Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe

Traces of Bronze Age globalization in East Asia: Insights from a revised phylogeography of the Y-chromosome haplogroup Q1a1a-M120

OBJECTIVE

In this study, we aim to explore the genetic imprint of Bronze Age globalization in East Asia from a phylogeographic perspective by examining the Y-chromosome haplogroup Q1a1a-M120, and to identify key demographic processes involved in the formation of early China and the ancient Huaxia people.

METHODS

Over the past few decades, we have collected the sequences of 347 Y chromosomes from the haplogroup Q1a1a-M120. These sequences were utilized to analyze and reconstruct a highly revised phylogenetic tree with age estimates. And we analyzed the geographical distribution and spatial autocorrelation of nine major sub-branches of Q1a1a-M120. Finally, we observed the expansion of Q1a1a-M120 from the beginning of the Bronze Age in East Asia, along with the continuous dissemination of its sub-lineages among East Asian populations.

RESULTS

We suggest that certain sub-lineages played a significant role in the formation of states and early civilizations in China, as well as in the development of the ancient Huaxia people, who are the direct ancestors of the Han population. Overall, we propose that haplogroup Q-M120 played a role in the introduction of Bronze Age culture to the central region of East Asia. Therefore, it is haplogroup Q-M120, rather than the Western Eurasian paternal lineage, that expanded and contributed to the gene pool of the East Asian population.

CONCLUSION

In summary, the globalization of the Bronze Age led to large-scale population replacement and admixture across various regions of Eurasia; our findings highlight the unique demographic processes that occurred in East Asia during this period.

Cultural transmission, networks, and clusters among Austronesian-speaking peoples

With its linguistic and cultural diversity, Austronesia is important in the study of evolutionary forces that generate and maintain cultural variation. By analysing publicly available datasets, we have identified four classes of cultural features in Austronesia and distinct clusters within each class. We hypothesized that there are differing modes of transmission and patterns of variation in these cultural classes and that geography alone would be insufficient to explain some of these patterns of variation. We detected relative differences in the verticality of transmission and distinct patterns of cultural variation in each cultural class. There is support for pulses and pauses in the Austronesian expansion, a west-to-east increase in isolation with explicable exceptions, and correspondence between linguistic and cultural outliers. Our results demonstrate how cultural transmission and patterns of variation can be analysed using methods inspired by population genetics.

Lactiplantibacillus plantarum KABP051: Stability in Fruit Juices and Production of Bioactive Compounds During Their Fermentation

The lactic fermentation of fruit and vegetable juices by well-characterised probiotics remains relatively underexplored. We have investigated the stability and impact of Lactiplantibacillus plantarum KABP051 fermentation on orange, apple, and peach juices by microbiological, physicochemical, and sensory evaluation means. For each fruit juice, three different samples were analysed: original fruit juice without probiotic as blank (B), fruit juice inoculated with 107 CFU/mL of probiotic without fermentation (P), and fruit juice inoculated with 107 CFU/mL of probiotic and fermented at 37 °C for 24 h (PF). P samples displayed good stability throughout the study, and PF samples showed an initial increase in CFUs accompanied by a change in pH, confirming the ability of the probiotic to ferment these juices. After 60 days of refrigeration, PF samples contained >107 CFU/mL. Total phenolic content and antioxidant capacity were equivalent in F, P, and PF. Remarkably, deep metabolomic analyses confirmed malolactic fermentation and revealed the production of several bioactive compounds including the antimicrobial substance phenyllactic acid, the immunomodulatory and anti-fatigue amino acid N-acetyl glutamine, the vitamin B3 form nicotinic acid, the monoterpene (-)-β-pinene, and the neurotransmitter acetylcholine, among others, during probiotic fermentation. Finally, a hedonic analysis involving 51 participants showed that probiotic fermented orange juice is well accepted by panellists, with scores comparable to those of the control juice. Overall, we here show that fruit juices are excellent carriers for the delivery of the probiotic L. plantarum KABP051 and its non-alcoholic fermentation can result in tasty functional fruit juices enriched with health-promoting compounds.

Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations

The tripartite ancestral structure is a recently proposed model for the genetic origin of modern Japanese, comprising indigenous Jomon hunter-gatherers and two additional continental ancestors from Northeast Asia and East Asia. To investigate the impact of the tripartite structure on genetic and phenotypic variation today, we conducted biobank-scale analyses by merging Biobank Japan (BBJ; n = 171,287) with ancient Japanese and Eurasian genomes (n = 22). We demonstrate the applicability of the tripartite model to Japanese populations throughout the archipelago, with an extremely strong correlation between Jomon ancestry and genomic variation among individuals. We also find that the genetic legacy of Jomon ancestry underlies an elevated body mass index (BMI). Genome-wide association analysis with rigorous adjustments for geographical and ancestral substructures identifies 132 variants that are informative for predicting individual Jomon ancestry. This prediction model is validated using independent Japanese cohorts (Nagahama cohort, n = 2993; the second cohort of BBJ, n = 72,695). We further confirm the phenotypic association between Jomon ancestry and BMI using East Asian individuals from UK Biobank (n = 2286). Our extensive analysis of ancient and modern genomes, involving over 250,000 participants, provides valuable insights into the genetic legacy of ancient hunter-gatherers in contemporary populations.

The rise and transformation of Bronze Age pastoralists in the Caucasus

The Caucasus and surrounding areas, with their rich metal resources, became a crucible of the Bronze Age1 and the birthplace of the earliest steppe pastoralist societies2. Yet, despite this region having a large influence on the subsequent development of Europe and Asia, questions remain regarding its hunter-gatherer past and its formation of expansionist mobile steppe societies3-5. Here we present new genome-wide data for 131 individuals from 38 archaeological sites spanning 6,000 years. We find a strong genetic differentiation between populations north and south of the Caucasus mountains during the Mesolithic, with Eastern hunter-gatherer ancestry4,6 in the north, and a distinct Caucasus hunter-gatherer ancestry7 with increasing East Anatolian farmer admixture in the south. During the subsequent Eneolithic period, we observe the formation of the characteristic West Eurasian steppe ancestry and heightened interaction between the mountain and steppe regions, facilitated by technological developments of the Maykop cultural complex8. By contrast, the peak of pastoralist activities and territorial expansions during the Early and Middle Bronze Age is characterized by long-term genetic stability. The Late Bronze Age marks another period of gene flow from multiple distinct sources that coincides with a decline of steppe cultures, followed by a transformation and absorption of the steppe ancestry into highland populations.

