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The Yellow River Delta played a vital role in the development of the Neolithic civilization of China. However, the population history of this region from the Neolithic transitions to the present remains poorly understood due to the lack of ancient human genomes. This especially holds for key Neolithic transitions and tumultuous turnovers of dynastic history. Here, we report genome-wide data from 69 individuals dating to 5,410-1,345 years before present (BP) at 0.008 to 2.49× coverages, along with 325 present-day individuals collected from 16 cities across Shandong. During the Middle to Late Dawenkou period, we observed a significant influx of ancestry from Neolithic Yellow River farmers in central China and some southern Chinese ancestry that mixed with local hunter-gatherers in Shandong. The genetic heritage of the Shandong Longshan people was found to be most closely linked to the Dawenkou culture. During the Shang to Zhou Dynasties, there was evidence of genetic admixture of local Longshan populations with migrants from the Central Plain. After the Qin to Han Dynasties, the genetic composition of the region began to resemble that of modern Shandong populations. Our genetic findings suggest that the middle Yellow River Basin farmers played a role in shaping the genetic affinity of neighboring populations in northern China during the Middle to Late Neolithic period. Additionally, our findings indicate that the genetic diversity in the Shandong region during the Zhou Dynasty may be linked with their complex ethnicities.
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China's Northern and Southern Dynasties period (3rd-6th centuries AD) marked a significant era of ethnic integration in northern China. However, previous ancient DNA studies have primarily focused on northern ethnic groups, with limited research on the genetic formation of the hereditary elite family, especially considering their abundant archaeological record and clear material identity. In this study, we obtained the ancient genome of a hereditary elite family, Gao Bin (, 503-572 AD), at 0.6473-fold coverage with 475132 single-nucleotide polymorphisms (SNPs) on the 1240k panel. His mitochondrial haplogroup belonged to Z4 and Y-haplogroup to O1a1a2b-F2444*. The genetic profile of Gao Bin was most similar to that of the northern Han Chinese. He could be modelled as deriving all his ancestry from Late Neolithic to Iron Age Yellow River farmers without influence from Northeast Asia, Korea, or the Mongolian Plateau. Our study sheds light on the genetic formation of hereditary elite families in the context of the Southern and Northern Dynasties ethnic integration.
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Shandong province, located in the Lower Yellow River, is one of the birthplaces of ancient Chinese civilization. However, the comprehensive genetic histories of this region have remained largely unknown until now due to a lack of ancient human genomes. Here, we present 21 ancient genomes from Shandong dating from the Warring States period to the Jin-Yuan Dynasties. Unlike the early Neolithic samples from Shandong, the historical samples are most closely related to post-Late Neolithic populations of the Middle Yellow River Basin, suggesting a population turnover in Shandong from the Neolithic Age to the Historical era. In addition, we detect a close genetic affinity between the historical samples in Shandong and present-day Han Chinese, showing long-term genetic stability in Han Chinese at least since the Warring States period.
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Soil contamination, land desertification and concrete cracking can have significant adverse impacts on sustainable human economic and societal development. Cost-effective and environmentally friendly approaches are recommended to resolve these issues. Microbially induced carbonate precipitation (MICP) is an innovative, attractive and cost-effective in situ biotechnology with high potential for remediation of polluted or desertified soils/lands and cracked concrete and has attracted widespread attention in recent years. Accordingly, the principles of MICP technology and its applications in the remediation of heavy metal-contaminated and desertified soils and self-healing of concrete were reviewed in this study. The production of carbonate mineral precipitates during the MICP process can effectively reduce the mobility of heavy metals in soils, improve the cohesion of dispersed sands and realize self-healing of cracks in concrete. Moreover, CO2 can be fixed during MICP, which can facilitate carbon neutrality and contribute to global warming mitigation. Overall, MICP technology exhibits great promise in environmental restoration and construction engineering applications, despite some challenges remaining in its large-scale implementation, such as the substantial impacts of fluctuating environmental factors on microbial activity and MICP efficacy. Several methods, such as the use of natural materials or wastes as nutrient and calcium sources and isolation of bacterial strains with strong resistance to harsh environmental conditions, are employed to improve the remediation performance of MICP. However, more studies on the efficiency enhancement, mechanism exploration and field-scale applications of MICP are needed.
