also explains the extreme pull of one of the Amhara samples toward the Oromos in the plot. The Amharas were sampled in Addis Abeba, where Amharas from all around Ethiopia (and Amharas native to areas around Addis Abeba) live.

    Allow me to clarify one more thing: although Oromos (or Oromo speakers) now inhabit southern and northern Ethiopia, that was due to a recent expansion. Their original homeland is southern Ethiopia.

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  • Anonymous • Disclaimer says:

    The post from “Anonymous at January 11th, 2011 at 8:12 am” illustrates this point by noting that Tishkoff’s analysis sees the Maasai as an admixture of Cushitic and Nilo-Saharans, while Dienekes’ plot shows them as a nearly pure type population in the admixture analysis (as does the 2010 paper that I cite which expands on Tishkoff’s analysis), and also appropriately notes that the sample sizes in whole gene analysis are small and prone to be less representative, with Dienekes’ analysis of the Oromo possibly failing to capture effects do to geographic variation within the Oromo since his Oromo samples are drawn from near the Kenyan border — small wonder that a population form near Kenya would be genetically similar to one from Kenya itself.

    Dienekes’ analysis is not comparable to Tishkoff’s, and the latter is more appropriate for “genetic” linguistic affiliations, because it has a wider range of samples. Most importantly Nilo-Saharans from Sudan and other parts of East Africa. It could be that what distinguishes Dienekes’ “East African” cluster from Tishkoff’s “Cushitic/Afroasiatic” cluster is the Nilo-Saharan “portion” of the East African cluster, i.e. that it can not be distinguished from the ancestry of the Maasai that is similar to Afroasiatic Ethiopians due to the lack of other Nilo-Saharan samples or some other factor that made it difficult for a split to occur (K value, genetic relationships between other populations included in the analysis).

    Tishkoff’s study shows Oromos from similar parts of Ethiopia as the Behar samples (that Dienekes uses) with only around 6% “Nilo-Saharan” ancestry. Meanwhile, Tishkoff’s Maasai samples from three different Maasai groups were all around 50% “Cushitic/Afroasiatic” on average.

    Of course, there are most likely older genetic links between Afroasiatic Ethiopians and neighboring Nilo-Saharans, but that is a different matter.

    Omotic is generally considered the most divergent branch of the Afroasiatic languages. Some argue it isn’t Afro-Asiatic at all http://www.uio.no/studier/emner/hf/iln/LING2110/v07/THEIL%20Is%20Omotic%20Afroasiatic.pdf noting that “Omotic has a very innovative and mixed lexicon with many intrusions from [AA] languages, especially Cushitic, and also from Nilo-Saharan.” The lexical blending of Cushitic and Nilo-Saharan, the Nilo-Saharan style tonality, and the suggestively Afro-Asiatic grammatical flourishes of Omotic that have caused many to classify it as Afro-Asiatic are together suggestive of an incomplete Afro-Asiatic language transition, or of an Cushitic-Nilo-Saharan creole, at the fringe of the Cushitic (and Afro-Asiatic) language area where the Afro-Asiatic influence would be weakest.
    As far as I know, the divergence of Omotic is not believed to be caused by the minor Nilo-Saharan substratum, but rather a more ancient split from the rest of Afroasiatic. But that is outside of my comfort zone.

    Sure Omotic is spoken at the fringe of the Cushitic language area, but I would not say that Afroasiatic influence should be weakest there, considering that it seems likely to be close to the area from which proto-Afroasiatic originally spread.

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  • The only exception is the Tigrayan ethnic group, which carries an elevated frequency of Eurasian lineages.

    did you note the clustering of the tigray with the ahmara in the PCA? were the ‘central cushitic’ then simply always closer to the semitic speakers than ‘eastern cushitic’?

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  • I have spoken of my somewhat atypical, for a South Asian, genetic results before. Recently Dienekes performed some cluster analysis which confirmed the initial findings, while adding a little detail: I am DOD075. The Southeast Asian component is modal in Malays, while the East Asian component is modal in the North Chinese. Vietnamese and Cambodians...
  • Any chance that East Asian component is from ruling islamic mogul?

    possible. though the ratio of “east asian” in the burmese communities likely high in any case. i assume i have some line of descent from a turk within the last 500 years, but i doubt it was that much.

