DOI: 10.5061/dryad.j9kd51cjp
title: Data from: Metabarcoding analysis provides insight into the link between prey and plant intake in a large alpine cat carnivore, the snow leopard

description: Species of the family Felidae (a group represented by cats) are thought to
 be obligate carnivores, specialized for hunting and consuming other
 animals. However, the detection of plants in the feces of felids raises
 questions about the role of plants in their diet. This is particularly
 true for the snow leopard (Panthera uncia), a big cat native to central
 and South Asia's high mountains. Our study aimed to
 comprehensively identify the prey and plants consumed by snow leopards as
 well as six other sympatric mammals. We applied DNA metabarcoding methods
 on 126 fecal samples collected from the Sarychat-Ertash Nature Reserve in
 Kyrgyzstan. We found that among the three most common plant
 families in snow leopard feces, Tamaricaceae (genus Myricaraia) was
 consumed often by snow leopards. The genus Myricaria frequently appeared
 in samples lacking any animal prey DNA, indicating that snow leopards
 might have consumed this plant especially when their digestive tracts were
 empty. We also observed a significant difference in plant composition
 between male and female snow leopards, and potentially between sampling
 seasons. We provide a comprehensive overview of the prey and
 plants detected in the feces of snow leopards and sympatric mammals. We
 believe our findings will help in formulating hypotheses and guiding
 future research to understand the adaptive significance of plant-eating
 behavior in felids and animal-plant relationships in the ecosystem.
description: # Metabarcoding analysis insights into the link between prey and plant
 intake in the alpine large cat carnivore, snow leopard
 [https://doi.org/10.5061/dryad.j9kd51cjp](https://doi.org/10.5061/dryad.j9kd51cjp) These files are datasets and scripts to generate data in "Metabarcoding analysis insights into the link between prey and plant intake in the alpine large cat carnivore, snow leopard" Illumina sequencing data was demultiplexed using bcl2fastq and Claident. After trimming primer sequences using Skewer, error collection, and OTU collation were conducted using scripts in miseq_.Rmd files. *T*axon assignment was conducted using Claident and results are in QCidentified files. Metadata, OTU table, and taxonomy table were integrated into phyloseq (McMurdie & Holmes., 2013, PLOS ONE.) object by scripts in afterClaident*.Rmd files. Data from different barcode regions were merged using mergeMarkers.Rmd file and a python3 script by da Silva et al. (2019). Subsequent statistical analysis was conducted using other.Rmd files. ## Description of the data and file structure * miseq*.Rmd are Rmarkdown files for processing Illumina sequencing data. The resulting OTU tables are OTU_table*.RData files. * metadata*.xlsx contains metadata of each sample. The precision of the geographic coordinates was decreased to generalize the location information of threatened species. Data for unused samples were marked as NA. * QCidentified* files are the results of taxonomy assignment by QCauto algorithm using Claident software (Tanabe & Toju., 2013, PLOS ONE.). * OTU_table*.RData are OTU tables collated with LULU (Frøslev et al., 2017, Nature Communications.) * track*.csv includes the number of reads recorded in each filtering process. * afterClaident*.Rmd are Rmarkdown files creating phyloseq objects and conducting filtering and rarefaction. * mergeMarkers.Rmd is an Rmarkdown file to prepare input for merge_markers.py (da Silva et al., 2019, Molecular Ecology Resources.). * Dietary metric.Rmd is a Rmarkdown file receiving merged data and converting it to pyloseq. It also calculates FOO and wPOO to generate figures. * Cooccur.Rmd is a Rmarkdown file conducting a post-hoc co-occurrence analysis (Griffith et al., 2016, Journal of Statistical Software.) * NMDS.Rmd is a Rmarkdown file depicting NMDS plots and conducting PERMANOVA. * CAP*.Rmd are Rmakrdown files conducting CAP with wPOO and FOO datasets, respectively. * Randomforest*.Rmd are Rmakrdown files conducting RandomForest with wPOO and FOO datasets, respectively. ## Sharing/Access information Sequence data is available here: DDBJ BioProject (PRJDB16690) ## Code/Software bcl2fastq v2.20.422 Skewer Claident v0.9.2022.04.28 VSEARCH v2.21.1 R version 4.2.2 (2022-10-31) Python 3.10.10