Genetic structure in China

After my experiment on Spain, I decided to carry out a similar experiment in China, for which there is a large number of regional/ethnic sub-populations.15 clusters were inferred with 22 MDS dimensions.

The Uygur are the clear outlier population, doubtlessly due to their substantial Caucasoid admixture and geographical position in Central Asia, a region that was traditionally at the outskirts of Chinese civilization. Other Altaic speakers (both Mongolic and Tungusic) are also divergent, as are the Dai/Lahu people from the China/Thailand/Laos area.

Interestingly, the Tujia people from Central China seem to be the ones most like the Han overall, with Hmongic Miaozu/She more like the southern Han.

Origin and dispersal of Y chromosome haplogroup C (Zhong et al. 2010)

A beautiful new paper has appeared that tackles the distribution and substructure of Y chromosome haplogroup C, a widely dispersed lineage that binds Asia, Oceania, and the Americas. This will be invaluable as a resource for students of East Eurasian anthropology and genetics. My only problem with the paper is in its use of the evolutionary mutation rate that I have criticized elsewhere.

From the paper:

Hg C is prevalent in various geographical areas (Figures 1 and 2), including Australia (65.74%), Polynesia (40.52%), Heilongjiang of northeastern China (Manchu, 44.00%), Inner Mongolia (Mongolian, 52.17%; Oroqen, 61.29%), Xinjiang of northwestern China (Hazak, 75.47%), Outer Mongolia (52.80%) and northeastern Siberia (37.41%). Hg C is also present in other regions, extending longitudinally from Sardinia in Southern Europe all the way to Northern Colombia, and latitudinally from Yakutia of Northern Siberia and Alaska of Northern America to India, Indonesia and Polynesia, but absent in Africa.

On the structure of haplogroup C:

As shown in Figure 1, most of the subhaplogroups of Hg C have a geographically pronounced distribution. Hg C6, which is defined by a recently identified marker, was not detected in our samples. Hg C1 and C4 are completely restricted to Japan and Australia, respectively, and not detected in the other samples from East Asia and Southeast Asia. Hg C5 occurs in India and its neighboring regions Pakistan and Nepal. In mainland East Asia, four Hg C5 individuals were detected, including two in Xibe, one in Uygur and one in Shanxi Han. Although the dispersal of Hg C2 is relatively wide, its distribution remains limited to Oceania and its neighboring regions, except Australia. In our samples, only three Hg C2 individuals were observed in Eastern Indonesia, which is consistent with previous reports. Hg C3 is the most widespread subhaplogroup, which was detected in Central Asia, South Asia, Southeast Asia, East Asia, Siberia and the Americas, but absent in Oceania. Different subhaplogroups of Hg C that do not overlap between the regions suggest that these individuals have undergone long-time isolation. As these subhaplogroups have a common origin by sharing the M130-derived allele, their geographical distributions enable us to infer the prehistoric migration routes of this lineage.

The MDS plot is quite instructive. Notice the duality of Japanese C chromosomes, which parallels what we know about the dual origins of the Japanese. It would be instructive to test European haplogroup C outliers to see where they fall within haplogroup C diversity.

The C3 MDS is quite instructive, and shows quite well the distribution of C3 diversity in Chinese ethnic populations.

Off the top of my head, I detect a top-right Mongolian-Manchu-Tibetan quadrant (note that Mongolians and Tibetans are also linked by the rare haplogroup D) and a left Central/Southern Chinese ethnic quadrant. Notice the closeness of Hani to Yi, which may validate the former's oral traditions.

Finally, getting back to the controversial issue of Y-chromosome age estimation, here are the dates proposed by the authors for the age of STR variation within haplogroups and their divergence times. In my opinion these are overestimates due to the use of the evolutionary rate.

A case in point is haplogroup C3b-P39; according to the authors' date, this ought to be related to the early arrival of the ancestors of Amerindians, but haplogroup C in the Americans has a strong relationship with Na-Dene speakers such as Athapaskans, and it seems to me that a late spread of this haplogroup is more consistent with its limited geographical distribution and strong linguistic associations.

Related: the Southern origin of O3

Journal of Human Genetics doi: 10.1038/jhg.2010.40

Global distribution of Y-chromosome haplogroup C reveals the prehistoric migration routes of African exodus and early settlement in East Asia

Hua Zhong et al.

The regional distribution of an ancient Y-chromosome haplogroup C-M130 (Hg C) in Asia provides an ideal tool of dissecting prehistoric migration events. We identified 465 Hg C individuals out of 4284 males from 140 East and Southeast Asian populations. We genotyped these Hg C individuals using 12 Y-chromosome biallelic markers and 8 commonly used Y-short tandem repeats (Y-STRs), and performed phylogeographic analysis in combination with the published data. The results show that most of the Hg C subhaplogroups have distinct geographical distribution and have undergone long-time isolation, although Hg C individuals are distributed widely across Eurasia. Furthermore, a general south-to-north and east-to-west cline of Y-STR diversity is observed with the highest diversity in Southeast Asia. The phylogeographic distribution pattern of Hg C supports a single coastal ‘Out-of-Africa’ route by way of the Indian subcontinent, which eventually led to the early settlement of modern humans in mainland Southeast Asia. The northward expansion of Hg C in East Asia started ~40 thousand of years ago (KYA) along the coastline of mainland China and reached Siberia ~15 KYA and finally made its way to the Americas.

