Assessing the origins of the European Plagues following the Black Death: A synthesis of genomic, historical, and ecological information Barbara Bramantia,b,1,2, Yarong Wuc,1, Ruifu Yangc, Yujun Cuic,2, and Nils Chr. Stensetha,d,2 aCentre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway; bDepartment of Neuroscience and Rehabilitation, Faculty of Medicine, Pharmacy and Prevention, University of Ferrara, 44121 Ferrara, Italy; cState Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; and dMinistry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China Edited by Joan E. Strassmann, Washington University in St. Louis, St. Louis, MO, and approved July 22, 2021 (received for review February 7, 2021) The second plague pandemic started in Europe with the Black Death newer hypothesis (Hypothesis 2) claims that the plague reservoir in 1346 and lasted until the 19th century. Based on ancient DNA was in Asia, possibly close to Eastern Europe (6, 7, 9, 11, 13). studies, there is a scientific disagreement over whether the bacterium, In order to more easily view the phylogeny from the second Yersinia pestis, came into Europe once (Hypothesis 1) or repeatedly plague pandemic and to better contrast the evidence for the two over the following four centuries (Hypothesis 2). Here, we synthesize hypotheses, we generated two schematic figures (Fig. 2) and a the most updated phylogeny together with historical, archeological, table (Table 1). evolutionary, and ecological information. On the basis of this holistic Hypothesis 1 is supported by a phylogenetic analysis based on view, we conclude that Hypothesis 2 is the most plausible. We also the currently available ancient genomes, which infers high posterior suggest that Y. pestis lineages might have developed attenuated vir- probability for a Western European source of the transmissions on ulence during transmission, which can explain the convergent evolu- the post–Black Death branch (SI Appendix, Fig. S1). However, as pla tionary signals, including decay, that appeared at the end of the the dataset includes 41 ancient genomes from Western Europe pandemics. against only 8 strains from Eastern Europe (including Gdansk and Riga), the proposed origins from Western Europe are likely to EVOLUTION Black Death | European plague | Yersinia pestis | molecular evolution | be biased toward a European reservoir due to a size-effect bias. ecological epidemiology Notably, the most basal genome LAI009 (4) (the Black Death’s lineage), Bolgar (at the root of Branch 1), and the most recent esearchers agree that the second plague pandemic was caused Yersinia pestis – genome [CHE1 (7)] all originated from Western Russia, implying Rby (1 9), which arrived in Europe from Caffa that they might have been closer to a putative Asian or Eastern transported by Genoese galleys on the Black Sea at the beginning European reservoir. This continuity does represent strong evi- of the Black Death (10). However, there is no consensus among dence in support of Hypothesis 2. researchersastotheoriginsofplagueepidemicsinEuropefollowing Using only genomic data, Hypothesis 1 might be seen as the most the Black Death and ravaging Europe until the 19th century, as parsimonious hypothesis since it proposes an internal source for all attested by historical documents (11). western Eurasian outbreaks. However, for two locations (Pestbacken, The two main theories are that one or more plague reservoirs Sweden 1710 [PEB10] and Marseille, France 1722 [OBS]), an origin remained in Western Europe during the entire second plague pandemic (referred to in the following as Hypothesis 1) (3, 4, 8, 12) or the bacteria repeatedly invaded Europe from non–Western Significance European reservoir(s) during the same period (referred to in the following as Hypothesis 2) (6, 7, 9, 11, 13). Here, we assess these Over the last few years, there has been a great deal of scientific two hypotheses using a broad spectrum of evidence, including debate regarding whether the plague bacterium, Yersinia pestis, historical and archeological, genetic, evolutionary, and ecological spread from a Western European reservoir during the second information. plague pandemic, or if it repeatedly came to Europe from Asia. Here, we make a synthesis of the available evidence, including Results and Discussion genomes of ancient DNA and historical, archeological, and eco- Assessment of the Two Hypotheses. For the purpose of understanding logical information. We conclude that the bacterium most likely the evolution of the plague bacteria, more than 100 ancient Y. pestis came to Europe from Asia several times during the second genomes have been published to date. The last 17 were recently plague pandemic. reported during a short period by four distinct research groups (7–9, 12). Using most of the ancient genomes (criteria for exclusion are Author contributions: B.B. conceived the