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  • In the open thread someone asked: "Any recent stuff on the genetics of Ethiopians." That prompted me to look around, because I'm curious too. Poking around Wikipedia I couldn't find anything recent. A lot of the studies are older uniparental lineage based works (NRY and mtDNA). Ethiopia is interesting because unlike almost all other Sub-Saharan...
  • Andrew,

    As we discussed on Dienekes’ Blog back in March 2010, I predict that once more discoveries are made Y-DNA E will be shown to be Eurasian, with only A and B left as African.

    I also wonder if the mystery component in Mozambique is Austronesian, likewise if Austronesians are the mystery component in the North Kannadi – who knows, but if I’m right, it would provide the stepping stones for Austronesians ending up in Madagascar, as I think a direct voyage is unlikely.

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  • I have spoken of my somewhat atypical, for a South Asian, genetic results before. Recently Dienekes performed some cluster analysis which confirmed the initial findings, while adding a little detail: I am DOD075. The Southeast Asian component is modal in Malays, while the East Asian component is modal in the North Chinese. Vietnamese and Cambodians...
  • Thank you for your candor that really gives life to an otherwise clinical discussion. Your conjectures seem to be on point.

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  • In the open thread someone asked: "Any recent stuff on the genetics of Ethiopians." That prompted me to look around, because I'm curious too. Poking around Wikipedia I couldn't find anything recent. A lot of the studies are older uniparental lineage based works (NRY and mtDNA). Ethiopia is interesting because unlike almost all other Sub-Saharan...
  • Could you elaborate on the extent to which the Bantu expansion was eliminationist and what evidence we have?

    A 2010 journal article http://www.nature.com/ejhg/journal/v19/n1/full/ejhg2010141a.html
    looking at whole genome comparisons in Sub-Saharan Africa, particularly Mozambique, addresses the issues somewhat. Basically, it suggests that there was more assimilation in some places than in others. For example, “we find a strong differentiation of the southeastern Bantu population from Mozambique, which suggests an assimilation of a pre-Bantu substrate by Bantu speakers in the region.” It goes on to say in the body of the open access article that:

    “ii.The southeastern Bantu from Mozambique are remarkably differentiated from the western Niger-Congo speaking populations, such as the Mandenka and the Yoruba, and also differentiated from geographically closer Eastern Bantu samples, such as Luhya. These results suggest that the Bantu expansion of languages, which started ~5000 years ago at the present day border region of Nigeria and Cameroon, and was probably related to the spread of agriculture and the emergence of iron technology, was not a demographic homogeneous migration with population replacement in the southernmost part of the continent, but acquired more divergence, likely because of the integration of pre-Bantu people. The complexity of the expansion of Bantu languages to the south (with an eastern and a western route), might have produced differential degrees of assimilation of previous populations of hunter gatherers. This assimilation has been detected through uniparental markers because of the genetic comparison of nowadays hunter gatherers (Pygmies and Khoisan) with Bantu speaker agriculturalists. Nonetheless, the singularity of the southeastern population of Mozambique (poorly related to present Khoisan) could be attributed to a complete assimilation of ancient genetically differentiated populations (presently unknown) by Bantu speakers in southeastern Africa, without leaving any pre-Bantu population in the area to compare with.”

    In other words, in addition to Pygmies and Khoisans, the two extant remnant hunter-gatherer populations of Africa, there was a third equally distinct Mozambiquian hunter-gatherer group that was entirely assimilated by Bantus to the point where no remnant hunter-gatherer group survived. Their genetics remain a large part of Mozambique’s Bantu population’s genetics (i.e. most Mozambiquans are mostly descended from this “lost race” of people), but their language and way of life has vanished every bit as completely as Western and Southern Europe’s hunter-gatherer populations.

    * * *

    Another interesting finding of the paper pertinent to the original post is to recall that the Maasai, which shows so much affinity with African part of the Ethiopian Oromo population, is proto-typical Nilo-Saharan language population. This is surprising because the Oromo are an Afro-Asiatic language family population. Naiively, given the Afro-Asiatic languages of Ethiopia, we would expect Ethiopians to be more genetically similar to other Afro-Asiatic language speakers than they actually are.

