Impacts of proactive health management on cattle and horse diets and dung biodiversity in Danish rewilding areas

Reintroducing megafauna to reinstate missing top-down trophic interactions (trophic rewilding) is increasingly being applied as a tool to promote self-regulating, biodiverse ecosystems. Even though the theoretical background is clear, and megafauna effects are documented from prehistoric ecosystems, the effects of reintroduced herbivores in contemporary ecosystems remain understudied. This includes how reintroduced megafauna interact with each other and the ecosystem, but also how current management practices affect the processes they provide. In this study, we investigated the effects of proactive health management, i.e., winter feeding and anti-parasitic treatments, on the ecosystem by examining diets of large herbivores and dung-associated invertebrate communities. We used environmental DNA metabarcoding to yield community compositions of plants and invertebrates in dung from cattle and horses from five comparable nature sites in Denmark, which differed in management, and site/p..., The dataset consists of DNA reads from high-throughput sequencing of 295 dung samples from cattle and horses collected at five sites in Denmark in 2022. From each of the five sites, 7 samples from cattle and 7 samples from horses (except the NM site where no horses were present) were collected in February, March, April, Jun,e and August, respectively. At each sampling event, a field blank was collected and sequenced alongside the other samples (see associated manuscript for details). Twenty-two of these samples (10 from the ML and SL sites respectively, and two field blanks collected in August) were sequenced alongside (and will also be used in) another project, and was thus not part of this raw data, but the filtered data from these samples are added as separate files (see description further below) and should be appended to the main dataset for the subsequent analysis.   
DNA was extracted from the samples with the Fast DNA Stool Mini Kit from Qiagen, and amplified by PCR re..., # Impacts of proactive health management on cattle and horse diets and dung biodiversity in Danish rewilding areas

**Content of this data repository:**

1. A compressed repository (.tar.gz) is uploaded for each dataset (ITS & COI). Each repository includes a directory for each library containing two raw sequencing output files (end in .fq.gz).
2. A compressed repository (tagfiles.tar.gz) including all the files for demultiplexing (one for each library, ends in tags.txt).
3. An example file for each dataset to use in MetaBarFlow (example_batchfileDADA2.list)
4. The following output files from MetaBarFlow for each dataset (file names start with RWDK_COI\_ and RWDK_ITS_*, respectively):
1. *classified.txt (the original taxonomic classification file of ASVs from MetaBarFlow)
2. *classified_corrected.txt (the manually corrected taxonomy file)
3. *DADA2_nochim.otus (List of all ASVs defines by MetaBarFlow)
4. *DADA2_nochim.table (ASV/sample read count matrix
5. The files containi...,