Sequencing data accompanying the study 'Lethal Plague Outbreaks in Lake Baikal Hunter–gatherers 5500 years ago'
DNA sequencing data (adapter-trimmed and merged using adapterRemoval2) generated for the study of plague strains (Yersinia pestis) among prehistoric hunter-gatherers at Lake Baikal, Siberia. DNA sequences generated from archaeological dental cementum. Metadata will be linked upon the publication of the paper accompanying this data.  Abstract: Plague is considered amongst the most devastating diseases in human history. However, early strains of the plague-causing bacterium Yersinia pestis lack virulence factors required for the bubonic form until around 3800 years ago. Consequently, the morbidity and mortality of early plague strains remains unclear. Here, we describe early plague strains reported associated with two phases of outbreaks among mid-Holocene hunter–gatherers near Lake Baikal in south-east Siberia, beginning from ~5500 years ago (cal. BP). These outbreaks occur across four hunter–gatherer cemeteries, with a 39% detection rate for plague infection. By reconstructing kinship pedigrees, we show that small familial groups are affected, consistent with human-to-human spread of disease, and that the first outbreak occurred within a single generation. The infections appear to have resulted in acute mortality, especially among children (aged 8 to 11-years-old). We further note functional differences, including in the ypm superantigen known from Y. pseudotuberculosis today. The new strains diverge ancestrally to known Y. pestis and constrain the timing of its emergence, indicating this happened before approximately 5700 years ago. These findings show that plague outbreaks happened earlier than previously thought and were indeed lethal. We contend that the occurrence of outbreaks among mid-Holocene hunter–gatherer communities well outside the sphere of Late Neolithic Europe challenges the notion that higher population densities and lifestyle changes during the Neolithic agricultural transition were prerequisites for plague epidemics.