Yersinia pestis, a zoonotic pathogen that spread from wild rodents to peridomestic rodents and humans, has caused three historic plague pandemics. Genomic evidence from ancient human remains reveals reduced copies of the virulence gene pla in later-dated strains from the first two pandemics, but the biological relevance of this remains unknown. In a recent study, Sidhu et al. analysed Y. pestis published ancient genomes from the first and second pandemic and confirmed substantial depletion of the pla gene. Genomic analyses of large, modern, third-pandemic Y. pestis strain collections identified three contemporary strains with pla depletion. Genetic characterization of the pla region — located on the high-copy number plasmid pPCP1 — using de novo assembly of ancient and modern pPCP1, revealed that reduced pla dosage probably resulted from excision via recombination between two flanking xrs regions, in combination with pPCP1 integration into the low-copy pCD1 plasmid. In vitro, pla depletion decreased Pla proteolytic activity, whereas in vivo, it decreased the mortality of mice in models of bubonic plague, but not in pneumonic and septicaemic models. In sum, pla depletion likely attenuated Y. pestis virulence, allowing the pathogen to persist in tolerant hosts.