RADseq data from eighteen species of snake and lizard from New Mexico Raw sequence reads. Squamate reptiles

While key elements of fitness in vertebrate animals are impacted by their gut microbiome community, the set of host genetic traits that drive microbiome composition and therefore can be selected on by the host-microbiome relationship is not fully understood. Using the correlation between host genetic diversity and gut microbiome phylogenetic diversity across a community of reptiles, we test hypotheses about the behavior of host genes that drive microbiome assembly. We find that microbiome communities are phylogenetically under-dispersed relative to random expectations, and host genetic diversity is not correlated with microbiome diversity. Our analyses reinforce results from host functional genomic work that identifies conserved host immune genes as key players in microbiome assembly. Our finding, in context of an emerging consensus that microbiomes are predictably differentiated at the host family level, indicates that host-microbiome relationships generally evolve slowly relative to host speciation rates. This pattern indicates that rapid host-microbiome evolution may be mediated by factors outside of strict host genetic changes.