The impact of cooking and burial on proteins: a characterisation of experimental foodcrusts and ceramics

Foodcrusts have received relatively little attention in the burgeoning field of proteomic analysis of ancient cuisine. We remain ignorant of how cooking and burial impact protein survival, and crucially, the extent to which the extractome reflects the composition of input ingredients. Therefore, through experimental analogues, we explore the extent of protein survival in unburied and buried foodcrusts and ceramics using 'typical' Mesolithic ingredients (red deer, Atlantic salmon and sweet chestnut). We then explore a number of physicochemical properties theorised to aid protein preservation. The results reveal that proteins were much more likely to be detected in foodcrusts than ceramics using the methodology employed, that input ingredient strongly influences protein preservation, and that degradation is not universal nor linear between proteins, indicating that multiple protein physicochemical properties are at play. While certain properties such as hydrophobicity apparently aid protein preservation, none single-handedly explain why particular proteins/peptides survive in buried foodcrusts: this complex interplay requires further investigation. The findings demonstrate that proteins indicative of the input ingredient can be identifiable in foodcrust, but that the full proteome is unlikely to preserve. While this shows promise for the survival of proteins in archaeological foodcrust, further research is needed to accurately interpret foodcrust extractomes.

Long shared haplotypes identify the Southern Urals as a primary source for the 10th century Hungarians

During the Hungarian Conquest in the 10th century CE, the early medieval Magyars, a group of mounted warriors from Eastern Europe, settled in the Carpathian Basin. They likely introduced the Hungarian language to this new settlement area, during an event documented by both written sources and archaeological evidence. Previous archaeogenetic research identified the newcomers as migrants from the Eurasian steppe. However, genome-wide ancient DNA from putative source populations has not been available to test alternative theories of their precise source. We generated genome-wide ancient DNA data for 131 individuals from candidate archaeological contexts in the Circum-Uralic region in present-day Russia. Our results tightly link the Magyars to people of the Early Medieval Karayakupovo archaeological horizon on both the European and Asian sides of the southern Urals. Our analyes show that ancestors of the people of the Karayakupovo archaeological horizon were established in the Southern Urals by the Iron Age and that their descendants persisted locally in the Volga-Kama region until at least the 14th century.

Cauldrons of Bronze Age nomads reveals 2700 year old yak milk and the deep antiquity of food preparation techniques

Cauldrons, vessels that are simultaneously common and enigmatic, offer insights into past cultural and social traditions. While assumed to possess a special function, what these cauldrons contained is still largely mysterious. These vessels, such as those made from bronze or copper alloys, function as reservoirs for ancient organics through the antibacterial qualities provided by the metal surfaces. Here we show, through protein analysis, that cauldrons from the Final Bronze Age (ca. 2700 BP) were primarily used to collect blood from ruminants, primarily caprines, likely for the production of sausages in a manner similar to contemporary practices in Mongolia's rural countryside. Our findings present a different function from the recent findings of cooked meat in copper-alloy vessels from the northern Caucasus 2000 years earlier, exposing the diversity in food preparation techniques. Our secondary findings of bovine milk within the cauldron, including peptides specific to Bos mutus, pushes back their regional domestication into the Bronze Age.

Network of large pedigrees reveals social practices of Avar communities

From AD 567-568, at the onset of the Avar period, populations from the Eurasian Steppe settled in the Carpathian Basin for approximately 250 years1. Extensive sampling for archaeogenomics (424 individuals) and isotopes, combined with archaeological, anthropological and historical contextualization of four Avar-period cemeteries, allowed for a detailed description of the genomic structure of these communities and their kinship and social practices. We present a set of large pedigrees, reconstructed using ancient DNA, spanning nine generations and comprising around 300 individuals. We uncover a strict patrilineal kinship system, in which patrilocality and female exogamy were the norm and multiple reproductive partnering and levirate unions were common. The absence of consanguinity indicates that this society maintained a detailed memory of ancestry over generations. These kinship practices correspond with previous evidence from historical sources and anthropological research on Eurasian Steppe societies2. Network analyses of identity-by-descent DNA connections suggest that social cohesion between communities was maintained via female exogamy. Finally, despite the absence of major ancestry shifts, the level of resolution of our analyses allowed us to detect genetic discontinuity caused by the replacement of a community at one of the sites. This was paralleled with changes in the archaeological record and was probably a result of local political realignment.

Reconstructing the Genetic Relationship between Ancient and Present-Day Siberian Populations

Human populations across a vast area in northern Eurasia, from Fennoscandia to Chukotka, share a distinct genetic component often referred to as the Siberian ancestry. Most enriched in present-day Samoyedic-speaking populations such as Nganasans, its origins and history still remain elusive despite the growing list of ancient and present-day genomes from Siberia. Here, we reanalyze published ancient and present-day Siberian genomes focusing on the Baikal and Yakutia, resolving key questions regarding their genetic history. First, we show a long-term presence of a unique genetic profile in southern Siberia, up to 6,000 yr ago, which distinctly shares a deep ancestral connection with Native Americans. Second, we provide plausible historical models tracing genetic changes in West Baikal and Yakutia in fine resolution. Third, the Middle Neolithic individual from Yakutia, belonging to the Belkachi culture, serves as the best source so far available for the spread of the Siberian ancestry into Fennoscandia and Greenland. These findings shed light on the genetic legacy of the Siberian ancestry and provide insights into the complex interplay between different populations in northern Eurasia throughout history.

Palaeoproteomic investigation of an ancient human skeleton with abnormal deposition of dental calculus

Detailed investigation of extremely severe pathological conditions in ancient human skeletons is important as it could shed light on the breadth of potential interactions between humans and disease etiologies in the past. Here, we applied palaeoproteomics to investigate an ancient human skeletal individual with severe oral pathology, focusing our research on bacterial pathogenic factors and host defense response. This female skeleton, from the Okhotsk period (i.e., fifth to thirteenth century) of Northern Japan, poses relevant amounts of abnormal dental calculus deposition and exhibits oral dysfunction due to severe periodontal disease. A shotgun mass-spectrometry analysis identified 81 human proteins and 15 bacterial proteins from the calculus of the subject. We identified two pathogenic or bioinvasive proteins originating from two of the three "red complex" bacteria, the core species associated with severe periodontal disease in modern humans, as well as two additional bioinvasive proteins of periodontal-associated bacteria. Moreover, we discovered defense response system-associated human proteins, although their proportion was mostly similar to those reported in ancient and modern human individuals with lower calculus deposition. These results suggest that the bacterial etiology was similar and the host defense response was not necessarily more intense in ancient individuals with significant amounts of abnormal dental calculus deposition.

Differentiated adaptative genetic architecture and language-related demographical history in South China inferred from 619 genomes from 56 populations

BACKGROUND

The underrepresentation of human genomic resources from Southern Chinese populations limited their health equality in the precision medicine era and complete understanding of their genetic formation, admixture, and adaptive features. Besides, linguistical and genetic evidence supported the controversial hypothesis of their origin processes. One hotspot case was from the Chinese Guangxi Pinghua Han people (GPH), whose language was significantly similar to Southern Chinese dialects but whose uniparental gene pool was phylogenetically associated with the indigenous Tai-Kadai (TK) people. Here, we analyzed genome-wide SNP data in 619 people from four language families and 56 geographically different populations, in which 261 people from 21 geographically distinct populations were first reported here.

