Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago.

The 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

The origins and spread of domestic horses from the Western Eurasian steppes

This is the final version. Available on open access from Nature Research via the DOI in this recordData availability: All collapsed and paired-end sequence data for samples sequenced in this study are available in compressed fastq format through the European Nucleotide Archive under accession number PRJEB44430, together with rescaled and trimmed bam sequence alignments against both the nuclear and mitochondrial horse reference genomes. Previously published ancient data used in this study are available under accession numbers PRJEB7537, PRJEB10098, PRJEB10854, PRJEB22390 and PRJEB31613, and detailed in Supplementary Table 1. The genomes of ten modern horses, publicly available, were also accessed as indicated in their corresponding original publications57,61,85-87.NOTE: see the published version available via the DOI in this record for the full list of authorsDomestication of horses fundamentally transformed long-range mobility and warfare. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling at Botai, Central Asia around 3500 BC. Other longstanding candidate regions for horse domestication, such as Iberia and Anatolia, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 BC, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 BC driving the spread of Indo-European languages. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium BC Sintashta culture

Strontium isotope ratios (87Sr/86Sr) analysis from various sources the southern Trans-Urals

The present dataset contains measurement of biovalable strontium isotopes (87Sr/86Sr) gathered in the southern Trans-Urals. There are four samples types, such as wormwood (n = 95), leached soil (n = 95), water (n = 93) and freshwater mollusks (n = 74), collected to measure bioavailable strontium isotopes. The analysis of Sr isotopic composition was carried out in the cleanrooms (6 and 7 ISO classes) of the Geoanalitik shared research facilities of the Institute of Geology and Geochemistry, the Ural Branch of the Russian Academy of Sciences (Ekaterinburg). Mollusk shell samples preliminarily cleaned with acetic acid, as well as vegetation samples rinsed with deionized water and ashed, were dissolved by open digestion in concentrated HNO 3 with the addition of H 2 O 2 on a hotplate at 150°C. Water samples were acidified with concentrated nitric acid and filtered. To obtain aqueous leachates, pre-ground soil samples weighing 1 g were taken into polypropylene containers, 10 ml of ultrapure water was added and shaken in for 1 hour, after which they were filtered through membrane cellulose acetate filters with a pore diameter of 0.2 μm. In all samples, the strontium content was determined by ICP-MS (NexION 300S). Then the sample volume corresponding to the Sr content of 600 ng was evaporated on a hotplate at 120°C, the precipitate was dissolved in 7M HNO 3 . Sample solutions were centrifuged at 6000 rpm and strontium was chromatographically isolated using SR resin (Triskem). The strontium isotopic composition was measured on a Neptune Plus multicollector mass spectrometer with inductively coupled plasma (MC-ICP-MS). To correct mass bias, a combination of bracketing and internal normalization according to the exponential law 88 Sr/ 86 Sr = 8.375209 was used. The results were additionally bracketed using the NIST SRM 987 strontium carbonate reference material using an average deviation from the reference value of 0.710245 for every two samples bracketed between NIST SRM 987 measurements. The long-term reproducibility of the strontium isotopic analysis was evaluated using repeated measurements of NIST SRM 987 during 2020-2022 and yielded 87 Sr/ 86 Sr = 0.71025, 2SD = 0.00012 (104 measurements in two replicates). The within-laboratory standard uncertainty (2σ) obtained for SRM-987 was ± 0.003 %

Strontium isotope ratios (87Sr/86Sr) from various sources of freshwater from the Southern Trans-Urals