    The strong genetic connection to the Maasai is particularly surprising given that “There is a strong differentiation of Nilo-Saharans, much beyond what would be expected by geography.” Within African populations, looking at autosomal genetics, “The first PC (Figure 2a) and STRUCTURE with K=2 (Figure 3) separate the Nilo-Saharan-speaking Maasai from all other populations, with neighboring Luhya and African Americans in an intermediate position.” Thus, the deepest and most obvious break in African component of African autosomal population genetics is between the cluster that includes the Maasai and the African component of Ethiopians on the one hand, and all other African specific populations on other.

    * * *

    What does this mean? We don’t know. The kind of comparisons one does in autosomal genetics don’t clearly resolve themselves into tree like structures in the way that uniparental genetic methods do. Adding new populations or permitting more putative ancesteral populations in an analysis can turn what looked like a “source” cluster, not admixed with anything else, into a mixture of other components. The whole gene comparisons also provide fuzzier estimates of the relative evolutionary age of different components (although the degree of uniformity of a mix in a population is suggestive of whether the mix has “fixed” in the population over many generations or is recent). The post from “Anonymous at January 11th, 2011 at 8:12 am” illustrates this point by noting that Tishkoff’s analysis sees the Maasai as an admixture of Cushitic and Nilo-Saharans, while Dienekes’ plot shows them as a nearly pure type population in the admixture analysis (as does the 2010 paper that I cite which expands on Tishkoff’s analysis), and also appropriately notes that the sample sizes in whole gene analysis are small and prone to be less representative, with Dienekes’ analysis of the Oromo possibly failing to capture effects do to geographic variation within the Oromo since his Oromo samples are drawn from near the Kenyan border — small wonder that a population form near Kenya would be genetically similar to one from Kenya itself.

    What kind of scenario could be a fit to those fact? Here is a simple one. Given that Ethiopian Oromo have substantial Southwest Asian admixture not attributable to the Ethio-Semitic language transition about 2800 years ago, but similar in character, while the Maasai do not, one possibility is that the Afro-Asiatic Cushitic languages may be an artifact of a similar pre-historic language transition that took place more than 2800 years ago (i.e. 800 BCE) that caused most Ethiopians to transition from some pre-Cushitic language to to Cushitic languages in connection with a population influx from Southwest Asia.

    In that scenario, prior to that Cushitic transition, the Ethiopians may have been more genetically similar to the Maasai.

    Barring any other plausible linguistic candidate, the genetic similarity of the Ethiopian’s African component to the Nilo-Saharan language speaking Maasi suggests that pre-Cushitic Ethiopians may have spoken Nilo-Saharan languages. The possibility that there were pre-Oromo languages in Ethiopia that were Nilo-Saharan is also supported by the fact that Nilo-Saharan languages are common in Ethiopia’s neighbors (Kenya 29% of the population), Sudan (29% of the population — and more in soon to be separated out Southern Sudan), Uganda (26%), Chad (41%), Niger (33%) (Source http://www.bookrags.com/tandf/nilo-saharan-languages-tf/); that Cushitic (http://en.wikipedia.org/wiki/Cushitic_languages) and Nilo-Saharan languages have a similar and intertwined geographic distribution; and that Cushitic languages are at the fringe of the Afro-Asiatic linguistic area. Cushitic languages are also found in some of those countries. About 0.7% of Ethiopians speak one of sixteen Nilo-Saharan languages which could be a remant of an older substrate of Ethiopian Nilo-Saharan languages.

    Another possible clue that there might have been a transition in relatively recent pre-history from Nilo-Saharan to Afro-Asiatic languages could be present in the group of Omotic languages spoken by a small number of people in Southwest Ethiopia, which share the strongly tonal character of the Nilo-Saharan languages. Omotic is generally considered the most divergent branch of the Afroasiatic languages. Some argue it isn’t Afro-Asiatic at all http://www.uio.no/studier/emner/hf/iln/LING2110/v07/THEIL%20Is%20Omotic%20Afroasiatic.pdf noting that “Omotic has a very innovative and mixed lexicon with many intrusions from [AA] languages, especially Cushitic, and also from Nilo-Saharan.” The lexical blending of Cushitic and Nilo-Saharan, the Nilo-Saharan style tonality, and the suggestively Afro-Asiatic grammatical flourishes of Omotic that have caused many to classify it as Afro-Asiatic are together suggestive of an incomplete Afro-Asiatic language transition, or of an Cushitic-Nilo-Saharan creole, at the fringe of the Cushitic (and Afro-Asiatic) language area where the Afro-Asiatic influence would be weakest.

