Inference of symbiotic adaptations in nature using experimental evolution

Microbes must adapt to the presence of other species, but it can be difficult to recreate the natural context for these interactions in the laboratory.  We describe a method for inferring the existence of symbiotic adaptations by experimentally evolving microbes that would normally interact in an artificial environment without access to other species.  By looking for changes in the fitness effects microbes adapted to isolation have on their partners, we can infer the existence of ancestral adaptations that were lost during experimental evolution.  The direction and magnitude of trait changes can offer useful insight as to whether the microbes have historically been selected to help or harm one another in nature.  We apply our method to the complex symbiosis between the social amoeba Dictyostelium discoideum and two intracellular bacterial endosymbionts, Paraburkholderia agricolaris and P. hayleyella.  Our results suggest P. hayleyella – but not P. agricolaris – has generally been select...