Dominant Contribution of Northern Chinese to the Paternal Genetic Structure of Chaoshanese in South China

We investigated the Y chromosome of various Chinese populations to determine the patrilineal origin of the Chaoshanese population. Admixture analysis of six specific Y short tandem repeat (STR) loci in 6,292 individual samples taken from 51 populations, including Chaoshanese and Minnanese of our earlier studies, showed that over 85% of the Chaoshanese Y chromosomes were derived from the Central China Han (M (RH): 0.8614; M (BE): 1.1868?±?0.2054), and a very small portion were from the southern aborigines. These results support a Central China Han origin of the Chaoshanese and additionally reveal that males from the Central China Han were the predominant contributor to the patrilineal genetics of the Chaoshanese. A phylogenetic tree and analysis of molecular variance signified a strong association between Y chromosomes of Chinese populations and their linguistic affiliations, revealing a coevolution of Y chromosome diversity and languages in East Asia.     

Genetic link between Chaoshan and other Chinese Han populations: Evidence from HLA-A and HLA-B allele frequency distribution

The genetic polymorphism of HLA-A and HLA-B loci was investigated in 505 Chaoshanese using PCR-SSP method. Among the HLA-A alleles detected, A*11 (35.64%) was most frequent, followed by A*02 (31.78%). Of 34 HLA-B alleles tested, 30 were observed, in which B*60 (21.68%), B*46 (14.46%), and B*58 (10.69%) were highly predominant. Comparison was made with other nine Chinese Han ethnic groups covering the Mainland China, Taiwan, Hong Kong, and Singapore. The high frequent alleles found in Chaoshanese were also common in other Chinese groups compared though the frequency levels varied from group to group. The phylogenic tree analysis based on the HLA-A and -B allele frequencies of all the 10 Chinese ethnic groups revealed that Chaoshanese, while clustering in general with the southern China-related Han Chinese, had the highest affinity to the Mainland Minnanese, but separated distinctively from the northern Han Chinese. The study, however, was yet to confirm the hypothesis of the Central Plains Han origin of Chaoshanese. Interestingly, the alleles (B*46, B*38, and B*58) and the related haplotypes (A*02-B*46 and A*33-B*58) that are positively associated with nasopharyngeal carcinoma (NPC), a disease prevailing predominantly among southern Chinese, were always at much higher frequencies among southern Chinese than among northern Chinese, whereas A*31 and B*13, the two alleles with highly protective effects for NPC, and the associated haplotype A*30-B*13 were predominantly high in northern Chinese. The different genetic background between northern and southern China may explain, at least partially, the prevalence of NPC among southern Chinese.     

STR Polymorphisms of the Henan Population and Investigation of the Central Plains Han Origin of Chaoshanese

Allele frequencies for 15 short tandem repeat (STR) loci were obtained from a Chinese Han population in Henan province of middle China. No deviation from Hardy–Weinberg equilibrium was observed for the STR loci except for D3S1358. The 15 STR loci are potentially useful for paternity testing and forensic casework in the Henan population. A phylogenetic tree based on CODIS STR allele frequencies of 25 Han populations revealed noticeable but far less clear distinctions between southern and northern Chinese populations; the Henan Han population was located at an intermediate position between south and north Chinese Han populations, relatively closer to Chaoshan and Minnan Han. Moreover, admixture analysis showed a large proportion of Central Plains Han origin in Chaoshanese and Minnanese. Admixture and phylogenetic analysis also reflected the genetic similarity shared by these two groups.     

Fine‐scale genetic structure of Tujia and central Han Chinese revealing massive genetic admixture under language borrowing

