Volume 163, Issue 3, 22 October 2015, Pages 571–582

Article

Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago

  • 1 Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark
  • 2 Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5–7, 1350 Copenhagen, Denmark
  • 3 Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden
  • 4 Section for Organismal Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
  • 5 Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
  • 6 Division of Armenology and Social Sciences, Institute of Archaeology and Ethnography, National Academy of Sciences, 0025 Yerevan, Republic of Armenia
  • 7 Institute of History and Archaeology RAS (South Ural Department), South Ural State University, 454080 Chelyabinsk, Russia
  • 8 Orenburg Museum of Fine Arts, 460000 Orenburg, Russia
  • 9 Department of Archaeology and Ethnography, Yerevan State University, 0025 Yerevan, Republic of Armenia
  • 10 Department of Archaeology, University of Tartu, 51003 Tartu, Estonia
  • 11 Institute of Archaeology, University of Wrocław, 50-139 Wrocław, Poland
  • 12 Department of Evolutionary Biology, Estonian Biocentre and University of Tartu, 51010 Tartu, Estonia
  • 13 Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
  • 14 Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, 0014 Yerevan, Armenia
  • 15 Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
  • 16 Center for Theoretical Evolutionary Genetics, University of California, Berkeley, California 94720-3140, USA
  • 17 Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK

Highlights

Yersinia pestis was common across Eurasia in the Bronze Age

The most recent common ancestor of all Y. pestis was 5,783 years ago

The ymt gene was acquired before 951 cal BC, giving rise to transmission via fleas

Bronze Age Y. pestis was not capable of causing bubonic plague


Summary

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.



Introduction

Plague is caused by the bacteria Yersinia pestis and is being directly transmitted through human-to-human contact (pneumonic plague) or via fleas as a common vector (bubonic or septicemic plague) ( Treille and Yersin, 1894). Three historic human plague pandemics have been documented: (1) the First Pandemic, which started with the Plague of Justinian (541–544 AD), but continued intermittently until ∼750 AD; (2) the Second Pandemic, which began with the Black Death in Europe (1347–1351 AD) and included successive waves, such as the Great Plague (1665–1666 AD), until the 18th century; (3) the Third Pandemic, which emerged in China in the 1850s and erupted there in a major epidemic in 1894 before spreading across the world as a series of epidemics until the middle of the 20th century ( Bos et al., 2011, Cui et al., 2013, Drancourt et al., 1998, Harbeck et al., 2013, Parkhill et al., 2001, Perry and Fetherston, 1997 and Wagner et al., 2014). Earlier outbreaks such as the Plague of Athens (430–427 BC) and the Antonine Plague (165–180 AD) may also have occurred, but there is no direct evidence that allows confident attribution to Y. pestis ( Drancourt and Raoult, 2002 and McNeill, 1976).

The consequences of the plague pandemics have been well-documented and the demographic impacts were dramatic (Little et al., 2007). The Black Death alone is estimated to have killed 30%–50% of the European population. Economic and political collapses have also been in part attributed to the devastating effects of the plague. The Plague of Justinian is thought to have played a major role in weakening the Byzantine Empire, and the earlier putative plagues have been associated with the decline of Classical Greece and likely undermined the strength of the Roman army.

Molecular clock estimates have suggested that Y. pestis diversified from the more prevalent and environmental stress-tolerant, but less pathogenic, enteric bacterium Y. pseudotuberculosis between 2,600 and 28,000 years ago ( Achtman et al., 1999, Achtman et al., 2004, Cui et al., 2013 and Wagner et al., 2014). However, humans may potentially have been exposed to Y. pestis for much longer than the historical record suggests, though direct molecular evidence for Y. pestis has not been obtained from skeletal material older than 1,500 years ( Bos et al., 2011 and Wagner et al., 2014). The most basal strains of Y. pestis (0.PE7 clade) recorded to date were isolated from the Qinghai-Tibet Plateau in China in 1961–1962 ( Cui et al., 2013).

We investigated the origin of Y. pestis by sequencing ancient bacterial genomes from the teeth of Bronze Age humans across Europe and Asia. Our findings suggest that the virulent, flea-borne Y. pestis strain that caused the historic bubonic plague pandemics evolved from a less pathogenic Y. pestis lineage infecting human populations long before recorded evidence of plague outbreaks.

Results

Identification of Yersinia pestis in Bronze Age Eurasian Individuals

We screened c. 89 billion raw DNA sequence reads obtained from teeth of 101 Bronze Age individuals from Europe and Asia (Allentoft et al., 2015) and found that seven individuals carried sequences resembling Y. pestis ( Figure 1, Table S1, Supplemental Experimental Procedures). Further sequencing allowed us to assemble the Y. pestis genomes to an average depth of 0.14–29.5X, with 12%–95% of the positions in the genome covered at least once ( Table 1, Table S2, S3, and S4). We also recovered the sequences of the three plasmids pCD1, pMT1, and pPCP1 (0.12 to 50.3X in average depth) the latter two of which are crucial for distinguishing Y. pestis from its highly similar ancestor Y. pseudotuberculosis ( Table 1, Figure 2, Table S3) ( Bercovier et al., 1980, Chain et al., 2004 and Parkhill et al., 2001). The host individuals from which Y. pestis was recovered belong to Eurasian Late Neolithic and Bronze Age cultures ( Allentoft et al., 2015), represented by the Afanasievo culture in Altai, Siberia (2782 cal BC, 2794 cal BC, n = 2), the Corded Ware culture in Estonia (2462 cal BC, n = 1), the Sintashta culture in Russia (2163 cal BC, n = 1), the Unetice culture in Poland (2029 cal BC, n = 1), the Andronovo culture in Altai, Siberia (1686 cal BC, n = 1), and an early Iron Age individual from Armenia (951 cal BC, n = 1) (Table S1).

Archaeological Sites of Bronze Age Yersinia pestis(A) Map of Eurasia indicating ...
Figure 1. 

Archaeological Sites of Bronze Age Yersinia pestis

(A) Map of Eurasia indicating the position, radiocarbon dated ages and associated cultures of the samples in which Y. pestis were identified. Dates are given as 95% confidence interval calendar BC years. IA: Iron Age.

(B) Burial four from Bulanovo site. Picture by Mikhail V. Khalyapin. See also Table S1.