RESULTS

We identified significant population stratification among ethnolinguistically diverse Guangxi populations, suggesting their differentiated genetic origin and admixture processes. GPH shared more alleles related to Zhuang than Southern Han Chinese but received more northern ancestry relative to Zhuang. Admixture models and estimates of genetic distances showed that GPH had a close genetic relationship with geographically close TK compared to Northern Han Chinese, supporting their admixture origin hypothesis. Further admixture time and demographic history reconstruction supported GPH was formed via admixture between Northern Han Chinese and Southern TK people. We identified robust signatures associated with lipid metabolisms, such as fatty acid desaturases (FADS) and medically relevant loci associated with Mendelian disorder (GJB2) and complex diseases. We also explored the shared and unique selection signatures of ethnically different but linguistically related Guangxi lineages and found some shared signals related to immune and malaria resistance.

CONCLUSIONS

Our genetic analysis illuminated the language-related fine-scale genetic structure and provided robust genetic evidence to support the admixture hypothesis that can explain the pattern of observed genetic diversity and formation of GPH. This work presented one comprehensive analysis focused on the population history and demographical adaptative process, which provided genetic evidence for personal health management and disease risk prediction models from Guangxi people. Further large-scale whole-genome sequencing projects would provide the entire landscape of southern Chinese genomic diversity and their contributions to human health and disease traits.

The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes

More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases at the time of writing and review of this manuscript, and crossed the threshold of >10,000 individuals with published genome-wide ancient DNA data at the end of 2022. This note is intended as a citable descriptor of the AADR.

Phylogeographic analysis of Y-chromosomal haplogroup C2a-M48-F8472, a minor paternal lineage of Han populations with possible ancestry of Xiongnu

BACKGROUND

Y-chromosome haplogroup C2a-M48-F8472, a unique paternal line in the ancient Xiongnu population, is concentrated in the modern Han people. The most closely related lineage of this paternal lineage is mainly distributed in Tungusic-, Mongolic-, and Turkic-speaking populations.

AIM

To investigate the formation process of this unique distribution state.

SUBJECTS AND METHODS

In total, 36 sequences of haplogroup C2a-M48-F8472 were analysed to generate a revised phylogenetic tree with age estimation and to explore the geographic distribution pattern.

RESULTS

The results suggested that northern China is likely the diffusion centre of this paternal haplogroup. This lineage is concentrated in the Liu clan () of Han populations and may have originated in the Tuge tribe () of Xiongnu populations. The initial expansion (∼2,600 years ago) and the second phase of expansion (∼1,570 years ago) of haplogroup C2a-M48-F8472 coincide with the earlier appearance and later disappearance of the Tuge tribe. As a sub-clade of M48, the history of F8472 suggested that ancient peoples related to Tungusic-speaking populations were intricately connected with the demographic history of populations in the Mongolian Plateau.

CONCLUSION

The appearance of this paternal line in the Han population is helpful for understanding the mixed history of ancient and modern people in the Mongolian Plateau and Central China.

Extraction Protocol for Parallel Analysis of Proteins and DNA from Ancient Teeth and Dental Calculus

Dental calculus is becoming a crucial material in the study of past populations with increasing interest in its proteomic and genomic content. Here, we suggest further development of a protocol for analysis of ancient proteins and a combined approach for subsequent ancient DNA extraction. We tested the protocol on recent teeth, and the optimized protocol was applied to ancient tooth to limit the destruction of calculus as it is a precious and irreplaceable source of dietary, microbiological, and ecological information in the archeological context. Finally, the applicability of the protocol was demonstrated on samples of the ancient calculus.

Genetic and cultural adaptations underlie the establishment of dairy pastoralism in the Tibetan Plateau

BACKGROUND

Domestication and introduction of dairy animals facilitated the permanent human occupation of the Tibetan Plateau. Yet the history of dairy pastoralism in the Tibetan Plateau remains poorly understood. Little is known how Tibetans adapted to milk and dairy products.

RESULTS

We integrated archeological evidence and genetic analysis to show the picture that the dairy ruminants, together with dogs, were introduced from West Eurasia into the Tibetan Plateau since ~ 3600 years ago. The genetic admixture between the exotic and indigenous dogs enriched the candidate lactase persistence (LP) allele 10974A > G of West Eurasian origin in Tibetan dogs. In vitro experiments demonstrate that - 13838G > A functions as a LP allele in Tibetans. Unlike multiple LP alleles presenting selective signatures in West Eurasians and South Asians, the de novo origin of Tibetan-specific LP allele - 13838G > A with low frequency (~ 6-7%) and absence of selection corresponds - 13910C > T in pastoralists across eastern Eurasia steppe.

CONCLUSIONS

Results depict a novel scenario of genetic and cultural adaptations to diet and expand current understanding of the establishment of dairy pastoralism in the Tibetan Plateau.

Descent, marriage, and residence practices of a 3,800-year-old pastoral community in Central Eurasia

Our understanding of prehistoric societal organization at the family level is still limited. Here, we generated genome data from 32 individuals from an approximately 3,800-y-old burial mound attributed to the Bronze Age Srubnaya-Alakul cultural tradition at the site of Nepluyevsky, located in the Southern Ural region of Central Eurasia. We found that life expectancy was generally very low, with adult males living on average 8 y longer than females. A total of 35 first-degree, 40 second-degree, and 48 third-degree biological relationships connected 23 of the studied individuals, allowing us to propose a family tree spanning three generations with six brothers at its center. The oldest of these brothers had eight children with two women and the most children overall, whereas the other relationships were monogamous. Notably, related female children above the age of five were completely absent from the site, and adult females were more genetically diverse than males. These results suggest that biological relationships between male siblings played a structural role in society and that descent group membership was based on patrilineality. Women originated from a larger mating network and moved to join the men, with whom they were buried. Finally, the oldest brother likely held a higher social position, which was expressed in terms of fertility.

Paleoproteomic evidence reveals dairying supported prehistoric occupation of the highland Tibetan Plateau

The extreme environments of the Tibetan Plateau offer considerable challenges to human survival, demanding novel adaptations. While the role of biological and agricultural adaptations in enabling early human colonization of the plateau has been widely discussed, the contribution of pastoralism is less well understood, especially the dairy pastoralism that has historically been central to Tibetan diets. Here, we analyze ancient proteins from the dental calculus (n = 40) of all human individuals with sufficient calculus preservation from the interior plateau. Our paleoproteomic results demonstrate that dairy pastoralism began on the highland plateau by ~3500 years ago. Patterns of milk protein recovery point to the importance of dairy for individuals who lived in agriculturally poor regions above 3700 m above sea level. Our study suggests that dairy was a critical cultural adaptation that supported expansion of early pastoralists into the region's vast, non-arable highlands, opening the Tibetan Plateau up to widespread, permanent human occupation.

