Museum genomics suggests long-term population decline in a putatively extinct bumble bee

Authors: Schweizer, Rena; GRUMMER, JARED - University Of Montana; TOBIN, KERRIGAN - Marquette University; GEIB, SCOTT - University Of Montana; Cox-Foster, Diana; KIMSEY, LYNN - University Of California, Davis; Koch, Jonathan; Branstetter, Michael

Submitted to: Proceedings of the National Academy of Sciences (PNAS)
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/16/2025
Publication Date: 10/20/2025
Citation: Schweizer, R.M., Grummer, J.A., Tobin, K.B., Geib, S.M., Cox-Foster, D.L., Kimsey, L.S., Koch, J., Branstetter, M.G. 2025. Museum genomics suggests long-term population decline in a putatively extinct bumble bee. Proceedings of the National Academy of Sciences (PNAS). https://doi.org/10.1073/pnas.2509749122.
DOI: https://doi.org/10.1073/pnas.2509749122

Interpretive Summary: The Franklin bumble bee, once found only in a small part of Oregon and California, hasn’t been seen since 2006 and is likely extinct. To better understand what led to its disappearance, we analyzed DNA from museum specimens collected over the last 40 years. We found that the bees had very low genetic diversity, and some showed signs of inbreeding, meaning individuals were closely related. This suggests the population was already small and isolated. Our results show the population began declining thousands of years ago, with further drops in the past 400 years likely due to environmental stress like wildfires and drought. We found no strong genetic evidence that disease played a major role. Instead, a long history of low population size and reduced genetic variation likely made the species more vulnerable to extinction. This study highlights the power of using museum collections to learn about rare species and suggests the Franklin bumble bee was already declining before modern human impacts began.

Technical Abstract: Global declines of pollinators threaten ecosystem stability and agricultural productivity. Reconstructing historic demographic patterns of pollinators provides an evolutionary perspective to contemporary population declines. The Franklin bumble bee (Bombus franklini), once endemic to a narrow range in Oregon and California and last observed alive in 2006, is emblematic of this phenomenon. We sequenced museum specimens collected across four decades to elucidate the genetic and demographic history of this endangered, potentially extinct species. Genome-wide heterozygosity of all individuals was remarkably low, and some individuals had almost entire chromosomes in runs of homozygosity (ROH). Overall, ROH patterns identified short segments suggestive of historical inbreeding, although one individual exhibited extensive ROH and potential evidence for localized recent inbreeding in fragmented colonies. Demographic reconstructions revealed a marked decline in effective population size beginning during the late Pleistocene, with further declines in the last 400 years reflecting climatic pressures likely related to episodic fires and drought. We find little to no genomic evidence implicating Varimorpha bombi or other pathogens in the species’ population decline, and use coalescent simulations to show that we would be able to detect recently reduced heterozygosity only when colony-level survival rates are below 30%. Instead, a combination of historically low effective population size, low genetic diversity, and environmental stochasticity likely heightened vulnerability to extinction prior to the effects of recent anthropogenic stressors. Our findings demonstrate the utility of natural history collections for clarifying the genetic and demographic dynamics of rare species and suggest that B. franklini may have already been on a trajectory of decline prior to human impacts.