Data from: Isolation by distance promotes gut microbial strain divergence in wild mouse populations

Bacterial species within the mammalian gut microbiota exhibit considerable
strain diversity associated with both geography and host genetic ancestry.
However, because geography and ancestry are typically confounded,
disentangling their contributions to the divergence of gut bacterial
strains has remained challenging. Here, we show that isolation by distance
(IBD) promotes gut bacterial strain divergence within host species
independently of host ancestry. Joint profiling of gut bacterial and
mitochondrial genomes from wild-living populations of deer mice
(Peromyscus maniculatus) sampled across the United States revealed
significant IBD in 27 predominant gut bacterial species, including
Muribaculaceae and Lachnospiraceae spp., but limited evidence for
co-inheritance of gut bacterial genomes with mitochondria during the
diversification of mouse populations. Spore-forming gut bacterial species
exhibited reduced IBD, suggesting that adaptations facilitating bacterial
dispersal can lessen geographic structuring of strain diversity. In
contrast to conspecific hosts sampled at the same field site, hosts of
different rodent genera sampled in sympatry with deer mice harbored
divergent strains within shared gut bacterial species. These results
indicate that geographic distance mediates the early stages of gut
bacterial strain divergence between conspecific hosts, whereas effects of
host ancestry on strain-level microbiota composition emerge over longer
evolutionary timescales, such as those separating host genera.