Genetic population structure of the Xiongnu Empire at imperial and local scales

The Xiongnu established the first nomadic imperial power, controlling the Eastern Eurasian steppe from ca. 200 BCE to 100 CE. Recent archaeogenetic studies identified extreme levels of genetic diversity across the empire, corroborating historical records of the Xiongnu Empire being multiethnic. However, it has remained unknown how this diversity was structured at the local community level or by sociopolitical status. To address this, we investigated aristocratic and local elite cemeteries at the western frontier of the empire. Analyzing genome-wide data from 18 individuals, we show that genetic diversity within these communities was comparable to the empire as a whole, and that high diversity was also observed within extended families. Genetic heterogeneity was highest among the lowest-status individuals, implying diverse origins, while higher-status individuals harbored less genetic diversity, suggesting that elite status and power was concentrated within specific subsets of the broader Xiongnu population.

Permafrost preservation reveals proteomic evidence for yak milk consumption in the 13th century

Domesticated yaks endure as iconic symbols of high-altitude frozen landscapes, where herding communities depend on their high-fat milk, transport, dung, and natural fibers. While there is established proteomic evidence for ancient consumption of ruminant and horse milk in the mountains and steppes of northern Eurasia, yak dairy products have yet to be detected. Yak domestication and the species' dispersal from Tibet into the mountainous zones to the north are also poorly resolved due to a paucity of zooarchaeological data. To examine the potential of paleoproteomics to shed light on domesticated yak in Mongolia, we analyzed human dental calculus from Mongol era elite individuals recovered from permafrost burials in Khovsgol province, where people continue to herd yak to this day. We report the first evidence for yak dairy consumption, linked to local resource control. In addition, we confirm a large diversity of recovered whey, curd, tissue, and blood proteins, likely reflecting the excellent preservation conditions found at permafrost sites.

Revealing Joseon period People's single nucleotide polymorphism associated with lactase gene by ancient DNA analysis of human remains from archaeological sites in Korea

Lactase non-persistence (LNP), one of the causes of lactose intolerance, is related to lactase gene associated single nucleotide polymorphisms (SNPs). Since the frequency of LNP varies by ethnic group and country, the research to reveal the presence or absence of LNP for specific people has been conducted worldwide. However, in East Asia, the study of lactase gene associated SNPs have not been sufficiently examined so far using ancient human specimens from archaeological sites. In our study of Joseon period human remains (n=14), we successfully revealed genetic information of lactase gene associated SNPs (rs1679771596, rs41525747, rs4988236, rs4988235, rs41380347, rs869051967, rs145946881 and rs182549), further confirming that as for eight SNPs, the pre-modern Korean people had a lactase non-persistent genotype. Our report contributes to the establishment of LNP associated SNP analysis technique that can be useful in forthcoming studies on human bones and mummy samples from East Asian archaeological sites.

The impacts of bronze age in the gene pool of Chinese: Insights from phylogeographics of Y-chromosomal haplogroup N1a2a-F1101

Objectives: Previous studies of archaeology and history suggested that the rise and prosperity of Bronze Age culture in East Asia had made essential contribution to the formation of early state and civilization in this region. However, the impacts in perspective of genetics remain ambiguous. Previous genetic researches indicated the Y-chromosome Q1a1a-M120 and N1a2a-F1101 may be the two most important paternal lineages among the Bronze Age people in ancient northwest China. Here, we investigated the 9,000-years history of haplogroup N1a2a-F1101 with revised phylogenetic tree and spatial autocorrelation analysis.

Materials and Methods: In this study, 229 sequences of N1a2a-F1101 were analyzed. We developed a highly-revised phylogenetic tree with age estimates for N1a2a-F1101. In addition, we also explored the geographical distribution of sub-lineages of N1a2a-F1101, and spatial autocorrelation analysis was conducted for each sub-branch.

Results: The initial differentiation location of N1a2a-F1101 and its most closely related branch, N1a2b-P43, a major lineage of Uralic-speaking populations in northern Eurasia, is likely the west part of northeast China. After ~4 thousand years of bottleneck effect period, haplgroup N1a2a-F1101 experienced continuous expansion during the Chalcolithic age (~ 4.5 kya to 4 kya) and Bronze age (~ 4 kya to 2.5 kya) in northern China. Ancient DNA evidence supported that this haplogroup is the lineage of ruling family of Zhou Dynasty (~ 3 kya-2.2 kya) of ancient China.

Discussion: In general, we proposed that the Bronze Age people in the border area between the eastern Eurasian steppe and northern China not only played a key role in promoting the early state and civilization of China, but also left significant traces in the gene pool of Chinese people.

Detection of dairy products from multiple taxa in Late Neolithic pottery from Poland: an integrated biomolecular approach

The detection of dairy processing is pivotal to our understanding of ancient subsistence strategies. This culinary process is linked to key arguments surrounding the evolution of lactase persistence in prehistory. Despite extensive evidence indicating the presence of dairy products in ceramics in the European Neolithic, questions remain about the nature and extent of milk (and lactose) processing and consumption. In order to investigate past patterns of dairy processing, here we analyse ancient proteins identified from Late Neolithic Funnel Beaker ceramics, scrutinizing the principle that curd and whey proteins partition during the production of dairy foods from milk. Our results indicate the presence of casein-rich dairy products in these vessels suggesting the creation of curd-enriched products from raw milk. Moreover, this analysis reveals the use of multiple species for their dairy products in the Late Neolithic, adding to a growing body of evidence for the period. Alongside palaeoproteomic analysis, we applied well-established lipid residue analysis. Differential interpretations between these two approaches show that palaeoproteomics is especially useful where the effects from isotope mixing may underestimate the frequency of dairy products in archaeological ceramics, highlighting the potential utility of a multi-stranded approach to understand life histories of vessel use.

Middle Holocene Siberian genomes reveal highly connected gene pools throughout North Asia

The peopling history of North Asia remains largely unexplored due to the limited number of ancient genomes analyzed from this region. Here, we report genome-wide data of ten individuals dated to as early as 7,500 years before present from three regions in North Asia, namely Altai-Sayan, Russian Far East, and the Kamchatka Peninsula. Our analysis reveals a previously undescribed Middle Holocene Siberian gene pool in Neolithic Altai-Sayan hunter-gatherers as a genetic mixture between paleo-Siberian and ancient North Eurasian (ANE) ancestries. This distinctive gene pool represents an optimal source for the inferred ANE-related population that contributed to Bronze Age groups from North and Inner Asia, such as Lake Baikal hunter-gatherers, Okunevo-associated pastoralists, and possibly Tarim Basin populations. We find the presence of ancient Northeast Asian (ANA) ancestry-initially described in Neolithic groups from the Russian Far East-in another Neolithic Altai-Sayan individual associated with different cultural features, revealing the spread of ANA ancestry ∼1,500 km further to the west than previously observed. In the Russian Far East, we identify 7,000-year-old individuals that carry Jomon-associated ancestry indicating genetic links with hunter-gatherers in the Japanese archipelago. We also report multiple phases of Native American-related gene flow into northeastern Asia over the past 5,000 years, reaching the Kamchatka Peninsula and central Siberia. Our findings highlight largely interconnected population dynamics throughout North Asia from the Early Holocene onward.

