Origin of ethnic groups, linguistic families, and civilizations in China viewed from the Y chromosome

Genomic insights into Neolithic founding paternal lineages around the Qinghai-Xizang Plateau using integrated YanHuang resource

Indigenous populations of the Qinghai-Xizang Plateau exhibit unique high-altitude adaptations, especially within Tibeto-Burman (TB) groups. However, the paternal genetic heritage of eastern Plateau regions remains less explored. We present one integrative Y chromosome dataset of 9,901 modern and ancient individuals, including whole Y chromosome sequences from 1,297 individuals and extensive Y-SNP/STR genotype data. We reveal the Paleolithic common origin and following divergence of Qinghai-Xizang Plateau ancestors from East Asian lowlands, marked by subsequent isolation and Holocene expansion involving local hunter-gatherers and millet-farming communities. We identified two key TB-related founding lineages, D-Z31591 and O-CTS4658, which underwent significant expansions around 5,000 years ago on the Qinghai-Xizang Plateau and its eastern Tibetan-Yi Corridor. The genetic legacy of these TB lineages highlights crucial migration pathways linking the Plateau and lowland southwestern China. Our findings align paternal genetic structures with East Asian geography and linguistic groups, underscoring the utility of Y chromosome analyses in unraveling complex paternal histories.

ERAP1 Gene Variants and Haplotypes Associated With Psoriasis Vulgaris of Han Chinese in Inner Mongolia

BACKGROUND

This study aimed to investigate the association between genetic variants of ERAP1 (OMIM: 606832) and psoriasis vulgaris (PsV) susceptibility in Inner Mongolia Han nationality.

METHODS

For primary screening, the subjects included 142 PsV cases and 100 healthy controls without psoriasis. The 27 exons of ERAP1 gene were sequenced to screen significant genetic variants. For the validation study, the subjects included 1030 PsV cases and 965 healthy controls. A total of 18 mutations were detected for genetic variants of significance in primary screening and previously reported genetic variants.

RESULTS

In primary screening stage, 13 genetic variants of ERAP1 showed an association with psoriasis. A total of 18 genetic variants were typed for the validation, and 12 genetic variants were associated with PsV in Inner Mongolia Han population. Stratified analysis showed significant differences in the allele frequencies of 8 ERAP1 genetic variants in cases with positive family history, and significant differences in allele frequencies among 9 ERAP1 genetic variants in patients with negative family history. A risk haplotype (TCCCTCCAGACC) was significantly associated with PsV, and the most risk haplotype was E730/K528/R127/E56.

CONCLUSION

ERAP1 gene mutation may be associated with PsV and HLA-C*06:02 in Han nationality in Inner Mongolia. A risk haplotype of four-nonsynonymous mutation (E730/K528/R127/E56) is associated with PsV.

Prevalence and risk factors for refractive error in older adults in eight ethnicities in China: The China national health survey

Purpose

This study aimed to investigate the prevalence of refractive error (RE) and risk factors for myopia among older adults in the Han and various minority ethnic groups across seven provinces in China.

Methods

This cross-sectional study forms a part of the ophthalmic dataset of the China National Health Survey (CNHS). Face-to-face interviews and ophthalmic examinations were conducted in seven provinces located in western and northern China. The age- and sex-adjusted prevalence of RE among Han and seven other ethnic groups aged 50-80 years were compared. A mixed-effects model was used to identify the risk factors associated with RE.

