ADMIXTURE across Eurasia: from Anatolia to Siberia

(Last Update: Oct 17)

Here is a result of an ADMIXTURE run of a few populations from Eurasia (left to right: Turks, Armenians, Georgians, followed by a mix of Uygur, Mongolians, Yakut, Hezhen in no order), combining the HGDP dataset with that of Behar et al. (2010).

It's more of a test, rather than a final result, as I've just finished integrating the two datasets, but it's a nice comparison of a wide assortment of linguistic families.

Notice Turks and Armenians being quite similar to each other, (green+blue), although Turks are differentiated by the presence of an east Eurasian component (5.5%). On the basis of uniparental markers, five years ago, I estimated this component as 6.2% which seems to be right on the money. In the combined Armenian/Georgian sample this admixture is only 0.14% and as can be seen is limited to a handful of Georgian individuals.

It is interesting that Georgians belong semi-uniquely to the green cluster. Turks' non-Mongoloid ancestors were Indo-European speaking like the Armenians still are. It would be tempting to see in the blue-green contrast an Indo-European/Caucasian one, especially as the Caucasoid component further east seems to be mainly blue, in agreement with the idea that it was Indo-Europeans (in particular mainly Iranic speakers) who brought Caucasoid genes to the heartland of Asia.

UPDATE I (Oct 17):

Moving to the north, we see (left-to-right) Han (red), Hungarian/Belorussian (blue), Chuvash (first red "step"), Uzbek (second red "step"). Unlike the Turks, the Hungarians, who also speak a language that came from the east, seem to lack a noticeable east Eurasian component.

Their linguistic conversion was one of elite dominance, where a handful of Mongoloid and quasi-Mongoloid upper echelons left their language but not their genes:

According to his observations, the “overlords” were characterized by Turanid, Uralian and Pamir race elements and also by certain long-headed components. The “middle layer” or “warriors’ layer”, however, showed an anthropological profile distinctly different from that of the overlords. It was essentially constituted by Mediterraneans, Nordoids (who might also have been tall robust Mediterraneans) and Pamir component while the absence of Turanid and Uralian race characteristics was remarkable. As regards the third layer, the so-called “common folk”, they were dominated, just as the middle layer was, by Mediterranean and Nordoid elements but, in addition, the Cromagnoid ones were also significant.

The Chuvash are Turkic and live in Europe, while the Uzbeks, closer to the Altaic homeland in Asia are also Turkic, and have a predictable higher percentage of east Eurasian genes.

Genetic structure in East Asia using 200K SNPs

The table of paired F_st values for East Asian populations is here. The PCA plots are seen on the left.

PLoS ONE 3(12): e3862. doi:10.1371/journal.pone.0003862

Analysis of East Asia Genetic Substructure Using Genome-Wide SNP Arrays

Chao Tian et al.

Abstract

Accounting for population genetic substructure is important in reducing type 1 errors in genetic studies of complex disease. As efforts to understand complex genetic disease are expanded to different continental populations the understanding of genetic substructure within these continents will be useful in design and execution of association tests. In this study, population differentiation (Fst) and Principal Components Analyses (PCA) are examined using >200 K genotypes from multiple populations of East Asian ancestry. The population groups included those from the Human Genome Diversity Panel [Cambodian, Yi, Daur, Mongolian, Lahu, Dai, Hezhen, Miaozu, Naxi, Oroqen, She, Tu, Tujia, Naxi, Xibo, and Yakut], HapMap [ Han Chinese (CHB) and Japanese (JPT)], and East Asian or East Asian American subjects of Vietnamese, Korean, Filipino and Chinese ancestry. Paired Fst (Wei and Cockerham) showed close relationships between CHB and several large East Asian population groups (CHB/Korean, 0.0019; CHB/JPT, 00651; CHB/Vietnamese, 0.0065) with larger separation with Filipino (CHB/Filipino, 0.014). Low levels of differentiation were also observed between Dai and Vietnamese (0.0045) and between Vietnamese and Cambodian (0.0062). Similarly, small Fst's were observed among different presumed Han Chinese populations originating in different regions of mainland of China and Taiwan (Fst's less than 0.0025 with CHB). For PCA, the first two PC's showed a pattern of relationships that closely followed the geographic distribution of the different East Asian populations. PCA showed substructure both between different East Asian groups and within the Han Chinese population. These studies have also identified a subset of East Asian substructure ancestry informative markers (EASTASAIMS) that may be useful for future complex genetic disease association studies in reducing type 1 errors and in identifying homogeneous groups that may increase the power of such studies.