Microbial foods for improving human and planetary health

The current food production system is negatively impacting planetary and human health. A transition to a sustainable and fair food system is urgently needed. Microorganisms are likely enablers of this process, as they can produce delicious and healthy microbial foods with low environmental footprints. We review traditional and current approaches to microbial foods, such as fermented foods, microbial biomass, and food ingredients derived from microbial fermentations. We discuss how future advances in science-driven fermentation, synthetic biology, and sustainable feedstocks enable a new generation of microbial foods, potentially impacting the sustainability, resilience, and health effects of our food system.

Isotopic and DNA analyses reveal multiscale PPNB mobility and migration across Southeastern Anatolia and the Southern Levant

Growing reliance on animal and plant domestication in the Near East and beyond during the Pre-Pottery Neolithic B (PPNB) (the ninth to eighth millennium BC) has often been associated with a "revolutionary" social transformation from mobility toward more sedentary lifestyles. We are able to yield nuanced insights into the process of the Neolithization in the Near East based on a bioarchaeological approach integrating isotopic and archaeogenetic analyses on the bone remains recovered from Nevalı Çori, a site occupied from the early PPNB in Turkey where some of the earliest evidence of animal and plant domestication emerged, and from Ba'ja, a typical late PPNB site in Jordan. In addition, we present the archaeological sequence of Nevalı Çori together with newly generated radiocarbon dates. Our results are based on strontium (⁸⁷Sr/⁸⁶Sr), carbon, and oxygen (δ¹⁸O and δ¹³C_carb) isotopic analyses conducted on 28 human and 29 animal individuals from the site of Nevalı Çori. ⁸⁷Sr/⁸⁶Sr results indicate mobility and connection with the contemporaneous surrounding sites during the earlier PPNB prior to an apparent decline in this mobility at a time of growing reliance on domesticates. Genome-wide data from six human individuals from Nevalı Çori and Ba'ja demonstrate a diverse gene pool at Nevalı Çori that supports connectedness within the Fertile Crescent during the earlier phases of Neolithization and evidence of consanguineous union in the PPNB Ba'ja and the Iron Age Nevalı Çori.

Ancient DNA from Protohistoric Period Cambodia indicates that South Asians admixed with local populations as early as 1st-3rd centuries CE

Indian cultural influence is remarkable in present-day Mainland Southeast Asia (MSEA), and it may have stimulated early state formation in the region. Various present-day populations in MSEA harbor a low level of South Asian ancestry, but previous studies failed to detect such ancestry in any ancient individual from MSEA. In this study, we discovered a substantial level of South Asian admixture (ca. 40-50%) in a Protohistoric individual from the Vat Komnou cemetery at the Angkor Borei site in Cambodia. The location and direct radiocarbon dating result on the human bone (95% confidence interval is 78-234 calCE) indicate that this individual lived during the early period of Funan, one of the earliest states in MSEA, which shows that the South Asian gene flow to Cambodia started about a millennium earlier than indicated by previous published results of genetic dating relying on present-day populations. Plausible proxies for the South Asian ancestry source in this individual are present-day populations in Southern India, and the individual shares more genetic drift with present-day Cambodians than with most present-day East and Southeast Asian populations.

Diverse dietary practices across the Early Bronze Age 'Kura-Araxes culture' in the South Caucasus

The Kura-Araxes (KA) cultural phenomenon (dated to the Early Bronze Age, c. 3500/3350-2500 BCE) is primarily characterised by the emergence of a homogeneous pottery style and a uniform 'material culture package' in settlements across the South Caucasus, as well as territories extending to the Ancient Near East and the Levant. It has been argued that KA societies practised pastoralism, despite a lack of direct examination of dietary and culinary practices in this region. Here, we report the first analyses of absorbed lipid residues from KA pottery to both determine the organic products produced and consumed and to reconstruct subsistence practices. Our results provide compelling evidence for a diversified diet across KA settlements in Armenia, comprising a mixed economy of meat and plant processing, aquatic fats and dairying. The preservation of diagnostic plant lipid biomarkers, notably long-chain fatty acids (C20 to C28) and n-alkanes (C23 to C33) has enabled the identification of the earliest processing of plants in pottery of the region. These findings suggest that KA settlements were agropastoral exploiting local resources. Results demonstrate the significance of applying biomolecular methods for examining dietary inferences in the South Caucasus region.

Integrated Spreadsheets for Nutritional Analysis of Population Diet Surveys

It can be challenging to calculate nutrient intakes in population diet surveys because existing nutritional analysis software is generally oriented toward analyzing intakes of individuals and may not allow users to input or easily modify the food composition data used in the analysis. These are drawbacks that are more problematic in low- and middle-income country settings. While there are numerous software-assisted dietary assessment platforms that conduct onboard nutritional analysis and are appropriate for use in large surveys, they are often similarly limited, and further restrict users to specific assessment modalities. This paper presents a multifunctional system of integrated spreadsheets for nutritional analysis of population diet surveys (ISNAPDS) that provides a solution for situations in which data have been collected but cannot be adequately analyzed with existing software. The protocol involves supplying the system with fully customizable data on food composition, food group classifications, and food intake (food intake in g/day may be entered directly or calculated based on user-supplied intake frequencies and either standard or variable serving sizes). Following data entry, the user modifies a set of simple pre-populated formulas to match them to the structure of the input data and the system applies these formulas to calculate nutrient and food group intakes, and the contributions of food groups to nutrient intakes for all members of the survey population. The flexibility of the ISNAPDS system allows it to accommodate the global diversity of foods consumed and analyze quantitative, semiquantitative, and nonquantitative food consumption data collected using prospective and retrospective assessment methods employing different reference periods and portion size estimation methods. To date, the system has been applied in published and ongoing analyses of 24 h recall, diet record, food frequency, and disaggregated household consumption data from population surveys in China, Ethiopia, India, Mongolia, Thailand, and a multi-country analysis of 10 sub-Saharan African countries.

Ancient Components and Recent Expansion in the Eurasian Heartland: Insights into the Revised Phylogeny of Y-Chromosomes from Central Asia

In the past two decades, studies of Y chromosomal single nucleotide polymorphisms (Y-SNPs) and short tandem repeats (Y-STRs) have shed light on the demographic history of Central Asia, the heartland of Eurasia. However, complex patterns of migration and admixture have complicated population genetic studies in Central Asia. Here, we sequenced and analyzed the Y-chromosomes of 187 male individuals from Kazakh, Kyrgyz, Uzbek, Karakalpak, Hazara, Karluk, Tajik, Uyghur, Dungan, and Turkmen populations. High diversity and admixture from peripheral areas of Eurasia were observed among the paternal gene pool of these populations. This general pattern can be largely attributed to the activities of ancient people in four periods, including the Neolithic farmers, Indo-Europeans, Turks, and Mongols. Most importantly, we detected the consistent expansion of many minor lineages over the past thousand years, which may correspond directly to the formation of modern populations in these regions. The newly discovered sub-lineages and variants provide a basis for further studies of the contributions of minor lineages to the formation of modern populations in Central Asia.