    Is this proof of this scenario? No. But, it is a scenario that would be consistent with the facts and there is suggestive circumstantial evidence to support it.

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  • Anonymous • Disclaimer says:

    First of all, you should know that Behar’s Oromos were sampled in areas neighboring the Kenyan border, while Ethiopian Oromos inhabit a large part of Ethiopia, all the way to the north.

    Allow me to give you a brief background on the demographic history of Ethiopia. In recent history, many Ethiopians, particularly those who now speak the Amharic language, underwent a language shift (in the case of Amharas, a switch from Cushitic to Semitic). You may ask yourself why there is such a clear distinction between Semitic speakers and Cushitic speakers in Dienekes’ ADMIXTURE runs.

    There are several explanations for this. One is, obviously, the geographic difference between the Semitic speakers and Cushitic speakers . Another explanation is that the “Cushitic” source population of most Semitic-speaking groups in Ethiopia were not Oromos, who speak an East Cushitic language, but “Agaws”, who speak a Central Cushitic language. Central Cushites speak a very distinct form of Cushitic, which split from the other Cushitic branches close to the proto-Cushitic root. Actually, the Ethiopian Jews went through a very recent, well-documented language shift from Central Cushitic to Semitic, although a small minority still speak their native language.

    Regarding Y-DNA and mtDNA differences between the ethnicities of Ethiopia, there is a lot of data available. Maternally, Oromos are just as close to Eurasians as Amharas are; they are basically identical. The only exception is the Tigrayan ethnic group, which carries an elevated frequency of Eurasian lineages.

    Paternally, Cushitic speakers are actually quite similar to Semitic speakers once all of the samples from different studies are put together. Regardless, the overwhelming majority of J in all of Ethiopia is old, much older than the entrance of Semitic. That is also why Ethiopian J1 lineages are among the most diverse in the whole world, the only region with higher diversity is parts of the northern Middle East.

    Just thought this information would be relevant.

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  • I have spoken of my somewhat atypical, for a South Asian, genetic results before. Recently Dienekes performed some cluster analysis which confirmed the initial findings, while adding a little detail: I am DOD075. The Southeast Asian component is modal in Malays, while the East Asian component is modal in the North Chinese. Vietnamese and Cambodians...
  • Any chance that East Asian component is from ruling islamic mogul?

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  • My goodness, we R1a guys get around. The highest density of my surname (not really Bigod) is in Shropshire, the limit of Anglo-Saxon conquest around 800 CE. The Immigrant in Virginia may have been born in London in 1746. Or a farm boy in NW England who hopped on a boat.

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  • In the open thread someone asked: "Any recent stuff on the genetics of Ethiopians." That prompted me to look around, because I'm curious too. Poking around Wikipedia I couldn't find anything recent. A lot of the studies are older uniparental lineage based works (NRY and mtDNA). Ethiopia is interesting because unlike almost all other Sub-Saharan...
  • Genetics of Ethiopians…

    Razib has done rounded up a nice review of Dienekes‘ Dodecad data to answer some prelim questions on the genetic of Ethiopia. Ethiopia is a very interesting cultural and paleontological area of the world. I had the pleasure of being a part of a f…

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  • The Bantus near Lake Victoria (Kenya, Tanzania etc) do show signs of admixture with the native Cushitic populations. Although it is highly variable in each tribe. According to Tishkoff et al. some Bantu speaking groups like the Tutsi, Mbugwe and Kikuyu have Cushitic ancestry in excess of 25%. While others like the Luhya only have it minimally (7%). The Tanzanian Iraqw people are remnants of the original Cushitic population which used to inhabit these lands before the Bantus (from West Africa) and Nilo-Saharans (from South Sudan) arrived. The Iraqw only have less than 15% admixture from those groups and are largely Cushitic.