Results

A total of 12,902 participants, including 8800 Han and 4102 from ethnic minorities, were included in the study. The age- and sex-adjusted prevalence of myopia, high myopia, hyperopia, and astigmatism ranged from 15.3 % (Manchu) to 22.9 % (Han), 0.2 % (Yugur) to 2.8 % (Han), 21.6 % (Tibetan) to 48.9 % (Uyghur), and 38.7 % (Yi) to 57.5 % (Manchu) across different ethnicities, respectively. Compared to the Han population, the Mongolian (odds ratios (OR) 0.62, 95 % confidence interval (CI) 0.46-0.84, p = 0.002), Tibetan (OR 0.66, 95 % CI 0.52-0.85, p = 0.001), Uyghur (OR 0.63, 95 % CI 0.49-0.80, p < 0.001), Yi (OR 0.65, 95 % CI 0.46-0.92, p = 0.014), and Yugur (OR 0.65, 95 % CI 0.50-0.85, p = 0.001) ethnicities were less likely to have myopia. There was no significant difference in the prevalence of myopia between the Manchu, Korean, and Han ethnic groups. Factors associated with a lower prevalence of myopia included rural residence (p < 0.001), a body mass index (BMI) > 18.5 kg/m2 (all p < 0.001), residence in higher latitude areas (p = 0.020), and a history of smoking (p = 0.002 in the past smoking group, p = 0.031 in the current smoking group). The Mongolian (p = 0.006) and Yugur (p = 0.007) populations, participants living in rural areas (p = 0.012), and those with a BMI >24 kg/m2 (p = 0.038 in the >24.0 ≤ 27.0 kg/m2 group or p = 0.041 in the >27.0 kg/m2 group) were less likely to have high myopia. Factors associated with a higher prevalence of hyperopia included older age (all p < 0.001), rural residence (p = 0.039), higher latitude areas (p = 0.031), smoking history (p = 0.040), and Mongolian (p = 0.001), Uyghur (p < 0.001), Yi (p < 0.001), and Yugur (p = 0.002) ethnicities. Conversely, the Manchu population (p = 0.004) and individuals with higher education levels than illiteracy (p = 0.024 or p < 0.001) were less likely to have hyperopia.

Conclusions

Myopia affected more than one-fifth of the older adults in the Han population in this survey. Significant differences in the prevalence of RE were observed between minority ethnicities and Han individuals, except for the Manchu and Korean groups.

Longitudinal Changes in Human Milk Minerals and Vitamins in the Chinese Population: A Scoping Review

This scoping review aims to investigate longitudinal changes in minerals and vitamins concentrations in human milk among the Chinese population. Following the PRISMA-ScR guidelines, a comprehensive and systematic literature search was conducted using both English and Chinese databases. Data were extracted and categorized into six defined lactation stages. We found that the concentration of most minerals decreased throughout the lactation period, although calcium (Ca) and magnesium (Mg) fluctuated slightly across lactation periods. Fat-soluble vitamins also showed a decline throughout the lactation period, while water-soluble vitamins exhibited an increasing trend. However, folic acid, biotin, and pantothenic acid demonstrated a downward trend. Overall, this review has identified the longitudinal changes in minerals and vitamins concentrations in human milk among the Chinese population. In order to conduct a more in-depth examination of maternal characteristics and nutritional factors of the composition of human milk, it is recommended to utilize standardized protocols for the collection and analysis of human milk samples.

Evolutionary profiles and complex admixture landscape in East Asia: New insights from modern and ancient Y chromosome variation perspectives

Human Y-chromosomes are characterized by nonrecombination and uniparental inheritance, carrying traces of human history evolution and admixture. Large-scale population-specific genomic sources based on advanced sequencing technologies have revolutionized our understanding of human Y chromosome diversity and its anthropological and forensic applications. Here, we reviewed and meta-analyzed the Y chromosome genetic diversity of modern and ancient people from China and summarized the patterns of founding lineages of spatiotemporally different populations associated with their origin, expansion, and admixture. We emphasized the strong association between our identified founding lineages and language-related human dispersal events correlated with the Sino-Tibetan, Altaic, and southern Chinese multiple-language families related to the Hmong-Mien, Tai-Kadai, Austronesian, and Austro-Asiatic languages. We subsequently summarize the recent advances in translational applications in forensic and anthropological science, including paternal biogeographical ancestry inference (PBGAI), surname investigation, and paternal history reconstruction. Whole-Y sequencing or high-resolution panels with high coverage of terminal Y chromosome lineages are essential for capturing the genomic diversity of ethnolinguistically diverse East Asians. Generally, we emphasized the importance of including more ethnolinguistically diverse, underrepresented modern and spatiotemporally different ancient East Asians in human genetic research for a comprehensive understanding of the paternal genetic landscape of East Asians with a detailed time series and for the reconstruction of a reference database in the PBGAI, even including new technology innovations of Telomere-to-Telomere (T2T) for new genetic variation discovery.

