Figure - available from: Nature
This content is subject to copyright. Terms and conditions apply.
map Depictions of the five main migratory events associated with the genomic history of the steppe pastoralists from 3000 bc to the present. a, Depiction of Early Bronze Age migrations related to the expansion of Yamnaya and Afanasievo culture. b, Depiction of Late Bronze Age migrations related to the Sintashta and Andronovo horizons. c, Depiction of Iron Age migrations and sources of admixture. d, Depiction of Hun-period migrations and sources of admixture. e, Depiction of Medieval migrations across the steppes.
Source publication
For thousands of years the Eurasian steppes have been a centre of human migrations and cultural change. Here we sequence the genomes of 137 ancient humans (about 1× average coverage), covering a period of 4,000 years, to understand the population history of the Eurasian steppes after the Bronze Age migrations. We find that the genetics of the Scyth...
Similar publications
The demographic history of East-Central Europe after the Neolithic period remains poorly explored, despite this region being on the confluence of various ecological zones and cultural entities. Here, the descendants of societies associated with steppe pastoralists form Early Bronze Age were followed by Middle Bronze Age populations displaying uniqu...
Citations
... This study presents the first large archaeogenetic dataset from present-day Georgia. Extending previous data 6, 8,41,42 , this temporally continuous genomic time transect allowed us to provide comprehensive insights into the population history of the South Caucasus. ...
... 73,74 and a recently published dataset from the Aegean 75 . In total, approximately 250 individuals from Armenia, Azerbaijan, Russia, and Eastern Turkey post-dating the Neolithic period 6, 28,29,41,42,51,76 were of high relevance to our study and were included in our analyses. ...
Archaeological and archaeogenetic studies have highlighted the pivotal role of the Caucasus region throughout prehistory, serving as a central hub for cultural, technological, and linguistic innovations. However, despite its dynamic history, the critical area between the Greater and Lesser Caucasus mountain ranges, mainly corresponding to modern-day Georgia, has received limited attention. Here, we generated an ancient DNA time transect consisting of 219 individuals with genome-wide data from 47 sites in this region, supplemented by 97 new radiocarbon dates. Spanning from the Early Bronze Age 5000 years ago to the so-called "Migration Period" that followed the fall of the Western Roman Empire, we document a largely persisting local gene pool that continuously assimilated migrants from Anatolia/Levant and the populations of the adjacent Eurasian steppe. More specifically, we observe these admixture events as early as the Middle Bronze Age. Starting with Late Antiquity (late first century AD), we also detect an increasing number of individuals with more southern ancestry, more frequently associated with urban centers - landmarks of the early Christianization in eastern Georgia. Finally, in the Early Medieval Period starting 400 AD, we observe genetic outlier individuals with ancestry from the Central Eurasian steppe, with artificial cranial deformations (ACD) in several cases. At the same time, we reveal that many individuals with ACD descended from native South Caucasus groups, indicating that the local population likely adopted this cultural practice.
... At the end of the Bronze Age and beginning of the Early Iron Age, the most archaeologically conspicuous activities of the North Pontic steppes were associated with Cimmerians and their military campaigns in Asia Minor 13 . The Cimmerians were followed by Scythians and Sarmatians, Early Iron Age political and military tribal unions 9,14 with variable combinations of local and East Asian ancestry, as indicated by previous ancient DNA studies 7,[15][16][17][18] . At this time, the Northern Black Sea coast was covered with a network of urbanized Greek colonies 19,20 . ...
The North Pontic region, which encompasses present-day Ukraine, was a crossroads of migration as it connected the vast Eurasian Steppe with Central Europe. We generated shotgun-sequenced genomic data for 91 individuals dating from around 7,000 BCE to 1,800 CE to study migration and mobility history in the region, with a particular focus on historically attested migrating groups during the Iron Age and the medieval period, such as Scythian, Chernyakhiv, Saltiv and Nogai associated peoples. We infer a high degree of temporal heterogeneity in ancestry, with fluctuating genetic affinities to present-day Western European, Eastern European, Western Steppe and East Asian groups. We also infer high heterogeneity in ancestry within geographically, culturally and socially defined groups. Despite this, we find that ancestry components which are widespread in Eastern and Central Europe have been present in the Ukraine region since the Bronze Age.
