Conservation museomics of the putatively extinct Franklin's bumble bee

The bumble bee Bombus franklini is a flagship species of conservation importance for insects. Historically, Franklin's bumble bee had a very limited distributed that included several sites found in the mountains of northern California and southern Oregon. However, since the late 1990s the species has been in decline and the last known record of the species was reported in 2006 from a single site in Oregon. The species is now thought to be extinct, or nearly so. The exact cause of the decline is unknown, but several factors, including disease, habitat alteration, and climate change, are possibilities. While the population dynamics of Franklin's bumble bee have been observed over time leading up to the decline, there have been no attempts to investigate the same period using population genetic methods, which can potentially provide additional insights into genetic diversity and population size. In this study we use next-generation sequencing methods and museum specimens to assemble a reference genome for Bombus franklini and investigate population genetic changes through time, including before and during the observed decline of the species. We use these data to test the hypothesis that genetic diversity in the species declined rapidly and in parallel with observed population declines. We also examine the genetic data for the presence of potential pathogens that might have contributed to declines. Our results demonstrate the value of museum specimens in conservation genomics research and present new insights into the decline of an iconic species.