Distinguished biological adaptation architecture aggravated population differentiation of Tibeto-Burman-speaking people

Tibeto-Burman (TB) people have endeavored to adapt to the hypoxic, cold, and high-UV high-altitude environments in the Tibetan Plateau and complex disease exposures in lowland rainforests since the late Paleolithic period. However, the full landscape of genetic history and biological adaptation of geographically diverse TB-speaking people, as well as their interaction mechanism, remain unknown. Here, we generate a whole-genome meta-database of 500 individuals from 39 TB-speaking populations and present a comprehensive landscape of genetic diversity, admixture history, and differentiated adaptative features of geographically different TB-speaking people. We identify genetic differentiation related to geography and language among TB-speaking people, consistent with their differentiated admixture process with incoming or indigenous ancestral source populations. A robust genetic connection between the Tibetan-Yi corridor and the ancient Yellow River people supports their Northern China origin hypothesis. We finally report substructure-related differentiated biological adaptative signatures between highland Tibetans and Loloish speakers. Adaptative signatures associated with the physical pigmentation (EDAR and SLC24A5) and metabolism (ALDH9A1) are identified in Loloish people, which differed from the high-altitude adaptative genetic architecture in Tibetan. TB-related genomic resources provide new insights into the genetic basis of biological adaptation and better reference for the anthropologically informed sampling design in biomedical and genomic cohort research.

The maternal phylogenetic insights of Yunnan Miao group revealed by complete mitogenomes

The Miao group is one of the representative Hmong-Mien-speaking populations and primarily scattered in southern China and Southeast Asia, which has experienced massive migrations in history and thus forms distinctive evolutionary genetics. Yet, the genetic explorations of Miao group are relatively limited based on complete mitochondrial genome (mitogenome), especially for the Miao group from Yunnan Province (YNM). Here, we sequenced complete mitogenomes of 132 Miao individuals from Yunnan Province using massively parallel sequencing method. Total 132 Miao individuals could be allocated to 119 various haplotypes, which were mainly dominated by haplogroups prevalent in southern East Asia (B, F, M7 and R9), and rarely occupied by northern lineages (A, D, G and M8). In order to dissect the genetic background of YNM more comprehensively, we introduced 99 published population data with 7135 complete mitochondrial sequences for population genetic comparisons. YNM exhibited closer genetic relationships with Hmong-Mien, Tai-Kadai, Sino-Tibetan and Austroasiatic populations, especially for Hmong-Mien populations; we further speculated that Miao group might have certain direct or indirect gene exchanges with ancient Baiyue groups. Several maternal lineages, such as B5a1c1a, F1g1, B4a5 and D4e1a3, were found to be specifically shared by YNM and other Hmong-Mien populations, and these matrilineal expansions occurred roughly during the Neolithic period. Eventually, according to the population dynamic analyses of YNM, the population size began to emerge recovery ∼1-0.5 kya after a long-term population reduction ∼1-5 kya, during which the B5a1c1a haplogroup manifested relatively apparent lineage expansion.