... Among the others, qpAdm (Haak et al., 2015;Harney et al., 2021) is one of the most widely used approaches on ancient data (Damgaard et al., 2018;Haber et al., 2017;Hajdinjak et al., 2018;Harney et al., 2018;Lazaridis et al., 2017Lazaridis et al., , 2016Narasimhan et al., 2019;Olalde et al., 2018;Skoglund et al., 2017), given its ability to deal with the challenges of aDNA data and model admixture events involving multiple sources (Haak et al., 2015;Harney et al., 2021;Patterson et al., 2012). This tool takes advantage of the fact that genetic variation within a specific population can be summarised by comparing its allele frequencies to those of three additional groups using a "treeness test" belonging to the F-statistics family, the f4 metric (Harney et al., the admixture coefficients (weights), assuming that their sum is equal to 1 (Haak et al., 2015). ...
The history of human populations has been strongly shaped by admixture events, contributing to the patterns of observed genetic diversity across populations. Given its significance for evolutionary and medical studies, many algorithms focusing on the inference of the genetic composition of admixed populations have been developed. In particular, the recent development of new ancestry estimation methods that consider the fragmentary nature of ancient genotype data, such as the f-statistics family and its derivations, have radically changed our understanding of the past. F-statistics capture similar genetic similarity information as Principal Component Analysis (PCA), which is widely used in population genetics to quantify genetic affinity between populations or individuals. In this study, we introduce ASAP (ASsessing ancestry proportions through Principal component Analysis) method that leverages PCA and Non-Negative Least Square (NNLS) to assess the ancestral compositions of admixed individuals given a large set of populations. We tested ASAP on different simulated models, incorporating high levels of missingness. Our results show its ability to reliably estimate ancestry across numerous scenarios, even those with a significant proportion of missing genotypes, in a fraction of the time required when using other tools. When harnessed on Eurasia's genotype data, ASAP helped replicate and extend findings from previous studies proving to be a fast, efficient, and straightforward new ancestry estimation tool.
... We kept 419 individuals for further analyses, 413 excluding one pair among the identical pairs found, and 424 including the previously published individuals from the KUP and KFJ sites 10 (Supplementary Table 1). We then merged them with a reference genome-wide panel of 2,280 modern individuals genotyped with microarray technology using the commercial HumanOrigins chip [54][55][56] and previously published ancient-individuals' genotypes sequenced with the same 1240k capture method or a 1240k SNPs subset from data obtained using whole-genome shotgun sequencing 10,27,54,55,[57][58][59][60][61][62][63][64][65][66][67][68][69][70][71][72][73][74] downloaded from Poseidon (https://poseidon-framework.github.io). We produced two datasets, one including the modern data and the SNPs overlap between the 1240k sites and the HumanOrigins SNP chip (1240KHO dataset, around 600,000 SNPs), and one with ancient data and the whole 1240k panel (the 1240k dataset). ...
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.
... According to the archeological background, DA45 (HBV genome published in 2018) 30,49 and AT19 originate from the same site and these two genomes define a branch with a 100% bootstrap support (Supplementary Fig. S3c). To explore the relationship between DA45 and AT19, we checked the mismatch SNPs of the human DNA of these two individuals and observed that these two samples are from the same individual (Supplementary Table S2). ...
... Only samples with more than 10k SNPs covered in the "1240k-Illumina" panel were involved in downstream human population genomic analysis. We compared the genome sequences of our HBV positive individuals with previously published ancient data 35,42,49,62,95 to the set of genotype panels based on the Affymetrix Axiom Genome-wide Human Origins 1 array (HumanOrigins; 593,124 autosomal SNPs) [96][97][98] . We grouped the ancient individuals based on archeological culture and genotype of HBV. ...
