Τwo papers on Genetic structure of Han Chinese in AJHG

A couple of new papers on population structure in the Han Chinese have just appeared in the American Journal of Human Genetics. My comments will follow once I read the two papers.

UPDATE (on Chen et al.):

The PCA plot on the left from Chen et al. shows clearly the north-south cline of genetic variation in China. While there are no apparent barriers within the Han ethnic group, it is clear that subsets of Han Chinese can be perfectly distinguished from each other by just looking at the first two principal components.

From the paper:

The one-dimensional subpopulation structure of the Han Chinese population (along PC1) showed a close resemblance to their sampling location son a geographic map, and there is a very high correlation of 0.93 between the mean PC1 values of samples and the median latitudes of the provinces

The results of the STRUCTURE analysis are also very interesting as they show the expected clinality of variation within China rather than sharp distinctions, paralleling the situation in the landmass of Europe. However, at K=3 the major component of the Japanese (JPT) is shown to be a low-level component within the Chinese. It's hard to interpret this, but a first hypothesis could be that the Japanese are descended from an earlier Mongoloid genetic stratum that has since been admixed in the Asian mainland with other Mongoloid groups, but retained its "purity" in the Japanese islands.

The American Journal of Human Genetics, 25 November 2009
doi:10.1016/j.ajhg.2009.10.016

Genetic Structure of the Han Chinese Population Revealed by Genome-wide SNP Variation

Jieming Chen et al.

Abstract

Population stratification is a potential problem for genome-wide association studies (GWAS), confounding results and causing spurious associations. Hence, understanding how allele frequencies vary across geographic regions or among subpopulations is an important prelude to analyzing GWAS data. Using over 350,000 genome-wide autosomal SNPs in over 6000 Han Chinese samples from ten provinces of China, our study revealed a one-dimensional “north-south” population structure and a close correlation between geography and the genetic structure of the Han Chinese. The north-south population structure is consistent with the historical migration pattern of the Han Chinese population. Metropolitan cities in China were, however, more diffused “outliers,” probably because of the impact of modern migration of peoples. At a very local scale within the Guangdong province, we observed evidence of population structure among dialect groups, probably on account of endogamy within these dialects. Via simulation, we show that empirical levels of population structure observed across modern China can cause spurious associations in GWAS if not properly handled. In the Han Chinese, geographic matching is a good proxy for genetic matching, particularly in validation and candidate-gene studies in which population stratification cannot be directly accessed and accounted for because of the lack of genome-wide data, with the exception of the metropolitan cities, where geographical location is no longer a good indicator of ancestral origin. Our findings are important for designing GWAS in the Chinese population, an activity that is expected to intensify greatly in the near future.

Link

The American Journal of Human Genetics, 25 November 2009
doi:10.1016/j.ajhg.2009.10.015

Genomic Dissection of Population Substructure of Han Chinese and Its Implication in Association Studies

Shuhua Xu et al.

Abstract

To date, most genome-wide association studies (GWAS) and studies of fine-scale population structure have been conducted primarily on Europeans. Han Chinese, the largest ethnic group in the world, composing 20% of the entire global human population, is largely underrepresented in such studies. A well-recognized challenge is the fact that population structure can cause spurious associations in GWAS. In this study, we examined population substructures in a diverse set of over 1700 Han Chinese samples collected from 26 regions across China, each genotyped at ∼160K single-nucleotide polymorphisms (SNPs). Our results showed that the Han Chinese population is intricately substructured, with the main observed clusters corresponding roughly to northern Han, central Han, and southern Han. However, simulated case-control studies showed that genetic differentiation among these clusters, although very small (FST = 0.0002 ∼0.0009), is sufficient to lead to an inflated rate of false-positive results even when the sample size is moderate. The top two SNPs with the greatest frequency differences between the northern Han and southern Han clusters (FST > 0.06) were found in the FADS2 gene, which associates with the fatty acid composition in phospholipids, and in the HLA complex P5 gene (HCP5), which associates with HIV infection, psoriasis, and psoriatic arthritis. Ingenuity Pathway Analysis (IPA) showed that most differentiated genes among clusters are involved in cardiac arteriopathy (p less than 10−101). These signals indicating significant differences among Han Chinese subpopulations should be carefully explained in case they are also detected in association studies, especially when sample sources are diverse.

Link

mtDNA of Hakka and Chaoshanese

Am J Phys Anthropol doi:10.1002/ajpa.21124

Tracing the origins of Hakka and Chaoshanese by mitochondrial DNA analysis

Wen-Zhi Wang et al.

