The gut microbiomes of Channel Island foxes and island spotted skunks
exhibit fine-scale differentiation across host species and island
populations
Abstract
California’s Channel Islands are home to two endemic mammalian
carnivores: island foxes (Urocyon littoralis) and island spotted skunks
(Spilogale gracilis amphiala). Although it is rare for two insular
terrestrial carnivores to coexist, these known competitors persist on
both Santa Cruz Island and Santa Rosa Island. We hypothesized that
examination of their gut microbial communities would provide insight
into the factors that enable this coexistence, as microbial symbionts
often reflect host evolutionary history and contemporary ecology. Using
rectal swabs collected from island foxes and island spotted skunks
sampled across both islands, we generated 16S rRNA amplicon sequencing
data to characterize their gut microbiomes. While island foxes and
island spotted skunks both harbored the core mammalian microbiome, host
species explained the largest proportion of variation in the dataset. We
further identified intraspecific variation between island populations,
with greater differentiation observed between more specialist island
spotted skunk populations compared to more generalist island fox
populations. This pattern may reflect differences in resource
utilization following fine-scale niche differentiation. It may further
reflect evolutionary differences regarding the timing of intraspecific
separation. Considered together, this study contributes to the growing
catalog of wildlife microbiome studies, with important implications for
understanding how eco-evolutionary processes enable the coexistence of
terrestrial carnivores – and their microbiomes – in island
environments.