    The Maasai from Kenya (East African HapMap samples used by Dienekes) have ancestral components which aren’t shown well in his admixture runs. The Maasai are a mixed people, in Tishkoff’s study they picked up the East African Cushitic cluster at 50%, the Nilotic (Southern Sudanese) at 25% and the remainder was mostly Bantu with minor traces from elsewhere in Africa. The Bantu/West African admixture in Maasai was about ~15-20%. Dienekes’ admixture run did pick that up quite well with the Yoruba (Nigerian) samples. Interestingly, the Ethiopian samples completely lack West African admixture.

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  • Could you elaborate on the extent to which the Bantu expansion was eliminationist and what evidence we have?

    we don’t have records of it, so only supposition. the main surprise to me is that khoisan and mbuti pygmy cluster together against the bantu populations. if the bantu expanded more through absorption that shouldn’t happen, the intervening populations would span the khoisan and pygmy. as it is, it looks like the khoisan, pygmy, and hazda, are relics in a sea of bantu.

    the bantu take pygmy wives, and there’s been assimilation of khoisan into the xhosa people. so i think mostly it was just low population density of the indigenes.

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  • Could you elaborate on the extent to which the Bantu expansion was eliminationist and what evidence we have?

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  • ah, is a better map.

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  • Razib your map gives a poor illustration of where Semitic and Cushitic languages are spoken.

    Many Cushitic languages are also spoken in Northern Ethiopia. In fact, Ethiopia is mostly Cushitic:

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  • One of the leading mtDNA papers on Ethiopia is here:

    http://www.ncbi.nlm.nih.gov/pubmed/15457403

    Most notably, on the mtDNA side, Ethiopia is the rough geographic center of the haplogroups of mtDNA haplogroup L3 that a closest to parent mtDNA lineage of macro-haplogroups M and N found predominantly in Eurasia.

    The leading view among linguists is that the Ethio-Semitic languages “reflect a single introduction of early Ethiosemitic from southern Arabia approximately 2800 years ago”, and that this single introduction of Ethiosemitic underwent “Rapid Diversification” within Ethiopia and Eritrea.”

    I have seen both Y-DNA and mtDNA papers dealing with Ethiopia (I can’t find the Y-DNA cite right at the moment) that clearly show a disproportionately male lineage distinction between Ethio-Semitic language speakers and non-Ethio-Semitic language speakers consistent with this hypothesis. The genome wide data clearly confirm the uniparental data in showing a distinction between admixed Ethio-Semitic language speakers and relatively unadmixed Oromo populations.

    Hence, the Oromo population is believed to be generally similar genetically to Ethiopia ca. 1000 BCE. Ethiopia has participated in maritime trade since ancient times providing one possible source of Southeast Asian admixture, although hardly the only possible scenario.

    The place of the non-Semitic Afro-Asiatic languages of Ethiopia, such as Oromo and other Cushitic languages in the Afro-Asiatic language family tree is unsettled and almost every combination of links has been proposed. One school of thought puts Oromo at the base of the Afro-Asiatic langauge family; others see the language family as originating in the Near East and back migrating (as a small number of minority mtDNA and Y-DNA haplogroups appear to have backmigrated). The age depth of the Afro-Asiatic language family is also a matter of great dispute, particularly over the question of whether it post-dates or pre-dates food production. An older date tends to favor an African origin for the language family; a more recent date tends to favor a Middle Eastern origin.

    The extent to which the Ethiopia’s original adoption of farming was independent of Sahel agriculture in the West African Sahel that ultimately merged with it, or was an extension of it that added supplmentary crops, and its timing, is also controversial. But, the Ethiopian and Sahel agricultural crops are generally viewed as distinct and independent in origin from the Fertile Crescent package. The point in time at which domesticated livestock arrived in the region is also a subject of considerable debate.

    Upper and Lower Egypt have population genetic differences in many respects, and it would be useful to know where the Egyptian samples come from in the ADMIXTURE plot to know what inferences we should draw from them.

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  • ok, might be informative:

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1181965/?tool=pmcentrez

    no time for a close read.

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  • But, I think part of the untold story here is that there may have been a larger genetic impact on Arabia after the rise of Islam from the Levant than vice versa!