Nutrition and Health in Human Evolution-Past to Present

Anyone who wants to understand the biological nature of humans and their special characteristics must look far back into evolutionary history. Today's way of life is drastically different from that of our ancestors. For almost 99% of human history, gathering and hunting have been the basis of nutrition. It was not until about 12,000 years ago that humans began domesticating plants and animals. Bioarchaeologically and biochemically, this can be traced back to our earliest roots. Modern living conditions and the quality of human life are better today than ever before. However, neither physically nor psychosocially have we made this adjustment and we are paying a high health price for it. The studies presented allow us to reconstruct food supply, lifestyles, and dietary habits: from the earliest primates, through hunter-gatherers of the Paleolithic, farming communities since the beginning of the Anthropocene, to the Industrial Age and the present. The comprehensive data pool allows extraction of all findings of medical relevance. Our recent lifestyle and diet are essentially determined by our culture rather than by our millions of years of ancestry. Culture is permanently in a dominant position compared to natural evolution. Thereby culture does not form a contrast to nature but represents its result. There is no doubt that we are biologically adapted to culture, but it is questionable how much culture humans can cope with.

Paleoproteomics

Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.

Emergence and intensification of dairying in the Caucasus and Eurasian steppes

Archaeological and archaeogenetic evidence points to the Pontic–Caspian steppe zone between the Caucasus and the Black Sea as the crucible from which the earliest steppe pastoralist societies arose and spread, ultimately influencing populations from Europe to Inner Asia. However, little is known about their economic foundations and the factors that may have contributed to their extensive mobility. Here, we investigate dietary proteins within the dental calculus proteomes of 45 individuals spanning the Neolithic to Greco-Roman periods in the Pontic–Caspian Steppe and neighbouring South Caucasus, Oka–Volga–Don and East Urals regions. We find that sheep dairying accompanies the earliest forms of Eneolithic pastoralism in the North Caucasus. During the fourth millennium bc, Maykop and early Yamnaya populations also focused dairying exclusively on sheep while reserving cattle for traction and other purposes. We observe a breakdown in livestock specialization and an economic diversification of dairy herds coinciding with aridification during the subsequent late Yamnaya and North Caucasus Culture phases, followed by severe climate deterioration during the Catacomb and Lola periods. The need for additional pastures to support these herds may have driven the heightened mobility of the Middle and Late Bronze Age periods. Following a hiatus of more than 500 years, the North Caucasian steppe was repopulated by Early Iron Age societies with a broad mobile dairy economy, including a new focus on horse milking.

Milk proteins from the North Caucasus and Eurasian steppe support the initial development of sheep dairying during the Eneolithic, followed by subsequent intensification and husbandry of different dairy animals during the Middle Bronze Age and later periods.

Stable Isotopic Evidence for Human and Animal Diets From the Late Neolithic to the Ming Dynasty in the Middle-Lower Reaches of the Hulu River Valley, NW China

The study of human and animal paleodiets, representing the unique subsistence strategies and human-environment interactions adopted over evolutionary time, has attracted intensive research attention. Historically, the western Loess Plateau (WLP) served as a key area for the evolution of human-land relationship. The human subsistence patterns in the WLP changed significantly from prehistoric to historical periods based on archaeobotanical data. However, the trajectory and influencing factors of ancient human and animal diets in the WLP remain unclear, mainly due to the lack of isotopic data in the upper reaches of the Wei River. In this paper, we reported 172 human and animal isotope samples (C and N) and 23 radiocarbon dates from three sites in the middle-lower reaches of the Hulu River Valley (HRV). At least three periods of dietary patterns for humans were observed in the WLP from the late Neolithic to Ming Dynasty. During 5300–4000 Before Present (BP), humans and domesticated animals such as pigs and dogs consumed a greater proportion of millets and millet byproducts. Between 3000 and 2200 BP, the diets of pigs and dogs remained largely comprised of C4 foods, while humans consumed both C3 and C4 foods, which contradicted the evidence of an overwhelming proportion of wheat and barley (C3 crops) from the contemporaneous cultural sediment. The contradictions between plant remains and human diets are probably related to geopolitical factors. Between 1000–500 BP, human diets were more diverse and heterogeneous in this region. Combined with environmental and archaeological evidence, the changes in diets and subsistence strategies over the three periods can be attributed to the comprehensive influence of regional cultural development, geopolitics and technological innovation. This paper not only reveals the trajectory and influencing factors of ancient human and animal diets in the middle-lower HRV, but also explores how subsistence strategies, particularly in terms of dietary structure, will change in the context of cultural exchange and diffusion, and emphasizes the important influence of geopolitical interactions in the WLP.

Genomic analyses of 10,376 individuals in the Westlake BioBank for Chinese (WBBC) pilot project

We initiate the Westlake BioBank for Chinese (WBBC) pilot project with 4,535 whole-genome sequencing (WGS) individuals and 5,841 high-density genotyping individuals, and identify 81.5 million SNPs and INDELs, of which 38.5% are absent in dbSNP Build 151. We provide a population-specific reference panel and an online imputation server ( https://wbbc.westlake.edu.cn/ ) which could yield substantial improvement of imputation performance in Chinese population, especially for low-frequency and rare variants. By analyzing the singleton density of the WGS data, we find selection signatures in SNX29, DNAH1 and WDR1 genes, and the derived alleles of the alcohol metabolism genes (ADH1A and ADH1B) emerge around 7,000 years ago and tend to be more common from 4,000 years ago in East Asia. Genetic evidence supports the corresponding geographical boundaries of the Qinling-Huaihe Line and Nanling Mountains, which separate the Han Chinese into subgroups, and we reveal that North Han was more homogeneous than South Han.

The spread of herds and horses into the Altai: How livestock and dairying drove social complexity in Mongolia

The initial movement of herders and livestock into the eastern steppe is of great interest, as this region has long been home to pastoralist groups. Due to a paucity of faunal remains, however, it has been difficult to discern the timing of the adoption of domesticated ruminants and horses into the region, though recent research on ancient dairying has started to shed new light on this history. Here we present proteomic evidence for shifts in dairy consumption in the Altai Mountains, drawing on evidence from sites dating from the Early Bronze to the Late Iron Age. We compare these finds with evidence for the rise of social complexity in western Mongolia, as reflected in material remains signaling population growth, the establishment of structured cemeteries, and the erection of large monuments. Our results suggest that the subsistence basis for the development of complex societies began at the dawn of the Bronze Age, with the adoption of ruminant livestock. Investments in pastoralism intensified over time, enabling a food production system that sustained growing populations. While pronounced social changes and monumental constructions occurred in tandem with the first evidence for horse dairying, ~1350 cal BCE, these shifts were fueled by a long-term economic dependence on ruminant livestock. Therefore, the spread into the Mongolian Altai of herds, and then horses, resulted in immediate dietary changes, with subsequent social and demographic transformations occurring later.

