Applying Evolutionary Theory to Understand Host-Microbiome Evolution: New Tricks for Old Dogs

Bob Week, Shelbi L. Russel, Hinrich Schulenburg, Brendan J. M. Bohannan, Marjolein Bruijning

All plants and animals are host to a community of microorganisms, their microbiomes, that have crucial influences on the life history and performance of their hosts. Despite the importance of such host-microbiome relationships, relatively little is known about the role microbiomes play in mediating evolution of the host as well as entire host-microbe assemblages. This knowledge gap is partly due to the lack of theoretical frameworks that generate testable predictions on the evolutionary dynamics of host-microbiome systems. In this Perspective, we argue that the foundation for such frameworks exists in evolutionary theory. We highlight four examples of theoretical models - niche construction, indirect genetic effects, maternal effects and multilevel selection – that capture important aspects of host-microbiome evolution. We outline how each of these frameworks can provide key insights into the \hl{evolution of host-microbiome systems} while also suggesting expansions of current theory to incorporate processes unique to host-microbe assemblages, for instance focusing on nuances in microbiome transmission and ecological microbial community dynamics. Expanding evolutionary theory to accommodate host-microbiome systems is key for a more integrative understanding of evolution, which is undoubtedly impacted by the association with microorganisms, guiding future empirical research on the function and evolution of these omnipresent interactions.