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 indicators of diet seasonality (R2 = 0.71-0.80). Compared to smaller species, bison and elk showed muted diet seasonality and maintained access to more unique foods when winter conditions constrained food availability. Evidence from GPS collars revealed size-based differences in species’ seasonal movements and habitat-use patterns, suggesting that better accounting for the allometry of foraging behaviours may help reconcile disparate ideas about the ecological drivers of seasonal diet switching.

Methods
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.

FastQC was used to ensure that both per-base and per-sequence quality scores exceeded Q20, and primers were removed from forward and reverse reads using cutadapt. All further sequence identifications were performed using obitools; forward and reverse sequences were aligned using the illuminapairedend command using a minimum alignment score of 40, and only joined sequences were retained. We used the obiuniq command to group identical sequences and tally them within samples, enabling us to quantify the relative read abundance (RRA) of each sequence. Sequences that occurred ≤2 times overall or that were <8 bp or >300bp were discarded. Sequences were considered to be likely PCR artifacts if they were highly similar to another sequence (1 bp difference) and had a much lower abundance (0.05%) in the majority of samples in which they occurred; we discarded these sequences using the obiclean command.

When inferring the taxonomy of dietary sequences to be included in the final diet profiles, we required a 100% match between each dietary sequence and a reference sequence from at least one of the libraries. After removing one sample with <1000 sequence reads, we rarefied the data to equal read counts (N = 1,453 reads per sample). The final dataset included 370 samples (25–162 per large herbivore species) and 685 plant taxa (94% identified to family, 65% to genus, and 42% to species). The taxonomic assignment of plant taxa was used to characterize plant functional types using the USDA Plants Database and the expert opinion of Yellowstone National Park’s botanists.