Archaeological, genetic, and linguistic evidence has supported the idea that northern China is the original center of modern Sino‐Tibetan‐speaking populations. However, the demographic history of subsequent southward migration and genetic admixture of Han Chinese with surrounding indigenous populations remain uncharacterized, and the language shifts and assimilations accompanied by movement of people, or just an adaptation of cultural ideas among populations in central China is still unclear, especially for Tibeto‐Burman‐speaking Tujia and central Han Chinese populations. To resolve this, we genotyped over 60K genome‐wide markers in 505 unrelated individuals from 63 indigenous populations. Our results showed both studied Han and Tujia were at the intermediate position in the modern East Asian North–South genetic cline and there was a correlation between the genetic composition and the latitude. We observed the strong genetic assimilation between Tujia people and central Han Chinese, which suggested massive population movements and genetic admixture under language borrowing. Tujia and central Han Chinese could be modeled as a two‐way admixture deriving primary ancestry from a northern ancestral population closely related to the ancient DevilsCave and present‐day Tibetans and a southern ancestral population closely related to the present‐day Tai‐Kadai and Austronesian‐speaking groups. The ancestral northern population we suspect to be related to the Neolithic millet farming groups in the Yellow River Basin or central China. We showed that the newly genotyped populations in Hubei Province had a higher proportion of DevilsCave or modern Tungusic/Mongolic‐related northern ancestries, while the Hunan populations harbored a higher proportion of Austronesian/Tai‐Kadai‐related southern ancestries.     

客家人起源的遗传学分析

客家人是南方讲客家话的特殊汉族民系,其来源学术界有一定争议。该研究对福建长汀的148个客家男子做了遗传分析。从父系遗传的Y染色体SNP的主成分分析看,客家人与中原汉族最近,又偏向于苗瑶语族群中的畲族,不同于其他南方汉族偏向于侗台语族群。混合分析发现客家人数据结构中汉族结构占80．2％,类畲族结构13％,类侗族结构6．8％。各族M7个体Y-STR单倍型的网络结构分析发现客家人中类苗瑶结构有两个来源,其一来自湖北,其一来自广东。客家人之类侗族结构应来自江西土著干越。客家人母系遗传的线粒体Region V区段9bp缺失频率为19．7％,与畲族很近,不同于中原汉族。客家人的主要成分应是中原汉人,畲族是对客家人影响最大的外来因素。与客家话中的苗瑶语特征相印证,客家人可能是古代荆蛮族的核心成分不断加上中原汉人移民形成的。客家话等南方汉语方言最初也可能是南方原住民语言在中原汉语不断影响下逐渐形成的。     

Ancient DNA Reveals That the Genetic Structure of the Northern Han Chinese Was Shaped Prior to 3,000 Years Ago

The Han Chinese are the largest ethnic group in the world, and their origins, development, and expansion are complex. Many genetic studies have shown that Han Chinese can be divided into two distinct groups: northern Han Chinese and southern Han Chinese. The genetic history of the southern Han Chinese has been well studied. However, the genetic history of the northern Han Chinese is still obscure. In order to gain insight into the genetic history of the northern Han Chinese, 89 human remains were sampled from the Hengbei site which is located in the Central Plain and dates back to a key transitional period during the rise of the Han Chinese (approximately 3,000 years ago). We used 64 authentic mtDNA data obtained in this study, 27 Y chromosome SNP data profiles from previously studied Hengbei samples, and genetic datasets of the current Chinese populations and two ancient northern Chinese populations to analyze the relationship between the ancient people of Hengbei and present-day northern Han Chinese. We used a wide range of population genetic analyses, including principal component analyses, shared mtDNA haplotype analyses, and geographic mapping of maternal genetic distances. The results show that the ancient people of Hengbei bore a strong genetic resemblance to present-day northern Han Chinese and were genetically distinct from other present-day Chinese populations and two ancient populations. These findings suggest that the genetic structure of northern Han Chinese was already shaped 3,000 years ago in the Central Plain area.     

Y-chromosome haplotype distribution in Han Chinese populations and modern human origin in East Asians

We investigated the distribution of Y-chromosome haplotype using 19 Y-SNPs in Han Chinese populations from 22 provinces of China. Our data indicate distinctive patterns of Y chromosome between southern and northern Han Chinese populations. The southern populations are much more polymorphic than northern populations. The latter has only a subset of the southern haplotypes. This result confirms the genetic difference observed between southern and northern ethnic populations in East Asia. It supports the hypothesis that the first settlement of modern humans of African origin occurred in the southern part of East Asia during the last Ice Age, and a northward migration led to the peopling of northern China.     