    If you think about this in terms of the traditional understanding of things, it’s a revolutionary idea. But if you fit the rise of Islam into your model of how herders affect agriculturalists (much more linguistically than genetically) then the Arabisation of the Middle East is sort of like the Turkisation of Anatolia. Granted, it’s stating the obvious – most Syrians are “white” in a way that Saudis often aren’t – but it’s still interesting to see it fit that general model you discussed a few weeks ago.

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  • ian, i think we need to look to NRY stuff for that. no time right now, but i’ll check it out if you don’t. there is a model that semitic languages come from northeast africa, so perhaps.

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  • Ethiopians, in particular highland Ethiopians, seem to me likely an ancient stabilized hybrid population between a population from Arabia, and a local Sub-Saharan population

    Forgive me if I’m missing something obvious, but is there some reason to assume that the “Southwest Asian” component originates in Arabia rather than Ethiopia? Could this just as well represent a substratum that colonised southwest Asia prior to the influx of East Africans? Or, for that matter (though less probably) could the absence of ancient East African lineages in Saudi Arabia reflect some sort of a bottleneck in the settlement of southwest Asia? Or is it possible to add some sort of temporal estimate into this?

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  • It’s Amhara.

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  • Over at his blog Dienekes Pontikos has taken some public data sets and his own Dodecad samples and generated a massive MDS plot of West Eurasian populations. The MDS is fine as it goes. It illustrates clearly that when you visualize an individual on a plot defined by the two largest dimensions of variation in...
  • It would interesting to see other races East Eurasians and Africans on the same plot, just to see where in what proximity to whom they would cluster.

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  • I’m surprised that the Bnei Menashe, who hail from eastern India and show noticeable Mongoloid features cluster soo close to the Brahui,Balochi and Pathan.

    i assume that is a cording error.

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  • Dienekes writes: “The people who lived in Anatolia 1500 years ago were not Turks. Hell, most of them were not Turks until quite recently when the Turkish Republic decided to forge a Turkish nation out of the heterogeneous Muslim population of the Ottoman Empire.”

    Dieneke, as a self-identity the “Turkish” identity itself is much more recent than you think, as I’ve explained in another thread of this blog:

    the “Turkish” identity of Anatolian + Rumelian (=Balkan) + Cypriot “Turks” is the result of nationalism imported from the West during the late 19th and early 20th centuries by the Ottoman intelligentsia, and it spread among the masses only after the establishment of the Turkish Republic and with the nationalist reforms of Kemal Ataturk. Before all these, there was no “Turkish” ethnicity or nation, Seljuqs and Ottomans were called “Turks” only by the West, but no individual or group in the Seljuq and Ottoman empires from the sultans to the lowest levels of the society applied the “Turkish” identity for themselves, the word “Turk” was just an insult and not an ethnic term (in fact, there was no concept of ethnicity or nation in the Seljuq and Ottoman empires, the Millet system was a religious system, not ethnic). Before the spread of the “Turkish” identity among the masses beginning from Ataturk, Turkish-speaking Muslims of the former Ottoman lands didn’t call themselves “Turk”, but only “Muslim”.

    unlike the “Arab” identity, the “Turkish” identity was never applied by the very people designated with that identity (not even by the conquerors from Central Asia) before the spread of nationalism from the West. Before nationalism, the “Turkish” identity was an identity of the other (and often a despised other), not oneself.

    “Turkmen” identity, OTOH, was used by the conquerors from Central Asia and by their descendants (not pure of course, there are apparently no pure descendants of them) for themselves, but its use has always been rather limited to a minority among the Turkish-speaking Muslims of the former Ottoman and Iranian lands.

    The country name “Turkey” (and its other versions in other languages) was also only used by the West (for the territories ruled by “Turkish” rulers) before the spread of nationalism among “Turks”. Seljuqs of Anatolia called their own country “Rum” (=Rome) and Ottomans called their own country “Osmaniyye” (=Ottoman state). The name “Türkiye” (Turkish version of Turkey) is a late 19th century borrowing from the Italian word “Turchia” (then used for the Ottoman Empire) and was subsequently applied to the republic founded by Kemal Ataturk.

    http://blogs.discovermagazine.com/gnxp/2010/12/are-turks-acculturated-armenians/

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  • Edit
    I meant to include the Makrani when mentioning the Brahui,Balochi and Pathan clusters and the omission is unintentional.

