DOI: 10.5061/dryad.j0zpc86h8
title: Dietary metabarcoding datasets for the southern meadow jumping mouse (Zapus luteus luteus)

description: The southern meadow jumping mouse (Zapus luteus luteus) is Endangered in
 the US due to loss of riparian habitat and knowledge of diet can focus
 conservation efforts. Context and life stages of diet have been documented
 for other species of Zapus (seeds, insect larvae, and hypogeous fungi),
 possibly shifting toward greater diversity in seed predations prior to
 hibernation. Yet, challenges in field observation, thorough digestion, and
 lack of scalability have hindered a thorough survey of dietary taxonomies.
 We collected the feces of 165 Z. l. luteus from across the geographic
 range. Emphasizing granivorous diet, we used DNA metabarcoding to resolve
 its dietary taxonomies. With negligible impact of field contamination, we
 found a varied diet most frequently of graminoids, forbs, and lepidoptera.
 Detecting up to nine dietary taxa in individuals, Z. l. luteus consumed
 more and different combinations of plant taxa as they approached the known
 hibernation window. Our work emphasizes the importance of forbs and
 graminoids as the foundation of the diet, providing primary sustenance and
 habitat for insect prey. The breadth of different diet items they consume
 suggests plasticity in resource use, potentially accommodating diverse
 patterns of seed production throughout their active period. We also
 hypothesize that a peak in seed availability in the late season could play
 a role in their accumulation of pre-hibernation fat stores.
description: We PCR amplified five DNA metabarcode markers (plant ITS2, plant
 rbcL, arthropod COI, fungal ITS2, and rodent cytochrome B) among two PCR
 multiplex reactions from the fecal DNA of <em>Zapus luteus
 luteus.</em> Libraries were prepared with strict non-combinatorial
 indexing and sequenced on an Illumina MiSeq V3 600 cycle kit (SRA
 BioProject accession: PRJNA833142). We demultiplexed samples and markers
 and processed data for marker datasets separately. Briefly we denoised and
 merged paired-end reads, post-clustered plant markers for diversity
 analysis, used a 1.1% relative read abundance filter to avoid exogneous
 contaminants and spurious features, filtered to exclude off-target
 amplifications within each marker, and classified using Naive Bayes
 classifiers. We used the cytochrome B marker to verify that the fecal
 sample belonged to <em>Zapus luteus luteus </em>(classified
 using BLAST alignment to NCBI and least common ancestor classification).
 Any fecal sample with the identifying DNA of other sympatric rodents was
 excluded from the dataset. We also sequenced bait used for live capture
 and excluded any features found in the bait from the entire dataset.
 Taxonomies were cross-referenced to a local database of plants available
 at capture localities or state-wide and national databases, and then
 collapsed a classification to a higher taxonomic level if the taxa were
 not known to occur there. Of the fungal taxonomies, we only retained
 hypogeous fungal taxa based on our study objectives. Both
 collapsed-filtered and annotated-unfiltered versions of the dataset are
 available. Diversity analyses (alpha and beta diversity) are limited to
 two study areas based on consistency in trapping and fecal sampling. Both
 diversity datasets have been rarified to 2500 reads following rarefaction
 analysis.
description: R scripts are available for statistical analyses of alpha and
 beta diversity. Datasets used as input and analysis procedures are noted
 at the beginning of and throughout the scripts. Please see README_file.txt
 for more information regarding the R scripts or contents of the
 datasets.