Dataset DOI: 10.5061/dryad.76hdr7tbk

Description of the data and file structure

Supplemental material from whole-genome sequencing data of North Carolina black bears

Project Overview
This dataset was generated to investigate the population genomic structure, genetic diversity, and connectivity of American black bears (Ursus americanus) in North Carolina, USA. The study focuses on individuals sampled from two primary management regions: the Mountain Bear Management Unit (MBMU) in western North Carolina and the Coastal Bear Management Unit (CBMU) in eastern North Carolina.

Experimental Design
Whole-genome sequencing was performed on tissue samples collected from 82 individual bears. Samples were obtained through state wildlife management and monitoring efforts to represent the geographic and ecological range of the study populations. The experimental design aimed to capture both broad-scale differentiation between management units and fine-scale population structure within regions.

Sequencing reads were aligned to the American black bear reference genome, followed by joint variant calling across all individuals. Standard quality control and filtering steps were applied to generate a high-confidence set of single nucleotide polymorphisms (SNPs). These included removal of low-quality variants, filtering based on minor allele frequency, exclusion of closely related individuals, and linkage disequilibrium pruning for downstream population genomic analyses.

Purpose of the Dataset
The resulting dataset supports analyses of population structure, genetic diversity, effective population size, and gene flow. In addition, the data were used to develop and validate a reduced SNP panel for applications in wildlife management, including individual identification, population assignment, and forensic investigations.

Intended Use
This dataset is intended for use in population genomics, conservation genetics, and applied wildlife management research. It provides a resource for understanding how landscape features and management history influence genetic structure in a large, wide-ranging mammal.

Files and variables

File: Supplemental_Figures_-_BearManuscript.pdf

Description: Supplementary Figure 1. Sensitivity of ROH-based inbreeding estimates to PLINK parameter settings. 

Supplementary Figure 2. Validation and Genomic Representation of the Targeted SNP Panel. 

Supplementary Figure 3. Genetic differentiation using the targeted 4,990 SNP dataset.

File: BearManuscript_SITables.xlsx

Description: Supplementary Tables with data for genetic diversity, land-use change, all bear metadata, and ROH analyses

Supplementary Table1: Metadata for all sample individuals included in the dataset. Data includes Sample ID, Sex, Sample Type used for DNA extraction, assigned Management Unit (CBMU = Coastal Bear Management Unit; MBMU = Mountain Bear Management Unit), Age, Location description, Year Collected, Geographic Location, post-filtering status, and inferred genetic grouping. “Kept post filtering” indicates whether an individual was retained following initial quality control and filtering steps performed in PLINK (e.g., missingness and relatedness thresholds), with “X” denoting retained samples. “Inferred Group” represents the genetic cluster assignment for each individual based on population structure analyses (E1 for CBMU; M1 and M2 for MBMU subclusters). Metadata completeness varied across individuals: while geographic location, collection data, and age information were available for some bears, these data were not consistently recorded for all samples. 

Supplementary Table 2: Parameters evaluated in sensitivity analyses for runs of homozygosity (ROH) detection. Alternative parameter combinations were tested to assess the robustness of ROH identification to variation in SNP density, minimum ROH length, SNP count, heterozygous calls, missing genotypes, and inter-SNP gap thresholds. These analyses were used to determine whether observed patterns in ROH abundance and length distribution were consistent across reasonable ROH-calling criteria.

Supplementary Table 3: Downsampling analyses of genomic diversity and inbreeding. The MBMU was downsampled to 27 individuals to match the CBMU.

Supplementary Table 4: Land cover change and composition across management units from 1985 - 2024. Summaries for land cover dynamics were averaged across all counties within the CBMU and MBMU. A.) Average percent change across land cover categories. B.) Percent net decrease in key habitat categories. C.) Average proportion of area by land cover type. * Denotes significant differences between the two management units. 

File: joint_filtered_final.vcf.gz

Description: Merged VCF with genotypes for all 82 bears across the final SNP dataset.

File: bear_snp_panel.txt

Description: List of SNPs included in the final targeted panel.