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  • I’m surprised that the Bnei Menashe, who hail from eastern India and show noticeable Mongoloid features cluster soo close to the Brahui,Balochi and Pathan.
    If it was lack of focus in South Asia groups for this particular plot??, then how are the Kalash clustering further away from the Brahui,Baloch and Pathan than the Bnei Menashe when they (Kalash) are geographically closer than the BMJ to the aforementioned 3 Pakistani ethnic groups?

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  • What’s interesting to me is that the British and Germans are so close, and surprisingly the Slovenians are right by them. Then the Irish and Orcadians bridge the gap between the British/German and the Scandinavians.

    My Mother is under the IRI – so typically Irish by this analysis, while my Father is on top of the SCD, so pulls more towards Scandinavia – maybe some unknown Viking (or Finnish/Russian/Chuvash??) ancestry.

    My wife’s Sicilian grandmother is right on top of the SIS towards the Sephardic Jews – I was expecting her to be nearer the Greeks. So maybe this is reflective of the fact that she has relatives with North African mtDNA and others with connections to Spain and Spanish names, so she may have Spanish/Moorish ancestry, which is pulling her away from the Greeks.

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  • oh, any retard discussion about whether ashkenazi jews are white or not will be deleted. i think they’re white personally, but i don’t give a shit if you agree or don’t agree. this stuff is moron bait, and i’m rather avoid that particular swarming of fish.

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  • So it’s settled. Ashkenazim are (basically) white Europeans. Agreed?

    i don’t agree. it isn’t “basically.” AJ are special in a variety of ways. but some people are invested in AJ being white europeans because of their racialist sympathies, and some are invested in them not being white europeans. you lot will continue to hold to your position no matter the PCA or bar plots i present from what i can tell, so wuteva. i.e., people can look at the same data visualization and come to exactly opposite viewpoints.

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  • So it’s settled. Ashkenazim are (basically) white Europeans. Agreed?

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  • One expects, but does not know, if Direction3 had been included in the analysis, Ashkanazis and Sicilians point clouds would separate out on the 3rd axis.

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  • It is somewhat surprising that one doesn’t see separate coastal and Danubian forks in the data, because that was one of the original big divides in the process of spreading farming to Europe, and because there pretty distinct divides (e.g. between Y-DNA haplogroups R1a and R1b) in some of the uniparental markers. Both European forks seem to spread out from a gateway in Greece, and the plot suggests more East-West axis admixture in Europe than one would expect.

    It isn’t too surprising but still worth noting that the Caucuses, while geographically compact and fairly modestly populated, have almost subcontinental levels of genetically diversity. The region is almost as thinly connected to the rest of West Eurasia genetically as it is linguistically in the autosomal markers. But, perhaps (as Dienekes has suggested) it is a common Caucuses component that is pulling the Northern European and Pakistani components towards it via Indo-European contributions. However, if that interpretation is correct, the extent to which Bronze Age and early Iron Age Indo-Europeans were replacing existing populations would have had to have been very great to have that effect.

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  • Nava,

    If you look at the legend, the are as follows:

    Green Circle = Saudi
    Green Diamond = Bedouin

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  • Who are those green circle and squares at the top right of the graph, if i may ask.

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  • probably. it is an interesting illustration of the difference between genes & culture: the former can be much more continuous than the latter. it looks like the pakistani iranian speakers are much more like pakistan indo-aryan speakers than iranian speakers from the west, the kurds and farsi speakers. as you note, filling the whole with afghans of various ethnicities, central asian tajiks, and iranians from khorasan would be be of interest.

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  • It seems reasonable to estimate that if there were samples from Afghanistan, they would form a bridge between the Iranian and Pakistani samples, to some degree.

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  • To the left you see a zoom in of a PCA which Dienekes produced for a post, Structure in West Asian Indo-European groups. The focus of the post is the peculiar genetic relationship of Kurds, an Iranian-speaking people, with Iranians proper, as well as Armenians (Indo-European) and Turks (not Indo-European). As you can see in...
  • [comment removed. i believe the commenter made some good points, but there was a lot of political stuff thrown in. not acceptable. i'm not an editor]

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  • I am not feeling well today and have no time to check the veracity of my claim. do not repeat the question. i will do the research when i have time, energy, and inclination. otherwise, you might be right. i don’t really care too much.

