A recent genomic survey of N.C. black bears from mountain and coastal habitats reveals distinct differences in genetic health and diversity between the populations, with coastal bears exhibiting greater genetic fragility than mountain bears. The results could be used by wildlife management and law enforcement to ensure the health of both bears and the ecosystems they are part of.
Using DNA samples collected over several years, the researchers generated whole genome sequences for 76 black bears selected from populations representing two of the three N.C. bear management units: 49 from the Mountain Bear Management Unit (MBMU) and 27 from the Coastal Bear Management Unit (CBMU). The data identified three genetic clusters, two from the MBMU and one from the CBMU. A genetic cluster refers to a group of genetically similar individuals within a species or population and is used by wildlife managers to help track the health of an animal community.
“We found that while mountain bears had two distinct, genetically healthy groups, the coastal bears had reduced genetic diversity and elevated inbreeding despite having a larger estimated population,” said Isabella Livingston, a postdoctoral researcher at North Carolina State University’s College of Veterinary Medicine and first author of a paper describing the work.
“We then added landscape data for context – we looked at how the landscapes in each of these management units have changed and saw that there’s been more change in the coastal region compared to the mountains,” said Livingston. “Coastal bears are running out of usable habitat, so there is evidence of potential isolation into breeding neighborhoods where they may not have access to every individual within the CBMU, resulting in inbreeding and genetic fragility.”
For bears in the MBMU, their ability to roam farther, more freely and encounter bears from other parts of the Appalachian Mountains could be contributing to the development of different genetic clusters.
“Bears don’t look at state borders and think, ‘Oh, well, better stop there,’” said Matthew Breen, professor of genomics and the Oscar J. Fletcher Distinguished Professor of Comparative Oncology Genetics at NC State’s College of Veterinary Medicine. “So it’s possible that the genetic diversity in that western part of the state might reflect a natural infusion and exchange with bears from other states, as opposed to the eastern population, which backs into an ocean.”
The genome-wide dataset also provided an opportunity to evaluate how genomic data could be translated into more targeted monitoring tools. The researchers generated a panel of single nucleotide polymorphisms, or SNPs, which are genetic variants that can be used to identify the management unit or group an individual bear belongs to.
“Basically groups of SNPs act as genetic fingerprints that we can use to find out where a bear is from and who it is,” said Livingston. “It’s a tool that can be used by wildlife managers in sustaining a healthy bear population. It can also be useful to law enforcement in poaching investigations and other forensically relevant contexts in determining where a bear came from.”
The researchers hope that the genomic data will aid wildlife managers, bears, and the ecosystems around them.
“This work shows that genome-wide data of wildlife populations can reveal population structure, demographic history, and emerging connectivity concerns that may not be apparent from census size or management boundaries alone,” said Breen. “We are delighted to be able to continue to work with the NC Wildlife Resources Commission and other constituents to explore how these data can be used to help them sustain a healthy, viable population of bears in our state.”
The paper appears in Genes and was supported in part by the Pittman–Robertson Federal Aid to Wildlife Restoration Grant under Cooperative Agreement WM-026. Other NC State contributors include Allison Dickey, Megan Dillon, Nicholas Gould, Jennifer Strules, Christopher DePerno, Michael Stoskopf and Kelly Meiklejohn.
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Note to editors : An abstract follows.
“Population Genomics of North Carolina’s Black Bears (Ursus americanus) Reveals Substructure and Identifies Informative SNPs for Population Assignment and Individualization”
Authors : Isabella G. Livingston, Allison N. Dickey, Megan N. Dillon, Nicholas P. Gould, Jennifer Strules, Christopher S. DePerno, Michael K. Stoskopf, Kelly A. Meiklejohn and Matthew Breen, North Carolina State University
Published : Sept. 29, 2026 in Genes
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.
Genes
Data/statistical analysis
Animals
29-Sep-2026
The authors declare no conflicts of interest.