Body size modulates the extent of seasonal diet switching by large mammalian herbivores in Yellowstone National Park

Prevailing theories about animal foraging behaviours and the food webs they occupy offer divergent predictions about whether seasonally limited food availability promotes dietary diversification or specialisation. Emphasis on how animals compete for food predominates in work on the foraging ecology of large mammalian herbivores, whereas emphasis on how the diversity of available foods generally constrains dietary opportunity predominates work on entire food webs. Reconciling predictions about what promotes dietary diversification is challenging because species’ different body sizes and mobilities modulate how they seek and compete for resources—the mechanistic bases of common predictions may not pertain to all species equally. We evaluated predictions about five large-herbivore species that differ in body size and mobility in Yellowstone National Park using GPS-tracking and dietary DNA. The data illuminated remarkably strong and significant correlations between body size and five key in..., We obtained high-resolution diet profiles for pronghorn (Antilocapra americana; 48 kg adult body mass), bighorn sheep (Ovis canadensis; 75 kg), mule deer (Odocoileus hemionus; 85 kg), elk (Cervus canadensis; 241 kg), bison (Bison bison; 625 kg). Fresh dung samples from 1–5 individuals per herd were combined in approximately equal volume and thoroughly mixed. 
We extracted DNA from 371 fecal samples and amplified the chloroplast trnL-P6 marker using PCR (Taberlet et al., 2007). To obtain dietary profiles, we produced 2 x 150 bp paired-end Nextera libraries for sequencing on Illumina MiSeq. To identify dietary DNA sequences, we developed two reference libraries: the ‘local’ library comprised 191 unique trnL-P6 sequences from 416 specimens representing 45 plant families from Yellowstone; the ‘global’ library was built using data from the European Molecular Biology Laboratory (release 143), which yielded 21,422 unique trnL-P6 sequences representing at least 615 plant families.
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[https://doi.org/10.5061/dryad.h18931zst](https://doi.org/10.5061/dryad.h18931zst)

CHANGES: Version 2 (May 2024) shows updated files that include a name change for one plant taxa included in each file.

CHANGES: Version 3 (August 2024) shows updated R script for data analyses that includes the addition of habitat Bray-Curtis dissimilarity calculations and the creation of maps which show sample collection sites across Yellowstone National Park.  

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Python scripts, R scripts, and input/output files used to quantify fine-grained dietary variation within and among populations of five large-herbivore species (pronghorn, bighorn sheep, mule deer, elk, bison) in Yellowstone National Park, USA.

First, global (step 1) and local (step 2) reference libraries are built for the *trn*L-P6 locus. Raw sequence reads from large-herbivore fecal samples are then cleaned and prepare...