Analysis of ancient human mitochondrial DNA from the Xiaohe cemetery: insights into prehistoric population movements in the Tarim Basin, China

Bronze Age cheese reveals human-Lactobacillus interactions over evolutionary history

Despite the long history of consumption of fermented dairy, little is known about how the fermented microbes were utilized and evolved over human history. Here, by retrieving ancient DNA of Bronze Age kefir cheese (∼3,500 years ago) from the Xiaohe cemetery, we explored past human-microbial interactions. Although it was previously suggested that kefir was spread from the Northern Caucasus to Europe and other regions, we found an additional spreading route of kefir from Xinjiang to inland East Asia. Over evolutionary history, the East Asian strains gained multiple gene clusters with defensive roles against environmental stressors, which can be a result of the adaptation of Lactobacillus strains to various environmental niches and human selection. Overall, our results highlight the role of past human activities in shaping the evolution of human-related microbes, and such insights can, in turn, provide a better understanding of past human behaviors.

Reconstructing complex admixture history using a hierarchical model

Various methods have been proposed to reconstruct admixture histories by analyzing the length of ancestral chromosomal tracts, such as estimating the admixture time and number of admixture events. However, available methods do not explicitly consider the complex admixture structure, which characterizes the joining and mixing patterns of different ancestral populations during the admixture process, and instead assume a simplified one-by-one sequential admixture model. In this study, we proposed a novel approach that considers the non-sequential admixture structure to reconstruct admixture histories. Specifically, we introduced a hierarchical admixture model that incorporated four ancestral populations and developed a new method, called HierarchyMix, which uses the length of ancestral tracts and the number of ancestry switches along genomes to reconstruct the four-way admixture history. By automatically selecting the optimal admixture model using the Bayesian information criterion principles, HierarchyMix effectively estimates the corresponding admixture parameters. Simulation studies confirmed the effectiveness and robustness of HierarchyMix. We also applied HierarchyMix to Uyghurs and Kazakhs, enabling us to reconstruct the admixture histories of Central Asians. Our results highlight the importance of considering complex admixture structures and demonstrate that HierarchyMix is a useful tool for analyzing complex admixture events.

Inferring the population history of Kyrgyz in Xinjiang, Northwest China from genome-wide array genotyping

OBJECTIVES

Xinjiang plays a vital role in the trans-Eurasian population migration, language diffusion, and culture and technology exchange. However, the underrepresentation of Xinjiang's genomes has hindered a more comprehensive understanding of Xinjiang's genetic structure and population history.

MATERIALS AND METHODS

We collected and genotyped 70 southern Xinjiang's Kyrgyz (SXJK) individuals and combined the data with modern and ancient Eurasians published. We used allele-frequency methods, including PCA, ADMIXTURE, f-statistics, qpWave/qpAdm, ALDER, Treemix, and haplotype-shared methods including shared-IBD segments, fineSTRUCTURE, and GLOBETROTTER to unveil the fine-scale population structure and reconstruct admixture history.

RESULTS

We identified genetic substructure within the SXJK population with subgroups showing different genetic affinities to West and East Eurasians. All SXJK subgroups were suggested to have close genetic relationships with surrounding Turkic-speaking groups that is, Uyghur, Kyrgyz from north Xinjiang and Tajikistan, and Chinese Kazakh, suggesting a shared ancestry among those populations. Outgroup-f3 and symmetrical f4 statistics showed a high genetic affinity of SXJK to present-day Tungusic, Mongolic-speaking populations and Ancient Northeast Asian (ANA) related groups. Allele sharing and haplotype sharing profiles revealed the east-west admixture pattern of SXJK. The qpAdm-based admixture models showed that SXJK derived ancestry from East Eurasian (ANA and East Asian, 42.7%-83.3%) and West Eurasian (Western Steppe herders and Central Asian, 16.7%-57.3%), the recent east-west admixture event could be traced to 1000 years ago based on ALDER and GLOBETROTTER analysis.

DISCUSSION

The high genetic affinity of SXJK to present-day Tungusic and Mongolic-speaking populations and short-shared IBD segments indicated their shared common ancestry. SXJK harbored a close genetic affinity to ANA-related populations, indicating the Northeast Asian origin of SXJK. The West and East Eurasian admixture models observed in SXJK further provided evidence of the dynamic admixture history in Xinjiang. The east-west admixture pattern and the identified ancestral makeup of SXJK suggested a genetic continuity from some Iron Age Xinjiang populations to present-day SXJK.

