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.

Author Correction: Ancient hepatitis B viruses from the Bronze Age to the Medieval period.

In Fig. 2 of this Letter, the 'E' and 'G' clade labels were inadvertently reversed, and in Table 2 the genotype of DA27 was 'D1' instead of 'D5'. These have been corrected online.

Ancient hepatitis B viruses from the Bronze Age to the Medieval period.

Hepatitis B virus (HBV) is a major cause of human hepatitis. There is considerable uncertainty about the timescale of its evolution and its association with humans. Here we present 12 full or partial ancient HBV genomes that are between approximately 0.8 and 4.5 thousand years old. The ancient sequences group either within or in a sister relationship with extant human or other ape HBV clades. Generally, the genome properties follow those of modern HBV. The root of the HBV tree is projected to between 8.6 and 20.9 thousand years ago, and we estimate a substitution rate of 8.04 × 10-6-1.51 × 10-5 nucleotide substitutions per site per year. In several cases, the geographical locations of the ancient genotypes do not match present-day distributions. Genotypes that today are typical of Africa and Asia, and a subgenotype from India, are shown to have an early Eurasian presence. The geographical and temporal patterns that we observe in ancient and modern HBV genotypes are compatible with well-documented human migrations during the Bronze and Iron Ages1,2. We provide evidence for the creation of HBV genotype A via recombination, and for a long-term association of modern HBV genotypes with humans, including the discovery of a human genotype that is now extinct. These data expose a complexity of HBV evolution that is not evident when considering modern sequences alone.

Population genomics of Bronze Age Eurasia.

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.

Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) 87Sr/86Sr isotope data from scythian Iron age barrows in Altai, Russia.

This paper reports LA-ICP-MS 87Sr/86Sr isotopic data collected from archaeological human remains uncovered in Manzherok region, Altai Republic, Russian Federation ("Mobility of nomads in central Asia: chronology and 87Sr/86Sr isotope evidence from the Pazyryk barrows of northern Altai, Russia" [1]. The skeletal remains derive from Scythian barrows dated to 6th - 3rd century BC located at Chultukov Log 1 cemetery. The Chultukov Log cemetery, located approximately 470km south of Novosibirsk, is considered the biggest nomadic burial ground in the Upper Altai and the Sayan Mountains. To enrich the information on prehistoric mobility of ancient nomadic populations in Central Asia, strontium isotopic data were collected using a Nu plasma (II) MC-ICP-MS equipped with ESI NWR193-based laser ablation system from premolar teeth of 8 adult individuals (4 males and 4 females), associated mainly with the Pazyryk culture. Additionally, we report bioavailable strontium data from single Equus caballus specimen (found at Chultukov Log 9 settlement) from Manzherok territory. In this study we have successfully applied and tested new in-depth decontamination protocol for total (<95%) removal of contaminants, necrotic tissue and dental calculus in archaeological materials based on a clinical irrigation procedure with NaOCl and EDTA. Strontium LA-ICP-MS 87Sr/86Sr isotopic data presented in this paper were obtained from prehistoric human teeth previously decontaminated according to this method. These data will provide valuable resources for isotopic analyses of prehistoric transportation systems in Central Asia, including residential mobility of ancient nomads inhabiting steppe zone, Mongolia and NW China.