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

Area of Science:

• Ecology and evolutionary biology
• Genomics
• Conservation biology

Background:

• Global pollinator declines pose significant threats to ecosystems and agriculture.
• Understanding historical population dynamics is crucial for addressing contemporary declines.
• The Franklin bumble bee (Bombus franklini) is a key example of a declining pollinator, last seen in 2006.

Purpose of the Study:

• To reconstruct the genetic and demographic history of the potentially extinct Franklin bumble bee.
• To investigate the factors contributing to its population decline using whole-genome data.
• To assess the utility of museum specimens for studying rare species' histories.

Main Methods:

• Whole-genome sequencing of museum specimens spanning four decades.
• Analysis of heterozygosity and runs of homozygosity (ROH) to infer inbreeding and population structure.
• Demographic reconstructions and coalescent simulations to model population size changes and detect recent declines.

Main Results:

• Remarkably low heterozygosity and extensive ROH patterns indicate historical inbreeding.
• Demographic reconstructions show a decline in effective population size since the late Pleistocene, with accelerated declines in the last 400 years.
• Genomic data provided little evidence for pathogen impact, suggesting environmental stressors and historical low genetic diversity were primary drivers.

Conclusions:

• The Franklin bumble bee's extinction vulnerability was heightened by historically low effective population size and genetic diversity, exacerbated by environmental stochasticity.
• The species may have been on a declining trajectory before recent anthropogenic stressors.
• Museum collections are valuable resources for understanding the genetic and demographic history of rare and potentially extinct species.