Kazak mitochondrial genomes provide insights into the human population history of Central Eurasia

As a historical nomadic group in Central Asia, Kazaks have mainly inhabited the steppe zone from the Altay Mountains in the East to the Caspian Sea in the West. Fine scale characterization of the genetic profile and population structure of Kazaks would be invaluable for understanding their population history and modeling prehistoric human expansions across the Eurasian steppes. With this mind, we characterized the maternal lineages of 200 Kazaks from Jetisuu at mitochondrial genome level. Our results reveal that Jetisuu Kazaks have unique mtDNA haplotypes including those belonging to the basal branches of both West Eurasian (R0, H, HV) and East Eurasian (A, B, C, D) lineages. The great diversity observed in their maternal lineages may reflect pivotal geographic location of Kazaks in Eurasia and implies a complex history for this population. Comparative analyses of mitochondrial genomes of human populations in Central Eurasia reveal a common maternal genetic ancestry for Turko-Mongolian speakers and their expansion being responsible for the presence of East Eurasian maternal lineages in Central Eurasia. Our analyses further indicate maternal genetic affinity between the Sherpas from the Tibetan Plateau with the Turko-Mongolian speakers.

Bronze and Iron Age population movements underlie Xinjiang population history

The Xinjiang region in northwest China is a historically important geographical passage between East and West Eurasia. By sequencing 201 ancient genomes from 39 archaeological sites, we clarify the complex demographic history of this region. Bronze Age Xinjiang populations are characterized by four major ancestries related to Early Bronze Age cultures from the central and eastern Steppe, Central Asian, and Tarim Basin regions. Admixtures between Middle and Late Bronze Age Steppe cultures continued during the Late Bronze and Iron Ages, along with an inflow of East and Central Asian ancestry. Historical era populations show similar admixed and diverse ancestries as those of present-day Xinjiang populations. These results document the influence that East and West Eurasian populations have had over time in the different regions of Xinjiang.

Ultrasensitive dual enhanced electrochemical immunosensor to detect ancient wool relics

The identification of ancient wool is of great significance in archaeology; however, conventional methods are unwieldy or even ineffective when testing contaminated or severely degraded ancient samples. Therefore, it is highly desirable to develop an ultrasensitive detection method for ancient wool. In this study, an ultrasensitive electrochemical immunosensor is proposed and developed to detect ancient wool, where graphene oxide (GO), aldehyde-functionalized ionic liquid (AFIL) composites and gold nanoparticles (AuNPs) are synthesized as efficient signal amplifiers. With their large surface area and excellent electron transfer efficiency, the combination of GO-AFIL and AuNPs endows the immunosensor with excellent electrochemical properties. The fabricated immunosensor measures over a wide linear range of 0.01-100 ng mL^-1 with a low detection limit of 0.9 ± 0.2 pg mL^-1. Moreover, the immunosensor demonstrates excellent performance for detecting ancient wool. The identification of wool fabrics unearthed from Xinjiang, Tibet and Kazakhstan supports the historicity of prosperous sheepherding and wool trade in Central Asia during the Bronze Age.

Ancient Xinjiang mitogenomes reveal intense admixture with high genetic diversity

Xinjiang is a key region in northwestern China, connecting East and West Eurasian populations and cultures for thousands of years. To understand the genetic history of Xinjiang, we sequenced 237 complete ancient human mitochondrial genomes from the Bronze Age through Historical Era (41 archaeological sites). Overall, the Bronze Age Xinjiang populations show high diversity and regional genetic affinities with Steppe and northeastern Asian populations along with a deep ancient Siberian connection for the Tarim Basin Xiaohe individuals. In the Iron Age, in general, Steppe-related and northeastern Asian admixture intensified, with North and East Xinjiang populations showing more affinity with northeastern Asians and South Xinjiang populations showing more affinity with Central Asians. The genetic structure observed in the Historical Era of Xinjiang is similar to that in the Iron Age, demonstrating genetic continuity since the Iron Age with some additional genetic admixture with populations surrounding the Xinjiang region.

Seasonal movements of Bronze Age transhumant pastoralists in western Xinjiang

The paper explores seasonal movements of Bronze Age mobile pastoralists in the western Tianshan mountainous region of Xinjiang, China. Fieldwork by a team from the Institute of Archaeology of the Chinese Academy of Social Science (CASS) and the University of Sydney, Australia have identified cyclical land use practices associated with the Andronovo cultural complex. Their pattern of seasonal movements has been reconstructed through ethnographic studies and analysis of modern snow and grass cover. Using this detailed combination of data, the study defines requirements for seasonal pastures–winter, summer and spring/autumn–and shows a clear correlation between modern land use and seasonal patterns of movement in the Bronze Age.