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Carbonato de Calcio , Materiales de Construcción , Restauración y Remediación Ambiental , Carbonato de Calcio/química , Restauración y Remediación Ambiental/métodos , Carbono/química , Suelo/química , Contaminantes del SueloRESUMEN
Phenotypic diversity, especially that of facial morphology, has not been fully investigated in the Han Chinese, which is the largest ethnic group in the world. In this study, we systematically analyzed a total of 14,838 facial traits representing 15 categories with both a large-scale three-dimensional (3D) manual landmarking database and computer-aided facial segmented phenotyping in 2379 Han Chinese individuals. Our results illustrate that homogeneous and heterogeneous facial morphological traits exist among Han Chinese populations across the three geographical regions: Zhengzhou, Taizhou, and Nanning. We identified 1560 shared features from extracted phenotypes, which characterized well the basic facial morphology of the Han Chinese. In particular, heterogeneous phenotypes showing population structures corresponded to geographical subpopulations. The greatest facial variation among these geographical populations was the angle of glabella, left subalare, and right cheilion (p = 3.4 × 10-161). Interestingly, we found that Han Chinese populations could be classified into northern Han, central Han, and southern Han at the phenotypic level, and the facial morphological variation pattern of central Han Chinese was between the typical differentiation of northern and southern Han Chinese. This result was highly consistent with the results revealed by the genetic data. These findings provide new insights into the analysis of multidimensional phenotypes as well as a valuable resource for further facial phenotype-genotype association studies in Han Chinese and East Asian populations. Supplementary Information: The online version contains supplementary material available at 10.1007/s43657-023-00109-x.
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Emperor Wu (, Wudi) of the Xianbei-led Northern Zhou dynasty, named Yuwen Yong (, 543-578 CE), was a highly influential emperor who reformed the system of regional troops, pacified the Turks, and unified the northern part of the country. His genetic profile and physical characteristics, including his appearance and potential diseases, have garnered significant interest from the academic community and the public. In this study, we have successfully generated a 0.343×-coverage genome of Wudi with 1,011,419 single-nucleotide polymorphisms (SNPs) on the 1240k panel. By analyzing pigmentation-relevant SNPs and conducting cranial CT-based facial reconstruction, we have determined that Wudi possessed a typical East or Northeast Asian appearance. Furthermore, pathogenic SNPs suggest Wudi faced an increased susceptibility to certain diseases, such as stroke. Wudi shared the closest genetic relationship with ancient Khitan and Heishui Mohe samples and modern Daur and Mongolian populations but also showed additional affinity with Yellow River (YR) farmers. We estimated that Wudi derived 61% of his ancestry from ancient Northeast Asians (ANAs) and nearly one-third from YR farmer-related groups. This can likely be attributed to continuous intermarriage between Xianbei royal families, and local Han aristocrats.1,2 Furthermore, our study has revealed genetic diversities among available ancient Xianbei individuals from different regions, suggesting that the formation of the Xianbei was a dynamic process influenced by admixture with surrounding populations.