Link

Y chromosome and mtDNA of Udegeys

American Journal of Physical Anthropology doi:10.1002/ajpa.21232

Genetic diversity of two haploid markers in the Udegey population from southeastern Siberia


Han-Jun Jin et al.

Abstract

The Udegeys are a small ethnic group who live along the tributaries of the Amur River Basin of southeastern Siberia in Russia. They are thought to speak a language belonging to a subdivision of the Tungusic-Manchu branch of the Altaic family. To understand the genetic features and genetic history of the Udegeys, we analyzed two haploid markers, mitochondrial DNA (mtDNA), and Y-chromosomal variation, in 51 individuals (including 21 males) from the Udegey population. In general, the Udegeys' mtDNA profiles revealed similarities to Siberians and other northeastern Asian populations, although a moderate European contribution was also detected. Interestingly, pairwise values of FST and the MDS plots based on the mtDNA variation showed that the Orok and Nivkh inhabiting the very same region of the Udegey were significantly different from the Udegey, implying that they may have been isolated and undergone substantial genetic drift. The Udegeys were characterized by a high frequency (66.7%) of Y chromosome haplogroup C, indicating a close genetic relationship with Mongolians and Siberians. On the paternal side, however, very little admixture was observed between the Udegeys and Europeans. Thus, the combined haploid genetic markers of both mtDNA and the Y chromosome imply that the Udegeys are overall closest to Siberians and northeast Asians of the Altaic linguistic family, with a minor maternal contribution from the European part of the continent.

Link

Y chromosomes and mtDNA of Koreans

Table 2 has a very useful listing of mtDNA haplogroup frequencies in several East Asian populations.

Table 5 has admixture estimates of NE and SE Asians in Korean populations; notice the gender asymmetry, with males of more southern origin than females.

Table S3 (Excel) has Y-chromosome haplogroup frequencies.

From the paper:

What could be the origin of the male-biased southern contribution to Korean gene pool illustrated, for example, by haplogroups O-M122 (42.2%) and O-SRY465 (20.1%) [29]. Recent molecular genetic analyses and the geographical distribution of haplogroup O-M122 lineages, found widely throughout East Asia at high frequencies (especially in southern populations and China), have suggested a link between these Y-chromosome expansions and the spread of rice agriculture in East Asia [62]–[64]. In general, Y-chromosomes might be spread via a process of demic diffusion during the early agricultural expansion period [65], [66]. If this interpretation were substantiated, the spatial pattern of Y-haplogroup O would imply a genetic contribution to Korea through the spread of male-mediated agriculture.

PLoS ONE 10.1371/journal.pone.0004210

The Peopling of Korea Revealed by Analyses of Mitochondrial DNA and Y-Chromosomal Markers

Han-Jun Jin, Chris Tyler-Smith, Wook Kim

Abstract

Background

The Koreans are generally considered a northeast Asian group because of their geographical location. However, recent findings from Y chromosome studies showed that the Korean population contains lineages from both southern and northern parts of East Asia. To understand the genetic history and relationships of Korea more fully, additional data and analyses are necessary.

Methodology and Results

We analyzed mitochondrial DNA (mtDNA) sequence variation in the hypervariable segments I and II (HVS-I and HVS-II) and haplogroup-specific mutations in coding regions in 445 individuals from seven east Asian populations (Korean, Korean-Chinese, Mongolian, Manchurian, Han (Beijing), Vietnamese and Thais). In addition, published mtDNA haplogroup data (N = 3307), mtDNA HVS-I sequences (N = 2313), Y chromosome haplogroup data (N = 1697) and Y chromosome STR data (N = 2713) were analyzed to elucidate the genetic structure of East Asian populations. All the mtDNA profiles studied here were classified into subsets of haplogroups common in East Asia, with just two exceptions. In general, the Korean mtDNA profiles revealed similarities to other northeastern Asian populations through analysis of individual haplogroup distributions, genetic distances between populations or an analysis of molecular variance, although a minor southern contribution was also suggested. Reanalysis of Y-chromosomal data confirmed both the overall similarity to other northeastern populations, and also a larger paternal contribution from southeastern populations.

Conclusion

The present work provides evidence that peopling of Korea can be seen as a complex process, interpreted as an early northern Asian settlement with at least one subsequent male-biased southern-to-northern migration, possibly associated with the spread of rice agriculture.

Link