Distinct but Intertwined Evolutionary Histories of Multiple Salmonella enterica Subspecies.

is responsible for many nontyphoidal foodborne infections and enteric (typhoid) fever in humans. Of the two species, is highly diverse and includes 10 known subspecies and approximately 2,600 serotypes. Understanding the evolutionary processes that generate the tremendous diversity in is important in reducing and controlling the incidence of disease outbreaks and the emergence of virulent strains. In this study, we aim to elucidate the impact of homologous recombination in the diversification of subspecies. Using a data set of previously published 926 genomes representing the 10 subspecies and , we calculated a genus-wide pan-genome composed of 84,041 genes and the pan-genome of 81,371 genes. The size of the accessory genomes varies between 12,429 genes in subsp. (subsp. IIIa) to 33,257 genes in subsp. (subsp. I). A total of 12,136 genes in the pan-genome show evidence of recombination, representing 14.44% of the pan-genome. We identified genomic hot spots of recombination that include genes associated with flagellin and the synthesis of methionine and thiamine pyrophosphate, which are known to influence host adaptation and virulence. Last, we uncovered within-species heterogeneity in rates of recombination and preferential genetic exchange between certain donor and recipient strains. Frequent but biased recombination within a bacterial species may suggest that lineages vary in their response to environmental selection pressure. Certain lineages, such as the more uncommon non- subspecies (non- subsp. ), may also act as a major reservoir of genetic diversity for the wider population. is a major foodborne pathogen, which can be transmitted via several distinct routes from animals and environmental sources to human hosts. Multiple subspecies and serotypes of exhibit considerable differences in virulence, host specificity, and colonization. This study provides detailed insights into the dynamics of recombination and its contributions to subspecies evolution. Widespread recombination within the species means that new adaptations arising in one lineage can be rapidly transferred to another lineage. We therefore predict that recombination has been an important factor in the emergence of several major disease-causing strains from diverse genomic backgrounds and their ability to adapt to disparate environments.