Data From: Characterizing patterns of genomic variation in the threatened Utah prairie dog: implications for conservation and management

Tissue Collection: We trapped Utah prairie dogs and collected hair and whiskers during a field trial of a sylvatic plague vaccine (Rocke et al., 2017). Samples were collected in 2014 from two plots within each site (assumed to be a single prairie dog colony), with plots located in proximity (0.15 – 2.10 km). Due to a high degree of movement between plots observed during the vaccine field trial, plots were treated as a single site for our analyses. Individuals were sampled throughout the Utah prairie dog range at three sites near Cedar City and Panguitch, Utah (CCUT) and four high-elevation sites within the Awapa Plateau (HEUT). DNA Collection and Sequencing: To generate single nucleotide polymorphisms (SNPs), samples with greater than 300 ng of total genomic DNA, quantified using a Qubit 2.0 Fluorometer (Invitrogen), were used for double digest restriction site-associated DNA sequencing (ddRAD) (Peterson et al., 2012). Genomic DNA was digested using the restriction enzymes HindIII and NlaIII, barcoded, and size selected for 250- to 500-bp fragments using a Pippin Prep (Sage Sciences). Fragments were paired-end sequenced on an Ilumina NovaSeq6000 at Texas A&M AgriLife Genomics. We aligned sequences to a Gunnison’s prairie dog (Cynomys gunnisoni) genome (Tsuchiya, Dikow, & Cassin-Sackett, 2020) using the BWA short-read aligner with default parameters and the MEM alignment algorithm (Li & Durbin, 2009). Contigs were assembled using the program STACKS v.1.48 software (Catchen et al., 2011, 2013), following the proposed workflow outlined by Rochette and Catchen (2017). After calling SNPs, several additional quality control measures were taken. First, in cases where more than 1 SNP per contig was present, only the first (most 5’) SNP was used. Second, only loci represented in 80% or more of individuals were retained. Third, only loci present in all 14 sampling locations were retained. Fourth, because low-frequency alleles may represent PCR errors, we removed loci with minor allele frequencies <0.05. Fifth, we removed potential paralogs by excluding loci with an observed heterozygosity exceeding 0.7 using the populations module of STACKS. These filters were used to make the .gen file in DRYAD. Additional filters, as outlined in our Evolutionary Applications article, were used for our analyses. References: Rocke, T. E., Tripp, D. W., Russell, R. E., Abbott, R. C., Richgels, K. L. D., Matchett, M. R., … Miller, M. W. (2017). Sylvatic plague vaccine partially protects prairie dogs (Cynomys spp.) in Field Trials. EcoHealth, 14(3), 438–450. https://doi.org/10.1007/s10393-017-1253-x Tsuchiya, M. T. N., Dikow, R. B., & Cassin-Sackett, L. (2020). First genome sequence of the Gunnison’s prairie dog (Cynomys gunnisoni), a keystone species and player in the transmission of sylvatic plague. Genome Biology and Evolution, 12(5), 618–625. https://doi.org/10.1093/gbe/evaa069 Li, H., & Durbin, R. (2009). Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 25(14), 1754–1760. https://doi.org/10.1093/bioinformatics/btp698 Catchen, J. M., Amores, A., Hohenlohe, P., Cresko, W., & Postlethwait, J. H. (2011). Stacks: Building and genotyping loci de novo from short-read sequences. Genes|Genomes|Genetics, 1(3), 171–182. https://doi.org/10.1534/g3.11000240 Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A., & Cresko, W. A. (2013). Stacks: An analysis tool set for population genomics. Molecular Ecology, 22(11), 3124–3140. https://doi.org/10.1111/mec.12354 Rochette, N. C., & Catchen, J. M. (2017). Deriving genotypes from RAD-seq short-read data using Stacks. Nature Publishing Group, 12(12), 2640–2659. https://doi.org/10.1038/nprot.2017.123