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  • Like the Armenians the Kurds are an antique population, claiming descent from the Medes, and referred to as Isaurians during the Roman and Byzantine period.

    kurds in byzantine lands. two byzantine emperors were isaurian, zeno and leo iii. leo may have been ethnic syrian, but zeno probably came from an iranic tribe. presumably the kurds were religiously diverse before islam, and some of this surely remained after islam. i don’t know the details of the areas inhabited by kurds then and now, but i don’t think the byzantine exclusion of muslims would be dispositive in the early period.

    Razib, what is your evidence for Isaurians being Kurds, Medes or any other Iranic-speaking people? As ZooKeeper states, they are much more likely to have been an Anatolian IE-speaking people. In any case, Isaurians had centuries ago totally switched to Greek language – probably also completely losing all their ethnic identity – by the time the Seljuqs and Turkmens arrived Asia Minor and today’s Kurds’ (including Zazas) “traditional” region has absolutely no intersection with that of historical Isaurians, who, we know, lived around the Taurus Mountains; so today’s Kurds shouldn’t be expected to have any descent from historical Isaurians.

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  • I’m wondering why you made the Isaurian = Kurdish connection, though. Taking into account the Isaurians’ location, isn’t it much more likely that they were an IE-Anatolian-speaking population or something like that?

    I agree with you, ZooKeeper. I am too waiting for an answer from Razib on this matter.

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  • Some corrections: “pre-historic times”, “transferred to the Balkans”. Pardon.

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  • -”Just as plausible to me is that eastern Anatolia as a whole exhibited little genetic difference between Greeks and Armenians, and the former were wholly assimilated or migrated”

    The Greek-speaking Chalcedonian Christians inhabiting the area from the Aegean to Cappadocia and the Pontus (the easternmost and northeasternmost locations where they could have been found in high numbers in the early 11th century, the local languages having gradually disappeared in a process beginning in the 4th century BC and where they were still found in smaller numbers – though barely in Cappadocia – in the 20th century) would have been mostly native in ancestry (despite the important colonization of Asia Minor from mainland Greece in Hellenistic times, it was obviously a very slow process of acculturation that eliminated the native languages) rather than mainland Greek so this must be the case. In other words, Turks are mostly acculturated Anatolians who were mostly Christian (of various “denominations”) and spoke a variety of languages, most importantly Greek, Armenian and Aramaic. Are genetic data offering us something that history doesn’t, so far?

    -”the Greek mainland may always have been subject to more influence from the lands to the north”

    That’s true from pre-historic ancient times, achaeology attests to that and quite likely that’s where the first IE-to-be-Greek speakers came from, after all, but Anatolian – Balkan contacts might have been somewhat important in historical times as well (you already mentioned the Greco-Turkish population exchange). For example, Slavs were settled in Bithynia, Anatolian Paulicians in Thrace etc. Also, some of the exchanged Balkan Muslims were, in part, Anatolian populations that had been transferred in the Balkans some centuries ago (e.g. Turkish-speaking Muslims in certain areas of Macedonia) so genetically speaking, those were essentially returning, at least in part.

    We also need to remember that modern Turkey is a vast country, with an important west-east axis, so the place of origin of the samples is important too.

    I’m wondering why you made the Isaurian = Kurdish connection, though. Taking into account the Isaurians’ location, isn’t it much more likely that they were an IE-Anatolian-speaking population or something like that?

    Considering the nature of this discussion and some rather rude posts (oh Elias!) I have to commend Onur on his attitude and replies!

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  • Steven Colson,

    A common J2a4b1 between us is indeed astonishing. The advent of DNA analysis will force a lot of history to be re-examined!

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  • Hi Corduene… in response:

    1) If it makes a difference to you, there were enough Armenians the eastern provinces for their political autonomy, if not outright secession.

    2) Land claims and other demands are not fully based on population percentages but rather are reparations for the genocide and for the survival of what remains of Armenia.

    3) It is best not to open this topic in this forum. I respectfully suggest you review http://www.regionalkinetics.com. You will find a contact email where this can be discussed more appropriately.

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  • You may be right, Davidian. Similarly to “Turks”, Kurds may have assimilated lots of Armenians and Assyrians in their last one thousand-year expansion in the east of what is now Turkey.

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