Hepatitis B virus is a globally distributed pathogen and the history of HBV infection in humans predates 10000 years. However, long-term evolutionary history of HBV in Eastern Eurasia remains elusive. We present 34 ancient HBV genomes dating between approximately 5000 to 400 years ago sourced from 17 sites across Eastern Eurasia. Ten sequences have full coverage, and only two sequences have less than 50% coverage. Our results suggest a potential origin of genotypes B and D in Eastern Asia. We observed a higher level of HBV diversity within Eastern Eurasia compared to Western Eurasia between 5000 and 3000 years ago, characterized by the presence of five different genotypes (A, B, C, D, WENBA), underscoring the significance of human migrations and interactions in the spread of HBV. Our results suggest the possibility of a transition from non-recombinant subgenotypes (B1, B5) to recombinant subgenotypes (B2 - B4). This suggests a shift in epidemiological dynamics within Eastern Eurasia over time. Here, our study elucidates the regional origins of prevalent genotypes and shifts in viral subgenotypes over centuries.
... In general, using aDNA analyses in an archaeological context represents an excellent example of the importance of scientific methods in archaeology. The "third scientific revolution" in archaeology, epitomized by the advent of aDNA analysis, has become pivotal in reconstructing past genetic lineages and migrations despite facing challenges such as preservation biases, contamination risks, and ethical issues surrounding the bioarchaeological study of ancient human remains (Brown, 2023;Dabney et al., 2013;Damgaard et al., 2018;Díaz-Andreu, 2015;Eisenmann et al., 2018;Foster and Sharp, 2002;Goodwin, 2014;Ho et al., 2014;Kristiansen, 2021Kristiansen, , 2022Kristiansen and Kroonen, 2023;Kroonen and Kristiansen, 2023;Orser, 2014;Otte, 2015;Ubelaker, 2014;Kristiansen et al., 2023). Recently, kinship or family burials from Neolithic times (Juras et al. 2017, Gomes et al 2020, Furtwängler et al. 2020, Bronze Age (Parson et al 2018(Parson et al , Ž egarac et al., 2021, Medieval (Gamba et al 2011, Zupanič Pajnič et al., 2023, Dzehverovic et al. 2023 or Early Modern times (Alterauge et al. 2021), have been increasingly confirmed by aDNA. ...
... For the population genomic analysis of the data, we started with principal component analysis (PCA) using the smartpca tool, by projecting the new and other previously published ancient individuals over the variation of modern European populations (Amorim et al., 2018;Antonio et al., 2019;Damgaard et al., 2018;Margaryan et al., 2020;Martiniano et al., 2016a,b;Mathieson et al., 2018;Narasimhan et al., 2019;Olalde et al., 2018Olalde et al., , 2019Patterson et al., 2006;Veeramah et al., 2018). We next used model-based clustering with ADMIXTURE to further understand the genetic composition of each individual based on components shared with other populations (Alexander et al., 2009). ...
... The aDNA analysis revealed mitochondrial haplogroups I2a for both individuals. In the published literature, haplogroup I2a has been found in Hungarian Scythian and Scottish Late Bronze Age individuals (Damgaard et al., 2018. A principal component analysis (PCA) using modern West Eurasian populations was performed to calculate the variation axes and then projected published ancient European individuals from the Roman Imperial, Antiquity, and Medieval periods (Fig. 5). ...
A human double burial combined with a horse interment, discovered in 2004 in the eastern cemetery of the Roman town of Ovilava (today Wels/AUT), has been the subject of a comprehensive interdisciplinary study. This burial was remarkable for two reasons: firstly, the arrangement of the two individuals, with individual 1 having an arm around individual 2, and secondly, the presence of equine skeletal remains in the same burial pit directly below the human remains. Based on this finding, an initial assessment suggested a mixed-sex pair buried together with a horse. The horse burial was interpreted as an indicator of an early medieval date. The position of the two human skeletons suggested that a male and female individual had been buried together. A thorough examination of both the human and horse skeletons disproved these initial interpretations. Radiocarbon dating of the human and horse skeletons dated them to the Roman period. In addition, ancient DNA (aDNA) analysis of the human remains corrected the earlier sex assumption, revealing that the individuals were two biological females who were first-degree relatives. The age difference of 15 to 25 years between the two suggests a probable mother-daughter relationship. Thus, the application of scientific methods confirmed a rare, combined human-horse burial from Roman antiquity and established the first genetically documented mother-daughter burial from this period in present-day Austria.