Ancient genomes reveal origin and rapid trans-Eurasian migration of 7th century Avar elites

The Avars settled the Carpathian Basin in 567/68 CE, establishing an empire lasting over 200 years. Who they were and where they came from is highly debated. Contemporaries have disagreed about whether they were, as they claimed, the direct successors of the Mongolian Steppe Rouran empire that was destroyed by the Turks in ∼550 CE. Here, we analyze new genome-wide data from 66 pre-Avar and Avar-period Carpathian Basin individuals, including the 8 richest Avar-period burials and further elite sites from Avar's empire core region. Our results provide support for a rapid long-distance trans-Eurasian migration of Avar-period elites. These individuals carried Northeast Asian ancestry matching the profile of preceding Mongolian Steppe populations, particularly a genome available from the Rouran period. Some of the later elite individuals carried an additional non-local ancestry component broadly matching the steppe, which could point to a later migration or reflect greater genetic diversity within the initial migrant population.

Understanding the microbial biogeography of ancient human dentitions to guide study design and interpretation

The oral cavity is a heterogeneous environment, varying in factors such as pH, oxygen levels, and salivary flow. These factors affect the microbial community composition and distribution of species in dental plaque, but it is not known how well these patterns are reflected in archaeological dental calculus. In most archaeological studies, a single sample of dental calculus is studied per individual and is assumed to represent the entire oral cavity. However, it is not known if this sampling strategy introduces biases into studies of the ancient oral microbiome. Here, we present the results of a shotgun metagenomic study of a dense sampling of dental calculus from four Chalcolithic individuals from the southeast Iberian peninsula (ca. 4500-5000 BP). Interindividual differences in microbial composition are found to be much larger than intraindividual differences, indicating that a single sample can indeed represent an individual in most cases. However, there are minor spatial patterns in species distribution within the oral cavity that should be taken into account when designing a study or interpreting results. Finally, we show that plant DNA identified in the samples is likely of postmortem origin, demonstrating the importance of including environmental controls or additional lines of biomolecular evidence in dietary interpretations.

A unified genealogy of modern and ancient genomes

The sequencing of modern and ancient genomes from around the world has revolutionized our understanding of human history and evolution. However, the problem of how best to characterize ancestral relationships from the totality of human genomic variation remains unsolved. Here, we address this challenge with nonparametric methods that enable us to infer a unified genealogy of modern and ancient humans. This compact representation of multiple datasets explores the challenges of missing and erroneous data and uses ancient samples to constrain and date relationships. We demonstrate the power of the method to recover relationships between individuals and populations as well as to identify descendants of ancient samples. Finally, we introduce a simple nonparametric estimator of the geographical location of ancestors that recapitulates key events in human history.

Genetic continuity of Indo-Iranian speakers since the Iron Age in southern Central Asia

Since prehistoric times, southern Central Asia has been at the crossroads of the movement of people, culture, and goods. Today, the Central Asian populations are divided into two cultural and linguistic groups: the Indo-Iranian and the Turko-Mongolian groups. Previous genetic studies unveiled that migrations from East Asia contributed to the spread of Turko-Mongolian populations in Central Asia and the partial replacement of the Indo-Iranian populations. However, little is known about the origin of the latters. To shed light on this, we compare the genetic data on two current-day Indo-Iranian populations — Yaghnobis and Tajiks — with genome-wide data from published ancient individuals. The present Indo-Iranian populations from Central Asia display a strong genetic continuity with Iron Age samples from Turkmenistan and Tajikistan. We model Yaghnobis as a mixture of 93% Iron Age individual from Turkmenistan and 7% from Baikal. For the Tajiks, we observe a higher Baikal ancestry and an additional admixture event with a South Asian population. Our results, therefore, suggest that in addition to a complex history, Central Asia shows a remarkable genetic continuity since the Iron Age, with only limited gene flow.

The Genetic Structure and East-West Population Admixture in Northwest China Inferred From Genome-Wide Array Genotyping

Northwest China is a contacting region for East and West Eurasia and an important center for investigating the migration and admixture history of human populations. However, the comprehensive genetic structure and admixture history of the Altaic speaking populations and Hui group in Northwest China were still not fully characterized due to insufficient sampling and the lack of genome-wide data. Thus, We genotyped genome-wide SNPs for 140 individuals from five Chinese Mongolic, Turkic speaking groups including Dongxiang, Bonan, Yugur, and Salar, as well as the Hui group. Analysis based on allele-sharing and haplotype-sharing were used to elucidate the population history of Northwest Chinese populations, including PCA, ADMIXTURE, pairwise Fst genetic distance, f-statistics, qpWave/qpAdm and ALDER, fineSTRUCTURE and GLOBETROTTER. We observed Dongxiang, Bonan, Yugur, Salar, and Hui people were admixed populations deriving ancestry from both East and West Eurasians, with the proportions of West Eurasian related contributions ranging from 9 to 15%. The genetic admixture was probably driven by male-biased migration- showing a higher frequency of West Eurasian related Y chromosomal lineages than that of mtDNA detected in Northwest China. ALDER-based admixture and haplotype-based GLOBETROTTER showed this observed West Eurasian admixture signal was introduced into East Eurasia approximately 700 ∼1,000 years ago. Generally, our findings provided supporting evidence that the flourish transcontinental communication between East and West Eurasia played a vital role in the genetic formation of northwest Chinese populations.

Is there still evolution in the human population?

It is often claimed that humanity has stopped evolving because modern medicine erased all selection on survival. Even if that would be true, and it is not, there would be other mechanisms of evolution which could still led to changes in allelic frequencies. Here I show, by applying basic evolutionary genetics knowledge, that we expect humanity to evolve. The results from genome sequencing projects have repeatedly affirmed that there are still recent signs of selection in our genomes. I give some examples of such adaptation. Then I briefly discuss what our evolutionary future has in store for us.