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Pueblo Asiatico , ADN Mitocondrial , Humanos , ADN Mitocondrial/genética , Pueblo Asiatico/genética , Genoma , Polimorfismo de Nucleótido Simple , China , Genética de PoblaciónRESUMEN
Y-chromosomal short tandem repeat polymorphisms (Y-STRs) and Y-chromosomal single nucleotide polymorphisms (Y-SNPs) are valuable genetic markers used in paternal lineage identification and population genetics. Currently, there is a lack of an effective panel that integrates Y-STRs and Y-SNPs for studying paternal lineages, particularly in East Asian populations. Hence, we developed a novel Y-chromosomal targeted panel called YARN (Y-chromosome Ancestry and Region Network) based on multiplex PCR and a single-end 400 massive parallel sequencing (MPS) strategy, consisting of 44 patrilineage Y-STRs and 260 evolutionary Y-SNPs. A total of 386 reactions were validated for the effectiveness and applicability of YARN according to SWGDAM validation guidelines, including sensitivity (with a minimum input gDNA of 0.125â¯ng), mixture identification (ranging from 1:1-1:10), PCR inhibitor testing (using substances such as 50⯵M hematin, 100⯵M hemoglobin, 100⯵M humic acid, and 2.5â¯mM indigo dye), species specificity (successfully distinguishing humans from other animals), repeatability study (achieved 100% accuracy), and concordance study (with 99.91% accuracy for 1121 Y-STR alleles). Furthermore, we conducted a pilot study using YARN in a cohort of 484 Han Chinese males from Huaiji County, Zhaoqing City, Guangdong, China (GDZQHJ cohort). In this cohort, we identified 52 different Y-haplogroups and 73 different surnames. We found weak to moderate correlations between the Y-haplogroups, Chinese surnames, and geographical locations of the GDZQHJ cohort (with λ values ranging from 0.050 to 0.340). However, when we combined two different categories into a new independent variable, we observed stronger correlations (with λ values ranging from 0.617 to 0.754). Overall, the YARN panel, which combines Y-STR and Y-SNP genetic markers, meets forensic DNA quality assurance guidelines and holds potential for East Asian geographical origin inference and paternal lineage analysis.
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Cromosomas Humanos Y , Dermatoglifia del ADN , Repeticiones de Microsatélite , Polimorfismo de Nucleótido Simple , Humanos , Masculino , Pueblos del Este de Asia/genética , Genética de Población , Secuenciación de Nucleótidos de Alto Rendimiento , Reacción en Cadena de la Polimerasa Multiplex , Reproducibilidad de los Resultados , Especificidad de la EspecieRESUMEN
The phenotype-first approach (PFA) and data-driven approach (DDA) have both greatly facilitated anthropological studies and the mapping of trait-associated genes. However, the pros and cons of the two approaches are poorly understood. Here, we systematically evaluated the two approaches and analyzed 14,838 facial traits in 2,379 Han Chinese individuals. Interestingly, the PFA explained more facial variation than the DDA in the top 100 and 1,000 except in the top 10 phenotypes. Accordingly, the ratio of heterogeneous traits extracted from the PFA was much greater, while more homogenous traits were found using the DDA for different sex, age, and BMI groups. Notably, our results demonstrated that the sex factor accounted for 30% of phenotypic variation in all traits extracted. Furthermore, we linked DDA phenotypes to PFA phenotypes with explicit biological explanations. These findings provide new insights into the analysis of multidimensional phenotypes and expand the understanding of phenotyping approaches.
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Introduction: Short Tandem Repeats (STRs) are highly valuable genetic markers in forensic science. However, the conventional PCR-CE technique has limitations, and the emergence of massively parallel sequencing (MPS) technology presents new opportunities for STR analysis. Yet, there is limited research on Chinese population diversity using MPS. Methods: In this study, we obtained genotype data for 52 A-STRs and 81 Y-STRs from the Hakka population in Meizhou, Guangdong, China, using the Forensic Analysis System Multiplecues SetB Kit on the MGISEQ-2000 platform. Results: Our findings demonstrate that these 133 STRs are highly efficient for forensic applications within the Meizhou Hakka population. Statistical analysis revealed Hobs values ranging from 0.61306 to 0.91083 and Hexp values ranging from 0.59156 to 0.91497 for A-STRs based on length polymorphism. For sequence polymorphism, Hobs values ranged from 0.61306 to 0.94586, and Hexp values fluctuated between 0.59156 and 0.94487. The CPE values were 1-5.0779620E-21 and 1-3.257436E-24 for length and sequence polymorphism, respectively, while the CPD values were 1-1.727007E-59 and 1-5.517015E-66, respectively. Among the 80 Y-STR loci, the HD values for length and sequence polymorphism were 0.99764282 and 0.99894195, respectively. The HMP values stood at 0.00418102 and 0.00288427, respectively, and the DC values were 0.75502742 and 0.83363803, respectively. For the 52 A-STR loci, we identified 554 and 989 distinct alleles based on length and sequence polymorphisms, respectively. For the 81 Y-STR loci, 464 and 652 unique alleles were detected at the length and sequence level, respectively. Population genetic analysis revealed that the Meizhou Hakka population has a close kinship relationship with the Asian populations THI and KOR based on length polymorphism data of A-STRs. Conversely, based on length polymorphism data of Y-STRs, the Meizhou Hakka population has the closest kinship relationship with the Henan Han population. Discussion: Overall, the variation information of repeat region sequences significantly enhances the forensic identification efficacy of STR genetic markers, providing an essential database for forensic individual and paternity testing in this region. Additionally, the data generated by our study will serve as a vital resource for research into the genetic structure and historical origins of the Meizhou Hakka population.
