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.

Rapid shifts in environmental variables associated with elevational changes in montane ecosystems provide opportunities to test hypotheses regarding the effects of environmental heterogeneity on gene flow and genetic structure. In tropical mountains, spatial environmental heterogeneity combined with seasonal environmental stability is predicted to result in low dispersal across elevations. Few studies have investigated the genetic consequences of elevational environmental heterogeneity in tropical montane mammals. Here, we use a population genomics approach to test the hypothesis that mountain treeshrews (Tupaia montana) exhibit limited gene flow across elevational gradients and between two neighboring peaks within Kinabalu National Park (KNP) in Borneo. We sampled 83 individuals across elevations on Mt. Tambuyukon (MT) and Mt. Kinabalu (MK) and sequenced mitogenomes and 4,106 ultraconserved elements containing an average of 1.9 single nucleotide polymorphisms per locus. We detected high gene flow across elevations and between peaks. We found greater genetic differentiation on MT than MK despite its lower elevation and associated environmental variation. This implies that, contrary to our hypothesis, genetic structure in this system is not primarily shaped by elevation. We propose that this pattern may instead be the result of colonization history combined with restricted upslope gene flow on MT due to unique plant communities associated with its upper montane habitats. Our results serve as a foundation to identify and mitigate future effects of climate change on mountain treeshrews in KNP. Given predictions for 2100 CE, we predict that mountain treeshrews will maintain genetic connectivity in KNP, making it an important conservation stronghold.