Link

August 1 update of YHRD

YHRD, the Y Chromosome Haplotype Reference Database has been updated on August 1:

The following populations were added today: Iceland, Elista (Russia, Kalmyks), Ecuador (Mestizo, Afroamerican, Quichua, Huaorani), Bama (China, Yao), Chengdu (China, Han), Zhenning (China, Buyi), Molidawa (China, Daur and Ewenki), Yuanjiang (China, Hani), Tongjiang (China, Hezhen), Tongxin (China, Hui), Yanji (China, Korean), Tongshi (China, Li), Xiuyan (China, Manchu), Alihe (China, Oroqen), Maowen (China, Qiang), Luoyuan (China, Fujian), Lhasa (China, Tibet), Yili (China, Xibe, Uigur and Han), Harbin (China, Han), Hailar (China, Mongolian), Lanzhou (China, Han), Liannan (China, Yao), Meixian (China, Han), Urumqi (China, Uigur), Mongolia, Japan, Korea, Gdansk (Poland), Nepal, Sao Paulo State (Brazil, European, African, Oriental and Pardo), Buenos Aires (Argentina), Santa Fe (Argentina), Mendoza (Argentina), Rio Negro (Argentina), Chubut (Argentina), Misiones (Argentina), Corrientes (Argentina), Formosa (Argentina), Chaco (Argentina), Salta (Argentina). We would like to thank the following colleagues for submitting these population samples: Daniel Corach and his group (Buenos Aires), Rune Andreassen and his group (Oslo, Norway), Ivan Nasidze and his group (Leipzig, Germany), Fabricio Gonzalez and his group (Quito, Ecuador), Chris Tyler-Smith, Yali Xue and their group (Cambridge, UK), Richard Pawlowski and his group (Gdansk, Poland), Rogerio Nogueira Oliveira and his group (Sao Paulo, Brazil), Gustavo Penacino and his group (Buenos Aires, Argentina), Emma Parkin, Mark Jobling and their group (Leicester, UK).

So, head on there to see if you get any new matches for your Y-chromosome samples.

Early human population centers in coastal habitats (?)

I am skeptical whether this result is an artefact of the composition of the 51 populations, or whether it reflects prehistoric realities, but the paper is worth reading nonetheless.

Examples of 50%-confidence kernels for population placement based on population average allele frequencies. Populations are: Columbian, Hezhen, Kalash, Karitiana, Lahu, Makrani, Mandega, Maya, Mbuti Pigmy, Melanesian, Mozabite, New Guinea, Orcadian, Palestinian, Pima, Russian, Sardinian, Uygur, Yakut, Yizu, and San. In most cases, a single kernel results, although, in populations Hezhen, Karitiana, and Pima, the kernel has broken into two or three regions.

Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0507991103

Global genetic positioning: Evidence for early human population centers in coastal habitats

William Amos and Andrea Manica

For an alternative perspective on relationships among human populations, we combined genetic and geographic information, using allele frequency gradients to place populations and individuals on the globe. Reanalyzing published data on 51 worldwide populations [Rosenberg, N. A., Pritchard, J. K., Weber, J. L., Cann, H. M., Kidd, K. K., Zhivitovsky, L. A. & Feldman, M. W. (2002) Science 298, 2381-2385] reveals five geographic clusters lying in plausible sites either of early agricultural innovation or on ancient migration routes. Also, the inferred sites show significant association with coastlines, suggesting that most early humans lived near large bodies of water. Our approach is flexible, and developments should prove useful both for exploring historical demography and for the identification of likely origin for unknown forensic samples.

Link