Y-chromosome haplotype distribution in Han Chinese populations and modern human origin in East Asians

We investigated the distribution of Y-chromosome haplotype using 19 Y-SNPs in Han Chinese populations from 22 provinces of China. Our data indicate distinctive patterns of Y chromosome between southern and northern Han Chinese populations. The southern populations are much more polymorphic than northern populations. The latter has only a subset of the southern haplotypes. This result confirms the genetic difference observed between southern and northern ethnic populations in East Asia. It supports the hypothesis that the first settlement of modern humans of African origin occurred in the southern part of East Asia during the last Ice Age, and a northward migration led to the peopling of northern China.     

利用近似贝氏计算推论台湾海峡沿岸秋茄种群的拓殖路线

由于地理关系,台湾海峡两岸的红树植物组成具有高度的相似性,都以耐寒性较强的秋茄为优势种。中国台湾(以下简称"台湾")与大陆仅一水之隔,因此台湾的秋茄种群来源最有可能来自东南沿海种群,然而台湾南、北红树植物种群的拓殖路线以及与大陆东南沿海种群的遗传关系的研究至今仍未见报道。通过SSR分子标记,利用近似贝氏计算(Approximate Bayesian Computation)推测海峡两岸4个分布区域秋茄的起源及其拓殖路线。结果表明4个区域的种群出现明显分化,大陆东南北部种群与其他种群间分化程度最高。通过推测台湾北部种群起源可追溯到29000—48400a前,早于末次冰期时间,且台湾北部种群遗传结构与大陆东南南部种群最相近,推测它们可能共同起源于南方祖先。大陆东南沿海南北种群的溯祖时间约为15.1万年至25.2a年前,约为更新世中期末,则意味东南沿海南、北种群的遗传分化可能受到更新世后期气候变化与海侵海退的影响而出现隔离,或东南沿海南、北种群可能来自不同的起源。而台湾南部种群与台湾北部种群的相似性,表明台湾南部种群是由北部种群拓殖而来,近似贝氏计算亦支持这个假说。因而,可以推测海峡两岸秋茄的拓殖路线是从大陆东南南方种群随黑潮迁移至台湾北部,再从北部拓殖到台湾南部。利用近似贝氏计算推论台湾海峡两岸红树林种群起源及拓殖路线,为未来我国东南沿海红树林植物的生物地理研究提供参考。     

海峡两岸汉民族与南岛民族肤纹之比较

本文研究与整理海峡两岸汉民族与南岛民族的肤纹数据,来比较与探讨目前他们的肤纹形态上的异同。研究群体包含台湾的汉人与原住民族群,以及大陆的汉族与海南的回辉人。研究结果显示两岸非官话(亦作北方方言)区汉族虽然在肤纹参数上有些许不同,但皆属于北方群。而南岛民族的回辉人和台湾原住民则分属南方和北方群,并且在肤纹参数上有非常显著的不同。这是第一个两岸南岛民族的肤纹比较研究,也是第一个非官话区汉人群体的肤纹比较研究。     

Autosomal STRs Provide Genetic Evidence for the Hypothesis That Tai People Originate from Southern China

Tai people are widely distributed in Thailand, Laos and southwestern China and are a large population of Southeast Asia. Although most anthropologists and historians agree that modern Tai people are from southwestern China and northern Thailand, the place from which they historically migrated remains controversial. Three popular hypotheses have been proposed: northern origin hypothesis, southern origin hypothesis or an indigenous origin. We compared the genetic relationships between the Tai in China and their “siblings” to test different hypotheses by analyzing 10 autosomal microsatellites. The genetic data of 916 samples from 19 populations were analyzed in this survey. The autosomal STR data from 15 of the 19 populations came from our previous study (Lin et al., 2010). 194 samples from four additional populations were genotyped in this study: Han (Yunnan), Dai (Dehong), Dai (Yuxi) and Mongolian. The results of genetic distance comparisons, genetic structure analyses and admixture analyses all indicate that populations from northern origin hypothesis have large genetic distances and are clearly differentiated from the Tai. The simulation-based ABC analysis also indicates this. The posterior probability of the northern origin hypothesis is just 0.04 [95%CI: (0.01–0.06)]. Conversely, genetic relationships were very close between the Tai and populations from southern origin or an indigenous origin hypothesis. Simulation-based ABC analyses were also used to distinguish the southern origin hypothesis from the indigenous origin hypothesis. The results indicate that the posterior probability of the southern origin hypothesis [0.640, 95%CI: (0.524–0.757)] is greater than that of the indigenous origin hypothesis [0.324, 95%CI: (0.211–0.438)]. Therefore, we propose that the genetic evidence does not support the hypothesis of northern origin. Our genetic data indicate that the southern origin hypothesis has higher probability than the other two hypotheses statistically, suggesting that the Tai people most likely originated from southern China.     

