DOI: 10.5061/dryad.tqjq2bvxn
title: Data From: Characterizing patterns of genomic variation in the threatened Utah prairie dog: implications for conservation and management

description: Utah prairie dogs (Cynomys parvidens) are federally threatened due to
 eradication campaigns, habitat destruction, and outbreaks of plague.
 Today, Utah prairie dogs exist in small, isolated populations, making them
 less demographically stable and more susceptible to erosion of genetic
 variation by genetic drift. We characterized patterns of genetic structure
 at neutral and putatively adaptive loci in order to evaluate the relative
 effects of genetic drift and local adaptation on population divergence. We
 sampled individuals across the Utah prairie dog species range and
 generated 2,955 single nucleotide polymorphisms (SNPs) using double digest
 restriction site associated DNA sequencing (ddRAD). Genetic diversity was
 lower in low elevation sites compared to high elevation sites. Population
 divergence was high among sites and followed an isolation-by-distance
 (IBD) model. Our results indicate that genetic drift plays a substantial
 role in the population divergence of the Utah prairie dog, and colonies
 would likely benefit from translocation of individuals between recovery
 units, which are characterized by distinct elevations, despite the
 detection of environmental associations with outlier loci. By
 understanding the processes that shape genetic structure, better informed
 decisions can be made with respect to the management of threatened species
 to ensure that adaptation is not stymied.
description: 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
 <i>HindIII</i> and <i>NlaIII</i>,
 barcoded,<i> </i>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
 (<i>Cynomys gunnisoni</i>) 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 &lt;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. <i>EcoHealth</i>,
 <i>14</i>(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. <i>Genome Biology and Evolution</i>, 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. <i>Bioinformatics</i>, <i>25</i>(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. <i>Genes|Genomes|Genetics</i>, <i>1</i>(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. <i>Molecular Ecology</i>, <i>22</i>(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. <i>Nature Publishing Group</i>, <i>12</i>(12), 2640–2659. https://doi.org/10.1038/nprot.2017.123
description: The .gen file has information regarding genotypes information for
 237 Utah prairie dogs at 3,549 loci.