Introduction
The Xerces Blue butterfly (Glaucopsyche xerces (Boisduval))(1) was native to the coastal sand dunes of San Francisco in association with its preferred larval host plant, Lotus scoparius (Fabaceae) (2). It was notable for its iridescent blue colouration on the dorsal (upper) wing surface, and conspicuous, variable white spots on the ventral surface. With the growth of San Francisco and the destruction of sand dune habitats, the Xerces Blue became restricted to a few sites in what is now Golden Gate National Recreation Area. The last specimens were reportedly collected by entomologist W. Harry Lange on March 23, 1941, and the Xerces blue has never been seen flying again (2). It is considered the first butterfly to have been driven to extinction by human activities (2).
The Xerces Blue and the closely related Silvery Blue, Glaucopsyche lygdamus (Doubleday), were recently proposed to be distinct species based on mtDNA data from a Xerces Blue museum specimen (3). However, two nuclear genes analysed (ribosomal 28S and histone H3) were invariable and genome-wide data were unavailable for the Xerces Blue, hampered by the inherent difficulties of retrieving genome-wide data from historical insect specimens (4, 5) and the absence of a suitable reference genome. The genus Glaucopsyche consists of 18 extant species distributed across the temperate regions of the northern hemisphere. To provide a relevant reference, we generated an annotated genome from the Palearctic Green-Underside Blue butterflyGlaucopsyche alexis (Poda). Using DNA extracted from five Xerces Blue and seven Silvery Blue (Glaucopsyche lygdamus incognitusTilden) historical specimens from the vicinity of San Francisco we generated whole genome resequencing data for both species and investigated their relationships and historical population genetics.