The present dataset contains measurement of biovalable strontium isotopes (87Sr/86Sr) gathered in the southern Trans-Urals. There are four samples types, such as wormwood (n = 95), leached soil (n = 95), water (n = 93) and freshwater mollusks (n = 74), collected to measure bioavailable strontium isotopes. The analysis of Sr isotopic composition was carried out in the cleanrooms (6 and 7 ISO classes) of the Geoanalitik shared research facilities of the Institute of Geology and Geochemistry, the Ural Branch of the Russian Academy of Sciences (Ekaterinburg). Mollusk shell samples preliminarily cleaned with acetic acid, as well as vegetation samples rinsed with deionized water and ashed, were dissolved by open digestion in concentrated HNO 3 with the addition of H 2 O 2 on a hotplate at 150°C. Water samples were acidified with concentrated nitric acid and filtered. To obtain aqueous leachates, pre-ground soil samples weighing 1 g were taken into polypropylene containers, 10 ml of ultrapure water was added and shaken in for 1 hour, after which they were filtered through membrane cellulose acetate filters with a pore diameter of 0.2 μm. In all samples, the strontium content was determined by ICP-MS (NexION 300S). Then the sample volume corresponding to the Sr content of 600 ng was evaporated on a hotplate at 120°C, the precipitate was dissolved in 7M HNO 3 . Sample solutions were centrifuged at 6000 rpm and strontium was chromatographically isolated using SR resin (Triskem). The strontium isotopic composition was measured on a Neptune Plus multicollector mass spectrometer with inductively coupled plasma (MC-ICP-MS). To correct mass bias, a combination of bracketing and internal normalization according to the exponential law 88 Sr/ 86 Sr = 8.375209 was used. The results were additionally bracketed using the NIST SRM 987 strontium carbonate reference material using an average deviation from the reference value of 0.710245 for every two samples bracketed between NIST SRM 987 measurements. The long-term reproducibility of the strontium isotopic analysis was evaluated using repeated measurements of NIST SRM 987 during 2020-2022 and yielded 87 Sr/ 86 Sr = 0.71025, 2SD = 0.00012 (104 measurements in two replicates). The within-laboratory standard uncertainty (2σ) obtained for SRM-987 was ± 0.003 %

Ancient pathogen DNA in human teeth and petrous bones.

Recent ancient DNA (aDNA) studies of human pathogens have provided invaluable insights into their evolutionary history and prevalence in space and time. Most of these studies were based on DNA extracted from teeth or postcranial bones. In contrast, no pathogen DNA has been reported from the petrous bone which has become the most desired skeletal element in ancient DNA research due to its high endogenous DNA content. To compare the potential for pathogenic aDNA retrieval from teeth and petrous bones, we sampled these elements from five ancient skeletons, previously shown to be carrying Yersinia pestis. Based on shotgun sequencing data, four of these five plague victims showed clearly detectable levels of Y. pestis DNA in the teeth, whereas all the petrous bones failed to produce Y. pestis DNA above baseline levels. A broader comparative metagenomic analysis of teeth and petrous bones from 10 historical skeletons corroborated these results, showing a much higher microbial diversity in teeth than petrous bones, including pathogenic and oral microbial taxa. Our results imply that although petrous bones are highly valuable for ancient genomic analyses as an excellent source of endogenous DNA, the metagenomic potential of these dense skeletal elements is highly limited. This trade-off must be considered when designing the sampling strategy for an aDNA project

Dairying enabled Early Bronze Age Yamnaya steppe expansions

During the Early Bronze Age, populations of the western Eurasian steppe expanded across an immense area of northern Eurasia. Combined archaeological and genetic evidence supports widespread Early Bronze Age population movements out of the Pontic-Caspian steppe that resulted in gene flow across vast distances, linking populations of Yamnaya pastoralists in Scandinavia with pastoral populations (known as the Afanasievo) far to the east in the Altai Mountains(1,2) and Mongolia(3). Although some models hold that this expansion was the outcome of a newly mobile pastoral economy characterized by horse traction, bulk wagon transport(4-6) and regular dietary dependence on meat and milk(5), hard evidence for these economic features has not been found. Here we draw on proteomic analysis of dental calculus from individuals from the western Eurasian steppe to demonstrate a major transition in dairying at the start of the Bronze Age. The rapid onset of ubiquitous dairying at a point in time when steppe populations are known to have begun dispersing offers critical insight into a key catalyst of steppe mobility. The identification of horse milk proteins also indicates horse domestication by the Early Bronze Age, which provides support for its role in steppe dispersals. Our results point to a potential epicentre for horse domestication in the Pontic-Caspian steppe by the third millennium bc, and offer strong support for the notion that the novel exploitation of secondary animal products was a key driver of the expansions of Eurasian steppe pastoralists by the Early Bronze Age.ISSN:0028-0836ISSN:1476-468