Population Genetic Analysis of Modern and Ancient DNA Variations Yields New Insights Into the Formation, Genetic Structure, and Phylogenetic Relationship of Northern Han Chinese

Modern East Asians derived from the admixture of aborigines and incoming farmers expanding from Yellow and Yangtze River Basins. Distinct genetic differentiation and subsequent admixture between Northeast Asians and Southeast Asians subsequently evidenced by the mitochondrial DNA, Y-chromosomal variations, and autosomal SNPs. Recently, population geneticists have paid more attention to the genetic polymorphisms and background of southern-Han Chinese and southern native populations. The genetic legacy of northern-Han remains uncharacterized. Thus, we performed this comprehensive population genetic analyses of modern and ancient genetic variations aiming to yield new insight into the formation of modern Han, and the genetic ancestry and phylogenetic relationship of the northern-Han Chinese population. We first genotyped 25 forensic associated markers in 3,089 northern-Han Chinese individuals using the new-generation of the Huaxia Platinum System. And then we performed the first meta-analysis focused on the genetic affinity between Asian Neolithic∼Iron Age ancients and modern northern-Han Chinese by combining mitochondrial variations in 417 ancient individuals from 13 different archeological sites and 812 modern individuals, as well as Y-chromosomal variations in 114 ancient individuals from 12 Neolithic∼Iron Age sites and 2,810 modern subjects. We finally genotyped 643,897 genome-wide nucleotide polymorphisms (SNPs) in 20 Shanxi Han individuals and combined with 1,927 modern humans and 40 Eurasian ancient genomes to explore the genetic structure and admixture of northern-Han Chinese. We addressed genetic legacy, population structure and phylogenetic relationship of northern-Han Chinese via various analyses. Our population genetic results from five different reference datasets indicated that Shanxi Han shares a closer phylogenetic relationship with northern-neighbors and southern ethnically close groups than with Uyghur and Tibetan. Genome-wide variations revealed that modern northern-Han derived their ancestry from Yakut-related population (25.2%) and She-related population (74.8%). Summarily, the genetic mixing that led to the emergence of a Han Chinese ethnicity occurred at a very early period, probably in Neolithic times, and this mixing involved an ancient Tibeto-Burman population and a local pre-Sinitic population, which may have been linguistically Altaic.

Tianshanbeilu and the Isotopic Millet Road: reviewing the late Neolithic/Bronze Age radiation of human millet consumption from north China to Europe

The westward expansion of human millet consumption from north China has important implications for understanding early interactions between the East and West. However, few studies have focused on the Xinjiang Uyghur Autonomous Region, the vast geographical area directly linking the ancient cultures of the Eurasian Steppe and the Gansu Corridor of China. In this study, we present the largest isotopic investigation of Bronze Age China (n = 110) on material from the key site of Tianshanbeilu, in eastern Xinjiang. The large range of δ¹³C values (–17.6‰ to –7.2‰; –15.5 ± 1.2‰) provides direct evidence of unique dietary diversity and consumption of significant C₄ resources (millets). The high δ¹⁵N results (10.3‰ to 16.7‰; 14.7 ± 0.8‰) likely reflect sheep/goat and wild game consumption and the arid climate of the Taklamakan Desert. Radiocarbon dates from four individuals indicate Tianshanbeilu was in use between 1940 and 1215 cal bc. The Tianshanbeilu results are then analysed with respect to 52 Bronze Age sites from across Eurasia, to investigate the spread and chronology of significant human millet consumption and human migration. This isotopic survey finds novel evidence that the second millennium bc was a dynamic period, with significant dietary interconnectivity occurring between north China, Central Asia and Siberia. Further, we argue that this ‘Isotopic Millet Road’ extended all the way to the Mediterranean and Central Europe, and conclude that these C₄ dietary signatures of millet consumption reflect early links (migration and/or resource transfer) between the Bronze Age inhabitants of modern-day China and Europe.

Phylogenetic and population structural inference from genomic ancestry maintained in present-day common wheat Chinese landraces