An Anthropometric Study of the Morphologic Facial Index of Tibetan Youth in Tibet

The purpose of this study was to understand sex differences and variations in facial indices among Tibetans and to create and evaluate anthropometric data on facial morphology. The study population consisted of 476 native Tibetans (241 males and 235 females) aged 18 to 24 years. The means and SD facial width was 133.53±7.31 mm for males and 133.95±8.10 mm for females; the difference between the sexes was not statistically significant. The means and SD facial height was 107.68±5.76 mm for males and 111.95±14.28 mm for females; the difference between the sexes was statistically significant (u=-8.394, P=0.000). The morphologic facial index was 80.86±5.82 (means±SD) for males and 83.91±11.90 (means±SD) for females; the difference between the sexes was statistically significant (u=-6.581, P=0.000). The proportion of the Tibetan male facial shape was hypereuryprosopic (45.6%) > euryprosopic (31.1%) > mesoprosopic (18.7%) > leptoprosopic (3.3%) > hyperleptoprosopic (1.2%). The proportion of the Tibetan female facial shape was hypereuryprosopic (25.5%) > mesoprosopic (22.6%) > euryprosopic (21.7%) > leptoprosopic (17.4%) > hyperleptoprosopic (12.8%). Facial width was positively correlated with height (male r=0.306, P=0.000; female r=0.144, P=0.027), weight (r=0.470, P=0.000 for males; r=0.337, P=0.000 for females), and BMI (r=0.378, P=0.000 for males; r=0.291, P=0.000 for females). Facial height was positively correlated with height (r=0.329, P=0.000 for males; r=0.137, P=0.035 for females) and weight (r=0.391, P=0.000 for males; r=0.170, P=0.009 for females). Facial height was positively correlated with BMI in Tibetan males (r=0.293, P=0.000), but no significant correlation was found in Tibetan females. The morphologic facial index of Tibetans was positively correlated with age (r=0.183, P=0.004 for males; r=0.171, P=0.009 for females). The results indicated that Tibetan youth in Tibet have a predominantly hypereuryprosopic facial shape and that facial features are related to age, height, and weight. Some common facial morphology features exist among the Tibet Tibetans, northeastern Indians, and Nepalese in the 3 different regions of the Sino-Tibetan language family. The data from this study provide basic information for the study of Tibetans in the fields of physical anthropology, forensic medicine, maxillofacial surgery, and plastic surgery.

Multiple migrations from East Asia led to linguistic transformation in NorthEast India and mainland Southeast Asia

NorthEast India, with its unique geographic location in the midst of the Himalayas and Bay of Bengal, has served as a passage for the movement of modern humans across the Indian subcontinent and East/Southeast Asia. In this study we look into the population genetics of a unique population called the Khasi, speaking a language (also known as the Khasi language) belonging to the Austroasiatic language family and residing amidst the Tibeto-Burman speakers as an isolated population. The Khasi language belongs to one of the three major broad classifications or phyla of the Austroasiatic language and the speakers of the three sub-groups are separated from each other by large geographical distances. The Khasi speakers are separated from their nearest Austroasiatic language-speaking sub-groups: the “Mundari” sub-family from East and peninsular India and the “Mon-Khmers” in Mainland Southeast Asia. We found the Khasi population to be genetically distinct from other Austroasiatic speakers, i.e. Mundaris and Mon-Khmers, but relatively similar to the geographically proximal Tibeto Burmans. The possible reasons for this genetic-linguistic discordance lie in the admixture history of different migration events that originated from East Asia and proceeded possibly towards Southeast Asia. We found at least two distinct migration events from East Asia. While the ancestors of today’s Tibeto-Burman speakers were affected by both, the ancestors of Khasis were insulated from the second migration event. Correlating the linguistic similarity of Tibeto-Burman and Sino-Tibetan languages of today’s East Asians, we infer that the second wave of migration resulted in a linguistic transition while the Khasis could preserve their linguistic identity.

Regional fauna-flora biodiversity and conservation strategy in China

Evolutionary and historical development and current profiles are essential to generating a tangible conservation strategy. It is also critical to distinguish the regions with vigorous potential growth from those meeting evolutionary development bottlenecks and those whose development has been severely devastated. We used two sizeable national data repositories of terrestrial fauna and flora of China to approach the issues. The results indicate that the Southwest and Coastal regions have the most significant terrestrial faunal-floral biodiversity (TFFB). Thus, they should be prioritized in conservation for great potential promotions. Although there has been remarkable evolutionary development, the Central region has been severely devastated. A solution is to uphold a balanced association between social-economic development and TFFB sustainability. As for the Northeast and the western Northwest, there is no need to invest heavily in conservation measures. This study sheds light on exploring more practical conservation strategies regionally, nationally, and globally to achieve pragmatic goals.