Fine-scale north-to-south genetic admixture profile in Shaanxi Han Chinese revealed by genome-wide demographic history reconstruction

The Han Chinese are the world's largest ethnic group residing across China. Shaanxi province in northern China was a pastoral–agricultural interlacing region sensitive to climate change since Neolithic times, which makes it a vital place for studying population dynamics. However, genetic studies of Shaanxi Han are underrepresented due to the lack of high-density sampling and genome-wide data. Here, we genotyped 700 000 single nucleotide polymorphisms (SNPs) in 200 Han individuals from nine populations in Shaanxi and compared with available modern and ancient Eurasian individuals. We revealed a north–south genetic cline in Han Chinese with Shaanxi Han locating at the northern side of the cline. We detected the western Eurasian-related admixture in Shaanxi populations, especially in Guanzhong and Shanbei Han Chinese in proportions of 2%–4.6%. Shaanxi Han were suggested to derive a large part of ancestry (39%–69%) from a lineage that also contributed largely to ancient and present-day Tibetans (85%) as well as southern Han, supporting the common northern China origin of modern Sino-Tibetan-speaking populations and southwestward expansion of millet farmers from the middle-upper Yellow River Basin to the Tibetan Plateau and to southern China. The rest of the ancestry of Shaanxi Han was from a lineage closely related to ancient and present-day Austronesian and Tai-Kadai speaking populations in southern China and Southeast Asia. We also observed a genetic substructure in Shaanxi Han in terms of north–south-related ancestry corresponding well to the latitudes. Maternal mitochondrial DNA and paternal Y-chromosome lineages further demonstrated the aforementioned admixture pattern of Han Chinese in Shaanxi province.     

现代中国人体质特征及其类型的分析

文章运用多元分析方法,分析了十六个地区的汉族和廿五个少数民族的体质特征,提出现代中国人的体质特征明显分为两大地区类型,即长江以北的为北部类型和长江以南的为南部类型。并且认为两大类型体征的形成始于我国文化发达的新石器时代.     

Northern gene flow into southeastern East Asians inferred from genome-wide array genotyping

The population history of Southeast (SE) China remains poorly understood due to the sparse sampling of present-day populations and limited modeling with ancient genomic data. We report genome-wide genotyping data from 207 present-day Han Chinese and Hmong-Mien (HM)-speaking She people from Fujian and Taiwan Island, SE China. We coanalyzed 66 Early Neolithic to Iron Age ancient Fujian and Taiwan Island individuals obtained from previously published works to explore the genetic continuity and admixture based on patterns of genetic variations of the high-resolution time transect. We found the genetic differentiation between northern and southern East Asians was defined by a north–south East Asian genetic cline and our studied southern East Asians were clustered in the southern end of this cline. The southeastern coastal modern East Asians are genetically similar to other southern indigenous groups as well as geographically close to Neolithic-to-Iron Age populations, but they also shared excess alleles with post-Neolithic Yellow River ancients, which suggested a southward gene flow on the modern southern coastal gene pool. In addition, we identified one new HM genetic cline in East Asia with the coastal Fujian HM-speaking She localizing at the intersection between HM and Han clines. She people show stronger genetic affinity with southern East Asian indigenous populations, with the main ancestry deriving from groups related to southeastern ancient indigenous rice farmers. The southeastern Han Chinese could be modeled with the primary ancestry deriving from the group related to the Yellow River Basin millet farmers and the remaining from groups related to rice farmers, which was consistent with the northern China origin of modern southeastern Han Chinese and in line with the historically and archaeologically attested southward migrations of Han people and their ancestors. Our estimated north–south admixture time ranges based on the decay of the linkage disequilibrium spanned from the Bronze Age to historic periods, suggesting the recent large-scale population migrations and subsequent admixture participated in the formation of modern Han in SE Asia.     

