Population Genomics of North Carolina's Black Bears (Ursus americanus) Reveals Substructure and Identifies Informative SNPs for Population Assignment and Individualization.
10 affiliations
- 1Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA.
- 2Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27607, USA.
- 3College of Natural Resources, North Carolina State University, Raleigh, NC 27695, USA.
- 4Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA.
- 5Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA.
- 6School of Science, Hawkesbury, Western Sydney University, Richmond, NSW 2753, Australia.
- 7Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27607, USA.
- 8Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27607, USA.
- 9Cancer Genetics, UNC Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.
- 10Duke Cancer Institute, Duke University, Durham, NC 27710, USA.
Abstract
Background/Objectives: Anthropogenic pressures increasingly fragment populations, reduce connectivity in large mammals, and threaten genetic diversity. Genetic diversity is essential for a population's ability to respond to environmental change and the long-term persistence of any species. The American black bear (Ursus americanus) is an important ecological regulator of many ecosystems. North Carolina (NC) is home to a large number of black bears that contribute to ecosystem function. In this study, we examined how rapidly changing environmental and anthropogenic effects influence the structure and genetic health of black bears in North Carolina. Methods: Whole genome sequencing data were generated from 82 black bears selected from populations representing two of the three state recognized management units, the Mountain Bear Management Unit (MBMU, n = 49) and the Coastal Bear Management Unit (CBMU, n = 27). Of the 82 black bears, 76 were retained after quality and relatedness filtering. These whole genome sequence data were used to identify almost 900,000 single nucleotide polymorphisms (SNPs) for population genetic analyses. Results: The data identified three genetic clusters, one within the CBMU and two within the MBMU, indicating regional substructure across the sampled populations. Compared with the MBMU, the CBMU exhibited significantly lower genetic diversity and higher inbreeding (p < 2.2 × 10⁻¹⁶), suggesting reduced connectivity and increased genetic vulnerability in the coastal population. Finally, a candidate panel of 4990 SNPs was developed that can be used for the population and individual assignment of black bears. Conclusions: These findings provide a valuable genome-wide resource for black bear conservation in North Carolina and support management strategies aimed at maintaining connectivity, preserving genetic diversity, and promoting long-term population resilience.
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BibTeX
@article{livingston2026population,
title = {{Population Genomics of North Carolina's Black Bears (Ursus americanus) Reveals Substructure and Identifies Informative SNPs for Population Assignment and Individualization.}},
author = {Isabella G Livingston and Allison N Dickey and Megan N Dillon and Nicholas P Gould and Jennifer Strules and Christopher S DePerno and Michael K Stoskopf and Kelly A Meiklejohn and Matthew Breen},
journal = {Genes},
year = {2026},
month = sep,
doi = {10.3390/genes17101206},
url = {https://europepmc.org/article/MED/42938322},
note = {CC BY},
}
RIS
TY - JOUR
TI - Population Genomics of North Carolina's Black Bears (Ursus americanus) Reveals Substructure and Identifies Informative SNPs for Population Assignment and Individualization.
AU - Isabella G Livingston
AU - Allison N Dickey
AU - Megan N Dillon
AU - Nicholas P Gould
AU - Jennifer Strules
AU - Christopher S DePerno
AU - Michael K Stoskopf
AU - Kelly A Meiklejohn
AU - Matthew Breen
PY - 2026
DA - 2026/09/29
JO - Genes
DO - 10.3390/genes17101206
UR - https://europepmc.org/article/MED/42938322
AB - Background/Objectives: Anthropogenic pressures increasingly fragment populations, reduce connectivity in large mammals, and threaten genetic diversity. Genetic diversity is essential for a population's ability to respond to environmental change and the long-term persistence of any species. The American black bear (Ursus americanus) is an important ecological regulator of many ecosystems. North Carolina (NC) is home to a large number of black bears that contribute to ecosystem function. In this study, we examined how rapidly changing environmental and anthropogenic effects influence the structure and genetic health of black bears in North Carolina. Methods: Whole genome sequencing data were generated from 82 black bears selected from populations representing two of the three state recognized management units, the Mountain Bear Management Unit (MBMU, n = 49) and the Coastal Bear Management Unit (CBMU, n = 27). Of the 82 black bears, 76 were retained after quality and relatedness filtering. These whole genome sequence data were used to identify almost 900,000 single nucleotide polymorphisms (SNPs) for population genetic analyses. Results: The data identified three genetic clusters, one within the CBMU and two within the MBMU, indicating regional substructure across the sampled populations. Compared with the MBMU, the CBMU exhibited significantly lower genetic diversity and higher inbreeding (p < 2.2 × 10⁻¹⁶), suggesting reduced connectivity and increased genetic vulnerability in the coastal population. Finally, a candidate panel of 4990 SNPs was developed that can be used for the population and individual assignment of black bears. Conclusions: These findings provide a valuable genome-wide resource for black bear conservation in North Carolina and support management strategies aimed at maintaining connectivity, preserving genetic diversity, and promoting long-term population resilience.
SN - 2073-4425
ER -