Stone Age Yersinia pestis genomes shed light on the early evolution, diversity, and ecology of plague

Abstract

Significance The bacterium Yersinia pestis has caused numerous historically documented outbreaks of plague and research using ancient DNA could demonstrate that it already affected human populations during the Neolithic. However, the pathogen’s genetic diversity, geographic spread, and transmission dynamics during this early period of Y. pestis evolution are largely unexplored. Here, we describe a set of ancient plague genomes up to 5,000 y old from across Eurasia. Our data demonstrate that two genetically distinct forms of Y. pestis evolved in parallel and were both distributed across vast geographic distances, potentially occupying different ecological niches. Interpreted within the archeological context, our results suggest that the spread of plague during this period was linked to increased human mobility and intensification of animal husbandry.

1,000 ancient genomes uncover 10,000 years of natural selection in Europe

“…There is direct ancient DNA evidence for pathogen infection being a major source of mortality in the Bronze Age. The earliest evidence for Yersinia pestis infections in Europe ascertained from ancient DNA comes from the Bronze Age at times particularly close to or after the arrival of pastoralists from the Eurasian Steppe, from where both of these pathogens have been recovered from humans several millennia prior to their first evidence in Europe 60,61 . Thus, pathogens entering Europe along with Steppe Pastoralists in the Bronze Age could have been a driving force behind changes in these immune related genes.…”

Emergence and spread of ancestral Yersinia pestis in Late-Neolithic and Bronze-Age Eurasia, ca . 5,000 to 2,500 y B.P.

“…In their study, Andrades Valtueña et al. ( 1 ) present a tour de force by reporting 17 new prehistoric Y. pestis genomes from Eurasian human burials (adding to 13 previously published) ( 1 – 7 ). Furthermore, their work, together with previously published data, lays the foundations for a new classification of Y. pestis strains and broadens our insight into the dynamics of emergence and spread of Y. pestis in prehistoric Eurasia.…”

“…Of the ancient genomes, the authors classify the two oldest (previously published) genomes as the “preLNBA–” (pre-Late Neolithic/Early Bronze Age) lineage and 26 others as the “LNBA–” lineage ( 1 ). PreLNBA– genomes are from Latvia and Sweden, dated, respectively, to 5,300 to 5,050 and 5,040 to 4,867 y B.P.…”

“…( 1 ) indicate that the LNBA– lineage had a different evolutionary story compared to later lineages, such as “Branch 1” causing the second and third plague pandemics, characterized by phylogenetic and global focal diversity ( 8 – 10 ). Conversely, the LNBA– lineage is characterized by a genetic monophyly, lacking distinct subbranches, containing many evolutionary dead ends, and showing no correlation between genetic and geographic distance ( 1 ). Interestingly, the two earliest LNBA– genomes from central Siberia and North Caucasus are both chronologically concurrent ( ca .…”

La paleomicrobiología molecular permite dilucidar el origen de la plaga

“…(B) Árbol ML de todos los SNPs de Yersinia pestis (n = 7506) y los intervalos de tiempo correspondientes a cada genoma. AndradesValtueña et al, (2022) Proc Nat Acad Sci USA, 119, e2116722119. https://www.pnas.org/doi/abs/10.1073/pnas.2116722119.…”