Data from: Comparing microsatellites and single nucleotide polymorphisms to evaluate genetic structure and diversity in wolverines (Gulo gulo) across Alaska and western Canada
Data files
Jan 09, 2025 version files 161.77 MB
-
gulo_msat_all_genotyped.csv
54.68 KB
-
gulo_msat_related_removed.csv
50.76 KB
-
gulo_snp_all_thinned_outliers_removed.vcf
31.09 MB
-
gulo_snp_all_thinned.vcf
32.98 MB
-
gulo_snp_all.vcf
93.89 MB
-
gulo_snp_related_removed.vcf
3.68 MB
-
msat_genotyped_related_removed.txt
266 B
-
outliers_removed.txt
3.40 KB
-
README.md
1.92 KB
-
snp_genotyped_related_removed.txt
179 B
-
UA_Museum_Samples_Loaned.xlsx
10.84 KB
Abstract
The Wolverine (Gulo gulo) is a cold-adapted species of conservation interest because it is sensitive to human development, disturbance, exploitation, and climate warming. Wolverine populations have been studied across much of their distributional range to evaluate patterns of genetic diversity, genetic structure, and gene flow. Little population structure has been detected in northwestern North America with microsatellite loci, but low genomic diversity in wolverines may limit detection of genetic differences in this highly vagile species. Here, we genotyped a relatively large sample of wolverines from across Alaska (US) and adjacent Yukon (Canada) with 12 microsatellite loci (n = 501) and 4,222 single nucleotide polymorphisms (SNPs; n = 201) identified using restriction-site associated DNA sequencing. We compared the relative ability of our microsatellite and SNP datasets to evaluate population genetic structure, genetic diversity, differentiation, and isolation by distance (IBD). We predicted that the SNP dataset would detect a higher degree of genetic structure and provide more significant support for IBD. We found evidence for multiple genetic clusters, including genetic distinctiveness of wolverines in southeast Alaska and on the Kenai Peninsula. The SNP dataset detected additional genetic clusters which align largely with ecoregions, and the SNP dataset showed stronger evidence of IBD, while the 2 datasets were generally consistent in estimates of genetic diversity and differentiation among regional groups. Our results highlight the importance of genomic methods to assess gene flow in wolverines. Identifying population genetic structure allows an assessment of the potential impacts of conservation threats and is an important precursor for designing population monitoring programs.
README: Comparing microsatellites and single nucleotide polymorphisms to evaluate genetic structure and diversity in wolverines (Gulo gulo) across Alaska and western Canada
https://doi.org/10.5061/dryad.crjdfn3dz
Description of the data and file structure
SNPs were discovered via restriction site-associated DNA sequencing. Sample location data contains sensitive trap line location information and can be requested with an added location buffer.
UA Museum Samples Loaned: Excel file of University of Alaska Museum of the North tissue archive identification numbers and lab sample identification labels. Includes some individuals not successfully genotyped in microsatellite and/or SNP datasets.
Microsatellite data files:
gulo_msat_all_genotyped: CSV of all microsatellite genotypes for all individuals, missing data encoded as -1
gulo_msat_related_removed: CSV of microsatellite genotypes for all individuals with highly related individuals removed, missing data encoded as -1
msat_genotyped_related_removed: TXT of lab identification labels of related microsatellite genotyped individuals removed
SNP data files: See github for RAD seq data processing code https://github.com/elisestacy
gulo_snp_all: VCF of SNP genotypes of unthinned loci, outlier loci not removed, and including all individuals
gulo_snp_all_thinned: VCF of SNP genotypes of thinned loci, outlier loci not removed, and including all individuals
gulo_snp_all_thinned_outliers_removed: VCF of SNP genotypes of thinned loci, outlier loci removed, and including all individuals
gulo_snp_related_removed: VCF of SNP genotypes of thinned loci, outlier loci removed, and related individuals removed
outliers_removed: TXT of SNP outlier loci removed
snp_genotyped_related_removed: TXT of lab identification labels of SNP genotyped related individuals removed
Methods
Microsatellite genotyping and single nucleotide polymorphism (SNP) genotyping via restriction site associated DNA sequencing (RAD seq).