Demographic history and diversity
We used the Pairwise Sequentially Markovian coalescent (PSMC) algorithm (10) to evaluate the demographic histories of both butterfly species, first exploring the two specimens with highest coverage (L05 and L13) (Fig. 2). We found an increase in effective population size in both species that is roughly coincident with the interglacial Marine Isotopic Stage (MIS) 7 (approximately from 240,000 to 190,000 years ago (11)). After this timepoint the trends differ. We estimated a continuous decrease in Xerces Blue population size in parallel to the Wisconsin Glacial Episode, which started about 75,000 years ago. However, the Silvery Blue does not appear to have been similarly affected by this event, suggesting different adaptive strategies to cope with cooling temperatures and/or food plant availability.