The Bronze Age of Eurasia (around 3000-1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought.

SummaryThe bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it originated remains contentious. Here, we report the oldest direct evidence of Yersinia pestis identified by ancient DNA in human teeth from Asia and Europe dating from 2,800 to 5,000 years ago. By sequencing the genomes, we find that these ancient plague strains are basal to all known Yersinia pestis. We find the origins of the Yersinia pestis lineage to be at least two times older than previous estimates. We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague. Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics.

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The transition from hunting and gathering to farming in Europe was brought upon by arrival of new people carrying novel material culture and genetic ancestry. The exact nature and scale of the transition-both material and genetic-varied in different parts of Europe [1-7]. Farming-based economies appear relatively late in Northeast Europe, and the extent to which they involve change in genetic ancestry is not fully understood due to the lack of relevant ancient DNA data. Here we present the results from new low-coverage whole-genome shotgun sequence data from five hunter-gatherers and five first farmers of Estonia whose remains date to 4,500 to 6,300 years before present. We find evidence of significant differences between the two groups in the composition of autosomal as well as mtDNA, X chromosome, and Y chromosome ancestries. We find that Estonian hunter-gatherers of Comb Ceramic culture are closest to Eastern hunter-gatherers, which is in contrast to earlier hunter-gatherers from the Baltics, who are close to Western hunter-gatherers [8, 9]. The Estonian first farmers of Corded Ware culture show high similarity in their autosomes with European hunter-gatherers, Steppe Eneolithic and Bronze Age populations, and European Late Neolithic/Bronze Age populations, while their X chromosomes are in addition equally closely related to European and Anatolian and Levantine early farmers. These findings suggest that the shift to intensive cultivation and animal husbandry in Estonia was triggered by the arrival of new people with predominantly Steppe ancestry but whose ancestors had undergone sex-specific admixture with early farmers with Anatolian ancestry.

Summary In this study we compare the genetic ancestry of individuals from two as yet genetically unstudied cultural traditions in Estonia in the context of available modern and ancient datasets: 15 from the Late Bronze Age stone-cist graves (1200–400 BC) (EstBA), and 6 from the Pre-Roman Iron Age tarand cemeteries (800/500 BC–50 AD) (EstIA). We also included 5 Pre-Roman to Roman Iron Age Ingrian (500 BC–450 AD) (IngIA) and 7 Middle Age Estonian (1200–1600 AD) (EstMA) individuals to build a dataset for studying the demographic history of the northern parts of the Eastern Baltic from the earliest layer of Mesolithic to modern times. Our findings are consistent with EstBA receiving gene flow from regions with strong Western hunter-gatherer (WHG) affinities, and EstIA from populations related to modern Siberians. The latter inference is in accordance with Y chromosome (chrY) distributions in present-day populations of the Eastern Baltic, as well as patterns of autosomal variation in the majority of the westernmost Uralic speakers [1–5]. This ancestry reached the coasts of the Baltic Sea no later than the mid-first millennium BC; i.e. in the same time window as the diversification of west Uralic/Finnic languages [6]. Furthermore, phenotypic traits often associated with modern Northern Europeans like light eyes, hair and skin as well as lactose tolerance can be traced back to the Bronze Age in the Eastern Baltic.

BackgroundThe genetic origins of Uralic speakers from across a vast territory in the temperate zone of North Eurasia have remained elusive. Previous studies have shown contrasting proportions of Eastern and Western Eurasian ancestry in their mitochondrial and Y chromosomal gene pools. While the maternal lineages reflect by and large the geographic background of a given Uralic-speaking population, the frequency of Y chromosomes of Eastern Eurasian origin is distinctively high among European Uralic speakers. The autosomal variation of Uralic speakers, however, has not yet been studied comprehensively.ResultsHere, we present a genome-wide analysis of 15 Uralic-speaking populations which cover all main groups of the linguistic family. We show that contemporary Uralic speakers are genetically very similar to their local geographical neighbours. However, when studying relationships among geographically distant populations, we find that most of the Uralic speakers and some of their neighbours share a genetic component of possibly Siberian origin. Additionally, we show that most Uralic speakers share significantly more genomic segments identity-by-descent with each other than with geographically equidistant speakers of other languages. We find that correlated genome-wide genetic and lexical distances among Uralic speakers suggest co-dispersion of genes and languages. Yet, we do not find long-range genetic ties between Estonians and Hungarians with their linguistic sisters that would distinguish them from their non-Uralic-speaking neighbours.ConclusionsWe show that most Uralic speakers share a distinct ancestry component of likely Siberian origin, which suggests that the spread of Uralic languages involved at least some demic component.Electronic supplementary materialThe online version of this article (10.1186/s13059-018-1522-1) contains supplementary material, which is available to authorized users.

The Iron and Classical Ages in the Near East were marked by population expansions carrying cultural transformations that shaped human history, but the genetic impact of these events on the people who lived through them is little-known. Here, we sequenced the whole genomes of 19 individuals who each lived during one of four time periods between 800 BCE and 200 CE in Beirut on the Eastern Mediterranean coast at the center of the ancient world’s great civilizations. We combined these data with published data to traverse eight archaeological periods and observed any genetic changes as they arose. During the Iron Age (∼1000 BCE), people with Anatolian and South-East European ancestry admixed with people in the Near East. The region was then conquered by the Persians (539 BCE), who facilitated movement exemplified in Beirut by an ancient family with Egyptian-Lebanese admixed members. But the genetic impact at a population level does not appear until the time of Alexander the Great (beginning 330 BCE), when a fusion of Asian and Near Easterner ancestry can be seen, paralleling the cultural fusion that appears in the archaeological records from this period. The Romans then conquered the region (31 BCE) but had little genetic impact over their 600 years of rule. Finally, during the Ottoman rule (beginning 1516 CE), Caucasus-related ancestry penetrated the Near East. Thus, in the past 4,000 years, three limited admixture events detectably impacted the population, complementing the historical records of this culturally complex region dominated by the elite with genetic insights from the general population.

11Farming-based economies appear relatively late in Northeast Europe and the extent to which 12