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The Datong Basin was an important arena for population movement and admixture between the Yellow River Valley and Eastern Steppe. In historical materials, the region was often the setting for a tug-of-war between Han farmers and non-Han nomads. The genetic makeup and population history of this Datong population has, however, remained uncertain. In this study, we analysed 289 mitogenomes from Datong individuals. Our primary findings were: (1) population summary statistics analysis revealed a high level of genetic diversity and strong signals of population expansion in the Datong population; (2) inter-population comparisons (PCA and Fst heatmap) exhibited a close clustering between the Datong population and Northern Han, especially northern frontier groups, such as the Inner Mongolia Han, Heilongjiang Han, Liaoning Han and Tianjin Han; (3) phylogeographic analysis of complete mitogenomes revealed the presence of different components in the maternal gene pools of Datong population-the northern East Asian component was dominant (66.44%), whereas the southern East Asians were the second largest component with 31.49%. We also observed a much reduced west Eurasian (2.07%) component; (4) direct comparisons with ancient groups showed closer relationship between Datong and Yellow River farmers than Eastern Steppe nomads. Despite, therefore, centuries of Eastern Steppe nomadic control over the Datong area, Yellow River farmers had a much more significant impact on the Datong population.
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Genoma Mitocondrial , Humanos , Genoma Mitocondrial/genética , Ríos , Filogeografía , Pueblo Asiatico , China , Genética de Población , ADN Mitocondrial/genéticaRESUMEN
Introduction: Viral hemorrhagic septicemia virus (VHSV) is the most lethal pathogen in aquaculture, infecting more than 140 fish species in marine, estuarine, and freshwater environments. Viral hemorrhagic septicemia virus is an enveloped RNA virus that belongs to the family Rhabdoviridae and the genus Novirhabdovirus. The current study is designed to infer the worldwide Viral hemorrhagic septicemia virus isolates' genetic diversity and evolutionary dynamics based on G-gene sequences. Methods: The complete G-gene sequences of viral hemorrhagic septicemia virus were retrieved from the public repositories with known timing and geography details. Pairwise statistical analysis was performed using Arlequin. The Bayesian model-based approach implemented in STRUCTURE software was used to investigate the population genetic structure, and the phylogenetic tree was constructed using MEGA X and IQ-TREE. The natural selection analysis was assessed using different statistical approaches, including IFEL, MEME, and SLAC. Results and Discussion: The global Viral hemorrhagic septicemia virus samples are stratified into five genetically distinct subpopulations. The STRUCTURE analysis unveiled spatial clustering of genotype Ia into two distinct clusters at K = 3. However, at K = 5, the genotype Ia samples, deposited from Denmark, showed temporal distribution into two groups. The analyses unveiled that the genotype Ia samples stratified into subpopulations possibly based on spatiotemporal distribution. Several viral hemorrhagic septicemia virus samples are characterized as genetically admixed or recombinant. In addition, differential or subpopulation cluster-specific natural selection signatures were identified across the G-gene codon sites among the viral hemorrhagic septicemia virus isolates. Evidence of low recombination events elucidates that genetic mutations and positive selection events have possibly driven the observed genetic stratification of viral hemorrhagic septicemia virus samples.
