Genetic Links to Gut Microbiome Variation in the Yellow-Rumped Warbler Hybrid Zone

The gut microbiome is a dynamic ecosystem wherein microbes can exert beneficial, neutral or harmful effects on their host organism. Previous research has supported a large role for the environment in shaping avian gut microbiome diversity, but host-specific factors that regulate gut microbiome variation remain elusive. In hybrid zones, genetic recombination shuffles divergent alleles among backcrossed individuals allowing associations between genomic regions and specific traits to be identified. In this study, we use an association mapping approach to investigate the contribution of host alleles in shaping gut microbiome composition. We collected samples from across the Yellow-rumped Warbler hybrid zone (Setophaga coronata coronata × S. c. auduboni), including from distantly allopatric sites. The narrow width of this hybrid zone suggests that selection acts against hybrids, although the source of that selection is unclear. We quantified gut microbiome variation using 16S amplicon sequencing and produced genome-wide sequence data for hosts to link warbler genotypes to microbiome traits. This study is one of the first to identify candidate genes underlying gut microbiome variation in wild passerines. Notably, candidate loci include genes with immune function, redox status and gene regulation functions; two genes overlap with candidate genes identified in another avian system. Genetic differentiation was weak among candidate loci, indicating that alleles associated with gut microbiome variation are shared between subspecies. Our analysis of microbiome variation across nearly the full breeding range of an avian species complex yields important insights on the genetic factors that shape symbiotic interactions in vertebrate systems.