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

Large mammalian herbivores vary their diets markedly with changes in resource availability. Yet the ways that seasonal changes in individual foraging behaviors scale up to reconfigure complex trophic networks are poorly understood. Two years of dietary DNA data enabled us to quantify fine-grained dietary variation within and among populations of five large herbivore species at Yellowstone National Park, revealing remarkably strong and significant correlations between body size and five key indicators of diet seasonality (R2 = 0.71–0.80). Data from GPS collars implicated seasonal changes in each species’ movement- and habitat-use patterns as potential determinants of foraging constraints and specializations that give rise to the strong allometry in diet composition. Bison and elk showed relatively muted seasonal changes compared to smaller species that exhibited stronger switches. Whereas the taxonomic breadth of individual diets contracted for all species in winter, larger species gene..., 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.

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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 prepared (step 3) for taxonomy assignment (step 4). The taxonomies assigned using the local and global reference libraries are combined (step 5) and then analyses are conducted to determine correlations between body size and key indicators of diet seasona...