Genetic admixture accelerates invasion via provisioning rapid adaptive evolution

Genetic admixture, the intraspecific hybridization among divergent introduced sources, can immediately facilitate colonization via hybrid vigor and profoundly enhance invasion via contributing novel genetic variation to adaption. As hybrid vigor is short‐lived, provisioning adaptation is anticipated to be the dominant and long‐term profit of genetic admixture, but the evidence for this is rare. We employed the 30 years' geographic‐scale invasion of the salt marsh grass, Spartina alterniflora, as an evolutionary experiment and evaluated the consequences of genetic admixture by combining the reciprocal transplant experiment with quantitative and population genetic surveys. Consistent with the documentation, we found that the invasive populations in China had multiple origins from the southern Atlantic coast and the Gulf of Mexico in the US. Interbreeding among these multiple sources generated a “hybrid swarm” that spread throughout the coast of China. In the northern and mid‐latitude China, natural selection greatly enhanced fecundity, plant height and shoot regeneration compared to the native populations. Furthermore, genetic admixture appeared to have broken the negative correlation between plant height and shoot regeneration, which was genetically‐based in the native range, and have facilitated the evolution of super competitive genotypes in the invasive range. In contrast to the evolved northern and mid‐latitude populations, the southern invasive populations showed slight increase of plant height and shoot regeneration compared to the native populations, possibly reflecting the heterotic effect of the intraspecific hybridization. Therefore, our study suggests a critical role of genetic admixture in accelerating the geographic invasion via provisioning rapid adaptive evolution.     

Population genetics analysis of the origin of the Oriental fruit fly, Bactrocera dorsalis Hendel (Diptera: Tephritidae), in northern Yunnan Province, China

We examined genetic variation in the Oriental fruit fly, Bactrocera dorsalis (Hendel), using six populations in two regions of Yunnan Province, China, to determine the distribution and likely mechanism for the dispersal of this fly. A 501‐bp portion of the mitochondrial cytochrome oxidase gene was sequenced from a minimum of eight individuals from each population, and 43 haplotypes were observed in the six Bactrocera dorsalis populations. When comparing the genetic diversity of populations in the northern and southern regions, which differ with respect to elevation, climate and plant phenology, we found a significantly greater haplotype diversity in the southern region (permutation test; P < 0.05), suggesting that the northern populations, those at Kunming and Qujing, probably originated from somewhere in the southern region. F_ST and number of pairwise differences revealed a high level of differentiation between the Panxi population and the other populations (permutation test; P < 0.05). Although the difference was marginally insignificant, the Shuitang population seemed to have differentiated from both northern populations. The Mantel test did not detect any isolation due to geographic distance. An amova analysis found that 2.56% of the variance was caused by the Panxi population. Haplotype network analysis showed that none of the six populations had a specific genetic lineage. Together, these analyses suggest that long‐distance dispersal has occurred for this species, and the species most probably took advantage of both a mountain pass and prevailing air currents. The Panxi population was significantly isolated from the others, probably because of its distinguishing habitat features, host plants or the recent reduction of the population size.     

中国南北方汉族人群DNA甲基化表观遗传差异研究

目的 族群地域、体貌特征等表型是基因型与环境共同作用的结果。大量基因组学研究表明,汉族人群具有混合特征,内部存在明显的南北遗传差异。本研究旨在探索研究表观基因组在中国南北方汉族人群之间是否存在差异,并筛选差异遗传位点。方法 使用GLINT软件对483份汉族样本的全基因组甲基化芯片数据进行EWAS分析,使用Lasso回归方法筛选位点。使用多元逻辑回归算法构建南北方汉族人群预测模型,通过十折交叉验证的方法评估。结果 筛选出一组南北方汉族之间差异显著的CpG位点,准确性为99.03%,Kappa系数为0.979 6。结论 本研究表明南北方汉族人群之间存在表观遗传差异,本研究为进一步开展不同地域汉族人群之间的表观遗传差异研究奠定了基础。     

