DOI: 10.5061/dryad.cnp5hqc2h
title: Spatial variation in diet-microbe associations across populations of a generalist North American carnivore

description: 1. Generalist species, by definition, exhibit variation in niche
 attributes that promote survival in changing environments. Increasingly,
 phenotypes previously associated with a species, particularly those with
 wide or expanding ranges, are dissolving and compelling greater emphasis
 on population-level characteristics. 2. In the present study, we assessed
 spatial variation in diet characteristics, gut microbiome, and the
 association between these two ecological traits across populations of
 coyotes (Canis latrans). We highlight the influence of the carnivore
 community in shaping these relationships, as the coyote varied from being
 an apex predator to a subordinate, mesopredator across sampled
 populations. 3. We implemented a scat survey across three distinct coyote
 populations in Michigan, USA. We used carbon (δ13C) and nitrogen (δ15N)
 isotopic values to reflect consumption patterns and trophic level,
 respectively. Corresponding samples were also paired with 16S rRNA
 sequencing to describe the microbial community and correlate with isotopic
 values. 4. Though consumption patterns were comparable, we found spatial
 variation in trophic level among coyote populations. Specifically, δ15N
 was highest where coyotes were the apex predator and lowest where coyotes
 co-occurred with gray wolves (Canis lupus). 5. The gut microbial community
 exhibited marked spatial variation across populations with the lowest OTU
 diversity found where coyotes occurred at their lowest trophic level.
 Bacteriodes and Fusobacterium dominated the microbiome and were positively
 correlated across all populations. We found no correlation between δ13C
 and microbial community attributes. However, positive associations between
 δ15N and specific microbial genera increased as coyotes ascended trophic
 levels. 6. Coyotes provide a model for exploring implications of niche
 plasticity because they are a highly adaptable, wide-ranging omnivore. As
 coyotes continue to vary in trophic position and expand their geographic
 range, we might expect increased divergence within their microbial
 community, changes in physiology, and alterations in behavior. 05-May-2020
description: We conducted systematic
 scat surveys from May-August 2016, collecting all carnivore feces found
 across our three study areas. Surveys occurred monthly for 7-10 days,
 utilizing hiking paths and wildlife trails, and usually included all
 available habitat types within the study area. We made concerted efforts
 during fieldwork to collect mostly “fresh” scat and collected from
 interior region to reduce contamination with collection tools cleaned with
 ethanol between samples. Opportunistic findings by other researchers,
 volunteers, and park rangers presumed to be carnivore were also included.
 Samples were stored in two of three liquid preservation solutions: DET,
 RNAlater or EtOH in 10ml sterile plastic vials as well as dry in sterile
 bags. However, nearly 3/4 of samples used for analysis were preserved in
 EtOH. All samples were stored at -20°C upon returning from the field until
 processed. Wet samples were used for molecular host confirmation and
 microbial community analysis while dry samples were processed for stable
 isotope analysis.