Abstract

Hakka and Chaoshanese are two unique Han populations residing in southern China but with northern Han (NH) cultural traditions and linguistic influences. Although most of historical records indicate that both populations migrated from northern China in the last two thousand years, no consensus on their origins has been reached so far. To shed more light on the origins of Hakka and Chaoshanese, mitochondrial DNAs (mtDNAs) of 170 Hakka from Meizhou and 102 Chaoshanese from Chaoshan area, Guangdong Province, were analyzed. Our results show that some southern Chinese predominant haplogroups, e.g. B, F, and M7, have relatively high frequencies in both populations. Although median network analyses show that Hakka/Chaoshanese share some haplotypes with NH, interpopulation comparison reveals that both populations show closer affinity with southern Han (SH) populations than with NH. In consideration of previous results from nuclear gene (including Y chromosome) research, it is likely that matrilineal landscapes of both Hakka and Chaoshanese have largely been shaped by the local people during their migration southward and/or later colonization in southern China, and factors such as cultural assimilation, patrilocality, and even sex-bias in the immigrants might have played important roles during the process.

Link

Cranial robusticity in Australians

From the paper:

Instead, cranial robusticity among the Australians and other modern humans can reasonably be explained on the basis of current knowledge of cranial development-function, as well as a phylogenetic scenario consistent with genetic studies of the population history of Aboriginal Australians (e.g. Hudjashov et al., 2006). Thus, the earliest Australians might be thought of as having evolved from the earliest modern humans who migrated from Africa into East/Southeast Asia around 60-70 kyr. The Australian Pleistocene/Early Holocene human record indicates the presence of marked variability in cranial form. However, it is not possible with present genetic data to determine whether the continent was colonised during a single migration by a population with a highly variable cranial form or in two major events by people with different cranial morphologies.

From Hudjashov et al. (2007) mentioned in the text:

The analysis reveals no evidence for any archaic maternal or paternal lineages in Australians, despite some suggestively robust features in the Australian fossil record, thus weakening the argument for continuity with any earlier Homo erectus populations in Southeast Asia. (ii) The tree of complete mtDNA sequences shows that Aboriginal Australians are most closely related to the autochthonous populations of New Guinea/Melanesia, indicating that prehistoric Australia and New Guinea were occupied initially by one and the same Palaeolithic colonization event approximately 50,000 years ago, in agreement with current archaeological evidence. (iii) The deep mtDNA and Y chromosomal branching patterns between Australia and most other populations around the Indian Ocean point to a considerable isolation after the initial arrival. (iv) We detect only minor secondary gene flow into Australia, and this could have taken place before the land bridge between Australia and New Guinea was submerged approximately 8,000 years ago, thus calling into question that certain significant developments in later Australian prehistory (the emergence of a backed-blade lithic industry, and the linguistic dichotomy) were externally motivated.

Journal of Archaeological Science doi:10.1016/j.jas.2008.11.021

Possible Causes and Significance of Cranial Robusticity Among Pleistocene-Early Holocene Australians

Darren Cunroe

Abstract

An analysis of possible developmental-functional causes of cranial form suggests that the unusual morphology of ‘robust’ Pleistocene/Early Holocene Australians such as Willandra Lakes Human 50 might best be explained by four underlying factors: possession of a 1) large neurocranium, 2) narrow cranial base, 3) viscerocranium with considerable midfacial projection, and 4) large dentition, especially the cheek teeth, with their associated large jaws and high volume masticatory muscles. Some of these features are likely to be highly heritable, while others are caused/exaggerated by influences from ageing processes, diet, and a hunter-gatherer lifestyle in an arid environment. These underlying ‘causes’ are either apomorphies of H. sapiens (1 & 2) and thus absent from pre-modern specimens such as from Ngandong, or represent plesiomorphic features of latter Homo (3 & 4). It is concluded that combining current knowledge of cranial development-function with genetic studies of the population history of Aboriginal Australians provides the most parsimonious solution to understanding their evolutionary origins.

Link

mtDNA of Mongolians

While I agree that the Mongol Empire played a major role in the admixture of Caucasoids and Mongoloids, we have very clear evidence now that the two races had been mixing in Central Asia long before that time.

J Hum Genet.

Genetic imprint of the Mongol: signal from phylogeographic analysis of mitochondrial DNA

Cheng B, Tang W, He L, Dong Y, Lu J, Lei Y, Yu H, Zhang J, Xiao C.