work; N.C.S. established the author team; B.B., Methods Y.C., and N.C.S. designed research; Y.W. analyzed the data, and designed and generated described in ), along with 499 modern ones, we present the phylogeny; B.B. wrote the paper with contributions from Y.W., R.Y., Y.C., and N.C.S.; here the most updated phylogeny (Fig. 1). and R.Y. and N.C.S. supervised the work. The updated phylogeny confirms the almost clonal nature of the The authors declare no competing interest. Black Death strains in comparison to all other lineages of the second This article is a PNAS Direct Submission. Pestis secunda plague pandemic, including the strains from the This open access article is distributed under Creative Commons Attribution-NonCommercial- [Ber37 and Ber 45, The Netherlands (6), and BolgarCity2370, Russia NoDerivatives License 4.0 (CC BY-NC-ND). (3)], which are placed on Branch 1 [see also London-Ind6330, See online for related content such as Commentaries. United Kingdom (3)], as well as to all other strains, which are placed 1B.B. and Y.W. contributed equally to this work. – on the post Black Death branch. There is general agreement that 2To whom correspondence may be addressed. Email: [email protected], n.c. the post–Black Death branch was hosted in a novel wild rodent [email protected], or [email protected]. reservoir—either in Europe or outside Europe (3–8, 12, 14). The This article contains supporting information online at https://www.pnas.org/lookup/suppl/ original hypothesis (Hypothesis 1) claims that such a plague reservoir doi:10.1073/pnas.2101940118/-/DCSupplemental. existed in Western Europe (15), perhaps in the Alps (16). However, a Published August 31, 2021. PNAS 2021 Vol. 118 No. 36 e2101940118 https://doi.org/10.1073/pnas.2101940118 | 1of6 Downloaded by guest on October 4, 2021 AB Fig. 1. Phylogeny and archaeological site locations of ancient genomes. (A) A maximum likelihood phylogeny was obtained with 574 genomes of Y. pestis (including 75 ancient genomes) involved based on 12,608 SNPs. The numbers at each node indicate the bootstrap values of 1,000 replicates. Branches highlighted in blue correspond to the second pandemic, which is subdivided in three groups: the 14th to 15th century group, which also includes the Black Death and the Pestis secunda (1,357 to 1,366) strains; the 15th to 17th century group; and the 18th century group (which also includes the BED genomes for homogeneity). Branches in purple correspond to the first Pandemic, and branches in green correspond to the prehistoric plague. The ratio between the depth of pla and that of the entire pPCP1 plasmid for all ancient genomes is shown in the rightmost heatmap, with a color scale ranging from 0 (dark blue) to 130+ (dark red). (B) Geographic distribution of the three waves during the second pandemic. 2of6 | PNAS Bramanti et al. https://doi.org/10.1073/pnas.2101940118 Assessing the origins of the European Plagues following the Black Death: A synthesis of genomic, historical, and ecological information Downloaded by guest on October 4, 2021 Hypothesis 1: The 18th c. Plague Hypothesis 2: CHE1 1720+ The 18th c. Plague Plague developed in CHE1 1720+ Plague was repeatedly reservoirs in the Alps imported to W-Eu where recirculated in chains of ROSTOV 2033,1762-73 ROSTOV 2033,1762-73 human transmission OBS 1722 OBS 1722 PEB10 1710-1 PEB10 1710-1 AZOV38 (15th-18th c.) AZOV38(15th-18th c.) BED, London (16th-17th c.) BED, London (16th-17th c.) = = GDANSK8 1425-1469 GDANSK8 1425-1469 ELLWANGEN (15th-17th c.) ROSTOV 2039,1762-73 ELLWANGEN (15th-17th c.) ROSTOV 2039,1762-73 SPN 1636 NMS002, Cambridge (15th-17th c.) SPN 1636 NMS002, Cambridge (15th-17th c.) BRA G701, Riga (15th-17th c.) BRA G701, Riga (15th-17th c.) The Thirty Years LAR LBG LAR LBG STN STN War’s Clade(1618-1648) The “Alpine” Clade STA001 (15th-17th c.) STA001 (15th-17th c.) Imported during war MAN008 COL001 MAN008 COL001 Imported by ship LAI009 Ber37, Ber45 LAI009 Ber37, Ber45 Branch0 BD Branch1 Branch 0 BD Branch 1 Port or trade center Bolgar Bolgar Eastern Europe/Central Asia BD 1346-1353 BD 1346-1353 Pestis secunda 1357-1366 Pestis secunda 1357-1366 Western Europe Fig. 2. Schematic comparison between the two main hypotheses for the interpretation of the Y. pestis phylogeny of the second plague pandemic. Historic and evolutionary information is included in the schematic figures. In addition to the symbols explained in the figure, we outlined in red the strains showing the 49-kb deletion. Pla decay (meaning both, full, or partial absence of the pla gene) is indicated by the names in bold. from the Ottoman Empire is historically and archaeologically well Hypothesis 1 assumes the existence of a wild rodent plague res- supported (7). Thus, Hypothesis 1 needs to account for a back and ervoir in the Alps, which is not supported by ecological evidence forth spread, which reintroduced plague on two occasions to the (13).