Genetic Structure and Demographic History Reveal Migration of the Diamondback Moth Plutella xylostella (Lepidoptera: Plutellidae) from the Southern to Northern Regions of China

The diamondback moth Plutella xylostella (Linnaeus) (Lepidoptera: Plutellidae) is one of the most destructive insect pests of cruciferous plants worldwide. Biological, ecological and genetic studies have indicated that this moth is migratory in many regions around the world. Although outbreaks of this pest occur annually in China and cause heavy damage, little is known concerning its migration. To better understand its migration pattern, we investigated the population genetic structure and demographic history of the diamondback moth by analyzing 27 geographical populations across China using four mitochondrial genes and nine microsatellite loci. The results showed that high haplotype diversity and low nucleotide diversity occurred in the diamondback moth populations, a finding that is typical for migratory species. No genetic differentiation among all populations and no correlation between genetic and geographical distance were found. However, pairwise analysis of the mitochondrial genes has indicated that populations from the southern region were more differentiated than those from the northern region. Gene flow analysis revealed that the effective number of migrants per generation into populations of the northern region is very high, whereas that into populations of the southern region is quite low. Neutrality testing, mismatch distribution and Bayesian Skyline Plot analyses based on mitochondrial genes all revealed that deviation from Hardy-Weinberg equilibrium and sudden expansion of the effective population size were present in populations from the northern region but not in those from the southern region. In conclusion, all our analyses strongly demonstrated that the diamondback moth migrates within China from the southern to northern regions with rare effective migration in the reverse direction. Our research provides a successful example of using population genetic approaches to resolve the seasonal migration of insects.     

Population structure of chum salmon Oncorhynchus keta in the Russian Far East, as revealed by microsatellite markers

Chum salmon populations in the Russian Far East have a complex multi-level genetic structure. A total of 53 samples (2446 fish) were grouped into five major regional clusters: the southern Kurils, eastern Sakhalin, southwestern Sakhalin, the Amur River, and a northern cluster. The northern cluster consists of chum salmon populations from a vast geographical region, including Chukotka, Kamchatka, and the continental coast of the Sea of Okhotsk. However, the degree of its genetic differentiation is low, 1.9%. In contrast, the southern population cluster exhibits much higher variation; for example, differentiation between chum salmon groups within Sakhalin Island reaches 4.6%, and the differentiation between Iturup Island and Sakhalin Island chum salmon is 7.7%. This suggests that southern populations of Asian chum salmon have a more ancient evolutionary history than northern populations. In contrast to the available data, our study indicates a great deviation of southwestern Sakhalin populations from other Sakhalin chum salmon. The Russian Far East chum salmon are genetically diverse and show statistically significant differentiation even within small geographic localities. This can be used to assign samples of unknown origins to definite local populations.     

X‐chromosome lineages and the settlement of the Americas

Most genetic studies on the origins of Native Americans have examined data from mtDNA and Y‐chromosome DNA. To complement these studies and to broaden our understanding of the origin of Native American populations, we present an analysis of 1,873 X‐chromosomes representing Native American (n = 438) and other continental populations (n = 1,435). We genotyped 36 polymorphic sites, forming an informative haplotype within an 8‐kb DNA segment spanning exon 44 of the dystrophin gene. The data reveal continuity from a common Eurasian ancestry between Europeans, Siberians, and Native Americans. However, the loss of two haplotypes frequent in Eurasia (18.8 and 7%) and the rise in frequency of a third haplotype rare elsewhere, indicate a major population bottleneck in the peopling of the Americas. Although genetic drift appears to have played a greater role in the genetic differentiation of Native Americans than in the latitudinally distributed Eurasians, we also observe a signal of a differentiated ancestry of southern and northern populations that cannot be simply explained by the serial southward dilution of genetic diversity. It is possible that the distribution of X‐chromosome lineages reflects the genetic structure of the population of Beringia, itself issued from founder effects and a source of subsequent southern colonization(s). Am J Phys Anthropol, 2009. © 2009 Wiley‐Liss, Inc.