Genetic Monitoring of California’s Burgeoning Black Bear Population

A new genetic study based at Pepperwood has found that Sonoma County-based matriarch black bears are raising healthy cubs. Through this study we can also see when male bears pass through the area and whether they’re mature or juvenile. We can determine and map the genetics of these bears, which gives us valuable information on their population’s health and resilience.  One goal of this study is to map black bear movement and teach residents how to coexist among black bears safely by employing best practices like keeping garbage secure.

The research is conducted by a large group of state agencies, nonprofit conservation groups, landowners and volunteers that have come together in a working group called the North Bay Bear Collaborative. The goal of the group is to mitigate future challenges that may arise from the North Bay’s increasing black bear population.

The following is an abridged version of an article on this subject that appeared in the San Jose Mercury News by Lisa Krieger (linked below).

“It’s giving us an idea of their relationships, and how they’re moving around,” said lead scientist Meghan Walla-Murphy. “We’re hoping to use this information to help inform the public that are now living with black bears, where they weren’t 10 to 15 years ago, to help both our human and bear communities stay safe and resilient.” Black bears are shy animals and usually avoid people. But they’re well-adapted to living alongside us, and as their numbers increase, our worlds will overlap.

About 70 bears are estimated to live in Sonoma County, according to the collaborative’s data. Based on anecdotal reports, between two and five different bears are in Marin County, although it is not known if they are permanent residents. Earlier this summer, one was seen in a tree in Larkspur and later strolling through a yard in San Rafael. A mother bear and her cubs were sighted at Novato’s 38-acre Miwok Park, with paths, picnic areas and a playground. Two years ago, a bear climbed 40 feet up a tree near downtown San Anselmo. How did they get here? Who are their parents, children, siblings and cousins? Where are they wandering?

DNA and photographs collected by the collaborative, reveal much about the collective ancestry of these bears. The study, led by Conservation Science Director Tosha Comendant, is currently focused on bears at Pepperwood’s 3,200-acre reserve. With sufficient funding, the team would expand its study to understand the genetic links between bears in 17 different regions of Sonoma County, perhaps even the entire state. It also seeks to study bears’ response to wildfires, and whether geographical barriers, such as freeways, cause inbreeding or other symptoms of population decline. In 2020, the project obtained data from 60 scat and fur samples from nine Pepperwood animals: six females and three males. It was able to link two generations of a mother and cubs, as well as half-brothers. In 2021, it identified seven females and two males. One male was later found wandering about 20 miles away, in Sugarloaf Ridge State Park. Those animals’ relationships are unknown, because the data is still being deciphered.

Collections from 2022 await processing. This summer and fall, scat and hair samples are being collected at Sonoma County plots, each 10 square miles. Samples will also be collected from four Marin County plots: Point Reyes National Seashore and Mt. Tamalpais, Olompali and Samuel P. Taylor state parks. Volunteers walk the rugged landscapes, searching for moist scat, rich in skin cells. They scoop the poop into a labeled vial and record its location with GPS. Back in the Pepperwood facility, each vial is filled with preservative and shipped to UC Davis for processing in the lab of Benjamin Sacks, Director of the university’s Mammalian Ecology and Conservation Unit. His lab extracts the DNA from the cells and then genotypes them using a suite of genetic markers that yield sex and individual DNA fingerprints. This data is sent back to Pepperwood, where geneticist Dr. Morgan Gray uses it to identify individuals and family relationships.

The approach was pioneered in Yellowstone National Park, where it revealed kinship and pack formation in 200 wolves. “In the same way that the wolves are introducing themselves and dispersing, I think we will see that phenomena in black bears, as well,” Walla-Murphy said. “We’re in a time where people have gone without living with bears,” she said. “Now we hope to build a bear culture in the North Bay again.”

A version of this story was originally featured in the San Jose Mercury News (Volume 173, issue 51), a subsidiary of Bay Area News Group, on August 9, 2023 by Lisa Krieger (contact at All rights of that article belong to the Bay Area News Group. To view the San Jose Mercury News article or leave comments for Bay Area News Group and the author, please visit

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