Populations Admixture Proportions

[Roderic]

Populations admixture proportions



The clusters can be loosely labeled as:

A: South Asian
B: Altaic
C: Irula (S Indian tribals)
D: !Kung (Khoisan speakers from Africa)
E: Sub-Saharan
F: Polynesian
G: Southeast Asian
H: Pygmy
I: West Asian
J: European
K: Amerindian
L: Northeast Asian

http://dienekes.blogspot.com/2010/09...t-al-2010.html

[Roderic]

Some ADMIXTURE estimates in Eurasia

Clustered European populations together with Mandenka and Han Chinese:



The populations are in the following order: Han, Mandenka, Orcadian, French Basque, French, North Italian, Tuscan, Sardinian, Russian.

Here are the admixture proportions:



Notice how the eastern component in Russians is now estimated as 10.9%. This probably reflects the inclusion of French Basque and Sardinians, i.e., populations which have historically no opportunity for eastern Eurasian admixture, rather than only Orcadians. This underscores the importance of having appropriate poles in inter-continental admixture estimates (see Appendix I).

Note also that the 100% value for the Han Chinese is not incompatible with the presence of the two aforementioned Caucasoid-admixed individuals, who are present here with an estimated 1.9% and 0.5% such admixture. However, this contributes little to the sample average of 40+ individuals.

The minor (0.1%) Sub-Saharan admixture in Tuscans and Sardinians is also interesting. As you can guess from the figure, this stems from a handful of individuals (green specks) with less than 1% admixture, which is, however more than the numerical low of 0.001% inferred for most Europeans by the software.

http://dienekes.blogspot.com/2010/09...n-eurasia.html

[Roderic]

African admixture in the Near East:

Here is the result of running ADMIXTURE for K=5 using 275K SNPs on the combined HGDP + HapMap African and West Asian populations, also including Adygei and Tuscans. The populations are in order: Luhya, Maasai, Tuscans, Yoruba, Adygei, Bedouins, Druze, Mozabites, Palestinians.



At this level of detail, Africans are divided into three clusters which can be labeled Sub-Saharan (red), East African (blue), and "Mozabite" or North African (purple). Europeans and West Asians form the green cluster, while the Arab samples have a substantial contribution of the yellow cluster.

Here are the admixture proportions:



African admixture in the two European populations is probably in the limits of statistical noise and consists of "Mozabite" (0.4%) for Tuscans and "E African" for Adygei (0.6%).

Druze, an Arab population that was religiously isolated from Arab Muslims for about a thousand years seems to have correspondingly missed most African admixture, registering 0.6% "Mozabite" and 1.1% "E African".

Non-Druze Arabs have clear traces of African admixture both in the form of "Mozabite" North African (4.5% for Palestinians, 4.9% for Bedouins), E African (6% for Palestinians and 5.7% for Bedouins) and a little Sub-Saharan (1.3% for Palestinians and 2.1% for Bedouins).

I had pointed the mainly eastern African admixture in Near Eastern Arabs a year ago in my review of HAPMIX. Clearly Maasai are a better stand-in than the Yoruba for whatever African ancestry Arabs have.

http://dienekes.blogspot.com/2010/10...ast-where.html

[Roderic]

Clustering European Populations with ADMIXTURE

Here is the result of running ADMIXTURE for K=6 using 275K SNPs on the combined HGDP+HapMap European populations + the CHB Chinese sample from HapMap. (Only the larger HapMap Tuscan sample was included, rather than the smaller HGDP one).

Using a large number of K in closely related populations makes convergence quite harder, but the end result does correspond to several identifiable clusters.



yellow: Northern European
green: "Adygei"
red: "Sardinian"
purple: "Basque"
light and dark blue: Chinese

It's interesting that the Chinese split before some Europeans do. Interestingly, one of the two Chinese components (light blue) is the one represented in Russians, so this split probably reflects some type of northern/southern differentiation in Chinese, as the east Eurasian component in Russians was introduced from northern Finno-Ugric speakers.

Here are the admixture proportions:



http://dienekes.blogspot.com/2010/10...ions-with.html

[Roderic]

ADMIXTURE in the New World


Here is the result of running ADMIXTURE on ~450K markers on six HapMap-3 populations; left-to-right: African Americans from the Southwest (ASW), Utah Whites (CEU), Beijing Chinese (CHB), Mexicans from Los Angeles (MEX), Toscans (TSI), and Yoruban from Nigeria (YRI).




Here are the admixture proportions (in %):



It is obvious, however, from the ADMIXTURE plot above, and the triangle plots below (for ASW and MEX), that the admixture is not uniformly distributed.

Notice the two African American individuals with substantial Amerindian admixture (14 and 29%), while the rest are a simple 2-way mix of Europeans and Sub-Saharans with minor Amerindian admixture in some of them. The standard deviation of European admixture is 8.3%, lower than in Mexicans.



Mexicans are variable in terms of their European-Amerindian mix, but with less variable tiny Sub-Saharan component (0.6% with a standard deviation of 1.2%). This is probably due to the fact that blacks were absorbed earlier in Mexico, while European-Amerindian social stratification and continued European immigration has fueled the retention of considerable variation.

European admixture in Mexicans is 27.7% on average, but with a standard deviation of 24.0% and minimum/maximum value of 0.0 to 90.5% in the sample I am considering.



Eva Longoria, for example, who recently learned that she is 70% European in "Faces of America" belongs to the top-5% of Mexican American "European-ness", although there is probably considerable variation of Mexican Americans within the country.

http://dienekes.blogspot.com/2010/10...new-world.html

[Roderic]

Eurasian ADMIXTURE

I took the 540,814 markers from the HGDP dataset that are also included in the 23andMe personal genomics test, and that have less than 1% no-call rate.

I ran ADMIXTURE on all the West- (and some mainly Caucasoid Central-) Eurasian populations, including Yoruba and Han Chinese to account for non-Caucasoid admixture in parts of Eurasia.




The populations are (left-to-right): Tuscan, North Italian, Sardinian, French, French Basque, Orcadian, Russian, Adygei, Palestinian, Bedouin, Druze, Mozabite, Pathan, Sindhi, Balochi, Brahui, Burusho, Yoruba, Han Chinese.

Here are the admixture proportions corresponding to this experiment:



APPENDIX

For the sake of completeness here are the ADMIXTURE runs for K=3 to K=5.

At K=3, the three major races (Caucasoid: green, Mongoloid: red, Negroid: blue) emerge.



At K=4, the Caucasoids are split into West Eurasians (red) and Central Asians (purple)



At K=5, the West Eurasians are split into Europeans (yellow) and West Asians (blue)



(K=7) The Druze get their own cluster (pink) with an average membership of 65.4% of Druze individuals



http://dienekes.blogspot.com/2010/10...cursor-to.html