Data for "Urbanization and host relatedness shape virome composition in a widespread, generalist carnivore"
This dataset contains virome data and related host data for bobcats sampled at the wildland-urban interface in Tucson, AZ, USA, between 2020-2023. DNA/RNA from scats (n=31) and buccal swabs (n=17) were used for virome sequencing. Virome next-generation sequencing libraries were hybridized using the Twist Comprehensive Viral Research Panel, followed by sequencing on a NextSeq 500 (2x75bp). Viral contigs were assembled by metaSPAdes v. 3.13.0 and MEGAHIT v. 1.1.3 as implemented in the metaWRAP pipeline v. 1.3.2. Here, we provide viral occurrence data (presence-absence) for contigs grouped by genus as viral taxonomic units (vOTUs). This data is provided for both sample types together, as well as for scats and swabs independently. For bobcats which also had SNP data generated from ddRADseq (https://doi.org/10.5061/dryad.7h44j104h), genotype information is provided in a genepop (.gen) file. Individual metadata is also provided, including sex, sample type used for viromics (scat, swab, or both), and latitude/longitude/date of capture. For Mantel tests, genetic distance was calculated as DPS (1 – the proportion of shared alleles) using the R package adegenet, geographic distance was calculated as Euclidean distance between UTM coordinates using the dist() function in R, and virome beta-diversity was calculated as Jaccard distance using the R package vegan.
For inquiries regarding the contents of this dataset, please contact the Corresponding Author listed in the README.txt file. Administrative inquiries (e.g., removal requests, trouble downloading, etc.) can be directed to data-management@arizona.edu
For inquiries regarding the contents of this dataset, please contact the Corresponding Author listed in the README.txt file. Administrative inquiries (e.g., removal requests, trouble downloading, etc.) can be directed to data-management@arizona.edu