... The putative connection among the Adriatic cultures was further investigated by imputing the genotypes in 815 (new and published) samples [8][9][10][18][19][20][21][22][23][24][25][26] and generating a PCA based on the shared identity-by-descent (IBD) fragments between individuals (Additional file 2: Table S10; Additional file 3: European populations with respect to Etruscans and Italy_IA_Romans (Additional file 3: Fig. S7B). ...
... files with bcftools-1.14 [67]. The Euroasiatic samples [8][9][10]18,19,[21][22][23][24][25][26][68][69][70] (Additional file 2: Table S5) were reconstructed with pathPhynder [71] starting from the .bam files, using standard parameters. ...
... We selected for imputation only samples with a coverage ≥ 0.1X, for shotgun data, or covering more than 300K SNPs from the 1240K panel, for chip data. To compare our data with other ancient populations, we selected unrelated individuals from different studies [8][9][10][18][19][20][21][22][23][24][25][26] for a total of 815 individuals. The complete list of samples and the corresponding publication can be found in Additional file 2: Table S5). ...
Background: The Italic Iron Age was characterized by the presence of various ethnic groups partially examined from a genomic perspective. To explore the evolution of Iron Age Italic populations and the genetic impact of Romanization, we focused on the Picenes, one of the most fascinating pre-Roman civilizations, who flourished on the Middle Adriatic side of Central Italy between the 9th and the 3rd century BCE, until the Roman colonization.
Results: We analyzed more than 50 samples, spanning more than 1,000 years of history from the Iron Age to Late Antiquity. Despite cultural diversity, our analysis reveals no major differences between the Picenes and other coeval populations, suggesting a shared genetic history of the Central Italian Iron Age ethnic groups. Nevertheless, a slight genetic differentiation between populations along the Adriatic and Tyrrhenian coasts can be observed, possibly due to genetic contacts between populations residing on the Italian and Balkan shores of the Adriatic Sea. Additionally, we found several individuals with ancestries deviating from their general population. Lastly, In the Late Antiquity period, the genetic landscape of the Middle Adriatic region drastically changed, indicating a relevant influx from the Near East.
Conclusions: Our findings, consistently with archeological hypotheses, suggest genetic interactions across the Adriatic Sea during the Bronze/Iron Age and a high level of individual mobility typical of cosmopolitan societies. Finally, we highlighted the role of the Roman Empire in shaping genetic and phenotypic changes that greatly impacted the Italian peninsula.
... Encompassing the expansive territory covering the eastern Eurasian Steppe and its surrounding regions in northern China, southern Siberia, and Central Asia and commanding the hub regions of the Silk Road, the Xiongnu fostered exchanges of materials, ideas, and people across the diverse parts of Eurasia. Recent archaeogenomic studies have provided an answer to a long-standing question of the genetic profiles of the Xiongnu people [3][4][5][6]. These studies highlighted dynamic changes in the genetic profiles of people in the Eastern Eurasian Steppe before and during the Xiongnu period, as well as in the subsequent Mongol Empire era. ...
... Previous studies have given a hint on the continued genetic changes during this period: while ancient individuals from the Xianbei (100-250 CE) [11] and Rouran (300-550 CE) [12] periods showed overall low genetic heterogeneity with a high proportion of their ancestry derived from the eastern Eurasian ancestral populations, the following Turkic (552-742 CE) and Uyghur (744-840 CE) period individuals showed highly heterogeneous genetic profiles presumably due to a recent mixture with Central Asian populations harboring an Iranian-or Bactria-Margiana Archaeological Complex (BMAC) related ancestry [3]. Medieval individuals from the Central Eurasian Steppe, from the Turkic and later periods (e.g., Kimak, Kipchak, and Karakhanid), show a similar genetic pattern with the Turkic/Uyghur period individuals from the Eastern Steppe [5]. Still, these tentative results are based on a small number of ancient genomes scattered across a large spatiotemporal space, thus unlikely to illuminate the whole dynamic history of the Medieval Eastern Steppe populations. ...
