A new genomic analysis of museum specimens reveals that the downfall of the Franklin’s bumble bee, a species last seen in the wild in 2006, began not in the 1990s but thousands of years ago. Researchers sequencing DNA from preserved bees found that the species was already on a trajectory toward extinction long before the pressures of modern agriculture and disease, suggesting a much deeper and more complex story of its disappearance.

This study challenges previous hypotheses that a sudden event, such as the introduction of a pathogen, was the primary cause of the bee’s rapid vanishing act. Instead, the findings point to a long-term vulnerability forged by ancient population bottlenecks, critically low genetic diversity, and environmental shifts stretching back to the late Pleistocene. By looking into the bee’s deep past, scientists have uncovered a cautionary tale about how historical fragility can set the stage for a species’ final collapse in the face of modern stressors.

A Bee Lost to Time

The Franklin’s bumble bee, or Bombus franklini, has become an emblem of the modern pollinator crisis. Once native to a small, specific ecoregion spanning southern Oregon and northern California, the bee experienced a severe population crash in the late 1990s. Despite intensive annual surveys in its former habitat, particularly around Mt. Ashland, Oregon, no confirmed sightings have occurred since 2006, leading experts to consider it potentially extinct. In 2019, its precarious situation was formally recognized with its protection under the U.S. Endangered Species Act.

Genomic Clues from Museum Collections

To unravel the mystery of the bee’s decline, researchers turned to an unconventional source: historical museum collections. Scientists collected whole-genome sequence data from 25 individual bee specimens that had been preserved over four decades. This process of “museum genomics” allowed the team to create a genetic timeline, tracking the species’ population dynamics and genetic health across different points in recent history and inferring its deeper ancestral past. By analyzing patterns of genetic variation, they could reconstruct the effective population size—the number of individuals contributing genes to the next generation—over thousands of years.

A Long and Ancient Decline

The genetic evidence painted a stark picture of a species that has been in trouble for millennia. The demographic reconstruction showed a significant drop in the bee’s effective population size that began during the late Pleistocene, approximately 100,000 years ago. This ancient decline was followed by further reductions over the last 400 years, long before the 20th century. The genomes of the Franklin’s bumble bee exhibited remarkably low heterozygosity, a measure of genetic diversity crucial for adaptation and resilience. Low diversity makes a species more susceptible to environmental changes and disease.

Evidence of Inbreeding

The study also found strong evidence of historical inbreeding. The analysis identified numerous “runs of homozygosity” (ROH), which are long stretches of the genome that are identical. In some individual bees, almost entire chromosomes were found in ROH, a pattern suggestive of prolonged periods of small population size where mating between related individuals was common. This genetic signature indicates that the species endured population bottlenecks that constrained its gene pool well before its recent, more visible collapse.

Rethinking the Role of Pathogens

For many declining North American bumble bee species, the spread of pathogens like Nosema bombi has been a leading hypothesis to explain their disappearance. This theory posits that diseases, possibly spread from commercially raised bees, overwhelmed wild populations. However, the genomic analysis of the Franklin’s bumble bee specimens found little to no evidence implicating pathogens as the primary driver of its initial, long-term decline. The researchers’ demographic models showed that while a recent pathogen-driven event could be detected under certain conditions, the deeper historical data pointed away from this explanation as the root cause. Instead, the study suggests that environmental stochasticity—random environmental events such as wildfires and droughts—likely played a more significant role in shaping its ancient population dynamics and heightened its extinction vulnerability over centuries.

Lessons for Modern Conservation

The findings underscore the immense value of natural history museums as archives of genetic information that can rewrite our understanding of extinction. By providing a window into a species’ past before modern anthropogenic influences became dominant, these collections help scientists distinguish between long-term vulnerabilities and recent threats. For the Franklin’s bumble bee, it appears its fate was largely sealed by its ancient history of low genetic diversity and small population size.

This research suggests that some species may already be on an extinction trajectory due to deep historical factors. Conservation strategies that focus only on immediate, observable threats may fail if they do not account for a species’ inherent, long-term fragility. Understanding the complete demographic and genetic history of a rare species is therefore critical for developing effective actions and identifying which populations are most at risk before they reach a point of no return.