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UW Researcher Leads Study Indicating Southern California Mountain Lions’ Genetic Connectivity Dangerously Low

January 25, 2022
moutain lion lying down in the wild
A Santa Ana Mountains puma rests in the shade near a “cubby” designed to collect hair DNA samples for a mark-recapture analysis. (UC-Davis Wildlife Health Center and Washington State University Photo)

Urbanization is decreasing wildlife habitat and connectivity worldwide, including for mountain lions in California. Mountain lion or puma populations along that state’s central and southern coastal habitats have experienced rapid fragmentation from development, leading to a call for demographic and genetic management.

University of Wyoming scientists led research that focuses on the conservation of a dangerously inbred puma population in Southern California.

“This work is a big deal for coastal mountain lion population conservation,” says Holly Ernest, a UW professor of wildlife genomics and disease ecology, and the Wyoming Excellence Chair in Disease Ecology in UW’s Department of Veterinary Sciences and the Program in Ecology. “Pacific coastal mountain lion populations in California have become isolated due to human-caused changes to their habitat. The result is that they have low interbreeding (gene flow) with other populations, and this has resulted in such low genetic diversity that their health is suffering.”

Ernest is senior author of a paper titled “Multi-Population Puma Connectivity Could Restore Genomic Diversity to At-Risk Coastal Populations in California” that was published in Evolutionary Applications today (Jan. 25). The journal publishes papers of interest to a diverse audience including evolutionary biologists, ecologists, biomedical researchers, environmental consultants and biologists within industry, government and health care.

Kyle Gustafson, an assistant professor of wildlife biology at Arkansas State University, was the paper’s lead and corresponding author. Gustafson started puma research in Ernest’s lab while a postdoctoral researcher at UW.

“Although several mountain lion populations in California are isolated and have low genetic diversity, this work shows that there is good potential to restore genetic diversity to those populations through gene flow,” Gustafson says.

“Kyle’s work was monumental. He did tons of work,” Ernest says. “This paper employed genome-wide sequencing to assess mountain lion genetic diversity; connectivity to provide vital information for wildlife managers to plan habitat restoration; and potentially population augmentation to mitigate inbreeding problems in coastal California populations.”

Other contributors to the paper with UW ties were Erick Gagne, a UW postdoctoral researcher in Ernest’s lab from 2015-17 and now an assistant professor at the University of Pennsylvania; and Melanie LaCava, a Ph.D. student in Ernest’s lab who graduated from UW in 2021 and is now a postdoctoral researcher at the University of California-Davis (UC-Davis). Additional collaborators were a wildlife veterinarian from UC-Davis One Health Institute; and wildlife biologists from the National Park Service and the California Department of Fish and Wildlife.

Looking Into the Research

Ernest’s team reviewed 354 puma tissue samples collected by the California Department of Fish and Wildlife between 2011-17. Tissue samples were used from pumas either hit by vehicles, found dead, poached or through depredation permits. The group looked at four large genetic clusters and a total of 10 mountain lion populations around the state.

Some key findings include:

-- The researchers suspect the Sierra Nevada mountain lion population had the highest genetic diversity in California because it has the largest habitat, likely the highest abundance and, therefore, the greatest ability to maintain levels of genetic diversity, Gustafson says.

Ernest adds that the Sierra Nevada habitat also has broad habitat connections with mountain lion habitat in Nevada and Oregon. Habitats in those other states provide mountain lion gene flow into the Sierra Nevada.

-- Results indicate that several Pacific coastal mountain lion populations are susceptible to inbreeding. The Central Coast South and the Santa Ana populations are both fragmented from urbanization as Los Angeles and San Diego continue to expand. The North Coast and Central Coast North populations appear to have some level of natural isolation because their populations extend as a habitat “peninsula” with the San Francisco Bay, highly agricultural Central Valley and Pacific Ocean as boundaries lacking habitat.

“However, the Central Coast South population also has increasing threats from the sprawling urbanization of the greater LA region from the south and the Santa Cruz region from the north,” Gustafson says.

Recovery Methods Underway

“There are several ways to assist recovery of these imperiled mountain lion populations, which serve as a bellwether for dangers to other wildlife living alongside the mountain lions,” Ernest says. “In one example, our data and findings have been and are used by California agencies and nonprofits to secure over $78 million in funds needed for building wildlife crossings near the Santa Monica Mountains of the greater Los Angeles region.”

Highway crossings -- overpasses and underpasses -- are developed specifically for safe wildlife crossing, Ernest says. Highly successful models for this exist in the state of Washington in the I-90 Snoqualmie Pass and Banff National Park in the Canadian Rocky Mountains, where there has been more than two decades of success with wildlife better able to traverse their habitat and not end up as roadkill, she says.

Ernest adds their research has been used by wildlife agencies and nonprofit conservancy advocates to improve futures for wildlife populations by helping prevent a massive development that would have effectively blocked gene flow between two very large habitat regions -- the Santa Ana Mountains just south of LA and the Eastern Peninsular ranges farther inland.

“The small bit of land near Temecula, Calif., is now protected as a wildlife corridor between these two large habitats for mountain lions and other species of wildlife,” Ernest says.

Ernest says the research has been years in the making and builds on 25-plus years of work since she started California mountain lion genetics work in the 1990s as a Ph.D. student and continued through her work as a professor at UC-Davis. The research continued with Gustafson and other postdoctoral researchers, graduate students and research members of her UW lab.

“Our research over the years has provided the genetic data to show that measures are needed to prevent Southern California mountain lion populations from collapsing,” Ernest says. “The really exciting aspect of genetic data is that it shows clear findings that are relatable to wildlife agencies and understandable to the public, especially as people become more familiar with genetic ancestry services for themselves. By engaging multitudes of people who might not otherwise be aware of threats to wildlife with these genetic findings, big improvements for wildlife conservation are being made.”

Funding for the research came from the California Department of Fish and Wildlife; University of California-Davis School of Veterinary Medicine Wildlife Health Center and One Health Institute; the National Park Service; California State Parks; the National Science Foundation; The Nature Conservancy; the U.S. Geological Survey; University of California-Los Angeles; and Arkansas State University.

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