... For this, we used the pileupCaller program v1.5.2 with option "--randomHaploid" (https://github.com/stschiff/sequenceTools). Then we merged newly generated genotype data with the previously published genotype data of present-day [22][23][24][25][26][27][28] and ancient individuals [3][4][5][6]11,12,[29][30][31][32][33]. These datasets had been genotyped on the two SNP sets: the Affymetrix Axiom Genome-Wide Human Origins 1 array ("HumanOrigins") [24] and a set of 1,233,013 SNPs including the HumanOrigins SNPs ("1240K") [31,34] (Table S2). ...
Recent archaeogenomic studies in Mongolia have elucidated the genetic origins of people from the Xiongnu and Mongol eras, but left the Medieval period between them only tangentially explored. Due to this dearth of ancient genomes, the dynamic history of Medieval Mongolia with the rise and fall of numerous polities still lacks a genomic perspective. To fill in this knowledge gap, here we report whole-genome sequences of nine ancient individuals from eastern Mongolia, who were excavated from two nearby cemeteries, Gurvan Dov and Tavan Khailaast. They are distributed from the Xiongnu-Xianbei period (ca. 200 CE) to the Mongol era (ca. 1,400 CE), forming a local time transect encompassing nearly 1,200 years. Remarkably, despite the long-time span, all nine individuals derive most of their ancestry (85–100%) from the eastern Eurasian lineages and show low heterogeneity in their genetic composition. This is in contrast to the general pattern observed in previously published Medieval genomes from central Mongolia, who showed higher heterogeneity and overall less eastern Eurasian ancestry, thus calling for a comprehensive archaeogenetic survey of Medieval Mongolia to fully capture the dynamic genetic history in this period.
... Recent ancient DNA has identified the genetic differentiation between Ancient Northern East Asian (ANEA) and Ancient Southern East Asian (ASEA) since the early Neolithic period, and then they experienced extensive population admixture events along different geographical corridors [7,8]. The patterns of evolutionary history observed in East Asia differed from those in Europe and Oceania, which had undergone large-scale population admixture and replacement processes [9]. Ancient human gene flow events outside East Asia have limited influence on the genetic backgrounds of East Asians [10]. ...
... Previous work has suggested that genomic variations could be used to trace the complex demographic history and recent population migration events that have resulted in the complex genetic admixture of previously geographically or culturally isolated populations, such as the Bantu expansion, the expansion of the Mongol Empire and Austronesian dispersal to Oceania [9,43,48]. ADMIXTURE and PCA results showed a close genetic relationship between Chinese inland HM and Southeast Asian HM people, which was also confirmed via the genetic distances (Fst and outgroup-f 3 values, Additional file 1: Tables S2~3). Ancient Gaohuahua people from Guangxi also had a solid genetic affinity with HM people from the Yungui Plateau and Southeast Asia. ...
... To analyze the comprehensive admixture and interaction landscape between HM people and other ancestral source groups, we merged the high-density Illumina dataset with ancient eastern Eurasians included in the 1240K dataset to form the merged middle-density 1240K dataset, including 146,802 SNPs. Ancient eastern Eurasians were included in both the merged HO and 1240K datasets, which included 47 ancient YRB farmers from 19 populations in Shandong, Henan, Shaanxi and Qinghai [7,13,85]; 30 ancient people from 13 populations in Amur River Basin or West Liao River Basin [11,85]; 23 ancient people from 9 populations in Guangxi province [12]; 54 ancient people from 9 populations in Fujian province and Taiwan island [7]; 26 ancient people from 10 populations in Japan and Korea Peninsula [10]; 33 ancient people from 7 populations on the southern fringe of the Tibetan Plateau in Nepal [86,87]; 54 ancient people from 9 populations in southern Russia around the Baikal regions [9,13,25,[88][89][90]; 243 ancient people from 20 populations in the Mongolian Plateau [25]; 18 ancient people from 4 populations in Xinjiang [91]; and a 40,000-year-old Tianyuan individual from Beijing [92]. In addition, the Illumina dataset was also merged with the HGDP and Oceanian genomic resources to generate the merged Illumina_WGS dataset, which included 460,678 SNPs and was mainly used for identifying signals of natural selection. ...
