October 01, 2010

Some ADMIXURE estimates on Eurafricans

Here is an ADMIXTURE run on the Xing et al. (2010) dataset using markers with less than 1% genotyping no-calls. Populations (left-to-right) are: Alur, Hema, Luhya (from Africa), and CEU, Tuscan, Slovenian, Urkarah, and Kurdish (from Western Eurasia).

Most West Eurasians have no trace of Sub-Saharan ancestry, except Kurds (estimated here at 2.3% overall, range: 1-3.6%), and a couple of Slovenians (4.5% and 1.6%, overall 0.2%). The fairly uniform distribution in Kurds suggests to me that this is an ancient phenomenon reflecting gene flow between the Near East and Africa and not a recent phenomenon.

The Hema are an African population exhibiting West Eurasian affinities (11.0%, range: 4.2-15.2%). Consult my comments on the original Xing et al. article on some information on these Nilo-Saharan pastoralists from the Democratic Republic of Congo.

17 comments:

Average Joe said...

Excellent work. Do you intend using any western European populations to see how closely related they are to other groups?

onur said...

Kurds don't show any Negroid component in the published results of the Xing et al. paper, so the red component at K=2 in your ADMIXTURE analysis may be related to something other than Negroid admixture (whether recent or ancient).

Dienekes said...

Kurds don't show any Negroid component in the published results of the Xing et al. paper

Where do you see that?

onur said...

Where do you see that?

This one is a particular example:

http://1.bp.blogspot.com/_Ish7688voT0/TEdq-EynHCI/AAAAAAAACgw/X11-JB_pz8U/s1600/african-xing.jpg

Ebizur said...

I understand that the Alur are more purely Nilo-Saharan than the Hema from a linguistic perspective (which is the only appropriate one in this case, since "Nilo-Saharan" is a linguistic classification). Some of the Hema do have E1b1b1 Y-DNA, and some of them do speak a Nilo-Saharan language (Lendu), but the original Hema seem to be a Bantu-speaking tribe, closely related to the majority populations of Burundi, Rwanda, and (at least the southern half of) Uganda.

Alur is a dialect of the Luo branch of the Nilotic languages; the Alur people are linguistically very closely related to the various Luo peoples of southern Sudan (e.g. Shilluk), northern Uganda, and the eastern shores of Lake Victoria in Kenya and Tanzania. Their next closest linguistic relatives are supposed to be the Dinka and Nuer of southern Sudan.

Lendu is a Central Sudanic language, so it is more closely related to the languages that are spoken by the Mbuti pygmies than it is related to the Nilotic languages of the Alur, Shilluk, or Maasai. It is curious that only the Hema, who are supposed to be an originally Bantu tribe that has been influenced by the Central Sudanic-speaking Lendu people, exhibit some Western Eurasian affinity, whereas the Nilotic-speaking Alur do not exhibit such affinity. I would like to see some research on the DNA of the Lendu, Mangbetu, and other Central Sudanic speakers (including the Bambuti, of course) in order to narrow down the list of potential sources of the Western Eurasian affinity that has been observed in this sample of Hema.

Dienekes said...

This one is a particular example:

Thanks, you are probably right. The Sub-Saharan "admixture" in Kurds is probably indicative of a shared genetic component, that is why I wrote "is an ancient phenomenon reflecting gene flow between the Near East and Africa"

However, Turks have about 2% Sub-Saharan admixture, and Arabs are known to have more, so I wouldn't be surprised if, when the relevant African populations are sampled, Kurds also turn out to have African admixture in that order.

onur said...

However, Turks have about 2% Sub-Saharan admixture

Autosomal studies don't show any Sub-Saharan or Negroid admixture in Turks:

http://2.bp.blogspot.com/_Ish7688voT0/Sfttv4ydl5I/AAAAAAAABVE/ycfoDOsujnQ/s1600-h/auton_structure.jpg

http://2.bp.blogspot.com/_Ish7688voT0/TA_8VX3jGkI/AAAAAAAACcM/HVkOLdPm94g/s1600/admixture-global.jpg

Dienekes said...

Autosomal studies don't show any Sub-Saharan or Negroid admixture in Turks:

"Turks" of Anatolia are not a homogeneous population, so the tiny samples of the studies you refer to are no substitute for the big samples studied with uniparental markers and show the unambiguous presence of Sub-Saharan elements.

Besides, I've seen with my own eyes "Black Turks" in Greece itself, so I very much doubt that they didn't exist in Anatolia.

ashraf said...

