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The gut microbiomes of Channel Island foxes and island spotted skunks exhibit fine-scale differentiation across host species and island populations
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  • Samantha Pasciullo Boychuck,
  • Lara Brenner,
  • Calypso Gagorik,
  • Juliann Schamel,
  • Stacy Baker,
  • Elton Tran,
  • Bridgett von Holdt,
  • Klaus-Peter Koepfli,
  • Jesús Maldonado,
  • Alexandra DeCandia
Samantha Pasciullo Boychuck
Georgetown University
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Lara Brenner
The Nature Conservancy
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Calypso Gagorik
Northern Arizona University
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Juliann Schamel
National Park Service
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Stacy Baker
National Park Service
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Elton Tran
Princeton University
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Bridgett von Holdt
Princeton University
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Klaus-Peter Koepfli
Smithsonian-Mason School of Conservation
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Jesús Maldonado
Smithsonian's National Zoo and Conservation Biology Institute
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Alexandra DeCandia
Georgetown University

Corresponding Author:alexandradecandia@gmail.com

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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.