Abstract

Mitochondrial deoxyribonucleic acid (DNA) from 201 unrelated Mongolian individuals in the three different regions was analyzed. The Mongolians took the dominant East Asian-specific haplogroups, and some European-prevalent haplogroups were detected. The East Asians-specific haplogroups distributed from east to west in decreasing frequencies, and the European-specific haplogroups distributed conversely. These genetic data suggest that the Mongolian empire played an important role in the maternal genetic admixture across Mongolians and even Central Asian populations, whereas the Silk Road might have contributed little in the admixture between the East Asians and the Europeans.

Link

YAP in 25 ethnic groups from Yunnan China

YAP defines haplogroup DE of the human Y-chromosome phylogeny, which joins together the haplogroup E, found in Negroids and Caucasoids, with haplogroup D, found mainly among Mongoloids, including the archaic Ainu, but also non-Mongoloid populations such as the Andaman Islanders.

The YAP frequencies listed here are, in all probability mostly of haplogroup D.

Sci China C Life Sci. 2003 Apr;46(2):135-140.

The geographic polymorphisms of Y chromosome at YAP locus among 25 ethnic groups in Yunnan, China.

Shi H, Dong Y, Li W, Yang J, Li K, Zan R, Xiao C.

The genetic polymorphisms of Y chromosome at YAP locus in 25 ethnic groups (33 populations) of China were analyzed in a total of 1294 samples. The average YAP+ frequency of the 33 populations was 9.2%, coinciding with published data of Chinese populations. Primi has the highest YAP+ frequency (72.3%), which is also the highest YAP+ among all the eastern Asian populations studied. The YAP+ occurred in 17 populations studied including Tibetan (36.0%), Naxi (37.5% and 25.5%), Zhuang (21.3%), Jingpo (12.5%), Miao (11.8%), Dai (11.4%, 10.0%, 3.3% and 2.0%), Yi (8.0%), Bai of Yunnan (6.7% and 6.0%), Mongol of Inner Mongolia (4.3%), Tujia of Hunan (2.6%), Yao (2.2%) and Nu (1.8%). The other 15 populations are YAP-including Lahu (2 populations), Hani, Achang, Drung, Lisu, Sui, Bouyei, Va, Bulang, Deang, Man and Hui and Mongol of Yunnan and Bai of Hunan. The YAP+ frequencies varied among the different ethnic groups studied, and even different among the same ethnic group living in different geographic locations. Using the genetic information, combined with the knowledge of ethnology, history and archaeology, the origin and prehistoric migrations of the ethnic groups in China, especially in Yunnan Province were discussed.

Link

Y chromosomes of Zhuang Populations

Yi Chuan Xue Bao. 2006 Dec;33(12):1060-72.

Y-chromosome Genotyping and Genetic Structure of Zhuang Populations.

Jing C, Hui L, Zhen-Dong Q, Wen-Hong L, Wei-Xiong L, Rui-Xing Y, Li J, Shang-Ling P.

Zhuang, the largest ethnic minority population in China, is one of the descendant groups of the ancient Bai-Yue. Linguistically, Zhuang languages are grouped into northern and southern dialects. To characterize its genetic structure, 13 East Asian-specific Y-chromosome biallelic markers and 7 Y-chromosome short tandem repeat (STR) markers were used to infer the haplogroups of Zhuang populations. Our results showed that O*, O2a, and O1 are the predominant haplogroups in Zhuang. Frequency distribution and principal component analysis showed that Zhuang was closely related to groups of Bai-Yue origin and therefore was likely to be the descendant of Bai-Yue. The results of principal component analysis and hierarchical clustering analysis contradicted the linguistically derived north-south division. Interestingly, a west-east clinal trend of haplotype frequency changes was observed, which was supported by AMOVA analysis that showed that between-population variance of east-west division was larger than that of north-south division. O* network suggested that the Hongshuihe branch was the center of Zhuang. Our study suggests that there are three major components in Zhuang. The O* and O2a constituted the original component; later, O1 was brought into Zhuang, especially eastern Zhuang; and finally, northern Han population brought O3 into the Zhuang populations.

Link

The second search for Peking Man

Many cranial fossils have strange histories. Some, like Piltdown Man and Galley Hill and Vogelherd persist for decades as important prehistoric remains, even though later dating reveals them to be much more recent than originally thought. Others like Kennewick Man become objects of a legal battle as to whether or not they should be buried and lost for science, or studied. And there are others like Combe Capelle who was lost during World War II, and then found decades later.

