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.

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:

1. 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
2. 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
3. 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
4. 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
5. 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
6. 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

The .gen file has information regarding genotypes information for 237 Utah prairie dogs at 3,549 loci.