University of Idaho Study Finds Major Genetic Shifts in Idaho Bighorn Sheep Populations
Sandpoint, Idaho — Rocky Mountain bighorn sheep across Idaho have undergone significant genetic changes over the past century, according to a new study from the University of Idaho and the Idaho Department of Fish and Game. The research, published in the journal Conservation Genetics, reveals that population declines have stripped wild sheep herds of genetic diversity and severed ancient connections between subspecies.
Bighorn sheep in Idaho were once far more genetically diverse, with Rocky Mountain and desert bighorn subspecies interbreeding across overlapping ranges. That cross-subspecies mixing helped build resilience against disease, environmental change, and physiological stress. Today, researchers say, that advantage has been largely lost.
A Century of Genetic Change
To measure how dramatically the species has changed, scientists compared DNA extracted from historic bighorn skulls — collected between 1897 and 1985 and held as part of the John Carrey collection at the Jack O’Connor Hunting Heritage and Education Center at Hells Gate State Park in Lewiston — with genetic samples taken from the same geographic areas between 2000 and 2017.
The contrast was stark. Roughly 35 percent of Idaho bighorn sheep in historical samples carried genetic markers linked to desert subspecies lineages, a clear sign of interbreeding between populations. In modern samples, that figure has dropped to approximately 1 percent — a near-total disappearance of that genetic bridge. Researchers attribute the loss to fragmented habitat and the regional extinction of bighorn populations from portions of their former range.
“Comparisons between historical and modern data reveal a consistent decline in genetic diversity,” said Frances Cassirer, a senior wildlife research biologist with the Idaho Department of Fish and Game and co-lead on the paper. “Historical populations showed higher genetic variation and contained more unique genetic variants, many of which have been lost.”
Cassirer noted that the patterns are consistent with genetic bottlenecks — the narrowing of a gene pool that occurs when a population shrinks sharply and fails to fully recover.
Six Isolated Populations, Shrinking Options
The research team, which included University of Idaho Distinguished Professor of Wildlife Science Lisette Waits along with scientists from the University of Montana and state fish and game personnel, identified six distinct genetic clusters in Idaho’s modern bighorn population. Those groupings largely align with five existing state wildlife management units in the Salmon River region, a critical stronghold for native bighorn sheep in North Idaho and central Idaho.
Some connectivity between groups persists, particularly in central portions of the range, but genetic separation among the clusters is evident — a sign that animals are not moving freely between areas and gene flow has diminished. The East Fork population, located within the Salmon-Challis National Forest, stands out as the most isolated and genetically distinct, shaped by long-term separation and a persistently small population size.
“Genetic diversity is essential for the health and long-term survival of species,” Cassirer said. “Isolated populations are at risk of further loss. Preserving this diversity is critical because these sheep have experienced local adaptation.”
Bighorn sheep were once broadly distributed across the western United States, but numbers collapsed in the late 1800s and early 1900s due to disease transmission from domestic livestock, overhunting, and competition for grazing habitat. While some herds have rebounded, many remain small and vulnerable.
What Comes Next
The study’s findings carry practical weight for wildlife managers. Understanding which populations are genetically isolated — and which retain some natural connectivity — can help guide decisions about translocation efforts, land management priorities, and habitat protection. The East Fork population’s distinct genetic profile, for instance, may warrant targeted conservation attention to prevent further erosion of its unique variation.
Idaho’s bighorn sheep remain a symbol of the state’s wild landscape, particularly along the rugged Salmon River corridor. Whether wildlife agencies can reverse the genetic fragmentation identified in this research will depend in part on broader land use decisions, including how grazing allotments and domestic sheep operations near bighorn habitat are managed in the years ahead. Readers following broader Idaho wildlife and natural resource management stories can find additional context at a recent report on Army Corps spring operations and updates on utility wildfire planning in North Idaho.