There are casts of all important skulls, so the loss of a specimen does not mean that it can no longer be studied by anthropologists. Unfortunately, newer techniques involving the extraction of DNA from bones only work with real skulls; hence, the urgency to rediscover misplaced fossils.

The Peking Man was lost during World War II as well. Thankfully, Franz Weidenreich had made casts of the skulls only years after they had been brought to the ground, and these casts have played a key role in subsequent discussions on human origins.

Now, a news story hints that Peking Man may not have been lost forever:

ZHOUKOUDIAN, CHINA -- For more than two decades, Yang Shoukai had hoarded his secret, unsure what to do with a possible clue to one of China's most baffling mysteries.

As construction supervisor on the site of an abandoned U.S. military barracks in Tianjin in 1982, he had discovered a strange cement box in the basement of the old wartime barracks. He tried to dig it up, but lacked the proper tools, and the box was buried under a new medical laboratory.

Mr. Yang, now retired and in poor health, is convinced that the box contains a 500,000-year-old archeological treasure that China has hunted for in vain since the Second World War: the missing skulls of Peking Man, one of the most famous links in the evolution of prehistoric humans.

...

Chinese specialists have conducted many failed searches for the skulls, but the new committee is optimistic. "I think we will find them," said Dong Cuiping, vice-director of the Peking Man Museum.

"Since 1941, the searches were always done by non-governmental people. Now this work is on the government's agenda. We're drawing more attention from society, and more clues - not only from China but outside China too."

If the skulls are recovered, they could become the basis for a major breakthrough in the understanding of human evolution, she said.

"When we first found the skulls, our science was not very advanced. Now we have much better technology. If we recover them, we could make new scientific discoveries."

Let's hope they succeed.

New evidence challenges hypothesis of modern human origins

WUHAN, April 27 (Xinhuanet) -- Chinese archaeologists said newly found evidence proves that a valley of Qingjiang River, a tributary on the middle reaches of the Yangtze River, might be one of the regions where Homo sapiens, or modern man, originated.

The finding challenges the "Out-of-Africa" hypothesis of modern human origins, according to which about 100,000 years ago modern humans originated in Africa, migrated to other continents, and replaced populations of archaic humans across the globe.

The finding comes from a large-scale excavation launched in the Qingjiang River Valley in 1980s when construction began on a rangeof hydropower stations on the Qingjiang River, a fellow researcher with the Hubei Provincial Institute of Cultural Relics and Archaeology.

Archaeologists discovered three human tooth fossils in one mountain cave in Mazhaping Village, in the Gaoping Township of Jianshi County, western Hubei Province, and found pieces of lithictechnology and evidence of fire usage in Minor Cave in Banxia. There were similar findings in Nianyu Mountain and in Zhadong Cavein Banxia, all in Changyang Prefecture of the Qiangjiang River Valley.

A special research panel named the Jianshi Man research team has been set up to analyze the findings.

Zheng Shaohua, a member of the Jianshi man research team from the Institute of Vertebrate Paleontology and Paleoanthropology of the Chinese Academy of Sciences, confirmed the tooth fossils belonged to humans dating back between 2.15 and 1.95 million yearsago.

The archaeologists also found fossils of bone implements in thecultural strata at the ruins where the human tooth fossils were discovered.

The fossilized bone implements bear traces of human beating, testifying that humans, not apes, lived inside the mountain cave, said Qiu Zhanxiang, another member on the Jianshi Man research team.

The pieces of lithic technology and traces of human fire usage found in Minor Cave in Banxia were said to date back 130,000 years,the ruins of human fire usage in Nianyu Mountain were dated as 120,000 years or 90,000 years old, while pieces of lithic technology and traces of fire usage found in Zhadong Cave in Banxia, were dated as 27,000 years old, said Professor Zheng.

Before these latest archaeological findings, Chinese archaeologists had found fossils of what is now known as ChangyangMan in 1957 under the leadership of renowned Chinese paleoanthropologist Jia Lanpo. Changyang Man represents early Homosapiens dating back 200,000 years.

The latest archaeological findings together with the earlier discovery of Changyang Man all prove there was continuity in Homo sapiens' development in China, said Liu Qingzhu, head of the Archaeology Institute of the Chinese Academy of Social Sciences.

"They are also of great significance to research on Paleolithic era in China and East Asia, and theories regarding multiple origins of mankind," said Liu.

Link (Xinhua)