Data from: Genomic diversity of cougars across Utah: Evidence for latitudinal differentiation in a continuous population
Data files
Mar 05, 2026 version files 702.12 MB
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admixture_popmap_lat_long.csv
26.49 KB
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cougar_ddRAD24_FinalFilter_LDthin_RelativesRemoved.vcf
238.32 MB
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cougar_ddRAD24_FinalFilter.vcf
461.91 MB
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cougar_ddRAD24_relatedness.csv
1.77 MB
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Metadata_cougar_ddRAD24_FinalFilter_LDthin_RelativesRemoved.csv
20.50 KB
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README.md
4.71 KB
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UT_Pumas.R
13.61 KB
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UtahNames.csv
46.61 KB
Abstract
Genetic data on wide-ranging wildlife species can inform population structure, management decisions, and landscape connectivity. The genetic structure of a population can change over time, alongside changes to population size and connectivity. We analyzed the population structure and genetic diversity of 316 cougars (Puma concolor) from Utah and southeastern Idaho using 24,597 single nucleotide polymorphisms (SNPs) generated from double digest restriction-site associated DNA (ddRAD) sequencing. We found linear trends in population structure across a latitudinal gradient but no support for distinct genetic populations. Similar to the findings of previous genetic studies, the cougar population in Utah remains well-connected, despite increased habitat fragmentation and urbanization over the last 30 years. Our results suggest a mismatch between the scale of the functional landscape for cougars and the wildlife management units used for cougar management. Our findings highlight the need to increase collaborative management over jurisdictional boundaries for wide-ranging species, such as the cougar.
Dataset DOI: 10.5061/dryad.v6wwpzh9g
Files and variables
1. cougar_ddRAD24_FinalFilter.vcf
Filtered Variant Call Format (VCF) file contains Single Nucleotide Polymorphism (SNP) data. Source: Stacks v2.2
2. cougar_ddRAD24_FinalFilter_LDthin_RelativesRemoved.vcf
Filtered Filtered Variant Call Format (VCF) file contains Single Nucleotide Polymorphism (SNP) data, subset to include only one random SNP per locus and to remove individuals flagged as close relatives. The final dataset contains 24,597 SNPs and 316 individuals. Source: Stacks v2.2
3. Metadata_cougar_ddRAD24_FinalFilter_LDthin_RelativesRemoved.csv
Metadata for cougar samples contained in final filtered dataset (cougar_ddRAD24_FinalFilter_LDthin_RelativesRemoved.vcf)
Variables
- SampleID: unique sample id number (UT indicates samples collected from Utah and ID indicates samples collected from Idaho)
- ClientID: alternative sample id used for archived tissue samples
- Barcode: barcode sequence assigned to sample during ddRAD library preparation
- Well: location of sample on ddRAD library preparation plate
- Library: library samples was assigned to during ddRAD library preparation and sequencing
- County: County within Utah / Idaho where sample was collected
- Updated_SampleID: sample id as listed in VCF files
- Latitude: approximate latitude
- Longitude: approximate longitude where sample was collected
4. cougar_ddRAD24_relatedness.csv
Estimates of pairwise relatedness between all samples. Source: VCFtools
Variables
- INDV1: id of first sample in pairwise comparison
- INDV2: id of second sample in pairwise comparison
- RELATEDNESS_AJK: estimated pairwise relatedness coefficient (Ajk)
4. UT_Pumas.R
R code used for data visualization and analyses.
5. admixture_popmap_lat_long.csv
Output of K=2 ADMIXTURE results. Used as input in UT_Pumas.R
Variables
- Column A: (equivalent to SampleID) unique sample id number (UT indicates samples collected from Utah and ID indicates samples collected from Idaho)
- Column B: approximate latitude where sample was collected
- Column C: approximate longitude where sample was collected
- Column D: (equivalent to Updated_SampleID) sample id as listed in VCF files
- Column E: county within Utah / Idaho where sample was collected
- Column F: alternative classification of sample collection location (used for data visualization and clustering purposes)
- Column G: alternative classification of sample collection location (used for data visualization and clustering purposes)
- Column H: alternative numerical classification of sample collection location (used for data visualization and clustering purposes)
- Column I: library samples was assigned to during ddRAD library preparation and sequencing
- Column J: ADMIXTURE cluster 1 estimate
- Column K: ADMIXTURE cluster 2 estimate
6. UtahNames.csv
Sample metadata information required as input for UT_Pumas.R
Variables
- index: row number
- x (equivalent to SampleID): unique sample id number (UT indicates samples collected from Utah and ID indicates samples collected from Idaho)
- ClientID: alternative sample id used for archived tissue samples
- SampleDate: date sample was collected (mm/dd/yyyy), listed as "unknown" if date of collection was not available
- Region.St: UTDWR management unit within which sample was obtained (not applicable for Idaho samples which are just listed as "Idaho")
- County: county within Utah / Idaho where sample was collected
- Latitude: approximate latitude
- Longitude: approximate longitude where sample was collected
- Source_of_Coordinates: description of how sample collection location accuracy was determined (e.g., estimated based on information provided by the sample collector, exact coordinates provided, etc.)
- OtherLocation: contains additional information, such as coordinates, provided by sample collector, if applicable (if no additional information was provided, field is the same as "Source_of_Coordinates")
- LocationDescription: description of sample collection location provided by sample collector (NA if no additional information was provided)
- AgeClass.jn: age class of collected sample, listed as "Unknown" if no age information was available
- SexCat: sex of collected sample (M= male, F=female, Unk=sex unknown)
Access information
Other publicly accessible locations of the data:
- Raw sequencing data generated from this study are available at NCBI's Sequence Read Archive [PRJNA1399492].