Genomic Insights Into the Genetic Structure and Natural Selection of Mongolians

Mongolians dwell at the Eastern Eurasian Steppe, where is the agriculture and pasture interlaced area, practice pastoral subsistence strategies for generations, and have their own complex genetic formation history. There is evidence that the eastward expansion of Western Steppe herders transformed the lifestyle of post-Bronze Age Mongolia Plateau populations and brought gene flow into the gene pool of Eastern Eurasians. Here, we reported genome-wide data for 42 individuals from the Inner Mongolia Autonomous Region of North China. We observed that our studied Mongolians were structured into three distinct genetic clusters possessing different genetic affinity with previous studied Inner Mongolians and Mongols and various Eastern and Western Eurasian ancestries: two subgroups harbored dominant Eastern Eurasian ancestry from Neolithic millet farmers of Yellow River Basin; another subgroup derived Eastern Eurasian ancestry primarily from Neolithic hunter-gatherers of North Asia. Besides, three-way/four-way qpAdm admixture models revealed that both north and southern Western Eurasian ancestry related to the Western Steppe herders and Iranian farmers contributed to the genetic materials into modern Mongolians. ALDER-based admixture coefficient and haplotype-based GLOBETROTTER demonstrated that the former western ancestry detected in modern Mongolian could be recently traced back to a historic period in accordance with the historical record about the westward expansion of the Mongol empire. Furthermore, the natural selection analysis of Mongolians showed that the Major Histocompatibility Complex (MHC) region underwent significantly positive selective sweeps. The functional genes, alcohol dehydrogenase (ADH) and lactase persistence (LCT), were not identified, while the higher/lower frequencies of derived mutations were strongly correlated with the genetic affinity to East Asian/Western Eurasian populations. Our attested complex population movement and admixture in the agriculture and pasture interlaced area played an important role in the formation of modern Mongolians.

Genomic Analysis of 18th-Century Kazakh Individuals and Their Oral Microbiome

The Asian Central Steppe, consisting of current-day Kazakhstan and Russia, has acted as a highway for major migrations throughout history. Therefore, describing the genetic composition of past populations in Central Asia holds value to understanding human mobility in this pivotal region. In this study, we analyse paleogenomic data generated from five humans from Kuygenzhar, Kazakhstan. These individuals date to the early to mid-18th century, shortly after the Kazakh Khanate was founded, a union of nomadic tribes of Mongol Golden Horde and Turkic origins. Genomic analysis identifies that these individuals are admixed with varying proportions of East Asian ancestry, indicating a recent admixture event from East Asia. The high amounts of DNA from the anaerobic Gram-negative bacteria Tannerella forsythia, a periodontal pathogen, recovered from their teeth suggest they may have suffered from periodontitis disease. Genomic analysis of this bacterium identified recently evolved virulence and glycosylation genes including the presence of antibiotic resistance genes predating the antibiotic era. This study provides an integrated analysis of individuals with a diet mostly based on meat (mainly horse and lamb), milk, and dairy products and their oral microbiome.

Ancient genome analyses shed light on kinship organization and mating practice of Late Neolithic society in China

Anthropology began in the late nineteenth century with an emphasis on kinship as a key factor in human evolution. From the 1960s, archaeologists attempted increasingly sophisticated ways of reconstructing prehistoric kinship but ancient DNA analysis has transformed the field, making it possible, to directly examine kin relations from human skeletal remains. Here, we retrieved genomic data from four Late Neolithic individuals in central China associated with the Late Neolithic Longshan culture. We provide direct evidence of consanguineous mating in ancient China, revealing inbreeding among the Longshan populations. By combining ancient genomic data with anthropological and archaeological evidence, we further show that Longshan society household was built based on the extended beyond the nuclear family, coinciding with intensified social complexity during the Longshan period, perhaps showing the transformation of large communities through a new role of genetic kinship-based extended family units.

Triangulation supports agricultural spread of the Transeurasian languages

The origin and early dispersal of speakers of Transeurasian languages-that is, Japanese, Korean, Tungusic, Mongolic and Turkic-is among the most disputed issues of Eurasian population history1-3. A key problem is the relationship between linguistic dispersals, agricultural expansions and population movements4,5. Here we address this question by 'triangulating' genetics, archaeology and linguistics in a unified perspective. We report wide-ranging datasets from these disciplines, including a comprehensive Transeurasian agropastoral and basic vocabulary; an archaeological database of 255 Neolithic-Bronze Age sites from Northeast Asia; and a collection of ancient genomes from Korea, the Ryukyu islands and early cereal farmers in Japan, complementing previously published genomes from East Asia. Challenging the traditional 'pastoralist hypothesis'6-8, we show that the common ancestry and primary dispersals of Transeurasian languages can be traced back to the first farmers moving across Northeast Asia from the Early Neolithic onwards, but that this shared heritage has been masked by extensive cultural interaction since the Bronze Age. As well as marking considerable progress in the three individual disciplines, by combining their converging evidence we show that the early spread of Transeurasian speakers was driven by agriculture.

The genomic origins of the Bronze Age Tarim Basin mummies

The identity of the earliest inhabitants of Xinjiang, in the heart of Inner Asia, and the languages that they spoke have long been debated and remain contentious¹. Here we present genomic data from 5 individuals dating to around 3000-2800 BC from the Dzungarian Basin and 13 individuals dating to around 2100-1700 BC from the Tarim Basin, representing the earliest yet discovered human remains from North and South Xinjiang, respectively. We find that the Early Bronze Age Dzungarian individuals exhibit a predominantly Afanasievo ancestry with an additional local contribution, and the Early-Middle Bronze Age Tarim individuals contain only a local ancestry. The Tarim individuals from the site of Xiaohe further exhibit strong evidence of milk proteins in their dental calculus, indicating a reliance on dairy pastoralism at the site since its founding. Our results do not support previous hypotheses for the origin of the Tarim mummies, who were argued to be Proto-Tocharian-speaking pastoralists descended from the Afanasievo^1,2 or to have originated among the Bactria-Margiana Archaeological Complex³ or Inner Asian Mountain Corridor cultures⁴. Instead, although Tocharian may have been plausibly introduced to the Dzungarian Basin by Afanasievo migrants during the Early Bronze Age, we find that the earliest Tarim Basin cultures appear to have arisen from a genetically isolated local population that adopted neighbouring pastoralist and agriculturalist practices, which allowed them to settle and thrive along the shifting riverine oases of the Taklamakan Desert.

Ancient Mitochondrial Genomes Reveal Extensive Genetic Influence of the Steppe Pastoralists in Western Xinjiang

The population prehistory of Xinjiang has been a hot topic among geneticists, linguists, and archaeologists. Current ancient DNA studies in Xinjiang exclusively suggest an admixture model for the populations in Xinjiang since the early Bronze Age. However, almost all of these studies focused on the northern and eastern parts of Xinjiang; the prehistoric demographic processes that occurred in western Xinjiang have been seldomly reported. By analyzing complete mitochondrial sequences from the Xiabandi (XBD) cemetery (3,500–3,300 BP), the up-to-date earliest cemetery excavated in western Xinjiang, we show that all the XBD mitochondrial sequences fall within two different West Eurasian mitochondrial DNA (mtDNA) pools, indicating that the migrants into western Xinjiang from west Eurasians were a consequence of the early expansion of the middle and late Bronze Age steppe pastoralists (Steppe_MLBA), admixed with the indigenous populations from Central Asia. Our study provides genetic links for an early existence of the Indo-Iranian language in southwestern Xinjiang and suggests that the existence of Andronovo culture in western Xinjiang involved not only the dispersal of ideas but also population movement.