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A high point of Tibetan Plateau (TP) civilization, the expansive Tubo Empire (618-842 AD) wielded great influence across ancient western China. However, whether the Tubo expansion was cultural or demic remains unclear due to sparse ancient DNA sampling. Here, we reported ten ancient genomes at 0.017- to 0.867-fold coverages from the Dulan site with typical Tubo archaeological culture dating to 1308-1130 BP. Nine individuals from three different grave types have close relationship with previously reported ancient highlanders from the southwestern Himalayas and modern core-Tibetan populations. A Dulan-related Tubo ancestry contributed overwhelmingly (95%-100%) to the formation of modern Tibetans. A genetic outlier with dominant Eurasian steppe-related ancestry suggesting a potential population movement into the Tubo-controlled regions from Central Asia. Together with archeological evidence from burial styles and customs, our study suggested the impact of the Tubo empire on the northeast edge of the TP involved both cultural and demic diffusion.
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As we continually reflect on the wars of the 20th century, identification of the remains of victims takes an increasingly prominent position in ongoing research. Existing work on the identification of human remains from 20th century wars primarily covers the determination of phenotypic characteristics, kinship and geographic origins, supporting the establishment of genetic information databases. Compared with standard forensic methods, DNA analyses have revealed greater effectiveness. The process of DNA analysis includes DNA extraction, genetic marker testing and data analysis. Protocols from ancient DNA research can be applied to degraded remains, and next-generation sequencing (NGS) techniques can compensate for shortcomings in the most commonly-used PCR-capillary electrophoresis typing. As it stands, wide-ranging inter-governmental and inter-institutional collaboration is necessary in order to set up NGS-based public databases, and thereby promote the identification of human remains and archaeological forensics.
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Dermatoglifia del ADN , Repeticiones de Microsatélite , Restos Mortales , Dermatoglifia del ADN/métodos , ADN Antiguo , Marcadores Genéticos , Secuenciación de Nucleótidos de Alto Rendimiento , HumanosRESUMEN
BACKGROUNDS: Y-chromosomal haplotypes based on Y-short tandem repeats (STRs) and Y-single nucleotide polymorphisms/insertion and deletion polymorphisms (SNPs/InDels) are used to characterize paternal lineages of unknown male trace donors. However, Y-chromosomal genetic markers are not currently sufficient for precise individual identification. Microhaplotype (MH), generally < 200 bp on autosomes and consisting of two or more SNPs, was recently introduced in forensic genetics with the development of massive parallel sequencing technology and may facilitate identification and DNA mixture deconvolution. Therefore, combining the two kinds of genetic markers may be beneficial in many forensic scenarios, especially crime scenes with male suspects, such as sexual assault cases. METHODS: In the present study, we developed a novel MPS-based panel, Microhaplotype and Y-SNP/STR (MY), by multiplex PCR and 150-bp paired-end sequencing, including 114 Y-SNPs (twelve dominant Y-DNA haplogroups), 45 Y-STRs (N-1 stutter < 0.09; estimated mutation rate < 5 × 10-3), and 22 MHs (allele coverage ratio > 0.91; pairwise distance > 10 Mb). Additionally, MY system-based genotype pattern recognition (GPR), a regression-based method to identify the genotype pattern for each MH locus, is proposed for two-person DNA mixture deconvolution. We integrated 26 two-person genotype combinations into nine genotype patterns and validated the application range of GPR based on DNA profiles of ten sets of simulated male-male DNA mixtures (1:10-1:2). RESULTS: The effective number of alleles (Ae) ranged from 3.62 to 14.72, with an average of 7.17, in 100 Chinese Guangdong Han individuals. The cumulative discrimination power was 1-5.00 × 10-31, and the cumulative power of exclusion was 1-5.00 × 10-8 and 1-4.85 × 10-12 for duo and trio paternity testing, respectively. Furthermore, the actual mixing ratio-depth of coverage (DoC) ratio (RDoC) regression relationships were established for different genetic markers and genotype patterns. In five overlapping areas, genotype differentiation of the major and minor contributors required likelihood ratio methods. In nonoverlapping areas, the genotype pattern could be recognized by comparing the observed RDoC and RDoC ranges. CONCLUSION: The GPR can be used to deconvolute two-person DNA mixtures (application range: 1:10-1:2) for individual identification.
