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.

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How Greek theaters filter out noise

Excerpt from Nature story:

The wonderful acoustics for which the ancient Greek theatre of Epidaurus is renowned may come from exploiting complex acoustic physics, new research shows.

The theatre, discovered under a layer of earth on the Peloponnese peninsula in 1881 and excavated, has the classic semicircular shape of a Greek amphitheatre, with 34 rows of stone seats (to which the Romans added a further 21).

Its acoustics are extraordinary: a performer standing on the open-air stage can be heard in the back rows almost 60 metres away. Architects and archaeologists have long speculated about what makes the sound transmit so well.

Now Nico Declercq and Cindy Dekeyser of the Georgia Institute of Technology in Atlanta say that the key is the arrangement of the stepped rows of seats. They calculate that this structure is perfectly shaped to act as an acoustic filter, suppressing low-frequency sound — the major component of background noise — while passing on the high frequencies of performers' voices1.

It's not clear whether this property comes from chance or design, Declercq says. But either way, he thinks that the Greeks and Romans appreciated that the acoustics at Epidaurus were something special, and copied them elsewhere.

...

In the first century BC the Roman authority on architecture, Vitruvius, implied that his predecessors knew very well how to design a theatre to emphasize the human voice. "By the rules of mathematics and the method of music," he wrote, "they sought to make the voices from the stage rise more clearly and sweetly to the spectators' ears... by the arrangement of theatres in accordance with the science of harmony, the ancients increased the power of the voice."

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.

The genetic legacy of the Manchu

A new paper in AJHG has identified a unique haplotype shared by many people from northeastern China and Mongolia. This haplotype belongs to haplogroup C3c, and is estimated to be about five centuries old. Its very recent spread corresponds with the rise to power of the Qing dynasty. As the authors write:

We reasoned that the events leading to the spread of this lineage might have been recorded in the historical record, as well as in the genetic record. The spread must have occurred after the cluster's TMRCA (∼500 years ago, corresponding to about A.D. 1500) and, most likely, before the Xibe migration in 1764. Notable features are the occurrence of the lineage in seven different populations but its apparent absence from the most populous Chinese ethnic group, the Han. A major historical event took place in this part of the world during this period—namely, the Manchu conquest of China and the establishment of the Qing dynasty, which ruled China from 1644 to 1912. This dynasty was founded by Nurhaci (1559–1626) and was dominated by the Qing imperial nobility, a hereditary class consisting of male-line descendants of Nurhaci's paternal grandfather, Giocangga (died 1582), with >80,000 official members by the end of the dynasty (Elliott 2001). The nobility were highly privileged; for example, a ninth-rank noble annually received ∼11 kg of silver and 22,000 liters of rice and maintained many concubines. A central part of the Qing social system was the army, the Eight Banners, which was made up of separate Manchu, Mongolian, and Chinese (Han) Eight Banners. The nobility occupied high ranks in the Manchu Eight Banners but not in the Mongolian or Chinese Eight Banners; the Manchu Eight Banners were recruited from the Manchu, Mongolian, Daur, Oroqen, Ewenki, Xibe, and a few other populations. A social mechanism was thus established that would have led to the increase of the specific Y lineage carried by Giocangga and Nurhaci and to its spread into a limited number of populations. We suggest that this lineage was the Manchu lineage.

Due to the very recent spread of this "Manchu" haplotype, it may be possible to find descendants of the Qing imperial nobility and test them. Presumably, they should have a high frequency of this haplotype. As the authors point out, the tumultuous events of recent times, have obscured the geneaological records. It may still be worthwhile to track such descendants though, or even remains of Qing noblemen. This would be a test for the validity of this theory.

An alternative explanation may be that the haplotype has been positively selected. There is, however, no direct evidence for this, and the limited geographical distribution of the haplotype may argue against this explanation:



American Journal of Human Genetics (early view)

Recent Spread of a Y-Chromosomal Lineage in Northern China and Mongolia

Yali Xue et al.

We have identified a Y-chromosomal lineage that is unusually frequent in northeastern China and Mongolia, in which a haplotype cluster defined by 15 Y short tandem repeats was carried by ∼3.3% of the males sampled from East Asia. The most recent common ancestor of this lineage lived 590 ± 340 years ago (mean ± SD), and it was detected in Mongolians and six Chinese minority populations. We suggest that the lineage was spread by Qing Dynasty (1644–1912) nobility, who were a privileged elite sharing patrilineal descent from Giocangga (died 1582), the grandfather of Manchu leader Nurhaci, and whose documented members formed ∼0.4% of the minority population by the end of the dynasty.

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