Hexaploid common wheat is one of the most important food crops worldwide. Common wheat domestication began in the Fertile Crescent of the Near East approximately 10 000 years ago and then spread west into Europe and eastward into East Asia and China. However, the possible spreading route into and within China is still unclear. In this study, we successfully extracted DNA from single ancient wheat seeds and sequenced the whole genome of seven ancient samples from Xiaohe and Gumugou cemeteries in Xinjiang, China. Genomic inference and morphological observation confirmed their identity as hexaploid common wheat grown in prehistoric China at least 3200 years before present (BP). Phylogenetic and admixture analyses with RNA-seq data of modern hexaploid wheat cultivars from both China and Western countries demonstrated a close kinship of the ancient wheat to extant common wheat landraces in southwestern China. The highly similar allelic frequencies in modern landraces of the Qinghai-Tibetan plateau with the ancient wheat support the previously suggested southwestern spreading route into highland China. A subsequent dispersal route from the Qinghai-Tibetan plateau margins to the Yangtze valley was proposed in this study. Furthermore, the common wheat populations grown in the Middle and Lower Yangtze valley wheat zones were also proposed to be established by population admixture with the wheat grown in the Upper Yangtze valley. Our study reports ancient common wheat sequences at a genome-wide scale, providing important information on the origin, dispersal, and genetic improvement under cultivation of present-day wheat landraces grown in China.

New genetic evidence of affinities and discontinuities between bronze age Siberian populations

OBJECTIVES

This work focuses on the populations of South Siberia during the Eneolithic and Bronze Age and specifically on the contribution of uniparental lineage and phenotypical data to the question of the genetic affinities and discontinuities between western and eastern populations.

MATERIALS AND METHODS

We performed molecular analyses on the remains of 28 ancient humans (10 Afanasievo (3600-2500 BC) and 18 Okunevo (2500-1800 BC) individuals). For each sample, two uniparentally inherited systems (mitochondrial DNA and Y-chromosome DNA) were studied, in order to trace back maternal and paternal lineages. Phenotype-informative SNPs (Single Nucleotide Polymorphisms) were also analyzed, along with autosomal STRs (Short Tandem Repeats).

RESULTS

Most of the Afanasievo men submitted to analysis belonged to a single sub-haplogroup, R1b1a1a, which reveals the predominance of this haplogroup in these early Bronze Age populations. Conversely, Okunevo individuals carried more diverse paternal lineages that mostly belonged to Asian/Siberian haplogroups. These differences are also apparent, although less strongly, in mitochondrial lineage composition and phenotype marker variant frequencies.

DISCUSSION

This study provides new elements that contribute to our understanding of the genetic interactions between populations in Eneolithic and Bronze Age southern Siberia. Our results support the hypothesis of a genetic link between Afanasievo and Yamnaya (in western Eurasia), as suggested by previous studies of other markers. However, we found no Y-chromosome lineage evidence of a possible Afanasievo migration to the Tarim Basin. Moreover, the presence of Y-haplogroup Q in Okunevo individuals links them to Native American populations, as was suggested by whole-genome sequencing.

Origin and spread of human mitochondrial DNA haplogroup U7

Human mitochondrial DNA haplogroup U is among the initial maternal founders in Southwest Asia and Europe and one that best indicates matrilineal genetic continuity between late Pleistocene hunter-gatherer groups and present-day populations of Europe. While most haplogroup U subclades are older than 30 thousand years, the comparatively recent coalescence time of the extant variation of haplogroup U7 (~16–19 thousand years ago) suggests that its current distribution is the consequence of more recent dispersal events, despite its wide geographical range across Europe, the Near East and South Asia. Here we report 267 new U7 mitogenomes that – analysed alongside 100 published ones – enable us to discern at least two distinct temporal phases of dispersal, both of which most likely emanated from the Near East. The earlier one began prior to the Holocene (~11.5 thousand years ago) towards South Asia, while the later dispersal took place more recently towards Mediterranean Europe during the Neolithic (~8 thousand years ago). These findings imply that the carriers of haplogroup U7 spread to South Asia and Europe before the suggested Bronze Age expansion of Indo-European languages from the Pontic-Caspian Steppe region.

Strontium isotope evidence for a highly mobile population on the Pamir Plateau 2500 years ago

Archeological researches have proposed arguments for human mobility and long-distance trading over the Eurasia before the Silk Roads. Here we utilize biologically available strontium isotope analysis to assess the extent of pre-Silk Road population movements and cultural communications across the Asian interior. From an early Iron Age cemetery (ca. 2500 yr B.P.) on the eastern Pamir Plateau, mean ⁸⁷Sr/⁸⁶Sr ratios from 34 individuals display considerable isotopic variability, and 10 individuals are distinguished as migrants based on the local strontium isotope range of 0.710296–0.710572 defined by 12 ovicaprine bones. Comparison of the proportion (10/34) with the regional census data completed in 1909 A.D. (3% non-locals) suggests a highly migratory behavior on the plateau 2500 years ago. Furthermore, exotic mortuary objects, such as silk fabrics from eastern China and angular harp originated from the Near East, clearly demonstrate an interaction between different cultures on the plateau before the establishment of the Silk Road.