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Dermatoglifia del ADN , Polimorfismo de Nucleótido Simple , ADN/análisis , ADN/genética , Dermatoglifia del ADN/métodos , Marcadores Genéticos , Genotipo , Haplotipos , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Masculino , Repeticiones de MicrosatéliteRESUMEN
The Hexi Corridor was an important arena for culture exchange and human migration between ancient China and Central and Western Asia. During the Han Dynasty (202 BCE-220 CE), subsistence strategy along the corridor shifted from pastoralism to a mixed pastoralist-agriculturalist economy. Yet the drivers of this transition remain poorly understood. In this study, we analyze the Y-chromosome and mtDNA of 31 Han Dynasty individuals from the Heishuiguo site, located in the center of the Hexi Corridor. A high-resolution analysis of 485 Y-SNPs and mitogenomes was performed, with the Heishuiguo population classified into Early Han and Late Han groups. It is revealed that (1) when dissecting genetic lineages, the Yellow River Basin origin haplogroups (i.e., Oα-M117, Oß-F46, Oγ-IMS-JST002611, and O2-P164+, M134-) reached relatively high frequencies for the paternal gene pools, while haplogroups of north East Asian origin (e.g., D4 and D5) dominated on the maternal side; (2) in interpopulation comparison using PCA and Fst heatmap, the Heishuiguo population shifted from Southern-Northern Han cline to Northern-Northwestern Han/Hui cline with time, indicating genetic admixture between Yellow River immigrants and natives. By comparison, in maternal mtDNA views, the Heishuiguo population was closely clustered with certain Mongolic-speaking and Northwestern Han populations and exhibited genetic continuity through the Han Dynasty, which suggests that Heishuiguo females originated from local or neighboring regions. Therefore, a sex-biased admixture pattern is observed in the Heishuiguo population. Additionally, genetic contour maps also reveal the same male-dominated migration from the East to Hexi Corridor during the Han Dynasty. This is also consistent with historical records, especially excavated bamboo slips. Combining historical records, archeological findings, stable isotope analysis, and paleoenvironmental studies, our uniparental genetic investigation on the Heishuiguo population reveals how male-dominated migration accompanied with lifestyle adjustments brought by these eastern groups may be the main factor affecting the subsistence strategy transition along the Han Dynasty Hexi Corridor.
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Northern Pakistan is home to many diverse ethnicities and languages. The region acted as a prime corridor for ancient invasions and population migrations between Western Eurasia and South Asia. Kho, one of the major ethnic groups living in this region, resides in the remote and isolated mountainous region in the Chitral Valley of the Hindu Kush Mountain range. They are culturally and linguistically distinct from the rest of the Pakistani population groups and their genetic ancestry is still unknown. In this study, we generated genome-wide genotype data of ~1 M loci (Illumina WeGene array) for 116 unrelated Kho individuals and carried out comprehensive analyses in the context of worldwide extant and ancient anatomically modern human populations across Eurasia. The results inferred that the Kho can trace a large proportion of their ancestry to the population who migrated south from the Southern Siberian steppes during the second millennium BCE ~110 generations ago. An additional wave of gene flow from a population carrying East Asian ancestry was also identified in the Kho that occurred ~60 generations ago and may possibly be linked to the expansion of the Tibetan Empire during 7th to 9th centuries CE (current era) in the northwestern regions of the Indian sub-continent. We identified several candidate regions suggestive of positive selection in the Kho, that included genes mainly involved in pigmentation, immune responses, muscular development, DNA repair, and tumor suppression.
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Etnicidad , Genética de Población , Pueblo Asiatico/genética , Etnicidad/genética , Flujo Génico , Humanos , PakistánRESUMEN
In kinship tests, the investigating of the forensic STRs usually provides decisive information to resolve relationship cases. We describe a parentage case with 3 genetic incompatibilities (D6S1043, D18S51 and D2S1338) between the child and alleged parent. With 90 STR loci and 100 SNP loci, the massively parallel sequencing (MPS)-based genotyping results support the certainty of parentage, and the mismatched alleles were considered to be mutations. MPS can provide additional allele sequence structures that can be used to infer the origins of the mutations. SNPs as supplementary markers can provide effective information to give an unequivocal statement of the parentage.