Those "black "turks"" (ironical appelation btw, since original turks are mongoloid with most likely 0% ss input) are descendants of relatively recent sudanese and other african people (especially 16 and 17 th century)to work in cotton (and other plants) fields, you can see many of them in countryside of Adana and inner Egean region.

onur said...

Besides, I've seen with my own eyes "Black Turks" in Greece itself, so I very much doubt that they didn't exist in Anatolia.

In westernmost Asia Minor, there is a tiny remnant population of Black slaves of the Ottoman times, some of them also migrated to the metropoles in recent times, but there is no other known Black remnant population in Turkey (at least in the Turkish-speaking parts, maybe there are some other Black remnant populations in the Arabic-speaking parts of Turkey, but I don't know any). But as I said, they are a tiny minority in the places they live and don't mix with the White folk around them much. I have very rarely seen Black or Black-mixed people in Turkey and all of them were probably either tourists or recent illegal workers from African countries.

In short, probably the "Black Turks" you saw were from that tiny population of Black slave remnants in Turkey.

horacioh said...

It’s a pity, that the study doesn’t include Ashkenazim. The ”L1” and "L2" mtDNA marker is present in the two populations – Ashkenazim and African Ethiopian Jews - also the derived and sibling mtDNA Hg "M" and "N1", as well as the Y markers Hg E3b and 4s too, all of this from East Africa and so. (Also is watching in autosomal markers in minor as well) They belong respectively at one of the three nucleous or center jewish ancient populations, that evolving the called "Syrian-European nucleous"(helenistic and Roman times).
The oldest center –Ethiopians likely belong these- were that developed in Napata and Elephantine (Kush) and whose nucleous or center was after Alexandria, and I called "Coptic Nucleous" derived in two bias, and split forwards the North via Europe -intermixed with the Syrian Europe nucleous- or the South, via Nile and the Horn Of Africa.
The "Babilonian and Persian nucleous" is other of the above three mentioned centers and included Bukara, Iranian and Iraki mainly.
All of this Nucleus take Judaea and Israel like a axis or pendulum.
Another fourth Nucleous or center I call "East Europe" -not mainly conected with ME-, is not ancient like the three others and was the Jewish Khazar Empire stiring into Askenazy current population and others. All of this events were naturaly intrajewish asimilations in all jews current populations.
The Ashkenazim hyperhaploydia and heterozygosis (not common in isolated population, the same for mtDNA coming in great rate from host population) is explained by the superposition and overlay of diverse fount or source population , that are all of this of Jewish origin (that consider converted into intraJewish assimilations) , one coming from the “Syrian European nucleous” – that Sephardic as well as preAshenazim bring inside -. The other convergence were the “Coptic Jewish nucleous”, coming from Alexandria, the main and largest Judaic center in ancient times – the buried and graves in Jewish graveyards and catacombs of Tuscan, and Alsace as too Rhineland cities take a lot of Egyptian ornaments and display figures from these, as well as Y and mtDNA markers - . The great Jews migration from Egypt beginning after the Muslim invaders from Arabia in the VII AE century. The “Babylonian and Persian nucleous” take place and contacts newly with and when the “preAshenazim second fase” were migrating to the East Europe. A remarkable contact was with the fourth “East Europe Jews nucleous”-not related or little related with ME-, with the descendant of the Jews Khazarians ones, spreading every where and carrying a lot of East Europe and Eurasian markers. That happen between the XI and XII century AE.
Remember also that Ethiopian Jews and non Jews are closely between them and are related in a whole to Middle Eastern by languages, traditions and genes associated too with the Horn of Africa. It is the difference between Hindu people – without these close relations with ME- and Ethiopians in Whole as well.
See, Table 2. Haplogroup distribution in non-Jewish local populations and Jews
From: Ashkenazi Jewish mtDNA haplogroup distribution varies among distinct subpopulations: lessons of population substructure in a closed group
Jeanette Feder, Ofer Ovadia, Benjamin Glaser and Dan Mishmar
See: when in other papers like this too, for example, Polish Jews mtDNA L1,L2 close to 4% Polish non Jews are 0%
Polish Jews Polish non-Jews Russian and Ukrainian (RU) Jews Russian non-Jews
Haplogroup N=192 % N=436 % N=150 % N=201 %
U (non K) 12 6.3 70 16.1 11 7.3 36 17.9
K 72 37.5 15 3.4 25 16.7 6 3
HV* 20 10.4 25 5.7 19 12.7 15 7.5
H 27 14.6 197 45.2 41 27.3 85 42.3
J 18 9.4 34 7.8 15 10 16 8
T 9 4.7 50 11.5 11 7.3 22 10.9
N1 12 6.3 2 0.5 11 7.3 0 0
I 3 1.6 8 1.8 0 0 5 2.5
W 6 3.1 16 3.7 4 2.7 4 2
X 1 0.5 8 1.8 0 0 7 3.5
L1 and L2 6 3.1 0 0 2 1.3 0 0
L3 0 0 1 0.2 0 0 0 0
R* 0 0 2 0.5 0 0 1 0.5
M 2 1 8 1.8 0 0 3 1.5
Pre-HV 2 1 0 0 6 4 1 0.5
Others 2 1 0 0 5 3.3 0 0

Gioiello said...

