Evolutionary history and recurrent host adaptation in ancient Salmonella enterica

AI interpretationAI-generated

Ancient Salmonella genomes reveal extinct lineages and repeated host adaptation across Eurasia.

This study presents 53 new ancient Salmonella enterica genomes from Eurasia, dated 3500 BCE to 1300 CE. It reconstructs the pathogen's evolutionary history, identifying extinct prehistoric lineages and multiple lineage replacement events. Bayesian analysis dates host adaptation events, showing that Paratyphi C, Choleraesuis, and Typhisuis evolved host specificity independently. Convergent adaptation signals were found via shared pseudogenes and gene gain/loss. The lineage's gradual adaptation to humans coincides with intensifying animal husbandry in pastoralist and farming societies.

• Multiple extinct prehistoric Salmonella lineages once caused infections across Eurasia.
• Host-adapted sublineages Paratyphi C, Choleraesuis, and Typhisuis evolved host specificity independently.
• Convergent host adaptation signals were detected through shared pseudogenes and recurrent gene gain/loss events.

Sample interpretation

The 54 site samples span the Iron Age (10), Bronze Age (4), Early Medieval (4), and other periods. Y-chromosome haplogroups are dominated by R-M269 (14), with R-L51, R-L2, R-PF6162, and R-L20 also present. Mitochondrial haplogroups include T1a1 (3), U2e1 (2), H (2), J1c (2), and K1b1a1 (2). Key sites include KNC181 (7), KNL026 (4), and SJL020 (3). These ancient individuals likely represent past human populations that carried or were exposed to Salmonella.

For genealogy enthusiasts

For ancestry enthusiasts, this study shows how ancient pathogen DNA can trace human-pathogen interactions. It highlights that Salmonella's adaptation to humans paralleled the rise of animal husbandry, offering a new lens on how ancient lifestyles shaped disease evolution.