The emergence of symbiotic interactions has been studied using population genomics in nature and experimental evolution in the laboratory, but the parallels between these processes are unknown. We compared the genetic patterns associated with the emergence of rhizobia after the horizontal transfer of a symbiotic plasmid in natural populations of Cupriavidus taiwanensis, over 10 MY ago, with an evolution experiment of Ralstonia solanacearum for a few hundred generations. In spite of major differences in terms of time-span, environment, genetic background and phenotypic achievement, both processes resulted in rapid diversification dominated by purifying selection concomitant with acquisition of key adaptive mutations. None of the processes produced adaptive mutations in the plasmid carrying the genes responsible for the ecological transition. Early stages of the adaptation to symbiosis involved the co-option of the same set of master regulators. Our results provide evidence for similarities in experimental and natural evolutionary transitions and highlight the potential of comparisons between both processes to guide experimentation on the molecular mechanisms driving symbiosis.
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