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Terrestrial faunal-floral biodiversity (TFFB) in China

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Regional variation assessment of TFFB in China

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China’s regional disparity in human impact and evolutionary development

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Regionalized conservation strategies in China

Forensic Features and Genetic Structure Analyses of the Beijing Han Nationality Disclosed by a Self-Developed Panel Containing a Series of Ancestry Informative Deletion/Insertion Polymorphism Loci

The utilization of the ancestry informative markers to disclose the ancestral composition of a certain population and explore the genetic affinities between diverse populations is beneficial to inferring the biogeographic ancestry of unknown individuals and assisting in case detection, as well as avoiding the impacts of population stratification during genome-wide association analysis studies. In the present study, we applied an in-house ancestry informative deletion/insertion polymorphic multiplex amplification system to investigate the ancestral compositions of the Beijing Han population and analyze the genetic relationships between the Beijing Han population and 31 global reference populations. The results demonstrated that 32 loci of this self-developed panel containing 39 loci significantly contributed to the inference of genetic information for the Beijing Han population. The results of multiple population genetics statistical analyses indicated that the ancestral component and genetic architecture of the Beijing Han population were analogous to the reference East Asian populations, and that the Beijing Han population was genetically close to the reference East Asian populations.

Genomic Insights Into the Population History and Biological Adaptation of Southwestern Chinese Hmong-Mien People

Hmong-Mien (HM) -speaking populations, widely distributed in South China, the north of Thailand, Laos, and Vietnam, have experienced different settlement environments, dietary habits, and pathogenic exposure. However, their specific biological adaptation remained largely uncharacterized, which is important in the population evolutionary genetics and Trans-Omics for regional Precision Medicine. Besides, the origin and genetic diversity of HM people and their phylogenetic relationship with surrounding modern and ancient populations are also unknown. Here, we reported genome-wide SNPs in 52 representative Miao people and combined them with 144 HM people from 13 geographically representative populations to characterize the full genetic admixture and adaptive landscape of HM speakers. We found that obvious genetic substructures existed in geographically different HM populations; one localized in the HM clines, and others possessed affinity with Han Chinese. We also identified one new ancestral lineage specifically existed in HM people, which spatially distributed from Sichuan and Guizhou in the north to Thailand in the south. The sharing patterns of the newly identified homogenous ancestry component combined the estimated admixture times via the decay of linkage disequilibrium and haplotype sharing in GLOBETROTTER suggested that the modern HM-speaking populations originated from Southwest China and migrated southward in the historic period, which is consistent with the reconstructed phenomena of linguistic and archeological documents. Additionally, we identified specific adaptive signatures associated with several important human nervous system biological functions. Our pilot work emphasized the importance of anthropologically informed sampling and deeply genetic structure reconstruction via whole-genome sequencing in the next step in the deep Chinese Population Genomic Diversity Project (CPGDP), especially in the regions with rich ethnolinguistic diversity.

Inferring the population structure and admixture history of three Hmong-Mien-speaking Miao tribes from southwest China based on Genome-wide SNP genotyping

BACKGROUND

Hmong-Mien speaking Miao, also called Hmong, is the sixthlargest ethnic group in mainland China. However, the fine-scale genetic profiles and population history of Miao populations in southwest China, especially in Guizhou province, remain uncharacterised due to a scarcity of samples of genome-wide data from different tribes.

AIM

To further investigate the population substructure and admixture history of the Guizhou Miao minority.

SUBJECTS AND METHODS

We collected 29 samples from three Miao tribes of Guizhou province in southwest China and genotyped about 700,000 genome-wide SNPs of each sample. We analysed newly generated data in together with published modern/ancient East Asian populations datasets via a series of population genetic methods, including principal component analysis (PCA), ADMIXTURE, Fst, TreeMix, f-statistics, qpWave, and qpAdm.

