Thursday, February 16, 2017

Ancestry Analysis In Han Chinese Populations With Functional Immunity Genes

The following excepts are from the results section of a new open access paper in variation in functional immune system genes call KIR to show ancestral relationships of populations, which will be cited at the end of this post.

Global Population Genetics And The Mysterious Distribution Of KIR Genetic Clusters

Its finding first confirmed a divide between West Eurasians, South Asians, Papuans, Oceanians and Native Americans on one hand, and East Asians, Southeast Asians and Africans on the other.
In the phylogenetic tree, we could clearly find two main clusters. The smaller cluster consisted of Palestinian, Adygei, Tuscan, Hazara, Sardinian, North Italian, Barusho, Karitiana, Pima, Pathan, Papuan and Melanesian. Eastern Chinese Han gathered with Jilin Han in another cluster, following the sub branch containing Shanghai Han, Miao, Japanese, Hezhen, Naxi, Daur and Tujia, then with Yunnan Han and Shaanxi Han. Interestingly, all 7 African populations were genetically closer to populations from East Asia than West Europe, America and Pacific Ocean[.] 
The somewhat atypical alignment of continental groups in their KIR genes may reflect selective sweeps that impacted some continental regions, but not others. The East Asian, Southeast Asian and African one would presumably be the ancestral one, while the other would have the more derived version of KIR genes. But, the source of the selective pressure would have to be quite ancient to include Papuans.

Han Population Genetics And History

The paper then looked at relationships of Han Chinese populations within China. This corroborates a mass migration of the Eastern Chinese to Northeast China, and the affects of admixture with British nationals in Hong Kong.

In particular, the Jilin Han who are ethnically Han Chinese people who live in Jilin province immediately to the north of North Korea migrated there as part of a deliberate plan to demographically overwhelm the ethnically Korean and ethnically Manchurian and linguistically Tungistic people who are indigenous to the region. These peoples have population genetic continuity in the region going back to the Mesolithic era, and managed to remain ethnically distinct within the sphere of greater Chinese influence. This area is also the likely penultimate source (before Korea) of the Yayoi contribution to the Japanese people whose ethnic and linguistic identity is not entirely clear. We also have evidence of a catastrophic disease outbreak of some kind in this region around 3000 BCE, just as the Holocene climate optimum was ending.

There was a similar migration of west to east into the Sichuan area by ethnically Han Chinese people at roughly the same time.

Han Chinese expansion pretty much culturally obliterated any trace of pre-existing ethnic populations in much of Eastern China and indeed substantially replaced them on a demic basis as well in a large part of China, although there are numerous intra-Han Chinese distinctions based upon regional topolects which share a common set of Chinese characters as the central part of their written language (although even these characters are not entirely uniform across the Chinese linguistic area).

Some of this, as the paper notes, is relatively recent (ca. 1650 CE to 1900 CE and later), while some of this is much more ancient.

A lot of this expansion took place between 4800 BCE and 3000 BCE during which half a dozen Y-DNA haplogroups that account for 65% of the Chinese population experienced a rapid expansion, that also coincides with the domestication of soybeans in Northern China, the expansion of millet agriculture, and the mastery of beer brewing. Climate factors around this time also provided a push factor that encouraged southern migration as "barbarian" populations migrated south placing pressure on the existing populations of Northern China to do likewise. This period of extremely rapid genetic expansion ends corresponds roughly to the Yangshao culture, which was replaced by the Longshan culture ca. 3000 BCE at the end of the Holocene climate optimum. Population growth apparently continued for another 1000 years during the Longshan period, and in both the Yangshao and Longshan cultures, millet, pig and dogs were the primary sources of sustenance, they cultivated silkworms, and they made minor use of rice, but had few cattle, sheep or goats. Soybeans were also probably an important source of sustenance in these cultures, but this is harder to establish archaeologically because soybean waste does not leave as much of an archaeological trace.

Rice farming was expanding around the same time, in parallel, in Southern China, which also cultivated pigs, peaches and chickens (which appear to have been domesticated in Taiwan).

Legendary history starts to receive some archaeological corroboration in the Yellow River region by about 1900 BCE, around the time that the Chinese Bronze age commenced with the Erlitou culture (which arguably corresponds to the legendary Xia culture, which is conventionally dated to about 150 years later). Ancient DNA evidence suggests that the population genetic makeup of the Han Chinese in China's central plains in northern China was pretty much in place in its modern form by at least 1000 BCE.

The only trace of what came before seems to be the residual cultural divide between populations influenced by the more individualist oriented millet and wheat farming cultural influence in the North which contrasts with the more collective cultural values associated with rice farming in the South, with some residual population genetic distinctions in the South.
Using KIR as the panel of genetic marker, the results showed that Eastern Han from Jiangsu province had the closest relationship with Jilin Han, followed by Shanghai Han, indicating that Eastern Han shared a common ancestry, which was consistent to the findings based on other genetic markers, such as autosomal STRs and Y-STRs by Yao et al. 
The notable association of Eastern Han with Jilin Han was confirmed by the famous large-scale migration literally called “Crashing into Guandong”. Since A.D. 1,650, to control the rapid expansion of Chinese Han population, Han from Eastern China was promoted by the national policy to migrate to Northeastern China. As a result, Chinese Han accounted for 80% of the total northeastern Chinese during the 18th century. Besides, that Eastern Han was genetically close to Shanghai Han could be explained by the close geographic location and long-term cultural interaction. 
We also found Hong Kong Han displayed the farthest genetic distance to Eastern Han compared to other Han populations, obviously, which could be explained by the fact that Hong Kong Han mixed with lineage from the United Kingdom. The genetic characteristics of Eastern Han revealed that subpopulations sharing the same ancestry may have genetically closer relationships than geographically close groups. 
Wen et al. revealed the southward expansion of Han on the basis of variance of Y-chromosomal and mitochondrial DNA. Chen et al. analyzed genome-wide SNP variation and demonstrated the population stratification of Hans from 10 provinces including over 6,000 Han Chinese samples. Both studies indicated the north-south migration of Han Chinese. In this research, the relationships between Eastern Han populations and others worldwide were emphasized. The strongest association between Eastern Han and Jilin Han showed the impact of historical event “Crashing into Guandong”, which was a south to north migration route in the history, on genome polymorphisms. 
Our research utilized KIR as markers to provide new evidences for illustrating the potential Han dispersal. 
The paper is Caiyojong Yin, et al., "Genetic polymorphism and evolutionary differentiation of Eastern Chinese Han: a comprehensive and comparative analysis on KIRs" 7 Scientific Reports 42486 (February 16, 2017).

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