Neolithic Yersinia pestis infections in humans and a dog

Abstract

Yersinia pestis has been infecting humans since the Late Neolithic (LN). Whether those early infections were isolated zoonoses or initiators of a pandemic remains unclear. We report Y. pestis infections in two individuals (of 133) from the LN necropolis at Warburg (Germany, 5300-4900 cal BP). Our analyses show that the two genomes belong to distinct strains and reflect independent infection events. All LN genomes known today (n = 4) are basal in the phylogeny and represent separate lineages that probably originated in different animal hosts. In the LN, an opening of the landscape resulted in the introduction of new rodent species, which may have acted as Y. pestis reservoirs. Coincidentally, the number of dogs increased, possibly leading to Y. pestis infections in canines. Indeed, we detect Y. pestis in an LN dog. Collectively, our data suggest that Y. pestis frequently entered human settlements at the time without causing significant outbreaks.

Fig. 1. Map of LN sites.

correctLocation of archaeological sites in which LN Y. pestis was identified in human (Warburg, Riņņukalns, Gökhem) and canine remains (Ajvide) (A). Warburg necropolis with the gallery graves I, III-V and building II (B).

Fig. 2. Phylogeny of ancient and modern Y. pestis genomes.

Maximum likelihood phylogenetic tree based on the SNP alignment (10,743 positions) of 226 modern genomes, 62 published ancient genomes, the novel genomes Warburg_1 and Warburg_2 (red) and the outgroup Y. pseudotuberculosis. LN strains are highlighted in green and LNBA strains in yellow. Dating of the ancient strains is given as calibrated years before the present (cal BP). Country abbreviation is given in brackets (CH = Switzerland, CG = Congo, CN = China, CZ = Czech Republic, DE = Germany, EE = Estonia, ES = Spain, FR = France, FSU = Former Soviet Union, HR = Croatia, IN = India, IR = Iran, KG = Kyrgyzstan, KZ = Kazakhstan, LT = Lithuania, LV = Latvia, MG = Madagascar, MM = Myanmar, MN = Mongolia, NP = Nepal, PL = Poland, RU = Russia, SE = Sweden, UA = Ukraine, UG = Uganda, UK = United Kingdom, US = United States). Unique positions to the outgroup were excluded to facilitate the visualisation. Bootstrap values were calculated for 1000 replicates and nodes with a support above 90 are marked with an asterisk. The scale corresponds to substitutions per site. Genomes included in the phylogeny are listed in Supplementary Data 5.

Fig. 3. Molecular dating of early Y. pestis.

Maximum clade credibility tree based on 42 modern and ancient Y. pestis genomes and the two genomes from Warburg (red). All dates are given as calibrated years before the present (cal BP). Country abbreviation is provided in brackets as described in Fig. 2. Genomes included in the molecular dating analysis are listed in Supplementary Data 6.