Population decline of Franklin’s bumble bee wasn’t due to pathogens, museum genomic research shows

The mysterious population decline of the imperiled Franklin’s bumble bee, which once flourished in a small area of northern California and southern Oregon, was not due to pathogens, but most likely to population bottlenecks and environmental issues such as fire and drought, according to research published Oct. 20 in the Proceedings of the National Academy of Sciences.

A team led by conservation geneticist Rena Schweizer of the USDA Agricultural Research Services Pollinating Insects Research Unit, Logan, Utah, collected whole-genome sequence data from museum specimens of Bombus franklini, spanning more than four decades, to reconstruct 300,000 years of the bee’s genetic history.

Most of the specimens are from the Bohart Museum of Entomology at the University of California, Davis. UC Davis Distinguished Emeritus and bumble bee conservationist Professor Robbin Thorp of the UC Davis Department of Entomology and Nematology monitored the B. franklini population and collected specimens from 1998 until his death in 2019. He was instrumental in obtaining species protection under the U.S. Endangered Species Act.

“Understanding what was happening to Franklin's bumble bee was Robbin Thorp's last major project before his death,” said Distinguished Professor Emeritus Lynn Kimsey, who directed the Bohart Museum for 34 years until her retirement in 2024. She is a co-author of the paper.

Franklin’s bumble bee has not been sighted in the wild since 2006 and is feared extinct. Its range, a 13,300-square-mile area confined to Siskiyou and Trinity counties in California and Jackson, Douglas and Josephine counties in Oregon, is thought to be the most limited geographic distribution of any bumble bee in North America and possibly the world.

The team described the bumble bee as a “rare U.S. pollinator” that “exemplifies the challenges of studying species with small ranges and declining populations that are no longer found in the wild. Using advanced genomic techniques on historical museum specimens, we reconstructed the species’ evolutionary history, revealing critically low genetic diversity and significant population declines since the late Pleistocene.”

“We found that, contrary to previous hypotheses, pathogens likely did not drive initial declines; rather, its extinction vulnerability may have arisen from population bottlenecks and environmental stochasticity over the last 100,000 years,“ the authors wrote. “This study underscores the significance of museum collections in unraveling species’ historical population dynamics before modern anthropogenic influences, thereby contributing to understanding extinction risk and helping guide conservation actions.”

“An analysis of 25 female museum specimens revealed evidence of very low genetic diversity and historical inbreeding,” the authors said. “We found evidence of a steep decrease in population size beginning in the late Pleistocene era, with further decline detected between 200 to 300 years ago, prior to human impact and the introduction of pathogens.

The scientists concluded that “a combination of historically low effective population size and genetic diversity along with environmental stochasticity heightened this species’ extinction vulnerability prior to recent anthropogenic stressors. This study demonstrates the utility of museum collections for clarifying genetic and demographic dynamics of rare species and suggests that B. franklini may have already been on a trajectory of decline prior to human impacts.”

In emphasizing the significance of the research, the authors noted that “Pollinator declines globally threaten ecosystem stability and agricultural productivity. Reconstructing pollinator historic demographies provides an evolutionary perspective to understand contemporary population declines.”

“The global decline of insect pollinators such as bees, beetles, butterflies, and flies is an issue of significant ecological and economic concern as they play an irreplaceable role in the reproduction of many plant species, including an estimated 35% of the crops essential for humans,” they wrote. “Bumble bees are among the most well-studied bee fauna, with many species observed to be in decline, considered at risk for extinction, or even putatively extinct. This is alarming given that wild bumble bees are critical pollinators in natural and agricultural landscapes and are vital to the production of agricultural crops. Assessing the status of bumble bees and other pollinator species and determining the drivers of their declines have become critical research areas.”

Between 1998 and 2005, the number of sightings of B. franklini declined precipitously from 94 individuals in 1998 to 20 in 1999, nine in 2000 and one in 2001. Although 20 were found in 2002 only three were sighted in 2003, all at a single locality. None were found in 2004 and 2005, and a single worker was sighted in 2006. This was at the same locality, Mt. Ashland, where the last B. franklini were found in 2003. No individuals were found in 2007 or 2008.

B. franklini was named for Henry J. Franklin, who monographed the bumble bees of North and South America in 1912-13. In a UC Davis interview, Thorp said that Franklin's bumble bee frequents California poppies, lupines, vetch, wild roses, blackberries, clover, sweet peas, horsemint and mountain penny royal during its flight season, from mid-May through September. It collects pollen primarily from lupines and poppies and gathers nectar mainly from mints.

The authors said the project could not have been completed without the work of Thorp and the approval of Kimsey to extract DNA from the specimens. They were able to genomically sample museum specimens at the Bohart for use in their study, with specimens ranging in age from 1950-1998, the only observations after this point. This allowed us to peek into the genetic history of the species both during the 1950-1998 period,” they said, “and thousands of years prior, using population genomics techniques.”

In addition to Kimsey, co-authors are Michael Branstetter (UC Davis doctoral alumnus), Diana Cox-Foster and Jonathan Uhuad Koch, all of USDA-ARS, Logan, Utah; Jared Grummer, University of Montana, Missoula; Kerrigan Tobin, Marquette University, Milwaukee; and Renee Corpuz and Scott Geib of USDA-ARS, Hilo, Hawaii.