RESULTS

PCA and ADMIXTURE results showed that the three studied Guizhou Miao groups consistently fell on the Hmong-Mien-related genetic cline and were relatively genetically homogeneous, displayingd a genetic affinity with neighbouring Tai-Kadai speaking populations such as Dong. These results were further confirmed by the observed genetic clade in Fst, TreeMix, outgroup-f₃ -statistics, and f₄ -statistics. Furthermore, f₄ -based allele sharing patterns illustrated that compared with Hunan Miao in central China, Guizhou Miao shared more alleles with Hmong-Mien-speaking Vietnam Hmong and Tai-Kadai-speaking CoLao, Dong, while exhibiting less northeast Asian-related ancestry. Admixture-f₃ and f₄ statistics revealed the North-South admixture pattern for the studied Guizhou Miao. A qpAdm-based two-way admixture model further revealed that the studied Guizhou Miao harboured 44%∼55.4% indigenous Austronesian-speaking Atayal-related ancestry and 44.6%∼56% Late Neolithic Yellow River farmer-related ancestry.

CONCLUSIONS

The population structure within Hmong-Mien-related populations showed a geographic correlation. Hmong-Mien speaking Hunan Miao, Guizhou Miao, and Vietnam Hmong presented closer genetic relationships although they dwelt in different regions, suggesting the preservation of the original Hmong-related genetic diversity. The results based on genome-wide SNPs data generally matched the migration history for the Miao population. Our study contributes to a better knowledge of Miao populations and the population structure in southwest China.

Fine-Scale Genetic Structure and Natural Selection Signatures of Southwestern Hans Inferred From Patterns of Genome-Wide Allele, Haplotype, and Haplogroup Lineages

The evolutionary and admixture history of Han Chinese have been widely discussed via traditional autosomal and uniparental genetic markers [e.g., short tandem repeats, low-density single nucleotide polymorphisms). However, their fine-scale genetic landscapes (admixture scenarios and natural selection signatures) based on the high-density allele/haplotype sharing patterns have not been deeply characterized. Here, we collected and generated genome-wide data of 50 Han Chinese individuals from four populations in Guizhou Province, one of the most ethnolinguistically diverse regions, and merged it with over 3,000 publicly available modern and ancient Eurasians to describe the genetic origin and population admixture history of Guizhou Hans and their neighbors. PCA and ADMIXTURE results showed that the studied four populations were homogeneous and grouped closely to central East Asians. Genetic homogeneity within Guizhou populations was further confirmed via the observed strong genetic affinity with inland Hmong-Mien people through the observed genetic clade in Fst and outgroup f₃/f₄-statistics. qpGraph-based phylogenies and f₄-based demographic models illuminated that Guizhou Hans were well fitted via the admixture of ancient Yellow River Millet farmers related to Lajia people and southern Yangtze River farmers related to Hanben people. Further ChromoPainter-based chromosome painting profiles and GLOBETROTTER-based admixture signatures confirmed the two best source matches for southwestern Hans, respectively, from northern Shaanxi Hans and southern indigenes with variable mixture proportions in the historical period. Further three-way admixture models revealed larger genetic contributions from coastal southern East Asians into Guizhou Hans compared with the proposed inland ancient source from mainland Southeast Asia. We also identified candidate loci (e.g., MTUS2, NOTCH4, EDAR, ADH1B, and ABCG2) with strong natural selection signatures in Guizhou Hans via iHS, nSL, and ihh, which were associated with the susceptibility of the multiple complex diseases, morphology formation, alcohol and lipid metabolism. Generally, we provided a case and ideal strategy to reconstruct the detailed demographic evolutionary history of Guizhou Hans, which provided new insights into the fine-scale genomic formation of one ethnolinguistically specific targeted population from the comprehensive perspectives of the shared unlinked alleles, linked haplotypes, and paternal and maternal lineages.