What does Horacioh mean? That these four sources of the Jewish people come from ancient Jews (from Abraham etc.) or are they due to admixture and introgression from many other peoples? If he does mean that all them are true Jews, this doesn’t fit with data at our disposal.
We will know this when Jewish archaeologists and geneticists will publish the results of their researches on ancient bones from Israel. MtDNA K, so diffused among Ashkenazim, and which is also mine, wasn’t found on the tested tombs around Jerusalem. It could be due by chance, but it is a little strange not finding it. We shall see next results.

onur said...

the tiny samples of the studies you refer to are no substitute for the big samples studied with uniparental markers and show the unambiguous presence of Sub-Saharan elements

I acknowledge that autosomal studies of Turks is in its infancy. But those "Sub-Saharan elements" you mention may actually be pre-Negroid in origin and might have arrived Asia Minor thousands of years ago from a completely non-Negroid source.

pconroy said...

Gioiello,

Have you had your autosome tested with 23AndMe (or DeCodeMe), as with even a little Jewish ancestry (1/32 for example) you will show lots of Jewish relatives - like hundreds.

That would solve your existential question once and for all?!

Gioiello said...

Which “existential question” are you speaking about? I was tested both by “deCODEme” and “23and ME”, and I was 23% and 19 % Ashkenazim: this said Warwick who ran my data when I wrote on “dna-forums”. But I have always thought that are Jews to be Italians and not me to be a Jew. The “existential question” belongs to Jews and not to me, because I’d have willingly accepted a Jewish origin. Are Jews who don’t accept an Italian one. My quest is only scientific, not personal. Many people and researchers are convinced that Jews (above all Ashkenazim but Sephardim too) have a little to do with Abraham and all Jewish mythology.

Corduene said...

"Most West Eurasians have no trace of Sub-Saharan ancestry, except Kurds (estimated here at 2.3% overall, range: 1-3.6%), and a couple of Slovenians (4.5% and 1.6%, overall 0.2%). The fairly uniform distribution in Kurds suggests to me that this is an ancient phenomenon reflecting gene flow between the Near East and Africa and not a recent phenomenon."

The above used Study Xing et al. 2010 is about Iraqi Kurds (6,5) Mio and not about Kurds As a whole Nation.

Quote:"Dispersion of a Caucasus/Middle East genetic component
In the ADMIXTURE analysis of Eurasia, we observed a clinal distribution of a
Caucasus/Middle East genetic component in several South Asian populations. Evidence from mitochondrial DNA, Y-chromosome, and autosomal loci suggests that the genetic composition of India has been influenced by west Eurasians .

We find that this ancestry component is most prevalent in West Asians (Iraqi
Kurd) and Caucasus populations (Daghestani)...This ancestry component also extends into Europe and is more prevalent in southern Europeans than in northern Europeans. Our results suggest that the northern Indian genetic component proposed by Reich et al could represent the dispersion of a genetic ancestry component originating near the Caucasus/Middle East region."

This 2,3% Sub-Saharan influence among iraqi Kurds is not found among Kurds from Anatolia and Iran. This has also nothing to do an ancient phenomenon reflecting gene flow between the Near East and Africa but is a recent phenomenon. like 40 Years ago their were some 1-2 thousand Ethiopian Jews settled in Iraq. some of them became Kurds. I know one who is half iraqi ethiopian half Kurd personally.

Here is a better Study from Nasidze et al. made about caucasian and anatolian Kurds.

http://www.zazaki.org/files/Kurds.pdf

Corduene said...

I is not very correct to talk about West Euroasian Kurds by showing a study made only about Iraqi Kurds which in fact are just 1/6 of the whole Kurdish Nation. There are 20 Mio Kurds in Turkey, 3-4 Mio In Syria and 7 Mio in Iran while only 6 Mio in Iraq. This is like showing a study made about Cretans as a study about all Greeks. If there is 2 % Sub Saharan ancestory found among Iraqi Kurds and absent among anatolian, syrian and Iranian Kurds than the impact of sub saharan influence is almost 0%.