Background
The underrepresentation of Hmong-Mien (HM) people in Asian genomic studies has hindered our comprehensive understanding of the full landscape of their evolutionary history and complex trait architecture. South China is a multi-ethnic region and indigenously settled by ethnolinguistically diverse HM, Austroasiatic (AA), Tai-Kadai (TK), Austronesian (AN), and Sino-Tibetan (ST) people, which is regarded as East Asia’s initial cradle of biodiversity. However, previous fragmented genetic studies have only presented a fraction of the landscape of genetic diversity in this region, especially the lack of haplotype-based genomic resources. The deep characterization of demographic history and natural-selection-relevant genetic architecture of HM people was necessary.
Results
We reported one HM-specific genomic resource and comprehensively explored the fine-scale genetic structure and adaptative features inferred from the genome-wide SNP data of 440 HM individuals from 33 ethnolinguistic populations, including previously unreported She. We identified solid genetic differentiation between HM people and Han Chinese at 7.64‒15.86 years ago (kya) and split events between southern Chinese inland (Miao/Yao) and coastal (She) HM people in the middle Bronze Age period and the latter obtained more gene flow from Ancient Northern East Asians. Multiple admixture models further confirmed that extensive gene flow from surrounding ST, TK, and AN people entangled in forming the gene pool of Chinese coastal HM people. Genetic findings of isolated shared unique ancestral components based on the sharing alleles and haplotypes deconstructed that HM people from the Yungui Plateau carried the breadth of previously unknown genomic diversity. We identified a direct and recent genetic connection between Chinese inland and Southeast Asian HM people as they shared the most extended identity-by-descent fragments, supporting the long-distance migration hypothesis. Uniparental phylogenetic topology and network-based phylogenetic relationship reconstruction found ancient uniparental founding lineages in southwestern HM people. Finally, the population-specific biological adaptation study identified the shared and differentiated natural selection signatures among inland and coastal HM people associated with physical features and immune functions. The allele frequency spectrum of cancer susceptibility alleles and pharmacogenomic genes showed significant differences between HM and northern Chinese people.
Conclusions
Our extensive genetic evidence combined with the historical documents supported the view that ancient HM people originated from the Yungui regions associated with ancient “Three-Miao tribes” descended from the ancient Daxi-Qujialing-Shijiahe people. Then, some have recently migrated rapidly to Southeast Asia, and some have migrated eastward and mixed respectively with Southeast Asian indigenes, Liangzhu-related coastal ancient populations, and incoming southward ST people. Generally, complex population migration, admixture, and adaptation history contributed to the complicated patterns of population structure of geographically diverse HM people.
... Ancient DNA analysis has recently developed into the field of ancient genomics with the development of massive sequencing technologies. Ancient genomic studies have offered important information, such as the lineages, migration, and history of human populations [1][2][3][4][5][6]. Biological remains, such as dental stones and coprolites, contain DNAs derived from the intraoral and enteral microbes of ancient humans and/or archaic hominins [7,8]. ...
Coprolites contain various kinds of ancient DNAs derived from gut micro-organisms, viruses, and foods, which can help to determine the gut environment of ancient peoples. Their genomic information should be helpful in elucidating the interaction between hosts and microbes for thousands of years, as well as characterizing the dietary behaviors of ancient people. We performed shotgun metagenomic sequencing on four coprolites excavated from the Torihama shell-mound site in the Japanese archipelago. The coprolites were found in the layers of the Early Jomon period, corresponding stratigraphically to 7000 to 5500 years ago. After shotgun sequencing, we found that a significant number of reads showed homology with known gut microbe, viruses, and food genomes typically found in the feces of modern humans. We detected reads derived from several types of phages and their host bacteria simultaneously, suggesting the coexistence of viruses and their hosts. The food genomes provide biological evidence for the dietary behavior of the Jomon people, consistent with previous archaeological findings. These results indicate that ancient genomic analysis of coprolites is useful for understanding the gut environment and lifestyle of ancient peoples.
