The microbiome responds to Evolve and Resequence experiments in Drosophila melanogaster

Abstract

BackgroundExperimental evolution has a long history of uncovering fundamental insights into evolutionary processes, but has largely neglected one underappreciated component--the microbiome. As eukaryotic hosts evolve, the microbiome may also evolve. However, the microbial contribution to host evolution remains poorly understood. Here, we re-analyzed genomic data to characterize the metagenomes from ten Evolve and Resequence (E&R) experiment in Drosophila melanogaster to determine how the microbiome changed in response to host selection. ResultsBacterial diversity was significantly different in 5/10 studies, primarily in traits associated with metabolism or immunity. Duration of selection did not significantly influence bacterial diversity, highlighting the importance of associations with specific host traits. Additionally, we find that excluding reads from a facultative symbiont, Wolbachia, in the analysis of bacterial diversity changes the inference, raising important questions for future E&R experiments in the D. melanogaster microbiome. ConclusionsOur genomic re-analysis suggests the microbiome often responds to host selection; thus, the microbiome may contribute to the response of Drosophila in E&R experiments. We outline important considerations for incorporating the microbiome into E&R experiments. The E&R approach may provide critical insights into host-microbiome interactions and fundamental insight into the genomic basis of adaptation.